Merge pull request #74 from simpeg/ci_mainenance

Ci mainenance

.github/environment_ci.yml

@@ -0,0 +1,34 @@
+name: geoana-test
+channels:
+  - conda-forge
+dependencies:
+  - numpy>=1.22.4
+  - scipy>=1.8
+  - libdlf
+
+  # optionals
+  - matplotlib
+  - utm
+
+  # documentation
+  - sphinx
+  - pydata-sphinx-theme==0.15.4
+  - sphinx-gallery>=0.1.13
+  - numpydoc>=1.5
+  - discretize
+  - jupyter
+  - graphviz
+  - pillow
+
+  # testing
+  - pytest
+  - pytest-cov
+
+  # Building
+  - pip
+  - meson-python>=0.15.0
+  - meson
+  - ninja
+  - cython>=3.0.8
+  - setuptools_scm
+  - python-build

.github/workflows/release.yml

@@ -6,76 +6,25 @@ on:
     - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
 
 jobs:
-  build_manylinux_x86_64_wheels:
-    name: Build manylinux_x86_64
-    runs-on: ubuntu-20.04
-    steps:
-      - uses: actions/checkout@v4
-      - name: Build wheels
-        uses: pypa/[email protected]
-        env:
-          CIBW_BUILD: "*manylinux_x86_64"
-          CIBW_ARCHS_LINUX: x86_64
-      - uses: actions/upload-artifact@v3
-        with:
-          path: ./wheelhouse/*.whl
-
-  build_manylinux_aarch64_wheels:
-    name: Build manylinux_aarch64
-    runs-on: ubuntu-20.04
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
-        with:
-          platforms: all
-      - name: Build wheels
-        uses: pypa/[email protected]
-        env:
-          CIBW_ARCHS_LINUX: aarch64
-          CIBW_BUILD: "*manylinux_aarch64"
-      - uses: actions/upload-artifact@v3
-        with:
-          path: ./wheelhouse/*.whl
+  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]
 
-  build_musllinux_x86_64_wheels:
-    name: Build musllinux_x86_64 wheels
-    runs-on: ubuntu-20.04
     steps:
       - uses: actions/checkout@v4
-      - name: Build wheels
-        uses: pypa/[email protected]
-        env:
-          CIBW_BUILD: "*musllinux_x86_64"
-          CIBW_ARCHS_LINUX: x86_64
-      - uses: actions/upload-artifact@v3
         with:
-          path: ./wheelhouse/*.whl
+          fetch-depth: 0
 
-  build_mac_wheels:
-    name: Build macos wheels
-    runs-on: macos-11
-    steps:
-      - uses: actions/checkout@v4
       - name: Build wheels
-        uses: pypa/[email protected]
-        env:
-          CIBW_ARCHS_MACOS: x86_64 arm64
-      - uses: actions/upload-artifact@v3
-        with:
-          path: ./wheelhouse/*.whl
+        uses: pypa/[email protected]
 
-  build_windows_wheels:
-    name: Build Windows wheels
-    runs-on: windows-2019
-    steps:
-      - uses: actions/checkout@v4
-      - name: Build wheels
-        uses: pypa/[email protected]
-        env:
-          CIBW_ARCHS_WINDOWS: AMD64
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
 
   # Don't upload this one to pypi, otherwise it will be preferred over every compiled one
@@ -85,6 +34,8 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
@@ -95,7 +46,7 @@ jobs:
           python -m build
           find ./dist/*.whl | xargs pip install
           python -c "import geoana; geoana.show_config()"
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           path: ./dist/geoana*.whl
 
@@ -106,36 +57,16 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-    - uses: actions/checkout@v2
-    - name: Setup environment
-      uses: mamba-org/setup-micromamba@v1
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Setup Conda
+      uses: conda-incubator/setup-miniconda@v3
       with:
-        environment-name: geoana-test
-        create-args: >-
-          python=3.11
-          numpy>=1.20
-          scipy>=1.8
-          libdlf
-          cython
-          setuptools_scm
-          meson-python>=0.14.0
-          meson
-          ninja
-          build
-          discretize
-          numba
-          matplotlib
-          jupyter
-          utm
-          pytest
-          pytest-cov
-          sphinx
-          sphinx-gallery>=0.1.13
-          pydata-sphinx-theme=0.13.3
-          numpydoc>=1.5
-          graphviz
-          pillow
-        cache-environment: true
+        auto-update-conda: true
+        environment-file: .github/environment_ci.yml
+        activate-environment: geoana-test
+        python-version: "3.11"
     - name: Prepare source distribution
       run: |
         python -m build --no-isolation --skip-dependency-check --sdist .
@@ -166,19 +97,15 @@ jobs:
   release:
     name: Create Release
     needs: [
-      build_manylinux_x86_64_wheels,
-      build_manylinux_aarch64_wheels,
-      build_musllinux_x86_64_wheels,
-      build_mac_wheels,
-      build_windows_wheels,
+      build_wheels,
       pure_python
     ]
     runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       name: Retrieve assets
       with:
         name: artifact

