diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 0c184e0..01a0710 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -23,14 +23,20 @@ jobs: run: | pip install poetry - - name: Configure Poetry - run: | - poetry config virtualenvs.create false + - name: Cache Poetry virtualenv and dependencies + uses: actions/cache@v4 + with: + path: | + ~/.cache/pypoetry + ~/.cache/pip + key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }} + restore-keys: | + poetry-${{ runner.os }}- - name: Install dependencies run: | - make install + make install-dev - name: Run linting checks run: | - make check-pylint \ No newline at end of file + make check-pylint diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index 611645d..5036281 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -23,14 +23,27 @@ jobs: run: | pip install poetry - - name: Configure Poetry - run: | - poetry config virtualenvs.create false - + - name: Cache Poetry virtualenv and dependencies + uses: actions/cache@v4 + with: + path: | + ~/.cache/pypoetry + ~/.cache/pip + key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }} + restore-keys: | + poetry-${{ runner.os }}- + + - name: Cache pre-commit + uses: actions/cache@v4 + with: + path: | + ~/.cache/pre-commit + key: pre-commit-3|${{ env.pythonLocation }}|${{ hashFiles('.pre-commit-config.yaml') }} + - name: Install dependencies run: | - make install + make install-dev - name: Run Pre-commit checks run: | - make precommit \ No newline at end of file + make precommit diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index c342052..4f0820f 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -23,14 +23,20 @@ jobs: run: | pip install poetry - - name: Configure Poetry - run: | - poetry config virtualenvs.create false + - name: Cache Poetry virtualenv and dependencies + uses: actions/cache@v4 + with: + path: | + ~/.cache/pypoetry + ~/.cache/pip + key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }} + restore-keys: | + poetry-${{ runner.os }}- - name: Install dependencies run: | - make install + make install-dev - name: Run tests run: | - make test \ No newline at end of file + make test diff --git a/.make/.bumpversion.toml b/.make/.bumpversion.toml index 79b246b..dbfd1e4 100644 --- a/.make/.bumpversion.toml +++ b/.make/.bumpversion.toml @@ -1,30 +1,31 @@ - [tool.bumpversion] -current_version = "0.4.0" +current_version = "0.7.1" commit = true message = "Makefile version {new_version} released." tag = true tag_name = "makefile-{new_version}" parse = '(?P\d+)\.(?P\d+)\.(?P\d+) (?P.*)?' serialize = [ - "{major}.{minor}.{patch}", - "{utcnow:%Y-%m-%dT%H:%M:%SZ}" + "{major}.{minor}.{patch}" ] [[tool.bumpversion.files]] filename = "CHANGES_MAKEFILE.md" search = ''' -[Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest) -------------------------------------------------------------------------------------- +## [Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest) + +______________________________________________________________________ ''' replace = ''' -[Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest) -------------------------------------------------------------------------------------- +## [Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest) + +______________________________________________________________________ + + -[//]: # (New changes here in list form) +## [{new_version}](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-{new_version}) ({utcnow:%Y-%m-%d}) -[{new_version}](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-{new_version}) ({utcnow:%Y-%m-%d}) -------------------------------------------------------------------------------------- +______________________________________________________________________ ''' [[tool.bumpversion.files]] diff --git a/.make/CHANGES_MAKEFILE.md b/.make/CHANGES_MAKEFILE.md index 20bccc5..c20049d 100644 --- a/.make/CHANGES_MAKEFILE.md +++ b/.make/CHANGES_MAKEFILE.md @@ -1,18 +1,52 @@ # CHANGES.md -[Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest) -------------------------------------------------------------------------------------- +## [Unreleased](https://github.com/RolnickLab/lab-advanced-template/tree/main) (latest) -[//]: # (New changes here in list form) +______________________________________________________________________ -[0.4.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.4.0) (2024-10-30) -------------------------------------------------------------------------------------- + -* Add cyclomatic complexity check target +## [0.7.1](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.7.1) (2025-09-17) -[0.3.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.3.0) (2024-10-30) -------------------------------------------------------------------------------------- +______________________________________________________________________ -* Add utilities to track makefile versions -* Fix many of the targets relating to standalone `poetry` installation + +## [0.7.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.7.0) (2025-09-10) + +______________________________________________________________________ + +- Add `mdformat` tool for markdown linting +- Modularize the Makefile structure, allowing to choose which tools are available +- Add tests for the Makefile + +## [0.6.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.6.0) (2025-05-29) + +______________________________________________________________________ + +- Improve venv support +- Add venv remove target +- Refactor `poetry-install-auto` to really be automatic +- Add `mamba-install` target as an alternative/complement to conda for local dev +- Add `autoflake`, `autopep8` and `ruff` targets +- Fix some typos that caused targets to fail + +## [0.5.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.5.0) (2025-03-11) + +______________________________________________________________________ + +- Add venv support +- Update and fix `poetry-install-auto` target + +## [0.4.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.4.0) (2024-10-30) + +______________________________________________________________________ + +- Add cyclomatic complexity check target + +## [0.3.0](https://github.com/RolnickLab/lab-advanced-template/tree/makefile-0.3.0) (2024-10-30) + +______________________________________________________________________ + +- Add utilities to track makefile versions +- Fix many of the targets relating to standalone `poetry` installation diff --git a/.make/Makefile b/.make/Makefile index 08d0974..293b7f5 100644 --- a/.make/Makefile +++ b/.make/Makefile @@ -10,7 +10,7 @@ # files to include. ######################################################################################## PROJECT_PATH := $(dir $(abspath $(firstword $(MAKEFILE_LIST)))) -MAKEFILE_VERSION := 0.4.0 +MAKEFILE_VERSION := 0.7.1 BUMP_TOOL := bump-my-version BUMP_CONFIG_FILE := $(PROJECT_PATH).bumpversion.toml @@ -73,12 +73,12 @@ dry: ## Add the dry target for a preview of changes; ex. `make bump-major dry` .PHONY: bump-major bump-major: ## Bump makefile major version - $(BUMP_TOOL) $(BUMP_ARGS) bump major --config-file $(BUMP_CONFIG_FILE) + $(BUMP_TOOL) bump $(BUMP_ARGS) major --config-file $(BUMP_CONFIG_FILE) .PHONY: bump-minor bump-minor: ## Bump makefile minor version <0.X.0> - $(BUMP_TOOL) $(BUMP_ARGS) bump minor --config-file $(BUMP_CONFIG_FILE) + $(BUMP_TOOL) bump $(BUMP_ARGS) minor --config-file $(BUMP_CONFIG_FILE) .PHONY: bump-patch bump-patch: ## Bump makefile patch version <0.0.X> - $(BUMP_TOOL) $(BUMP_ARGS) bump patch --config-file $(BUMP_CONFIG_FILE) + $(BUMP_TOOL) bump $(BUMP_ARGS) patch --config-file $(BUMP_CONFIG_FILE) diff --git a/.make/README.md b/.make/README.md index 0135556..eb26919 100644 --- a/.make/README.md +++ b/.make/README.md @@ -2,16 +2,28 @@ This folder contains the base makefile targets. -It should not be modified outside of the [Template's repository](https://github.com/RolnickLab/lab-advanced-template). +It should not be modified outside the [Template's repository](https://github.com/RolnickLab/lab-advanced-template). -If there is a problem with the contents of these targets, please open an issue [here](https://github.com/RolnickLab/lab-advanced-template/issues). +If there is a problem with the contents of these targets, please open an +issue [here](https://github.com/RolnickLab/lab-advanced-template/issues). -If you know how to fix the problem, please also consider opening a pull request with +If you know how to fix the problem, please also consider opening a pull request with your proposed solution. You can always override the faulty targets located here by creating new targets with the same names inside [Makefile.targets](../Makefile.targets). The Makefile and `bump-my-version` related files in this directory are to help with -change tracking for the makefile itself. If you are using this makefile as part of a -template in another repository \ No newline at end of file +change tracking for the makefile itself. If you are using this makefile as part of a +template in another repository, you won't have to interact with them. + +## Tests + +Makefile tests can be found in the [.make/tests/](tests) folder. Current tests are +essentially bash scripts to test the different makefile targets. + +These should only be run when modifying the makefiles inside the +[Template's repository](https://github.com/RolnickLab/lab-advanced-template). + +They should never be run in a project implemented from the template, as they could cause +side effects to your project. diff --git a/.make/base.make b/.make/base.make index cd6622d..5f40e6c 100644 --- a/.make/base.make +++ b/.make/base.make @@ -3,7 +3,7 @@ # If necessary, override the corresponding variable and/or target, or create new ones # in one of the following files, depending on the nature of the override : # -# Makefile.variables, Makefile.targets or Makefile.private`, +# Makefile.variables, Makefile.targets or Makefile.private, # # The only valid reason to modify this file is to fix a bug or to add new # files to include. @@ -16,7 +16,7 @@ PROJECT_PATH := $(dir $(abspath $(firstword $(MAKEFILE_LIST)))) MAKEFILE_NAME := $(word $(words $(MAKEFILE_LIST)),$(MAKEFILE_LIST)) SHELL := /usr/bin/env bash BUMP_TOOL := bump-my-version -MAKEFILE_VERSION := 0.4.0 +MAKEFILE_VERSION := 0.7.1 DOCKER_COMPOSE ?= docker compose AUTO_INSTALL ?= @@ -26,12 +26,22 @@ CONDA_TOOL := conda CONDA_ENVIRONMENT ?= CONDA_YES_OPTION ?= +# Default environment to install package +# Can be overridden in Makefile.private file +DEFAULT_INSTALL_ENV ?= +DEFAULT_POETRY_INSTALL_ENV ?= + # Colors _SECTION := \033[1m\033[34m _TARGET := \033[36m _NORMAL := \033[0m .DEFAULT_GOAL := help + +# Project and Private variables and targets import to override variables for local +# This is to make sure, sometimes the Makefile includes don't work. +-include Makefile.variables +-include Makefile.private ## -- Informative targets ------------------------------------------------------------------------------------------- ## .PHONY: all @@ -70,397 +80,48 @@ targets: help version: ## display current version @echo "version: $(APP_VERSION)" -## -- Conda targets ------------------------------------------------------------------------------------------------- ## - -.PHONY: conda-install -conda-install: ## Install Conda on your local machine - @echo "Looking for [$(CONDA_TOOL)]..."; \ - $(CONDA_TOOL) --version; \ - if [ $$? != "0" ]; then \ - echo " "; \ - echo "Your defined Conda tool [$(CONDA_TOOL)] has not been found."; \ - echo " "; \ - echo "If you know you already have [$(CONDA_TOOL)] or some other Conda tool installed,"; \ - echo "Check your [CONDA_TOOL] variable in the Makefile.private for typos."; \ - echo " "; \ - echo "If your conda tool has not been initiated through your .bashrc file,"; \ - echo "consider using the full path to its executable instead when"; \ - echo "defining your [CONDA_TOOL] variable"; \ - echo " "; \ - echo "If in doubt, don't install Conda and manually create and activate"; \ - echo "your own Python environment."; \ - echo " "; \ - echo -n "Would you like to install Miniconda ? [y/N]: "; \ - read ans; \ - case $$ans in \ - [Yy]*) \ - echo "Fetching and installing miniconda"; \ - echo " "; \ - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh; \ - bash ~/miniconda.sh -b -p $${HOME}/.conda; \ - export PATH=$${HOME}/.conda/bin:$$PATH; \ - conda init; \ - /usr/bin/rm ~/miniconda.sh; \ - ;; \ - *) \ - echo "Skipping installation."; \ - echo " "; \ - ;; \ - esac; \ - else \ - echo "Conda tool [$(CONDA_TOOL)] has been found, skipping installation"; \ - fi; - -.PHONY: conda-create-env -conda-create-env: conda-install ## Create a local Conda environment based on `environment.yml` file - @$(CONDA_TOOL) env create $(CONDA_YES_OPTION) -f environment.yml - -.PHONY: conda-env-info -conda-env-info: ## Print information about active Conda environment using - @$(CONDA_TOOL) info - -.PHONY: _conda-poetry-install -_conda-poetry-install: - @$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) python --version; \ - if [ $$? != "0" ]; then \ - echo "Target environment doesn't seem to exist..."; \ - if [ "$(AUTO_INSTALL)" = "true" ]; then \ - ans="y";\ - else \ - echo ""; \ - echo -n "Do you want to create it? [y/N] "; \ - read ans; \ - fi; \ - case $$ans in \ - [Yy]*) \ - echo "Creating conda environment : [$(CONDA_ENVIRONMENT)]"; \ - make -s conda-create-env; \ - ;; \ - *) \ - echo "Exiting..."; \ - exit 1;\ - ;; \ - esac;\ - fi; - $(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) $(CONDA_TOOL) install $(CONDA_YES_OPTION) -c conda-forge poetry; \ - CURRENT_VERSION=$$($(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) poetry --version | awk '{print $$NF}' | tr -d ')'); \ - REQUIRED_VERSION="1.6.0"; \ - if [ "$$(printf '%s\n' "$$REQUIRED_VERSION" "$$CURRENT_VERSION" | sort -V | head -n1)" != "$$REQUIRED_VERSION" ]; then \ - echo "Poetry installed version $$CURRENT_VERSION is less than minimal version $$REQUIRED_VERSION, fixing urllib3 version to prevent problems"; \ - $(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) poetry add "urllib3<2.0.0"; \ - fi; +## -- Virtualenv targets -------------------------------------------------------------------------------------------- ## -.PHONY:conda-poetry-install -conda-poetry-install: ## Install Poetry in the project's Conda environment. Will fail if Conda is not found - @poetry --version; \ - if [ $$? != "0" ]; then \ - echo "Poetry not found, proceeding to install Poetry..."; \ - echo "Looking for [$(CONDA_TOOL)]...";\ - $(CONDA_TOOL) --version; \ - if [ $$? != "0" ]; then \ - echo "$(CONDA_TOOL) not found; Poetry will not be installed"; \ - else \ - echo "Installing Poetry with Conda in [$(CONDA_ENVIRONMENT)] environment"; \ - make -s _conda-poetry-install; \ - fi; \ - else \ - echo ""; \ - echo "Poetry has been found on this system :"; \ - echo " Install location: $$(which poetry)"; \ - echo ""; \ - if [ "$(AUTO_INSTALL)" = "true" ]; then \ - ans="y";\ - else \ - echo -n "Would you like to install poetry in the project's conda environment anyway ? [y/N]: "; \ - read ans; \ - fi; \ - case $$ans in \ - [Yy]*) \ - echo "Installing Poetry with Conda in [$(CONDA_ENVIRONMENT)] environment"; \ - make -s _conda-poetry-install; \ - ;; \ - *) \ - echo "Skipping installation."; \ - echo " "; \ - ;; \ - esac; \ - fi; +VENV_PATH := $(PROJECT_PATH).venv +VENV_ACTIVATE := $(VENV_PATH)/bin/activate -.PHONY: conda-poetry-uninstall -conda-poetry-uninstall: ## Uninstall Poetry located in currently active Conda environment - $(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) $(CONDA_TOOL) remove $(CONDA_YES_OPTION) poetry +.PHONY: venv-create +venv-create: ## Create a virtualenv '.venv' at the root of the project folder + @virtualenv $(VENV_PATH) + @make -s venv-activate -.PHONY: conda-clean-env -conda-clean-env: ## Completely removes local project's Conda environment - $(CONDA_TOOL) env remove $(CONDA_YES_OPTION) -n $(CONDA_ENVIRONMENT) +.PHONY: venv-activate +venv-activate: ## Print out the shell command to activate the project's virtualenv. + @echo "source $(VENV_ACTIVATE)" -## -- Poetry targets ------------------------------------------------------------------------------------------------ ## - -.PHONY: poetry-install-auto -poetry-install-auto: ## Install Poetry in Conda environment, or with pipx in a virtualenv if Conda not found - @poetry --version; \ - if [ $$? != "0" ]; then \ - echo "Poetry not found, proceeding to install Poetry..."; \ - echo "Looking for [$(CONDA_TOOL)]...";\ - $(CONDA_TOOL) --version; \ - if [ $$? != "0" ]; then \ - echo "$(CONDA_TOOL) not found, trying with pipx"; \ - pipx --version; \ - if [ $$? != "0" ]; then \ - make AUTO_INSTALL=true -s poetry-install-venv; \ - fi; \ - else \ - echo "Installing poetry with Conda"; \ - make AUTO_INSTALL=true -s conda-poetry-install; \ - fi; \ - fi; - -.PHONY: poetry-install -poetry-install: ## Install standalone Poetry using pipx. Will ask where to install pipx. - @echo "Looking for Poetry version...";\ - poetry --version; \ - if [ $$? != "0" ]; then \ - if [ "$(AUTO_INSTALL)" = "true" ]; then \ +.PHONY: venv-remove +venv-remove: ## Delete the virtualenv '.venv' at the root of the project folder. + @if [ -d $(VENV_PATH) ]; then \ + echo "Current venv folder is [$(VENV_PATH)]"; \ + if [ "$(AUTO_INSTALL)" = "true" ]; then \ ans="y";\ - else \ - echo "Poetry not found..."; \ - echo "Looking for pipx version...";\ - pipx_found=0; \ - pipx --version; \ - if [ $$? != "0" ]; then \ - pipx_found=1; \ - echo "pipx not found..."; \ - echo""; \ - echo -n "Would you like to install pipx and Poetry? [y/N]: "; \ - else \ - echo""; \ - echo -n "Would you like to install Poetry using pipx? [y/N]: "; \ - fi; \ - read ans; \ - fi; \ - case $$ans in \ + else \ + echo ""; \ + echo -n "Would you like to completely delete this virtual environment? [y/N]: "; \ + read ans; \ + fi; \ + case $$ans in \ [Yy]*) \ - if [ $$pipx_found == "1" ]; then \ - echo""; \ - echo -e "\e[1;39;41m-- WARNING --\e[0m The following pip has been found and will be used to install pipx: "; \ - echo " -> "$$(which pip); \ - echo""; \ - echo "If you do not have write permission to that environment, using it to install pipx will fail."; \ - echo "If this is the case, you should install pipx using a virtual one."; \ - echo""; \ - echo "See documentation for more information."; \ - echo""; \ - echo -n "Would you like to use the local available pip above, or create virtual environment to install pipx? [local/virtual]: "; \ - read ans_how; \ - case $$ans_how in \ - "LOCAL" | "Local" |"local") \ - make -s poetry-install-local; \ - ;; \ - "VIRTUAL" | "Virtual" | "virtual") \ - make -s poetry-install-venv; \ - ;; \ - *) \ - echo ""; \ - echo -e "\e[1;39;41m-- WARNING --\e[0m Option $$ans_how not found, exiting process."; \ - echo ""; \ - exit 1; \ - esac; \ - else \ - echo "Installing Poetry"; \ - pipx install poetry; \ - fi; \ + echo ""; \ + echo "Starting deletion process for [$(VENV_PATH)]"; \ + rm -rf $(VENV_PATH); \ + echo ""; \ + echo "-- Deletion complete --"; \ ;; \ *) \ - echo "Skipping installation."; \ + echo ""; \ + echo "Skipping virtual environment deletion."; \ echo " "; \ ;; \ esac; \ - fi; - -PIPX_VENV_PATH := $$HOME/.pipx_venv -.PHONY: poetry-install-venv -poetry-install-venv: ## Install standalone Poetry. Will install pipx in $HOME/.pipx_venv - @pipx --version; \ - if [ $$? != "0" ]; then \ - echo "Creating virtual environment using venv here : [$(PIPX_VENV_PATH)]"; \ - python3 -m venv $(PIPX_VENV_PATH); \ - echo "Activating virtual environment [$(PIPX_VENV_PATH)]"; \ - source $(PIPX_VENV_PATH)/bin/activate; \ - pip3 install pipx; \ - pipx ensurepath; \ - fi; - source $(PIPX_VENV_PATH)/bin/activate && pipx install poetry - -.PHONY: poetry-install-local -poetry-install-local: ## Install standalone Poetry. Will install pipx with locally available pip. - @pipx --version; \ - if [ $$? != "0" ]; then \ - echo "pipx not found; installing pipx"; \ - pip3 install pipx; \ - pipx ensurepath; \ - fi; - @echo "Installing Poetry" - @pipx install poetry - - -.PHONY: poetry-env-info -poetry-env-info: ## Information about the currently active environment used by Poetry - @poetry env info - -.PHONY: poetry-create-env -poetry-create-env: ## Create a Poetry managed environment for the project (Outside of Conda environment). - @echo "Creating Poetry environment that will use Python $(PYTHON_VERSION)"; \ - poetry env use $(PYTHON_VERSION); \ - poetry env info - @echo"" - @echo "This environment can be accessed either by using the " - @echo "command, or activated with the command." - @echo"" - @echo "Use and for more information" - @echo"" - -.PHONY: poetry-remove-env -poetry-remove-env: ## Remove