From ef477d0760079d63e87be3b95ede60559c3d6437 Mon Sep 17 00:00:00 2001
From: "luka.pavageau" <luka.pavageau@etu.univ-nantes.fr>
Date: Fri, 6 Mar 2026 15:27:19 +0100
Subject: [PATCH 01/40] proposed fix for
 https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/419

---
 snakemake_executor_plugin_slurm/__init__.py | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/snakemake_executor_plugin_slurm/__init__.py b/snakemake_executor_plugin_slurm/__init__.py
index 7d3aaf83..db0616de 100644
--- a/snakemake_executor_plugin_slurm/__init__.py
+++ b/snakemake_executor_plugin_slurm/__init__.py
@@ -355,6 +355,18 @@ def __post_init__(self):
     auto_deploy_default_storage_provider=False,
 )
 
+def _select_logdir(workflow) : 
+    """Selects where slurm_logdir should be created"""
+    logdir = workflow.executor_settings.logdir
+    # logdir is defined as absolute, keep "as is"
+    if logdir and str(logdir).startswith("/"):  
+        return Path(logdir)
+    # logdir is relative, we ensure it stays relative to the wokflow's workdir
+    elif logdir : 
+        return Path(workflow.workdir_init) / workflow.executor_settings.logdir
+    # logdir is unset
+    else : 
+        return Path(".snakemake/slurm_logs").resolve()
 
 # Required:
 # Implementation of your executor
@@ -398,11 +410,7 @@ def __post_init__(self, test_mode: bool = False):
         self._status_query_min_seconds = None
         self._status_query_max_seconds = 0.0
         self._status_query_cycle_rows = []
-        self.slurm_logdir = (
-            Path(self.workflow.executor_settings.logdir)
-            if self.workflow.executor_settings.logdir
-            else Path(".snakemake/slurm_logs").resolve()
-        )
+        self.slurm_logdir = _select_logdir(self.workflow)
         # Check the environment variable "SNAKEMAKE_SLURM_PARTITIONS",
         # if set, read the partitions from the given file. Let the CLI
         # option override this behavior.

From b1df606c37d9a9f1f994c0c40f29348fe6fd6d51 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Wed, 17 Jun 2026 16:38:48 +0200
Subject: [PATCH 02/40] feat: first non-tested, intermediate version

---
 pixi.toml      | 27 ++++++++++++++++++++++++
 pyproject.toml | 16 +++++++++-----
 setup.cfg      |  9 --------
 setup.py.bck   | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 95 insertions(+), 14 deletions(-)
 create mode 100644 pixi.toml
 delete mode 100644 setup.cfg
 create mode 100644 setup.py.bck

diff --git a/pixi.toml b/pixi.toml
new file mode 100644
index 00000000..1b896efb
--- /dev/null
+++ b/pixi.toml
@@ -0,0 +1,27 @@
+[project]
+name = "snakemake-executor-plugin-slurm"
+channels = ["conda-forge", "bioconda"]
+platforms = ["linux-64"]
+
+[dependencies]
+python = "3.11.*"
+ruff = ">=0.10.0,<0.11"
+pytest = ">=9.0.3,<10"
+coverage = ">=7.14.0,<8"
+snakemake = ">=9.21.0,<10"
+
+[feature.dev.pypi-dependencies]
+snakemake-executor-plugin-slurm = { path = ".", editable = true }
+
+[feature.conda_pkg.dependencies]
+snakemake-executor-plugin-slurm = "==2.7.1"
+
+[environments]
+default = { features = ["dev"] }
+conda-pkg = { features = ["conda_pkg"] }
+
+[tasks]
+format = "ruff format"
+lint = "ruff check"
+test = "coverage run -m pytest tests/ -sv --tb=short --disable-warnings"
+coverage-report = "coverage report -m"
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 4dc84588..2b42073a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,12 +20,11 @@ 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"
+throttler = ">=1.2.2,<2"
 pyyaml = ">=6.0.3,<7"
 
 [tool.poetry.group.dev.dependencies]
-black = "==26.3.1"
-flake8 = ">=6.1.0,<7"
+ruff = ">=0.10.0,<0.11"
 coverage = ">=7.14.0,<8"
 pytest = ">=9.0.3,<10"
 snakemake = ">=9.21.0,<10"
@@ -37,9 +36,16 @@ generate-slurm-partition-config = "snakemake_executor_plugin_slurm.cli:main"
 [tool.coverage.run]
 omit = [".*", "*/site-packages/*", "Snakefile"]
 
-[tool.black]
+[tool.ruff]
 line-length = 88
-extend-exclude = 'tests/test_scontrol_parsing\.py'
+target-version = "py311"
+extend-exclude = ["tests/test_scontrol_parsing.py"]
+
+[tool.ruff.lint]
+ignore = ["E203"]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/test_scontrol_parsing.py" = ["E501"]
 
 [tool.pytest.ini_options]
 python_files = ["test_*.py", "tests.py"]
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 34599d0e..00000000
--- a/setup.cfg
+++ /dev/null
@@ -1,9 +0,0 @@
-[flake8]
-# Recommend matching the black line length (default 88),
-# rather than using the flake8 default of 79:
-max-line-length = 88
-extend-ignore =
-    # See https://github.com/PyCQA/pycodestyle/issues/373
-    E203,
-per-file-ignores =
-    tests/test_scontrol_parsing.py:E501
\ No newline at end of file
diff --git a/setup.py.bck b/setup.py.bck
new file mode 100644
index 00000000..d49d55ab
--- /dev/null
+++ b/setup.py.bck
@@ -0,0 +1,57 @@
+import os
+from setuptools import setup, find_packages, Extension
+from Cython.Build import cythonize
+import toml
+
+# Parse pyproject.toml for metadata
+pyproject_path = os.path.join(os.path.dirname(__file__), "pyproject.toml")
+with open(pyproject_path, "r") as f:
+    pyproject = toml.load(f)
+
+project = pyproject.get("tool", {}).get("poetry", {})
+dependencies = pyproject.get("tool", {}).get("poetry", {}).get("dependencies", {}).copy()
+
+# Remove python version constraint from dependencies
+dependencies.pop("python", None)
+dependencies.pop("Cython", None)
+
+# Collect all .py files in snakemake_executor_plugin_slurm directory for Cython compilation
+base_dir = "snakemake_executor_plugin_slurm"
+py_files = []
+
+for filename in os.listdir(base_dir):
+    if filename.endswith(".py"):
+        file_path = os.path.join(base_dir, filename)
+        py_files.append(file_path)
+
+# Create a single Extension with all Python files
+extensions = [
+    Extension(
+        'snakemake_executor_plugin_slurm._core',
+        py_files
+    )
+]
+
+# gcc arguments for optimization
+os.environ["CFLAGS"] = "-O3"
+
+setup(
+    name=project.get("name", "snakemake-executor-plugin-slurm"),
+    version=project.get("version", "2.1.0"),
+    description=project.get("description", ""),
+    author=", ".join(project.get("authors", [])),
+    license=project.get("license", ""),
+    url=project.get("repository", ""),
+    py_modules=[],
+    ext_modules=cythonize(extensions, language_level=3, compiler_directives={"linetrace": True}),
+    install_requires=list(dependencies.keys()),
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],
+)
+
+
+
+

