Merge pull request #200 from NSLS-II/fix-osx-compilation

Fix OSX compilation

.github/workflows/ci-test.yml

@@ -1,91 +1,145 @@
 name: CI-Test
 
-on: [push, pull_request]
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+  release:
+    types: [published, created]
 
 jobs:
 
   lint:
+    # pull requests are a duplicate of a branch push if within the same repo.
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
+
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v4
-    - uses: pre-commit/[email protected]
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+      - uses: pre-commit/[email protected]
 
   test:
+    # pull requests are a duplicate of a branch push if within the same repo.
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
+
     name: Tests
     runs-on: ${{ matrix.host-os }}
     needs: lint
+
     strategy:
       matrix:
+        # host-os: ["ubuntu-latest", "macos-13", "macos-14"]
         host-os: ["ubuntu-latest"]
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
       fail-fast: false
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
     steps:
-      - name: Set env.REPOSITORY_NAME  # just the repo, as opposed to org/repo
+      - name: Checkout the code
+        uses: actions/checkout@v4
+
+      - name: Set env vars
         run: |
-          export REPOSITORY_NAME=${GITHUB_REPOSITORY#*/}
+          export REPOSITORY_NAME=${GITHUB_REPOSITORY#*/}  # just the repo, as opposed to org/repo
           echo "REPOSITORY_NAME=${REPOSITORY_NAME}" >> $GITHUB_ENV
 
-      - name: Checkout the code
-        uses: actions/checkout@v4
+          python_version="${{ matrix.python-version }}"
+          export PYTHON_VERSION_NODOT="${python_version//\./}"
+          echo "PYTHON_VERSION_NODOT=${PYTHON_VERSION_NODOT}" >> $GITHUB_ENV
+
+      - name: Set MacOS Deployment Target
+        if: runner.os == 'macOS'
+        run: |
+          export MACOSX_DEPLOYMENT_TARGET="10.15"
+          echo "MACOSX_DEPLOYMENT_TARGET=${MACOSX_DEPLOYMENT_TARGET}" >> $GITHUB_ENV
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+      - name: Install micromamba with build dependencies
+        uses: mamba-org/setup-micromamba@v1
+        # if: runner.os == 'macOS'
         with:
-          python-version: ${{ matrix.python-version }}
+          init-shell: bash
+          environment-name: build-env
+          create-args: >-
+            python=${{ matrix.python-version }}
+            arpack=*=mpi_openmpi*
+            gfortran
+            openmpi=4
+
+
+      # - name: Set up Python ${{ matrix.python-version }}
+      #   # if: matrix.host-os != 'macos-latest'
+      #   if: runner.os != 'macOS'
+      #   uses: actions/setup-python@v5
+      #   with:
+      #     python-version: ${{ matrix.python-version }}
+
+      - name: Install MacOS dependencies
+        if: runner.os == 'macOS'
+        run: |
+          set -vxeuo pipefail
+          brew install tree
+      #     python -m pip install delocate
 
       - name: Install dependencies
         run: |
           set -vxeuo pipefail
           bash ./scripts/install-deps.sh
+          tree .
           ls -Al .
           ls -Al ./dist/
-          tree .
+
+      # - name: Delocate wheels for MacOS
+      #   if: runner.os == 'macOS'
+      #   run: |
+      #     set -vxeuo pipefail
+      #     delocate-wheelpython -v ./dist/${{ env.REPOSITORY_NAME }}-*-cp${PYTHON_VERSION_NODOT}*.whl
 
       - uses: actions/upload-artifact@v3
         with:
           name: ${{ env.REPOSITORY_NAME }}-wheels
-          path: dist/*.whl
+          path: dist/*
 
       - name: Test with pytest
         run: |
           set -vxeuo pipefail
           bash ./scripts/run-tests.sh
 