current project's Poetry managed environment. - @if [ "$(AUTO_INSTALL)" = "true" ]; then \ - ans_env="y";\ - env_path=$$(poetry env info -p); \ - env_name=$$(basename $$env_path); \ - else \ - echo""; \ - echo "Looking for poetry environments..."; \ - env_path=$$(poetry env info -p); \ - if [[ "$$env_path" != "" ]]; then \ - echo "The following environment has been found for this project: "; \ - env_name=$$(basename $$env_path); \ - echo""; \ - echo "Env name : $$env_name"; \ - echo "PATH : $$env_path"; \ - echo""; \ - echo "If the active environment listed above is a Conda environment,"; \ - echo "Choosing to delete it will have no effect; use the target "; \ - echo""; \ - echo -n "Would you like delete the environment listed above? [y/N]: "; \ - read ans_env; \ - else \ - env_name="None"; \ - env_path="None"; \ - fi; \ - fi; \ - if [[ $$env_name != "None" ]]; then \ - case $$ans_env in \ - [Yy]*) \ - poetry env remove $$env_name || echo "No environment was removed"; \ - ;; \ - *) \ - echo "No environment was found/provided - skipping environment deletion"; \ - ;;\ - esac; \ - else \ - echo "No environments were found... skipping environment deletion"; \ - fi; \ - -.PHONY: poetry-uninstall -poetry-uninstall: poetry-remove-env ## Uninstall pipx-installed Poetry and the created environment - @if [ "$(AUTO_INSTALL)" = "true" ]; then \ - ans="y";\ - else \ - echo""; \ - echo -n "Would you like to uninstall pipx-installed Poetry? [y/N]: "; \ - read ans; \ - fi; \ - case $$ans in \ - [Yy]*) \ - pipx uninstall poetry; \ - ;; \ - *) \ - echo "Skipping uninstallation."; \ - echo " "; \ - ;; \ - esac; \ - -.PHONY: poetry-uninstall-pipx -poetry-uninstall-pipx: poetry-remove-env ## Uninstall pipx-installed Poetry, the created Poetry environment and pipx - @if [ "$(AUTO_INSTALL)" = "true" ]; then \ - ans="y";\ - else \ - echo""; \ - echo -n "Would you like to uninstall pipx-installed Poetry and pipx? [y/N]: "; \ - read ans; \ - fi; \ - case $$ans in \ - [Yy]*) \ - pipx uninstall poetry; \ - pip uninstall -y pipx; \ - ;; \ - *) \ - echo "Skipping uninstallation."; \ - echo " "; \ - ;; \ - esac; \ - -.PHONY: poetry-uninstall-venv -poetry-uninstall-venv: poetry-remove-env ## Uninstall pipx-installed Poetry, the created Poetry environment, pipx and $HOME/.pipx_venv - @if [ "$(AUTO_INSTALL)" = "true" ]; then \ - ans="y";\ - else \ - echo""; \ - echo -n "Would you like to uninstall pipx-installed Poetry and pipx? [y/N]: "; \ - read ans; \ - fi; \ - case $$ans in \ - [Yy]*) \ - (source $(PIPX_VENV_PATH)/bin/activate && pipx uninstall poetry); \ - (source $(PIPX_VENV_PATH)/bin/activate && pip uninstall -y pipx); \ - ;; \ - *) \ - echo "Skipping uninstallation."; \ - echo " "; \ - ;; \ - esac; \ - - @if [ "$(AUTO_INSTALL)" = "true" ]; then \ - ans="y";\ - else \ - echo""; \ - echo -n "Would you like to remove the virtual environment located here : [$(PIPX_VENV_PATH)] ? [y/N]: "; \ - read ans; \ - fi; \ - case $$ans in \ - [Yy]*) \ - rm -r $(PIPX_VENV_PATH); \ - ;; \ - *) \ - echo "Skipping [$(PIPX_VENV_PATH)] virtual environment removal."; \ - echo ""; \ - ;; \ - esac; \ - -## -- Install targets (All install targets will install Poetry if not found using `make poetry-install-auto`)-------- ## - -.PHONY: install -install: install-precommit ## Install the application package, developer dependencies and pre-commit hook - -.PHONY: install-precommit -install-precommit: install-dev## Install the pre-commit hooks (also installs developer dependencies) - @if [ -f .git/hooks/pre-commit ]; then \ - echo "Pre-commit hook found"; \ - else \ - echo "Pre-commit hook not found, proceeding to configure it"; \ - poetry run pre-commit install; \ - fi; - -.PHONY: install-dev -install-dev: poetry-install-auto ## Install the application along with developer dependencies - @poetry install --with dev - -.PHONY: install-with-lab -install-with-lab: poetry-install-auto ## Install the application and it's dev dependencies, including Jupyter Lab - @poetry install --with dev --with lab - - -.PHONY: install-package -install-package: poetry-install-auto ## Install the application package only - @poetry install + else \ + echo "Venv [$(VENV_PATH)] does not exist, nothing to do"; \ + fi; ## -- Versioning targets -------------------------------------------------------------------------------------------- ## @@ -472,89 +133,20 @@ ifeq ($(filter dry, $(MAKECMDGOALS)), dry) endif .PHONY: dry -dry: ## Add the dry target for a preview of changes; ex. `make bump-major dry` +dry: ## Add the dry target for a preview of changes; ex. 'make bump-major dry' @-echo > /dev/null .PHONY: bump-major bump-major: ## Bump application major version - $(BUMP_TOOL) $(BUMP_ARGS) bump major + $(BUMP_TOOL) bump $(BUMP_ARGS) major .PHONY: bump-minor bump-minor: ## Bump application minor version <0.X.0> - $(BUMP_TOOL) $(BUMP_ARGS) bump minor + $(BUMP_TOOL) bump $(BUMP_ARGS) minor .PHONY: bump-patch bump-patch: ## Bump application patch version <0.0.X> - $(BUMP_TOOL) $(BUMP_ARGS) bump patch - -## -- Docker targets ------------------------------------------------------------------------------------------------ ## - -## -- Apptainer/Singularity targets --------------------------------------------------------------------------------- ## - -## -- Linting targets ----------------------------------------------------------------------------------------------- ## - -.PHONY: check-lint -check-lint: ## Check code linting (black, isort, flake8, docformatter and pylint) - poetry run nox -s check - -.PHONY: check-pylint -check-pylint: ## Check code with pylint - poetry run nox -s pylint - -.PHONY: check-complexity -check-complexity: ## Check code cyclomatic complexity with Flake8-McCabe - poetry run nox -s complexity - -.PHONY: fix-lint -fix-lint: ## Fix code linting (black, isort, flynt, docformatter) - poetry run nox -s fix - -.PHONY: precommit -precommit: ## Run Pre-commit on all files manually - poetry run nox -s precommit - -## -- Tests targets ------------------------------------------------------------------------------------------------- ## - -.PHONY: test -test: ## Run all tests - poetry run nox -s test + $(BUMP_TOOL) bump $(BUMP_ARGS) patch -TEST_ARGS ?= -MARKER_TEST_ARGS = -m "$(TEST_ARGS)" -SPECIFIC_TEST_ARGS = -k "$(TEST_ARGS)" -CUSTOM_TEST_ARGS = "$(TEST_ARGS)" -.PHONY: test-marker -test-marker: ## Run tests using pytest markers. Ex. make test-marker TEST_ARGS="" - @if [ -n "$(TEST_ARGS)" ]; then \ - poetry run nox -s test_custom -- -- $(MARKER_TEST_ARGS); \ - else \ - echo "" ; \ - echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \ - echo "" ; \ - echo ' make test-marker TEST_ARGS=""' ; \ - echo "" ; \ - fi -.PHONY: test-specific -test-specific: ## Run specific tests using the -k option. Ex. make test-specific TEST_ARGS="" - @if [ -n "$(TEST_ARGS)" ]; then \ - poetry run nox -s test_custom -- -- $(SPECIFIC_TEST_ARGS); \ - else \ - echo "" ; \ - echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \ - echo "" ; \ - echo ' make test-specific TEST_ARGS=""' ; \ - echo "" ; \ - fi -.PHONY: test-custom -test-custom: ## Run tests with custom args. Ex. make test-custom TEST_ARGS="-m 'not offline'" - @if [ -n "$(TEST_ARGS)" ]; then \ - poetry run nox -s test_custom -- -- $(CUSTOM_TEST_ARGS); \ - else \ - echo "" ; \ - echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \ - echo "" ; \ - echo ' make test-custom TEST_ARGS=""' ; \ - echo "" ; \ - fi \ No newline at end of file diff --git a/.make/conda.make b/.make/conda.make new file mode 100644 index 0000000..855f80e --- /dev/null +++ b/.make/conda.make @@ -0,0 +1,176 @@ + + +## -- Conda targets ------------------------------------------------------------------------------------------------- ## + +CONDA_ENVIRONMENT_FILE := environment.yml +.PHONY: conda-install +conda-install: ## Install Miniconda on your local machine + @echo "Looking for [$(CONDA_TOOL)]..."; \ + $(CONDA_TOOL) --version; \ + if [ $$? != "0" ]; then \ + echo " "; \ + echo "Your defined Conda tool [$(CONDA_TOOL)] has not been found."; \ + echo " "; \ + echo "If you know you already have [$(CONDA_TOOL)] or some other Conda tool installed,"; \ + echo "Check your [CONDA_TOOL] variable in the Makefile.private for typos."; \ + echo " "; \ + echo "If your conda tool has not been initiated through your .bashrc file,"; \ + echo "consider using the full path to its executable instead when"; \ + echo "defining your [CONDA_TOOL] variable"; \ + echo " "; \ + echo "If in doubt, don't install Conda and manually create and activate"; \ + echo "your own Python environment."; \ + echo " "; \ + echo "It is strongly NOT advisable to execute this command if you are on a"; \ + echo "Compute Cluster (ie. Mila/DRAC), as they either have modules available (Mila),"; \ + echo "or even prohibit the installation and use of Conda (DRAC) based environments."; \ + echo " "; \ + echo -n "Would you like to install and initialize Miniconda ? [y/N]: "; \ + read ans; \ + case $$ans in \ + [Yy]*) \ + echo "Fetching and installing miniconda"; \ + echo " "; \ + wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh; \ + bash ~/miniconda.sh -b -p $${HOME}/.conda; \ + export PATH=$${HOME}/.conda/bin:$$PATH; \ + conda init; \ + /usr/bin/rm ~/miniconda.sh; \ + ;; \ + *) \ + echo "Skipping installation."; \ + echo " "; \ + ;; \ + esac; \ + else \ + echo "Conda tool [$(CONDA_TOOL)] has been found, skipping installation"; \ + fi; + +.PHONY: mamba-install +mamba-install: ## Install Micromamba on you local machine + @echo "Looking for [micromamba]..."; \ + micromamba --version; \ + if [ $$? != "0" ]; then \ + echo ""; \ + echo "[micromamba] has not been found."; \ + echo ""; \ + echo "If you know you already have installed [micromamba] installed, it might not have"; \ + echo "been properly activated (which can also be on purpose)."; \ + echo ""; \ + echo "If your Conda/Micromamba tool has not been initiated through your .bashrc file,"; \ + echo "consider using the full path to its executable instead when"; \ + echo "defining your [CONDA_TOOL] variable"; \ + echo " "; \ + echo "If you do decide to install Micromamba, please take care to define the [CONDA_TOOL]"; \ + echo "variable in you personal 'Makefile.private' file as CONDA_TOOL := micromamba."; \ + echo " "; \ + echo "If in doubt, don't install Micromamba and manually create and activate"; \ + echo "your own Python environment."; \ + echo ""; \ + echo "It is strongly NOT advisable to execute this command if you are on a"; \ + echo "Compute Cluster (ie. Mila/DRAC), as they either have modules available (Mila),"; \ + echo "or even prohibit the installation and use of Conda based environments (DRAC)."; \ + echo ""; \ + echo -n "Would you like to install and initialize [micromamba] ? [y/N]: "; \ + read ans; \ + case $$ans in \ + [Yy]*) \ + echo 'Installing Micromamba' + wget -qO- https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba;\ + mv bin/micromamba ~/.local/bin/micromamba;\ + rm -rf bin/;\ + ~/.local/bin/micromamba shell init -s bash ~/.micromamba;\ + ;; \ + *) \ + echo "Skipping installation."; \ + echo " "; \ + ;; \ + esac; \ + + +.PHONY: conda-create-env +conda-create-env: conda-install ## Create a local Conda environment based on 'environment.yml' file + @$(CONDA_TOOL) env create $(CONDA_YES_OPTION) -f $(CONDA_ENVIRONMENT_FILE) + +.PHONY: conda-env-info +conda-env-info: ## Print information about active Conda environment using + @$(CONDA_TOOL) info + +.PHONY: conda-activate +conda-activate: ## Print the shell command to activate the project's Conda env. + @echo "$(CONDA_TOOL) activate $(CONDA_ENVIRONMENT)" + +.PHONY: _conda-poetry-install +_conda-poetry-install: + @$(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) python --version; \ + if [ $$? != "0" ]; then \ + echo "Target environment doesn't seem to exist..."; \ + if [ "$(AUTO_INSTALL)" = "true" ]; then \ + ans="y";\ + else \ + echo ""; \ + echo -n "Do you want to create it? [y/N] "; \ + read ans; \ + fi; \ + case $$ans in \ + [Yy]*) \ + echo "Creating conda environment : [$(CONDA_ENVIRONMENT)]"; \ + make -s conda-create-env; \ + ;; \ + *) \ + echo "Exiting..."; \ + exit 1;\ + ;; \ + esac;\ + fi; + $(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) $(CONDA_TOOL) install $(CONDA_YES_OPTION) -c conda-forge poetry; \ + CURRENT_VERSION=$$($(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) poetry --version | awk '{print $$NF}' | tr -d ')'); \ + REQUIRED_VERSION="1.6.0"; \ + if [ "$$(printf '%s\n' "$$REQUIRED_VERSION" "$$CURRENT_VERSION" | sort -V | head -n1)" != "$$REQUIRED_VERSION" ]; then \ + echo "Poetry installed version $$CURRENT_VERSION is less than minimal version $$REQUIRED_VERSION, fixing urllib3 version to prevent problems"; \ + $(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) poetry add "urllib3<2.0.0"; \ + fi; + +.PHONY:conda-poetry-install +conda-poetry-install: ## Install Poetry in the project's Conda environment. Will fail if Conda is not found + @poetry --version; \ + if [ $$? != "0" ]; then \ + echo "Poetry not found, proceeding to install Poetry..."; \ + echo "Looking for [$(CONDA_TOOL)]...";\ + $(CONDA_TOOL) --version; \ + if [ $$? != "0" ]; then \ + echo "$(CONDA_TOOL) not found; Poetry will not be installed"; \ + else \ + echo "Installing Poetry with Conda in [$(CONDA_ENVIRONMENT)] environment"; \ + make -s _conda-poetry-install; \ + fi; \ + else \ + echo ""; \ + echo "Poetry has been found on this system :"; \ + echo " Install location: $$(which poetry)"; \ + echo ""; \ + if [ "$(AUTO_INSTALL)" = "true" ]; then \ + ans="y";\ + else \ + echo -n "Would you like to install poetry in the project's conda environment anyway ? [y/N]: "; \ + read ans; \ + fi; \ + case $$ans in \ + [Yy]*) \ + echo "Installing Poetry with Conda in [$(CONDA_ENVIRONMENT)] environment"; \ + make -s _conda-poetry-install; \ + ;; \ + *) \ + echo "Skipping installation."; \ + echo " "; \ + ;; \ + esac; \ + fi; + +.PHONY: conda-poetry-uninstall +conda-poetry-uninstall: ## Uninstall Poetry located in currently active Conda environment + $(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) $(CONDA_TOOL) remove $(CONDA_YES_OPTION) poetry + +.PHONY: conda-clean-env +conda-clean-env: ## Completely removes local project's Conda environment + $(CONDA_TOOL) env remove $(CONDA_YES_OPTION) -n $(CONDA_ENVIRONMENT) diff --git a/.make/lint.make b/.make/lint.make new file mode 100644 index 0000000..022edf3 --- /dev/null +++ b/.make/lint.make @@ -0,0 +1,37 @@ +## -- Linting targets ----------------------------------------------------------------------------------------------- ## + +.PHONY: check-lint +check-lint: ## Check code linting (black, isort, flake8, docformatter and pylint) + $(ENV_COMMAND_TOOL) nox -s check + +.PHONY: check-pylint +check-pylint: ## Check code with pylint + $(ENV_COMMAND_TOOL) nox -s pylint + +.PHONY: check-complexity +check-complexity: ## Check code cyclomatic complexity with Flake8-McCabe + $(ENV_COMMAND_TOOL) nox -s complexity + +.PHONY: fix-lint +fix-lint: ## Fix code linting (autoflake, autopep8, black, isort, flynt, docformatter) + $(ENV_COMMAND_TOOL) nox -s fix + +.PHONY: markdown-lint +markdown-lint: ## Fix markdown linting using mdformat + $(ENV_COMMAND_TOOL) nox -s mdformat + +.PHONY: precommit +precommit: ## Run Pre-commit on all files manually + $(ENV_COMMAND_TOOL) nox -s precommit + +.PHONY: ruff +ruff: ## Run the ruff linter + $(ENV_COMMAND_TOOL) nox -s ruff-lint + +.PHONY: ruff-fix +ruff-fix: ## Run the ruff linter and fix automatically fixable errors + $(ENV_COMMAND_TOOL) nox -s ruff-fix + +.PHONY: ruff-format +ruff-format: ## Run the ruff code formatter + $(ENV_COMMAND_TOOL) nox -s ruff-format diff --git a/.make/poetry.make b/.make/poetry.make new file mode 100644 index 0000000..92af1ad --- /dev/null +++ b/.make/poetry.make @@ -0,0 +1,387 @@ +# Project and Private variables and targets import to override variables for local +# This is to make sure, sometimes the Makefile includes don't work. +-include Makefile.variables +-include Makefile.private + +ENV_COMMAND_TOOL := poetry run + +## -- Poetry targets ------------------------------------------------------------------------------------------------ ## + +.PHONY: poetry-install-auto +poetry-install-auto: ## Install Poetry automatically using DEFAULT_POETRY_INSTALL_ENV. Defaults to venv install + @poetry --version; \ + if [ $$? != "0" ]; then \ + echo "Poetry not found, proceeding to install Poetry..."; \ + if [ "$(DEFAULT_POETRY_INSTALL_ENV)" == "conda" ]; then \ + echo ""; \ + echo "[DEFAULT_POETRY_INSTALL_ENV] is defined as 'conda', installing poetry with the 'poetry-install-conda' target"; \ + echo ""; \ + ans_where="conda"; \ + elif [ "$(DEFAULT_POETRY_INSTALL_ENV)" == "venv" ]; then \ + echo ""; \ + echo "[DEFAULT_POETRY_INSTALL_ENV] is defined as 'venv', installing poetry with the 'poetry-install-venv' target"; \ + echo ""; \ + ans_where="venv"; \ + else\ + echo ""; \ + echo "[DEFAULT_POETRY_INSTALL_ENV] is not defined, defaulting to installing poetry with the 'poetry-install-venv' target"; \ + echo ""; \ + ans_where="venv"; \ + fi; \ + case $$ans_where in \ + "venv" | "Venv" |"VENV") \ + make AUTO_INSTALL=true -s poetry-install-venv; \ + ;; \ + "conda" | "Conda" | "CONDA") \ + echo "Installing poetry with Conda"; \ + make AUTO_INSTALL=true -s conda-poetry-install; \ + ;; \ + *) \ + echo ""; \ + echo -e "\e[1;39;41m-- WARNING --\e[0m There was an unexpected error. Option $$ans_how not found, exiting process."; \ + echo ""; \ + exit 1; \ + esac; \ + fi; + +.PHONY: _pipx_install_poetry +_pipx_install_poetry: + @output="$$(pip install poetry --dry-run)"; \ + if echo "$$output" | grep -q computecanada ; then \ + echo ""; \ + echo -e "\e[1;39;41m-- WARNING --\e[0m Compute Canada (DRAC) environment detected: Installing Poetry < 2.0.0"; \ + echo ""; \ + pipx install 'poetry<2.0.0' ; \ + else \ + pipx install poetry ; \ + fi; + + +.PHONY: poetry-install +poetry-install: ## Install Poetry interactively. + @echo "Looking for Poetry version...";\ + poetry --version; \ + if [ $$? != "0" ]; then \ + if [ "$(AUTO_INSTALL)" = "true" ]; then \ + ans="y";\ + else \ + echo "Poetry not found..."; \ + echo "Looking for pipx version...";\ + pipx_found=0; \ + pipx --version; \ + if [ $$? != "0" ]; then \ + pipx_found=1; \ + echo "pipx not found..."; \ + echo""; \ + echo -n "Would you like to install pipx and Poetry? [y/N]: "; \ + else \ + echo""; \ + echo -n "Would you like to install Poetry using pipx? [y/N]: "; \ + fi; \ + read ans; \ + fi; \ + case $$ans in \ + [Yy]*) \ + if [ $$pipx_found == "1" ]; then \ + echo""; \ + echo -e "\e[1;39;41m-- WARNING --\e[0m The following pip has been found and will be used to install pipx: "; \ + echo " -> "$$(which pip); \ + echo""; \ + echo "If you do not have write permission to that environment, using it to install pipx will fail."; \ + echo "If this is the case, you should install pipx using a virtual one."; \ + echo""; \ + echo "See documentation for more information."; \ + echo""; \ + echo -n "Would you like to use the local available pip above, or create virtual environment to install pipx? [local/virtual]: "; \ + read ans_how; \ + case $$ans_how in \ + "LOCAL" | "Local" |"local") \ + make -s poetry-install-local; \ + ;; \ + "VIRTUAL" | "Virtual" | "virtual") \ + make -s poetry-install-venv; \ + ;; \ + *) \ + echo ""; \ + echo -e "\e[1;39;41m-- WARNING --\e[0m Option $$ans_how not found, exiting process."; \ + echo ""; \ + exit 1; \ + esac; \ + else \ + echo "Installing Poetry"; \ + make -s _pipx_install_poetry; \ + fi; \ + ;; \ + *) \ + echo "Skipping installation."; \ + echo " "; \ + ;; \ + esac; \ + fi; + +PIPX_VENV_PATH := $$HOME/.pipx_venv +.PHONY: poetry-install-venv +poetry-install-venv: ## Install standalone Poetry. Will install pipx in $HOME/.pipx_venv + @pipx --version; \ + if [ $$? != "0" ]; then \ + echo "Creating virtual environment using venv here : [$(PIPX_VENV_PATH)]"; \ + python3 -m venv $(PIPX_VENV_PATH); \ + echo "Activating virtual environment [$(PIPX_VENV_PATH)]"; \ + source $(PIPX_VENV_PATH)/bin/activate; \ + pip3 install pipx; \ + pipx ensurepath; \ + source $(PIPX_VENV_PATH)/bin/activate && make -s _pipx_install_poetry ; \ + else \ + make -s _pipx_install_poetry ; \ + fi; + +.PHONY: poetry-install-local +poetry-install-local: ## Install standalone Poetry. Will install pipx with locally available pip. + @pipx --version; \ + if [ $$? != "0" ]; then \ + echo "pipx not found; installing pipx"; \ + pip3 install pipx; \ + pipx ensurepath; \ + fi; + @echo "Installing Poetry" + @make -s _pipx_install_poetry + + +.PHONY: poetry-env-info +poetry-env-info: ## Information about the currently active environment used by Poetry + @poetry env info + +.PHONY: poetry-create-env +poetry-create-env: ## Create a Poetry managed environment for the project (Outside of Conda environment). + @echo "Creating Poetry environment that will use Python $(PYTHON_VERSION)"; \ + poetry env use $(PYTHON_VERSION); \ + poetry env info + @echo"" + @echo "This environment can be accessed either by using the " + @echo "command, or activated with the command." + @echo"" + @echo "Use and for more information" + @echo"" + +.PHONY: poetry-activate +poetry-activate: ## Print the shell command to activate the project's poetry env. + poetry env activate + +.PHONY: poetry-remove-env +poetry-remove-env: ## Remove current project's Poetry managed environment. + @if [ "$(AUTO_INSTALL)" = "true" ]; then \ + ans_env="y";\ + env_path=$$(poetry env info -p); \ + env_name=$$(basename $$env_path); \ + else \ + echo""; \ + echo "Looking for poetry environments..."; \ + env_path=$$(poetry env info -p); \ + if [[ "$$env_path" != "" ]]; then \ + echo "The following environment has been found for this project: "; \ + env_name=$$(basename $$env_path); \ + echo""; \ + echo "Env name : $$env_name"; \ + echo "PATH : $$env_path"; \ + echo""; \ + echo "If the active environment listed above is a Conda environment,"; \ + echo "Choosing to delete it will have no effect; use the target "; \ + echo""; \ + echo""; \ + echo "If the active environment listed above is a venv environment,"; \ + echo "Choosing to delete it will have no effect; use the bash command $ rm -rf "; \ + echo""; \ + echo -n "Would you like delete the environment listed above? [y/N]: "; \ + read ans_env; \ + else \ + env_name="None"; \ + env_path="None"; \ + fi; \ + fi; \ + if [[ $$env_name != "None" ]]; then \ + case $$ans_env in \ + [Yy]*) \ + poetry env remove $$env_name || echo "No environment was removed"; \ + ;; \ + *) \ + echo "No environment was found/provided - skipping environment deletion"; \ + ;;\ + esac; \ + else \ + echo "No environments were found... skipping environment deletion"; \ + fi; \ + +.PHONY: poetry-uninstall +poetry-uninstall: poetry-remove-env ## Uninstall pipx-installed Poetry and the created environment + @if [ "$(AUTO_INSTALL)" = "true" ]; then \ + ans="y";\ + else \ + echo""; \ + echo -n "Would you like to uninstall pipx-installed Poetry? [y/N]: "; \ + read ans; \ + fi; \ + case $$ans in \ + [Yy]*) \ + pipx --version ; \ + if [ $$? != "0" ]; then \ + echo "" ; \ + echo "Pipx not found globally, trying with $(PIPX_VENV_PATH) env" ;\ + echo "" ; \ + source $(PIPX_VENV_PATH)/bin/activate && pipx uninstall poetry ; \ + else \ + pipx uninstall poetry ; \ + fi; \ + ;; \ + *) \ + echo "Skipping uninstallation."; \ + echo " "; \ + ;; \ + esac; \ + +.PHONY: poetry-uninstall-pipx +poetry-uninstall-pipx: poetry-remove-env ## Uninstall pipx-installed Poetry, the created Poetry environment and pipx + @if [ "$(AUTO_INSTALL)" = "true" ]; then \ + ans="y";\ + else \ + echo""; \ + echo -n "Would you like to uninstall pipx-installed Poetry and pipx? [y/N]: "; \ + read ans; \ + fi; \ + case $$ans in \ + [Yy]*) \ + pipx --version ; \ + if [ $$? != "0" ]; then \ + echo "" ; \ + echo "Pipx not found globally, trying with $(PIPX_VENV_PATH) env" ;\ + echo "" ; \ + source $(PIPX_VENV_PATH)/bin/activate && pipx uninstall poetry && pip uninstall -y pipx; \ + else \ + pipx uninstall poetry ; \ + pip uninstall -y pipx ;\ + fi; \ + ;; \ + *) \ + echo "Skipping uninstallation."; \ + echo " "; \ + ;; \ + esac; \ + +.PHONY: poetry-uninstall-venv +poetry-uninstall-venv: poetry-remove-env ## Uninstall pipx-installed Poetry, the created Poetry environment, pipx and $HOME/.pipx_venv + @if [ "$(AUTO_INSTALL)" = "true" ]; then \ + ans="y";\ + else \ + echo""; \ + echo -n "Would you like to uninstall pipx-installed Poetry and pipx? [y/N]: "; \ + read ans; \ + fi; \ + case $$ans in \ + [Yy]*) \ + (source $(PIPX_VENV_PATH)/bin/activate && pipx uninstall poetry); \ + (source $(PIPX_VENV_PATH)/bin/activate && pip uninstall -y pipx); \ + ;; \ + *) \ + echo "Skipping uninstallation."; \ + echo " "; \ + ;; \ + esac; \ + + @if [ "$(AUTO_INSTALL)" = "true" ]; then \ + ans="y";\ + else \ + echo""; \ + echo -n "Would you like to remove the virtual environment located here : [$(PIPX_VENV_PATH)] ? [y/N]: "; \ + read ans; \ + fi; \ + case $$ans in \ + [Yy]*) \ + rm -r $(PIPX_VENV_PATH); \ + ;; \ + *) \ + echo "Skipping [$(PIPX_VENV_PATH)] virtual environment removal."; \ + echo ""; \ + ;; \ + esac; \ + +## -- Install targets (All install targets will install Poetry if not found using 'make poetry-install-auto')-------- ## + + +POETRY_COMMAND := poetry + +ifeq ($(DEFAULT_INSTALL_ENV),venv) +POETRY_COMMAND := source $(VENV_ACTIVATE) && poetry +else ifeq ($(DEFAULT_INSTALL_ENV),poetry) +POETRY_COMMAND := poetry +else ifeq ($(DEFAULT_INSTALL_ENV),conda) +POETRY_COMMAND := $(CONDA_TOOL) run -n $(CONDA_ENVIRONMENT) poetry +endif + +.PHONY: _check-env +_check-env: + @if ! [ $(DEFAULT_INSTALL_ENV) ]; then \ + echo -e "\e[1;39;41m-- WARNING --\e[0m No installation environment have been defined." ; \ + echo "" ; \ + echo "[DEFAULT_INSTALL_ENV] is not defined - Poetry will use the currently activated environment." ; \ + echo "If there is no currently active environment (ie. conda or venv)," ; \ + echo "Poetry will create and manage it's own environment." ; \ + elif [ $(DEFAULT_INSTALL_ENV) = "venv" ]; then \ + if [ ! -f $(VENV_ACTIVATE) ]; then \ + make -s venv-create ;\ + fi; \ + elif [ $(DEFAULT_INSTALL_ENV) = "conda" ]; then \ + if ! $(CONDA_TOOL) env list | grep -q $(CONDA_ENVIRONMENT) ; then \ + make -s conda-create-env ; \ + fi; \ + fi; + +.PHONY: _remind-env-activate +_remind-env-activate: + @echo "" + @echo "Activate your environment using the following command:" + @echo "" + @if ! [ $(DEFAULT_INSTALL_ENV) ] || [ $(DEFAULT_INSTALL_ENV) = "poetry" ]; then \ + make -s poetry-activate ; \ + echo "" ; \ + echo "You can also use the eval bash command : eval \$$(make poetry-activate)"; \ + echo "" ; \ + echo "The environment can also be used through the 'poetry run ' command."; \ + echo "" ; \ + echo " Ex: poetry run python "; \ + elif [ $(DEFAULT_INSTALL_ENV) = "venv" ]; then \ + make -s venv-activate ; \ + echo "" ; \ + echo "You can also use the eval bash command : eval \$$(make venv-activate)"; \ + elif [ $(DEFAULT_INSTALL_ENV) = "conda" ]; then \ + make -s conda-activate ; \ + echo "" ; \ + echo "You can also use the eval bash command : eval \$$(make conda-activate)"; \ + fi; + @echo "" + +.PHONY: install +install: install-precommit ## Install the application package, developer dependencies and pre-commit hook + +.PHONY: install-precommit +install-precommit: install-dev ## Install the pre-commit hooks (also installs developer dependencies) + @if [ -f .git/hooks/pre-commit ]; then \ + echo "Pre-commit hook found"; \ + else \ + echo "Pre-commit hook not found, proceeding to configure it"; \ + $(POETRY_COMMAND) run pre-commit install; \ + fi; + +.PHONY: install-dev +install-dev: poetry-install-auto _check-env ## Install the application along with developer dependencies + @$(POETRY_COMMAND) install --with dev + @make -s _remind-env-activate + +.PHONY: install-with-lab +install-with-lab: poetry-install-auto _check-env ## Install the application and it's dev dependencies, including Jupyter Lab + @$(POETRY_COMMAND) install --with dev --with lab + @make -s _remind-env-activate + + +.PHONY: install-package +install-package: poetry-install-auto _check-env ## Install the application package only + @$(POETRY_COMMAND) install + @make -s _remind-env-activate diff --git a/.make/test.make b/.make/test.make new file mode 100644 index 0000000..6c31024 --- /dev/null +++ b/.make/test.make @@ -0,0 +1,45 @@ +## -- Tests targets ------------------------------------------------------------------------------------------------- ## + +.PHONY: test +test: ## Run all tests + $(ENV_COMMAND_TOOL) nox -s test + +TEST_ARGS ?= +MARKER_TEST_ARGS = -m "$(TEST_ARGS)" +SPECIFIC_TEST_ARGS = -k "$(TEST_ARGS)" +CUSTOM_TEST_ARGS = "$(TEST_ARGS)" + +.PHONY: test-marker +test-marker: ## Run tests using pytest markers. Ex. make test-marker TEST_ARGS="" + @if [ -n "$(TEST_ARGS)" ]; then \ + $(ENV_COMMAND_TOOL) nox -s test_custom -- -- $(MARKER_TEST_ARGS); \ + else \ + echo "" ; \ + echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \ + echo "" ; \ + echo ' make test-marker TEST_ARGS=""' ; \ + echo "" ; \ + fi +.PHONY: test-specific +test-specific: ## Run specific tests using the -k option. Ex. make test-specific TEST_ARGS="" + @if [ -n "$(TEST_ARGS)" ]; then \ + $(ENV_COMMAND_TOOL) nox -s test_custom -- -- $(SPECIFIC_TEST_ARGS); \ + else \ + echo "" ; \ + echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \ + echo "" ; \ + echo ' make test-specific TEST_ARGS=""' ; \ + echo "" ; \ + fi + +.PHONY: test-custom +test-custom: ## Run tests with custom args. Ex. make test-custom TEST_ARGS="-m 'not offline'" + @if [ -n "$(TEST_ARGS)" ]; then \ + $(ENV_COMMAND_TOOL) nox -s test_custom -- -- $(CUSTOM_TEST_ARGS); \ + else \ + echo "" ; \ + echo 'ERROR : Variable TEST_ARGS has not been set, please rerun the command like so :' ; \ + echo "" ; \ + echo ' make test-custom TEST_ARGS=""' ; \ + echo "" ; \ + fi \ No newline at end of file diff --git a/.make/tests/test-script.sh b/.make/tests/test-script.sh new file mode 100755 index 0000000..4536f5b --- /dev/null +++ b/.make/tests/test-script.sh @@ -0,0 +1,244 @@ +#!/usr/bin/env bash + +SCRIPT_PATH="$(readlink -f "$0")" + +# Get the directory of the script +SCRIPT_DIR="$(dirname "$SCRIPT_PATH")" +MAKE_DIR="$(dirname "$SCRIPT_DIR")" +PROJECT_DIR="$(dirname "$MAKE_DIR")" + +TEST_ENV="$PROJECT_DIR/.testvenv" +PIPX_TEST_ENV="$PROJECT_DIR/.testvenvpipx" + +# Test base.make + +base() { + echo "" + echo "###" + echo "### Test base targets" + echo "###" + echo "" + echo "### Running 'make targets': ###" + echo "" + cd "$PROJECT_DIR" && make targets + + echo "### Running 'make version': ###" + echo "" + cd "$PROJECT_DIR" && make version + + # Test venv + + echo "" + echo "### Running 'make venv-create' and 'make venv-remove: ###" + echo "" + ( + cd "$PROJECT_DIR" && \ + make VENV_PATH="$PROJECT_PATH.testvenv" venv-create && \ + make VENV_PATH="$PROJECT_PATH.testvenv" AUTO_INSTALL=true venv-remove + ) + # Versioning + + echo "" + echo "### Running 'make bump' targets ###" + echo "" + ( + cd "$PROJECT_DIR" && \ + make bump-major dry && \ + make bump-minor dry && \ + make bump-patch dry + ) +} + +TEST_CONDA_ENV="lab-advanced-template-testing" +MAKEFILE_ARGS_CONDA_OVERRIDE="-f $PROJECT_DIR/Makefile -f $PROJECT_DIR/.make/conda.make" +conda(){ + echo "" + echo "###" + echo "### Test conda targets" + echo "###" + echo "" + ( + cd "$PROJECT_DIR" && + make $MAKEFILE_ARGS_CONDA_OVERRIDE CONDA_ENVIRONMENT_FILE="$SCRIPT_DIR/test_environment.yml" CONDA_YES_OPTION="-y" conda-create-env && \ + make $MAKEFILE_ARGS_CONDA_OVERRIDE conda-env-info && \ + make $MAKEFILE_ARGS_CONDA_OVERRIDE CONDA_ENVIRONMENT="$TEST_CONDA_ENV" conda-activate && \ + make $MAKEFILE_ARGS_CONDA_OVERRIDE CONDA_ENVIRONMENT="$TEST_CONDA_ENV" AUTO_INSTALL=true conda-poetry-install && \ + make $MAKEFILE_ARGS_CONDA_OVERRIDE CONDA_ENVIRONMENT="$TEST_CONDA_ENV" AUTO_INSTALL=true conda-poetry-uninstall && \ + make $MAKEFILE_ARGS_CONDA_OVERRIDE CONDA_ENVIRONMENT="$TEST_CONDA_ENV" AUTO_INSTALL=true conda-clean-env + ) +} + +MAKEFILE_ARGS_POETRY_OVERRIDE="-f $PROJECT_DIR/Makefile -f $PROJECT_DIR/.make/conda.make -f $PROJECT_DIR/.make/poetry.make" +lint() { + echo "" + echo "###" + echo "### Test pipx poetry targets" + echo "###" + echo "" + ( + cd "$PROJECT_DIR" && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry poetry-create-env && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry install && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry check-lint && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry check-pylint && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry check-complexity && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry fix-lint && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry precommit && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry ruff && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry ruff-fix && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry ruff-format + make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry AUTO_INSTALL=true poetry-remove-env + ) +} + +poetry(){ + echo "" + echo "###" + echo "### Test Poetry managed and venv managed installs" + echo "###" + echo "" + ( + cd "$PROJECT_DIR" && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry poetry-create-env && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry install && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=poetry AUTO_INSTALL=true poetry-remove-env && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=venv VENV_PATH="$TEST_ENV" install && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=venv VENV_PATH="$TEST_ENV" AUTO_INSTALL=true venv-remove + ) + echo "" + echo "### Test conda managed installs" + echo "" + ( + cd "$PROJECT_DIR" && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE CONDA_ENVIRONMENT_FILE="$SCRIPT_DIR/test_environment.yml" CONDA_YES_OPTION="-y" conda-create-env && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE DEFAULT_INSTALL_ENV=conda CONDA_ENVIRONMENT="$TEST_CONDA_ENV" install && \ + make $MAKEFILE_ARGS_POETRY_OVERRIDE CONDA_ENVIRONMENT="$TEST_CONDA_ENV" AUTO_INSTALL=true conda-clean-env + ) + +} + +poetry-pipx(){ + echo "" + echo "###" + echo "### Test pipx poetry targets" + echo "###" + echo "" + ( + cd "$PROJECT_DIR" && \ + make PIPX_VENV_PATH="$PIPX_TEST_ENV" poetry-install-venv && \ + make PIPX_VENV_PATH="$PIPX_TEST_ENV" AUTO_INSTALL=true poetry-uninstall-venv && \ + make poetry-install-venv + ) +} + +MAKEFILE_ARGS_UV_OVERRIDE="-f $PROJECT_DIR/Makefile -f $PROJECT_DIR/.make/uv.make" + +uv(){ + echo "" + echo "###" + echo "### Test uv managed managed installs" + echo "###" + echo "" + ( + cd "$PROJECT_DIR" && \ + make $MAKEFILE_ARGS_UV_OVERRIDE AUTO_INSTALL=true uv-migrate-from-poetry && \ + make $MAKEFILE_ARGS_UV_OVERRIDE uv-create-env && \ + make $MAKEFILE_ARGS_UV_OVERRIDE AUTO_INSTALL=true install && \ + make $MAKEFILE_ARGS_UV_OVERRIDE AUTO_INSTALL=true uv-remove-env && \ + make $MAKEFILE_ARGS_UV_OVERRIDE AUTO_INSTALL=true uv-migrate-undo && \ + rm -rf pyproject.toml.uv.backup + ) +} + +uv-pipx(){ + echo "" + echo "###" + echo "### Test pipx uv pipx targets" + echo "###" + echo "" + ( + cd "$PROJECT_DIR" && \ + make $MAKEFILE_ARGS_UV_OVERRIDE PIPX_VENV_PATH="$PIPX_TEST_ENV" uv-install-venv && \ + make $MAKEFILE_ARGS_UV_OVERRIDE PIPX_VENV_PATH="$PIPX_TEST_ENV" AUTO_INSTALL=true uv-uninstall-venv && \ + make $MAKEFILE_ARGS_UV_OVERRIDE uv-install-venv + ) +} + +all() { + base + conda + lint + poetry +} + +list () { + echo + echo "!!! Do not run this script outside of the 'lab-advanced-template' repository." + echo "This script exists only to test the makefiles for integrity when adding or" + echo "modifying targets !!!" + echo + echo " List of available tests:" + echo + echo " - base : Test 'base' targets" + echo " - conda : Test 'conda' targets" + echo " - lint : Test 'linting' targets" + echo " - poetry : Test 'poetry' targets" + echo " - poetry-pipx : Test 'poetry' targets related to pipx" + echo " - uv : Test 'uv' targets" + echo " - uv-pipx : Test 'uv' targets related to pipx" + echo " - test : Test 'test' targets" + + echo + echo " Full test suite" + echo + echo " - all : Run most tests, except 'poetry-pipx'" + echo + +} + +if [[ "$#" -eq 0 ]]; then + list +fi + +for var in "$@" +do + # Order is set according to use, not alphabetical order + case "$var" in + "list") + list + ;; + "base") + base + ;; + "conda") + conda + ;; + "lint") + lint + ;; + "poetry") + poetry + ;; + "poetry-pipx") + poetry-pipx + ;; + "uv") + uv + ;; + "uv-pipx") + uv-pipx + ;; + "all") + all + ;; + *) + echo "* * * * * * * * * * * * * * * * * * * * * * * * * " + echo "* ""$var"" is not a valid input " + echo "* Use the list command to see available inputs" + echo "* * * * * * * * * * * * * * * * * * * * * * * * *" + echo + list + echo + exit 1 + esac +done \ No newline at end of file diff --git a/.make/tests/test_environment.yml b/.make/tests/test_environment.yml new file mode 100644 index 0000000..3cd99a6 --- /dev/null +++ b/.make/tests/test_environment.yml @@ -0,0 +1,6 @@ +name: lab-advanced-template-testing +channels: + - conda-forge +dependencies: + - python=3.11 + diff --git a/.make/uv.make b/.make/uv.make new file mode 100644 index 0000000..13c07dd --- /dev/null +++ b/.make/uv.make @@ -0,0 +1,312 @@ +# Project and Private variables and targets import to override variables for local +# This is to make sure, sometimes the Makefile includes don't work. + +## -- UV targets ------------------------------------------------------------------------------------------------ ## +ENV_COMMAND_TOOL := uv run + +.PHONY: uv-install-auto +uv-install-auto: + uv --version; \ + if [ $$? != "0" ]; then \ + @make -s uv-install-venv; \ + fi; + +.PHONY: uv-install +uv-install: ## Install uv interactively. + @echo "Looking for uv version...";\ + uv --version; \ + if [ $$? != "0" ]; then \ + if [ "$(AUTO_INSTALL)" = "true" ]; then \ + ans="y";\ + else \ + echo "uv not found..."; \ + echo "Looking for pipx version...";\ + pipx_found=0; \ + pipx --version; \ + if [ $$? != "0" ]; then \ + pipx_found=1; \ + echo "pipx not found..."; \ + echo""; \ + echo -n "Would you like to install pipx and uv? [y/N]: "; \ + else \ + echo""; \ + echo -n "Would you like to install uv using pipx? [y/N]: "; \ + fi; \ + read ans; \ + fi; \ + case $$ans in \ + [Yy]*) \ + if [ $$pipx_found == "1" ]; then \ + echo""; \ + echo -e "\e[1;39;41m-- WARNING --\e[0m The following pip has been found and will be used to install pipx: "; \ + echo " -> "$$(which pip); \ + echo""; \ + echo "If you do not have write permission to that environment, using it to install pipx will fail."; \ + echo "If this is the case, you should install pipx using a virtual one."; \ + echo""; \ + echo "See documentation for more information."; \ + echo""; \ + echo -n "Would you like to use the local available pip above, or create virtual environment to install pipx? [local/virtual]: "; \ + read ans_how; \ + case $$ans_how in \ + "LOCAL" | "Local" |"local") \ + make -s uv-install-local; \ + ;; \ + "VIRTUAL" | "Virtual" | "virtual") \ + make -s uv-install-venv; \ + ;; \ + *) \ + echo ""; \ + echo -e "\e[1;39;41m-- WARNING --\e[0m Option $$ans_how not found, exiting process."; \ + echo ""; \ + exit 1; \ + esac; \ + else \ + echo "Installing uv"; \ + make -s _pipx_install_uv; \ + fi; \ + ;; \ + *) \ + echo "Skipping installation."; \ + echo " "; \ + ;; \ + esac; \ + fi; + +.PHONY: _pipx_install_uv +_pipx_install_uv: + @pipx install uv + + +PIPX_VENV_PATH := $$HOME/.pipx_venv +.PHONY: uv-install-venv +uv-install-venv: ## Install standalone uv. Will install pipx in $HOME/.pipx_venv + @pipx --version; \ + if [ $$? != "0" ]; then \ + echo "Creating virtual environment using venv here : [$(PIPX_VENV_PATH)]"; \ + python3 -m venv $(PIPX_VENV_PATH); \ + echo "Activating virtual environment [$(PIPX_VENV_PATH)]"; \ + source $(PIPX_VENV_PATH)/bin/activate; \ + pip3 install pipx; \ + pipx ensurepath; \ + source $(PIPX_VENV_PATH)/bin/activate && make -s _pipx_install_uv ; \ + else \ + make -s _pipx_install_uv ; \ + fi; + +.PHONY: uv-install-local +uv-install-local: ## Install standalone uv. Will install pipx with locally available pip. + @pipx --version; \ + if [ $$? != "0" ]; then \ + echo "pipx not found; installing pipx"; \ + pip3 install pipx; \ + pipx ensurepath; \ + fi; + @echo "Installing UV" + @make -s _pipx_install_uv + +.PHONY: uv-create-env +uv-create-env: ## Create a virtual environment for uv, using the project's python version. + @uv python install $(PYTHON_VERSION) + @uv venv --python $(PYTHON_VERSION) + +.PHONY: uv-activate +uv-activate: ## Print out the shell command to activate the project's uv environment. + @make -s venv-activate + +.PHONY: uv-remove-env +uv-remove-env: ## Remove current project's uv managed environment. + @make -s venv-remove + +.PHONY: uv-uninstall +uv-uninstall: uv-remove-env ## Uninstall pipx-installed uv and the created environment + @if [ "$(AUTO_INSTALL)" = "true" ]; then \ + ans="y";\ + else \ + echo""; \ + echo -n "Would you like to uninstall pipx-installed uv? [y/N]: "; \ + read ans; \ + fi; \ + case $$ans in \ + [Yy]*) \ + pipx --version ; \ + if [ $$? != "0" ]; then \ + echo "" ; \ + echo "Pipx not found globally, trying with $(PIPX_VENV_PATH) env" ;\ + echo "" ; \ + source $(PIPX_VENV_PATH)/bin/activate && pipx uninstall uv ; \ + else \ + pipx uninstall uv ; \ + fi; \ + ;; \ + *) \ + echo "Skipping uninstallation."; \ + echo " "; \ + ;; \ + esac; \ + +.PHONY: uv-uninstall-pipx +uv-uninstall-pipx: uv-remove-env ## Uninstall pipx-installed uv, the created uv environment and pipx + @if [ "$(AUTO_INSTALL)" = "true" ]; then \ + ans="y";\ + else \ + echo""; \ + echo -n "Would you like to uninstall pipx-installed uv and pipx? [y/N]: "; \ + read ans; \ + fi; \ + case $$ans in \ + [Yy]*) \ + pipx --version ; \ + if [ $$? != "0" ]; then \ + echo "" ; \ + echo "Pipx not found globally, trying with $(PIPX_VENV_PATH) env" ;\ + echo "" ; \ + source $(PIPX_VENV_PATH)/bin/activate && pipx uninstall uv && pip uninstall -y pipx; \ + else \ + pipx uninstall uv ; \ + pip uninstall -y pipx ;\ + fi; \ + ;; \ + *) \ + echo "Skipping uninstallation."; \ + echo " "; \ + ;; \ + esac; \ + +.PHONY: uv-uninstall-venv +uv-uninstall-venv: uv-remove-env ## Uninstall pipx-installed uv, the created uv environment, pipx and $HOME/.pipx_venv + @if [ "$(AUTO_INSTALL)" = "true" ]; then \ + ans="y";\ + else \ + echo""; \ + echo -n "Would you like to uninstall pipx-installed uv and pipx? [y/N]: "; \ + read ans; \ + fi; \ + case $$ans in \ + [Yy]*) \ + (source $(PIPX_VENV_PATH)/bin/activate && pipx uninstall uv); \ + (source $(PIPX_VENV_PATH)/bin/activate && pip uninstall -y pipx); \ + ;; \ + *) \ + echo "Skipping uninstallation."; \ + echo " "; \ + ;; \ + esac; \ + + @if [ "$(AUTO_INSTALL)" = "true" ]; then \ + ans="y";\ + else \ + echo""; \ + echo -n "Would you like to remove the virtual environment located here : [$(PIPX_VENV_PATH)] ? [y/N]: "; \ + read ans; \ + fi; \ + case $$ans in \ + [Yy]*) \ + rm -r $(PIPX_VENV_PATH); \ + ;; \ + *) \ + echo "Skipping [$(PIPX_VENV_PATH)] virtual environment removal."; \ + echo ""; \ + ;; \ + esac; \ + +PHONY: uv-migrate-from-poetry +uv-migrate-from-poetry: ## Migrate the project's default poetry 'pyproject.toml' to uv. + @if [ "$(AUTO_INSTALL)" = "true" ]; then \ + ans="y";\ + else \ + echo""; \ + echo -n "Would you like to convert your current pyproject.toml file to use uv instead of poetry ? [y/N]: "; \ + read ans; \ + fi; \ + case $$ans in \ + [Yy]*) \ + echo "Creating backup copy of current pyproject.toml file"; \ + cp pyproject.toml pyproject.toml.poetry.backup ; \ + echo "Migrating pyproject.toml file to use uv"; \ + uvx migrate-to-uv --dependency-groups-strategy keep-existing; \ + if [ -e pyproject.toml.uv.backup ]; then \ + echo "pyproject.toml.uv.backup file found. Proceeding to delete it."; \ + rm pyproject.toml.uv.backup ; \ + fi; \ + ;; \ + *) \ + echo "Skipping pyproject.toml migration."; \ + echo ""; \ + ;; \ + esac; \ + +PHONY: uv-migrate-undo +uv-migrate-undo: ## Undo previous migration of the project's default poetry 'pyproject.toml' to uv. + @if [ "$(AUTO_INSTALL)" = "true" ]; then \ + ans="y";\ + else \ + echo""; \ + echo -n "Would you like to revert your current pyproject.toml file to use the previous backup of the file ? [y/N]: "; \ + read ans; \ + fi; \ + case $$ans in \ + [Yy]*) \ + echo "Checking if backup pyproject.toml file exists"; \ + if [ -e "$(PROJECT_PATH)/pyproject.toml.poetry.backup" ]; then \ + echo "Backup file found"; \ + echo "Making backup of current uv pyproject.toml"; \ + cp "$(PROJECT_PATH)/pyproject.toml" "$(PROJECT_PATH)/pyproject.toml.uv.backup" ; \ + echo "Reverting pyproject.toml file to previous poetry backup."; \ + cp "$(PROJECT_PATH)pyproject.toml.poetry.backup" "$(PROJECT_PATH)/pyproject.toml" ; \ + echo "Removing previous poetry backup."; \ + rm "$(PROJECT_PATH)/pyproject.toml.poetry.backup" ; \ + echo "Removing uv.lock file."; \ + rm "$(PROJECT_PATH)/uv.lock" ; \ + else \ + echo ""; \ + echo "Backup file not found. Skipping migration undo"; \ + fi; \ + ;; \ + *) \ + echo "Skipping pyproject.toml migration."; \ + echo ""; \ + ;; \ + esac; \ + + +## -- Install targets (All install targets will install uv if not found using 'make uv-install-auto')---------------- ## +.PHONY: _remind-env-activate +_remind-env-activate: + @echo "" + @echo "Activate your environment using the following command:" + @echo "" + @make -s uv-activate + @echo "" + @echo "You can also use the following command line to interact with the environment" + @echo "" + @echo " $$ uv run " + @echo "" + +.PHONY: install +install: install-precommit ## Install the application package, developer dependencies and pre-commit hook + +.PHONY: install-precommit +install-precommit: install-dev ## Install the pre-commit hooks (also installs developer dependencies) + @if [ -f .git/hooks/pre-commit ]; then \ + echo "Pre-commit hook found"; \ + else \ + echo "Pre-commit hook not found, proceeding to configure it"; \ + $(ENV_COMMAND_TOOL) pre-commit install; \ + fi; + +.PHONY: install-dev +install-dev: uv-install-auto ## Install the application along with developer dependencies + @uv sync --group dev + @make -s _remind-env-activate + +.PHONY: install-with-lab +install-with-lab: uv-install-auto ## Install the application and it's dev dependencies, including Jupyter Lab + @uv --group dev --group lab + @make -s _remind-env-activate + + +.PHONY: install-package +install-package: uv-install-auto ## Install the application package only + @uv sync + @make -s _remind-env-activate diff --git a/.mdformat.toml b/.mdformat.toml new file mode 100644 index 0000000..802e359 --- /dev/null +++ b/.mdformat.toml @@ -0,0 +1,2 @@ +number = true +extensions = ["gfm", "gfm_alerts"] diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 3971ae8..5057701 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,4 +1,4 @@ -exclude: "^docs/|/migrations/" +exclude: "^docs/|/migrations/|Makefile*" default_stages: [ commit ] repos: @@ -18,8 +18,18 @@ repos: args: ["--maxkb=5000"] files: '^(?!data/usa_polygon_5070\.gpkg$)(?!data/s2_grid_usa_polygon_5070\.gpkg$).*$' + - repo: https://github.com/PyCQA/autoflake + rev: v2.3.1 + hooks: + - id: autoflake + + - repo: https://github.com/hhatto/autopep8 + rev: v2.3.2 + hooks: + - id: autopep8 + - repo: https://github.com/psf/black - rev: 23.12.1 + rev: 24.8.0 hooks: - id: black @@ -46,6 +56,21 @@ repos: hooks: - id: flynt + - repo: https://github.com/tcort/markdown-link-check + rev: v3.13.7 + hooks: + - id: markdown-link-check + args: [ -q ] + + - repo: https://github.com/hukkin/mdformat + rev: 0.7.22 + hooks: + - id: mdformat + additional_dependencies: + - mdformat-gfm + - mdformat-gfm-alerts + + # sets up .pre-commit-ci.yaml to ensure pre-commit dependencies stay up to date ci: autoupdate_schedule: weekly diff --git a/CHANGES.md b/CHANGES.md index 655d322..f09b30e 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,29 +1,36 @@ # CHANGES.md -[Unreleased](https://github.com/RolnickLab/geospatial-tools/tree/main) (latest) -------------------------------------------------------------------------------------- +## [Unreleased](https://github.com/RolnickLab/geospatial-tools/tree/main) (latest) -[//]: # (New changes here in list form) +______________________________________________________________________ -[0.1.3](https://github.com/RolnickLab/geospatial-tools/tree/0.1.3) (2024-09-23) -------------------------------------------------------------------------------------- +- Refactor the stac.py module to extract logic that belongs more in raster.py +- Update the makefile +- Update the project dependencies +- Add new QA tools : `autoflake`, `autopep8` and `ruff` + +## [0.1.3](https://github.com/RolnickLab/geospatial-tools/tree/0.1.3) (2024-09-23) + +______________________________________________________________________ - Convert project to use `nox` instead of `tox` for cluster storage optimization. -[0.1.2](https://github.com/RolnickLab/geospatial-tools/tree/0.1.2) (2024-09-23) -------------------------------------------------------------------------------------- +## [0.1.2](https://github.com/RolnickLab/geospatial-tools/tree/0.1.2) (2024-09-23) + +______________________________________________________________________ - Fix `docformatter` with missing extra dependency for use with `pyproject.toml` +## [0.1.1](https://github.com/RolnickLab/geospatial-tools/tree/0.1.1) (2024-09-20) -[0.1.1](https://github.com/RolnickLab/geospatial-tools/tree/0.1.1) (2024-09-20) -------------------------------------------------------------------------------------- +______________________________________________________________________ - Fix `black` dependency that was not correctly setup in dev dependency group -[0.1.0](https://github.com/RolnickLab/geospatial-tools/tree/0.1.0) (2024-09-20) -------------------------------------------------------------------------------------- - +## [0.1.0](https://github.com/RolnickLab/geospatial-tools/tree/0.1.0) (2024-09-20) + +______________________________________________________________________ + - Add `resample_tiff_raster.py` script - Implement functions for clipping and reprojecting raster images - Implement vector functions for grid creation @@ -32,4 +39,4 @@ - Implement functions and scripts to search for and process Sentinel 2 products from Microsoft's Planetary Computer - Add examples of the above in Jupyter notebook formats -- Add tests and notebook tests \ No newline at end of file +- Add tests and notebook tests diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 81f0991..e439538 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -17,7 +17,7 @@ To add a new dependency with a specific version: poetry add "==" ``` -To add a new dependency to a specific group of dependencies +To add a new dependency to a specific group of dependencies (for example, the development dependencies): ``` @@ -25,36 +25,37 @@ poetry add --group dev ``` ## Design patterns + Two main considerations should be made when contributing to this package. First, a polymorphic approach, using abstract classes and their concrete implementation, should be prioritized in order to increase maintainability and extensibility. Therefore, new additions should try to follow this design pattern and either implement -new concrete classes or create new abstract classes and their implementations for +new concrete classes or create new abstract classes and their implementations for completely new behavior or needs. -Avoid multiple levels of inheritance; the approach should be _AbstractClass -> -[ConcreteClass1, ConcreteClass2, ...]_ and not +Avoid multiple levels of inheritance; the approach should be _AbstractClass -> +[ConcreteClass1, ConcreteClass2, ...]_ and not _AbstractClass -> ChildClass -> GrandChildClass -> ..._ -Next, a dependency-injection approach is to be preferred, as well as a composition +Next, a dependency-injection approach is to be preferred, as well as a composition approach when creating new modules or extending existing ones. Functional approaches are also acceptable when appropriate, but classes should still -be used for data management/representation. This can be done with either regular +be used for data management/representation. This can be done with either regular classes, `dataclasses`, or `pydantic` models. ## Tests -New contributions should include appropriate tests. Pytest is the preferred library to +New contributions should include appropriate tests. Pytest is the preferred library to use for testing in this project. To get started and to learn more about testing in Python: -* [Getting started with testing](https://realpython.com/python-testing/) -* [Testing in the contest of Machine Learning](https://fullstackdeeplearning.com/course/2022/lecture-3-troubleshooting-and-testing/) -* [Pytest Documentation](https://docs.pytest.org/en/stable/how-to/index.html) +- [Getting started with testing](https://realpython.com/python-testing/) +- [Testing in the contest of Machine Learning](https://fullstackdeeplearning.com/course/2022/lecture-3-troubleshooting-and-testing/) +- [Pytest Documentation](https://docs.pytest.org/en/stable/how-to/index.html) ## Docstring and type hinting diff --git a/Makefile b/Makefile index 1bc3994..7ca3c48 100644 --- a/Makefile +++ b/Makefile @@ -1,19 +1,48 @@ ######################################################################################## # -# DO NOT MODIFY!!! +# MODIFY WITH CARE!!! # If necessary, override the corresponding variable and/or target, or create new ones # in one of the following files, depending on the nature of the override : # # `Makefile.variables`, `Makefile.targets` or `Makefile.private`, # -# The only valid reason to modify this file is to fix a bug or to add new +# The only valid reason to modify this file is to fix a bug or to add/remove # files to include. +# +# REMEMBER!!! +# This is a project level config, any changes here will affect all other users +# ######################################################################################## - -#Include base makefile +# +# Necessary make files +# include .make/base.make -# Include custom targets and variables + +# +# Optional makefiles - Comment/uncomment the targets you want for the project +# +## Conda targets +include .make/conda.make + +## Poetry targets - !!! If using Poetry, you should comment out the UV file below and consider +## if you need the conda file above !!! +include .make/poetry.make + +## UV targets - !!! If using UV, you should comment out the poetry file above, and possibly the conda file too !!! +#include .make/uv.make + +## Linting targets +include .make/lint.make + +## Test related targets +include .make/test.make + +# +# Project related makefiles +# +## Custom targets and variables -include Makefile.targets -include Makefile.variables -# Private variables and targets import to override variables for local + +## Private variables and targets import to override variables for local -include Makefile.private diff --git a/Makefile.private.example b/Makefile.private.example index be83cd0..148bd0d 100644 --- a/Makefile.private.example +++ b/Makefile.private.example @@ -16,13 +16,28 @@ ## Private variables +# Most, but not all install/remove targets use this variable. A 'false' value will ask +# users to confirm some steps. A 'true' value will automatically install/remove without +# asking beforehand. +AUTO_INSTALL := false + +# The default environment to use. The choices are as follow: [venv, poetry, conda] +# If this is not set, the makefile will use the `poetry` command without activating +# an environment before hand. +DEFAULT_INSTALL_ENV := venv + +# The default environment where Poetry will be installed. The choices are as follow: [venv, conda] +# If this is not set, the makefile will ask the user where they want to install Poetry +#DEFAULT_POETRY_INSTALL_ENV := venv + + +# This variable is to enable the '-y' flag when newer version of conda is available. +# The default Mila conda module does not allow this flag; leave blanks or commented out +#CONDA_YES_OPTION := -y + # If you use a different Conda tool, say `micromamba`, or if you use a different alias # CONDA_TOOL := DOCKER_COMPOSE := docker compose -# Some targets use this variable. A 'false' value will ask user to confirm some steps. -# a 'true' value will automatically install/remove without asking beforehand. -AUTO_INSTALL := false - ## -- Private targets ------------------------------------------------------------------------------------------------## diff --git a/Makefile.targets b/Makefile.targets index 078a1eb..e4f8a33 100644 --- a/Makefile.targets +++ b/Makefile.targets @@ -5,4 +5,4 @@ .PHONY: test-notebooks test-notebooks: ## Execute test notebooks using pytest and nbval - nox -s test_nb \ No newline at end of file + $(ENV_COMMAND_TOOL) nox -s test_nb \ No newline at end of file diff --git a/README.md b/README.md index 9a4fb48..1d303af 100644 --- a/README.md +++ b/README.md @@ -1,23 +1,31 @@ # Geospatial-Tools +## Description + +This repository is a collection of tools and scripts for geospatial use cases. + ## Requirements This project has only been tested in a Linux (Debian based) environment and assumes some basic tools for development are already installed. -The project uses a Makefile to automate most operations. If `make` is available on your +The project uses a Makefile to automate most operations. If `make` is available on your machine there's a good chance this will work. The following Makefile files should not be modified, but can be consulted: -* [Makefile](Makefile) : Orchestration of the different files -* [base.make](.make/base.make) : Shared utilities, project agnostic. +- [Makefile](Makefile) : Orchestration of the different files +- [base.make](.make/base.make) : Shared utilities, project agnostic. The following Makefile files are project or user specific: -* [Makefile.variables](Makefile.variables) : Shared project variables. -* [Makefile.targets](Makefile.targets) : Shared project targets. -* [Makefile.private](Makefile.private.example) : User specific variables and targets. +- [Makefile.variables](Makefile.variables) : Shared project variables. +- [Makefile.targets](Makefile.targets) : Shared project targets. +- [Makefile.private](Makefile.private.example) : User specific variables and targets. + - This file is ignored by git and should never be committed, as it can also contain + secrets. + - You can create your own version locally by copying from + [Makefile.private.example](Makefile.private.example) ## Basic Information @@ -32,136 +40,261 @@ This project uses Python version 3.11 ## Build Tool -This project uses Poetry as a build tool. Using a build tool has the advantage of +This project uses `poetry` as a build tool. Using a build tool has the advantage of streamlining script use as well as fix path issues related to imports. -## Installation - -This project assumes environment management will be done with `Conda` or directly through -`Poetry`. +## First Time User Quick Setup -* [Poetry](https://python-poetry.org/docs/basic-usage/) -* [Conda](https://conda.io/projects/conda/en/latest/user-guide/getting-started.html) +### Installing poetry -While it is possible to manage the environment with, for example, pyenv or virtualenv, -those specific use cases are not supported by the Makefile and require users to set up -their own environments beforehand. +If on a compute cluster, first load the appropriate python module: -For detailed information about `Poetry` and `Conda`: +- [How to create a virtual environment for the Mila cluster](docs/environment_creation_mila.md) +- [How to create an environment for the DRAC cluster](docs/environment_creation_drac.md) -If you want to use something else than `Conda` or `Poetry` to manage environment isolation, -it is recommended to follow -[Poetry's guidelines on managing environments](https://python-poetry.org/docs/managing-environments/) +Installing `pipx` and `poetry`: -Poetry is not included in the [environment.yml](environment.yml), due to some possible problems -in compute cluster environments, but will be installed automatically if needed -by most `install` targets. - -### Environment Management +```shell +make poetry-install +``` -You will need to create a virtual environment for your dependencies. +Next, let's choose how to manage our development environment -* [How to create a virtual environment for the Mila cluster](docs/environment_creation_mila.md) -* [How to create an environment for the DRAC cluster](docs/environment_creation_drac.md) -* [How to create a Conda environment](docs/conda_environment_creation.md) -* [Migrating to DRAC from another environment](docs/migrating_to_drac.md) +### Environment management choice -Do note that Conda is not available on the DRAC cluster, and there are some extra steps -to use Conda on the Mila cluster compared to a workstation. +Choose between managing your development with either `virtualenv`, `poetry` or `conda`. -#### Environment management choices +#### Virtualenv (or Venv) -Environment management can become quite complicated. Using Conda allows a certain -ease of management since the Poetry installation is contained inside the created Conda -environment. +This is the simplest way and what most people in the lab are already used to. -However, some computing environments do not permit the use of Conda (like certain SLURM -clusters). This is why the `pipx` option for Poetry is also enabled. To -install `pipx`, a user needs to have write access for the current environment, which is -why, for compatibility reasons, we install it in a lightweight, standalone virtual environment. +Make sure that `python 3.10 or 3.11` is available either locally, through loaded cluster +modules (ex. `module load python/`) or `pyenv` before executing the +following command: -*Disclaimer for those that already know a lot about Poetry...