From 10e947d8aee26055003791da7971e7245c7dd001 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Thu, 18 Jun 2026 18:41:46 +0200
Subject: [PATCH 03/40] fix: relaxing system requirements for local cluster OS

---
 pixi.toml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/pixi.toml b/pixi.toml
index 1b896efb..7af18a1b 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -24,4 +24,7 @@ conda-pkg = { features = ["conda_pkg"] }
 format = "ruff format"
 lint = "ruff check"
 test = "coverage run -m pytest tests/ -sv --tb=short --disable-warnings"
-coverage-report = "coverage report -m"
\ No newline at end of file
+coverage-report = "coverage report -m"
+
+[system-requirements]
+linux = "4.18"

From f4a13a8430fefb65977fc956be6551072a726f4a Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Fri, 19 Jun 2026 10:06:45 +0200
Subject: [PATCH 04/40] fix: updated checkout versions

---
 .github/workflows/ci.yml | 38 +++++++++++++-------------------------
 1 file changed, 13 insertions(+), 25 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f5954074..f93c6acf 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -11,41 +11,25 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
-
-      - name: Install poetry
-        run: pip install poetry
-
-      - name: Install dependencies
-        run: |
-          poetry install --sync
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixiv0
 
       - name: Check formatting
-        run: poetry run black --check .
+        run: pixi run format --check .
 
   linting:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the code
-        uses: actions/checkout@v4
-
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
+        uses: actions/checkout@v6
 
-      - name: Install poetry
-        run: pip install poetry
-
-      - name: Install dependencies
-        run: |
-          poetry install --sync
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixiv0
 
       - name: Check code
-        run: poetry run flake8
+        run: poetry run lint
 
   testing:
     runs-on: ubuntu-latest
@@ -58,10 +42,14 @@ 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
 
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixiv0
+
+
       - uses: actions/setup-python@v5
         with:
           python-version: "3.11"

From 7092cdc63a70b16ea62978f06feb37422fa1b5f1 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Fri, 19 Jun 2026 10:11:13 +0200
Subject: [PATCH 05/40] fix: typo

---
 .github/workflows/ci.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f93c6acf..e2ae3394 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,7 +14,7 @@ jobs:
         uses: actions/checkout@v6
 
       - name: Setup pixi
-        uses: prefix-dev/setup-pixiv0
+        uses: prefix-dev/setup-pixi@v0
 
       - name: Check formatting
         run: pixi run format --check .
@@ -26,7 +26,7 @@ jobs:
         uses: actions/checkout@v6
 
       - name: Setup pixi
-        uses: prefix-dev/setup-pixiv0
+        uses: prefix-dev/setup-pixi@v0
 
       - name: Check code
         run: poetry run lint
@@ -47,7 +47,7 @@ jobs:
       - uses: koesterlab/setup-slurm-action@v1
 
       - name: Setup pixi
-        uses: prefix-dev/setup-pixiv0
+        uses: prefix-dev/setup-pixi@v0
 
 
       - uses: actions/setup-python@v5

From 6c13ec8bd922bcf4248a85ae57ad671d86675ac3 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Fri, 19 Jun 2026 10:27:24 +0200
Subject: [PATCH 06/40] refactor: updates

---
 .github/workflows/release-please.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml
index 3ea672d1..dd851322 100644
--- a/.github/workflows/release-please.yml
+++ b/.github/workflows/release-please.yml
@@ -11,7 +11,7 @@ jobs:
     outputs:
       release_created: ${{ steps.release.outputs.release_created }}
     steps:
-      - uses: googleapis/release-please-action@v4
+      - uses: googleapis/release-please-action@v5
         id: release
         with:
           release-type: python
@@ -22,11 +22,11 @@ jobs:
     needs: release-please
     if: ${{ needs.release-please.outputs.release_created }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install poetry
         run: pip install poetry
@@ -34,9 +34,9 @@ jobs:
       - name: Determine dependencies
         run: poetry lock
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           cache: poetry
 
       - name: Install dependencies

From 40fc0dedab0c996d0f3523744e76e9c52d903920 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Fri, 19 Jun 2026 10:36:02 +0200
Subject: [PATCH 07/40] fix: formatting

---
 snakemake_executor_plugin_slurm/__init__.py | 9 +++------
 tests/tests.py                              | 6 +++---
 upgrade_dependencies.py                     | 2 +-
 3 files changed, 7 insertions(+), 10 deletions(-)

diff --git a/snakemake_executor_plugin_slurm/__init__.py b/snakemake_executor_plugin_slurm/__init__.py
index 8c6092c9..cbc56a00 100644
--- a/snakemake_executor_plugin_slurm/__init__.py
+++ b/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)
diff --git a/tests/tests.py b/tests/tests.py
index 0f78f1b5..35874bca 100644
--- a/tests/tests.py
+++ b/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"
 
diff --git a/upgrade_dependencies.py b/upgrade_dependencies.py
index 398e8952..99ffd36f 100644
--- a/upgrade_dependencies.py
+++ b/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")

From 65add9cff9ca56ade09649660919b9fa5cd1fa4d Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Fri, 19 Jun 2026 11:26:27 +0200
Subject: [PATCH 08/40] refactor: sould resemble snakemake's main release
 script

---
 .github/workflows/release-please.yml | 65 ++++++++++++++--------------
 1 file changed, 33 insertions(+), 32 deletions(-)

diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml
index dd851322..2f98163a 100644
--- a/.github/workflows/release-please.yml
+++ b/.github/workflows/release-please.yml
@@ -8,43 +8,44 @@ name: release-please
 jobs:
   release-please:
     runs-on: ubuntu-latest
-    outputs:
-      release_created: ${{ steps.release.outputs.release_created }}
     steps:
-      - uses: googleapis/release-please-action@v5
-        id: release
-        with:
-          release-type: python
+
+        - uses: googleapis/release-please-action@v5
+          id: release
+          with: release-type: python
           token: ${{ secrets.RELEASE_PLEASE_PR_CI_TOKEN }}
 
-  publish:
-    runs-on: ubuntu-latest
-    needs: release-please
-    if: ${{ needs.release-please.outputs.release_created }}
-    steps:
-      - uses: actions/checkout@v6
+        - uses: actions/checkout@v6
+          if: ${{ steps.release.outputs.release_created }}
+          with:
+              fetch-depth: 0
 
-      - uses: actions/setup-python@v6
-        with:
-          python-version: "3.12"
+        - name: Set up Pixi
+          if: ${{ steps.release.outputs.release_created }}
+          uses: prefix/setup-pixi@v0.9.6
 
-      - name: Install poetry
-        run: pip install poetry
+        - name: Build and check package
+          if: ${{ steps.release.outputs.release_created }}
+          run: |
+            pixi run --environment publish build-check
 
-      - name: Determine dependencies
-        run: poetry lock
+        - name: Publish to PyPI
+          if: ${{ steps.release.outputs.release_created }}
+          uses: pypa/gh-action-pypi-publish@release/v1
+          with:
+            user: __token__
+        
 
