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Build(deps): Bump conda-incubator/setup-miniconda from 2 to 3 #381

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Build(deps): Bump conda-incubator/setup-miniconda from 2 to 3

Build(deps): Bump conda-incubator/setup-miniconda from 2 to 3 #381

Workflow file for this run

.github/workflows/workflows.yml at f761257
---
name: "CI build and test jobs"
on:
pull_request:
branches-ignore:
- /doc\/.*/
push:
branches:
- dev
- maint/*
tags:
- '*'
schedule:
# 7am EST / 8am EDT, daily
- cron: '0 12 * * *'
env:
REGISTRY: ghcr.io
IMAGE_NAME: ${{ github.repository }}
INSTALL_TYPE: pip
defaults:
run:
shell: bash -l {0}
jobs:
build:
runs-on: ubuntu-latest
steps:
- name: Setup python
uses: actions/setup-python@v4
with:
python-version: 3.9
- uses: actions/checkout@v4
with:
fetch-depth: 0
submodules: recursive
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
- name: Add version to environment
run: |
python -c 'import fitlins; print(f"VERSION={fitlins.__version__}")' >> $GITHUB_ENV
- name: Check version matches tag
if: startsWith(github.ref, 'refs/tags/')
run: test "$VERSION" = "${{ github.ref_name }}"
- name: Build image and export
timeout-minutes: 30
uses: docker/build-push-action@v5
with:
context: .
build-args: |
BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")"
VCS_REF="$(git rev-parse --short HEAD)"
VERSION=${{ env.VERSION }}
push: false
tags: |
${{ env.IMAGE_NAME }}:latest
${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest
load: true
- name: Verify executable can be run
run: |
docker images
docker run --rm $IMAGE_NAME:latest --help
- name: Check version
run: |
DOCKERVERSION=$(docker run --rm $IMAGE_NAME:latest --version \
| tail -n 1 | sed -e 's/.*fit/fit/' -e 's/[\r\n]//g')
echo "$VERSION"
echo "$DOCKERVERSION"
test "$DOCKERVERSION" = "fitlins v$VERSION"
- name: Export docker image to a tar file
run: |
docker save ${{ github.repository }} > /tmp/docker.tar
ls -l /tmp/
- name: Upload docker.tar as artifact
uses: actions/upload-artifact@v3
with:
name: docker
path: /tmp/docker.tar
cache_test_data:
runs-on: ubuntu-latest
steps:
- name: "Make cachedir"
run: |
mkdir -p /tmp/.cache/data && \
chmod 777 /tmp/.cache/data
- name: Set git ID
run: |
git config --global user.name 'Fitlins GH-Action User' && \
git config --global user.email 'shashankbansal56@gmail.com'
- name: Set up Python 3.9
uses: actions/setup-python@v4
with:
python-version: 3.9
- name: Install dependencies
shell: bash -l {0}
run: |
sudo apt-get update -y
sudo apt-get install -y git-annex
python -m pip install --upgrade pip
pip install datalad==0.14.7
- name: Datalad WTF
run: |
datalad wtf
- name: Install cached data
uses: actions/cache@v3
id: cache
with:
path: /tmp/.cache/data
key: ds003-v5-${{ github.ref_name }}-${{ github.sha }}
restore-keys: |
ds003-v5-${{ github.ref_name }}-
ds003-v5-
- name: "Install fMRIPrep derivatives of ds000003 and reference data"
# if: steps.cache.outputs.cache-hit != 'true'
run: |
cd /tmp/.cache/data
datalad install -r -s https://gin.g-node.org/markiewicz/fitlins-tests
datalad update --merge -d fitlins-tests
cd fitlins-tests
datalad get inputs/ds000003-fmriprep/sub-0{1,2,3}/func/*_space-MNI152NLin2009cAsym_desc-*.nii.gz \
inputs/ds000003-fmriprep/sub-0{1,2,3}/func/*_desc-confounds_*.tsv \
inputs/ds000003-fmriprep/dataset_description.json \
inputs/ds000003-fmriprep/sub-*/*/*.json \
outputs
datalad status
- name: "Check installed derivatives data"
run: |
cd /tmp/.cache/data/fitlins-tests/
git log --oneline --graph
du -sh .
