Merge remote-tracking branch 'upstream/master' into pr/yarikoptic/601

.github/workflows/bootstrap.yml

@@ -1,3 +1,4 @@
+---
 # this workflow bootstraps the testing of the build the docker images
 #
 # - this will run the python script used to generate the workflows
@@ -8,16 +9,16 @@
 name: bootstrap
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
 
 on:
-  push:
-    branches: [ "master" ]
-    paths:
-      - .github/workflows/bootstrap.yml
-      - .github/workflows/create_workflows.py
-      - neurodocker/**
+    push:
+        branches: [master]
+        paths:
+        -   .github/workflows/bootstrap.yml
+        -   .github/workflows/create_workflows.py
+        -   neurodocker/**
 
 # Uses the cron schedule for github actions
 #
@@ -33,53 +34,53 @@ on:
 #         │ │   │    │ │
 #         * *   *    * *
 
-  schedule:
-  - cron: 0 0 1,15 * *
+    schedule:
+    -   cron: 0 0 1,15 * *
 
   # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
-    inputs:
-      software_name:
-        description: 'software to test'
-        required: true
-        default: 'all'
+    workflow_dispatch:
+        inputs:
+            software_name:
+                description: software to test
+                required: true
+                default: all
 
 permissions:
-  contents: write
-  actions: write
+    contents: write
+    actions: write
 jobs:
-  bootstrap:
-    runs-on: ubuntu-22.04
+    bootstrap:
+        runs-on: ubuntu-22.04
 
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          token: ${{ secrets.CI_FLOW }}
+        steps:
+        -   uses: actions/checkout@v4
+            with:
+                token: ${{ secrets.CI_FLOW }}
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.11'
+        -   name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+                python-version: '3.11'
 
-      - name: Install dependencies
-        run: python -m pip install jinja2 pyyaml
+        -   name: Install dependencies
+            run: python -m pip install jinja2 pyyaml
 
-      - name: Create workflows
-        run: |
-          software_name=${{ inputs.software_name }}
-          if [ -z "$software_name" ]; then
-            software_name="all"
-          fi
-          if [ "$software_name" = "all" ]; then
-            echo "testing all software"
-          else
-            echo "testing ${software_name}"
-          fi
-          git checkout -b test_docker_build
-          python .github/workflows/create_workflows.py --software_name ${software_name}
-          ls -l .github/workflows
-          git add .
-          git config --global user.email "[email protected]"
-          git config --global user.name "Repronim neurodocker bot"
-          git commit -am "added new workflows"
-          git push origin --force test_docker_build
+        -   name: Create workflows
+            run: |
+                software_name=${{ inputs.software_name }}
+                if [ -z "$software_name" ]; then
+                  software_name="all"
+                fi
+                if [ "$software_name" = "all" ]; then
+                  echo "testing all software"
+                else
+                  echo "testing ${software_name}"
+                fi
+                git checkout -b test_docker_build
+                python .github/workflows/create_workflows.py --software_name ${software_name}
+                ls -l .github/workflows
+                git add .
+                git config --global user.email "[email protected]"
+                git config --global user.name "Repronim neurodocker bot"
+                git commit -am "added new workflows"
+                git push origin --force test_docker_build

.github/workflows/create_workflows.py

@@ -23,6 +23,7 @@
 and on the branch where the workflows are pushed to (currently "test_docker_build").
 
 """
+
 import argparse
 from pathlib import Path
 

.github/workflows/docs.yml

@@ -1,26 +1,27 @@
+---
 on:
-  push:
-    branches:
-    - master
+    push:
+        branches:
+        -   master
 permissions:
-  contents: write
+    contents: write
 jobs:
-  build_docs:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.10"
-      - name: Install neurodocker
-        run: python -m pip install --editable .[all]
-      - name: build docs
-        run: |
-          make -C docs cli
-          make -C docs list
-          sphinx-build docs docs-build
-      - name: Deploy
-        uses: JamesIves/github-pages-deploy-action@v4
-        with:
-          folder: docs-build # The folder the action should deploy.
+    build_docs:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+        -   name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+                python-version: '3.10'
+        -   name: Install neurodocker
+            run: python -m pip install --editable .[all]
+        -   name: build docs
+            run: |
+                make -C docs cli
+                make -C docs list
+                sphinx-build docs docs-build
+        -   name: Deploy
+            uses: JamesIves/github-pages-deploy-action@v4
+            with:
+                folder: docs-build # The folder the action should deploy.