-      - uses: actions/setup-python@v6
+
+
+          
+          
+    outputs:
+      release_created: ${{ steps.release.outputs.release_created }}
+    steps:
+      - uses: googleapis/release-please-action@v5
+        id: release
         with:
-          python-version: "3.12"
-          cache: poetry
-
-      - name: Install dependencies
-        run: |
-          poetry install
-
-      - name: Publish to PyPi
-        env:
-          PYPI_USERNAME: __token__
-          PYPI_PASSWORD: ${{ secrets.PYPI_TOKEN }}
-        run: poetry publish --build --username $PYPI_USERNAME --password $PYPI_PASSWORD
+          release-type: python
+          token: ${{ secrets.RELEASE_PLEASE_PR_CI_TOKEN }}
+          password: ${{ secrets.PYPI_TOKEN }}

From 8ecf6204995641fcd65b40bb8ae3719d227af36f Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Fri, 19 Jun 2026 12:04:59 +0200
Subject: [PATCH 09/40] fix: poetry -> pixi

---
 .github/workflows/ci.yml | 18 +++---------------
 1 file changed, 3 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index e2ae3394..3a718581 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -29,7 +29,7 @@ jobs:
         uses: prefix-dev/setup-pixi@v0
 
       - name: Check code
-        run: poetry run lint
+        run: pixi run lint
 
   testing:
     runs-on: ubuntu-latest
@@ -49,20 +49,8 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0
 
-
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
-
-      - name: Install poetry
-        run: pip install poetry
-
-      - name: Install dependencies
-        run: |
-          poetry install --sync
-
       - name: Run pytest
-        run: poetry run coverage run -m pytest tests/ -sv --tb=short --disable-warnings
+        run: pixi run test
 
       - name: Run Coverage
-        run: poetry run coverage report -m
+        run: pixi run coverage-report

From f01b42c178fa18756d3b203c3100005e77c6a635 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Fri, 19 Jun 2026 12:10:54 +0200
Subject: [PATCH 10/40] refactor: release please versions

---
 .github/workflows/release-please.yml | 54 +++++++++++-----------------
 1 file changed, 21 insertions(+), 33 deletions(-)

diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml
index 2f98163a..e4526e34 100644
--- a/.github/workflows/release-please.yml
+++ b/.github/workflows/release-please.yml
@@ -9,43 +9,31 @@ jobs:
   release-please:
     runs-on: ubuntu-latest
     steps:
-
-        - uses: googleapis/release-please-action@v5
-          id: release
-          with: release-type: python
+      - uses: googleapis/release-please-action@v5
+        id: release
+        with:
+          release-type: python
           token: ${{ secrets.RELEASE_PLEASE_PR_CI_TOKEN }}
 
-        - uses: actions/checkout@v6
-          if: ${{ steps.release.outputs.release_created }}
-          with:
-              fetch-depth: 0
-
-        - name: Set up Pixi
-          if: ${{ steps.release.outputs.release_created }}
-          uses: prefix/setup-pixi@v0.9.6
-
-        - name: Build and check package
-          if: ${{ steps.release.outputs.release_created }}
-          run: |
-            pixi run --environment publish build-check
-
-        - name: Publish to PyPI
-          if: ${{ steps.release.outputs.release_created }}
-          uses: pypa/gh-action-pypi-publish@release/v1
-          with:
-            user: __token__
-        
+      - uses: actions/checkout@v6
+        if: ${{ steps.release.outputs.release_created }}
+        with:
+          fetch-depth: 0
 
+      - uses: actions/setup-python@v6
+        if: ${{ steps.release.outputs.release_created }}
+        with:
+          python-version: "3.11"
 
+      - name: Build package
+        if: ${{ steps.release.outputs.release_created }}
+        run: |
+          python -m pip install --upgrade pip build
+          python -m build
 
-          
-          
-    outputs:
-      release_created: ${{ steps.release.outputs.release_created }}
-    steps:
-      - uses: googleapis/release-please-action@v5
-        id: release
+      - name: Publish to PyPI
+        if: ${{ steps.release.outputs.release_created }}
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          release-type: python
-          token: ${{ secrets.RELEASE_PLEASE_PR_CI_TOKEN }}
+          user: __token__
           password: ${{ secrets.PYPI_TOKEN }}

From 0bc77b9ca9c56bb35b04f3bc92e3fbf69f847f5f Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Fri, 19 Jun 2026 12:14:05 +0200
Subject: [PATCH 11/40] fix: the setup experiment does not belong to the repo -
 has been accidentally pushed

---
 setup.py.bck | 57 ----------------------------------------------------
 1 file changed, 57 deletions(-)
 delete mode 100644 setup.py.bck

diff --git a/setup.py.bck b/setup.py.bck
deleted file mode 100644
index d49d55ab..00000000
--- a/setup.py.bck
+++ /dev/null
@@ -1,57 +0,0 @@
-import os
-from setuptools import setup, find_packages, Extension
-from Cython.Build import cythonize
-import toml
-
-# Parse pyproject.toml for metadata
-pyproject_path = os.path.join(os.path.dirname(__file__), "pyproject.toml")
-with open(pyproject_path, "r") as f:
-    pyproject = toml.load(f)
-
-project = pyproject.get("tool", {}).get("poetry", {})
-dependencies = pyproject.get("tool", {}).get("poetry", {}).get("dependencies", {}).copy()
-
-# Remove python version constraint from dependencies
-dependencies.pop("python", None)
-dependencies.pop("Cython", None)
-
-# Collect all .py files in snakemake_executor_plugin_slurm directory for Cython compilation
-base_dir = "snakemake_executor_plugin_slurm"
-py_files = []
-
-for filename in os.listdir(base_dir):
-    if filename.endswith(".py"):
-        file_path = os.path.join(base_dir, filename)
-        py_files.append(file_path)
-
-# Create a single Extension with all Python files
-extensions = [
-    Extension(
-        'snakemake_executor_plugin_slurm._core',
-        py_files
-    )
-]
-
-# gcc arguments for optimization
-os.environ["CFLAGS"] = "-O3"
-
-setup(
-    name=project.get("name", "snakemake-executor-plugin-slurm"),
-    version=project.get("version", "2.1.0"),
-    description=project.get("description", ""),
-    author=", ".join(project.get("authors", [])),
-    license=project.get("license", ""),
-    url=project.get("repository", ""),
-    py_modules=[],
-    ext_modules=cythonize(extensions, language_level=3, compiler_directives={"linetrace": True}),
-    install_requires=list(dependencies.keys()),
-    classifiers=[
-        "Programming Language :: Python :: 3",
-        "License :: OSI Approved :: MIT License",
-        "Operating System :: OS Independent",
-    ],
-)
-
-
-
-

From 0e25162904a1d8dd2a8e721749645e0ce0594c59 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Fri, 19 Jun 2026 12:15:27 +0200
Subject: [PATCH 12/40] fix: not applying E501 exception to scontrol parsing
 test any longer

---
 pyproject.toml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2b42073a..5e8e1f88 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -44,9 +44,6 @@ extend-exclude = ["tests/test_scontrol_parsing.py"]
 [tool.ruff.lint]
 ignore = ["E203"]
 
-[tool.ruff.lint.per-file-ignores]
-"tests/test_scontrol_parsing.py" = ["E501"]
-
 [tool.pytest.ini_options]
 python_files = ["test_*.py", "tests.py"]
 

From a8811883708791cf42d39f7b9f37fa98b4fa6198 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Mon, 22 Jun 2026 15:21:01 +0200
Subject: [PATCH 13/40] fix: deleted unnecessarry pixi.toml file

