diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml new file mode 100644 index 0000000..270fbf5 --- /dev/null +++ b/.github/workflows/black.yml @@ -0,0 +1,15 @@ +name: Black +on: push + +jobs: + black: + runs-on: ubuntu-24.04 + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 # Python ≥3.11 required for use_pyproject + with: + python-version: "3.12" + - uses: psf/black@stable + with: + use_pyproject: true + options: "--check" diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml index 28e5759..6773db6 100644 --- a/.github/workflows/docker-publish.yml +++ b/.github/workflows/docker-publish.yml @@ -10,10 +10,10 @@ on: jobs: publish: - runs-on: ubuntu-20.04 + runs-on: ubuntu-24.04 steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Publish to Registry uses: docker/build-push-action@v1 with: diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index 10e394a..7b5fc70 100644 --- a/.github/workflows/python-ci.yml +++ b/.github/workflows/python-ci.yml @@ -4,36 +4,36 @@ on: push jobs: test: - - runs-on: ubuntu-20.04 + runs-on: ubuntu-24.04 strategy: matrix: - python-version: [3.7, 3.8] + python-version: ["3.11", "3.12"] steps: - - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - env: - PIP_INDEX_URL: https://pypi.pacificclimate.org/simple - CPLUS_INCLUDE_PATH: /usr/include/gdal - C_INCLUDE_PATH: /usr/include/gdal - run: | - sudo apt-get update - sudo apt-get install libpq-dev python-dev libhdf5-dev libnetcdf-dev libgdal-dev - pip install -U pip pytest - pip install -r requirements.txt - pip install -e .[dev] - - name: Test with pytest (full) - if: github.ref == 'refs/heads/master' - run: | - py.test -m "not online" -v - - name: Test with pytest (fast) - if: github.ref != 'refs/heads/master' - run: | - py.test -m "not online and not slow" -v - - name: Code Quality - run: black . --check + - uses: actions/checkout@v4 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + env: + PIP_INDEX_URL: https://pypi.pacificclimate.org/simple + CPLUS_INCLUDE_PATH: /usr/include/gdal + C_INCLUDE_PATH: /usr/include/gdal + run: | + sudo apt-get update + sudo apt-get install -y libpq-dev python3-dev libhdf5-dev libnetcdf-dev gdal-bin libgdal-dev curl + curl -sSL https://install.python-poetry.org | python3 - + echo "$HOME/.local/bin" >> $GITHUB_PATH + - name: Install dependencies + run: | + poetry config virtualenvs.create false + poetry install --extras "dev" + - name: Test with pytest (full) + if: github.ref == 'refs/heads/master' + run: | + py.test -m "not online" -v + - name: Test with pytest (fast) + if: github.ref != 'refs/heads/master' + run: | + py.test -m "not online and not slow" -v diff --git a/Dockerfile b/Dockerfile index 8b16253..127e075 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,28 +1,37 @@ -FROM pcic/geospatial-python:gdal3 +FROM pcic/geospatial-python:3.8.4 -LABEL Maintainer="https://github.com/pacificclimate/sandpiper" Description="sandpiper WPS" Vendor="pacificclimate" Version="1.7.1" +LABEL Maintainer="https://github.com/pacificclimate/sandpiper" \ + Description="sandpiper WPS" \ + Vendor="pacificclimate" \ + Version="1.7.1" ENV PIP_INDEX_URL="https://pypi.pacificclimate.org/simple/" -ENV THREDDS_URL_ROOT="https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets" +ENV THREDDS_URL_ROOT="https://marble-dev01.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets" # Update system -RUN apk upgrade --update && \ - apk add \ +RUN apt-get update && apt-get upgrade -y && \ + apt-get install -y \ libxml2-dev \ libxslt-dev \ - linux-headers + wget + -COPY . /tmp WORKDIR /tmp -# Install WPS -RUN pip install --upgrade pip && \ - pip install sphinx psutil && \ - pip install . --ignore-installed && \ - pip install gunicorn +ENV POETRY_HOME="/opt/poetry" +ENV PATH="$POETRY_HOME/bin:$PATH" + +RUN apt-get update && \ + apt-get install -y --no-install-recommends python3-pip curl && \ + curl -sSL https://install.python-poetry.org | python3 + +COPY . . + +RUN poetry config virtualenvs.in-project true && \ + poetry install # Start WPS service on port 5000 on 0.0.0.0 EXPOSE 5000 -CMD gunicorn --bind=0.0.0.0:5000 --timeout 150 sandpiper.wsgi:application +CMD ["poetry", "run","gunicorn", "--bind=0.0.0.0:5000", "--timeout", "150", "sandpiper.wsgi:application"] # docker build -t pcic/sandpiper . # docker run -p 5000:5000 pcic/sandpiper diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 700b794..0000000 --- a/MANIFEST.in +++ /dev/null @@ -1,6 +0,0 @@ -include Makefile -include *.txt -include *.md -recursive-include sandpiper * -global-exclude __pycache__ -global-exclude *.py[co] diff --git a/Makefile b/Makefile deleted file mode 100644 index 8d64a21..0000000 --- a/Makefile +++ /dev/null @@ -1,181 +0,0 @@ -# Configuration -APP_ROOT := $(abspath $(lastword $(MAKEFILE_LIST))/..) -APP_NAME := sandpiper -VENV?