* +```shell +make venv-create +``` -Yes, `Poetry` can manage environments directly, and there are a lot of other more advanced -uses that are not explored in this repository. This is done on purpose, as an introduction -to this tool in a context that is familiar for most users (i.e. creating virtual environments -with venv/virtualenv/conda). If you are comfortable with `Poetry` and especially its use -on compute clusters, feel free to disregard the recommendations below. Just don't forget -to document its use for the project! +You can see the shell command to activate the environment with the following target: -### First Time User Quick Setup +```shell +make venv-activate +``` #### Poetry -The easiest and quickest way to get up and running with Poetry. - -Install pipx and Poetry and activate project environment : +Make sure that `python 3.10 or 3.11` is available either locally, through loaded cluster +modules (ex. `module load python/`) or `pyenv` before executing the +following command: ```shell -make poetry-install-venv +make poetry-create-env ``` -**Or, if Poetry is already available:** +Make sure to read up +on [how to use your poetry virtual environment](https://python-poetry.org/docs/basic-usage/#using-your-virtual-environment) + +You can: + +- Use the `poetry run` command to access your executables + - ex. `poetry run python your_script.py`, or `poetry run pylint src/` +- Use the `poetry shell` command to activate and step in your project environment + +#### Conda + +Reminder: `conda` is not available on DRAC. + +If working on the Mila cluster, first load the appropriate module : +`module load anaconda/3` + +1. Create `conda` environment (will check for `conda` and install it if not found): ```shell -make poetry-create-env +make conda-create-env ``` -Install package: +2. Activate `conda` environment (substitute with your \ if something else + than `conda`: -```shell -make install +``` +conda activate ``` -#### Conda -The easiest and quickest way to get up and running with Conda. +### Install -Create Conda environment (will check for Conda and install it if not found): +Once the environment is taken care of, you can verify everything with the following +command before continuing: ```shell -make conda-create-env +make poetry-env-info ``` -Activate Conda environment (substitute with your if something else -than `conda`: +or -``` -conda activate geospatial-tools +```shell +poetry env info ``` -Install package: +To install the package and its dependencies: ```shell make install ``` -### In depth Environment and Install Targets +This also installs and configures the `pre-commit` hook. See ... + +### Development + +1. [Add required dependencies](./CONTRIBUTING.md#adding-dependencies) +2. Create some new modules in the [src](./src) folder! + +## Detailed documentation + +This project assumes environment management will be done with `conda`, a classic +python virtual environment, or directly through `poetry`. + +- [Poetry](https://python-poetry.org/docs/basic-usage/) +- [Conda](https://conda.io/projects/conda/en/latest/user-guide/getting-started.html) + +While it is possible to manage the environment with, for example, pyenv or virtualenv, +those specific use cases are not supported by the Makefile and require users to set up +their own environments beforehand. + +If you want to use something else than `conda` or `poetry` to manage environment isolation, +it is recommended to follow +[Poetry's guidelines on managing environments](https://python-poetry.org/docs/managing-environments/) + +`poetry` is not included in the [environment.yml](environment.yml), due to some possible problems +in compute cluster environments, but will be installed automatically if needed +by most `install` targets. + +See [Environment and Install targets](docs/makefile_environment_targets.md) for more +information. + +### Environment Management + +Your project will need a virtual environment for your dependencies. + +- [How to create a virtual environment for the Mila cluster](docs/environment_creation_mila.md) +- [How to create an environment for the DRAC cluster](docs/environment_creation_drac.md) +- [How to create a Conda environment](docs/conda_environment_creation.md) +- [Migrating to DRAC from another environment](docs/migrating_to_drac.md) + +There are different ways of managing your python version in these environments. On the +clusters, you have access to different python modules, and through `conda` you have access +to practically all the versions that are available. + +However, on your own system, if you do not wish to use `conda`, you will have to either +manually install different versions of python manually for them to be usable by `poetry` +or use a tool like [pyenv](https://github.com/pyenv/pyenv). + +Do note that `conda` is not available on the DRAC cluster, and there are some extra steps +to use `conda` on the Mila cluster compared to a workstation. + +#### How to use conda with poetry + +When using `conda`, it is important to understand that it is both an environment management +tool AND a dependency management tool... and so is `poetry`. The difference is that with `conda` +you can install different versions of python, as well as have access to non +python applications and binary packages. -See [Environment and Install targets](docs/makefile_environment_targets.md) +To use them together, it is recommended to use `conda` as the environment and python +version manager, for non-python dependencies, and use `poetry` as the python +dependency manager. -## Useful targets for development +Using both `conda` and `poetry` (and `pip` directly, for that matter), to install and +manage python dependencies is a great recipe for breaking your environment. + +If you do need to install python dependencies in both (ex. pytorch through `conda`, and +others using `poetry`), you need to be cautious as one dependency manager can and will +interfere with the dependencies managed by the other one and will make dependency +conflicts challenging to fix. + +If there are no ways around it, you could also manage and use two environments at the same time +(one via conda and one via poetry). This, however, requires an enormous amount of discipline +to work and is strongly discouraged. + +#### Environment management choices + +The choice of which environment manager to use between `conda` and `poetry` is ultimately +determined by either project requirements or personal preference. Both are allowed and +supported by this project. + +### Installation + +There are a few installation targets available. + +![](img/install_targets.png) + +Generally, `make install` is the most useful, but the others can have their uses. +For example, using `make install-package` is great for an environment where +you will only be executing your code and do no development. + +### Useful Makefile targets for development + +To run linting checks with `flake8`, `pylint`, `black`, `isort` and `docformatter`: -To run linting checks with `flake8`, `pylint`, `black` and `isort`: ```shell make check-lint ``` -To fix linting with `black`, `flynt` and `isort`: +To fix linting with `autoflake`,`autopep8`,`black`, `isort`, `flynt` and `docformatter`: + ```shell make fix-lint ``` To run a `pre-commit` check before actually committing: + ```shell make precommit ``` To run tests: + ```shell make test ``` +#### The use of Nox + +Behind the scenes, the targets in this section make use of the +[Nox automation tool](https://nox.thea.codes/en/stable/). + +The configurations can be found in the [noxfile.py](noxfile.py) file. + +For more information about how `nox` is used in this project, see +[Nox session descriptions](docs/nox_session_descriptions.md). + +#### Experimental targets + +The `ruff` tool is now also available in the makefile. This tool is not yet integrated +into the `pre-commit` configuration and should be used, optionally, as a complement to +the other code quality tools. + +To run linting using `ruff`: + +```shell +make ruff +``` + +To run linting using `ruff` and fix automatically fixable warnings: + +```shell +make ruff-fix +``` + +To run code formatting using `ruff` + +```shell +make ruff-format +``` + +For more information of `ruff`, see it's [official documentation here](https://docs.astral.sh/ruff/). + ## Configurations + Configurations are in the [config/](configs) folder. ## Data diff --git a/data/README.md b/data/README.md index ce6b693..f52f328 100644 --- a/data/README.md +++ b/data/README.md @@ -4,10 +4,10 @@ ### International -* [NASA's EarthData](https://www.earthdata.nasa.gov/) -* [USGS Earth Explorer](https://earthexplorer.usgs.gov/) -* [Copernicus Open Access Hub](https://scihub.copernicus.eu/) -* [Climate Data Store](https://cds.climate.copernicus.eu/cdsapp#!/home) +- [NASA's EarthData](https://www.earthdata.nasa.gov/) +- [USGS Earth Explorer](https://earthexplorer.usgs.gov/) +- [Copernicus Open Access Hub](https://scihub.copernicus.eu/) +- [Climate Data Store](https://cds.climate.copernicus.eu/cdsapp#!/home) ## Satellite data @@ -25,9 +25,9 @@ The tiling grid can be found here in KML format : [](https://sentiwiki.copernicu ### Canada -* [GEO.ca](https://geo.ca/) : Canada's geographic information portal -* [Données Québec](https://www.donneesquebec.ca/) : Quebec's open data portal +- [GEO.ca](https://geo.ca/) : Canada's geographic information portal +- [Données Québec](https://www.donneesquebec.ca/) : Quebec's open data portal ### USA -* [Cartographic Boundaries, Census Office](https://www.census.gov/geographies/mapping-files/time-series/geo/carto-boundary-file.html) +- [Cartographic Boundaries, Census Office](https://www.census.gov/geographies/mapping-files/time-series/geo/carto-boundary-file.html) diff --git a/docs/conda_environment_creation.md b/docs/conda_environment_creation.md index 982222d..9ce51ef 100644 --- a/docs/conda_environment_creation.md +++ b/docs/conda_environment_creation.md @@ -1,23 +1,49 @@ # Creating a Conda Environment -First, read the [Conda section](https://docs.mila.quebec/Userguide.html#conda) +First, read the [Conda section](https://docs.mila.quebec/Userguide.html#conda) in Mila's documentation. +To make full use of the Conda makefile target, make sure to define the variables found +in [Makefile.variables](../Makefile.variables) appropriately, and ensure that +the `CONDA_ENVIRONMENT` variable lines up with the name defined in the +[environment.yml](../environment.yml) file. + ## Install Conda -If you still need to install a newer version of Conda, or if you want to install -it on your personal computer: + +**Warning!!!** + +**Unless absolutely necessary, it is not recommended to install a local +version of Conda when using a compute cluster like Mila or DRAC. You should only +install Conda if you will be working directly on your local machine.** + +If you need to install a newer version of Miniconda, or if you want to install +it for the first time on your personal computer: ```shell make conda-install ``` +### Alternative : Mamba + +You can also choose to install [micromamba](https://mamba.readthedocs.io/en/latest/index.html) +as an alternative or a complement to miniconda. + +If you do install mamba, make sure to create a renamed copy of +[Makefile.private.example](../Makefile.private.example) -> `Makefile.private` and set +the `CONDA_TOOL` variable to `CONDA_TOOL := micromamba` so the Makefile can use it. + +```shell +make mamba-install +``` + ## Environment Creation Creating a Conda Environment is relatively straightforward with the makefile. -First, make sure the name of the environment has been updated in the +First, make sure the name of the environment has been updated in the [environment.yml file](../environment.yml) before running the following command: -``` + +```shell make conda-create-env ``` @@ -26,5 +52,18 @@ make conda-create-env Once created, the environment must be activated: ``` +# If using micromamba, replace 'conda' with 'micromamba' conda activate -``` \ No newline at end of file +``` + +You can use this command to see the command as configured for the project: + +```shell +make conda-activate +``` + +You can also use the eval command to activate the environment: + +```shell +eval $(make conda-activate) +``` diff --git a/docs/environment_creation_drac.md b/docs/environment_creation_drac.md index c3b0802..6b2956d 100644 --- a/docs/environment_creation_drac.md +++ b/docs/environment_creation_drac.md @@ -1,109 +1,115 @@ - # Environment Creation and Management for DRAC First things first, read the amazing [DRAC Python documentation](https://docs.alliancecan.ca/wiki/Python). -If you are also new to using Slurm clusters, please read -[Getting started with DRAC](https://docs.alliancecan.ca/wiki/Getting_started) and +If you are also new to using Slurm clusters, please read +[Getting started with DRAC](https://docs.alliancecan.ca/wiki/Getting_started) and [How to run jobs on the DRAC cluster](https://docs.alliancecan.ca/wiki/Running_jobs) -Below are simplified steps on how to create and manage a virtual environment on the +Below are simplified steps on how to create and manage a virtual environment on the DRAC cluster. ## Pre-built Python wheels and available modules -DRAC offers pre-build Python wheels for commonly used libraries. You can [consult them +DRAC offers pre-build Python wheels for commonly used libraries. You can [consult them here](https://docs.alliancecan.ca/wiki/Available_Python_wheels). -However, many libraries, or newer versions of those libraries, are not available through +However, many libraries, or newer versions of those libraries, are not available through those wheels. -For some libraries, like Pytorch or scientific libraries like Numpy, it can be +For some libraries, like Pytorch or scientific libraries like Numpy, it can be better/simpler to use the pre-built versions. -For secondary or simple utility libraries, like `pytest`, `flake8` or `requests`, using -versions from the pre-built wheels might not be critical or even preferred, as using +For secondary or simple utility libraries, like `pytest`, `flake8` or `requests`, using +versions from the pre-built wheels might not be critical or even preferred, as using the latest versions might be better overall. -While there are generally no problems with building your virtual environment with -Pypi versions of the libraries on DRAC, sometimes this can lead to poorer performance and/or -runtime errors. What's more, you also won't be available to build your environment -inside your job ([like recommended here](https://docs.alliancecan.ca/wiki/Python#Creating_virtual_environments_inside_of_your_jobs)), +While there are generally no problems with building your virtual environment with +Pypi versions of the libraries on DRAC, sometimes this can lead to poorer performance and/or +runtime errors. What's more, you also won't be available to build your environment +inside your +job ([like recommended here](https://docs.alliancecan.ca/wiki/Python#Creating_virtual_environments_inside_of_your_jobs)), unless you are working on Cedar, since its nodes have access to internet. -Do note that building your environment inside your job can help with some performance +Do note that building your environment inside your job can help with some performance issues, but it is not required. -See [Managing Dependencies](#managing-dependencies-on-drac) below for more information +See [Managing Dependencies](#managing-dependencies-on-drac) below for more information on how to install dependencies from the local pre-built wheels. **Important note** -While working on DRAC with pre-built Python wheels, the use of the `poetry.lock` file is not recommended; -use [Tilde requirements](https://python-poetry.org/docs/dependency-specification/#tilde-requirements) +While working on DRAC with pre-built Python wheels, the use of the `poetry.lock` file is not recommended; +use [Tilde requirements](https://python-poetry.org/docs/dependency-specification/#tilde-requirements) instead to ensure reproducibility across different environments. ## Creating an environment on the DRAC cluster -The preferred method of creating a virtual environment for the DRAC cluster is +The preferred method of creating a virtual environment for the DRAC cluster is with `virtualenv` First, a python module is loaded by default on DRAC. To see the available modules: + ``` module avail python ``` + To load a particular model (assuming 3.11.5 is available): + ``` module load python/3.11.5 ``` Then create the environment: + ``` virtualenv ``` ## Managing dependencies on DRAC -### The 3 choices +### The three choices -* Limit your self exclusively to DRAC's pre-built wheels, and code anything that's +- Limit yourself exclusively to DRAC's pre-built wheels, and code anything that's missing yourself. -* Don't use pre-build wheels at all -* Use a mix of the 2. +- Don't use pre-build wheels at all +- Use a mix of the 2. -The first 2 are pretty straight forward, but using a mix of dependency sources will +The first 2 are pretty straight forward, but using a mix of dependency sources will require careful tracking and documentation. -Dependencies intended to be installed from pre-built wheels should go in the -`[tool.poetry.dependencies]` section of the `pyproject.toml` file, while other -dependencies should be added to an optional dependency group, which can then be installed +Dependencies intended to be installed from pre-built wheels should go in the +`[tool.poetry.dependencies]` section of the `pyproject.toml` file, while other +dependencies should be added to an optional dependency group, which can then be installed with `poetry` ([See Adding Dependencies](../CONTRIBUTING.md#adding-dependencies)) -For example, dependencies intended to be installed from DRAC's pre-build wheels should -be added manually in the `[tool.poetry.dependencies]` section of the `pyproject.toml` file -and installed using the `pip install -e . --no-index` command from the root of your -repository root. +For example, dependencies intended to be installed from DRAC's pre-build wheels should +be added manually in the `[tool.poetry.dependencies]` section of the `pyproject.toml` file +and installed using the `pip install -e . --no-index` command from the root of your +repository root. -For the other dependencies, an optional dependency group should be created in the -`pyproject.toml` file. Make sure to [make the group optional](https://python-poetry.org/docs/managing-dependencies/#optional-groups). -Dependencies can be added to this group using the `poetry add --group ` +For the other dependencies, an optional dependency group should be created in the +`pyproject.toml` file. Make sure +to [make the group optional](https://python-poetry.org/docs/managing-dependencies/#optional-groups). +Dependencies can be added to this group using the `poetry add --group ` and can be installed with the command `poetry install --with ` ### Reproducibility -If using any dependencies from the DRAC pre-built wheels, you will still need to -document the versions in a way that users outside DRAC can still use your code. +If using any dependencies from the DRAC pre-built wheels, you will still need to +document the versions in a way that users outside DRAC can still use your code. -For example : the requests library +For example, the requests library *as of July 24th, 2024* -* Version available on DRAC : `2.31.0` -* Full version (what we see with `pip list`) : `requests==2.31.0+computecanada` - * This version is obviously not available outside DRAC -* How to add it to the pyproject.toml: - * If not on DRAC, you can use poetry to add it using `poetry add requests~2.31.0` - * If on DRAC, add it manually to the pyproject.toml file under the `[tool.poetry.dependencies]` section : `requests = "~2.31.0"` +- Version available on DRAC : `2.31.0` +- Full version (what we see with `pip list`) : `requests==2.31.0+computecanada` + - This version is not available outside DRAC +- How to add it to the pyproject.toml: + - If not on DRAC, you can use poetry to add it using `poetry add requests~2.31.0` + - If on DRAC, add it manually to the pyproject.toml file under the `[tool.poetry.dependencies]` section : + `requests = "~2.31.0"` -This will help ensure reproducibility between environments even when using pre-built +This will help ensure reproducibility between environments even when using pre-built wheel versions of Python dependencies. diff --git a/docs/environment_creation_mila.md b/docs/environment_creation_mila.md index c79b6d7..bbc6e37 100644 --- a/docs/environment_creation_mila.md +++ b/docs/environment_creation_mila.md @@ -1,26 +1,43 @@ # Creating a Virtual Environment on the Mila Cluster -On the Mila cluster, both `venv` and `virtualenv` can be used to create a virtual +On the Mila cluster, both `venv` and `virtualenv` can be used to create a virtual environment. First, load the python module: + ``` -module load python/3.11 +module load python/3.10 ``` Then, for `venv`: + ``` python3 -m venv ``` or for `virtualenv`: + ``` virtualenv ``` -where `` is the path where the environment will be created. It normally -should be inside your project's folder (but ignored by git), and commonly named `.env`, -`.venv`. +where `` is the path where the environment will be created. It normally +should be inside your project's folder (but ignored by git), and commonly named ` `.venv\`. + +- _On a side note, `.env` is generally reserved for a text file listing + environment variables, used by various tools like `python-dotenv` and `docker compose`_ + +You can also make use of the following makefile targets: + +```shell +# To create a .venv environment +make venv-create +``` + +```shell +# To remove the .venv environment +make venv-remove +``` You can then activate your environment using the following commandline: @@ -28,4 +45,17 @@ You can then activate your environment using the following commandline: source /bin/activate ``` -After the environment is created and activated, follow the [Poetry Instructions](../README.md#poetry) \ No newline at end of file +If you used the `make venv-create` target, or create it at `/.venv`, +you can also use: + +```shell +# To get the path for activation +make venv-activate +``` + +```shell +# To activate it +eval $(make venv-activate) +``` + +After the environment is created and activated, follow the [Poetry Instructions](../README.md#poetry) diff --git a/docs/makefile_environment_targets.md b/docs/makefile_environment_targets.md index 8b6adc8..aefaedf 100644 --- a/docs/makefile_environment_targets.md +++ b/docs/makefile_environment_targets.md @@ -1,90 +1,175 @@ # Environment and Installation Related Makefile Targets -## Poetry targets +## Venv targets -There are 2 possibilities available in how to manage `Poetry` if it is not already +There are three targets in the makefile to help with streamling classic python virtual +environments. + +```shell +# Create a virtual environment at /.venv/ +make venv-create +``` + +```shell +# Get the path to activate the virtual environment created at /.venv/ +make venv-activate +``` + +```shell +# Activate the virtual environment using the path returned by 'make venv-activate' +eval $(make venv-activate) +``` + +```shell +# Remove a virtual environment at /.venv/ +make venv-remove +``` + +## Poetry install targets + +### Installing poetry + +There are two possibilities available to manage `poetry` if it is not already configured on your system. -**It is not recommended to install `Poetry` in the same environment that will be managed -by `Poetry`; It should be installed by `Conda` (as in, `conda install poetry`) or -on the system using `pipx`, in order to minimize dependency conflicts.