---
 pixi.toml | 30 ------------------------------
 1 file changed, 30 deletions(-)
 delete mode 100644 pixi.toml

diff --git a/pixi.toml b/pixi.toml
deleted file mode 100644
index 7af18a1b..00000000
--- a/pixi.toml
+++ /dev/null
@@ -1,30 +0,0 @@
-[project]
-name = "snakemake-executor-plugin-slurm"
-channels = ["conda-forge", "bioconda"]
-platforms = ["linux-64"]
-
-[dependencies]
-python = "3.11.*"
-ruff = ">=0.10.0,<0.11"
-pytest = ">=9.0.3,<10"
-coverage = ">=7.14.0,<8"
-snakemake = ">=9.21.0,<10"
-
-[feature.dev.pypi-dependencies]
-snakemake-executor-plugin-slurm = { path = ".", editable = true }
-
-[feature.conda_pkg.dependencies]
-snakemake-executor-plugin-slurm = "==2.7.1"
-
-[environments]
-default = { features = ["dev"] }
-conda-pkg = { features = ["conda_pkg"] }
-
-[tasks]
-format = "ruff format"
-lint = "ruff check"
-test = "coverage run -m pytest tests/ -sv --tb=short --disable-warnings"
-coverage-report = "coverage report -m"
-
-[system-requirements]
-linux = "4.18"

From 7e246ed8dbbd8d75c88564e68879005b5e8ebfcd Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Tue, 23 Jun 2026 09:11:47 +0200
Subject: [PATCH 14/40] fix: working pyproject toml version

---
 pyproject.toml | 105 ++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 77 insertions(+), 28 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 5e8e1f88..e19963f3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,37 +1,90 @@
-[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."
-authors = [
-    "Christian Meesters <meesters@uni-mainz.de>",
-    "David Lähnemann <david.laehnemann@dkfz-heidelberg.de>",
-    "Johannes Koester <johannes.koester@uni-due.de>",
-]
 readme = "README.md"
+requires-python = ">=3.11"
 license = "MIT"
-repository = "https://github.com/snakemake/snakemake-executor-plugin-slurm"
-documentation = "https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html"
+authors = [
+    { 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",
+]
+  
 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 = ">=1.2.2,<2"
-pyyaml = ">=6.0.3,<7"
-
-[tool.poetry.group.dev.dependencies]
-ruff = ">=0.10.0,<0.11"
-coverage = ">=7.14.0,<8"
+[project.urls]
+Repository = "https://github.com/snakemake/snakemake-executor-plugin-slurm"
+Documentation = "https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html"
+
+[project.scripts]
+generate-slurm-partition-config = "snakemake_executor_plugin_slurm.cli:main"
+
+[tool.setuptools.packages.find]
+include = ["snakemake_executor_plugin_slurm*"]
+
+
+[tool.codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = '.git,*.pdf,*.svg,versioneer.py,*.css,test_*'
+check-hidden = true
+
+####################################################################
+# Pixi Configuration
+####################################################################
+[tool.pixi.workspace]
+name = "snakemake-executor-plugin-slurm"
+channels = ["conda-forge", "bioconda"]
+platforms = ["linux-64"]
+
+[tool.pixi.dependencies]
+python = ">=3.11,<3.14"
+
+[tool.pixi.pypi-dependencies]
+snakemake-executor-plugin-slurm = { path = ".", editable = true }
+
+[tool.pixi.environments]
+dev = { features = ["test", "style"] }
+
+[tool.pixi.feature.test.pypi-dependencies]
 pytest = ">=9.0.3,<10"
+coverage = ">=7.14.0,<8"
 snakemake = ">=9.21.0,<10"
-pandas = ">=2.3.3,<4"
 
-[tool.poetry.scripts]
-generate-slurm-partition-config = "snakemake_executor_plugin_slurm.cli:main"
+[tool.pixi.feature.test.tasks]
+test = { cmd = "pytest" }
+coverage-report = { cmd = "coverage run -m pytest && 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.coverage.run]
 omit = [".*", "*/site-packages/*", "Snakefile"]
@@ -46,7 +99,3 @@ ignore = ["E203"]
 
 [tool.pytest.ini_options]
 python_files = ["test_*.py", "tests.py"]
-
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"

From f27d7e2d179015a5827a809fa1d700b07266e5dd Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Tue, 23 Jun 2026 09:54:40 +0200
Subject: [PATCH 15/40] fix: restored functionality of release-please -
 hopefully

---
 .github/workflows/release-please.yml | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml
index e4526e34..de822959 100644
--- a/.github/workflows/release-please.yml
+++ b/.github/workflows/release-please.yml
@@ -9,6 +9,7 @@ jobs:
   release-please:
     runs-on: ubuntu-latest
     steps:
+
       - uses: googleapis/release-please-action@v5
         id: release
         with:
@@ -20,16 +21,17 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v6
+      - name: Set up Pixi
         if: ${{ steps.release.outputs.release_created }}
+        uses: prefix-dev/setup-pixi@v0.9.6
         with:
-          python-version: "3.11"
+          environments: quality
+          cache: true
 
-      - name: Build package
+      - name: Build and check package
         if: ${{ steps.release.outputs.release_created }}
         run: |
-          python -m pip install --upgrade pip build
-          python -m build
+          pixi run --environment publish build-check
 
       - name: Publish to PyPI
         if: ${{ steps.release.outputs.release_created }}

From 3521d667f97db832eb82bcf747f8abfa22fc8421 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Tue, 23 Jun 2026 18:52:45 +0200
Subject: [PATCH 16/40] fix: attempt to run pixi install correctly

---
 pyproject.toml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index e19963f3..4142cea0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ 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"
+requires-python = ">=3.11,<4"
 license = "MIT"
 authors = [
     { name = "Christian Meesters", email = "meesters@uni-mainz.de" },
@@ -63,6 +63,12 @@ platforms = ["linux-64"]
 
 [tool.pixi.dependencies]
 python = ">=3.11,<3.14"
+pip = ">=24,<26"
+packaging = ">=24,<26"
+poetry = ">=2.4.1" # for local use
+
+[tool.pixi.tasks]
+install = { cmd = "poetry install" }
 
 [tool.pixi.pypi-dependencies]
 snakemake-executor-plugin-slurm = { path = ".", editable = true }

From da3151ab97aac410182ecde1ad67caf932b68ae8 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Tue, 23 Jun 2026 19:54:21 +0200
Subject: [PATCH 17/40] fix: added publish and build envs and check

---
 pyproject.toml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 4142cea0..60754c9f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -75,6 +75,8 @@ snakemake-executor-plugin-slurm = { path = ".", editable = true }
 
 [tool.pixi.environments]
 dev = { features = ["test", "style"] }
+quality = { features = ["style"] }
+publish = { features = ["build"] }
 
 [tool.pixi.feature.test.pypi-dependencies]
 pytest = ">=9.0.3,<10"
@@ -92,6 +94,13 @@ ruff = ">=0.10.0,<0.11"
 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/*" }
+
 [tool.coverage.run]
 omit = [".*", "*/site-packages/*", "Snakefile"]
 

From 3f6aa2614ddfe2ab2bbf6eb632dece90187c9158 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Tue, 23 Jun 2026 20:54:22 +0200
Subject: [PATCH 18/40] fix: cleanup (removed empty task)