=/tmp/sandpiper-venv -PYTHON=${VENV}/bin/python3 -PIP=${VENV}/bin/pip -export PIP_INDEX_URL=https://pypi.pacificclimate.org/simple -export THREDDS_URL_ROOT=https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets - -# Notebook targets -LOCAL_URL = http://localhost:5000 -DEV_PORT ?= $(shell bash -c 'read -ep "Target port: " port; echo $$port') - -# Used in target refresh-notebooks to make it looks like the notebooks have -# been refreshed from the production server below instead of from the local dev -# instance so the notebooks can also be used as tutorial notebooks. -OUTPUT_URL = https://docker-dev03.pcic.uvic.ca/wpsoutputs -SANITIZE_FILE := https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/raw/master/notebooks/output-sanitize.cfg - - -.PHONY: all -all: apt install develop test-all clean-test test-notebooks-prod - -.PHONY: help -help: - @echo "Please use 'make ' where is one of:" - @echo " help to print this help message. (Default)" - @echo " install to install app by running 'pip install -e .'" - @echo " develop to install with additional development requirements." - @echo " start to start $(APP_NAME) service as daemon (background process)." - @echo " stop to stop $(APP_NAME) service." - @echo " restart to restart $(APP_NAME) service." - @echo " status to show status of $(APP_NAME) service." - @echo " clean to remove all files generated by build and tests." - @echo "\nTesting targets:" - @echo " test to run tests (but skip long running tests)." - @echo " test-all to run all tests (including long running tests)." - @echo " lint to run code style checks with flake8." - @echo "\nSphinx targets:" - @echo " docs to generate HTML documentation with Sphinx." - @echo "\nDeployment targets:" - @echo " dist to build source and wheel package." - -## Build targets - -.PHONY: apt -apt: - @echo "Installing gdal ..." - @-bash -c "sudo apt-get install -y gdal-bin libgdal-dev" - -.PHONY: install -install: venv - @echo "Installing application ..." - @-bash -c '${PIP} install .' - @echo "\nStart service with \`sandpiper start'" - -.PHONY: develop -develop: venv - @echo "Installing development requirements for tests and docs ..." - @-bash -c '${PIP} install -e ".[dev]"' - -.PHONY: start -start: venv - @echo "Starting application ..." - @-bash -c "${VENV}/bin/$(APP_NAME) start -d" - -.PHONY: stop -stop: venv - @echo "Stopping application ..." - @-bash -c "${VENV}/bin/$(APP_NAME) stop" - -.PHONY: restart -restart: venv stop start - @echo "Restarting application ..." - -.PHONY: status -status: venv - @echo "Show status ..." - @-bash -c "${VENV}/bin/$(APP_NAME) status" - -.PHONY: clean -clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts - -.PHONY: clean-build -clean-build: - @echo "Remove build artifacts ..." - @-rm -fr build/ - @-rm -fr dist/ - @-rm -fr .eggs/ - @-find . -name '*.egg-info' -exec rm -fr {} + - @-find . -name '*.egg' -exec rm -f {} + - @-find . -name '*.log' -exec rm -fr {} + - @-find . -name '*.sqlite' -exec rm -fr {} + - -.PHONY: clean-pyc -clean-pyc: - @echo "Remove Python file artifacts ..." - @-find . -name '*.pyc' -exec rm -f {} + - @-find . -name '*.pyo' -exec rm -f {} + - @-find . -name '*~' -exec rm -f {} + - @-find . -name '__pycache__' -exec rm -fr {} + - -.PHONY: clean-test -clean-test: - @echo "Remove test artifacts ..." - @-rm -fr .pytest_cache - -.PHONY: clean-dist -clean-dist: clean - @echo "Running 'git clean' ..." - @git diff --quiet HEAD || echo "There are uncommitted changes! Aborting 'git clean' ..." - ## do not use git clean -e/--exclude here, add them to .gitignore instead - @-git clean -dfx - -.PHONY: venv -venv: - test -d $(VENV) || python3 -m venv $(VENV) - -## Test targets - -.PHONY: test -test: venv - @echo "Running tests (skip slow and online tests) ..." - @bash -c '${PYTHON} -m pytest -v -m "not slow and not online" tests/' - -.PHONY: test-all -test-all: venv - @echo "Running all tests (including slow and online tests) ..." - @bash -c '${PYTHON} -m pytest -v tests/' - -.PHONY: notebook-sanitizer -notebook-sanitizer: - @echo "Copying notebook output sanitizer ..." - @-bash -c "curl -L $(SANITIZE_FILE) -o $(CURDIR)/docs/output-sanitize.cfg --silent" - -.PHONY: test-notebooks -test-notebooks: notebook-sanitizer - @echo "Running notebook-based tests" - @bash -c "source $(VENV)/bin/activate && env LOCAL_URL=$(LOCAL_URL) pytest --nbval --verbose $(CURDIR)/notebooks/ --sanitize-with $(CURDIR)/docs/output-sanitize.cfg --ignore $(CURDIR)/notebooks/.ipynb_checkpoints" - -.PHONY: test-notebooks-prod -test-notebooks-prod: notebook-sanitizer - @echo "Running notebook-based tests against production instance of sandpiper" - @bash -c "source $(VENV)/bin/activate && pytest --nbval --verbose $(CURDIR)/notebooks/ --sanitize-with $(CURDIR)/docs/output-sanitize.cfg --ignore $(CURDIR)/notebooks/.ipynb_checkpoints" - -.PHONY: test-notebooks-dev -test-notebooks-dev: notebook-sanitizer - @echo "Running notebook-based tests against development instance of sandpiper" - @bash -c "source $(VENV)/bin/activate && env DEV_URL=http://docker-dev03.pcic.uvic.ca:30101/wps pytest --nbval --verbose $(CURDIR)/notebooks/ --sanitize-with $(CURDIR)/docs/output-sanitize.cfg --ignore $(CURDIR)/notebooks/.ipynb_checkpoints" - -.PHONY: test-notebooks-custom -test-notebooks-custom: notebook-sanitizer - @echo "Running notebook-based tests against custom instance of sandpiper" - @bash -c "source $(VENV)/bin/activate && env DEV_URL=http://docker-dev03.pcic.uvic.ca:$(DEV_PORT)/wps pytest --nbval --verbose $(CURDIR)/notebooks/ --sanitize-with $(CURDIR)/docs/output-sanitize.cfg --ignore $(CURDIR)/notebooks/.ipynb_checkpoints" - - -.PHONY: lint -lint: venv - @echo "Running black code style checks ..." - @bash -c '${PYTHON} -m black . --check' - -.PHONY: refresh-notebooks -refresh-notebooks: - @echo "Refresh all notebook outputs under docs/source/notebooks" - @bash -c 'for nb in $(CURDIR)/notebooks/*.ipynb; do LOCAL_URL="$(LOCAL_URL)" jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=60 --output "$$nb" "$$nb"; sed -i "s@$(LOCAL_URL)/outputs/@$(OUTPUT_URL)/@g" "$$nb"; done; cd $(APP_ROOT)' - -## Documentation - -.PHONY: docs -docs: - @echo "Updating notebook docs" - @bash -c 'source $(VENV)/bin/activate && jupyter nbconvert --to html notebooks/* --output-dir docs/formatted_demos/' - -## Deployment targets - -.PHONY: dist -dist: clean - @echo "Building source and wheel package ..." - @-python setup.py sdist - @-python setup.py bdist_wheel - @-bash -c 'ls -l dist/' diff --git a/conftest.py b/conftest.py new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/conftest.py @@ -0,0 +1 @@ + diff --git a/docs/formatted_demos/test_wps_resolve_rules_errors.html b/docs/formatted_demos/test_wps_resolve_rules_errors.html new file mode 100644 index 0000000..7376b12 --- /dev/null +++ b/docs/formatted_demos/test_wps_resolve_rules_errors.html @@ -0,0 +1,7649 @@ + + + + + +test_wps_resolve_rules_errors + + + + + + + + + + + + +
+ +
+ + diff --git a/docs/formatted_demos/wps_evaluate_rules_demo.html b/docs/formatted_demos/wps_evaluate_rules_demo.html index 6ca70b0..05694bd 100644 --- a/docs/formatted_demos/wps_evaluate_rules_demo.html +++ b/docs/formatted_demos/wps_evaluate_rules_demo.html @@ -1,18 +1,14 @@ - - - + + + wps_evaluate_rules_demo - - - - - - - - - - +/* Hiding the collapser by default */ +.jp-Collapser { + display: none; +} +@page { + margin: 0.5in; /* Margin for each printed piece of paper */ +} +@media print { + .jp-Cell-inputWrapper, + .jp-Cell-outputWrapper { + display: block; + } +} + - - - + + - - + + + + +
+
- - - - - - - diff --git a/docs/formatted_demos/wps_parser_demo.html b/docs/formatted_demos/wps_parser_demo.html index 7cd355e..a03348a 100644 --- a/docs/formatted_demos/wps_parser_demo.html +++ b/docs/formatted_demos/wps_parser_demo.html @@ -1,18 +1,14 @@ - - - + + + wps_parser_demo - - - - - - - +.jp-Cell-Placeholder { + padding-left: 55px; +} + +.jp-Cell-Placeholder-wrapper { + background: #fff; + border: 1px solid; + border-color: #e5e6e9 #dfe0e4 #d0d1d5; + border-radius: 4px; + -webkit-border-radius: 4px; + margin: 10px 15px; +} + +.jp-Cell-Placeholder-wrapper-inner { + padding: 15px; + position: relative; +} + +.jp-Cell-Placeholder-wrapper-body { + background-repeat: repeat; + background-size: 50% auto; +} + +.jp-Cell-Placeholder-wrapper-body div { + background: #f6f7f8; + background-image: -webkit-linear-gradient( + left, + #f6f7f8 0%, + #edeef1 20%, + #f6f7f8 40%, + #f6f7f8 100% + ); + background-repeat: no-repeat; + background-size: 800px 104px; + height: 104px; + position: absolute; + right: 15px; + left: 15px; + top: 15px; +} + +div.jp-Cell-Placeholder-h1 { + top: 20px; + height: 20px; + left: 15px; + width: 150px; +} + +div.jp-Cell-Placeholder-h2 { + left: 15px; + top: 50px; + height: 10px; + width: 100px; +} + +div.jp-Cell-Placeholder-content-1, +div.jp-Cell-Placeholder-content-2, +div.jp-Cell-Placeholder-content-3 { + left: 15px; + right: 15px; + height: 10px; +} + +div.jp-Cell-Placeholder-content-1 { + top: 100px; +} + +div.jp-Cell-Placeholder-content-2 { + top: 120px; +} - + - +/* Hiding the collapser by default */ +.jp-Collapser { + display: none; +} +@page { + margin: 0.5in; /* Margin for each printed piece of paper */ +} +@media print { + .jp-Cell-inputWrapper, + .jp-Cell-outputWrapper { + display: block; + } +} + - - - + + - - + + + + +
+
- - - - - - - diff --git a/docs/formatted_demos/wps_resolve_rules_demo.html b/docs/formatted_demos/wps_resolve_rules_demo.html index 078203b..d0712d6 100644 --- a/docs/formatted_demos/wps_resolve_rules_demo.html +++ b/docs/formatted_demos/wps_resolve_rules_demo.html @@ -1,18 +1,14 @@ - - - + + + wps_resolve_rules_demo - - - - - - - - - - +/* Hiding the collapser by default */ +.jp-Collapser { + display: none; +} +@page { + margin: 0.5in; /* Margin for each printed piece of paper */ +} +@media print { + .jp-Cell-inputWrapper, + .jp-Cell-outputWrapper { + display: block; + } +} + - - - + + - - + + + + +
+
- - - - - - - diff --git a/notebooks/test_wps_resolve_rules_errors.ipynb b/notebooks/test_wps_resolve_rules_errors.ipynb index fd322de..073e686 100644 --- a/notebooks/test_wps_resolve_rules_errors.ipynb +++ b/notebooks/test_wps_resolve_rules_errors.ipynb @@ -11,7 +11,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "id": "74f92779", "metadata": {}, "outputs": [], @@ -21,23 +21,12 @@ "import json\n", "import os\n", "from wps_tools.testing import get_target_url\n", - "from pkg_resources import resource_filename" + "from importlib.resources import files" ] }, { "cell_type": "code", - "execution_count": 10, - "id": "223b4190", - "metadata": {}, - "outputs": [], - "source": [ - "while os.path.basename(os.getcwd()) != \"sandpiper\":\n", - " os.chdir('../')" - ] - }, - { - "cell_type": "code", - "execution_count": 11, + "execution_count": null, "id": "221e60e0", "metadata": {}, "outputs": [ @@ -45,7 +34,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Using sandpiper on https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/sandpiper/wps\n" + "Using sandpiper on https://marble-dev01.pcic.uvic.ca/twitcher/ows/proxy/sandpiper/wps\n" ] } ], @@ -58,34 +47,32 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "id": "fc5bc8b6", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - " owslib.wps.WPSException : {'code': 'NoApplicableCode', 'locator': 'None', 'text': 'Process error: ArgumentError: Could not parse rfc1738 URL from string bad_connection_string'}\n", - " owslib.wps.WPSException : {'code': 'NoApplicableCode', 'locator': 'None', 'text': 'Process error: MissingSchema: Invalid URL bad_geoserver: No schema supplied. Perhaps you meant http://bad_geoserver?'}\n" - ] - } - ], + "outputs": [], "source": [ "# NBVAL_IGNORE_OUTPUT\n", - "csv = resource_filename(\"tests\", \"data/rules_small.csv\")\n", - "with open(csv, \"r\") as csv_file:\n", + "from pathlib import Path\n", + "\n", + "current = Path.cwd()\n", + "while not (current / \"pyproject.toml\").exists():\n", + " current = current.parent\n", + "\n", + "csv_path = current / \"tests/data/rules_small.csv\"\n", + "\n", + "with open(csv_path, \"r\") as f:\n", " with pytest.raises(Exception):\n", " sandpiper.resolve_rules(\n", - " csv_content=csv_file.read(),\n", - " geoserver=\"https://docker-dev03.pcic.uvic.ca/geoserver/bc_regions/ows\",\n", + " csv_content=f.read(),\n", + " geoserver=\"https://beehive.pacificclimate.org/plan2adapt/bc_regions/ows\",\n", " connection_string=\"bad_connection_string\"\n", " )\n", " output.get()[0]\n", "\n", " with pytest.raises(Exception):\n", " output = sandpiper.resolve_rules(\n", - " csv_content=csv_file.read(), \n", + " csv_content=f.read(), \n", " geoserver=\"bad_geoserver\",\n", " )\n", " output.get()[0]" @@ -102,7 +89,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -116,7 +103,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.5" + "version": "3.12.1" } }, "nbformat": 4, diff --git a/notebooks/wps_evaluate_rules_demo.ipynb b/notebooks/wps_evaluate_rules_demo.ipynb index b81a091..5d5338a 100644 --- a/notebooks/wps_evaluate_rules_demo.ipynb +++ b/notebooks/wps_evaluate_rules_demo.ipynb @@ -10,14 +10,14 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ "from birdy import WPSClient\n", "import os\n", "from wps_tools.testing import get_target_url\n", - "from pkg_resources import resource_filename\n", + "from importlib.resources import files\n", "\n", "# Ensure we are in the working directory with access to the data\n", "while os.path.basename(os.getcwd()) != \"sandpiper\":\n", @@ -33,7 +33,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Using sandpiper on https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/sandpiper/wps\n" + "Using sandpiper on https://marble-dev01.pcic.uvic.ca/twitcher/ows/proxy/sandpiper/wps\n" ] } ], @@ -67,15 +67,14 @@ { "data": { "text/plain": [ - "\u001b[0;31mSignature:\u001b[0m\n", - "\u001b[0msandpiper\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mevaluate_rule\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\u001b[0m\n", - "\u001b[0;34m\u001b[0m \u001b[0mrules\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", - "\u001b[0;34m\u001b[0m \u001b[0mparse_tree\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", - "\u001b[0;34m\u001b[0m \u001b[0mvariables\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", - "\u001b[0;34m\u001b[0m \u001b[0mloglevel\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'INFO'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", - "\u001b[0;34m\u001b[0m \u001b[0moutput_formats\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n", - "\u001b[0;34m\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mDocstring:\u001b[0m\n", + "\u001b[31mSignature:\u001b[39m\n", + "sandpiper.evaluate_rule(\n", + " rules,\n", + " parse_tree=\u001b[38;5;28;01mNone\u001b[39;00m,\n", + " variables=\u001b[38;5;28;01mNone\u001b[39;00m,\n", + " loglevel=\u001b[33m'INFO'\u001b[39m,\n", + ")\n", + "\u001b[31mDocstring:\u001b[39m\n", "Evaluate parse trees to determine truth value of a rule\n", "\n", "Parameters\n", @@ -93,8 +92,8 @@ "-------\n", "json : ComplexData:mimetype:`application/json`\n", " JSON file\n", - "\u001b[0;31mFile:\u001b[0m ~/code/birds/sandpiper/\n", - "\u001b[0;31mType:\u001b[0m method\n" + "\u001b[31mFile:\u001b[39m ~/python-sprint/py-repos/sandpiper/\n", + "\u001b[31mType:\u001b[39m method" ] }, "metadata": {}, @@ -115,14 +114,14 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# Evaluate truth value of expression 1\n", "rules = ['rule_snow', 'rule_rain', 'rule_hybrid']\n", - "parse_tree = resource_filename('tests', 'data/parse_tree.json')\n", - "variables = resource_filename('tests', 'data/collected_variables.json') \n", + "parse_tree = str((files(\"tests\") / \"data/parse_tree.json\").resolve()),\n", + "variables = str((files(\"tests\") / \"data/collected_variables.json\").resolve()), \n", "output = sandpiper.evaluate_rule(\n", " rules=rules,\n", " parse_tree=parse_tree,\n", @@ -172,7 +171,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -186,7 +185,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.5" + "version": "3.12.1" } }, "nbformat": 4, diff --git a/notebooks/wps_parser_demo.ipynb b/notebooks/wps_parser_demo.ipynb index b38be64..acd0768 100644 --- a/notebooks/wps_parser_demo.ipynb +++ b/notebooks/wps_parser_demo.ipynb @@ -31,7 +31,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Using sandpiper on https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/sandpiper/wps\n" + "Using sandpiper on https://marble-dev01.pcic.uvic.ca/twitcher/ows/proxy/sandpiper/wps\n" ] } ], @@ -65,8 +65,8 @@ { "data": { "text/plain": [ - "\u001b[0;31mSignature:\u001b[0m \u001b[0msandpiper\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mparser\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mconditions\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mloglevel\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'INFO'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutput_formats\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mDocstring:\u001b[0m\n", + "\u001b[31mSignature:\u001b[39m sandpiper.parser(conditions, loglevel=\u001b[33m'INFO'\u001b[39m)\n", + "\u001b[31mDocstring:\u001b[39m\n", "Process a condition into a parse tree\n", "\n", "Parameters\n", @@ -80,8 +80,8 @@ "-------\n", "json : ComplexData:mimetype:`application/json`\n", " JSON file\n", - "\u001b[0;31mFile:\u001b[0m ~/code/birds/sandpiper/notebooks/\n", - "\u001b[0;31mType:\u001b[0m method\n" + "\u001b[31mFile:\u001b[39m ~/python-sprint/py-repos/sandpiper/notebooks/\n", + "\u001b[31mType:\u001b[39m method" ] }, "metadata": {}, @@ -141,7 +141,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -155,7 +155,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.5" + "version": "3.12.1" } }, "nbformat": 4, diff --git a/notebooks/wps_resolve_rules_demo.ipynb b/notebooks/wps_resolve_rules_demo.ipynb index c2f75f9..8ac717d 100644 --- a/notebooks/wps_resolve_rules_demo.ipynb +++ b/notebooks/wps_resolve_rules_demo.ipynb @@ -11,14 +11,14 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ "from birdy import WPSClient\n", "import os\n", "from wps_tools.testing import get_target_url\n", - "from pkg_resources import resource_filename\n", + "from importlib.resources import files\n", "\n", "# Ensure we are in the working directory with access to the data\n", "while os.path.basename(os.getcwd()) != \"sandpiper\":\n", @@ -140,12 +140,12 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ "output_local = sandpiper.resolve_rules(\n", - " csv = open(resource_filename('tests', 'data/rules_small.csv')).read()\n", + " csv = (files(\"tests\") / \"data/rules_small.csv\").read_text(),\n", ")" ] }, diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..8a70683 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,5787 @@ +# This file is automatically @generated by Poetry 2.1.2 and should not be changed by hand. + +[[package]] +name = "affine" +version = "2.4.0" +description = "Matrices describing affine transformation of the plane" +optional = false +python-versions = ">=3.7" +groups = ["main"] +files = [ + {file = "affine-2.4.0-py3-none-any.whl", hash = "sha256:8a3df80e2b2378aef598a83c1392efd47967afec4242021a0b06b4c7cbc61a92"}, + {file = "affine-2.4.0.tar.gz", hash = "sha256:a24d818d6a836c131976d22f8c27b8d3ca32d0af64c1d8d29deb7bafa4da1eea"}, +] + +[package.extras] +dev = ["coveralls", "flake8", "pydocstyle"] +test = ["pytest (>=4.6)", "pytest-cov"] + +[package.source] +type = "legacy" +url = 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Science/Research", + "Operating System :: MacOS :: MacOS X", + "Operating System :: POSIX", + "Programming Language :: Python", + "Natural Language :: English", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Topic :: Scientific/Engineering :: Atmospheric Science", + "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", +] +keywords = [ + "wps", + "pywps", + "birdhouse", + "sandpiper", + "plan2adapt", + "climate", + "adaptation", +] +license = { text = "GNU General Public License v3" } +readme = "README.md" +requires-python = ">=3.11, <=3.14" +dependencies = [ + "click>=8.2.1,<9.0.0", + "cf_cell_methods>=0.1.0,<1.0.0", + "gdal>=3.3.3,<3.4", + "gunicorn>=23.0.0,<24.0.0", + "jinja2>=3.1.6,<4.0.0", + "numpy>=1.26.4,<2.0.0", + "pint>=0.24.4,<0.25", + "psutil>=7.0.0,<8.0.0", + "pyproj>=3.7.1,<4.0.0", + "pywps>=4.6.0,<5.0.0", + "shapely>=2.1.1,<3.0.0", + "pywps>=4.6.0", + 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marks tests that are slow (deselect with '-m \"not slow\"')", +] + +[[tool.poetry.include]] +path = "*.txt" +format = ["sdist", "wheel"] + +[[tool.poetry.include]] +path = "*.md" +format = ["sdist", "wheel"] + +[[tool.poetry.include]] +path = "sandpiper" +format = ["sdist", "wheel"] + +[[tool.poetry.include]] +path = "tests/data/configs/*.cfg" +format = ["sdist", "wheel"] + +[[tool.poetry.source]] +name = "pcic" +url = "https://pypi.pacificclimate.org/simple/" +priority = "primary" + +[tool.flake8] +max-line-length = 120 +exclude = [".git", "__pycache__", "docs/source/conf.py", "build", "dist", "src"] + +[tool.doc8] +ignore-path = ["docs/build", "docs/source/_templates", "docs/source/_static"] +max-line-length = 120 + + +[tool.poe.tasks] + + +# ── Python env via Poetry ──────────────────────────────────── +[tool.poe.tasks.lock] +cmd = "poetry lock" +help = "Build the lock file for the project" + +[tool.poe.tasks.install] +cmd = "poetry install" +help = "Install Python project dependencies using Poetry" + +[tool.poe.tasks.develop] +cmd = "poetry install --extras dev" +help = "Install development dependencies using Poetry" + +[tool.poe.tasks.start] +cmd = "poetry run sandpiper start -d" +help = "Start the Sandpiper service in detached mode" + +[tool.poe.tasks.stop] +cmd = "poetry run sandpiper stop" +help = "Stop the Sandpiper service" + +[tool.poe.tasks.restart] +sequence = ["stop", "start"] +help = "Restart the Sandpiper service" + +[tool.poe.tasks.status] +cmd = "poetry run sandpiper status" +help = "Show the status of the Sandpiper service" + +[tool.poe.tasks.dist] +cmd = "poetry build" +help = "Build a distribution package for the project" + +# ── Tests & lint ───────────────────────────────────────────── + +[tool.poe.tasks.test] +cmd = "pytest -v -m 'not slow and not online' tests/" +help = "Run fast, offline unit tests" + +[tool.poe.tasks.test-all] +cmd = "pytest -v tests/" +help = "Run all tests, including online ones" + +[tool.poe.tasks.lint] +cmd = "black . --check" +help = "Check code formatting using Black" + +# ── Notebook tasks ────────────────────────────────────────── + +[tool.poe.tasks.prepare-notebooks] +cmd = "curl -L https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/raw/master/notebooks/output-sanitize.cfg -o docs/output-sanitize.cfg --silent" +help = "Download the output sanitizer config for notebook tests" + +[tool.poe.tasks.test-notebooks] +sequence = ["prepare-notebooks", "test-notebooks-local"] +help = "Run all local notebook tests with sanitized output" + +[tool.poe.tasks.test-notebooks-local] +cmd = "pytest --nbval --verbose notebooks/ --sanitize-with docs/output-sanitize.cfg --ignore notebooks/.ipynb_checkpoints" +env = { LOCAL_URL = "http://localhost:5000" } +help = "Run notebook tests locally using nbval with sanitization" + +# [tool.poe.tasks.test-notebooks-prod] +# sequence = ["prepare-notebooks", "test-notebooks-prod-run"] +# help = "Run notebook tests against the production environment" + +# [tool.poe.tasks.test-notebooks-prod-run] +# cmd = "pytest --nbval --verbose notebooks/ --sanitize-with docs/output-sanitize.cfg --ignore notebooks/.ipynb_checkpoints" + +# [tool.poe.tasks.test-notebooks-dev] +# sequence = ["prepare-notebooks", "test-notebooks-dev-run"] +# help = "Run notebook tests against the dev environment" + +# [tool.poe.tasks.test-notebooks-dev-run] +# cmd = "pytest --nbval --verbose notebooks/ --sanitize-with docs/output-sanitize.cfg --ignore notebooks/.ipynb_checkpoints" +# env = { DEV_URL = "http://docker-dev03.pcic.uvic.ca:30101/wps" } + +# [tool.poe.tasks.test-notebooks-custom] +# sequence = ["prepare-notebooks", "run-custom-port-test"] +# help = "Run notebook tests against a custom dev server port" + +# [tool.poe.tasks.run-custom-port-test] +# shell = "read -p 'Target port: ' PORT && env DEV_URL=http://docker-dev03.pcic.uvic.ca:$PORT/wps pytest --nbval --verbose notebooks/ --sanitize-with docs/output-sanitize.cfg --ignore notebooks/.ipynb_checkpoints" + +# TODO: Convert to Poe task +# .PHONY: refresh-notebooks +# refresh-notebooks: +# @echo "Refresh all notebook outputs under docs/source/notebooks" +# @bash -c 'for nb in $(CURDIR)/notebooks/*.ipynb; do LOCAL_URL="$(LOCAL_URL)" jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=60 --output "$$nb" "$$nb"; sed -i "s@$(LOCAL_URL)/outputs/@$(OUTPUT_URL)/@g" "$$nb"; done; cd $(APP_ROOT)' + +# ── Documentation ──────────────────────────────────────────── + +[tool.poe.tasks.docs] +cmd = "jupyter nbconvert --to html notebooks/* --output-dir docs/formatted_demos/" +help = "Convert notebooks to HTML for documentation" diff --git a/pytest.ini b/pytest.ini deleted file mode 100644 index 7332916..0000000 --- a/pytest.ini +++ /dev/null @@ -1,4 +0,0 @@ -[pytest] -markers = - online: marks tests that use online resources (deselect with '-m "not online"') - slow: marks tests that are slow (deselect with '-m "not slow"') diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 52a9ad0..0000000 --- a/requirements.txt +++ /dev/null @@ -1,9 +0,0 @@ -pywps==4.4.5 -gdal==3.0.4 -jinja2 -click>=8.0 -psutil -pyproj==3.0.0 -p2a_impacts==0.4.0 -wps-tools==2.0.0 -ce==3.2.0 diff --git a/requirements_dev.txt b/requirements_dev.txt deleted file mode 100644 index 87da2de..0000000 --- a/requirements_dev.txt +++ /dev/null @@ -1,22 +0,0 @@ -pytest>=6.0 -flake8 -pytest-flake8 -ipython -pytest-notebook -nbsphinx -nbval>=0.9.6 -nbconvert -Sphinx==2.4.4 -bumpversion -twine -cruft -# Changing dependencies above this comment will create merge conflicts when updating the cookiecutter template with cruft. Add extra requirements below this line. -black==22.3.0 -nbclient~=0.5.10 - -# notebook requirements -jupyterlab -ipywidgets -nodejs -birdhouse-birdy -beautifulsoup4 diff --git a/sandpiper/processes/wps_resolve_rules.py b/sandpiper/processes/wps_resolve_rules.py index cfa35f0..d59b712 100644 --- a/sandpiper/processes/wps_resolve_rules.py +++ b/sandpiper/processes/wps_resolve_rules.py @@ -5,7 +5,7 @@ from pywps.app.Common import Metadata from p2a_impacts.resolver import resolve_rules -from p2a_impacts.utils import get_region, REGIONS +from p2a_impacts.utils import get_region, REGIONS, create_session from wps_tools.logging import log_handler from wps_tools.io import log_level, collect_args, csv_input from wps_tools.error_handling import custom_process_error @@ -28,7 +28,7 @@ def __init__(self): "date_range", "Date Range", abstract="30 year period for data", - allowed_values=["2020", "2050", "2080"], + allowed_values=["2030", "2050", "2080"], default="2080", data_type="string", ), @@ -48,7 +48,7 @@ def __init__(self): abstract="Geoserver URL", min_occurs=1, max_occurs=1, - default="https://docker-dev03.pcic.uvic.ca/geoserver/bc_regions/ows", + default="https://beehive.pacificclimate.org/plan2adapt/bc_regions/ows", data_type="string", ), LiteralInput( @@ -66,7 +66,7 @@ def __init__(self): abstract="Ensemble name filter for data files", min_occurs=1, max_occurs=1, - default="p2a_rules", + default="p2a_rules_cmip6_mbcn", data_type="string", ), LiteralInput( @@ -156,7 +156,7 @@ def _handler(self, request, response): date_range, get_region(region, geoserver), ensemble, - connection_string, + create_session(connection_string), thredds, loglevel, ) diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index