GHA & Installation improvements (#1025)

* Improved GHA

---------

Co-authored-by: Hsin Fan <57552401+hsinfan1996@users.noreply.github.com>

.flake8

@@ -0,0 +1,7 @@
+[flake8]
+ignore = E741,E226,W503,W504
+exclude = 
+    build/,
+    .eggs/,
+    benchmarks/data,
+    pyccl/ccllib.py

.github/environment.yml

@@ -0,0 +1,14 @@
+name: test  # default testing environment name from conda-incubator
+dependencies:
+  - pip
+  - cmake
+  - gsl
+  - swig
+  - pyyaml
+  - numpy
+  - scipy
+  - camb=1.3.6
+  - isitgr
+  - fast-pt
+  - pytest
+  - pytest-cov

.github/workflows/ci.yml

@@ -1,4 +1,5 @@
 name: continuous-integration
+
 on:
   push:
     branches:
@@ -7,129 +8,123 @@ on:
       - releases/*
   pull_request: null
 
+env:
+  CACHE_NUMBER: 0  # increase to reset cache manually
+  CONDA_ENV: .github/environment.yml
+
 jobs:
   build:
     runs-on: ${{ matrix.os }}
     defaults:
       run:
         shell: bash -l {0}
+
     strategy:
       fail-fast: false
       matrix:
-        os:
-          - macos-11
-          - ubuntu-latest
+        os: [macos-latest, ubuntu-latest]
+        include:
+          - os: macos-latest
+            label: osx-64
+            prefix: /Users/runner/miniconda3
+
+          - os: ubuntu-latest
+            label: linux-64
+            prefix: /usr/share/miniconda3
         py:
           - 3.8
 
     steps:
-      - name: cancel previous runs
-        uses: styfle/cancel-workflow-action@0.6.0
+      - name: Cancel previous runs
+        uses: styfle/cancel-workflow-action@0.11.0
         with:
           access_token: ${{ github.token }}
 
-      - uses: actions/checkout@v2
+      - name: Checkout CCL repository
+        uses: actions/checkout@v3
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - name: Set up conda
+        uses: conda-incubator/setup-miniconda@v2
         with:
           python-version: ${{ matrix.py }}
-          channels: conda-forge,defaults
+          channels: conda-forge, defaults
           channel-priority: strict
           show-channel-urls: true
           miniforge-version: latest
           miniforge-variant: Mambaforge
 
-      - name: remove homebrew
-        if: matrix.os == 'macos-11'
+      - name: "macOS: set env variables"
+        if: matrix.label == 'osx-64'
         run: |
-          curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/uninstall.sh -o uninstall_homebrew.sh
-          chmod u+x ./uninstall_homebrew.sh
-          ./uninstall_homebrew.sh -f -q >& /dev/null
-          rm -f uninstall_homebrew.sh
+          mamba install llvm-openmp
+          echo "DYLD_FALLBACK_LIBRARY_PATH=${CONDA_PREFIX}/lib" >> $GITHUB_ENV
+          SDKROOT=$(xcrun --sdk macosx --show-sdk-path)
+          echo "SDKROOT: ${SDKROOT}"
+          echo "SDKROOT=${SDKROOT}" >> $GITHUB_ENV
+          echo "CONDA_BUILD_SYSROOT=${SDKROOT}" >> $GITHUB_ENV
 
-      - name: lint
-        run: |
-          export MAMBA_NO_BANNER=1
-          mamba install flake8
-          flake8 pyccl
-          flake8 --exclude=data benchmarks
-          if [[ `grep "$(printf '\t')" pyccl/*.py` != "" ]]; then
-            exit 1
-          fi
-
-      - name: install deps
-        run: |
-          mamba install \
-            pip \
-            numpy nose coveralls pyyaml gsl fftw cmake swig scipy \
-            compilers pkg-config setuptools_scm pytest pandas pytest-cov \
-            cython "camb=1.3.6" isitgr traitlets fast-pt
-
-          if [[ ${MATRIX_OS} == "macos-11" ]]; then
-            mamba install llvm-openmp
-            echo "DYLD_FALLBACK_LIBRARY_PATH=${CONDA_PREFIX}/lib" >> $GITHUB_ENV
-            SDKROOT=$(xcrun --sdk macosx --show-sdk-path)
-            echo "SDKROOT: ${SDKROOT}"
-            echo "SDKROOT=${SDKROOT}" >> $GITHUB_ENV
-            echo "CONDA_BUILD_SYSROOT=${SDKROOT}" >> $GITHUB_ENV
-          fi
-        env:
-          MATRIX_OS: ${{ matrix.os }}
-
-      - name: install class
-        run: |
-          if [[ ${MATRIX_OS} == "macos-11" ]]; then
-            export LDFLAGS="-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
-            export LDFLAGS="$LDFLAGS -L/Users/runner/miniconda3/envs/test/lib"
-            . ci_scripts/install_class_osx.sh
-          else
-            . ci_scripts/install_class_linux.sh
-          fi
-        env:
-          MATRIX_OS: ${{ matrix.os }}
-
-      - name: build CCL
-        run: |
-          python setup.py build
-          python setup.py develop
+          export CFLAGS="-I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include"
+          export LDFLAGS="-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
 
-      - name: c unit tests
+      - name: Set current date as environment variable
+        run: echo "TODAY=$(date +'%Y.%m.%d')" >> $GITHUB_ENV
+
+      - name: Get cached environment
+        uses: actions/cache@v3
+        id: cache
+        with:
+          path: ${{ matrix.prefix }}
+          key:
+            conda-py${{ matrix.py }}--${{
+            matrix.os }}--${{
+            hashFiles(env.CONDA_ENV) }}-${{
+            hashFiles('setup.py') }}--${{
+            env.TODAY }}-${{
+            env.CACHE_NUMBER }}
+
+      - name: Install environment packages
+        if: steps.cache.outputs.cache-hit != 'true'
         run: |
-          cd build
-          make -j4
-          CLASS_PARAM_DIR=./extern/share/class/ OMP_NUM_THREADS=2 ./check_ccl
+          export MAMBA_NO_BANNER=1  # hide mamba banner from output
+          mamba env update --file ${{ env.CONDA_ENV }} --prune
+          pip install "classy<3"
 
-      - name: python unit tests
+      - name: Install CCL
         run: |
-          OMP_NUM_THREADS=2 pytest -vv pyccl --cov=pyccl
+          pip install -e .
 
-      - name: benchmarks
+      - name: Unit tests
         run: |
-          OMP_NUM_THREADS=2 pytest -vv benchmarks --cov=pyccl --cov-append
+          OMP_NUM_THREADS=2 pytest -vv pyccl --cov=pyccl --cov-report=lcov:lcov.info
 
-      - name: coveralls
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Benchmarks
         run: |
-          coveralls --service=github
-
-#  build-doc-only-ubuntu:
-#    runs-on: ubuntu-latest
-#
-#    steps:
-#      - uses: actions/checkout@v2
-#      - name: install latex
-#        run: |
-#
-#          sudo apt install \
-#            texlive texlive-bibtex-extra texlive-science texlive-publishers \
-#            latexmk python3-sphinx python3-sphinx-rtd-theme python3-nbconvert \
-#            python3-jupyter-client jupyter-client jupyter-nbconvert sphinx-common \
-#            pandoc python3-setuptools \
-#            -y
-#          sudo pip3 install mkauthlist
-#
-#      - name: build docs
-#        run: |
-#          cd doc/0000-ccl_note
-#          make
+          OMP_NUM_THREADS=2 pytest -vv benchmarks --cov=pyccl --cov-report=lcov:lcov.info --cov-append
+
+      - name: Code coverage
+        if: matrix.label == 'linux-64'
+        uses: coverallsapp/github-action@v2
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path-to-lcov: lcov.info
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout CCL repository
+        uses: actions/checkout@v3
+
+      - name: Lint
+        uses: py-actions/flake8@v2
+        with:
+          args: "--config .flake8"
+
+
+# Legacy step: uninstall homebrew (CI works without it).
+# - name: "macOS: remove homebrew"
+#   if: matrix.label == 'osx-64'
+#   run: |
+#     curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/uninstall.sh -o uninstall_homebrew.sh
+#     chmod u+x ./uninstall_homebrew.sh
+#     ./uninstall_homebrew.sh -f -q >& /dev/null
+#     rm -f uninstall_homebrew.sh

.gitignore

@@ -59,8 +59,9 @@ tests/benchmark/codes/.ipynb_checkpoints/*
 # Ignore rope project
 .ropeproject
 
-# Ignore the automatically generated coverage file
-.coverage
+# Ignore the automatically generated coverage files
+.coverage*
+*cov.info
 
 # Ignore DS_Store file
 .DS_Store

README.md

@@ -54,9 +54,10 @@ or
 $ pip install pyccl
 ```
 
-For the PyPi installation, you will need ``CMake`` installed locally. See
-[Getting CMake](https://ccl.readthedocs.io/en/latest/source/installation.html#getting-cmake)
-for instructions. Note that the code only supports Linux or Mac OS, but no Windows.
+For the PyPi installation, you will need ``CMake`` and ``SWIG`` installed locally.
+See [Getting CMake](https://ccl.readthedocs.io/en/latest/source/installation.html#getting-cmake)
+and [Installing SWIG](https://pypi.org/project/swig/) for instructions.
+Note that the code only supports Linux or Mac OS, but no Windows.
 
 Once you have the code installed, you can take it for a spin!
 
@@ -81,7 +82,7 @@ lens2 = ccl.WeakLensingTracer(cosmo, dndz=(z_n, n))
 
 # Calculate the angular cross-spectrum of the two tracers as a function of ell
 ell = np.arange(2, 10)
-cls = ccl.angular_cl(cosmo, lens1, lens2, ell)
+cls = cosmo.angular_cl(lens1, lens2, ell)
 print(cls)
 ```
 
@@ -113,7 +114,7 @@ for more information.
 If you have comments, questions, or feedback, please
 [write us an issue](https://github.com/LSSTDESC/CCL/issues).
 
-The current lead of the LSST DESC CCL Topical Team is David Alonso (damonge, david.alonso at physics.ox.ac.uk)
+The current lead of the LSST DESC CCL Topical Team is David Alonso (damonge, david.alonso at physics.ox.ac.uk).
 
 
 # Acknowledgements

cmake/Modules/BuildFFTW.cmake

@@ -5,7 +5,7 @@ set(FFTWMD5 0d5915d7d39b3253c1cc05030d79ac47)
 
 find_package(FFTW)
 
-# If GSL is not installed, lets go ahead and compile it
+# If FFTW is not installed, lets go ahead and compile it
 if(NOT FFTW_FOUND )
     message(STATUS "FFTW not found, downloading and compiling from source")
     ExternalProject_Add(FFTW

setup.py

@@ -92,18 +92,19 @@ def run(self):
     include_package_data=True,
     use_scm_version=True,
     distclass=Distribution,
-    python_requires='>=3.7.0',
+    python_requires='>=3.7',
     setup_requires=['setuptools_scm'],
-    install_requires=['numpy', 'pyyaml'],
+    install_requires=['numpy'],
     cmdclass={'build_py': Build, 'develop': Develop, 'clean': Clean},
     classifiers=[
-        'Development Status :: 4 - Beta',
+        'Development Status :: 5 - Production/Stable',
         'Intended Audience :: Science/Research',
-        'License :: OSI Approved',
+        'License :: OSI Approved :: BSD License',
         'Operating System :: MacOS :: MacOS X',
         'Operating System :: POSIX :: Linux',
         'Programming Language :: C',
         'Programming Language :: Python',
-        'Topic :: Scientific/Engineering :: Physics'
+        'Topic :: Scientific/Engineering :: Physics',
+        'Topic :: Scientific/Engineering :: Astronomy',
     ]
 )