fix: update to latest interface

.github/workflows/ci.yml

@@ -6,73 +6,49 @@ on:
       - main
   pull_request:
 
-env:
-  PYTHON_VERSION: 3.11
-
 jobs:
-  linting:
+  formatting:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the code
-        uses: actions/checkout@v3
-
-      - uses: actions/setup-python@v4
-        with:
-          python-version: ${{ env.PYTHON_VERSION }}
-
-      - name: Install poetry
-        run: pip install poetry
+        uses: actions/checkout@v5
 
-      - name: Determine dependencies
-        run: poetry lock
-
-      - uses: actions/setup-python@v4
-        with:
-          python-version: ${{ env.PYTHON_VERSION }}
-          cache: poetry
-
-      - name: Install Dependencies using Poetry
-        run: poetry install
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0
 
       - name: Check formatting
-        run: poetry run ruff format --check .
-
-      - name: Lint
-        run: poetry run ruff check .
+        run: pixi run format --check .
 
-  testing:
+  linting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-
-      - uses: actions/setup-python@v4
-        with:
-          python-version: ${{ env.PYTHON_VERSION }}
+      - name: Check out the code
+        uses: actions/checkout@v5
 
-      - name: Install poetry
-        run: pip install poetry
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0
 
-      - name: Determine dependencies
-        run: poetry lock
+      - name: Check code
+        run: pixi run lint
 
-      - uses: actions/setup-python@v4
-        with:
-          python-version: ${{ env.PYTHON_VERSION }}
-          cache: poetry
+  testing:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
 
-      - name: Install dependencies
-        run: poetry install
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0
 
       - name: Setup envmodules
         run: |
           sudo apt-get update
           sudo apt-get install -y environment-modules
 
       - name: Run pytest
+        shell: bash -el {0}
         run: |
-          source /etc/profile.d/modules.sh
-          module --help
-          poetry run coverage run -m pytest
+          command -v module
+          pixi run test -v
 
       - name: Run Coverage
-        run: poetry run coverage report -m
+        run: pixi run coverage-report

.github/workflows/release-please.yml

@@ -18,36 +18,23 @@ jobs:
         id: release
         with:
           release-type: python
-          package-name: 
 
   publish:
     runs-on: ubuntu-latest
     needs: release-please
     if: ${{ needs.release-please.outputs.release_created }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v5
 
-      - uses: actions/setup-python@v4
-        with:
-          python-version: ${{ env.PYTHON_VERSION }}
-
-      - name: Install poetry
-        run: pip install poetry
-
-      - name: Determine dependencies
-        run: poetry lock
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0
 
-      - uses: actions/setup-python@v4
-        with:
-          python-version: ${{ env.PYTHON_VERSION }}
-          cache: poetry
-
-      - name: Install Dependencies using Poetry
+      - name: Build source and wheel distribution + check build
         run: |
-          poetry install
+          pixi run check-build
 
-      - name: Publish to PyPi
-        env:
-          PYPI_USERNAME: __token__
-          PYPI_PASSWORD: ${{ secrets.PYPI_TOKEN }}
-        run: poetry publish --build --username $PYPI_USERNAME --password $PYPI_PASSWORD
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}

.gitignore

@@ -159,4 +159,4 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 
-poetry.lock
+pixi.lock

pyproject.toml

@@ -1,26 +1,67 @@
 [project]
 name = "snakemake-software-deployment-plugin-envmodules"
 version = "0.1.4"
-description = ""
+authors = [{ name = "Johannes Köster", email = "johannes.koester@uni-due.de" }]
+description = "Software deployment plugin for Snakemake using environment modules."
 readme = "README.md"
 requires-python = ">=3.11,<4.0"
-dependencies = ["snakemake-interface-software-deployment-plugins >=0.6.1,<1.0.0"]
-repository = "https://github.com/your/plugin"
+dependencies = [
+    "snakemake-interface-common (>=1.17.4,<2.0.0)",
+    "snakemake-interface-software-deployment-plugins (>=0.7.7,<1.0)",
+]
+
+[tool.pixi.pypi-dependencies]
+snakemake-software-deployment-plugin-envmodules = { path = ".", editable = true }
+#snakemake-interface-software-deployment-plugins = { path = "../snakemake-interface-software-deployment-plugins", editable = true }
+
+[project.urls]
+repository = "https://github.com/snakemake/snakemake-software-deployment-plugin-envmodules"
 documentation = "https://snakemake.github.io/snakemake-plugin-catalog/plugins/software-deployment/envmodules.html"
-[[project.authors]]
-name = "Johannes Koester"
-email = "johannes.koester@uni-due.de"
 
