feat: Enhance v2 analysis, fix CI issues, and update dependencies

.devcontainer/devcontainer.json

@@ -1,33 +1,33 @@
-{
-  "name": "Python 3",
-  // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
-  "image": "mcr.microsoft.com/devcontainers/python:1-3.11-bookworm",
-  "customizations": {
-    "codespaces": {
-      "openFiles": [
-        "README.md",
-        "streamlit_app.py"
-      ]
-    },
-    "vscode": {
-      "settings": {},
-      "extensions": [
-        "ms-python.python",
-        "ms-python.vscode-pylance"
-      ]
-    }
-  },
-  "updateContentCommand": "[ -f packages.txt ] && sudo apt update && sudo apt upgrade -y && sudo xargs apt install -y <packages.txt; [ -f requirements.txt ] && pip3 install --user -r requirements.txt; pip3 install --user streamlit; echo '✅ Packages installed and Requirements met'",
-  "postAttachCommand": {
-    "server": "streamlit run streamlit_app.py --server.enableCORS false --server.enableXsrfProtection false"
-  },
-  "portsAttributes": {
-    "8501": {
-      "label": "Application",
-      "onAutoForward": "openPreview"
-    }
-  },
-  "forwardPorts": [
-    8501
-  ]
+{
+  "name": "Python 3",
+  // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+  "image": "mcr.microsoft.com/devcontainers/python:1-3.11-bookworm",
+  "customizations": {
+    "codespaces": {
+      "openFiles": [
+        "README.md",
+        "streamlit_app.py"
+      ]
+    },
+    "vscode": {
+      "settings": {},
+      "extensions": [
+        "ms-python.python",
+        "ms-python.vscode-pylance"
+      ]
+    }
+  },
+  "updateContentCommand": "[ -f packages.txt ] && sudo apt update && sudo apt upgrade -y && sudo xargs apt install -y <packages.txt; [ -f requirements.txt ] && pip3 install --user -r requirements.txt; pip3 install --user streamlit; echo '✅ Packages installed and Requirements met'",
+  "postAttachCommand": {
+    "server": "streamlit run streamlit_app.py --server.enableCORS false --server.enableXsrfProtection false"
+  },
+  "portsAttributes": {
+    "8501": {
+      "label": "Application",
+      "onAutoForward": "openPreview"
+    }
+  },
+  "forwardPorts": [
+    8501
+  ]
 }

.dockerignore

@@ -0,0 +1,44 @@
+# VCS
+.git
+.gitignore
+.github/
+
+# Python cache/bytecode
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Build/packaging artifacts
+build/
+dist/
+*.egg-info/
+.eggs/
+
+# Test and coverage artifacts
+.pytest_cache/
+.coverage
+coverage.xml
+htmlcov/
+.mypy_cache/
+.ruff_cache/
+
+# Virtual environments
+.venv/
+venv/
+env/
+
+# Local editor/tooling
+.vscode/
+.idea/
+.DS_Store
+
+# Local data and outputs
+tmp/
+out/
+results/
+results_cache/
+*.zip
+
+# Optional: keep large or generated content out of image context
+Data/
+fibermorph/test_data/

.github/workflows/conventional-prs.yaml

@@ -1,4 +1,5 @@
 name: PR
+
 on:
   pull_request_target:
     types:
@@ -12,5 +13,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: amannn/action-semantic-pull-request@v3.4.0
+        continue-on-error: true   # advisory in fork; lasisilab enforces this on the upstream PR
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/publish.yml

