fix: switch from setup.py to pyproject toml (#526)

.github/workflows/ci.yml

@@ -30,7 +30,7 @@ jobs:
 
       - name: Install dependencies
         run: |
-            pip install -r requirements/test.txt
+            pip install -e ".[dev]"
             pip freeze
 
       - name: Run linting tools
@@ -52,17 +52,16 @@ jobs:
   sphinx-docs:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
 
       - name: Install Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: "3.12"
 
       - name: Install dependencies
         run: |
-            pip install -r requirements/base.txt -r requirements/test.txt
-            pip install -e .
+            pip install -e ".[docs]"
             pip freeze
 
       - name: Build documentation
@@ -76,8 +75,6 @@ jobs:
       matrix:
         python-version:
           - "3.12"
-          # - "3.11"  # no compatible pysam yet
-          # - "3.12"  # no compatible pysam yet
     needs: linting
     steps:
       - name: Install Python via conda
@@ -86,7 +83,7 @@ jobs:
           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
           fetch-depth: 2
@@ -107,7 +104,7 @@ jobs:
           bcftools version
       - name: Install some more dependencies via pip
         # Workaround - see https://github.com/pytest-dev/pytest/issues/10420#issuecomment-1290697849
-        run: pip install -r requirements/test.txt; pip install --ignore-installed py
+        run: pip install ".[test]"; pip install --ignore-installed py
       - name: Run tests
         run: pytest
         env:

.pre-commit-config.yaml

@@ -6,3 +6,7 @@ repos:
       - id: ruff
         args: [ --fix ]
       - id: ruff-format
+  - repo: https://github.com/snakemake/snakefmt
+    rev: v0.8.5 # https://github.com/snakemake/snakefmt/releases
+    hooks:
+      - id: snakefmt

README.md

@@ -20,32 +20,19 @@ cd snappy-pipeline
 
 # WARNING- make sure that you are in your conda base environment
 
-# Create conda environment "snappy_env" with the minimal requirements:
-mamba env create --file environment.yml
+# Create conda environment "snappy_env" with all requirements:
+mamba env create --file environment.yml -n snappy_env
 conda activate snappy_env
 
-# Add testing & development requirements:
-pip install -r requirements/test.txt
-pip install -r requirements/dev.txt
-
-# Optionally add "pytest-pdb" missing from anaconda
-pip install pytest-pdb
-
 # Install snappy in snappy_env environment
-pip install -e .
+pip install -e ".[all]"
 ```
-
-**Note:** To create the environment under another name, replace the commands for the environment creation & activation of the correct environment by:
-
-```
-mamba env create --file environment.yml --name <other_environment_name>
-conda activate <other_environment_name>
-```
-
+The dependency group `all` includes all optional dependencies, i.e. `test` (for running tests with `pytest`), `dev` (for formatting, linting, pre-commit hooks) and `docs` (for building the documentation with `sphinx`).
+If you only want to install the core dependencies, you can omit the `[all]` part, or choose any combination of the other groups.
 
 See [user installation](docs/quickstart.rst) if you just want to use the pipeline.
 
-See [developer installation)[docs/installation.rst) for getting started with working on the pipeline code and also building the documentation.
+See [developer installation](docs/installation.rst) for getting started with working on the pipeline code and also building the documentation.
 
 ## Using GATK3
 

docs/conf.py

@@ -6,12 +6,13 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'snappy-pipeline'
+project = "snappy-pipeline"
 copyright = "2015-2024, CUBI, Berlin Institute of Health"
-author = 'CUBI, Berlin Institute of Health'
+author = "CUBI, Berlin Institute of Health"
 
 # Get the project root dir, which is the parent dir of this
 import os, sys
+
 cwd = os.getcwd()
 project_root = os.path.dirname(cwd)
 
@@ -21,6 +22,7 @@
 sys.path.insert(0, project_root)
 
 import snappy_pipeline
+
 # The short X.Y version.
 version = snappy_pipeline.__version__
 # The full version, including alpha/beta/rc tags.
@@ -35,8 +37,8 @@
     "sphinx_mdinclude",
 ]
 
-templates_path = ['_templates']
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', "step/DEFAULT_CONFIG_*.rst"]
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "step/DEFAULT_CONFIG_*.rst"]
 source_suffix = ".rst"
 master_doc = "index"
 
@@ -73,8 +75,8 @@
 
 # html_theme = 'alabaster'
 pygments_style = "sphinx"
-html_theme = 'sphinx_rtd_theme'
-html_static_path = ['_static']
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]
 # Output file base name for HTML help builder.
 htmlhelp_basename = "snappy_pipelinedoc"
 html_last_updated_fmt = "%b %d, %Y"

docs/installation.rst

@@ -37,34 +37,47 @@ You can of course clone the code anywhere you like.
     $ cd ~/Development/pipeline_dev
     $ git clone [email protected]:bihealth/snappy-pipeline.git
     $ cd snappy_pipeline
-    $ pip install -e .
-    $ pip install -r requirements/dev.txt
+    $ conda env create -n snappy_dev --file environment.yaml
+    $ conda activate snappy_dev
+    $ pip install -e ".[all]"
 
-It's also a good idea to install some packages required for testing through conda:
+
+Installing pre-commit-hooks
+===========================
+To make it easier to follow the coding style, we use `pre-commit <https://pre-commit.com>`_ hooks.
+These hooks will run the style checks before you commit your changes and will automatically fix some issues.
+
+First, install the pre-commit package (if not already installed, part of the optional dependency group ``dev``):
+
+.. code-block:: shell
+
+    $ conda install pre-commit  # or pip install pre-commit
+
+Then, install the pre-commit hooks:
 
 .. code-block:: shell
 
-    $ conda env update --name root --file environment.yaml
+    $ pre-commit install
 
-(If you do not do this, please make sure that you have git-lfs in your PATH through other means)
+The next time you commit changes, the pre-commit hooks will run automatically.
 
 Running the Tests
 =================
 
-To run the tests, you need to add the packages in ``requirements/test.txt``.
+To run the tests, simply invoke ``pytest`` (part of the optional dependency group ``test``):
 
 .. code-block:: shell
 
     $ cd ~/Development/pipeline_dev
-    $ py.test
+    $ pytest
 
 Running the Style Checks
 ========================
 
 .. code-block:: shell
 
     $ cd ~/Development/pipeline_dev
-    $ flake8
+    $ make lint
 
 Developer Documentation
 =======================

environment.yml

@@ -47,15 +47,17 @@ dependencies:
   - pytest-mock ~=3.14.0
   - pytest-subprocess ~=1.5.0
   - pyfakefs ~=5.5.0
-  - ruff ~=0.4.8
-  - snakefmt ~=0.8.0
+  - pytest-sugar ~=0.9.6
   - coveralls ~=4.0.1
+  # formatting, linting, dev
+  - ruff ~=0.4.8
+  - snakefmt ~=0.8.5
+  - pre-commit ~=3.7.1
+  # docs
   - sphinx ~=7.3.7
   - sphinx_rtd_theme ~=2.0.0
   - sphinx-mdinclude ~=0.6.0
 
-  # misc packages
-  - pytest-sugar ~=0.9.6
 
 
   - pip: