Begin work to integrate cibuildwheel tests. (#351)

* Test and deploy binary pip wheels: - Add scripts to be run inside a cibuildwheel docker image on both linux and macos which installs static versions of OpenBLAS (linux only), fftw, and suitesparse. Link our internal _libtoast extension to these static packages, which ensures consistency regardless of other shared libraries loaded by other packages. - Add a github workflow which tests pip wheel building daily, and preserves the wheels as artifacts which can be downloaded and tested as needed. This also runs the unit tests on the installed wheel packages (linux and macos, python 3.6-3.8). - Add a deployment workflow executed on git tags which uploads to pypi. this will likely need some testing during 2.3.7 tag preparation. - Cleanup package definitions in setup.py, version generation, and add a MANIFEST.in file to ensure that extra package files are bundled. * Use path relative to setup.py when generating version. * Require python 3.6.0 or newer. Add documentation for the release process.
hpc4cmb · May 30, 2020 · 6c02c9f · 6c02c9f
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diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -0,0 +1,110 @@
+# Deploy tagged releases.
+
+name:  Deploy Release
+
+on:
+  push:
+    tags:
+      - '*'
+
+env:
+  TWINE_USERNAME: __token__
+  TWINE_PASSWORD: ${{ secrets.TWINE_PASSWORD }}
+
+jobs:
+  py36:
+    name: Python 3.6 wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    env:
+      CIBW_BUILD: cp36-macosx_x86_64 cp36-manylinux_x86_64
+      CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+      CIBW_MANYLINUX_I686_IMAGE: manylinux2014
+      CIBW_BUILD_VERBOSITY: 3
+      CIBW_ENVIRONMENT_LINUX: "TOAST_STATIC_DEPS=1 TOAST_BUILD_BLAS_LIBRARIES='-lopenblas -fopenmp -lm -lgfortran' TOAST_BUILD_LAPACK_LIBRARIES='-lopenblas -fopenmp -lm -lgfortran'"
+      CIBW_ENVIRONMENT_MACOS: "TOAST_STATIC_DEPS=1"
+      CIBW_BEFORE_BUILD_LINUX: ./wheels/install_deps_linux.sh
+      CIBW_BEFORE_BUILD_MACOS: ./wheels/install_deps_osx.sh
+      CIBW_BEFORE_TEST: echo "" >/dev/null
+      CIBW_TEST_COMMAND: export OMP_NUM_THREADS=2; python -c 'import toast.tests; toast.tests.run()'
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      name: Install Python
+      with:
+        python-version: '3.7'
+    - name: Install cibuildwheel
+      run: |
+        python -m pip install twine cibuildwheel==1.4.2
+    - name: Build wheel
+      run: |
+        python -m cibuildwheel --output-dir wheelhouse
+    - name: Upload to PyPI
+      run: |
+        python -m twine upload wheelhouse/toast*.whl
+  py37:
+    name: Python 3.7 wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    env:
+      CIBW_BUILD: cp37-macosx_x86_64 cp37-manylinux_x86_64
+      CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+      CIBW_MANYLINUX_I686_IMAGE: manylinux2014
+      CIBW_BUILD_VERBOSITY: 3
+      CIBW_ENVIRONMENT_LINUX: "TOAST_STATIC_DEPS=1 TOAST_BUILD_BLAS_LIBRARIES='-lopenblas -fopenmp -lm -lgfortran' TOAST_BUILD_LAPACK_LIBRARIES='-lopenblas -fopenmp -lm -lgfortran'"
+      CIBW_ENVIRONMENT_MACOS: "TOAST_STATIC_DEPS=1"
+      CIBW_BEFORE_BUILD_LINUX: ./wheels/install_deps_linux.sh
+      CIBW_BEFORE_BUILD_MACOS: ./wheels/install_deps_osx.sh
+      CIBW_BEFORE_TEST: echo "" >/dev/null
+      CIBW_TEST_COMMAND: export OMP_NUM_THREADS=2; python -c 'import toast.tests; toast.tests.run()'
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      name: Install Python
+      with:
+        python-version: '3.7'
+    - name: Install cibuildwheel
+      run: |
+        python -m pip install twine cibuildwheel==1.4.2
+    - name: Build wheel
+      run: |
+        python -m cibuildwheel --output-dir wheelhouse
+    - name: Upload to PyPI
+      run: |
+        python -m twine upload wheelhouse/toast*.whl
+  py38:
+    name: Python 3.8 wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    env:
+      CIBW_BUILD: cp38-macosx_x86_64 cp38-manylinux_x86_64
+      CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+      CIBW_MANYLINUX_I686_IMAGE: manylinux2014
+      CIBW_BUILD_VERBOSITY: 3
+      CIBW_ENVIRONMENT_LINUX: "TOAST_STATIC_DEPS=1 TOAST_BUILD_BLAS_LIBRARIES='-lopenblas -fopenmp -lm -lgfortran' TOAST_BUILD_LAPACK_LIBRARIES='-lopenblas -fopenmp -lm -lgfortran'"
+      CIBW_ENVIRONMENT_MACOS: "TOAST_STATIC_DEPS=1"
+      CIBW_BEFORE_BUILD_LINUX: ./wheels/install_deps_linux.sh
+      CIBW_BEFORE_BUILD_MACOS: ./wheels/install_deps_osx.sh
+      CIBW_BEFORE_TEST: echo "" >/dev/null
+      CIBW_TEST_COMMAND: export OMP_NUM_THREADS=2; python -c 'import toast.tests; toast.tests.run()'