** +**It is generally not recommended to install `poetry` in the same environment that will +be managed by `poetry`; It is preferable to install it on the system using `pipx`, +to minimize dependency conflicts.** + +That being said, having `poetry` installed in a `conda` environment, and using `poetry` +to manage that same `conda` environment is not the end of the world and is an acceptable +workaround for some projects. + +See the [official documentation on how to install poetry](https://python-poetry.org/docs/#installation) +for more details if you prefer to install `poetry` manually. + +The following target will install `poetry` interactively, asking questions along the way: + +```shell +make poetry-install +``` -The following target will first try to install `Poetry` in the active `Conda` -environment; if it can't find `Conda`, it will proceed to install via `pipx` +To install `poetry` in a non-interactive way, you can instead use this target: ```shell make poetry-install-auto ``` -To install `Poetry` using `Conda`: +The above target will try to install `poetry` according to the `DEFAULT_POETRY_INSTALL_ENV` +Makefile variable; if it's not defined, installation of `poetry` will proceed via `pipx`. + +The `DEFAULT_POETRY_INSTALL_ENV` variable can be set in your local `Makefile.private` file. +If you don't have one, this file can be created by copying from the +[Makefile.private.example](../Makefile.private.example) file. + +If you know exactly how you want to install `poetry`, you have three options: + +```shell +# This will install poetry using pipx. If pipx needs to be installed, it will be installed +# using the locally available pip. This does not work on the different compute clusters. +make poetry-install-local +``` + +```shell +# This will install poetry with pipx. If pipx needs to be install, it will be installed +# in a newly created virtual environment in $HOME/.pipx_venv. +make poetry-install-venv +``` ```shell +# This will install poetry in the projects conda environment, along side all other python +# dependencies. make conda-poetry-install ``` -Using `pipx` will instead allow environment management directly with `Poetry`. The -following target will also make `Poetry` use a Python 3.11 environment for this -project. +Both install methods have their respective cleanup targets: ```shell -make poetry-install-venv +make poetry-uninstall +``` + +```shell +make conda-poetry-uninstall ``` -This will also create a virtual environment managed by `Poetry`. +You can also use `make poetry-uninstall-pipx` or `make poetry-uninstall-venv` to also +remove the `pipx` library and the `pipx` virtualenv, respectively, depending on how you +chose to install `pipx` and `poetry`. -A standalone environment can also be created later using the `make poetry-create-env` -command, and removed with the `make poetry-remove-env` command. +### Environment creation with Poetry -Information about the currently active environment used by Poetry, -whether Conda or Poetry, can be seen using the `make poetry-env-info` command. +Using `poetry` to create a virtual environment is different from creating one using `venv` +or `virtualenv`, as they are centralized and managed by `poetry`. -Both install methods can also be cleaned up: +A `poetry` virtual environment can be created using the following target: ```shell -make conda-poetry-uninstall +make poetry-create-env ``` -or + +and be removed with: + ```shell -make poetry-uninstall-pipx +make poetry-remove-env ``` -**Important note!** +Information about the currently active environment used by Poetry, +whether Conda or Poetry, can be seen using: -If you have an active `Conda` environment and install `Poetry` using `pipx`, -you will have to use `poetry run python ` instead of -`python `, (which is normal when using Poetry) as -`python` will use Conda's active environment. +```shell +poetry-env-info +``` ## Conda Targets +### Installing Conda + If you need or want to install Conda: + ```shell make conda-install ``` +```shell +# Alternatively, you can also install micromamba. +make mamba-install +``` + +On the Mila cluster, it is preferable to use the available `anaconda` module instead: + +```shell +module load anaconda/3 +``` + +### Environment creation + To create the conda environment: + ```shell make conda-create-env ``` To remove the conda environment: + ```shell make conda-clean-env ``` -Make sure to activate the configured environment before installing. +Make sure to activate the configured environment before using the install targets. ## Install targets **All `install` targets will first check if `Poetry` is available and try to install it with the `make poetry-install-auto` target.** -To install the package, development dependencies and CLI tools (if available): +To install the package, development dependencies, and CLI tools (if available): + ```shell make install ``` To install only the package, without development tools: + ```shell make install-package ``` diff --git a/docs/migrating_to_drac.md b/docs/migrating_to_drac.md index 5e3f091..dbb0924 100644 --- a/docs/migrating_to_drac.md +++ b/docs/migrating_to_drac.md @@ -2,28 +2,29 @@ DISCLAIMER -Working across multiple clusters (ex. Mila and DRAC) at the same time can quickly -become quite complex, as you will have to manage your project dependencies very -attentively. Different versions of the same libraries can have different secondary +Working across multiple clusters (ex. Mila and DRAC) at the same time can quickly +become quite complex, as you will have to manage your project dependencies very +attentively. Different versions of the same libraries can have different secondary dependencies and their behavior can change. -While usually only true for major version changes (i.e. version X.2.1, where "X" is the number that changes), -sometimes minor version changes (i.e. 2.X.0) can also introduce breaking changes, like -function names changing, functions not working the same way or even being removed. +While usually only true for major version changes (i.e. version X.2.1, where "X" is the +number that changes), sometimes minor version changes (i.e. 2.X.0) can also introduce +breaking changes, like function names changing, functions not working the same way or +even being removed. ## Things to consider when migrating to DRAC -If your project has been initiated somewhere else, either on your own workstation -or on the Mila cluster, chances are you are using the most recent (at the time of your +If your project has been initiated somewhere else, either on your own workstation +or on the Mila cluster, chances are you are using the most recent (at the time of your project's creation) versions of your Python libraries. -The first things to consider are therefore : Are those versions available in DRAC's +The first things to consider are therefore: Are those versions available in DRAC's pre-built wheels, and do I need to use these pre-built versions? -Version differences also need to take into account. If downgrading a -library to match the version available on DRAC requires drastic changes to your code -because of breaking changes between those versions, it might be better off not -using the DRAC version if you don't have the time to make these changes (or don't +Version differences also need to take into account. If downgrading a +library to match the version available on DRAC requires drastic changes to your code +because of breaking changes between those versions. It might be better off not +using the DRAC version if you don't have the time to make these changes (or don't want to break your code in other environments outside DRAC) [See the Environment Creation and Management for DRAC document](environment_creation_drac.md) diff --git a/docs/nox_session_descriptions.md b/docs/nox_session_descriptions.md new file mode 100644 index 0000000..6dc10eb --- /dev/null +++ b/docs/nox_session_descriptions.md @@ -0,0 +1,40 @@ +# Nox sessions + +The configurations can be found in the [noxfile.py](../noxfile.py) file. + +Feel free to modify the contents of existing sessions, as well as add new ones for your +project. + +However, it would be best to avoid renaming existing ones as the Makefile expects the +current session names unless you also plan to override the existing Makefile targets +that use them. + +With the `nox` tool, individual _commands_ are called sessions, and can be executed using +the following syntax: + +```shell +nox -s +``` + +- Main `nox` sessions: + + - No session specified; executing `nox` : Runs the pre-commit configuration + - `check` Runs all checks on the code base without modifying the code + - `fix` : Runs the autoflake, autopep8, black, isort, docformatter and flynt tools on the code base + - `flake8` : Runs the `flake8` linter + - `autoflake` : Run the `autoflake` lint fixer to remove unused imports and variables + - `autopep8` : Run the `autopep8` lint fixer to automatically fix most other `flake8` warnings + - `black` : Runs the code formatter + - `isort` : Runs the import sorter + - `flynt` : Runs the `f-string` formatter + - `mdformat` : Runs the markdown formatter + - `docformatter` : Runs the docstring formatter + - `test` : Runs tests found in the `tests/` folder with `pytest` + +- `ruff` - Experimental sessions: + + - `ruff-lint` : Check lint using the `ruff` linter. This linter is stricter + than `flake8`, but less than `pylint` + - `ruff-fix` : Check lint using the `ruff` linter and automatically fix the + warnings that can be fixed by `ruff` + - `ruff-format` : Format the code using the `ruff` formatter diff --git a/docs/poetry_documentation.md b/docs/poetry_documentation.md new file mode 100644 index 0000000..1ed2612 --- /dev/null +++ b/docs/poetry_documentation.md @@ -0,0 +1,80 @@ +# Poetry Documentation + +## Considerations when using Poetry in a Compute Cluster environment + +### Version concerns on DRAC + +As of this writing (February 2025), the newest available version on DRAC for `poetry` is +`2.0.1+computecanada`, and is the version causing problems. + +Newer versions of `poetry`, `>=2.0.0` are raising errors when trying to +resolve dependencies when installing projects and adding new dependencies. + +If you encounter such issues, please try reinstalling `poetry` at a lesser version: +`pipx install 'poetry<2.0.0'`, or newer, non-computecanada versions if available. + +### Poetry Cache Management + +Whether installing `poetry` as a standalone tool or in a conda environment, cache +management is an important consideration in a shared compute cluster. + +If you maintain the default configuration, `poetry`'s cache is located +somewhere in your `$HOME` folder, ex. `$HOME/.cache/pypoetry`. + +The cache can get big quite fast. It is also something that can change a lot +over time, which is not ideal for drive that are backed up regularly, like `/projects/`. + +Since a cache is supposed to be temporary by nature, and easy to recreate +(most of the time), it can make sense to move the cache to `$SCRATCH`, +as there are very few and limited consequences if it ends up being deleted by the +`purge` policies. + +To see current configs and current `cache-dir` path : + +```bash +poetry config --list +``` + +There are a few options available in managing `poetry`'s cache in a cluster environment + +### Option 1: move the cache + +To set a new cache path: + +```bash +poetry config cache-dir /PATH/TO/SCRATCH/.cache/pypoetry +``` + +### Option 2: clean your caches periodically, or disable them + +You can view the existing caches (typically `PyPI` and `_default_cache`) : + +```bash +poetry cache list +``` + +You can clean your caches directly: + +```bash +poetry cache clear --all +``` + +Or disable them altogether: + +```bash +poetry cache clear --no-cache +``` + +### Option 3: manually skip cache when installing dependencies + +When adding dependencies : + +```bash +poetry add --no-cache +``` + +When installing a project: + +```bash +poetry install --no-cache +``` diff --git a/docs/uv_documentation.md b/docs/uv_documentation.md new file mode 100644 index 0000000..083e647 --- /dev/null +++ b/docs/uv_documentation.md @@ -0,0 +1,291 @@ +# UV + +`uv` is an alternative tool for dependency management, like `poetry` and `conda`. +It is blazingly fast and also comes with the possibility of easily getting access to +other versions of Python without tools like `pyenv`. + +However, using `conda` together with `uv` can be very cumbersome and is not really recommended, +as the most useful dependency management features of `uv` will not work. If you really +want to use `uv` together with `conda`, see [using uv-pip](#note-about-using-pip-with-uv) + +Therefore, if you require binary dependencies from `conda` (non-python dependencies likes +`cdo`, for example), it is recommended to use the classic `poetry` version of this +template, unless you have other ways of installing those dependencies. + +This README is a quick and concise guide to get you started. Reading the +[official documentation](https://docs.astral.sh/uv/) is wholeheartedly recommended, as +you'll find yourself rapidly limited in what you can do. + +## Getting started. + +The only thing you have to do is start your project off from the template, like +[described here](https://github.com/RolnickLab/lab-basic-template/blob/main/README.md#initialization), +and then replace the contents of the +`pyproject.toml` file with the one present in this branch. + +## Install UV + +`uv` first needs to be installed. + +The recommended way to install `uv` is with `pipx`. + +On your personal computer, you can do the following: + +```shell +pip install pipx +pipx ensurepath +pipx install uv +``` + +On compute clusters, like Mila and DRAC, you won't be able to use the default pip +available after loading a python module. + +You will first need to create and activate a base virtual environment in which you have +write access. + +For example, on the Mila cluster: + +``` +module load python/3.10 +python3 -m venv ~/.pipx_env +source ~/.base_env/bin/activate +``` + +Next, `pipx` and `uv` can be installed using this new virtual environment's `pip`: + +``` +pip install pipx +pipx ensurepath +pipx install uv +``` + +The `pipx` way is pretty straightforward, but you can also install `uv` +many other ways, which are documented here: +[uv installation methods](https://docs.astral.sh/uv/getting-started/installation/#installation-methods) + +## Setting up your environment + +First download the version of python you want for your environment with `uv`: + +```shell +# As an example, here is for python 3.12 +uv python install 3.12 +``` + +Then create your environment: + +```shell +uv venv --python 3.12 +``` + +### DRAC problems with uv venv + +Creating an environment using `uv` on DRAC can create problems, most probably because +of the custom indexing and python wheels (exact reason has not been confirmed yet). + +On the DRAC cluster, it is therefore preferred to load the python module and then create the environment +manually: + +```shell +module load python/3.12 +virtualenv --no-download .venv +source .venv/bin/activate +``` + +## Using uv with the makefile + +First, make sure that the `uv` targets are activated, and that the `poetry` targets +are commented out in the [Makefile](../Makefile) main file. + +To install `uv` on your system: + +```shell +make uv-install +``` + +To create a new virtual environment: + +```shell +make uv-create-env +``` + +To see the required command to activate your new environment: + +```shell +make uv-activate +``` + +To migrate a `poetry` `pyproject.toml` file to uv: + +```shell +make uv-migrate-from-poetry +``` + +For more information, see the `uv` target description with the following command: + +```shell +make targets +``` + +To install the application: + +```shell +make install +``` + +## Installing and managing dependencies manually + +To first install the dependencies, after creating and activating the environment: + +```shell +uv sync +``` + +To install the dev dependencies: + +```shell +uv sync --group dev +``` + +To add a dependency: + +```shell +uv add +``` + +To add a dependency to the dev group: + +```shell +uv add --group dev +``` + +For more information about managing dependencies with `uv`, see the following +documentation [Managing dependencies with uv](https://docs.astral.sh/uv/guides/projects/#managing-dependencies) + +### Installing DRAC custom wheels + +To install dependencies like described in the +[DRAC documentation](https://docs.alliancecan.ca/wiki/Python#Creating_and_using_a_virtual_environment), +you can use the `--offline` flag, with either `sync` or `add`. + +Ex: + +```shell +uv sync --offline +``` + +You should also consider updating your `pyproject.toml` file with the following: + +```toml +[tool.uv] +python-preference = "system" + +## From https://docs.astral.sh/uv/reference/settings/#index-strategy: +## "Only use results from the first index that returns a match for a given package name." +## In other words: only get the package from PyPI if there isn't a version of it in the DRAC wheelhouse. +# index-strategy = "first-index" + +## "Search for every package name across all indexes, exhausting the versions from the first index before +## moving on to the next" +## In other words: Only get the package from PyPI if the requested version is higher than the version +## in the DRAC wheelhouse. +# index-strategy = "unsafe-first-match" + +## "Search for every package name across all indexes, preferring the "best" version found. +## If a package version is in multiple indexes, only look at the entry for the first index." +## In other words: Consider all versions of the package DRAC + PyPI, and use the version that best matches +## the requested version. In a tie, choose the DRAC wheel. +index-strategy = "unsafe-best-match" + +[[tool.uv.index]] +name = "drac-gentoo2023-x86-64-v3" +url = "/cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo2023/x86-64-v3" +format = "flat" + +[[tool.uv.index]] +name = "drac-gentoo2023-generic" +url = "/cvmfs/soft.computecanada.ca/custom/python/wheelhouse/gentoo2023/generic" +format = "flat" + +[[tool.uv.index]] +name = "drac-generic" +url = "/cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic" +format = "flat" +``` + +### Note about using pip with uv + +While it is possible to use `pip`, you should try to avoid it when possible, for two reasons: + +- If you do have to use `pip`, you should always use `uv pip`, as you will benefit + from `uv`'s speed. Moreover, you could have another active `pip`, even if your `.venv` has + been sourced; which will cause your use of `pip` to interact with another environment. +- Using `uv pip` does not update the `pyproject.toml` file, and does not update OR use + the `uv.lock` file, which means you have to set your dependencies manually. + +This last point is not necessarily a dealbreaker, and in some situations it might even +be necessary, like if you want to use `uv` with existing repositories that use +`requirements.txt` files. + +You will, however, lose one of the most powerful features of `uv` that ensures your +environment is easily reproducible. + +One more thing that is **very important** to note: + +`uv pip` will always interact with the **active** +**environment**. This means that if you have your `.venv` environment in your repository, +but you also have, say, the base `conda` environment active, `uv pip` will interact +with the `conda` environment. + +This is one way of working with both `conda` and `uv`, +but like mentioned above, you lose the ability to automatically manage your +`pyproject.toml` file and won't be able to use `uv.lock` file. + +Consult the documentation to learn more about [uv's pip interfare](https://docs.astral.sh/uv/pip/). + +## Using uv + +To list the installed dependencies: + +```shell +uv pip list +``` + +If you have sourced your `.venv`, you can use `python` and other tools through the +command line like you are used to. + +You can also use the `uv run` command instead. Without the need to +manually source your `.venv` folder, this command allows access to your environment and +the installed dependencies - This is already taken into account in the Makefile targets: + +```shell +# Execute a python script +uv run python scripts/my_python_script.py +``` + +```shell +# Execute the pre-commit check +uv run pre-commit run --all-files +``` + +For the development tool `nox`, you still have to be at the root of the repository, as +the command requires the presence of the `noxfile.py`: + +```shell +# Don't forget to install the dev dependencies first with +# uv sync --group dev + +uv run nox -s ruff-lint +``` + +## Converting to UV from poetry manually + +You can easily convert your current `poetry` pyproject.toml file to `uv` with the following commands: + +```shell +echo "Creating backup copy of current pyproject.toml file" +cp pyproject.toml pyproject.toml.poetry.backup + +echo "Migrating pyproject.toml file to use uv" +uvx migrate-to-uv --dependency-groups-strategy keep-existing +``` diff --git a/geospatial_tools/geotools_types.py b/geospatial_tools/geotools_types.py index 5ea9d0e..b13de62 100644 --- a/geospatial_tools/geotools_types.py +++ b/geospatial_tools/geotools_types.py @@ -1,7 +1,5 @@ """This module contains constants and functions pertaining to data types.""" -from typing import Tuple, Union - from shapely.geometry import ( GeometryCollection, LineString, @@ -12,5 +10,5 @@ Polygon, ) -BBoxLike = Tuple[float, float, float, float] -IntersectsLike = Union[Point, Polygon, LineString, MultiPolygon, MultiPoint, MultiLineString, GeometryCollection] +BBoxLike = tuple[float, float, float, float] +IntersectsLike = Point | Polygon | LineString | MultiPolygon | MultiPoint | MultiLineString | GeometryCollection diff --git a/geospatial_tools/planetary_computer/sentinel_2.py b/geospatial_tools/planetary_computer/sentinel_2.py index 46ebffb..9fef5f7 100644 --- a/geospatial_tools/planetary_computer/sentinel_2.py +++ b/geospatial_tools/planetary_computer/sentinel_2.py @@ -2,7 +2,6 @@ import logging import pathlib from concurrent.futures import ThreadPoolExecutor, as_completed -from typing import Optional, Union from geopandas import GeoDataFrame @@ -35,7 +34,7 @@ def __init__( sentinel2_tiling_grid_column: str, vector_features: GeoDataFrame, vector_features_column: str, - date_ranges: Optional[list[str]] = None, + date_ranges: list[str] | None = None, max_cloud_cover: int = 5, max_no_data_value: int = 5, logger: logging.Logger = LOGGER, @@ -127,7 +126,7 @@ def create_date_ranges(self, start_year: int, end_year: int, start_month: int, e ) return self.date_ranges - def find_best_complete_products(self, max_cloud_cover: Optional[int] = None, max_no_data_value: int = 5) -> dict: + def find_best_complete_products(self, max_cloud_cover: int | None = None, max_no_data_value: int = 5) -> dict: """ Finds the best complete products for each Sentinel 2 tiles. This function will filter out all products that have more than 5% of nodata values. @@ -193,7 +192,7 @@ def select_best_products_per_feature(self) -> GeoDataFrame: self.vector_features_with_products = spatial_join_results return self.vector_features_with_products - def to_file(self, output_dir: Union[str, pathlib.Path]) -> None: + def to_file(self, output_dir: str | pathlib.Path) -> None: write_results_to_file( cloud_cover=self.max_cloud_cover, successful_results=self.successful_results, @@ -208,7 +207,7 @@ def sentinel_2_complete_tile_search( date_ranges: list[str], max_cloud_cover: int, max_no_data_value: int = 5, -) -> Optional[tuple[int, str, Optional[float], Optional[float]]]: +) -> tuple[int, str, float | None, float | None] | None: client = StacSearch(PLANETARY_COMPUTER) collection = "sentinel-2-l2a" tile_ids = [tile_id] @@ -280,7 +279,7 @@ def find_best_product_per_s2_tile( def _get_best_product_id_for_each_grid_tile( s2_tile_search_results: dict, feature_s2_tiles: GeoDataFrame, logger: logging.Logger = LOGGER -) -> Optional[str]: +) -> str | None: search_result_keys = s2_tile_search_results.keys() all_keys_present = all(item in search_result_keys for item in feature_s2_tiles) if not all_keys_present: @@ -321,9 +320,9 @@ def write_best_product_ids_to_dataframe( def write_results_to_file( cloud_cover: int, successful_results: dict, - incomplete_results: Optional[list] = None, - error_results: Optional[list] = None, - output_dir: Union[str, pathlib.Path] = DATA_DIR, + incomplete_results: list | None = None, + error_results: list | None = None, + output_dir: str | pathlib.Path = DATA_DIR, logger: logging.Logger = LOGGER, ) -> dict: tile_filename = output_dir / f"data_lt{cloud_cover}cc.json" @@ -358,8 +357,8 @@ def download_and_process_sentinel2_asset( product_id: str, product_bands: list[str], collections: str = "sentinel-2-l2a", - target_projection: Optional[Union[int, str]] = None, - base_directory: Union[str, pathlib.Path] = DATA_DIR, + target_projection: int | str | None = None, + base_directory: str | pathlib.Path = DATA_DIR, delete_intermediate_files: bool = False, logger: logging.Logger = LOGGER, ) -> Asset: diff --git a/geospatial_tools/raster.py b/geospatial_tools/raster.py index f7b44c7..9f4cd12 100644 --- a/geospatial_tools/raster.py +++ b/geospatial_tools/raster.py @@ -6,7 +6,6 @@ import time from concurrent.futures import ProcessPoolExecutor from multiprocessing import cpu_count -from typing import Optional, Union import geopandas as gpd import rasterio @@ -21,11 +20,11 @@ def reproject_raster( - dataset_path: Union[str, pathlib.Path], - target_crs: Union[str, int], - target_path: Union[str, pathlib.Path], + dataset_path: str | pathlib.Path, + target_crs: str | int, + target_path: str | pathlib.Path, logger: logging.Logger = LOGGER, -) -> Union[pathlib.Path, None]: +) -> pathlib.Path | None: """ Parameters @@ -76,12 +75,12 @@ def reproject_raster( def _clip_process( - raster_image: Union[pathlib.Path, str], + raster_image: pathlib.Path | str, id_polygon: tuple[int, GeoDataFrame], - base_output_filename: Optional[str], - output_dir: Union[pathlib.Path, str], + base_output_filename: str | None, + output_dir: pathlib.Path | str, logger: logging.Logger = LOGGER, -) -> Union[tuple[int, GeoDataFrame, pathlib.Path], None]: +) -> tuple[int, GeoDataFrame, pathlib.Path] | None: """ Parameters @@ -132,17 +131,17 @@ def _clip_process( else: logger.warning( f"There was an error writing the file :[Polygon ID: {polygon_id}" - f"\nPolygon: {polygon}\nError message: {str(e)}]" + f"\nPolygon: {polygon}\nError message: {e!s}]" ) return None def clip_raster_with_polygon( - raster_image: Union[pathlib.Path, str], - polygon_layer: Union[pathlib.Path, str, GeoDataFrame], - base_output_filename: Optional[str] = None, - output_dir: Union[str, pathlib.Path] = DATA_DIR, - num_of_workers: Optional[int] = None, + raster_image: pathlib.Path | str, + polygon_layer: pathlib.Path | str | GeoDataFrame, + base_output_filename: str | None = None, + output_dir: str | pathlib.Path = DATA_DIR, + num_of_workers: int | None = None, logger: logging.Logger = LOGGER, ) -> list[pathlib.Path]: """ @@ -195,7 +194,7 @@ def clip_raster_with_polygon( polygons = gdf["geometry"] ids = gdf.index - id_polygon_list = zip(ids, polygons) + id_polygon_list = zip(ids, polygons, strict=False) logger.info(f"Clipping raster image with {len(polygons)} polygons") with ProcessPoolExecutor(max_workers=workers) as executor: futures = [ @@ -219,7 +218,7 @@ def clip_raster_with_polygon( return path_list -def get_total_band_count(raster_file_list: list[Union[pathlib.Path, str]], logger: logging.Logger = LOGGER) -> int: +def get_total_band_count(raster_file_list: list[pathlib.Path | str], logger: logging.Logger = LOGGER) -> int: """ Parameters @@ -244,7 +243,7 @@ def get_total_band_count(raster_file_list: list[Union[pathlib.Path, str]], logge def create_merged_raster_bands_metadata( - raster_file_list: list[Union[pathlib.Path, str]], logger: logging.Logger = LOGGER + raster_file_list: list[pathlib.Path | str], logger: logging.Logger = LOGGER ) -> dict: """ @@ -266,12 +265,12 @@ def create_merged_raster_bands_metadata( def merge_raster_bands( - raster_file_list: list[Union[pathlib.Path, str]], - merged_filename: Union[pathlib.Path, str], + raster_file_list: list[pathlib.Path | str], + merged_filename: pathlib.Path | str, merged_band_names: list[str] = None, merged_metadata: dict = None, logger: logging.Logger = LOGGER, -) -> Optional[pathlib.Path]: +) -> pathlib.Path | None: """ This function aims to combine multiple overlapping raster bands into a single raster image. diff --git a/geospatial_tools/stac.py b/geospatial_tools/stac.py index 3a820cc..75c77c3 100644 --- a/geospatial_tools/stac.py +++ b/geospatial_tools/stac.py @@ -3,7 +3,6 @@ import logging import pathlib import time -from typing import Optional, Union import pystac import pystac_client @@ -30,7 +29,7 @@ PLANETARY_COMPUTER_API = "https://planetarycomputer.microsoft.com/api/stac/v1" -def create_planetary_computer_catalog(max_retries=3, delay=5, logger=LOGGER) -> Union[pystac_client.Client, None]: +def create_planetary_computer_catalog(max_retries=3, delay=5, logger=LOGGER) -> pystac_client.Client | None: """ Creates a Planetary Computer Catalog Client. @@ -53,7 +52,7 @@ def create_planetary_computer_catalog(max_retries=3, delay=5, logger=LOGGER) -> return None -def catalog_generator(catalog_name, logger=LOGGER) -> Optional[pystac_client.Client]: +def catalog_generator(catalog_name, logger=LOGGER) -> pystac_client.Client | None: catalog_dict = {PLANETARY_COMPUTER: create_planetary_computer_catalog} if catalog_name not in catalog_dict: logger.error(f"Unsupported catalog name: {catalog_name}") @@ -70,7 +69,7 @@ def list_available_catalogs(logger: logging.Logger = LOGGER) -> frozenset[str]: class AssetSubItem: - def __init__(self, asset, item_id: str, band: str, filename: Union[str, pathlib.Path]): + def __init__(self, asset, item_id: str, band: str, filename: str | pathlib.Path): if isinstance(filename, str): filename = pathlib.Path(filename) self.asset = asset @@ -83,10 +82,10 @@ class Asset: def __init__( self, asset_id: str, - bands: Optional[list[str]] = None, - asset_item_list: Optional[list[AssetSubItem]] = None, - merged_asset_path: Optional[Union[str, pathlib.Path]] = None, - reprojected_asset: Optional[Union[str, pathlib.Path]] = None, + bands: list[str] | None = None, + asset_item_list: list[AssetSubItem] | None = None, + merged_asset_path: str | pathlib.Path | None = None, + reprojected_asset: str | pathlib.Path | None = None, logger: logging.Logger = LOGGER, ): self.asset_id = asset_id @@ -110,8 +109,8 @@ def show_asset_items(self): self.logger.info(f"Asset list for asset [{self.asset_id}] : \n\t{asset_list}") def merge_asset( - self, base_directory: Optional[Union[str, pathlib.Path]] = None, delete_sub_items: bool = False - ) -> Union[pathlib.Path, None]: + self, base_directory: str | pathlib.Path | None = None, delete_sub_items: bool = False + ) -> pathlib.Path | None: if not base_directory: base_directory = "" if isinstance(base_directory, str): @@ -142,8 +141,8 @@ def merge_asset( def reproject_merged_asset( self, - target_projection: Union[str, int], - base_directory: Union[str, pathlib.Path] = None, + target_projection: str | int, + base_directory: str | pathlib.Path = None, delete_merged_asset: bool = False, ): if not base_directory: @@ -199,25 +198,25 @@ class StacSearch: def __init__(self, catalog_name, logger=LOGGER): self.catalog: pystac_client.Client = catalog_generator(catalog_name=catalog_name) - self.search_results: Optional[list[pystac.Item]] = None - self.cloud_cover_sorted_results: Optional[list[pystac.Item]] = None - self.filtered_results: Optional[list[pystac.Item]] = None - self.downloaded_search_assets: Optional[list[Asset]] = None - self.downloaded_cloud_cover_sorted_assets: Optional[list[Asset]] = None + self.search_results: list[pystac.Item] | None = None + self.cloud_cover_sorted_results: list[pystac.Item] | None = None + self.filtered_results: list[pystac.Item] | None = None + self.downloaded_search_assets: list[Asset] | None = None + self.downloaded_cloud_cover_sorted_assets: list[Asset] | None = None self.downloaded_best_sorted_asset = None self.logger = logger def search( self, date_range=None, - max_items: Optional[int] = None, - limit: Optional[int] = None, - ids: Optional[list] = None, - collections: Optional[Union[str, list]] = None, - bbox: Optional[geotools_types.BBoxLike] = None, - intersects: Optional[geotools_types.IntersectsLike] = None, - query: Optional[dict] = None, - sortby: Optional[Union[list, dict]] = None, + max_items: int | None = None, + limit: int | None = None, + ids: list | None = None, + collections: str | list | None = None, + bbox: geotools_types.BBoxLike | None = None, + intersects: geotools_types.IntersectsLike | None = None, + query: dict | None = None, + sortby: list | dict | None = None, max_retries=3, delay=5, ) -> list: @@ -312,13 +311,13 @@ def search( def search_for_date_ranges( self, date_ranges: list[str], - max_items: Optional[int] = None, - limit: Optional[int] = None, - collections: Optional[Union[str, list]] = None, - bbox: Optional[geotools_types.BBoxLike] = None, - intersects: Optional[geotools_types.IntersectsLike] = None, - query: Optional[dict] = None, - sortby: Optional[Union[list, dict]] = None, + max_items: int | None = None, + limit: int | None = None, + collections: str | list | None = None, + bbox: geotools_types.BBoxLike | None = None, + intersects: geotools_types.IntersectsLike | None = None, + query: dict | None = None, + sortby: list | dict | None = None, max_retries=3, delay=5, ) -> list: @@ -401,14 +400,14 @@ def search_for_date_ranges( def _base_catalog_search( self, date_range: str, - max_items: Optional[int] = None, - limit: Optional[int] = None, - ids: Optional[list] = None, - collections: Optional[Union[str, list]] = None, - bbox: Optional[geotools_types.BBoxLike] = None, - intersects: Optional[geotools_types.IntersectsLike] = None, - query: Optional[dict] = None, - sortby: Optional[Union[list, dict]] = None, + max_items: int | None = None, + limit: int | None = None, + ids: list | None = None, + collections: str | list | None = None, + bbox: geotools_types.BBoxLike | None = None, + intersects: geotools_types.IntersectsLike | None = None, + query: dict | None = None, + sortby: list | dict | None = None, ): search = self.catalog.search( datetime=date_range, @@ -431,7 +430,7 @@ def _base_catalog_search( log_state(log_msg) return list(items) - def sort_results_by_cloud_coverage(self) -> Optional[list]: + def sort_results_by_cloud_coverage(self) -> list | None: """ Sort results by cloud coverage. @@ -449,7 +448,7 @@ def sort_results_by_cloud_coverage(self) -> Optional[list]: self.logger.warning("No results found: please run a search before trying to sort results") return None - def filter_no_data(self, property_name: str, max_no_data_value: int = 5) -> Optional[list[pystac.Item]]: + def filter_no_data(self, property_name: str, max_no_data_value: int = 5) -> list[pystac.Item] | None: """ Filter results and sorted results that are above a nodata value threshold. @@ -511,7 +510,7 @@ def _download_assets(self, item: pystac.Item, bands: list, base_directory: pathl return downloaded_files def _download_results( - self, results: Optional[list[pystac.Item]], bands: list, base_directory: Union[str, pathlib.Path] + self, results: list[pystac.Item] | None, bands: list, base_directory: str | pathlib.Path ) -> list[Asset]: if not results: return [] @@ -527,7 +526,7 @@ def _download_results( downloaded_search_results.append(downloaded_item) return downloaded_search_results - def download_search_results(self, bands: list, base_directory: Union[str, pathlib.Path]) -> list[Asset]: + def download_search_results(self, bands: list, base_directory: str | pathlib.Path) -> list[Asset]: """ Parameters @@ -561,7 +560,7 @@ def _generate_best_results(self): return results def download_sorted_by_cloud_cover_search_results( - self, bands: list, base_directory: Union[str, pathlib.Path], first_x_num_of_items: Optional[int] = None + self, bands: list, base_directory: str | pathlib.Path, first_x_num_of_items: int | None = None ) -> list[Asset]: """ @@ -589,9 +588,7 @@ def download_sorted_by_cloud_cover_search_results( self.downloaded_cloud_cover_sorted_assets = downloaded_search_results return downloaded_search_results - def download_best_cloud_cover_result( - self, bands: list, base_directory: Union[str, pathlib.Path] - ) -> Optional[Asset]: + def download_best_cloud_cover_result(self, bands: list, base_directory: str | pathlib.Path) -> Asset | None: """ Parameters diff --git a/geospatial_tools/utils.py b/geospatial_tools/utils.py index ac7b2a8..683d29a 100644 --- a/geospatial_tools/utils.py +++ b/geospatial_tools/utils.py @@ -8,7 +8,6 @@ import pathlib import sys import zipfile -from typing import Optional, Union import requests import yaml @@ -90,7 +89,7 @@ def get_yaml_config(yaml_config_file: str, logger: logging.Logger = LOGGER) -> d for path in potential_paths: if path.exists(): config_filepath = path - logger.info(f"Yaml config file [{str(path)}] found.") + logger.info(f"Yaml config file [{path!s}] found.") break params = {} @@ -137,7 +136,7 @@ def get_json_config(json_config_file: str, logger=LOGGER) -> dict: for path in potential_paths: if path.exists(): config_filepath = path - logger.info(f"JSON config file [{str(path)}] found.") + logger.info(f"JSON config file [{path!s}] found.") break if not config_filepath: @@ -153,7 +152,7 @@ def get_json_config(json_config_file: str, logger=LOGGER) -> dict: return {} -def create_crs(dataset_crs: Union[str, int], logger=LOGGER): +def create_crs(dataset_crs: str | int, logger=LOGGER): """ Parameters @@ -183,11 +182,10 @@ def create_crs(dataset_crs: Union[str, int], logger=LOGGER): return CRS.from_epsg(recovered_code) logger.error(f"Encountered problem while trying to format EPSG code from input : [{dataset_crs}]") + return None -def download_url( - url: str, filename: Union[str, pathlib.Path], overwrite: bool = False, logger=LOGGER -) -> Optional[pathlib.Path]: +def download_url(url: str, filename: str | pathlib.Path, overwrite: bool = False, logger=LOGGER) -> pathlib.Path | None: """ This function downloads a file from a given URL. @@ -223,9 +221,7 @@ def download_url( return None -def unzip_file( - zip_path: Union[str, pathlib.Path], extract_to: Union[str, pathlib.Path], logger: logging.Logger = LOGGER -): +def unzip_file(zip_path: str | pathlib.Path, extract_to: str | pathlib.Path, logger: logging.Logger = LOGGER): """ This function unzips an archive to