create a ci environment.yml with python script

Author: jcapriot

.github/make_ci_environ.py

@@ -0,0 +1,88 @@
+import tomllib
+from pathlib import Path
+import yaml
+import os
+
+def parse_pyproject(path: str, optional_sections_to_skip=None):
+    with open(path, "rb") as f:
+        data = tomllib.load(f)
+
+    deps = set()
+
+    # project.dependencies (PEP 621)
+    for dep in data.get("project", {}).get("dependencies", []):
+        if "numpy" in dep:
+            # numpy is also listed in build requirements with a higher version number
+            # so we skip it here to avoid conflicts.
+            continue
+        deps.add(dep)
+
+    # optional dependencies (PEP 621)
+    if optional_sections_to_skip is None:
+        optional_sections_to_skip = []
+    for group, group_deps in data.get("project", {}).get("optional-dependencies", {}).items():
+        if group in optional_sections_to_skip:
+            print("Skipping optional dependency group:", group)
+            continue
+        deps.update(group_deps)
+
+    deps.discard("geoana[all]")
+    deps.discard("geoana[doc,all]")
+    deps.discard("geoana[plot,extras,jittable]")
+
+    if "matplotlib" in deps:
+        deps.remove("matplotlib")
+        deps.add("matplotlib-base")
+    return deps
+
+def create_env_yaml(deps, name="env", python_version=None, free_threaded=False):
+    conda_pkgs = []
+    pip_pkgs = []
+
+    for dep in deps:
+        # crude split: try to detect conda vs pip-only packages
+        if any(dep.startswith(pip_only) for pip_only in ["git+", "http:", "https:", "file:"]):
+            pip_pkgs.append(dep)
+        else:
+            conda_pkgs.append(dep)
+
+    dependencies = conda_pkgs
+    if pip_pkgs:
+        dependencies.append({"pip": pip_pkgs})
+
+    if python_version:
+        if free_threaded:
+            dependencies.insert(0, f"python-freethreading={python_version}")
+        else:
+            dependencies.insert(0, f"python={python_version}")
+
+    return {
+        "name": name,
+        "channels": ["conda-forge"],
+        "dependencies": dependencies,
+    }
+
+if __name__ == "__main__":
+    pyproject_path = Path("pyproject.toml")
+
+    py_vers = os.environ.get("PYTHON_VERSION", "3.11")
+    mkl_vers = os.environ.get("MKL_VERSION", "2024")
+    is_free_threaded = os.environ.get("FREE_THREADED", "false").lower() == "true"
+    is_coverage = os.environ.get("DO_COVERAGE", "false").lower() == "true"
+    env_name = os.environ.get("ENV_NAME", "pydiso-ci")
+
+    optional_to_skip = []
+    if not is_coverage:
+        optional_to_skip.append("coverage")
+    
+    deps = parse_pyproject(pyproject_path, optional_sections_to_skip=optional_to_skip)
+    deps.add("mkl-devel")
+    deps.add("pkg-config")
+    deps.add(f"mkl={mkl_vers}")
+    env_data = create_env_yaml(deps, name=env_name, python_version=py_vers, free_threaded=is_free_threaded)
+
+    out_name = "environment_ci.yml"
+    with open(out_name, "w") as f:
+        yaml.safe_dump(env_data, f, sort_keys=False)
+
+    print("✅ Generated environment_ci.yml with", len(deps), "dependencies")

.github/workflows/python-package-conda.yml

@@ -22,7 +22,7 @@ jobs:
         include:
           - os: ubuntu-latest
             python-version: "3.12"
-            coverage: ${{ true }}
+            coverage: true
           - os: macos-15-intel
             python-version: "3.11"
             mkl-version: "2023"
@@ -36,27 +36,35 @@ jobs:
             free-threaded: true
           - python-version: "3.12"
             free-threaded: true
+          - python-version: "3.14"
+            free-threaded: true
+            mkl-version: "2025"
 
     steps:
     - uses: actions/checkout@v5
       with:
         fetch-depth: 0
 
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.13"
+    
+    - name: Create Conda environment file
+      run: |
+        python -m pip install pyyaml
+        python .github/make_ci_environ.py
+      env:
+        PYTHON_VERSION: ${{ matrix.python-version}}
+        MKL_VERSION: ${{ matrix.mkl-version }}
+        FREE_THREADED: ${{ matrix.free-threaded && 'true' || 'false' }}
+        DO_COVERAGE: ${{ matrix.coverage && 'true' || 'false' }}
+        ENV_NAME: pydiso-ci
+
     - name: Setup Conda
       uses: conda-incubator/setup-miniconda@v3
       with:
-        channels: conda-forge, defaults
-        channel-priority: true
-        activate-environment: dev
-
-    - name: Create environment
-      run: |
-        conda install --quiet --yes -c conda-forge \
-          ${{ matrix.free-threaded && 'python-freethreading' || 'python' }}=${{ matrix.python-version }} \
-          pip numpy scipy cython mkl=${{ matrix.mkl-version }} pytest \
-          mkl-devel pkg-config meson-python meson ninja setuptools_scm \
-          ${{ matrix.coverage && 'coverage' || ''}} \
-          ${{ matrix.os == 'windows-latest' && '"libblas=*=*mkl"' || ''}}
+        activate-environment: pydiso-ci
 
     - name: Conda information
       run: |
@@ -71,8 +79,6 @@ jobs:
           ${{ matrix.coverage && '--config-settings=setup-args="-Db_coverage=true"' || ''}} \
           ${{ matrix.os == 'windows-latest' && '--config-settings=setup-args="-Dvsenv=true"' || ''}}
 
-        conda list
-
     - name: Run Tests
       run: |
         ${{ matrix.coverage && 'coverage run -m' || '' }} pytest -s -v

.gitignore

@@ -12,3 +12,5 @@ coverage.xml
 .idea/
 
 .vscode/
+
+environment_ci.yml

pyproject.toml

@@ -53,7 +53,10 @@ file = 'LICENSE'
 [project.optional-dependencies]
 test = [
     "pytest",
-    "pytest-cov",
+]
+
+coverage = [
+    "coverage",
 ]
 
 build = [