Merge pull request #165 from XAITK/main

Incoming Updates from GitLab

.gitattributes

@@ -1 +1,13 @@
+# :auto shared:
 *.rst conflict-marker-size=79
+**.pt filter=lfs diff=lfs merge=lfs -text
+**.pth filter=lfs diff=lfs merge=lfs -text
+**.pkl filter=lfs diff=lfs merge=lfs -text
+**.png filter=lfs diff=lfs merge=lfs -text
+**.jpg filter=lfs diff=lfs merge=lfs -text
+**.jpeg filter=lfs diff=lfs merge=lfs -text
+**.tiff filter=lfs diff=lfs merge=lfs -text
+**.bin filter=lfs diff=lfs merge=lfs -text
+**.tiff filter=lfs diff=lfs merge=lfs -text
+**.npy filter=lfs diff=lfs merge=lfs -text
+# :auto shared:

.github/actions/build-stage/action.yml

@@ -0,0 +1,32 @@
+name: "build-stage"
+description: "Setup user python environment with poetry and enable caching."
+runs:
+  using: "composite"
+  steps:
+    - name: Environment Variables
+      run: |
+        export PIP_CACHE_DIR="$GITHUB_WORKSPACE/.cache/pip"
+        export POETRY_CACHE_DIR="$GITHUB_WORKSPACE/.cache/poetry"
+        echo "${HOME}/.local/bin" >> $GITHUB_PATH
+      shell: bash
+    - name: Setup Poetry
+      run: |
+        pip install --root-user-action=ignore --upgrade pip -q
+        pip install --root-user-action=ignore --user -U poetry -q
+      shell: bash
+    - name: Configure Poetry
+      run: |
+        poetry config --local virtualenvs.in-project true
+        poetry config --local virtualenvs.prefer-active-python true
+      shell: bash
+    - name: Versions of things used here
+      run: |
+        python --version
+        poetry -q run python --version
+        pip --version
+        poetry --version
+        poetry check
+      shell: bash
+    - name: Install Environment
+      run: poetry install --sync --only main,linting,tests,docs
+      shell: bash

.github/actions/quality-stage/action.yml

@@ -0,0 +1,10 @@
+name: "quality-stage"
+description: "Setup user python environment with poetry and enable caching."
+runs:
+  using: "composite"
+  steps:
+    - name: Setup Environment
+      uses: ./.github/actions/build-stage
+    - name: Synchronize Poetry Environment
+      run: poetry install --sync --only main,linting,tests
+      shell: bash

.github/actions/test-stage/action.yml

@@ -0,0 +1,17 @@
+name: "test-stage"
+description: "Setup user python environment with poetry and enable caching."
+
+inputs:
+  extras:
+    description: "Parameterize the 'extras' required for testing"
+    required: true
+    default: ""
+
+runs:
+  using: "composite"
+  steps:
+    - name: Setup Environment
+      uses: ./.github/actions/build-stage
+    - name: Synchronize Poetry Environment
+      run: poetry install --sync --only main,linting,tests --extras "${{ inputs.extras }}"
+      shell: bash

.github/workflows/publish.yml → .github/workflows/.github-publish.yml

@@ -26,27 +26,30 @@ jobs:
     # This should only be run for tags on the "official" repository org.
     if: github.repository_owner == 'XAITK'
     steps:
+      - name: Install Git LFS
+        run: |
+          apt-get -qq update
+          apt-get -qq install -y git-lfs
+        shell: bash
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          lfs: true
       # Cache local python environment artifacts for the current python version
       # and poetry lockfile hash.
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         id: env-cache
         with:
           # Confirmed that the `.local` directory doesn't exist until the
           # `pip install --user` is invoked below, so we can be confident that
           # only our python stuff is being captured in this cache (intentional).
           path: |
-            ~/.cache/pypoetry/virtualenvs/
-            ~/.local
+            ~/.cache
           key: python-3.9-${{ hashFiles('poetry.lock') }}
 
       - name: Setup Environment
-        # Using non-relative path for correct behavior when used as a remote
-        # workflow.
-        uses: Kitware/SMQTK-Core/.github/actions/python-poetry-setup@master
+        uses: ./.github/actions/build-stage
 
       # Ensure there is alignment with the tag reference and the reported
       # version of the package

.github/workflows/ci-unittests.yml → .github/workflows/.github-quality.yml

@@ -1,6 +1,6 @@
 # This is a basic workflow to help you get started with Actions
 
-name: CI Unittests
+name: Quality Assurance
 
 # Controls when the action will run.
 on:
@@ -26,14 +26,20 @@ defaults:
 # NOTE: Github actions does not support anchors apparently. Forgive duplication of job
 #       steps.
 jobs:
-  lint:
+  mypy:
     runs-on: ubuntu-latest
     container: python:3.9
     steps:
+      - name: Install Git LFS
+        run: |
+          apt-get -qq update
+          apt-get -qq install -y git-lfs
+        shell: bash
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          lfs: true
       # Cache local python environment artifacts for the current python version
       # and poetry lockfile hash.
       - uses: actions/cache@v4
@@ -42,24 +48,28 @@ jobs:
           # Confirmed that the `.local` directory doesn't exist until the
           # `pip install --user` is invoked below, so we can be confident that
           # only our python stuff is being captured in this cache (intentional).
-          path: |
-            ~/.cache/pypoetry/virtualenvs/
-            ~/.local
+          path: ~/.cache
           key: python-3.9-${{ hashFiles('poetry.lock') }}
       - name: Setup Environment
-        # See: https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#example-using-a-public-action-in-a-subdirectory
-        uses: Kitware/SMQTK-Core/.github/actions/python-poetry-setup@master
-      - name: Lint with Flake8
-        run: poetry run flake8
+        uses: ./.github/actions/quality-stage
+      - name: Typecheck with MyPy
+        run: poetry run mypy --config-file pyproject.toml src/ tests/
+        shell: bash
 
-  typecheck:
+  ruff-lint:
     runs-on: ubuntu-latest
     container: python:3.9
     steps:
+      - name: Install Git LFS
+        run: |
+          apt-get -qq update
+          apt-get -qq install -y git-lfs
+        shell: bash
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          lfs: true
       # Cache local python environment artifacts for the current python version
       # and poetry lockfile hash.
       - uses: actions/cache@v4
@@ -68,37 +78,28 @@ jobs:
           # Confirmed that the `.local` directory doesn't exist until the
           # `pip install --user` is invoked below, so we can be confident that
           # only our python stuff is being captured in this cache (intentional).
-          path: |
-            ~/.cache/pypoetry/virtualenvs/
-            ~/.local
+          path: ~/.cache
           key: python-3.9-${{ hashFiles('poetry.lock') }}
       - name: Setup Environment
-        # See: https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#example-using-a-public-action-in-a-subdirectory
-        uses: Kitware/SMQTK-Core/.github/actions/python-poetry-setup@master
-      - name: Typecheck with MyPy
-        run: poetry run mypy
+        uses: ./.github/actions/quality-stage
+      - name: Lint with Ruff
+        run: poetry run ruff check --config pyproject.toml
+        shell: bash
 
-  unittests:
+  ruff-format:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.9","3.10","3.11","3.12"]
-        # Extras for included, optional plugin support (space-separated lists)
-        opt-extra: [
-            "",  # no extras
-            "tools",
-        ]
-      # We want all python versions tested even if one of them happens to fail
-      fail-fast: false
-
-    container: python:${{ matrix.python-version }}
-
-    # Steps represent a sequence of tasks that will be executed as part of the job
+    container: python:3.9
     steps:
+      - name: Install Git LFS
+        run: |
+          apt-get -qq update
+          apt-get -qq install -y git-lfs
+        shell: bash
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          lfs: true
       # Cache local python environment artifacts for the current python version
       # and poetry lockfile hash.
       - uses: actions/cache@v4
@@ -107,30 +108,40 @@ jobs:
           # Confirmed that the `.local` directory doesn't exist until the
           # `pip install --user` is invoked below, so we can be confident that
           # only our python stuff is being captured in this cache (intentional).
-          path: |
-            ~/.cache/pypoetry/virtualenvs/
-            ~/.local
-          key: python-${{ matrix.python-version }}-${{ hashFiles('poetry.lock') }}-${{ matrix.opt-extra }}
-          restore-keys: |
-            python-${{ matrix.python-version }}-${{ hashFiles('poetry.lock') }}
+          path: ~/.cache
+          key: python-3.9-${{ hashFiles('poetry.lock') }}
       - name: Setup Environment
-        # See: https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#example-using-a-public-action-in-a-subdirectory
-        uses: Kitware/SMQTK-Core/.github/actions/python-poetry-setup@master
-      - name: Optionally install additional requirements
-        env:
-          OPT_EXTRA: ${{ matrix.opt-extra }}
-        run: |
-          if [[ -n "$OPT_EXTRA" ]]
-          then
-            poetry install --extras "$OPT_EXTRA"
-          fi
-      - name: Run Unittests
-        run: poetry run pytest
+        uses: ./.github/actions/quality-stage
+      - name: Format check with Ruff
+        run: poetry run ruff format --config pyproject.toml --check
+        shell: bash
 
-      - name: CodeCov report submission
-        uses: codecov/codecov-action@v4
+  sphinx-lint:
+    runs-on: ubuntu-latest
+    container: python:3.9
+    steps:
+      - name: Install Git LFS
+        run: |
+          apt-get -qq update
+          apt-get -qq install -y git-lfs
+        shell: bash
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v4
         with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          fail_ci_if_error: true
-          files: coverage.xml
-          flags: unittests
+          fetch-depth: 0
+          lfs: true
+      # Cache local python environment artifacts for the current python version
+      # and poetry lockfile hash.
+      - uses: actions/cache@v4
+        id: env-cache
+        with:
+          # Confirmed that the `.local` directory doesn't exist until the
+          # `pip install --user` is invoked below, so we can be confident that
+          # only our python stuff is being captured in this cache (intentional).
+          path: ~/.cache
+          key: python-3.9-${{ hashFiles('poetry.lock') }}
+      - name: Setup Environment
+        uses: ./.github/actions/quality-stage
+      - name: Lint docs with Spinx-lint
+        run: poetry run sphinx-lint --enable all --disable leaked-markup --max-line-length 120 -i docs/_implementations docs
+        shell: bash