chore: Migrate to pyproject.toml (#241)

- the old setuptools setup.py is replaced by a pyproject.toml (e.g. for use with uv).
- package layout is migrated to the src/ package layout
- github workflows for linting and testing are updated
- linting and formatting is now done via ruff (instead of flake + isort + black)
- readthedocs setup has been adjusted for v2

.github/workflows/main.yml

@@ -7,6 +7,10 @@ on:
   pull_request:
     branches_ignore: []
 
+defaults:
+  run:
+    shell: bash -el {0}
+
 jobs:
   cancel-previous:
     runs-on: ubuntu-latest
@@ -20,18 +24,34 @@ jobs:
 
   linting:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version:
+          - "3.12"
     steps:
-      - uses: actions/checkout@v1
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: Install system dependencies
+        run: sudo apt-get install -y libbz2-dev liblzma-dev
+
+      - name: Setup environment variables
+        run: echo "GIT_LFS_SKIP_SMUDGE=1" >> $GITHUB_ENV
 
-      - name: Install Python
-        uses: actions/setup-python@v2
+      - name: Setup conda
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: "3.10"
+          channels: conda-forge,bioconda,nodefaults
+          environment-file: 'environment.yaml'
+          python-version: ${{ matrix.python-version }}
 
-      - name: Install dependencies
-        run: |
-            pip install -r requirements/test_black.txt
-            pip freeze
+      - name: Set up Python
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
 
       - name: Run linting tools
         run: |
@@ -41,51 +61,42 @@ jobs:
         if: github.event_name == 'pull_request' && failure()
         uses: marocchino/[email protected]
         with:
-          message: 'Please format your code with [black](https://black.readthedocs.io): `make black`.'
+          message: 'Please check your code via `make lint`.'
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
   testing:
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version:
-          - '3.10'
-          # - "3.11"  # no compatible pysam yet
-          # - "3.12"  # no compatible pysam yet
+          - "3.12"
     needs: linting
     steps:
-      - name: Install Python via conda
-        uses: s-weigand/setup-conda@v1
-        with:
-          python-version: ${{ matrix.python-version }}
-          conda-channels: defaults,bioconda,conda-forge
-
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           lfs: true
 
-      - name: Install mamba
-        run: conda install -y mamba
+      - name: Install system dependencies
+        run: sudo apt-get install -y libbz2-dev liblzma-dev
 
-      - name: Prepare environment.yaml file
-        run: >
-          cp environment.yaml /tmp/environment.yaml && sed -i -e
-          's/- python/- python=${{ matrix.python-version }}/'
-          /tmp/environment.yaml
+      - name: Setup environment variables
+        run: echo "GIT_LFS_SKIP_SMUDGE=1" >> $GITHUB_ENV
 
-      - name: Update environment using mamba
-        run: mamba env update --name root --file /tmp/environment.yaml
+      - name: Setup conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          channels: conda-forge,bioconda,nodefaults
+          environment-file: 'environment.yaml'
+          python-version: ${{ matrix.python-version }}
 
-      - name: Save time by installing packages via mamba.
-        run: mamba install -y pysam
+      - name: Set up Python
+        run: uv python install ${{ matrix.python-version }}
 
-      - name: Install dependencies
-        run: |
-            pip install -r requirements/test_black.txt
-            pip freeze
+      - name: Install the project
+        run: uv sync --all-extras --dev
 
       - name: Run tests
-        run: pytest
+        run: uv run pytest
 
       - uses: codecov/codecov-action@v3

.github/workflows/release-please.yml

@@ -10,28 +10,27 @@ jobs:
     runs-on: ubuntu-latest
     steps:
 
-      - uses: GoogleCloudPlatform/release-please-action@v2
+      - uses: GoogleCloudPlatform/release-please-action@v4
         id: release
         with:
           release-type: python
-          package-name: cubi-tk
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         if: ${{ steps.release.outputs.release_created }}
         with:
           fetch-depth: 0
 
-      - name: Set up Python
+      - name: Setup uv
         if: ${{ steps.release.outputs.release_created }}
-        uses: actions/setup-python@v2
+        uses: astral-sh/setup-uv@v3
         with:
-          python-version: '3.x'
+          version: "0.5.16"
+          enable-cache: true
 
