refactor: ci using pixi and ruff/flake8

.github/workflows/ci.yml

@@ -11,41 +11,29 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
-      - uses: actions/setup-python@v5
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0
         with:
-          python-version: "3.11"
-
-      - name: Install poetry
-        run: pip install poetry
-
-      - name: Install dependencies
-        run: |
-          poetry install --sync
+          environments: dev
 
       - name: Check formatting
-        run: poetry run black --check .
+        run: pixi run --environment dev format --check .
 
   linting:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
-      - uses: actions/setup-python@v5
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0
         with:
-          python-version: "3.11"
-
-      - name: Install poetry
-        run: pip install poetry
-
-      - name: Install dependencies
-        run: |
-          poetry install --sync
+          environments: dev
 
       - name: Check code
-        run: poetry run flake8
+        run: pixi run --environment dev lint
 
   testing:
     runs-on: ubuntu-latest
@@ -58,23 +46,22 @@ jobs:
           - "8888:3306"
         options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: koesterlab/setup-slurm-action@v1
 
-      - uses: actions/setup-python@v5
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0
         with:
-          python-version: "3.11"
-
-      - name: Install poetry
-        run: pip install poetry
+          environments: dev
 
-      - name: Install dependencies
-        run: |
-          poetry install --sync
+      - name: Install plugin package
+        run: pixi run --environment dev python -m pip install -e .
 
       - name: Run pytest
-        run: poetry run coverage run -m pytest tests/ -sv --tb=short --disable-warnings
+        run: |
+            pixi run --environment dev \
+            python -m pytest -vv --capture=no tests
 
       - name: Run Coverage
-        run: poetry run coverage report -m
+        run: pixi run --environment dev coverage-report

.gitignore

@@ -160,3 +160,6 @@ cython_debug/
 #.idea/
 
 .aider*
+# pixi environments
+.pixi/*
+!.pixi/config.toml

pyproject.toml

@@ -1,49 +1,113 @@
-[tool.poetry]
+[build-system]
+requires = ["setuptools>=64"]
+build-backend = "setuptools.build_meta"
+
+
+[project]
 name = "snakemake-executor-plugin-slurm"
 version = "2.7.1"
 description = "A Snakemake executor plugin for submitting jobs to a SLURM cluster."
+readme = "README.md"
+requires-python = ">=3.11,<4"
+license = {text = "MIT"}
 authors = [
-    "Christian Meesters <meesters@uni-mainz.de>",
-    "David Lähnemann <david.laehnemann@dkfz-heidelberg.de>",
-    "Johannes Koester <johannes.koester@uni-due.de>",
+    {name = "Christian Meesters", email = "meesters@uni-mainz.de"},
+    {name = "David Lähnemann",   email = "david.laehnemann@dkfz-heidelberg.de"},
+    {name = "Johannes Koester",  email = "johannes.koester@uni-due.de"},
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering",
 ]
-readme = "README.md"
-license = "MIT"
-repository = "https://github.com/snakemake/snakemake-executor-plugin-slurm"
-documentation = "https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html"
 keywords = ["snakemake", "plugin", "executor", "cluster", "slurm"]
+dependencies = [
+    "snakemake-interface-common>=1.23.0,<2",
+    "snakemake-interface-executor-plugins>=9.4.0,<10",
+    "snakemake-executor-plugin-slurm-jobstep>=0.6.0,<1",
+    "pandas>=2.3.3,<4",
+    "numpy>=2.4.5,<3",
+    "throttler>=1.2.2,<2",
+    "pyyaml>=6.0.3,<7",
+]
 
-[tool.poetry.dependencies]
-python = "^3.11"
-snakemake-interface-common = ">=1.23.0,<2"
-snakemake-interface-executor-plugins = ">=9.4.0,<10"
-snakemake-executor-plugin-slurm-jobstep = ">=0.6.0,<1"
-pandas = ">=2.3.3,<4"
-numpy = ">=2.4.5,<3"
-throttler = ">=1.2.3,<2"
-pyyaml = ">=6.0.3,<7"
-
-[tool.poetry.group.dev.dependencies]
-black = "==26.3.1"
-flake8 = ">=6.1.0,<7"
-coverage = ">=7.14.0,<8"
-pytest = ">=9.0.3,<10"
-snakemake = ">=9.21.0,<10"
-pandas = ">=2.3.3,<4"
+[project.urls]
+Repository    = "https://github.com/snakemake/snakemake-executor-plugin-slurm"
+Documentation = "https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html"
 
-[tool.poetry.scripts]
+[project.scripts]
 generate-slurm-partition-config = "snakemake_executor_plugin_slurm.cli:main"
 