run_pytest:
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: ['ubuntu-latest']
python-version: ["3.7", "3.8", "3.9", "3.10"]
pip-flags: ['']
check: ['test']
env:
CHECK_TYPE: ${{ matrix.check }}
EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
OS_TYPE: ${{ matrix.os }}
steps:
- uses: actions/checkout@v4
with:
submodules: recursive
fetch-depth: 0
- uses: conda-incubator/setup-miniconda@v3
with:
miniconda-version: "latest"
auto-update-conda: true
activate-environment: fitlins-ci
environment-file: tools/ci/conda_environment.yml
python-version: ${{ matrix.python-version }}
show-channel-urls: true
auto-activate-base: false
- name: Test conda installation
run: |
conda info
conda list
conda env list
conda config --show-sources
conda config --show
- name: Install dependencies
run: |
conda install -y --channel leej3 "afni-minimal"
conda list | grep afni
- name: Display Python version
run: |
which python
which pip
python -c "import sys; print(sys.version)"
- name: Install fitlins
run: tools/ci/install.sh
- name: Run tests
run: tools/ci/check.sh
- uses: codecov/codecov-action@v3
with:
verbose: true
if: ${{ always() }}
pre-release:
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: ['ubuntu-latest']
python-version: ['3.10']
# Check pre-release pybids and pre-release everything
pip-flags: ['', 'PRE_PIP_FLAGS']
check: ['test']
env:
CHECK_TYPE: ${{ matrix.check }}
EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
OS_TYPE: ${{ matrix.os }}
steps:
- uses: actions/checkout@v4
with:
submodules: recursive
fetch-depth: 0
- uses: conda-incubator/setup-miniconda@v3
with:
activate-environment: fitlins-ci
environment-file: tools/ci/conda_environment.yml
python-version: ${{ matrix.python-version }}
- name: Test conda installation
run: |
conda info
conda list
conda env list
conda config --show-sources
conda config --show
- name: Install dependencies
run: |
conda install -y --channel leej3 "afni-minimal"
conda list | grep afni
- name: Display Python version
run: |
which python
which pip
python -c "import sys; print(sys.version)"
- name: Install fitlins
run: tools/ci/install.sh
- name: Install pybids from GitHub
run: pip install git+https://github.com/bids-standard/pybids.git
- name: Run tests
run: tools/ci/check.sh
- uses: codecov/codecov-action@v3
with:
verbose: true
if: ${{ always() }}
test_ds003_nistats_smooth:
needs: [cache_test_data]
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
python-version: [3.9]
test_name: ["nistats_smooth"]
pip-flags: ['']
check: ['workflow']
env:
CHECK_TYPE: ${{ matrix.check }}
EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
OS_TYPE: ${{ matrix.os }}
steps:
- uses: actions/checkout@v4
with:
submodules: recursive
fetch-depth: 0
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install fitlins
run: tools/ci/install.sh
- name: Restore cached test data
uses: actions/cache@v3
id: cache
with:
path: /tmp/.cache/data
key: ds003-v5-${{ github.ref_name }}-${{ github.sha }}
- name: Run fitlins tests
timeout-minutes: 240
run: |
mkdir -p $WORK_DIR $OUTPUT_DIR
chmod 777 $WORK_DIR $OUTPUT_DIR
tools/ci/check.sh
env:
DATA: /tmp/.cache/data/fitlins-tests
TEST_NAME: ${{ matrix.test_name }}
OUTPUT_DIR: /tmp/ds003/derivatives
WORK_DIR: /tmp/ds003/work
- name: Combine coverage and submit
uses: codecov/codecov-action@v3
with:
verbose: true
test_ds003_afni:
needs: [cache_test_data]
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
python-version: [3.9]
test_name: ["afni_smooth", "afni_blurto"]
pip-flags: ['']
check: ['workflow']
env:
CHECK_TYPE: ${{ matrix.check }}
EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
OS_TYPE: ${{ matrix.os }}
