brainiak · mihaic · Nov 15, 2024 · Apr 29, 2024 · Apr 29, 2024 · Apr 29, 2024
diff --git a/.conda/bin/build b/.conda/bin/build
@@ -14,11 +14,6 @@ then
     out_dir=conda_build_out_dir/
 fi
 
-export BRAINIAK_HOME=$DIR/../../
-
-# See run-tests.sh
-export MKL_THREADING_LAYER=GNU
-
 # See https://github.com/brainiak/brainiak/issues/377
 export KMP_DUPLICATE_LIB_OK=TRUE
 

diff --git a/.conda/build.sh b/.conda/build.sh
diff --git a/.conda/meta.yaml b/.conda/meta.yaml
@@ -1,72 +1,79 @@
-{% set conda_package_nonexistent = (
-    "pymanopt<=0.2.5",
-) %}
-{% set data = load_setup_py_data() %}
-
 package:
   # Repeating name because of the following issue:
   # https://github.com/conda/conda-build/issues/2475
   name: brainiak
-  version: {{ environ.get('GIT_DESCRIBE_TAG', 'v0.1.dev1')[1:] }}
+
+  # Can't find a good way to get this from setuptools_scm. This needs to be defined before running conda-build
+  version: {{ environ.get('BRAINIAK_VERSION') }}
 
 about:
-  home: {{ data.get('url') }}
-  license: {{ data.get('license') }}
-  summary: {{ data.get('description') }}
+  home: http://brainiak.org
+  license: Apache-2.0
+  license_family: Apache
+  license_file: LICENSE
+  summary: |
+    The Brain Imaging Analysis Kit is a package of Python modules 
+    useful for neuroscience, primarily focused on functional 
+    Magnetic Resonance Imaging (fMRI) analysis. The package was originally 
+    created by a collaboration between Intel and the 
+    Princeton Neuroscience Institute (PNI).
 
 source:
   path: ../
 
 build:
   number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }}
   script_env:
-
-    # We need the source directory because conda removes source / working
-    # directories by the time we reach the test phase. We can optionally pass in
-    # the --keep-old-work flag later on to use the $PREFIX/work directory
-    - BRAINIAK_HOME
-    - MKL_THREADING_LAYER
     - KMP_DUPLICATE_LIB_OK
 
+  script:
+    - PIP_NO_INDEX=False {{ PYTHON }} -m pip install pymanopt
+    - {{ PYTHON }} -m pip install . -v
+
 requirements:
   build:
+    - python
     - {{ compiler('cxx') }}
 
   host:
     - python
     - pip
-    - mpich
+    - mpich # [not win]
     - llvm-openmp
-    - setuptools>=42 
-    - wheel
+    - scikit-build-core
+    - cmake
+    - setuptools_scm>=8.0
     - pybind11>=2.9.0
     - scipy!=1.0.0
     - cython
-    - numpy<=1.23.1
-    - setuptools_scm
+    - numpy
 
   run:
     - python
-    - numpy<=1.23.1
-    - mpich
-    - llvm-openmp
-    - tensorflow
-    - tensorflow-probability
-    {% for req in data.get('install_requires', [])
-        if req not in conda_package_nonexistent -%}
-    - {{req}}
-    {% endfor %}
+    - {{ pin_compatible('numpy') }}
+    - mpi4py>=3
+    - nitime
+    - scikit-learn>=0.18
+    - scipy!=1.0.0
+    - statsmodels
+    - psutil
+    - nibabel
+    - joblib
+    - wheel
+    - pydicom
+    - tensorflow  # [not win]
+    - tensorflow-probability # [not win]
 