.github/workflows/publish.yml

@@ -1,27 +1,28 @@
+---
 name: Publish to pypi on Github release
 
 on:
-  release:
-    types: [published]
+    release:
+        types: [published]
 
 jobs:
-  pypi-release:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
+    pypi-release:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.10"
+        -   name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+                python-version: '3.10'
 
-      - name: Install build & twine
-        run: python -m pip install build twine
+        -   name: Install build & twine
+            run: python -m pip install build twine
 
-      - name: Publish to pypi
-        run: |
-          python -m build
-          twine upload dist/*
-        env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        -   name: Publish to pypi
+            run: |
+                python -m build
+                twine upload dist/*
+            env:
+                TWINE_USERNAME: __token__
+                TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}

.github/workflows/pull-request.yml

@@ -1,43 +1,44 @@
+---
 name: CI
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
 
 on:
-  pull_request:
-    branches: [ master ]
+    pull_request:
+        branches: [master]
 
 jobs:
-  run-tests:
-    runs-on: ubuntu-22.04
-    strategy:
-      matrix:
-        python-version: ['3.12', '3.11', '3.10', '3.9', '3.8']
-      fail-fast: false
-    steps:
-      - name: Install Apptainer
-        env:
-          VERSION: 1.1.5
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y wget
-          wget https://github.com/apptainer/apptainer/releases/download/v${VERSION}/apptainer_${VERSION}_amd64.deb
-          wget https://github.com/apptainer/apptainer/releases/download/v${VERSION}/apptainer-suid_${VERSION}_amd64.deb
-          sudo apt-get install --yes ./apptainer*
-      - name: Set Apptainer/Singularity environment variables
-        run: |
-          # Give reproenv the full path to apptainer, so it still works with `sudo`.
-          echo REPROENV_APPTAINER_PROGRAM=apptainer >> $GITHUB_ENV
-          echo APPTAINER_CACHEDIR=/dev/shm/$(whoami)/singularity >> $GITHUB_ENV
-      - uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install neurodocker
-        run: python -m pip install --editable .[dev]
-      - name: Run python tests
-        run: pytest --numprocesses auto
-      - name: Get code coverage
-        run: codecov
+    run-tests:
+        runs-on: ubuntu-22.04
+        strategy:
+            matrix:
+                python-version: ['3.12', '3.11', '3.10', '3.9', '3.8']
+            fail-fast: false
+        steps:
+        -   name: Install Apptainer
+            env:
+                VERSION: 1.1.5
+            run: |
+                sudo apt-get update
+                sudo apt-get install -y wget
+                wget https://github.com/apptainer/apptainer/releases/download/v${VERSION}/apptainer_${VERSION}_amd64.deb
+                wget https://github.com/apptainer/apptainer/releases/download/v${VERSION}/apptainer-suid_${VERSION}_amd64.deb
+                sudo apt-get install --yes ./apptainer*
+        -   name: Set Apptainer/Singularity environment variables
+            run: |
+                # Give reproenv the full path to apptainer, so it still works with `sudo`.
+                echo REPROENV_APPTAINER_PROGRAM=apptainer >> $GITHUB_ENV
+                echo APPTAINER_CACHEDIR=/dev/shm/$(whoami)/singularity >> $GITHUB_ENV
+        -   uses: actions/checkout@v4
+        -   name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+                python-version: ${{ matrix.python-version }}
+        -   name: Install neurodocker
+            run: python -m pip install --editable .[dev]
+        -   name: Run python tests
+            run: pytest --numprocesses auto
+        -   name: Get code coverage
+            run: codecov