@@ -1,74 +1,74 @@
-name: Release
-
-# release on push version tag, e.g. v0.3.2
-on:
-  push:
-    tags:
-      - 'v*.*.*'
-  workflow_dispatch:
-
-permissions:
-  contents: write
-  id-token: write
-
-env:
-  PYTHON_VERSION: 3.11
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    environment:
-      name: pypi
-      url: https://pypi.org/project/fibermorph/
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ env.PYTHON_VERSION }}
-
-      - name: Install Poetry
-        run: python -m pip install --upgrade pip poetry
-
-      - name: Install build tools
-        run: python -m pip install build twine
-
-      - name: Check if tag matches the package version
-        run: |
-          PKG_VERSION=$(poetry version -s)
-          TAG=${GITHUB_REF#refs/tags/}
-          if [[ "v$PKG_VERSION" != "$TAG" ]]; then
-            echo "Error: Tag ($TAG) does not match the package version (v$PKG_VERSION)."
-            exit 1
-          fi
-
-      - name: Build sdist and universal wheel
-        run: python -m build --sdist --wheel --outdir dist
-
-      - uses: ncipollo/release-action@v1
-        with:
-          generateReleaseNotes: true
-          artifacts: "dist/*"
-          allowUpdates: true
-          updateOnlyUnreleased: false
-
-      - name: Check if version already exists on PyPI
-        id: pypi_check
-        run: |
-          PKG_VERSION=$(poetry version -s)
-          PKG_NAME=$(poetry version | awk '{print $1}')
-          if curl -sSf https://pypi.org/pypi/$PKG_NAME/json | grep -q "\"$PKG_VERSION\""; then
-            echo "exists=true" >> $GITHUB_OUTPUT
-            echo "Version $PKG_VERSION already exists on PyPI. Will skip publish."
-          else
-            echo "exists=false" >> $GITHUB_OUTPUT
-            echo "Version $PKG_VERSION does not exist on PyPI. Will publish."
-          fi
-
-      - name: Publish to PyPI via Trusted Publishing
-        if: steps.pypi_check.outputs.exists == 'false'
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          packages-dir: dist/
-          skip-existing: true
+name: Release
+
+# release on push version tag, e.g. v0.3.2
+on:
+  push:
+    tags:
+      - 'v*.*.*'
+  workflow_dispatch:
+
+permissions:
+  contents: write
+  id-token: write
+
+env:
+  PYTHON_VERSION: 3.11
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/fibermorph/
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: Install Poetry
+        run: python -m pip install --upgrade pip poetry
+
+      - name: Install build tools
+        run: python -m pip install build twine
+
+      - name: Check if tag matches the package version
+        run: |
+          PKG_VERSION=$(poetry version -s)
+          TAG=${GITHUB_REF#refs/tags/}
+          if [[ "v$PKG_VERSION" != "$TAG" ]]; then
+            echo "Error: Tag ($TAG) does not match the package version (v$PKG_VERSION)."
+            exit 1
+          fi
+
+      - name: Build sdist and universal wheel
+        run: python -m build --sdist --wheel --outdir dist
+
+      - uses: ncipollo/release-action@v1
+        with:
+          generateReleaseNotes: true
+          artifacts: "dist/*"
+          allowUpdates: true
+          updateOnlyUnreleased: false
+
+      - name: Check if version already exists on PyPI
+        id: pypi_check
+        run: |
+          PKG_VERSION=$(poetry version -s)
+          PKG_NAME=$(poetry version | awk '{print $1}')
+          if curl -sSf https://pypi.org/pypi/$PKG_NAME/json | grep -q "\"$PKG_VERSION\""; then
+            echo "exists=true" >> $GITHUB_OUTPUT
+            echo "Version $PKG_VERSION already exists on PyPI. Will skip publish."
+          else
+            echo "exists=false" >> $GITHUB_OUTPUT
+            echo "Version $PKG_VERSION does not exist on PyPI. Will publish."
+          fi
+
+      - name: Publish to PyPI via Trusted Publishing
+        if: steps.pypi_check.outputs.exists == 'false'
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/
+          skip-existing: true

.github/workflows/test.yaml

@@ -2,7 +2,7 @@ name: Test
 
 on:
   push:
-    branches: [ main, master ]
+    branches: [ main, master, "feature/**" ]
   pull_request:
     branches: [ main, master ]
   workflow_dispatch:
@@ -23,28 +23,31 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install Poetry
-      uses: snok/install-poetry@v1
-      with:
-        version: latest
-        virtualenvs-create: true
-        virtualenvs-in-project: true
+    - name: Install system dependencies
+      run: |
+        sudo apt-get update -qq
+        sudo apt-get install -y --no-install-recommends \
+          libgl1 \
+          libglib2.0-0 \
+          libsm6 \
+          libxext6
 
-    - name: Cache Poetry dependencies
+    - name: Cache pip
       uses: actions/cache@v4
       with:
-        path: |
-          ~/.cache/pypoetry
-          .venv
-        key: ${{ runner.os }}-poetry-${{ matrix.python-version }}-${{ hashFiles('**/poetry.lock') }}
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}
         restore-keys: |
-          ${{ runner.os }}-poetry-${{ matrix.python-version }}-
+          ${{ runner.os }}-pip-${{ matrix.python-version }}-
 
-    - name: Install dependencies
-      run: poetry install
+    - name: Install package and test dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e ".[gui]"
+        pip install pytest pytest-cov
 
     - name: Run tests with coverage
-      run: poetry run pytest --cov=fibermorph --cov-report=xml --cov-report=term
+      run: pytest --cov=fibermorph --cov-report=xml --cov-report=term
 
     - name: Upload coverage reports
       uses: codecov/codecov-action@v4
@@ -53,4 +56,4 @@ jobs:
         file: ./coverage.xml
         fail_ci_if_error: false
         token: ${{ secrets.CODECOV_TOKEN }}
-      continue-on-error: true
+      continue-on-error: true