---
 pyproject.toml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 60754c9f..389e7cf2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -65,10 +65,6 @@ platforms = ["linux-64"]
 python = ">=3.11,<3.14"
 pip = ">=24,<26"
 packaging = ">=24,<26"
-poetry = ">=2.4.1" # for local use
-
-[tool.pixi.tasks]
-install = { cmd = "poetry install" }
 
 [tool.pixi.pypi-dependencies]
 snakemake-executor-plugin-slurm = { path = ".", editable = true }

From 02f034d723bafdaebed317d960b6870e02a6dd04 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Tue, 23 Jun 2026 20:54:58 +0200
Subject: [PATCH 19/40] fix: added minor versions for actions - no need to
 update for every fix

---
 .github/workflows/release-please.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml
index de822959..17f9288c 100644
--- a/.github/workflows/release-please.yml
+++ b/.github/workflows/release-please.yml
@@ -10,13 +10,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
 
-      - uses: googleapis/release-please-action@v5
+      - uses: googleapis/release-please-action@v5.0
         id: release
         with:
           release-type: python
           token: ${{ secrets.RELEASE_PLEASE_PR_CI_TOKEN }}
 
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v6.0
         if: ${{ steps.release.outputs.release_created }}
         with:
           fetch-depth: 0

From db1f47fad8c4618c40bd6dc3b19c4cfd2925df58 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Wed, 24 Jun 2026 09:00:38 +0200
Subject: [PATCH 20/40] fix: need to specify dev env? + explicit install step

---
 .github/workflows/ci.yml | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3a718581..fdc8d560 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -17,7 +17,7 @@ jobs:
         uses: prefix-dev/setup-pixi@v0
 
       - name: Check formatting
-        run: pixi run format --check .
+        run: pixi run --environment quality format --check .
 
   linting:
     runs-on: ubuntu-latest
@@ -29,7 +29,7 @@ jobs:
         uses: prefix-dev/setup-pixi@v0
 
       - name: Check code
-        run: pixi run lint
+        run: pixi run --environment quality lint
 
   testing:
     runs-on: ubuntu-latest
@@ -49,8 +49,11 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0
 
+      - name: Install package for plugin discovery
+        run: pixi run --environment dev python -m pip install -e .
+
       - name: Run pytest
-        run: pixi run test
+        run: pixi run --environment dev test
 
       - name: Run Coverage
-        run: pixi run coverage-report
+        run: pixi run --environment dev coverage-report

From 0c22b8b4a60c69c605fbdd71933a85794a66cb42 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 24 Jun 2026 07:12:11 +0000
Subject: [PATCH 21/40] fix: install package in non-editable mode for plugin
 discovery

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index fdc8d560..4c0dfcb7 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -50,7 +50,7 @@ jobs:
         uses: prefix-dev/setup-pixi@v0
 
       - name: Install package for plugin discovery
-        run: pixi run --environment dev python -m pip install -e .
+        run: pixi run --environment dev python -m pip install .
 
       - name: Run pytest
         run: pixi run --environment dev test

From f4fa3522ae31cedca3b1314040b2b86615c8cc0d Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Wed, 24 Jun 2026 09:57:13 +0200
Subject: [PATCH 22/40] fix: another attempt

---
 .github/workflows/ci.yml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4c0dfcb7..d56bbd7f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -15,6 +15,8 @@ jobs:
 
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0
+        with:
+          environments: quality
 
       - name: Check formatting
         run: pixi run --environment quality format --check .
@@ -27,6 +29,8 @@ jobs:
 
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0
+        with:
+          environments: quality
 
       - name: Check code
         run: pixi run --environment quality lint
@@ -48,9 +52,8 @@ jobs:
 
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0
-
-      - name: Install package for plugin discovery
-        run: pixi run --environment dev python -m pip install .
+        with:
+          environments: dev
 
       - name: Run pytest
         run: pixi run --environment dev test

From 17f82cde9980125bce10167db53a02711c6b9573 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Wed, 24 Jun 2026 14:26:03 +0200
Subject: [PATCH 23/40] fix: attempting explicit install step

---
 .github/workflows/ci.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d56bbd7f..6d27be87 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -55,6 +55,9 @@ jobs:
         with:
           environments: dev
 
+      - name: Install plugin package (non-editable)
+        run: pixi run --environment dev python -m pip install --no-deps --force-reinstall .
+
       - name: Run pytest
         run: pixi run --environment dev test
 

From 223a06cc7c9f8759bc66f158acfdd260357a025a Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Wed, 24 Jun 2026 17:34:09 +0200
Subject: [PATCH 24/40] fix: added entry point

---
 pyproject.toml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 389e7cf2..77369068 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -44,6 +44,9 @@ Documentation = "https://snakemake.github.io/snakemake-plugin-catalog/plugins/ex
 [project.scripts]
 generate-slurm-partition-config = "snakemake_executor_plugin_slurm.cli:main"
 
+[project.entry-points."snakemake executor plugins"]
+slurm = "snakemake_executor_plugin_slurm:ExecutorPlugin"
+
 [tool.setuptools.packages.find]
 include = ["snakemake_executor_plugin_slurm*"]
 

From cc5a286ddd33c8a48105c60df406add415718cc9 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Wed, 24 Jun 2026 17:34:31 +0200
Subject: [PATCH 25/40] fix: attempting editable install

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6d27be87..50949aa5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -55,8 +55,8 @@ jobs:
         with:
           environments: dev
 
-      - name: Install plugin package (non-editable)
-        run: pixi run --environment dev python -m pip install --no-deps --force-reinstall .
+      - name: Install plugin package
+        run: pixi run --environment dev python -m pip install -e.
 
       - name: Run pytest
         run: pixi run --environment dev test

From 6e171781e17bb4532a0f60176be79c3859907d54 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Wed, 24 Jun 2026 17:42:23 +0200
Subject: [PATCH 26/40] fix: syntax breaking typo

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 50949aa5..2c15953e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -56,7 +56,7 @@ jobs:
           environments: dev
 
       - name: Install plugin package
-        run: pixi run --environment dev python -m pip install -e.
+        run: pixi run --environment dev python -m pip install -e .
 
       - name: Run pytest
         run: pixi run --environment dev test

From 8d1ff56c77b7c947335f4c6adf357f15df544973 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Wed, 24 Jun 2026 17:52:55 +0200
Subject: [PATCH 27/40] fix: unified env name scheme

---
 .github/workflows/ci.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2c15953e..df47f044 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -16,10 +16,10 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0
         with:
-          environments: quality
+          environments: dev
 
       - name: Check formatting
-        run: pixi run --environment quality format --check .
+        run: pixi run --environment dev format --check .
 
   linting:
     runs-on: ubuntu-latest
@@ -30,10 +30,10 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0
         with:
-          environments: quality
+          environments: dev
 
       - name: Check code
-        run: pixi run --environment quality lint
+        run: pixi run --environment dev lint
 
   testing:
     runs-on: ubuntu-latest

From 82860f1cfc4aa525f6783cd0bfb848e534306ea0 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Wed, 24 Jun 2026 19:52:40 +0200
Subject: [PATCH 28/40] fix: trying to get envs straight

---
 pyproject.toml | 23 +++++++++++++++++------
 1 file changed, 17 insertions(+), 6 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 77369068..0dc2dda1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -59,11 +59,27 @@ check-hidden = true
 ####################################################################
 # Pixi Configuration
 ####################################################################
-[tool.pixi.workspace]
+[tool.pixi]
 name = "snakemake-executor-plugin-slurm"
 channels = ["conda-forge", "bioconda"]
 platforms = ["linux-64"]
 