.github/workflows/test_with_conda.yml

@@ -18,50 +18,33 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: [3.8, 3.9, "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Setup environment
-      uses: mamba-org/setup-micromamba@v1
+    - uses: actions/checkout@v4
+
+    - name: Setup Conda
+      uses: conda-incubator/setup-miniconda@v3
       with:
-        environment-name: geoana-test
-        create-args: >-
-          python=${{ matrix.python-version }}
-          numpy>=1.20
-          scipy>=1.8
-          libdlf
-          cython
-          setuptools_scm
-          meson-python>=0.14.0
-          meson
-          ninja
-          build
-          discretize
-          matplotlib
-          jupyter
-          utm
-          pytest
-          pytest-cov
-          sphinx
-          sphinx-gallery>=0.1.13
-          pydata-sphinx-theme=0.13.3
-          numpydoc>=1.5
-          graphviz
-          pillow
-        cache-environment: true
-    - name: Install numba
-      if: matrix.python-version != '3.12'
-      # Numba doesn't work on python 3.12 just yet, so conditionally install it into the environment:
+        auto-update-conda: true
+        environment-file: .github/environment_ci.yml
+        activate-environment: geoana-test
+        python-version: ${{ matrix.python-version }}
+
+    - name: Conda information
       run: |
-        micromamba install numba
+        conda info
+        conda list
+        conda config --show
+
     - name: Install Our Package
       run: |
-        pip install --no-build-isolation --editable . --config-settings=setup-args="-Dwith_extensions=true"
-        conda list
+        pip install . --config-settings=setup-args="-Dwith_extensions=true"
+
     - name: Run Tests
       run: |
         pytest --cov-config=.coveragerc --cov=geoana --cov-report=xml -s -v -W ignore::DeprecationWarning
+
     - name: "Upload coverage to Codecov"
       if: matrix.python-version == '3.11'
       uses: codecov/codecov-action@v3

.gitignore

@@ -106,3 +106,5 @@ geoana/kernels/_extensions/potential_field_prism_api.h
 
 # setuptools_scm
 geoana/version.py
+
+.idea/

geoana/kernels/_extensions/meson.build

@@ -1,38 +1,7 @@
+
 # NumPy include directory
-# The try-except is needed because when things are
-# split across drives on Windows, there is no relative path and an exception
-# gets raised. There may be other such cases, so add a catch-all and switch to
-# an absolute path. Relative paths are needed when for example a virtualenv is
-# placed inside the source tree; Meson rejects absolute paths to places inside
-# the source tree.
-# For cross-compilation it is often not possible to run the Python interpreter
-# in order to retrieve numpy's include directory. It can be specified in the
-# cross file instead:
-#   [properties]
-#   numpy-include-dir = /abspath/to/host-pythons/site-packages/numpy/core/include
-#
-# This uses the path as is, and avoids running the interpreter.
-incdir_numpy = meson.get_external_property('numpy-include-dir', 'not-given')
-if incdir_numpy == 'not-given'
-  incdir_numpy = run_command(py,
-    [
-      '-c',
-      '''import os
-import numpy as np
-try:
-  incdir = os.path.relpath(np.get_include())
-except Exception:
-  incdir = np.get_include()
-print(incdir)
-  '''
-    ],
-    check: true
-  ).stdout().strip()
-else
-  _incdir_numpy_abs = incdir_numpy
-endif
-inc_np = include_directories(incdir_numpy)
-np_dep = declare_dependency(include_directories: inc_np)
+np_dep = dependency('numpy')
+numpy_nodepr_api = ['-DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION']
 
 # Deal with M_PI & friends; add `use_math_defines` to c_args or cpp_args
 # Cython doesn't always get this right itself (see, e.g., gh-16800), so
@@ -44,7 +13,6 @@ else
   use_math_defines = []
 endif
 
-numpy_nodepr_api = '-DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION'
 c_undefined_ok = ['-Wno-maybe-uninitialized']
 
 cython_c_args = [numpy_nodepr_api, use_math_defines]
@@ -56,7 +24,6 @@ module_path = 'geoana/kernels/_extensions'
 py.extension_module(
     'potential_field_prism',
     'potential_field_prism.pyx',
-    include_directories: incdir_numpy,
     c_args: cython_c_args,
     install: true,
     subdir: module_path,
@@ -66,7 +33,6 @@ py.extension_module(
 py.extension_module(
     'rTE',
     ['rTE.pyx', '_rTE.cpp'],
-    include_directories: incdir_numpy,
     cpp_args: cython_cpp_args,
     install: true,
     subdir: module_path,