 [build-system]
-requires = [ "poetry-core>=2.0.0,<3.0.0",]
-build-backend = "poetry.core.masonry.api"
-
-[tool.poetry]
-[[tool.poetry.packages]]
-include = "snakemake_software_deployment_plugin_envmodules"
-from = "src"
-
-[tool.poetry.group.dev.dependencies]
-coverage = "^7.6.12"
-pytest = "^8.3.5"
-ruff = "^0.9.9"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.pixi.project]
+channels = ["conda-forge"]
+platforms = ["osx-arm64", "linux-64"]
+
+[tool.pixi.environments]
+dev = { features = ["dev"] }
+publish = { features = ["publish"] }
+
+[tool.pixi.feature.dev.dependencies]
+pytest = ">=8.3.5,<9"
+ruff = ">=0.10.0,<0.11"
+pytest-cov = ">=6.0.0,<7"
+
+[tool.pixi.feature.dev.tasks]
+format = "ruff format"
+lint = "ruff check"
+qc = { depends-on = ["format", "lint"] }
+coverage-report = "coverage report -m"
+
+[tool.pixi.feature.dev.tasks.test]
+cmd = [
+    "pytest",
+    "--cov=snakemake_software_deployment_plugin_envmodules",
+    "--cov-report=xml:coverage-report/coverage.xml",
+    "--cov-report=term-missing",
+    "tests/test_plugin.py",
+]
+
+[tool.coverage.report]
+exclude_lines = ["pass", "\\.\\.\\."]
+fail_under = 70.0
+
+# Publish
+[tool.pixi.feature.publish.dependencies]
+twine = ">=6.1.0,<7"
+python-build = ">=1.2.2,<2"
+
+
+[tool.pixi.feature.publish.tasks]
+build = { cmd = "python -m build", description = "Build the package into the dist/ directory" }
+check-build = { cmd = "python -m twine check dist/*", depends-on = [
+    "build",
+], description = "Check that the package can be uploaded" }

src/snakemake_software_deployment_plugin_envmodules/__init__.py

@@ -1,4 +1,5 @@
-from typing import Iterable, Tuple
+import shlex
+from typing import Iterable
 import subprocess as sp
 from snakemake_interface_software_deployment_plugins import (
     EnvBase,
@@ -15,7 +16,7 @@
 class EnvSpec(EnvSpecBase):
     def __init__(self, *names: str):
         super().__init__()
-        self.names: Tuple[str] = names
+        self.names: tuple[str, ...] = tuple(names)
 
     def identity_attributes(self) -> Iterable[str]:
         # The identity of the env spec is given by the names of the modules.
@@ -25,6 +26,9 @@ def source_path_attributes(self) -> Iterable[str]:
         # no paths involved here
         return ()
 
+    def __str__(self) -> str:
+        return ",".join(self.names)
+
 
 class Env(EnvBase):
     def __post_init__(self):
@@ -33,19 +37,20 @@ def __post_init__(self):
 
     @EnvBase.once
     def check(self) -> None:
-        if self.run_cmd("type module", stdout=sp.PIPE, stderr=sp.PIPE).returncode != 0:
+        res = self.run_cmd("type module", stdout=sp.PIPE, stderr=sp.STDOUT)
+        if res.returncode != 0:
             raise WorkflowError(
                 "The module command is not available. "
-                "Please make sure that the environment modules are "
-                "available on your system."
+                "Please make sure that environment modules are "
+                f"available on your system: {res.stdout.decode()}"
             )
 
     def decorate_shellcmd(self, cmd: str) -> str:
         # Decorate given shell command such that it runs within the environment.
         # Unclear why that happens.
         # one might have to say 'shopt -s expand_aliases;', but that did not
         # help either...
-        return f"module purge && module load {' '.join(self.spec.names)}; {cmd}"
+        return f"module purge && module load {' '.join(shlex.quote(name) for name in self.spec.names)} && {cmd}"
 
     def record_hash(self, hash_object) -> None:
         # We just hash the names here as the best thing we can do for envmodules

tests/test_plugin.py

@@ -1,19 +1,20 @@
 import os
 from typing import Optional, Type
-from snakemake_interface_software_deployment_plugins import EnvBase
+from snakemake_interface_software_deployment_plugins import EnvBase, EnvSpecBase
 from snakemake_interface_software_deployment_plugins.tests import (
     TestSoftwareDeploymentBase,
 )
 from snakemake_interface_software_deployment_plugins.settings import (
     SoftwareDeploymentSettingsBase,
 )
-from snakemake_software_deployment_plugin_envmodules import Env, EnvSpec, EnvSpecBase
+from snakemake_software_deployment_plugin_envmodules import Env, EnvSpec
 
 os.environ["MODULEPATH"] = "tests/modules"
 
 
-class TestSoftwareDeployment(TestSoftwareDeploymentBase):
+class Test(TestSoftwareDeploymentBase):
     __test__ = True  # activate automatic testing
+    shell_executable = ["bash", "-l", "-c"]
 
     def get_software_deployment_provider_settings(
         self,
@@ -30,6 +31,17 @@ def get_env_spec(self) -> EnvSpecBase:
         # testing.
         return EnvSpec("somecmd")
 
+    def get_settings_cls(self) -> Optional[Type[SoftwareDeploymentSettingsBase]]:
+        # Return the settings class that should be used for this plugin.
+        return None
+
+    def get_settings(
+        self,
+    ) -> Optional[SoftwareDeploymentSettingsBase]:
+        # If your plugin has settings, return a valid settings object here.
+        # Otherwise, return None.
+        return None
+
     def get_test_cmd(self) -> str:
         # Return a command that should be executable without error in the environment
         return "somecmd"