Merge branch 'master' into master

.github/workflows/pre-commit.yml

@@ -10,25 +10,21 @@ on:
 jobs:
 
   pre-commit-checks:
-    strategy:
-      matrix:
-        os: [ "macos-latest", "windows-latest", "ubuntu-18.04", "ubuntu-20.04",  "macos-10.15"]
-        python-version: [3.6, 3.7, 3.8]
 
-    runs-on: ${{ matrix.os }}
+    runs-on: ubuntu-latest
     steps:
 
       - name: Checkout repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Setup Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v3
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: 3.8
 
       - name: Cache pip dependencies
         id: cache-pip-dependencies
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           # Ubuntu-specific, see
           # https://github.com/actions/cache/blob/main/examples.md#python---pip
@@ -40,9 +36,7 @@ jobs:
       - name: Install dependencies
         run: |
               python -m pip install --upgrade pip
-              if [[ -f requirements_dev.txt ]]; then pip install -r requirements_dev.txt; fi
-              pip install -e .
-              pre-commit install
+              pip install 'pre-commit>=2.10.1'
         shell: bash
 
       - name: Run pre-commit large file check

.github/workflows/publish_package.yml

@@ -7,25 +7,17 @@ on:
   # publish from the Releases page:
   release:
     types: [published]
-  # publish from the Actions page:
-  workflow_dispatch:
-    inputs:
-      version:
-        description: 'Version (e.g. 2.0.3)'
-        required: true
 
 jobs:
   deploy:
 
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Set up Python
-      uses: actions/setup-python@v1
-      with:
-        python-version: '3.6'
+      uses: actions/setup-python@v3
 
     - name: Install dependencies
       run: |
@@ -41,10 +33,8 @@ jobs:
       with:
         files: 'dist/*'
         fail_on_unmatched_files: true
-        tag_name: ${{ github.event.inputs.version }} # in the workflow_dispatch case, make a new tag from the given input; in the published release case, this will be empty and will fall back to updating that release.
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
+        prerelease: ${{ contains(github.ref, 'rc') || contains(github.ref, 'dev') }}
+
     - name: Publish to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:

.github/workflows/run_tests.yml

@@ -8,9 +8,33 @@ on:
   push:
     branches:
       - master
+    paths-ignore:
+      - '**.md'
+      - '**.rst'
+      - '**.bib'
+      - '.github/**'
+      - '!.github/workflows/run_tests.yml'
+      - 'dev/**'
+      - 'docs/**'
+      - 'images/**'
+      - '.gitignore'
+      - '.pre-commit-config.yaml'
+      - '.readthedocs.yml'
   # Trigger the workflow on pull requests, but reveal no secrets, do not use pull_request_target, see:
   # https://docs.github.com/en/actions/reference/events-that-trigger-workflows#pull_request_target
   pull_request:
+    paths-ignore:
+      - '**.md'
+      - '**.rst'
+      - '**.bib'
+      - '.github/**'
+      - '!.github/workflows/run_tests.yml'
+      - 'dev/**'
+      - 'docs/**'
+      - 'images/**'
+      - '.gitignore'
+      - '.pre-commit-config.yaml'
+      - '.readthedocs.yml'
 
 env:
   # Even when given -y, apt will still sometimes hang at a prompt if a package
@@ -19,14 +43,16 @@ env:
   # (TravisCI quietly defined this on all their platforms, but we have to give it manually on GithubCI.)
   DEBIAN_FRONTEND: 'noninteractive'
   HDF5_USE_FILE_LOCKING: 'FALSE'
+  # Skip to the headless matplotlib renderer, which is less
+  # bug-prone in the constrained environment of CI
+  # Tip from a matplotlib dev: https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/3388#issuecomment-846091012
+  # Ref: https://matplotlib.org/stable/users/explain/backends.html
+  MPLBACKEND: 'Agg'
 
 jobs:
   ultra_matrix_test:
     name: Matrix Test of Python ${{ matrix.python-version }} on ${{ matrix.os }}
 