 test:
+  source_files:
+    - tests
+    - pyproject.toml
+  imports:
+    - brainiak
   commands:
-    - find $BRAINIAK_HOME/tests | grep pycache | xargs rm -rf
-    - mpiexec -n 2 pytest $BRAINIAK_HOME
-
-      # Known issue: https://github.com/travis-ci/travis-ci/issues/4704#issuecomment-348435959
-    - python -c 'import os,sys,fcntl; flags = fcntl.fcntl(sys.stdout, fcntl.F_GETFL); fcntl.fcntl(sys.stdout, fcntl.F_SETFL, flags&~os.O_NONBLOCK);'
-    - conda inspect linkages -p $PREFIX brainiak  # [not win]
-    - conda inspect objects -p $PREFIX brainiak  # [osx]
+    - pytest
   requires:
     - pytest
     - testbook
     - numdifftools
+    - pytest-reportlog
diff --git a/.flake8 b/.flake8
@@ -0,0 +1,10 @@
+[flake8]
+max-complexity = 10
+extend-ignore =
+    # Docstrings
+    D,
+    E721,
+    E231
+
+per-file-ignores =
+    src/brainiak/__init__.py:F401
diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml
@@ -0,0 +1,200 @@
+name: wheels and conda
+
+on:
+  workflow_dispatch:
+  release:
+    types:
+      - published
+  pull_request:
+    paths:
+      - .github/workflows/cd.yml
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
+  FORCE_COLOR: 3
+
+jobs:
+  make_sdist:
+    name: Make SDist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Build SDist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  build_wheels:
+    name: Wheel on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+      fail-fast: true
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      # Use intel mpi on windows
+      - uses: mpi4py/setup-mpi@v1
+        if: ${{ contains(matrix.os, 'windows') }}
+        with:
+          mpi: msmpi
+
+      # Else, use the default for the OS and setup-mpi action
+      - uses: mpi4py/setup-mpi@v1
+        if: ${{ !contains(matrix.os, 'windows') }}
+
+      - name: Checkout LLVM on macOS
+        if: runner.os == 'macOS'
+        uses: actions/checkout@v4
+        with:
+          repository: llvm/llvm-project
+          ref: release/18.x
+          path: llvm-project
+
+      - name: Build OpenMP on macOS
+        if: runner.os == 'macOS'
+        env:
+          MACOSX_DEPLOYMENT_TARGET: "10.9"
+        working-directory: llvm-project
+        run: |
+          cmake \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DCMAKE_INSTALL_PREFIX=$(brew --prefix) \
+            -DCMAKE_INSTALL_NAME_DIR=$(brew --prefix)/lib \
+            -DCMAKE_C_COMPILER=clang \
+            -DCMAKE_CXX_COMPILER=clang++ \
+            -DLIBOMP_INSTALL_ALIASES=OFF \
+            -S openmp \
+            -B build
+          cmake --build build --parallel
+          cmake --install build
+
+      - uses: actions/setup-python@v5
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel
+
+      - name: Build wheels
+        run: python -m cibuildwheel --output-dir wheelhouse
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  build_conda:
+    name: Conda on ${{ matrix.os }} with Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -leo pipefail {0}
+    strategy:
+      matrix:
+        os: [ ubuntu-latest, macos-13, macos-latest ]
+        python-version: [ '3.9', '3.10', '3.11', '3.12' ]
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      # Can't figure out a way to get the package version from setuptools_scm inside the conda build
+      # We need to install setuptools_scm, call it as a module, and store the version in an environment variable
+      - name: Run setuptools_scm to get package version and store in environment variable BRAINIAK_VERSION (Linux\Mac)
+        if: ${{ !contains(matrix.os, 'windows') }}
+        run: |
+          python -m pip install setuptools_scm
+          export BRAINIAK_VERSION=$(python -m setuptools_scm)
+          echo "BRAINIAK_VERSION=${BRAINIAK_VERSION}" >> "$GITHUB_ENV"
+
+      - name: Run setuptools_scm to get package version and store in environment variable BRAINIAK_VERSION (Windows)
+        if: ${{ contains(matrix.os, 'windows') }}
+        run: |
+          python -m pip install setuptools_scm
+          set BRAINIAK_VERSION=$(python -m setuptools_scm)
+          echo "BRAINIAK_VERSION=${BRAINIAK_VERSION}" >> "$GITHUB_ENV" 
+
+      - name: Setup micromamba and boa
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
+            conda-forge::conda-build
+            boa
+          init-shell: >-
+            bash
+            powershell
+
+      - name: Build and test package
+        id: build-package
+        run: |
+          conda config --add channels conda-forge
+          conda config --set channel_priority strict
+          conda mambabuild --output-folder=conda-package .conda/
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: conda-package-${{ matrix.os }}-${{ matrix.python-version }}
+          path: conda-package
+
+  publish_pypi:
+    name: Publish to PyPI
+    needs: [ build_wheels, build_conda, make_sdist ]
+    environment:
+      name: pypi
+      url: https://pypi.org/p/brainiak
+    permissions:
+      id-token: write
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && contains(github.ref, 'refs/tags/v')
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - name: List files in artifact(s)
+        run: ls -l dist
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+
+  publish_conda:
+    name: Publish to Anaconda
+    needs: [ build_conda, build_wheels, make_sdist ]
+    environment: anaconda
+    permissions:
+      id-token: write
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && contains(github.ref, 'refs/tags/v')
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: conda-package-*
+          path: conda-packages
+          merge-multiple: false
+
+      - name: List files in artifact
+        run: find conda-packages -type f -name "*.tar.bz2"
+
+      - name: Upload to Anaconda
+        run: |
+          export ANACONDA_API_TOKEN=${{ secrets.ANACONDA_TOKEN }}
+          find conda-packages -type f -name "*.tar.bz2" -exec echo "anaconda upload {}" \;
+