build: Migrate to uv

Use uv for management of development dependencies and building in CI. This also migrates the "docs" and "test" extras to dependency groups, as they were only used to facilitate the dev setup, and did not actually add any functionality.
DSD-DBS · Dec 23, 2024 · ba41a65 · ba41a65
1 parent 8d820a5
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diff --git a/.github/workflows/code-qa.yml b/.github/workflows/code-qa.yml
@@ -31,34 +31,29 @@ jobs:
             python_version: "3.10"
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python ${{matrix.python_version}}
-        uses: actions/setup-python@v5
         with:
-          cache: pip
-          cache-dependency-path: pyproject.toml
+          fetch-depth: 0
+      - uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+          cache-dependency-glob: "**/pyproject.toml"
           python-version: ${{matrix.python_version}}
-      - name: Upgrade Pip
-        run: python -m pip install -U pip
-      - name: Install test dependencies
-        run: python -m pip install '.[test]'
       - name: Run unit tests
-        run: python -m pytest --cov-report=term --cov=capellambse --rootdir=.
+        run: uv run -m coverage run
 
   pre-commit:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
         with:
-          cache: pip
-          cache-dependency-path: pyproject.toml
+          fetch-depth: 0
+      - uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+          cache-dependency-glob: "**/pyproject.toml"
           python-version: "3.12"
-      - name: Upgrade pip
-        run: python -m pip install -U pip
-      - name: Install pre-commit
-        run: python -m pip install 'pre-commit'
       - name: Run Pre-Commit
-        run: pre-commit run --all-files
+        run: uv run pre-commit run --all-files
 
   build:
     name: Build wheel
@@ -67,18 +62,15 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - name: Setup Python
-        uses: actions/setup-python@v5
+      - uses: astral-sh/setup-uv@v4
         with:
-          cache: pip
-          cache-dependency-path: pyproject.toml
+          enable-cache: true
+          cache-dependency-glob: "**/pyproject.toml"
           python-version: "3.12"
-      - name: Install dependencies
-        run: python -m pip install -U pip build twine
       - name: Build packages
-        run: python -m build
+        run: uv build
       - name: Verify packages
-        run: python -m twine check dist/*
+        run: uvx twine check dist/*
       - name: Upload artifacts
         uses: actions/upload-artifact@v4
         with:
@@ -120,15 +112,11 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v5
+      - uses: astral-sh/setup-uv@v4
         with:
-          cache: pip
-          cache-dependency-path: pyproject.toml
+          enable-cache: true
+          cache-dependency-glob: "**/pyproject.toml"
           python-version: "3.12"
-      - name: Upgrade pip
-        run: python -m pip install -U pip
-      - name: Install dependencies
-        run: python -m pip install jupyter '.[docs,png]' capellambse-context-diagrams
       - name: Run example notebooks
         run: |
           jq --version
@@ -142,7 +130,7 @@ jobs:
           }
           for file in docs/source/examples/*.ipynb; do
             old_outputs="$(celloutputs "$file")"
-            if ! jupyter nbconvert --to notebook --execute "$file" --output "${file##*/}" --ExecutePreprocessor.timeout "${NOTEBOOK_TIMEOUT_SEC:-300}"; then
+            if ! uv run --all-extras jupyter nbconvert --to notebook --execute "$file" --output "${file##*/}" --ExecutePreprocessor.timeout "${NOTEBOOK_TIMEOUT_SEC:-300}"; then
               ok=false
               continue
             fi
@@ -160,17 +148,13 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v5
+      - uses: astral-sh/setup-uv@v4
         with:
-          cache: pip
-          cache-dependency-path: pyproject.toml
+          enable-cache: true
+          cache-dependency-glob: "**/pyproject.toml"
           python-version: "3.12"
-      - name: Upgrade pip
-        run: python -m pip install -U pip
-      - name: Install dependencies
-        run: |
-          sudo apt-get install -y pandoc
-          python -m pip install '.[docs]'
+      - name: Install system-level dependencies
+        run: sudo apt-get install -y pandoc
       - name: Auto-generate APIDOC sources
         run: make -C docs apidoc
       - name: Create docs

diff --git a/.gitignore b/.gitignore
@@ -3,7 +3,7 @@
 
 # Ignore all custom known_models by default, to avoid accidental information
 # leaks. To commit one anyway, use: git add -f filename.json
-capellambse/known_models/*.json
+src/capellambse/known_models/*.json
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -162,6 +162,9 @@ dmypy.json
 # Cython debug symbols
 cython_debug/
 
+# don't commit lock files for library projects
+uv.lock
+
 # Mac garbage
 .DS_Store
 

