Integrate new qa tools

.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
+          make check-pylint

.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
+          make precommit

.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
+          make test

.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<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+) (?P<releaseTime>.*)?'
 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 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]]

.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)
--------------------------------------------------------------------------------------
+<!-- (New changes here in list form) -->
 
-* 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
+<!-- (New changes here in list form) -->
 
+## [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

.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  <X.0.0>
-	$(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)

.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
+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.