-    # Matrix driven OS
-    runs-on: ${{ matrix.os }}
-
     # Default shell for ALL subsequent steps.
     defaults:
       run:
@@ -39,32 +65,34 @@ jobs:
       fail-fast: false
 
       matrix:
-        os: [ "macos-latest", "windows-latest", "ubuntu-18.04", "ubuntu-20.04",  "macos-10.15" ]
-        python-version: [ 3.6, 3.7, 3.8 ]
+        os: [ "macos-latest", "windows-latest", "ubuntu-20.04" ]
+        python-version: [ '3.8', '3.9', '3.10' ]
         test-name:
           - integration-test
 
+    # Matrix driven OS
+    runs-on: ${{ matrix.os }}
+
     # Main steps for the test to be reproduced across OS x Python
     steps:
       # Step 0: Checkout code.
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       # Step 1: Setup python version
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
 
-      # Step 2: Install requirement dependencies.
-      - name: Install dependencies
-        uses: py-actions/py-dependency-install@v2
-        with:
-          path: "requirements_dev.txt"
+      # Step 2: Install dependencies
+      - name: Install ivadomed
+        run: |
+          pip install -e .[dev]
 
-      # Step 3: install additional pytest/dev related dependencies
-      - name: Install IvadoMed Main Modules
+      # Step 3: List installed packages
+      - name: List installed packages
         run: |
-          pip install -e .
+          pip list
 
       # Step 4: Lint.
       - name: Lint with flake8

.github/workflows/run_tests_dummy.yml

@@ -0,0 +1,39 @@
+# This is a dummy version of run_tests.yml, which allows for conditional checks to still be "Required Statuses" for pull requests to be allowed to be merged
+
+name: Run tests on all platforms
+
+# see https://docs.github.com/en/enterprise-cloud@latest/repositories/configuring-branches-and-merges-in-your-repository/defining-the-mergeability-of-pull-requests/troubleshooting-required-status-checks#handling-skipped-but-required-checks
+# and https://github.com/orgs/community/discussions/13690
+on:
+  pull_request:
+    paths:
+      # this list needs to be kept in sync manually with the opposite list in run_tests.yml
+      - '**.md'
+      - '**.rst'
+      - '**.bib'
+      - '.github/**'
+      - '!.github/workflows/run_tests.yml'
+      - 'dev/**'
+      - 'docs/**'
+      - 'images/**'
+      - '.gitignore'
+      - '.pre-commit-config.yaml'
+      - '.readthedocs.yml'
+
+jobs:
+  ultra_matrix_test:
+    name: Matrix Test of Python ${{ matrix.python-version }} on ${{ matrix.os }}
+
+    # this section also needs to be kept in sync with run_tests.yml
+    strategy:
+      matrix:
+        # This list must be kept **in sync** with the Required Statuses in https://github.com/ivadomed/ivadomed/settings/branch_protection_rules/5051948
+        os: [ "macos-latest", "windows-latest", "ubuntu-20.04" ]
+        python-version: [ 3.8 ]
+        test-name:
+          - integration-test
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - run: 'echo "No code changes, so no build required" '

.gitignore

@@ -21,15 +21,19 @@ log.txt
 # Pycharm stuff
 .idea
 
+# VSCode stuff
+.vscode
+
 # Pytest Cache, anywhere:
 .pytest_cache/
 
 # IvadoMed pytest downloaded data file, anywhere:
 data_testing/
 data_functional_testing/
+data_multi_testing/
 
 # OS Specific hidden file
 .DS_Store
 
 # venv
-venv/
+venv/

.readthedocs.yml

@@ -5,17 +5,20 @@
 # Required
 version: 2
 
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/source/conf.py
 
 python:
-  version: 3.7
   install:
-    # Ensure the Find External Link PyTorch version is installed
-    - requirements: requirements_dev.txt
     # Install IvadoMed package via setup.py content
     - method: pip
       path: .
       extra_requirements:
-        - docs
+        - dev