+[tool.pixi.environment.dev]
+features = ["test", "style"]
+
+[tool.pixi.environment.quality]
+features = ["style"]
+
+[tool.pixi.feature.test.pypi-dependencies]
+pytest = ">=9.0.3,<10"
+coverage = ">=7.14.0,<8"
+snakemake = ">=9.21.0,<10"
+
+[tool.pixi.feature.style.pypi-dependencies]
+# e.g. black, ruff, isort … (list whatever you need for style checks)
+black = ">=24.2,<25"
+ruff = ">=0.6.0,<0.7"
+
 [tool.pixi.dependencies]
 python = ">=3.11,<3.14"
 pip = ">=24,<26"
@@ -77,11 +93,6 @@ 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.pixi.feature.test.tasks]
 test = { cmd = "pytest" }
 coverage-report = { cmd = "coverage run -m pytest && coverage report -m" }

From d5fbd53abc2ef57d48b60f5efa1dcf9e1f2fb4d8 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Wed, 24 Jun 2026 20:03:45 +0200
Subject: [PATCH 29/40] fix: again ...

---
 pyproject.toml | 106 ++++++++++++++++++++++++++++---------------------
 1 file changed, 61 insertions(+), 45 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0dc2dda1..531e368c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,31 +1,36 @@
+# ----------------------------------------------------------------------
+# Build system
+# ----------------------------------------------------------------------
 [build-system]
 requires = ["setuptools>=64"]
 build-backend = "setuptools.build_meta"
 
+# ----------------------------------------------------------------------
+# PEP‑621 project metadata (used by pip / setuptools)
+# ----------------------------------------------------------------------
 [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 = "MIT"
+license = {text = "MIT"}
 authors = [
-    { 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" },
+    {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",
+    "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",
 ]
-  
 keywords = ["snakemake", "plugin", "executor", "cluster", "slurm"]
 dependencies = [
     "snakemake-interface-common>=1.23.0,<2",
@@ -36,7 +41,6 @@ dependencies = [
     "throttler>=1.2.2,<2",
     "pyyaml>=6.0.3,<7",
 ]
-
 [project.urls]
 Repository = "https://github.com/snakemake/snakemake-executor-plugin-slurm"
 Documentation = "https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html"
@@ -47,70 +51,82 @@ generate-slurm-partition-config = "snakemake_executor_plugin_slurm.cli:main"
 [project.entry-points."snakemake executor plugins"]
 slurm = "snakemake_executor_plugin_slurm:ExecutorPlugin"
 
+# ----------------------------------------------------------------------
+# Setuptools helper
+# ----------------------------------------------------------------------
 [tool.setuptools.packages.find]
 include = ["snakemake_executor_plugin_slurm*"]
 
-
+# ----------------------------------------------------------------------
+# Codespell configuration (optional, unrelated to Pixi)
+# ----------------------------------------------------------------------
 [tool.codespell]
-# Ref: https://github.com/codespell-project/codespell#using-a-config-file
-skip = '.git,*.pdf,*.svg,versioneer.py,*.css,test_*'
+skip = ".git,*.pdf,*.svg,versioneer.py,*.css,test_*"
 check-hidden = true
 
-####################################################################
-# Pixi Configuration
-####################################################################
+# ----------------------------------------------------------------------
+# Pixi configuration (new schema – version 0.8+)
+# ----------------------------------------------------------------------
 [tool.pixi]
 name = "snakemake-executor-plugin-slurm"
 channels = ["conda-forge", "bioconda"]
 platforms = ["linux-64"]
 
+# Conda‑only dependencies (python, pip, packaging)
+[tool.pixi.dependencies]
+python = ">=3.11,<3.14"
+pip = ">=24,<26"
+packaging = ">=24,<26"
+
+# The plugin itself – installed in editable mode for the CI tests
+[tool.pixi.pypi-dependencies]
+snakemake-executor-plugin-slurm = { path = ".", editable = true }
+
+# ----------------------------------------------------------------------
+# Environments (used by `pixi install -e <name>`)
+# ----------------------------------------------------------------------
 [tool.pixi.environment.dev]
 features = ["test", "style"]
 
 [tool.pixi.environment.quality]
 features = ["style"]
 
+[tool.pixi.environment.publish]
+features = ["build"]
+
+# ----------------------------------------------------------------------
+# Feature definitions
+# ----------------------------------------------------------------------
+# ---- Test -------------------------------------------------------------
 [tool.pixi.feature.test.pypi-dependencies]
 pytest = ">=9.0.3,<10"
 coverage = ">=7.14.0,<8"
 snakemake = ">=9.21.0,<10"
 
-[tool.pixi.feature.style.pypi-dependencies]
-# e.g. black, ruff, isort … (list whatever you need for style checks)
-black = ">=24.2,<25"
-ruff = ">=0.6.0,<0.7"
-
-[tool.pixi.dependencies]
-python = ">=3.11,<3.14"
-pip = ">=24,<26"
-packaging = ">=24,<26"
-
-[tool.pixi.pypi-dependencies]
-snakemake-executor-plugin-slurm = { path = ".", editable = true }
-
-[tool.pixi.environments]
-dev = { features = ["test", "style"] }
-quality = { features = ["style"] }
-publish = { features = ["build"] }
-
 [tool.pixi.feature.test.tasks]
-test = { cmd = "pytest" }
-coverage-report = { cmd = "coverage run -m pytest && coverage report -m" }
+test = {cmd = "pytest"}
+coverage-report = {cmd = "coverage run -m pytest && coverage report -m"}
 
+# ---- Style ------------------------------------------------------------
 [tool.pixi.feature.style.pypi-dependencies]
+black = ">=24.2,<25"
 ruff = ">=0.10.0,<0.11"
 
 [tool.pixi.feature.style.tasks]
-format = { cmd = "ruff format" }
-lint = { cmd = "ruff check ." }
+format = {cmd = "ruff format"}
+lint   = {cmd = "ruff check ."}
 
+# ---- Build ------------------------------------------------------------
 [tool.pixi.feature.build.pypi-dependencies]
 build = "*"
 twine = "*"
 
 [tool.pixi.feature.build.tasks]
-build-check = { cmd = "python -m build && twine check dist/*" }
+build-check = {cmd = "python -m build && twine check dist/*"}
 
+# ----------------------------------------------------------------------
+# Coverage, Ruff, Pytest configuration (unchanged)
+# ----------------------------------------------------------------------
 [tool.coverage.run]
 omit = [".*", "*/site-packages/*", "Snakefile"]
 
@@ -123,4 +139,4 @@ extend-exclude = ["tests/test_scontrol_parsing.py"]
 ignore = ["E203"]
 
 [tool.pytest.ini_options]
-python_files = ["test_*.py", "tests.py"]
+python_files = ["test_*.py", "tests.py"]
\ No newline at end of file

From 60c79cdf7ace8a4de9c93c506e76c8fbcf9e9575 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Thu, 25 Jun 2026 10:21:49 +0200
Subject: [PATCH 30/40] fix: gitignore added some auto generated files

---
 .gitignore | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.gitignore b/.gitignore
index ad6672d8..557dc0ac 100644
--- a/.gitignore
+++ b/.gitignore
@@ -160,3 +160,6 @@ cython_debug/
 #.idea/
 
 .aider*
+# pixi environments
+.pixi/*
+!.pixi/config.toml

From 5cf1020b6d2bee6ad985e2125598e590112297e4 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Thu, 25 Jun 2026 10:22:08 +0200
Subject: [PATCH 31/40] fix: pyproject.toml restructured

---
 pyproject.toml | 110 +++++++++++++++++++++----------------------------
 1 file changed, 46 insertions(+), 64 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 531e368c..edbe907d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,13 +1,8 @@
-# ----------------------------------------------------------------------
-# Build system
-# ----------------------------------------------------------------------
 [build-system]
 requires = ["setuptools>=64"]
 build-backend = "setuptools.build_meta"
 
-# ----------------------------------------------------------------------
-# PEP‑621 project metadata (used by pip / setuptools)
-# ----------------------------------------------------------------------
+
 [project]
 name = "snakemake-executor-plugin-slurm"
 version = "2.7.1"
@@ -17,8 +12,8 @@ requires-python = ">=3.11,<4"
 license = {text = "MIT"}
 authors = [
     {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"},
+    {name = "David Lähnemann",   email = "david.laehnemann@dkfz-heidelberg.de"},
+    {name = "Johannes Koester",  email = "johannes.koester@uni-due.de"},
 ]
 classifiers = [
     "Development Status :: 5 - Production/Stable",
@@ -41,102 +36,89 @@ dependencies = [
     "throttler>=1.2.2,<2",
     "pyyaml>=6.0.3,<7",
 ]
+
 [project.urls]
-Repository = "https://github.com/snakemake/snakemake-executor-plugin-slurm"
+Repository    = "https://github.com/snakemake/snakemake-executor-plugin-slurm"
 Documentation = "https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html"
 
 [project.scripts]
 generate-slurm-partition-config = "snakemake_executor_plugin_slurm.cli:main"
 
-[project.entry-points."snakemake executor plugins"]
+[python-entrypoint-group."snakemake executor plugins"]
 slurm = "snakemake_executor_plugin_slurm:ExecutorPlugin"
 
 # ----------------------------------------------------------------------
-# Setuptools helper
-# ----------------------------------------------------------------------
-[tool.setuptools.packages.find]
-include = ["snakemake_executor_plugin_slurm*"]
-
-# ----------------------------------------------------------------------
-# Codespell configuration (optional, unrelated to Pixi)
+# Misc. developer tools (codespell, coverage, ruff, pytest) – unchanged
 # ----------------------------------------------------------------------
 [tool.codespell]
 skip = ".git,*.pdf,*.svg,versioneer.py,*.css,test_*"
 check-hidden = true
 
-# ----------------------------------------------------------------------
-# Pixi configuration (new schema – version 0.8+)
-# ----------------------------------------------------------------------
+[tool.coverage.run]
+omit = [".*", "*/site-packages/*", "Snakefile"]
+
+[tool.ruff]
+line-length = 88
+target-version = "py311"
+extend-exclude = ["tests/test_scontrol_parsing.py"]
+
+[tool.ruff.lint]
+ignore = ["E203"]
+
+[tool.pytest.ini_options]
+python_files = ["test_*.py", "tests.py"]
+
+
 [tool.pixi]
-name = "snakemake-executor-plugin-slurm"
+
+# Workspace table (required for preview features)
+[tool.pixi.workspace]
+preview = ["pixi-build"]
 channels = ["conda-forge", "bioconda"]
 platforms = ["linux-64"]
 
-# Conda‑only dependencies (python, pip, packaging)
+# Conda-only dependencies (must be a table)
 [tool.pixi.dependencies]
-python = ">=3.11,<3.14"
-pip = ">=24,<26"
+python    = ">=3.11,<3.14"
+pip       = ">=24,<26"
 packaging = ">=24,<26"
 
-# The plugin itself – installed in editable mode for the CI tests
+# Pip-only dependencies (install the plugin from local path)
 [tool.pixi.pypi-dependencies]
-snakemake-executor-plugin-slurm = { path = ".", editable = true }
+snakemake-executor-plugin-slurm = { path = "." }
 
-# ----------------------------------------------------------------------
-# Environments (used by `pixi install -e <name>`)
-# ----------------------------------------------------------------------
-[tool.pixi.environment.dev]
-features = ["test", "style"]
+# Environments (must be a single mapping under the plural key)
+[tool.pixi.environments]
+dev     = { features = ["test", "style"] }
+quality = { features = ["style"] }
+publish = { features = ["build"] }
 
-[tool.pixi.environment.quality]
-features = ["style"]
-
-[tool.pixi.environment.publish]
-features = ["build"]
-
-# ----------------------------------------------------------------------
-# Feature definitions
-# ----------------------------------------------------------------------
-# ---- Test -------------------------------------------------------------
+# Feature definitions (unchanged)
 [tool.pixi.feature.test.pypi-dependencies]
-pytest = ">=9.0.3,<10"
-coverage = ">=7.14.0,<8"
+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*"]
+
 [tool.pixi.feature.test.tasks]
-test = {cmd = "pytest"}
+test            = {cmd = "pytest"}
 coverage-report = {cmd = "coverage run -m pytest && coverage report -m"}
 
-# ---- Style ------------------------------------------------------------
 [tool.pixi.feature.style.pypi-dependencies]
 black = ">=24.2,<25"
-ruff = ">=0.10.0,<0.11"
+ruff  = ">=0.10.0,<0.11"
 
 [tool.pixi.feature.style.tasks]
 format = {cmd = "ruff format"}
 lint   = {cmd = "ruff check ."}
 
-# ---- Build ------------------------------------------------------------
 [tool.pixi.feature.build.pypi-dependencies]
 build = "*"
 twine = "*"
 
 [tool.pixi.feature.build.tasks]
 build-check = {cmd = "python -m build && twine check dist/*"}
-
-# ----------------------------------------------------------------------
-# Coverage, Ruff, Pytest configuration (unchanged)
-# ----------------------------------------------------------------------
-[tool.coverage.run]
-omit = [".*", "*/site-packages/*", "Snakefile"]
-
-[tool.ruff]
-line-length = 88
-target-version = "py311"
-extend-exclude = ["tests/test_scontrol_parsing.py"]
-
-[tool.ruff.lint]
-ignore = ["E203"]
-
-[tool.pytest.ini_options]
-python_files = ["test_*.py", "tests.py"]
\ No newline at end of file

From 0312c686ae37d4fd132ed1f5255944da3704b271 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Thu, 25 Jun 2026 10:28:28 +0200
Subject: [PATCH 32/40] fix: removed on-fly comments

---
 pyproject.toml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index edbe907d..a4b100d4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -47,9 +47,6 @@ generate-slurm-partition-config = "snakemake_executor_plugin_slurm.cli:main"
 [python-entrypoint-group."snakemake executor plugins"]
 slurm = "snakemake_executor_plugin_slurm:ExecutorPlugin"
 
-# ----------------------------------------------------------------------
-# Misc. developer tools (codespell, coverage, ruff, pytest) – unchanged
-# ----------------------------------------------------------------------
 [tool.codespell]
 skip = ".git,*.pdf,*.svg,versioneer.py,*.css,test_*"
 check-hidden = true
@@ -87,13 +84,11 @@ packaging = ">=24,<26"
 [tool.pixi.pypi-dependencies]
 snakemake-executor-plugin-slurm = { path = "." }
 
