Maintenance for Geoana

.github/make_ci_environ.py

@@ -0,0 +1,89 @@
+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")
+    is_free_threaded = os.environ.get("FREE_THREADED", "false").lower() == "true"
+    no_doc = os.environ.get("NO_DOC_BUILD", "false").lower() == "true"
+    no_numba = os.environ.get("NO_NUMBA", "false").lower() == "true"
+    env_name = os.environ.get("ENV_NAME", "geoana_env")
+
+    skips = ["all"]
+    if no_numba or is_free_threaded:
+        skips.append("jittable")
+    if no_doc:
+        skips.append("doc")
+
+    deps = parse_pyproject(pyproject_path, optional_sections_to_skip=skips)
+    if is_free_threaded:
+        deps.discard("matplotlib-base")
+    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/release.yml

@@ -1,26 +1,26 @@
-name: Release
-on:
-  push:
-    # Sequence of patterns matched against refs/tags
-    tags:
-    - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+name: Build Distribution artifacts
+
+on: [push, pull_request]
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   build_wheels:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # macos-13 is an intel runner, macos-14 is apple silicon
-        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        # macos-15-intel is an Intel runner, macos-14 is Apple silicon
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, windows-11-arm, macos-15-intel, macos-14]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.21.3
+        uses: pypa/cibuildwheel@v3.2.0
 
       - uses: actions/upload-artifact@v4
         with:
@@ -31,7 +31,9 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
 
       - name: Build sdist
         run: pipx run build --sdist
@@ -45,9 +47,9 @@ jobs:
   # We can host it here on github though for those that need it (re: jupyter-light).
   pure_python:
     name: Create pure-python wheel
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Set up Python
@@ -68,20 +70,35 @@ jobs:
   distribute:
     name: Distribute documentation
     runs-on: ubuntu-latest
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
     defaults:
       run:
         shell: bash -l {0}
     steps:
-    - uses: actions/checkout@v4
+    - 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: "3.13"
+        ENV_NAME: geoana-test
+        NO_NUMBA: "true"
+
     - name: Setup Conda
       uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
         environment-file: .github/environment_ci.yml
-        activate-environment: geoana-test
-        python-version: "3.11"
+        activate-environment: geoana-test 
     - name: Install Our Package
       run: |
         pip install --no-build-isolation --editable . --config-settings=setup-args="-Dwith_extensions=true"
@@ -108,6 +125,7 @@ jobs:
       pure_python
     ]
     runs-on: ubuntu-latest
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/test_with_conda.yml

@@ -1,15 +1,12 @@
 name: Testing With Conda
+on: [push, pull_request]
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
-on:
-  push:
-    branches:
-      - '*'
-  pull_request:
-    branches:
-      - '*'
 jobs:
   build_and_test:
-    name: Testing (${{ matrix.python-version }}, ${{ matrix.os }})
+    name: Testing (${{ matrix.python-version }}${{ matrix.free-threaded && 't' || '' }}, ${{ matrix.os }})
     runs-on: ${{ matrix.os }}
     defaults:
       run:
@@ -18,39 +15,47 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
+        free-threaded: [false, true]
+        include:
+          - free-threaded: true
+            no_doc: true
+          - python-version: "3.14"
+            no_numba: true
+        exclude:
+          - python-version: "3.11"
+            free-threaded: true
+          - python-version: "3.12"
+            free-threaded: true
 
     steps:
-    - uses: actions/checkout@v4
+    - 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}}
+        FREE_THREADED: ${{ matrix.free-threaded && 'true' || 'false' }}
+        NO_DOC_BUILD: ${{ matrix.no_doc && 'true' || 'false' }}
+        NO_NUMBA: ${{ matrix.no_numba && 'true' || 'false' }}
+        ENV_NAME: geoana-test
+
+
     - name: Setup Conda
       uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
-        environment-file: .github/environment_ci.yml
+        environment-file: environment_ci.yml
         activate-environment: geoana-test
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install numba
-      if: matrix.python-version != '3.13'
-      # Numba doesn't work on python 3.13 just yet:
-      run: |
-        conda install --yes -c conda-forge numba
-
-      # Install discretize from it's repo until wheels/conda-forge built against numpy2.0 available:
-    - name: Pull Discretize
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-        repository: 'simpeg/discretize'
-        ref: 'main'
-        path: 'discretize'
-
-    - name: Install discretize
-      run: |
-        pip install ./discretize
 
     - name: Conda information
       run: |
@@ -64,7 +69,7 @@ jobs:
 
     - name: Run Tests
       run: |
-        pytest tests --cov-config=.coveragerc --cov=geoana --cov-report=xml -s -v -W ignore::DeprecationWarning
+        pytest tests --cov-config=.coveragerc --cov=geoana --cov-report=xml -s -v -W ignore::DeprecationWarning ${{ matrix.NO_DOC_BUILD && ' -k "not docs"'|| ''}}
 
     - name: "Upload coverage to Codecov"
       if: matrix.python-version == '3.11'

.gitignore

@@ -108,3 +108,7 @@ geoana/kernels/_extensions/potential_field_prism_api.h
 geoana/version.py
 
 .idea/
+
+.vscode/
+
+environment_ci.yml

docs/conf.py

@@ -441,9 +441,9 @@
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
     'python': ('https://docs.python.org/3/', None),
-    'numpy': ('https://docs.scipy.org/doc/numpy/', None),
-    'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
-    'matplotlib': ('http://matplotlib.org/', None),
+    'numpy': ('https://numpy.org/doc/stable/', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/', None),
+    'matplotlib': ('https://matplotlib.org/stable/', None),
 }
 
 

geoana/kernels/_extensions/meson.build

@@ -1,3 +1,25 @@
+add_languages('c', 'cpp', 'cython')
+
+py_dep = py.dependency()
+cc = meson.get_compiler('c')
+cpp = meson.get_compiler('cpp')
+cy = meson.get_compiler('cython')
+
+_global_c_args = cc.get_supported_arguments(
+  '-Wno-unused-but-set-variable',
+  '-Wno-unused-function',
+  '-Wno-conversion',
+  '-Wno-misleading-indentation',
+)
+add_project_arguments(_global_c_args, language : 'c')
+
+# We need -lm for all C code (assuming it uses math functions, which is safe to
+# assume for SciPy). For C++ it isn't needed, because libstdc++/libc++ is
+# guaranteed to depend on it.
+m_dep = cc.find_library('m', required : false)
+if m_dep.found()
+  add_project_link_arguments('-lm', language : 'c')
+endif
 
 numpy_nodepr_api = ['-DNPY_NO_DEPRECATED_API=NPY_1_22_API_VERSION']
 

geoana/kernels/_extensions/potential_field_prism.pyx

@@ -1,3 +1,6 @@
+# cython: freethreading_compatible = True
+# cython: language_level=3
+# cython: embedsignature=True
 cimport cython
 
 from libc.math cimport sqrt, log, atan