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Out unit tests for operators and functions no longer pass if something is not implemented #1398

Out unit tests for operators and functions no longer pass if something is not implemented

Out unit tests for operators and functions no longer pass if something is not implemented #1398

Workflow file for this run

name: build
on:
release:
types: [published]
push:
branches: [master]
tags: ['**']
paths-ignore:
- 'CHANGELOG.md'
- 'CITATION.cff'
- 'LICENSE'
- 'scripts/**'
- 'NOTICE.txt'
- 'README.md'
pull_request:
branches: [master]
paths-ignore:
- 'CHANGELOG.md'
- 'CITATION.cff'
- 'LICENSE'
- 'scripts/**'
- 'NOTICE.txt'
- 'README.md'
jobs:
test-cuda:
defaults: {run: {shell: 'bash -el {0}'}}
runs-on: [self-hosted, python, cuda]
strategy:
matrix:
python-version: [3.11]
numpy-version: [1.25]
steps:
- uses: actions/checkout@v4
with: {fetch-depth: 0, submodules: recursive}
- id: reqs
name: set requirements
run: |
envname="${GITHUB_REPOSITORY##*/}-${GITHUB_RUN_ID}.${GITHUB_RUN_NUMBER}"
echo "envname=$envname" >> $GITHUB_OUTPUT
sed -ri -e 's/^(name: ).*/\1$envname/' -e '/ python /d' -e 's/(.* numpy) .*/\1=${{ matrix.numpy-version }}/' scripts/requirements-test.yml
- uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.python-version }}
environment-file: scripts/requirements-test.yml
activate-environment: ${{ steps.reqs.outputs.envname }}
run-post: false
- id: build
name: build
run: |
conda activate "${{ steps.reqs.outputs.envname }}"
cmake -S . -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX"
cmake --build ./build --target install
- name: test
run: |
conda activate "${{ steps.reqs.outputs.envname }}"
TESTS_FORCE_GPU=1 python -m unittest discover -v -k tigre -k TIGRE -k astra -k ASTRA -k gpu -k GPU ./Wrappers/Python/test
- if: always()
name: Post Run conda-incubator/setup-miniconda@v3
shell: bash
run: |
sed -i '/${{ steps.reqs.outputs.envname }}/d' ~/.profile
source ~/.profile
conda env remove -n "${{ steps.reqs.outputs.envname }}"
test:
defaults: {run: {shell: 'bash -el {0}'}}
runs-on: ubuntu-latest
strategy:
matrix:
include:
- python-version: '3.10'
numpy-version: 1.23
- python-version: 3.12
numpy-version: 1.26
steps:
- uses: actions/checkout@v4
with: {fetch-depth: 0, submodules: recursive}
- name: set requirements
run: sed -ri -e '/ python /d' -e 's/(.* numpy) .*/\1=${{ matrix.numpy-version }}/' -e 's/=cuda*//' -e '/tigre/d' scripts/requirements-test.yml
- uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.python-version }}
environment-file: scripts/requirements-test.yml
activate-environment: cil_dev
- name: build
run: |
cmake -S . -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX"
cmake --build ./build --target install
- name: test
run: python -m unittest discover -v ./Wrappers/Python/test
conda-matrix:
runs-on: ubuntu-latest
outputs:
python-version: ${{ steps.matrix.outputs.python-version }}
numpy-version: ${{ steps.matrix.outputs.numpy-version }}
steps:
- id: matrix
run: |
if ${{ github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags') }}; then
echo "python-version=['3.10', 3.11]" >> $GITHUB_OUTPUT
echo "numpy-version=[1.23, 1.24, 1.25, 1.26]" >> $GITHUB_OUTPUT
else
echo "python-version=['3.10']" >> $GITHUB_OUTPUT
echo "numpy-version=[1.23]" >> $GITHUB_OUTPUT
fi
conda:
defaults: {run: {shell: 'bash -el {0}'}}
runs-on: ubuntu-latest
needs: conda-matrix
strategy:
matrix:
python-version: ${{ fromJson(needs.conda-matrix.outputs.python-version) }}
numpy-version: ${{ fromJson(needs.conda-matrix.outputs.numpy-version) }}
include:
- python-version: 3.12
numpy-version: 1.26
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
submodules: recursive
ref: ${{ github.event.pull_request.head.sha || github.ref }} # fix SHA
- uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.python-version }}
mamba-version: "1.5"
channels: conda-forge
- name: conda build & test
working-directory: recipe
run: |
conda install boa
conda mambabuild . -c conda-forge -c https://tomography.stfc.ac.uk/conda --override-channels --python=${{ matrix.python-version }} --numpy=${{ matrix.numpy-version }} --output-folder .
- uses: actions/upload-artifact@v4
with:
name: cil-package-py${{ matrix.python-version }}-np${{ matrix.numpy-version }}
path: recipe/linux-64/cil*
- name: anaconda upload -c ccpi
if: github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags')
run: |
conda install anaconda-client
anaconda -v -t ${{ secrets.CCPI_CONDA_TOKEN }} upload --force --label ${{ startsWith(github.ref, 'refs/tags') && 'main' || 'dev' }} recipe/linux-64/cil*
- name: conda upload -c tomography.stfc.ac.uk/conda
if: startsWith(github.ref, 'refs/tags')
run: |
echo '${{ secrets.STFC_SSH_KEY }}' > ./key
chmod 600 ./key
rsync -e 'ssh -o StrictHostKeyChecking=no -i ./key' -P recipe/linux-64/cil* \
'${{ secrets.STFC_SSH_HOST }}:${{ secrets.STFC_SSH_CONDA_DIR }}/linux-64/'
conda-reindex:
if: startsWith(github.ref, 'refs/tags')
needs: conda
runs-on: ubuntu-latest
steps:
- name: conda index tomography.stfc.ac.uk/conda
run: |
echo '${{ secrets.STFC_SSH_KEY }}' > ./key
chmod 600 ./key
ssh -o StrictHostKeyChecking=no -i ./key ${{ secrets.STFC_SSH_HOST }} \
'conda index --bz2 --zst --run-exports --channeldata --rss -n ccpi ${{ secrets.STFC_SSH_CONDA_DIR }}'
docs:
defaults: {run: {shell: 'bash -el {0}', working-directory: docs}}
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
submodules: recursive
ref: ${{ github.event.pull_request.head.sha || github.ref }} # fix SHA
- uses: conda-incubator/setup-miniconda@v3
with: {python-version: 3.11}
- uses: ruby/setup-ruby@v1
with:
ruby-version: '3.2'
bundler-cache: true
cache-version: 0
- name: install dependencies
run: |
conda install -c conda-forge -yq conda-merge
conda-merge ../scripts/requirements-test.yml docs_environment.yml > environment.yml
conda env update -n test
conda list
- name: build cil
working-directory: .
run: |
cmake -S . -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX"
cmake --build ./build --target install
- name: checkout docs
uses: actions/checkout@v4
with:
path: docs/build
ref: gh-pages
- id: pages
uses: actions/configure-pages@v5
- name: update web pages (jekyll)
run: make JEKYLLOPTS="--baseurl ${{ steps.pages.outputs.base_path }}" web-deps web
env: {JEKYLL_ENV: production}
- name: update docs pages (sphinx)
run: |
docs_dir="${{ github.ref_name }}"
docs_dir="${docs_dir//\//_}"
if test "$docs_dir" = master; then docs_dir=nightly; fi
make BUILDSUBDIR="$docs_dir" dirhtml
- uses: actions/upload-artifact@v4
with:
name: DocumentationHTML
path: docs/build
- name: Push changes
if: github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags')
uses: casperdcl/push-dir@v1
with:
message: Update documentation
branch: gh-pages
dir: docs/build
nojekyll: true
docker:
runs-on: ubuntu-latest
permissions:
contents: read
packages: write
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
submodules: recursive
ref: ${{ github.event.pull_request.head.sha || github.ref }} # fix SHA
- uses: jlumbroso/[email protected]
with:
docker-images: false
large-packages: false
- uses: docker/setup-buildx-action@v3
- uses: docker/metadata-action@v5
id: meta
with:
images: ghcr.io/${{ github.repository }}
tags: |
type=ref,event=branch
type=semver,pattern={{version}}
type=semver,pattern={{major}}.{{minor}}
labels: |
org.opencontainers.image.licenses=Apache-2.0 AND BSD-3-Clause AND GPL-3.0
- uses: docker/login-action@v3
if: github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags')
with:
registry: ghcr.io
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
- uses: docker/build-push-action@v6
with:
cache-from: type=gha
cache-to: type=gha,mode=max
context: .
load: true
tags: tomographicimaging/cil:test
- name: test
run: >
docker run --rm -v .:/CIL tomographicimaging/cil:test /bin/bash -c
'python -m unittest discover -v /CIL/Wrappers/Python/test'
- uses: docker/build-push-action@v6
with:
cache-from: type=gha
cache-to: type=gha,mode=max
context: .
push: ${{ github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags') }}
tags: ${{ steps.meta.outputs.tags }}
labels: ${{ steps.meta.outputs.labels }}
pass:
needs: [test-cuda, test, conda, docs, docker]
runs-on: ubuntu-latest
steps: [{run: echo success}]