d1b3ae8..0000000 --- a/setup.cfg +++ /dev/null @@ -1,47 +0,0 @@ -[bumpversion] -current_version = 0.1.0 -commit = True -tag = True - -[metadata] -description-file = README.md - -[bumpversion:file:sandpiper/__version__.py] -search = __version__ = '{current_version}' -replace = __version__ = '{new_version}' - -[bumpversion:file:docs/source/conf.py] -search = version|release = {current_version} -replace = {new_version} - -[bumpversion:file:Dockerfile] -search = Version="{current_version}" -replace = Version="{new_version}" - -[bumpversion:file:.cruft.json] -search = "version": "{current_version}", -replace = "version": "{new_version}", - -[tool:pytest] -addopts = - --strict - --tb=native - tests/ -python_files = test_*.py -markers = - online: mark test to need internet connection - slow: mark test to be slow - -[flake8] -max-line-length = 120 -exclude = - .git, - __pycache__, - docs/source/conf.py, - build, - dist, - src, - -[doc8] -ignore-path = docs/build,docs/source/_templates,docs/source/_static -max-line-length = 120 diff --git a/setup.py b/setup.py deleted file mode 100644 index 37b1e86..0000000 --- a/setup.py +++ /dev/null @@ -1,65 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - -"""The setup script.""" - -import os - -from setuptools import setup, find_packages - -here = os.path.abspath(os.path.dirname(__file__)) -README = open(os.path.join(here, "README.md")).read() -CHANGES = open(os.path.join(here, "CHANGES.md")).read() -REQUIRES_PYTHON = ">=3.7.0" - -about = {} -with open(os.path.join(here, "sandpiper", "__version__.py"), "r") as f: - exec(f.read(), about) - -reqs = [line.strip() for line in open("requirements.txt")] -dev_reqs = [line.strip() for line in open("requirements_dev.txt")] - -classifiers = [ - "Development Status :: 3 - Alpha", - "Intended Audience :: Developers", - "Intended Audience :: Science/Research", - "Operating System :: MacOS :: MacOS X", - "Operating System :: POSIX", - "Programming Language :: Python", - "Natural Language :: English", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", - "Topic :: Scientific/Engineering :: Atmospheric Science", - "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", -] - -setup( - name="sandpiper", - version=about["__version__"], - description="A Web Processing Service for the Plan2Adapt Rule Engine.", - long_description=README + "\n\n" + CHANGES, - long_description_content_type="text/x-rst", - author=about["__author__"], - author_email=about["__email__"], - url="https://github.com/nikola-rados/sandpiper", - python_requires=REQUIRES_PYTHON, - classifiers=classifiers, - license="GNU General Public License v3", - keywords="wps pywps birdhouse sandpiper", - packages=find_packages(), - package_data={ - "sandpiper": ["tests/data/*.nc"], - "tests": ["data/*.nc"], - }, - include_package_data=True, - install_requires=reqs, - extras_require={ - "dev": dev_reqs, - }, # pip install ".[dev]" - entry_points={ - "console_scripts": [ - "sandpiper=sandpiper.cli:cli", - ] - }, -) diff --git a/tests/conftest.py b/tests/conftest.py index ee50e36..198e817 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -5,5 +5,5 @@ def mock_thredds_url_root(monkeypatch): monkeypatch.setenv( "THREDDS_URL_ROOT", - "https://docker-dev03.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets", + "https://marble-dev01.pcic.uvic.ca/twitcher/ows/proxy/thredds/dodsC/datasets", ) diff --git a/tests/test_wps_parser.py b/tests/test_wps_parser.py index f48ec76..69dd4c7 100644 --- a/tests/test_wps_parser.py +++ b/tests/test_wps_parser.py @@ -19,9 +19,9 @@ def build_condition_input(conditions): ("conditions"), [ [ - "(temp_djf_iamean_s100p_hist < 5)", - "(temp_djf_iamean_s0p_hist < -6)", - "(temp_djf_iamean_s0p_hist < -6) && (temp_djf_iamean_s100p_hist > -6)", + "(temp_djf_iamean_s100p_hist < 5)", + "(temp_djf_iamean_s0p_hist < -6)", + "(temp_djf_iamean_s0p_hist < -6) && (temp_djf_iamean_s100p_hist > -6)", ] ], ) diff --git a/tests/test_wps_resolve_rules.py b/tests/test_wps_resolve_rules.py index 5c87830..dd211b9 100644 --- a/tests/test_wps_resolve_rules.py +++ b/tests/test_wps_resolve_rules.py @@ -1,5 +1,5 @@ import pytest -from pkg_resources import resource_filename +from importlib.resources import files from wps_tools.testing import run_wps_process from sandpiper.processes.wps_resolve_rules import ResolveRules @@ -16,10 +16,10 @@ ), [ ( - resource_filename("tests", "data/rules_small.csv"), + str((files("tests") / "data/rules_small.csv").resolve()), "2050", "vancouver_island", - "http://docker-dev01.pcic.uvic.ca:30123/geoserver/bc_regions/ows", + "https://beehive.pacificclimate.org/plan2adapt/bc_regions/ows", "p2a_rules", ), ],