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Add new tutorials to how to page in docs #1440

Add new tutorials to how to page in docs

Add new tutorials to how to page in docs #1440

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 }} \
'bash -lic "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: ${{ github.event.pull_request.head.sha || github.ref }} # fix SHA
- uses: jlumbroso/free-disk-space@v1.3.1
with:
docker-images: false
large-packages: false
- uses: docker/setup-buildx-action@v3
- uses: docker/metadata-action@v5
id: meta
with:
images: ghcr.io/${{ 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}]