       - name: Build package
         if: ${{ steps.release.outputs.release_created }}
         run: |
-          python -m pip install --upgrade pip
-          python setup.py sdist
+          uv build
 
       - name: Publish to PyPI
         if: ${{ steps.release.outputs.release_created }}

.readthedocs.yaml

@@ -0,0 +1,25 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+   os: ubuntu-22.04
+   jobs:
+    post_create_environment:
+      - pip install uv
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install --upgrade pip setuptools
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install --upgrade sphinx readthedocs-sphinx-ext
+    post_install:
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv sync --all-extras --group docs
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install '.[all]'
+    build:
+      html:
+        - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv run sphinx-build --fail-on-warning --show-traceback --keep-going -D language=de docs_manual $READTHEDOCS_OUTPUT/html
+
+## Build documentation in the docs/ directory with Sphinx
+#sphinx:
+#   configuration: docs_manual/conf.py

MANIFEST.in

@@ -4,13 +4,13 @@ include CHANGELOG.md
 include LICENSE
 include README.md
 
+graft src
+
 recursive-include tests *
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 
 recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
 
-include cubi_tk/version.py
 recursive-include cubi_tk/isa_tpl *.json *.txt
 
-include requirements.txt requirements/*.txt

Makefile

@@ -1,35 +1,18 @@
 .PHONY: all
-all: black
+all: lint format
 
-.PHONY: black
-black:
-	black -l 100 .
+.PHONY: format
+format:
+	uv run ruff format .
 
-.PHONY: black-check
-black-check:
-	black -l 100 --check .
-
-.PHONY: isort
-isort:
-	isort --force-sort-within-sections --profile=black .
-
-.PHONY: isort-check
-isort-check:
-	isort --force-sort-within-sections --profile=black --check .
-
-.PHONY: flake8
-flake8:
-	flake8
-
-# .PHONY: mypy
-# mypy: export MYPYPATH=stubs
-# mypy:
-# 	mypy clinvar_this clinvar_api tests
+.PHONY: format-check
+format-check:
+	uv run ruff format --check .
 
 .PHONY: lint
-lint: flake8 isort-check black-check
-# lint: flake8 isort-check black-check mypy
+lint:
+	uv run ruff check
 
 .PHONY: pytest
 pytest:
-	pytest .
+	uv run pytest

README.md

@@ -12,7 +12,7 @@ Tooling for connecting GitLab, pipelines, and SODAR at CUBI.
 Prerequisites when using conda:
 
 ```bash
-$ conda create -n cubi-tk python=3.10
+$ conda env create -n cubi-tk -f environment.yaml
 $ conda activate cubi-tk
 ```
 
@@ -21,15 +21,18 @@ Clone CUBI-TK and install.
 ```bash
 $ git clone [email protected]:bihealth/cubi-tk.git
 $ cd cubi-tk
-$ pip install -e .
+$ uv sync
+$ uv pip install -e .
+# or, if you need snappy kickoff:
+#$ GIT_LFS_SKIP_SMUDGE=1 uv pip install -e '.[snappy]'
 ```
 
 ## Building the Manual
 
 ```bash
-$ pip install -r requirements/develop.txt
+$ uv sync --all-extras --group docs
 $ cd docs_manual
-$ make clean html
+$ uv run make clean html
 $ ls _build/html/index.html
 ```
 

docs_manual/Makefile

@@ -4,7 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = python -msphinx
-SPHINXPROJ    = altamisa
+SPHINXPROJ    = cubi-tk
 SOURCEDIR     = .
 BUILDDIR      = _build
 

docs_manual/conf.py

@@ -74,7 +74,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

docs_manual/make.bat

@@ -9,7 +9,7 @@ if "%SPHINXBUILD%" == "" (
 )
 set SOURCEDIR=.
 set BUILDDIR=_build
-set SPHINXPROJ=altamisa
+set SPHINXPROJ=cubi-tk
 
 if "%1" == "" goto help
 

environment.yaml

@@ -1,11 +1,16 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 
 name: cubi-tk
 
 dependencies:
-  - python
+  - python >=3.9
   - pip
+  - uv >=0.5
   - hashdeep
+  - pysam >=0.22
+  - vcfpy >=0.13.8
+  - gcc_linux-64 >=13,<14
+  - zlib ~=1.3.0