-# Environments (must be a single mapping under the plural key)
 [tool.pixi.environments]
 dev     = { features = ["test", "style"] }
 quality = { features = ["style"] }
 publish = { features = ["build"] }
 
-# Feature definitions (unchanged)
 [tool.pixi.feature.test.pypi-dependencies]
 pytest    = ">=9.0.3,<10"
 coverage  = ">=7.14.0,<8"

From 1c1fa3ab65332bff5e4c52f97f4ff99993ebc314 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Thu, 25 Jun 2026 10:49:26 +0200
Subject: [PATCH 33/40] fix: attempt to run tests with more verbosity

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index a4b100d4..45d1646b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -101,7 +101,7 @@ exclude = ["pr_logo*"]
 
 [tool.pixi.feature.test.tasks]
 test            = {cmd = "pytest"}
-coverage-report = {cmd = "coverage run -m pytest && coverage report -m"}
+coverage-report = {cmd = "coverage run -m pytest -vv --capture=no && coverage report -m"}
 
 [tool.pixi.feature.style.pypi-dependencies]
 black = ">=24.2,<25"

From ef052c0bef7f56a6ea89a5a87b1a0b6585a23a97 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Thu, 25 Jun 2026 11:03:23 +0200
Subject: [PATCH 34/40] fix: trying alternate, more verbose test

---
 .github/workflows/ci.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index df47f044..f65d7d5f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -59,7 +59,9 @@ jobs:
         run: pixi run --environment dev python -m pip install -e .
 
       - name: Run pytest
-        run: pixi run --environment dev test
+        run: |
+            pixi run --environment dev \
+            python -m pytest -vv --capture=no tests
 
       - name: Run Coverage
         run: pixi run --environment dev coverage-report

From 424018f94184ae8fa8cc198d13557974b6611554 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Thu, 25 Jun 2026 11:23:23 +0200
Subject: [PATCH 35/40] fix: reverted change of release-please script - this PR
 should focus on the CI, only

---
 .github/workflows/release-please.yml | 47 +++++++++++++++++-----------
 1 file changed, 28 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml
index 17f9288c..3ea672d1 100644
--- a/.github/workflows/release-please.yml
+++ b/.github/workflows/release-please.yml
@@ -8,34 +8,43 @@ name: release-please
 jobs:
   release-please:
     runs-on: ubuntu-latest
+    outputs:
+      release_created: ${{ steps.release.outputs.release_created }}
     steps:
-
-      - uses: googleapis/release-please-action@v5.0
+      - uses: googleapis/release-please-action@v4
         id: release
         with:
           release-type: python
           token: ${{ secrets.RELEASE_PLEASE_PR_CI_TOKEN }}
 
-      - uses: actions/checkout@v6.0
-        if: ${{ steps.release.outputs.release_created }}
+  publish:
+    runs-on: ubuntu-latest
+    needs: release-please
+    if: ${{ needs.release-please.outputs.release_created }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
         with:
-          fetch-depth: 0
+          python-version: "3.11"
 
-      - name: Set up Pixi
-        if: ${{ steps.release.outputs.release_created }}
-        uses: prefix-dev/setup-pixi@v0.9.6
+      - name: Install poetry
+        run: pip install poetry
+
+      - name: Determine dependencies
+        run: poetry lock
+
+      - uses: actions/setup-python@v5
         with:
-          environments: quality
-          cache: true
+          python-version: "3.11"
+          cache: poetry
 
-      - name: Build and check package
-        if: ${{ steps.release.outputs.release_created }}
+      - name: Install dependencies
         run: |
-          pixi run --environment publish build-check
+          poetry install
 
-      - name: Publish to PyPI
-        if: ${{ steps.release.outputs.release_created }}
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_TOKEN }}
+      - name: Publish to PyPi
+        env:
+          PYPI_USERNAME: __token__
+          PYPI_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        run: poetry publish --build --username $PYPI_USERNAME --password $PYPI_PASSWORD

From 0cb497820d62108d138f5d38a829190126d12d20 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Fri, 26 Jun 2026 11:18:10 +0200
Subject: [PATCH 36/40] fix: removed entry point which is supposed to guarantee
 recognition - but installment with pip works - testing in the CI now

---
 pyproject.toml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 45d1646b..85863a52 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -44,9 +44,6 @@ Documentation = "https://snakemake.github.io/snakemake-plugin-catalog/plugins/ex
 [project.scripts]
 generate-slurm-partition-config = "snakemake_executor_plugin_slurm.cli:main"
 
-[python-entrypoint-group."snakemake executor plugins"]
-slurm = "snakemake_executor_plugin_slurm:ExecutorPlugin"
-
 [tool.codespell]
 skip = ".git,*.pdf,*.svg,versioneer.py,*.css,test_*"
 check-hidden = true

From 4cb00a9ec8a748e9a8a3ab73e03c8ae43a526c41 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Fri, 26 Jun 2026 11:56:59 +0200
Subject: [PATCH 37/40] fix: removed unnecessary exception

---
 pyproject.toml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 85863a52..7772b37e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -56,13 +56,9 @@ line-length = 88
 target-version = "py311"
 extend-exclude = ["tests/test_scontrol_parsing.py"]
 
-[tool.ruff.lint]
-ignore = ["E203"]
-
 [tool.pytest.ini_options]
 python_files = ["test_*.py", "tests.py"]
 
-
 [tool.pixi]
 
 # Workspace table (required for preview features)

From db8a7a4249972c424038edc69de0b364ced262f2 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Mon, 29 Jun 2026 10:41:42 +0200
Subject: [PATCH 38/40] fix: trying without pixi.build workspace spec

---
 pyproject.toml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 7772b37e..6ec2148a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -52,7 +52,6 @@ check-hidden = true
 omit = [".*", "*/site-packages/*", "Snakefile"]
 
 [tool.ruff]
-line-length = 88
 target-version = "py311"
 extend-exclude = ["tests/test_scontrol_parsing.py"]
 
@@ -63,7 +62,7 @@ python_files = ["test_*.py", "tests.py"]
 
 # Workspace table (required for preview features)
 [tool.pixi.workspace]
-preview = ["pixi-build"]
+#preview = ["pixi-build"]
 channels = ["conda-forge", "bioconda"]
 platforms = ["linux-64"]
 

From 6b58bceec4757cfc0ed9b12cd424f413be684cfd Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Mon, 29 Jun 2026 10:52:41 +0200
Subject: [PATCH 39/40] fix: deleted black dependency (leftover)

---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6ec2148a..5d9a2fa0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -96,7 +96,6 @@ test            = {cmd = "pytest"}
 coverage-report = {cmd = "coverage run -m pytest -vv --capture=no && coverage report -m"}
 
 [tool.pixi.feature.style.pypi-dependencies]
-black = ">=24.2,<25"
 ruff  = ">=0.10.0,<0.11"
 
 [tool.pixi.feature.style.tasks]

From f33ab236eb62f9ca315d818ea6439e44749d8803 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Wed, 1 Jul 2026 13:06:38 +0200
Subject: [PATCH 40/40] fix: added snakemake as depencdency to dev env

---
 pyproject.toml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 5d9a2fa0..26934a7f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -91,6 +91,9 @@ 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"}