steps:
- uses: actions/checkout@v4
with:
submodules: recursive
fetch-depth: 0
- uses: conda-incubator/setup-miniconda@v3
with:
miniconda-version: "latest"
auto-update-conda: true
activate-environment: fitlins-ci
environment-file: tools/ci/conda_environment.yml
python-version: ${{ matrix.python-version }}
show-channel-urls: true
auto-activate-base: false
- name: Test conda installation
run: |
conda info
conda list
conda env list
- name: Install dependencies
run: |
conda install -y --channel leej3 "afni-minimal"
conda list | grep afni
- name: Install fitlins
run: tools/ci/install.sh
- name: Restore cached test data
uses: actions/cache@v3
id: cache
with:
path: /tmp/.cache/data
key: ds003-v5-${{ github.ref_name }}-${{ github.sha }}
- name: Run fitlins tests
timeout-minutes: 240
run: |
mkdir -p $WORK_DIR $OUTPUT_DIR
chmod 777 $WORK_DIR $OUTPUT_DIR
tools/ci/check.sh
env:
DATA: /tmp/.cache/data/fitlins-tests
TEST_NAME: ${{ matrix.test_name }}
OUTPUT_DIR: /tmp/ds003/derivatives
WORK_DIR: /tmp/ds003/work
- name: Combine coverage and submit
uses: codecov/codecov-action@v3
with:
verbose: true
test_ds003_nistats_blurto:
needs: [build, cache_test_data]
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
test_name: ["nistats_blurto"]
steps:
- uses: actions/checkout@v4
- name: Set up docker buildx
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
with:
name: docker
path: /tmp
- name: Load docker image
run: |
docker info
set +o pipefail
ls -l /tmp/docker.tar
docker load < /tmp/docker.tar
docker images
- name: Restore cached test data
uses: actions/cache@v3
id: cache
with:
path: /tmp/.cache/data
key: ds003-v5-${{ github.ref_name }}-${{ github.sha }}
- name: Run fitlins tests
timeout-minutes: 240
run: |
mkdir -p $WORK_DIR $OUTPUT_DIR
chmod 777 $WORK_DIR $OUTPUT_DIR
docker run --rm \
-v $DATA:$DATA \
-v $WORK_DIR:$WORK_DIR \
-v $OUTPUT_DIR:$OUTPUT_DIR \
-v $PWD:/work \
-e CHECK_TYPE -e TEST_NAME \
-e DATA -e WORK_DIR -e OUTPUT_DIR \
-u $UID \
--entrypoint=/neurodocker/startup.sh \
$IMAGE tools/ci/check.sh
env:
IMAGE: ${{ github.repository }}:latest
CHECK_TYPE: workflow
DATA: /tmp/.cache/data/fitlins-tests
TEST_NAME: ${{ matrix.test_name }}
OUTPUT_DIR: /tmp/ds003/derivatives
WORK_DIR: /tmp/ds003/work
- name: Combine coverage and submit
uses: codecov/codecov-action@v3
with:
verbose: true
deploy_docker:
needs: [test_ds003_afni, test_ds003_nistats_smooth, test_ds003_nistats_blurto]
if: github.ref == 'refs/heads/dev' || startsWith(github.ref, 'refs/tags/')
runs-on: ubuntu-latest
steps:
- name: Set up docker buildx
uses: docker/setup-buildx-action@v3
- name: Download artifact
uses: actions/download-artifact@v3
with:
name: docker
path: /tmp
- name: Load docker image
run: |
docker info
set +o pipefail
ls -l /tmp/docker.tar
docker load < /tmp/docker.tar
docker images
- name: Set version/dev tags
run: |
# GHCR
docker tag $IMAGE_NAME $REGISTRY/$IMAGE_NAME:${{ github.ref_name }}
# DockerHub
docker tag $IMAGE_NAME $IMAGE_NAME:${{ github.ref_name }}
- name: Check images
run: docker images
- name: Login to Github Container Registry
uses: docker/login-action@v3
with:
registry: ghcr.io
username: ${{ github.repository_owner }}
password: ${{ secrets.GITHUB_TOKEN }}
- name: Deploy to GHCR
timeout-minutes: 60
run: docker push $REGISTRY/$IMAGE_NAME:${{ github.ref_name }}
- name: Login to DockerHub
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
- name: Deploy to DockerHub
timeout-minutes: 60
run: docker push $IMAGE_NAME:${{ github.ref_name }}
- name: Deploy ":latest" to DockerHub
timeout-minutes: 10
if: startsWith(github.ref, 'refs/tags/')
run: docker push $IMAGE_NAME:latest