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -98,7 +98,7 @@ repos:
         name: mypy
         types_or: [python, pyi, toml, yaml]
         pass_filenames: false
-        args: [capellambse, tests]
+        args: [src/capellambse, tests]
         additional_dependencies:
           - mypypp==0.1.1
 

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -22,14 +22,48 @@ our style guidelines outlined below.
 Developing
 ----------
 
-We recommend that you [develop inside of a virtual
-environment](README.md#installation). After you have set it up, simply run the
-unit tests to verify that everything is set up correctly:
+Use [uv](https://docs.astral.sh/uv/) to set up a local development environment.
+
+```bash
+git clone https://github.com/DSD-DBS/py-capellambse
+cd py-capellambse
+uv sync
+uv run pre-commit install
+
+# You may need to explicitly activate the project venv
+# to make code completion and tools available:
+source .venv/bin/activate.sh  # for Linux / Mac
+.venv\Scripts\activate  # for Windows
+```
+
+You can use `uv run <tool>` to avoid having to manually activate the project
+venv. For example, to run the unit tests, use:
 
 ```sh
-pytest
+uv run pytest
 ```
 
+The example notebooks (see above) are verified during CI, to ensure their
+output is up to date. This means they have to be re-run whenever the expected
+output changes.
+
+Use the following command to start a Jupyter server, which can be used to
+develop and re-run the example notebooks:
+
+```bash
+cd docs/source/examples
+CAPELLAMBSE_UUID_SEED=0 uv run jupyter lab
+```
+
+> [!NOTE]
+> The above command provides a static seed for the internal pseudo-random
+> number generator. This is not recommended for production environments. [Read
+> more about
+> CAPELLAMBSE_UUID_SEED.](https://dsd-dbs.github.io/py-capellambse/start/envvars.html)
+
+If your browser did not open automatically, follow the instructions in the
+terminal to start it manually.
+
 We additionally recommend that you set up your editor / IDE as follows.
 
 - Indent with 4 spaces per level of indentation

diff --git a/README.md b/README.md
@@ -181,47 +181,8 @@ pip install capellambse
 Development
 -----------
 
-To set up a development environment, clone the project and install it into a
-virtual environment.
-
-```bash
-git clone https://github.com/DSD-DBS/py-capellambse
-cd py-capellambse
-python -m venv .venv
-
-source .venv/bin/activate.sh  # for Linux / Mac
-.venv\Scripts\activate  # for Windows
-
-pip install -U pip pre-commit
-pip install -e '.[docs,test]'
-pre-commit install
-```
-
-The example notebooks (see above) are verified during CI, to ensure their
-output is up to date. This means they have to be re-run whenever the expected
-output changes.
-
-Use the following command to start a Jupyter server, which can be used to
-develop and re-run the example notebooks:
-
-```bash
-pip install jupyter capellambse
-cd docs/source/examples
-CAPELLAMBSE_UUID_SEED=0 jupyter-notebook
-```
-
-> [!NOTE]
-> The above command provides a static seed for the internal pseudo-random
-> number generator. This is not recommended for production environments. [Read
-> more about
-> CAPELLAMBSE_UUID_SEED.](https://dsd-dbs.github.io/py-capellambse/start/envvars.html)
-
-If your browser did not open automatically, follow the instructions in the
-terminal to start it manually.
-
-Once in the browser, simply click on the [01
-Introduction.ipynb](https://dsd-dbs.github.io/py-capellambse/examples/01%20Introduction.html)
-notebook to start!
+For details on how to set up a local development environment, please refer to
+the [CONTRIBUTING guide](CONTRIBUTING.md).
 
 Current limitations
 -------------------

diff --git a/docs/Makefile b/docs/Makefile
@@ -11,25 +11,27 @@ SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = source
 BUILDDIR      = build
 
+export UV_PYTHON = 3.12
+
 # Put it first so that "make" without argument is like "make help".
 help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@uv run --no-dev --group docs $(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 .PHONY: help Makefile
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@uv run --no-dev --group docs $(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 
 # Auto-generate API documentation
 apidoc:
-	sphinx-apidoc --module-first --output-dir source/code --force .. \
-		../capellambse/aird/diagram.py \
-		../capellambse/extensions/reqif/elements.py \
-		../capellambse/repl.py \
-		../capellambse/sphinx.py
+	uv run --no-dev --group docs sphinx-apidoc --module-first --output-dir source/code --force ../src \
+		../src/capellambse/aird/diagram.py \
+		../src/capellambse/extensions/reqif/elements.py \
+		../src/capellambse/repl.py \
+		../src/capellambse/sphinx.py
 	sed -i -e '/^\.\. automodule:: capellambse$$/a \   :no-index:' source/code/capellambse.rst
 
 clean-apidoc: