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Gradient generation tool to support GENN models in FOQUS #795

Gradient generation tool to support GENN models in FOQUS

Gradient generation tool to support GENN models in FOQUS #795

Workflow file for this run

name: Checks
on:
push:
branches:
- master
- '*_rel'
repository_dispatch:
# to run this, send a POST API call at repos/<user>/<repo>/dispatches with the specified event_type
# e.g. `gh repos/CCSI-Toolset/FOQUS/dispatches -F event_type=ci_run_tests`
types: [ci_run_tests]
workflow_dispatch:
pull_request:
types:
- opened
# ready_for_review occurs when a draft PR is turned to non-draft
- ready_for_review
# synchronize occurs whenever commits are pushed to the PR branch
- synchronize
defaults:
run:
# the -l flag is needed for the Conda environment to be activated properly
shell: bash -l {0}
env:
FOQUS_CONDA_ENV_NAME_DEV: ccsi-foqus-dev
PYTEST_BASETEMP: .pytest
jobs:
code-formatting:
name: Code formatting (Black)
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
with:
python-version: '3.8'
- name: Install Black
# unlike the other jobs, we don't need to install FOQUS and/or all the dev dependencies,
# but we still want to specify the Black version to use in requirements-dev.txt for local development
# so we extract the relevant line and pass it to a simple `pip install`
run: |
# we store the version
black_requirement="$(grep '^black.*$' requirements-dev.txt)"
pip --no-cache-dir install --progress-bar off "$black_requirement"
- name: Run Black to verify that the committed code is formatted
run: |
black --check .
pytest:
name: pytest (py${{ matrix.python-version }}/${{ matrix.os }})
needs: [code-formatting]
runs-on: ${{ matrix.os-version }}
strategy:
fail-fast: false
matrix:
python-version:
- '3.7'
- '3.8'
- '3.9'
# - '3.10'
os:
- linux
- win64
- macos
include:
- os: macos
os-version: macos-12
- os: linux
os-version: ubuntu-20.04
- os: win64
os-version: windows-2019
- python-version: "3.8" # avoid uploading coverage for full matrix
use_coverage: true
- python-version: "3.8" # this is to avoid installing optional dependencies in all environments
optional-dependencies: tensorflow sympy torch scikit-learn
env:
# uncomment this to debug Qt initialization errors
# QT_DEBUG_PLUGINS: '1'
MPLBACKEND: AGG
steps:
- uses: actions/checkout@v2
- name: Set up Conda
uses: conda-incubator/setup-miniconda@v2
with:
activate-environment: ${{ env.FOQUS_CONDA_ENV_NAME_DEV }}
python-version: ${{ matrix.python-version }}
- name: Set up FOQUS
uses: ./.github/actions/setup-foqus
with:
pip-install-target: -r requirements-dev.txt ${{ matrix.optional-dependencies }}
- name: Set common pytest flags
run:
echo 'PYTEST_ADDOPTS=--pyargs foqus_lib --verbose --color=yes --basetemp "${{ env.PYTEST_BASETEMP }}"' >> $GITHUB_ENV
- name: Set up GUI test environment (Linux)
if: contains(matrix.os, 'linux')
run: |
echo "QT_QPA_PLATFORM=minimal" >> $GITHUB_ENV
- name: Run pytest (default options)
if: "! matrix.use_coverage"
run: |
pytest foqus_lib/
- name: Run pytest (coverage)
if: matrix.use_coverage
run: |
pytest foqus_lib/ --cov=./ --cov-report=xml --cov-report=term
- name: Upload pytest artifacts
uses: actions/upload-artifact@v2
if: always()
with:
# TODO decide if we need a separate upload for each Python version
name: pytest-dir-${{ matrix.os }}-py${{ matrix.python-version }}
path: ${{ env.PYTEST_BASETEMP }}
retention-days: 7
- name: Upload coverage report to Codecov
if: matrix.use_coverage
uses: codecov/codecov-action@v2
pylint:
name: pylint (py${{ matrix.python-version }})
runs-on: ubuntu-20.04
strategy:
fail-fast: false
matrix:
python-version:
- '3.7'
- '3.8'
- '3.9'
# - '3.10'
steps:
- uses: actions/checkout@v2
- name: Set up Conda
uses: conda-incubator/setup-miniconda@v2
with:
activate-environment: ${{ env.FOQUS_CONDA_ENV_NAME_DEV }}
python-version: ${{ matrix.python-version }}
- name: Set up FOQUS
uses: ./.github/actions/setup-foqus
with:
pip-install-target: -r requirements-dev.txt
- name: Run pylint
run: |
pylint --rcfile=.pylint/pylintrc --disable=W,C,R,I foqus_lib/
docs:
name: Build docs
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
- name: Set up Conda
uses: conda-incubator/setup-miniconda@v2
with:
activate-environment: ${{ env.FOQUS_CONDA_ENV_NAME_DEV }}
python-version: ${{ matrix.python-version }}
- name: Set up FOQUS
uses: ./.github/actions/setup-foqus
with:
pip-install-target: -r requirements-dev.txt
- name: Build docs
run: |
cd docs/
make CLOPTS="-qW --keep-going" clean dummy