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      name: Install Python
+      with:
+        python-version: '3.7'
+    - name: Install cibuildwheel
+      run: |
+        python -m pip install twine cibuildwheel==1.4.2
+    - name: Build wheel
+      run: |
+        python -m cibuildwheel --output-dir wheelhouse
+    - name: Upload to PyPI
+      run: |
+        python -m twine upload wheelhouse/toast*.whl
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -0,0 +1,115 @@
+
+name:  Test Binary Wheels
+
+# Uncomment here for testing and comment out schedule below.
+# on:
+#   push:
+#     branches: [ master ]
+#   pull_request:
+#     branches: [ master ]
+
+# Uncomment here for production and comment out push / PR above.
+on:
+  schedule:
+    - cron: '0 4 * * *'
+
+jobs:
+  py36:
+    name: Python 3.6 wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    env:
+      CIBW_BUILD: cp36-macosx_x86_64 cp36-manylinux_x86_64
+      CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+      CIBW_MANYLINUX_I686_IMAGE: manylinux2014
+      CIBW_BUILD_VERBOSITY: 3
+      CIBW_ENVIRONMENT_LINUX: "TOAST_STATIC_DEPS=1 TOAST_BUILD_BLAS_LIBRARIES='-lopenblas -fopenmp -lm -lgfortran' TOAST_BUILD_LAPACK_LIBRARIES='-lopenblas -fopenmp -lm -lgfortran'"
+      CIBW_ENVIRONMENT_MACOS: "TOAST_STATIC_DEPS=1"
+      CIBW_BEFORE_BUILD_LINUX: ./wheels/install_deps_linux.sh
+      CIBW_BEFORE_BUILD_MACOS: ./wheels/install_deps_osx.sh
+      CIBW_BEFORE_TEST: echo "" >/dev/null
+      CIBW_TEST_COMMAND: export OMP_NUM_THREADS=2; python -c 'import toast.tests; toast.tests.run()'
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      name: Install Python
+      with:
+        python-version: '3.7'
+    - name: Install cibuildwheel
+      run: |
+        python -m pip install cibuildwheel==1.4.2
+    - name: Build wheel
+      run: |
+        python -m cibuildwheel --output-dir wheelhouse
+    - uses: actions/upload-artifact@v2
+      with:
+        name: wheels
+        path: ./wheelhouse
+  py37:
+    name: Python 3.7 wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    env:
+      CIBW_BUILD: cp37-macosx_x86_64 cp37-manylinux_x86_64
+      CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+      CIBW_MANYLINUX_I686_IMAGE: manylinux2014
+      CIBW_BUILD_VERBOSITY: 3
+      CIBW_ENVIRONMENT_LINUX: "TOAST_STATIC_DEPS=1 TOAST_BUILD_BLAS_LIBRARIES='-lopenblas -fopenmp -lm -lgfortran' TOAST_BUILD_LAPACK_LIBRARIES='-lopenblas -fopenmp -lm -lgfortran'"
+      CIBW_ENVIRONMENT_MACOS: "TOAST_STATIC_DEPS=1"
+      CIBW_BEFORE_BUILD_LINUX: ./wheels/install_deps_linux.sh
+      CIBW_BEFORE_BUILD_MACOS: ./wheels/install_deps_osx.sh
+      CIBW_BEFORE_TEST: echo "" >/dev/null
+      CIBW_TEST_COMMAND: export OMP_NUM_THREADS=2; python -c 'import toast.tests; toast.tests.run()'
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      name: Install Python
+      with:
+        python-version: '3.7'
+    - name: Install cibuildwheel
+      run: |
+        python -m pip install cibuildwheel==1.4.2
+    - name: Build wheel
+      run: |
+        python -m cibuildwheel --output-dir wheelhouse
+    - uses: actions/upload-artifact@v2
+      with:
+        name: wheels
+        path: ./wheelhouse
+  py38:
+    name: Python 3.8 wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    env:
+      CIBW_BUILD: cp38-macosx_x86_64 cp38-manylinux_x86_64
+      CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+      CIBW_MANYLINUX_I686_IMAGE: manylinux2014
+      CIBW_BUILD_VERBOSITY: 3
+      CIBW_ENVIRONMENT_LINUX: "TOAST_STATIC_DEPS=1 TOAST_BUILD_BLAS_LIBRARIES='-lopenblas -fopenmp -lm -lgfortran' TOAST_BUILD_LAPACK_LIBRARIES='-lopenblas -fopenmp -lm -lgfortran'"
+      CIBW_ENVIRONMENT_MACOS: "TOAST_STATIC_DEPS=1"
+      CIBW_BEFORE_BUILD_LINUX: ./wheels/install_deps_linux.sh
+      CIBW_BEFORE_BUILD_MACOS: ./wheels/install_deps_osx.sh
+      CIBW_BEFORE_TEST: echo "" >/dev/null
+      CIBW_TEST_COMMAND: export OMP_NUM_THREADS=2; python -c 'import toast.tests; toast.tests.run()'
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      name: Install Python
+      with:
+        python-version: '3.7'
+    - name: Install cibuildwheel
+      run: |
+        python -m pip install cibuildwheel==1.4.2
+    - name: Build wheel
+      run: |
+        python -m cibuildwheel --output-dir wheelhouse
+    - uses: actions/upload-artifact@v2
+      with:
+        name: wheels
+        path: ./wheelhouse
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -24,13 +24,6 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 # Auxiliary files
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake")
 
-# Copy the RELEASE file into the build directory
-configure_file(
-    "${CMAKE_CURRENT_SOURCE_DIR}/RELEASE"
-    "${CMAKE_CURRENT_BINARY_DIR}/RELEASE"
-    COPYONLY
-)
-
 # Use GNUInstallDirs to install libraries into correct locations on all
 # platforms.
 include(GNUInstallDirs)
@@ -69,8 +62,10 @@ if(BLAS_FOUND)
     if(LAPACK_FOUND)
         find_package(LAPACKnames)
     else(LAPACK_FOUND)
-        message(SEND_ERROR "Could not find a working LAPACK installation")
+        message(FATAL_ERROR "Could not find a working LAPACK installation")
     endif(LAPACK_FOUND)
+else(BLAS_FOUND)
+    message(FATAL_ERROR "Could not find a working BLAS installation")
 endif(BLAS_FOUND)
 
 find_package(FFTW)

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,10 @@
+include README.md
+include AUTHORS
+include LICENSE
+include src
+include CMakeLists.txt
+include tutorial
+include example
+include platforms
+include cmake
+include docs
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # Time Ordered Astrophysics Scalable Tools
 
-[![Build Status](https://travis-ci.org/hpc4cmb/toast.svg?branch=master)](https://travis-ci.org/hpc4cmb/toast)
+![Build Status](https://github.com/hpc4cmb/toast/workflows/Run%20Test%20Suite/badge.svg?branch=master)
 
 See the full documentation here:
 

diff --git a/RELEASE b/RELEASE
diff --git a/cmake/FindAATM.cmake b/cmake/FindAATM.cmake
@@ -26,19 +26,18 @@ if(PKG_CONFIG_FOUND AND NOT AATM_ROOT)
 endif()
 
 # Check whether to search static or dynamic libs
-set(CMAKE_FIND_LIBRARY_SUFFIXES_SAV ${CMAKE_FIND_LIBRARY_SUFFIXES})
+
+set(AATM_LIB_NAME "aatm")
 
 if(${AATM_USE_STATIC_LIBS})
-  set(CMAKE_FIND_LIBRARY_SUFFIXES ${CMAKE_STATIC_LIBRARY_SUFFIX})
-else()
-  set(CMAKE_FIND_LIBRARY_SUFFIXES ${CMAKE_FIND_LIBRARY_SUFFIXES_SAV})
+  set(AATM_LIB_NAME "aatm_static")
 endif()
 
 if(AATM_ROOT)
     # find libs
     find_library(
         AATM_LIB
-        NAMES "aatm"
+        NAMES ${AATM_LIB_NAME}
         PATHS ${AATM_ROOT}
         PATH_SUFFIXES "lib" "lib64"
         NO_DEFAULT_PATH
@@ -54,7 +53,7 @@ if(AATM_ROOT)
 else(AATM_ROOT)
     find_library(
         AATM_LIB
-        NAMES "aatm"
+        NAMES ${AATM_LIB_NAME}
         PATHS "${PKG_AATM_PREFIX}"
         PATH_SUFFIXES "lib" "lib64"
     )
@@ -70,9 +69,6 @@ if(AATM_LIB)
     set(AATM_LIBRARIES ${AATM_LIB})
 endif(AATM_LIB)
 
-# Restore variable
-set(CMAKE_FIND_LIBRARY_SUFFIXES ${CMAKE_FIND_LIBRARY_SUFFIXES_SAV})
-
 include(FindPackageHandleStandardArgs)
 
 find_package_handle_standard_args(AATM

diff --git a/docs/dev.rst b/docs/dev.rst
@@ -102,3 +102,37 @@ exposed through pybind11 should also have docstrings defined in the bindings.  C
 that is not exposed to python is considered internal, expert-level code that does not
 require formal documentation.  However, such code should have sufficient comments to
 describe the algorithm and design choices.
+
+Testing Workflow
+--------------------------
+
+We are using a github workflow to pull docker containers with our dependencies and run
+our unit tests.  Those docker containers are re-generated whenever a new tag is made on
+the `cmbenv git repository <https://github.com/hpc4cmb/cmbenv>`_.  So if there are
+dependencies that need to be updated, open a PR against cmbenv which updates the version
+or build in the package file.  After merging and tagging a new cmbenv release the
+updated docker images will be available in an hour or two and be used automatically.
+
+Release Process
+---------------------------
+
+There are some github workflows that only run when a new tag is created.  Unless you are
+sure everything works, create a "release candidate" tag first.  Before making a tag,
+ensure that the `docs/changes.rst` file contains all pull requests that have been merged
+since the last tag.  Also edit the `src/toast/RELEASE` file and set the version to a
+`PEP-440 compatible string <https://www.python.org/dev/peps/pep-0440/>`_.  Next go onto
+the github releases page and create a new release from the master branch.  Briefly, the
+format for a stable release, a release candidate or alpha version is:
+
+    2.6.9
+    2.6.7rc2
+    2.6.8a1
+
+After tagging the release, verify that the github workflow to deploy pip wheels runs and
+uploads these to PyPI.  The conda-forge bots will automatically detect the new tag and
+open a PR to update the feedstock.  Also, after the release is complete, update the
+`RELEASE` file to be at the "alpha" of the next release.  For example, after tagging
+version 3.4.5, set the version in the RELEASE file to 3.4.6a1.  This version is **only**
+used when building pip wheels.  Anyone installing locally with setup.py or with pip
+running on the local source tree will get a version constructed from the number of
+commits since the last git tag.