a specific directory. diff --git a/geospatial_tools/vector.py b/geospatial_tools/vector.py index f2083d9..e6852c2 100644 --- a/geospatial_tools/vector.py +++ b/geospatial_tools/vector.py @@ -6,7 +6,6 @@ from concurrent.futures import ProcessPoolExecutor from multiprocessing import cpu_count from pathlib import Path -from typing import Union import dask_geopandas as dgpd import geopandas as gpd @@ -22,7 +21,7 @@ def create_grid_coordinates( - bounding_box: Union[list, tuple], grid_size: float, logger: logging.Logger = LOGGER + bounding_box: list | tuple, grid_size: float, logger: logging.Logger = LOGGER ) -> tuple[ndarray, ndarray]: """ Create grid coordinates based on input bounding box and grid size. @@ -90,7 +89,7 @@ def _create_polygons_from_coords_chunk(chunk: tuple[ndarray, ndarray, float]) -> """ lon_coords, lat_coords, grid_size = chunk polygons = [] - for lon, lat in zip(lon_coords, lat_coords): + for lon, lat in zip(lon_coords, lat_coords, strict=False): polygons.append( Polygon([(lon, lat), (lon + grid_size, lat), (lon + grid_size, lat + grid_size), (lon, lat + grid_size)]) ) @@ -98,7 +97,7 @@ def _create_polygons_from_coords_chunk(chunk: tuple[ndarray, ndarray, float]) -> def create_vector_grid( - bounding_box: Union[list, tuple], grid_size: float, crs: str = None, logger: logging.Logger = LOGGER + bounding_box: list | tuple, grid_size: float, crs: str = None, logger: logging.Logger = LOGGER ) -> GeoDataFrame: """ Create a grid of polygons within the specified bounds and cell size. This function uses NumPy vectorized arrays for @@ -142,9 +141,9 @@ def create_vector_grid( def create_vector_grid_parallel( - bounding_box: Union[list, tuple], + bounding_box: list | tuple, grid_size: float, - crs: Union[str, int] = None, + crs: str | int = None, num_of_workers: int = None, logger: logging.Logger = LOGGER, ) -> GeoDataFrame: @@ -338,7 +337,7 @@ def select_polygons_by_location( return filtered_result_gdf -def to_geopackage(gdf: GeoDataFrame, filename: Union[str, Path], logger=LOGGER) -> str: +def to_geopackage(gdf: GeoDataFrame, filename: str | Path, logger=LOGGER) -> str: """ Save GeoDataFrame to a Geopackage file. @@ -459,11 +458,13 @@ def add_and_fill_contained_column( logger.info(f"Selecting all vector features that are within {feature_name}") selected_features = select_all_within_feature(polygon_feature=polygon_feature, vector_features=vector_features) logger.info(f"Writing [{feature_name}] to selected vector features") - [ # pylint: disable=W0106 - vector_features.at[idx, vector_column_name].add(feature_name) for idx in selected_features.index - ] + + vector_features.loc[selected_features.index, vector_column_name] = vector_features.loc[ + selected_features.index, vector_column_name + ].apply(lambda s: s | {feature_name}) +# Potential outdated function def find_and_write_all_contained_features( polygon_features: gpd.GeoDataFrame, polygon_column: str, diff --git a/notebooks/README.md b/notebooks/README.md index 260fe6c..09a7493 100644 --- a/notebooks/README.md +++ b/notebooks/README.md @@ -1,3 +1,3 @@ # Notebooks -Place to store all the project's notebooks \ No newline at end of file +Place to store all the project's notebooks diff --git a/noxfile.py b/noxfile.py index f5dee8f..d89ca63 100644 --- a/noxfile.py +++ b/noxfile.py @@ -1,22 +1,28 @@ +import re from pathlib import Path import nox +ARG_RE = re.compile(r"^-[-\w=]+$") # e.g. "-k", "--maxfail=1", "tests/foo.py" + nox.options.reuse_existing_virtualenvs = True # Reuse virtual environments nox.options.sessions = ["precommit"] def get_paths(session): package_path = Path(session.bin).parent.parent.parent + main_package = package_path / "geospatial_tools" + tests = package_path / "tests" + scripts = package_path / "scripts" return { "all": [ - package_path / "geospatial_tools", - package_path / "tests", - package_path / "scripts", + main_package, + tests, + scripts, ], "module": [ - package_path / "geospatial_tools", - package_path / "scripts", + main_package, + scripts, ], } @@ -29,27 +35,25 @@ def get_paths(session): @nox.session() def pylint(session): paths = get_paths(session) - session.run("poetry", "run", "pylint", *paths["module"], external=True) + session.run("pylint", *paths["module"], external=True) @nox.session() def flake8(session): paths = get_paths(session) - session.run("poetry", "run", "flake8", *paths["all"], external=True) + session.run("flake8", *paths["all"], external=True) @nox.session() def complexity(session): paths = get_paths(session) - session.run("poetry", "run", "flake8", "--max-complexity", "7", *paths["all"], external=True) + session.run("flake8", "--max-complexity", "7", *paths["all"], external=True) @nox.session() def docformatter(session): paths = get_paths(session) session.run( - "poetry", - "run", "docformatter", "--config", f"{paths['all'][0].parent}/pyproject.toml", @@ -61,31 +65,29 @@ def docformatter(session): @nox.session() def check(session): paths = get_paths(session) - session.run("poetry", "run", "black", "--check", *paths["all"], external=True) - session.run("poetry", "run", "isort", *paths["all"], "--check", external=True) - session.run("poetry", "run", "flynt", *paths["all"], external=True) + session.run("black", "--check", *paths["all"], external=True) + session.run("isort", *paths["all"], "--check", external=True) + session.run("flynt", *paths["all"], external=True) session.run( - "poetry", - "run", "docformatter", "--config", f"{paths['all'][0].parent}/pyproject.toml", *paths["all"], external=True, ) - session.run("poetry", "run", "flake8", *paths["all"], external=True) - session.run("poetry", "run", "pylint", *paths["module"], external=True) + session.run("flake8", *paths["all"], external=True) + session.run("pylint", *paths["module"], external=True) @nox.session() def fix(session): paths = get_paths(session) - session.run("poetry", "run", "black", *paths["all"], external=True) - session.run("poetry", "run", "isort", *paths["all"], external=True) - session.run("poetry", "run", "flynt", *paths["all"], external=True) + session.run("autoflake", "-v", *paths["all"], external=True) + session.run("autopep8", *paths["all"], external=True) + session.run("black", *paths["all"], external=True) + session.run("isort", *paths["all"], external=True) + session.run("flynt", *paths["all"], external=True) session.run( - "poetry", - "run", "docformatter", "--in-place", "--config", @@ -93,48 +95,87 @@ def fix(session): *paths["all"], external=True, ) + session.run("mdformat", *paths["root"], external=True) @nox.session() def precommit(session): - session.run("poetry", "run", "pre-commit", "run", "--all-files", external=True) + session.run("pre-commit", "run", "--all-files", external=True) + + +@nox.session() +def autoflake(session): + paths = get_paths(session) + session.run("autoflake", "-v", *paths["all"], external=True) + + +@nox.session() +def autopep(session): + paths = get_paths(session) + session.run("autopep8", *paths["all"], external=True) @nox.session() def black(session): paths = get_paths(session) - session.run("poetry", "run", "black", "--check", *paths["all"], external=True) + session.run("black", "--check", *paths["all"], external=True) @nox.session() def isort(session): paths = get_paths(session) - session.run("poetry", "run", "isort", *paths["all"], "--check", external=True) + session.run("isort", *paths["all"], "--check", external=True) @nox.session() def flynt(session): paths = get_paths(session) - session.run("poetry", "run", "flynt", *paths["all"], external=True) + session.run("flynt", *paths["all"], external=True) + + +@nox.session() +def mdformat(session): + paths = get_paths(session) + session.run("mdformat", *paths["root"], external=True) + + +@nox.session(name="ruff-lint") +def ruff_lint(session): + paths = get_paths(session) + session.run("ruff", "check", *paths["all"], external=True) + + +@nox.session(name="ruff-fix") +def ruff_fix(session): + paths = get_paths(session) + session.run("ruff", "check", "--fix", *paths["all"], external=True) + + +@nox.session(name="ruff-format") +def ruff_format(session): + paths = get_paths(session) + session.run("ruff", "format", *paths["all"], external=True) @nox.session() def test(session): - session.run("poetry", "run", "pytest", external=True) + session.run("pytest", external=True) @nox.session() def test_custom(session): + for a in session.posargs: + if not ARG_RE.match(a): + session.error(f"unsafe pytest argument detected: {a!r}") + session.run( - "poetry", "run", "pytest", external=True, *session.posargs + "python", "-m", "pytest", external=True, *session.posargs ) # Pass additional arguments directly to pytest @nox.session() def test_nb(session): session.run( - "poetry", - "run", "pytest", "--nbval", "tests/test_notebooks/", diff --git a/poetry.lock b/poetry.lock index 0ddd3da..f1e2289 100644 --- a/poetry.lock +++ b/poetry.lock @@ -28,25 +28,25 @@ files = [ [[package]] name = "anyio" -version = "4.4.0" +version = "4.9.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "anyio-4.4.0-py3-none-any.whl", hash = "sha256:c1b2d8f46a8a812513012e1107cb0e68c17159a7a594208005a57dc776e1bdc7"}, - {file = "anyio-4.4.0.tar.gz", hash = "sha256:5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94"}, + {file = "anyio-4.9.0-py3-none-any.whl", hash = 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+version = "3.22.0" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"}, - {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"}, + {file = "zipp-3.22.0-py3-none-any.whl", hash = "sha256:fe208f65f2aca48b81f9e6fd8cf7b8b32c26375266b009b413d45306b6148343"}, + {file = "zipp-3.22.0.tar.gz", hash = "sha256:dd2f28c3ce4bc67507bfd3781d21b7bb2be31103b51a4553ad7d90b84e57ace5"}, ] [package.extras] @@ -4907,10 +4842,10 @@ check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler = ["pytest-enabler (>=2.2)"] -test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +test = ["big-O", "importlib_resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] type = ["pytest-mypy"] [metadata] lock-version = "2.0" -python-versions = ">=3.10,<3.12" -content-hash = "d1e1443c0d29d8cf6c156197f7c1f7991d093beaf1a8e88e9a9d7036f081184f" +python-versions = ">=3.10,<3.13" +content-hash = "e3601ca1b1f2b6d6a9f268da4403a9c2f87840fd2f0c8626a834cb121b11bb8b" diff --git a/pyproject.toml b/pyproject.toml index afd6154..0f600f4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ optional = true optional = true [tool.poetry.dependencies] -python = ">=3.10,<3.12" +python = ">=3.10,<3.13" rasterio = "^1.3.10" geopandas = "^1.0.1" leafmap = "^0.31.9" @@ -40,8 +40,11 @@ pre-commit = "^3.7.0" flake8-pyproject = "^1.2.3" docformatter = {extras = ["tomli"], version = "^1.7.5"} nbval = "^0.11.0" -black = "^24.8.0" +black = {extras = ["jupyter"], version = "^25.1.0"} nox = "^2024.4.15" +autoflake = "^2.3.1" +autopep8 = "^2.3.2" +ruff = "^0.11.10" [tool.poetry.group.lab.dependencies] jupyterlab = "^4.0.10" @@ -70,23 +73,25 @@ tag_name = "{new_version}" parse = '(?P\d+)\.(?P\d+)\.(?P\d+) (?P.*)?' serialize = [ "{major}.{minor}.{patch}", - "{utcnow:%Y-%m-%dT%H:%M:%SZ}" ] [[tool.bumpversion.files]] filename = "CHANGES.md" search = ''' -[Unreleased](https://github.com/RolnickLab/geospatial-tools/tree/main) (latest) -------------------------------------------------------------------------------------- +## [Unreleased](https://github.com/RolnickLab/geospatial-tools/tree/main) (latest) + +______________________________________________________________________ ''' replace = ''' -[Unreleased](https://github.com/RolnickLab/geospatial-tools/tree/main) (latest) -------------------------------------------------------------------------------------- +## [Unreleased](https://github.com/RolnickLab/geospatial-tools/tree/main) (latest) + +______________________________________________________________________ + + -[//]: # (New changes here in list form) +## [{new_version}](https://github.com/RolnickLab/geospatial-tools/tree/{new_version}) ({utcnow:%Y-%m-%d}) -[{new_version}](https://github.com/RolnickLab/geospatial-tools/tree/{new_version}) ({utcnow:%Y-%m-%d}) -------------------------------------------------------------------------------------- +______________________________________________________________________ ''' [[tool.bumpversion.files]] @@ -105,6 +110,7 @@ max-line-length = 120 max-locals = 20 max-args = 16 max-attributes = 20 +max-positional-arguments = 16 [tool.flake8] max-line-length = 120 @@ -118,6 +124,20 @@ exclude = [ "__pycache__" ] +[tool.autoflake] +remove-all-unused-imports = true +in-place = true +ignore-init-module-imports = true +remove-unused-variables = true +recursive = true + +[tool.autopep8] +max_line_length = 120 +in-place = true +aggressive = 2 +ignore = ["W503", "E203", "E501"] +recursive = true + [tool.black] line-length = 120 target-version = ["py311"] @@ -138,3 +158,64 @@ wrap-summaries = 120 blank = false exclude = [] recursive = true + +[tool.ruff] +line-length = 120 + +target-version = "py311" + +exclude = [ + ".git", + "migrations", + "__pycache__", +] + +[tool.ruff.lint] +select = [ + "A", # Flake8 Built ins + "E", # Error (Flake8) + "F", # Pyflakes (Flake8) + "W", # Warning (Flake8) + "I", # isort (import sorting) + "N", # Naming conventions (Pylint, etc.) + "C90", # mccabe complexity (replaces flake8 --max-complexity and mccabe) + "B", # Bugbear (common linting issues) + "UP", # pyupgrade (suggests modern Python syntax) + "PLR", # Pylint refactor + "PLE", # Pylint error (specific Pylint error rules) + "PLW", # Pylint warning (specific Pylint warning rules) + "PLC", # Pylint convention (specific Pylint convention rules) + "R", # Refactor (Pylint refactoring suggestions) + "TID", # TO DO comments + "FAST",# FastAPI + "C4", # List and dict comprehensions + "DJ", # Django + "PIE", # Returns and unnecessary returns + "Q", # Double quotes + "RET", # Fix return statements + "PTH", # Enforce pathlib + "ARG", # Unused argument + "FLY", # Flynt + "NPY", # Numpy specific + "PD", # Pandas specific + "RUF", # Ruff specific +] + +ignore = [ + "E203", # whitespace before ':', Black already handles this + "E266", # too many leading '#' for comments + "E501", # line too long (we enforce via line-length instead) + "RET504", + "RUF013", + "PTH123" +] + +[tool.ruff.lint.pydocstyle] +convention = "numpy" # Corresponds to flake8's docstring-convention and docformatter style. + +[tool.ruff.lint.pylint] +max-args = 16 + +[tool.ruff.lint.mccabe] +# cyclomatic complexity +max-complexity = 18 diff --git a/scripts/README.md b/scripts/README.md index b8bd76c..f09de6e 100644 --- a/scripts/README.md +++ b/scripts/README.md @@ -1,13 +1,13 @@ # Scripts ----- +______________________________________________________________________ **Important note for SLURM scripts** -All Slurm scripts need to be run from the [scripts/](.) folder, as they use the +All Slurm scripts need to be run from the [scripts/](.) folder, as they use the [config.sh](config.sh.example) that also needs to be configured by each user. ----- +______________________________________________________________________ This folder is dedicated to scripts, whether python, bash or sbatch. @@ -18,4 +18,4 @@ itself. ## Scripts -* [resample_tiff_raster.py](resample_tiff_raster.py) : Script to resample a target tiff image, so it matches a source image's grid size and area. Resampling strategy is using a Nearest Neighbor algorythm to keep original values. Use the scripts CLI for more information : `python3 resample_tiff_raster.py --help` +- [resample_tiff_raster.py](resample_tiff_raster.py) : Script to resample a target tiff image, so it matches a source image's grid size and area. Resampling strategy is using a Nearest Neighbor algorythm to keep original values. Use the scripts CLI for more information : `python3 resample_tiff_raster.py --help` diff --git a/scripts/sentinel_2_search_and_process/README.md b/scripts/sentinel_2_search_and_process/README.md index cff67c7..40378a0 100644 --- a/scripts/sentinel_2_search_and_process/README.md +++ b/scripts/sentinel_2_search_and_process/README.md @@ -2,8 +2,8 @@ Scripts to run in order: -* [product_search.py](product_search.py) : Execute the search for products for a given region of interest -* [download_and_process.py](download_and_process.py) : Process the products found in previous scripts +- [product_search.py](product_search.py) : Execute the search for products for a given region of interest +- [download_and_process.py](download_and_process.py) : Process the products found in previous scripts Both scripts can be used with the `--help` option to have more information. @@ -19,5 +19,5 @@ python download_and_process.py --help The above scripts have their Slurm equivalent: -* [search.py](search.sh) : Execute the search for products for a given region of interest -* [process.py](process.sh) : Process the products found in previous scripts +- [search.py](search.sh) : Execute the search for products for a given region of interest +- [process.py](process.sh) : Process the products found in previous scripts diff --git a/scripts/sentinel_2_search_and_process/download_and_process.py b/scripts/sentinel_2_search_and_process/download_and_process.py index 5bbd757..448f1a2 100644 --- a/scripts/sentinel_2_search_and_process/download_and_process.py +++ b/scripts/sentinel_2_search_and_process/download_and_process.py @@ -29,7 +29,7 @@ def _handle_product_list(product_list: str) -> list: parsed_product_list = [] if product_list.endswith(".txt") and pathlib.Path(product_list).exists(): - with open(product_list, "r", encoding="utf-8") as f: + with open(product_list, encoding="utf-8") as f: for line in f: parsed_product_list.append(line.strip()) if not product_list.endswith(".txt"): @@ -87,7 +87,7 @@ def download_and_process( LOGGER.info(f"Will download and process the following products: {parsed_product_list}") if not parsed_product_list: LOGGER.error("Error - Product list not found!") - return None + return LOGGER.info(f"Loading best results file {best_products_file}") best_results = gpd.read_file(best_products_file) diff --git a/tests/test_notebooks/test_planetary_computer_sentinel2.ipynb b/tests/test_notebooks/test_planetary_computer_sentinel2.ipynb index b113487..85647d0 100644 --- a/tests/test_notebooks/test_planetary_computer_sentinel2.ipynb +++ b/tests/test_notebooks/test_planetary_computer_sentinel2.ipynb @@ -2,6 +2,7 @@ "cells": [ { "cell_type": "code", + "execution_count": 1, "id": "26590ffa", "metadata": { "ExecuteTime": { @@ -9,22 +10,23 @@ "start_time": "2025-05-22T18:12:04.226800Z" } }, + "outputs": [], "source": [ "import shutil\n", "\n", - "import leafmap\n", "import geopandas as gpd\n", + "import leafmap\n", + "\n", "from geospatial_tools import DATA_DIR, TESTS_DIR\n", + "from geospatial_tools.planetary_computer.sentinel_2 import BestProductsForFeatures, download_and_process_sentinel2_asset\n", "from geospatial_tools.raster import clip_raster_with_polygon\n", "from geospatial_tools.stac import Asset\n", - "from geospatial_tools.planetary_computer.sentinel_2 import BestProductsForFeatures, download_and_process_sentinel2_asset\n", - "from geospatial_tools.vector import create_vector_grid_parallel, to_geopackage, select_polygons_by_location" - ], - "outputs": [], - "execution_count": 1 + "from geospatial_tools.vector import create_vector_grid_parallel, select_polygons_by_location, to_geopackage" + ] }, { "cell_type": "code", + "execution_count": 2, "id": "bbf8d1aede2a4fd2", "metadata": { "ExecuteTime": { @@ -32,12 +34,11 @@ "start_time": "2025-05-22T18:12:05.677670Z" } }, + "outputs": [], "source": [ "TEST_TMP_DIR = TESTS_DIR / \"test_notebooks/tmp_sentinel2\"\n", "TEST_TMP_DIR.mkdir(exist_ok=True)" - ], - "outputs": [], - "execution_count": 2 + ] }, { "cell_type": "markdown", @@ -62,6 +63,7 @@ }, { "cell_type": "code", + "execution_count": 3, "id": "fcb67d1eb21aafc1", "metadata": { "ExecuteTime": { @@ -69,17 +71,17 @@ "start_time": "2025-05-22T18:12:05.727177Z" } }, + "outputs": [], "source": [ "USA_POLYGON_FILE = DATA_DIR / \"usa_polygon_5070.gpkg\"\n", "S2_USA_GRID_FILE = DATA_DIR / \"s2_grid_usa_polygon_5070.gpkg\"\n", "usa_polygon = gpd.read_file(USA_POLYGON_FILE)\n", "s2_grid = gpd.read_file(S2_USA_GRID_FILE)" - ], - "outputs": [], - "execution_count": 3 + ] }, { "cell_type": "code", + "execution_count": 4, "id": "314e7c068786ad4d", "metadata": { "ExecuteTime": { @@ -87,19 +89,9 @@ "start_time": "2025-05-22T18:12:05.780131Z" } }, - "source": [ - "usa_polygon" - ], "outputs": [ { "data": { - "text/plain": [ - " AFFGEOID GEOID NAME \\\n", - "0 0100000US US United States \n", - "\n", - " geometry \n", - "0 MULTIPOLYGON (((-2116048.733 3142966.552, -211... " - ], "text/html": [ "
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