+[tool.codespell]
+skip = ".git,*.pdf,*.svg,versioneer.py,*.css,test_*"
+check-hidden = true
+
 [tool.coverage.run]
 omit = [".*", "*/site-packages/*", "Snakefile"]
 
-[tool.black]
-line-length = 88
-extend-exclude = 'tests/test_scontrol_parsing\.py'
+[tool.ruff]
+target-version = "py311"
+extend-exclude = ["tests/test_scontrol_parsing.py"]
 
 [tool.pytest.ini_options]
 python_files = ["test_*.py", "tests.py"]
 
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+[tool.pixi]
+
+# Workspace table (required for preview features)
+[tool.pixi.workspace]
+#preview = ["pixi-build"]
+channels = ["conda-forge", "bioconda"]
+platforms = ["linux-64"]
+
+# Conda-only dependencies (must be a table)
+[tool.pixi.dependencies]
+python    = ">=3.11,<3.14"
+pip       = ">=24,<26"
+packaging = ">=24,<26"
+
+# Pip-only dependencies (install the plugin from local path)
+[tool.pixi.pypi-dependencies]
+snakemake-executor-plugin-slurm = { path = "." }
+
+[tool.pixi.environments]
+dev     = { features = ["test", "style"] }
+quality = { features = ["style"] }
+publish = { features = ["build"] }
+
+[tool.pixi.feature.test.pypi-dependencies]
+pytest    = ">=9.0.3,<10"
+coverage  = ">=7.14.0,<8"
+snakemake = ">=9.21.0,<10"
+
+[tool.setuptools.packages.find]
+include = ["snakemake_executor_plugin_slurm*"]
+# Exclude the `pr_logo` directory (and any sub‑files) from the packaged source
+exclude = ["pr_logo*"]
+
+[dependency-groups]
+dev = ["snakemake"]
+
+[tool.pixi.feature.test.tasks]
+test            = {cmd = "pytest"}
+coverage-report = {cmd = "coverage run -m pytest -vv --capture=no && coverage report -m"}
+
+[tool.pixi.feature.style.pypi-dependencies]
+ruff  = ">=0.10.0,<0.11"
+
+[tool.pixi.feature.style.tasks]
+format = {cmd = "ruff format"}
+lint   = {cmd = "ruff check ."}
+
+[tool.pixi.feature.build.pypi-dependencies]
+build = "*"
+twine = "*"
+
+[tool.pixi.feature.build.tasks]
+build-check = {cmd = "python -m build && twine check dist/*"}

snakemake_executor_plugin_slurm/__init__.py

@@ -510,8 +510,7 @@ def __post_init__(self, test_mode: bool = False):
                 "the array_limit setting to enable array job submission."
             )
             raise WorkflowError(
-                "Array job submission is effectively disabled due to "
-                "low array_limit."
+                "Array job submission is effectively disabled due to low array_limit."
             )
         self.slurm_logdir = _select_logdir(self.workflow)
         # Check the environment variable "SNAKEMAKE_SLURM_PARTITIONS",
@@ -675,10 +674,8 @@ def run_jobs(self, jobs: List[JobExecutorInterface]):
                 "all" in self.array_jobs or rule_name in self.array_jobs
             )
             # TODO: use more sensible logging information, once finished
-            self.logger.debug(
-                f"Running jobs for rule: {rule_name}, " f"{same_rule_jobs}"
-            )
-            self.logger.debug("Current array job settings: " f"{self.array_jobs}")
+            self.logger.debug(f"Running jobs for rule: {rule_name}, {same_rule_jobs}")
+            self.logger.debug(f"Current array job settings: {self.array_jobs}")
 
             if array_selected_for_rule:
                 dag = getattr(self.workflow, "dag", None)

tests/tests.py

@@ -184,9 +184,9 @@ def test_simple_workflow(self, tmp_path):
                 report_found = True
                 report_path = os.path.join(expected_path, fname)
                 # Verify it's not empty
-                assert (
-                    os.stat(report_path).st_size > 0
-                ), f"Efficiency report {report_path} is empty"
+                assert os.stat(report_path).st_size > 0, (
+                    f"Efficiency report {report_path} is empty"
+                )
                 break
         assert report_found, "Efficiency report file not found"
 

upgrade_dependencies.py

@@ -58,7 +58,7 @@ def sensible_range(ver):
         if not m:
             return None
         major, minor, patch = map(int, m.groups())
-        return f">={major}.{minor}.{patch},<{major+1}"
+        return f">={major}.{minor}.{patch},<{major + 1}"
 
     print("Upgrading pyproject.toml dependencies to sensible ranges...")
     print(f"(dry-run mode: {dry_run})\n")