-  docs:
-    name: Documentation
-    runs-on: ubuntu-latest
-    needs: test
-    strategy:
-      matrix:
-        python-version: [3.8]
-      fail-fast: false
-
-    steps:
-      - name: Set env.REPOSITORY_NAME  # just the repo, as opposed to org/repo
-        run: |
-          export REPOSITORY_NAME=${GITHUB_REPOSITORY#*/}
-          echo "REPOSITORY_NAME=${REPOSITORY_NAME}" >> $GITHUB_ENV
-
-      - name: Checkout the code
-        uses: actions/checkout@v4
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install dependencies
-        run: |
-          set -vxeuo pipefail
-          bash ./scripts/install-deps.sh
-
       - name: Build Docs
         run: |
           set -vxeuo pipefail
           bash ./scripts/build-docs.sh
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          name: ${{ env.REPOSITORY_NAME }}-docs
+          name: ${{ env.REPOSITORY_NAME }}-${{ matrix.python-version }}-${{ matrix.host-os }}-docs
           path: docs/build/html/
+
+
+  publish-to-pypi:
+    # Hints from:
+    #   - https://github.com/pypa/gh-action-pypi-publish/discussions/28
+    #   - https://github.com/Lightning-AI/lightning/blob/master/.github/workflows/release-pypi.yml
+    if: github.event_name == 'release'
+    name: Publish to PyPI
+    needs: test
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Download wheels from GitHub artifacts
+        uses: actions/download-artifact@v3
+        with:
+          name: wheels
+          path: dist/
+
+      - name: Publish wheels to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: ./dist/

.gitignore

@@ -100,3 +100,6 @@ target/
 
 #Ipython Notebook
 .ipynb_checkpoints
+
+# cibuildwheel artifacts
+wheelhouse/

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-yaml
       - id: check-toml
@@ -19,7 +19,7 @@ repos:
             docs/
           )
   - repo: https://github.com/PyCQA/flake8.git
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: flake8
         exclude: ^examples/

scripts/install-deps.sh

@@ -2,29 +2,43 @@
 
 set -vxeuo pipefail
 
-sudo apt-get update -y
-sudo apt-get install -y \
-    gfortran \
-    openmpi-bin \
-    openmpi-doc \
-    libopenmpi-dev \
-    libopenblas-dev \
-    libarpack2-dev \
-    libparpack2-dev
+platform="$(uname)"
+
+if [ "${platform}" == "Linux" ]; then
+    # sudo apt-get update -y
+    # sudo apt-get install -y \
+    #     gfortran \
+    #     openmpi-bin \
+    #     openmpi-doc \
+    #     libopenmpi-dev \
+    #     libopenblas-dev \
+    #     libarpack2-dev \
+    #     libparpack2-dev
+    echo "Skipping system packages installation in favor of conda packages for building."
+elif [ "${platform}" == "Darwin" ]; then
+    echo "gfortran is expected to exist already."
+fi
+
+gfortran --version
+which gfortran
 
 # These packages are installed in the base environment but may be older
 # versions. Explicitly upgrade them because they often create
 # installation problems if out of date.
+which python
+python -VV
+
 python -m pip install --upgrade pip setuptools wheel numpy
 
 # # Generate .whl file.
 python setup.py sdist bdist_wheel
+ls -la dist/
 
 # Install this package and the packages listed in requirements.txt.
-pip install -v .
+python -m pip install dist/edrixs-*-cp${PYTHON_VERSION_NODOT}*.whl
 
 # Install extra requirements for running tests and building docs.
-pip install -r requirements-dev.txt
+python -m pip install -r requirements-dev.txt
 
 # List the depencencies
-pip list
+python -m pip list

setup.py

@@ -12,7 +12,7 @@
 # NOTE: This file must remain Python 2 compatible for the foreseeable future,
 # to ensure that we error out properly for people with outdated setuptools
 # and/or pip.
-min_version = (3, 6)
+min_version = (3, 8)
 if sys.version_info < min_version:
     error = """
 edrixs does not support Python {0}.{1}.

src/CMakeLists.txt

@@ -57,11 +57,22 @@ if (EDRIXS_PY_INTERFACE)
   target_include_directories(${f2py_module_name} PUBLIC ${Python3_INCLUDE_DIRS} ${F2PY_INCLUDE_DIR} ${Python3_NumPy_INCLUDE_DIRS})
   target_link_libraries(${f2py_module_name} PUBLIC edrixs)
 
-  set_target_properties(
-       ${f2py_module_name}
+  if (LINUX)
+    set_target_properties(
+        ${f2py_module_name}
+        PROPERTIES
+            PREFIX ""
+            OUTPUT_NAME ${generated_module_file}
+            LINKER_LANGUAGE C
+      )
+  elseif(APPLE)
+    set_target_properties(
+      ${f2py_module_name}
       PROPERTIES
           PREFIX ""
           OUTPUT_NAME ${generated_module_file}
           LINKER_LANGUAGE C
-      )
+          LINK_FLAGS "-undefined dynamic_lookup"
+    )
+  endif()
 endif()