Bump version to 0.1.8

.github/workflows/check-pr-main-version.yml

@@ -17,16 +17,24 @@ jobs:
 
     steps:
       - name: Checkout PR branch (head)
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           ref: ${{ github.head_ref }}
           fetch-depth: 0
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
+
+      - name: Ensure uv.lock is up to date
+        run: |
+          if ! uv lock --check; then
+            echo "❌ uv.lock is out of date."
+            echo "Please update uv.lock before versioning can proceed."
+            exit 1
+          fi
 
       - name: Install the project
-        run: uv sync --all-extras --dev --no-editable
+        run: uv sync --locked --group test
 
       - name: Get PR branch version
         id: pr_version
@@ -86,7 +94,7 @@ jobs:
             echo "Version matches — bumping version and creating new release branch"
 
             uv version --bump patch
-            uv sync
+            uv sync --locked --group test
             NEXT_VERSION=$(uv version --short)
 
             if [[ "$NEXT_VERSION" == "$PR_VERSION" ]]; then

.github/workflows/check-uv-lock.yml

@@ -0,0 +1,83 @@
+name: Check uv.lock is up to date
+
+on:
+  pull_request:
+    branches:
+      - main
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  check-uv-lock:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout PR branch
+        uses: actions/checkout@v6
+        with:
+          ref: ${{ github.head_ref }}
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Check lock file
+        id: lockcheck
+        run: |
+          if uv lock --check; then
+            echo "up_to_date=true" >> $GITHUB_OUTPUT
+          else
+            echo "up_to_date=false" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Exit early if lock is up to date
+        if: steps.lockcheck.outputs.up_to_date == 'true'
+        run: echo "uv.lock is up to date ✔"
+
+      - name: Regenerate lock file
+        if: steps.lockcheck.outputs.up_to_date == 'false'
+        run: |
+          if [[ "${GITHUB_HEAD_REF}" == release/* ]]; then
+            echo "❌ Release branch — uv.lock must already be up to date."
+            exit 1
+          fi
+
+          uv lock
+
+      - name: Commit updated lock file
+        if: steps.lockcheck.outputs.up_to_date == 'false'
+        run: |
+          SAFE_REF=$(echo "${GITHUB_HEAD_REF}" | tr '/' '-')
+
+          git config user.name "quantem-bot"
+          git config user.email "[email protected]"
+
+          git checkout -b lockfix/${SAFE_REF}
+          git commit -am "Update uv.lock"
+          git push origin lockfix/${SAFE_REF}
+
+      - name: Create PR for updated lock file
+        if: steps.lockcheck.outputs.up_to_date == 'false'
+        env:
+          GH_TOKEN: ${{ secrets.QUANTEM_BOT_PAT }}
+        run: |
+          SAFE_REF=$(echo "${GITHUB_HEAD_REF}" | tr '/' '-')
+
+          if gh pr list --head "lockfix/${SAFE_REF}" --json number --jq 'length > 0'; then
+            echo "Lockfix PR already exists — skipping."
+            exit 1
+          fi
+
+          gh pr create \
+            --base "${{ github.base_ref }}" \
+            --head "lockfix/${SAFE_REF}" \
+            --title "Update uv.lock" \
+            --body "This PR updates \`uv.lock\` to match the current dependency specification."
+
+      - name: Fail original PR
+        if: steps.lockcheck.outputs.up_to_date == 'false'
+        run: |
+          echo "❌ uv.lock was out of date — a fix PR has been opened."
+          exit 1

.github/workflows/deploy.yml

@@ -13,10 +13,13 @@ jobs:
       UV_PUBLISH_TOKEN: ${{ secrets.PYPI_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
+
+      - name: Verify lock file is up to date
+        run: uv lock --check
 
       - name: Build the project
         run: uv build

.github/workflows/sync-dev-main.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Open PR from main to dev
         env:

.github/workflows/update-lock-file-cron.yml

@@ -0,0 +1,56 @@
+name: Update dependencies
+on:
+  schedule:
+    # Run weekly on Mondays at 9 AM UTC
+    - cron: '0 9 * * 1'
+  workflow_dispatch:
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  update-deps:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: dev
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Update dependencies
+        env:
+          GH_TOKEN: ${{ secrets.QUANTEM_BOT_PAT }}
+          REPO: ${{ github.repository }}
+        run: |
+          set -e
+
+          git config user.name "quantem-bot"
+          git config user.email "[email protected]"
+
+          # Update the lock file
+          uv lock --upgrade
+
+          # Check if there are changes
+          if git diff --quiet uv.lock; then
+            echo "No dependency updates available"
+            exit 0
+          fi
+
+          # Create branch and commit
+          BRANCH="chore/update-lockfile-$(date +%Y%m%d)"
+          git checkout -b "$BRANCH"
+          git add uv.lock
+          git commit -m "chore: update lock file"
+          git push origin "$BRANCH"
+
+          # Create PR
+          PR_BODY=$(printf "Automated dependency update via \`uv lock --upgrade\`.\n\nPlease review the changes and run tests before merging.")
+          gh pr create \
+            --repo "$REPO" \
+            --head "$BRANCH" \
+            --base dev \
+            --title "chore: Update dependencies" \
+            --body "$PR_BODY"

.github/workflows/uv-pytests.yml

@@ -4,28 +4,32 @@ on:
   pull_request:
     branches:
       - dev
+      - main
 
 jobs:
   uv-pytests:
-    name: python
-    runs-on: ubuntu-latest
+    name: ${{ matrix.os }} / python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
+        # Test other OSs main branch PRs
+        os: ${{ github.base_ref == 'main' && fromJSON('["ubuntu-latest", "windows-latest", "macos-latest", "macos-15-intel"]') || fromJSON('["ubuntu-latest"]') }}
         python-version:
           - "3.11"
           - "3.12"
           - "3.13"
+          - "3.14"
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Install uv and set python version
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install the project
-        run: uv sync --locked --all-extras --group test
+        run: uv sync --locked --group test
 
       - name: Run pytests
         run: uv run pytest tests

.gitignore

@@ -187,3 +187,7 @@ ipynb-playground/
 
 # cursor
 .cursor
+
+# widget (JS build artifacts)
+node_modules/
+widget/src/quantem/widget/static/

CONTRIBUTORS.md

@@ -7,6 +7,13 @@ Getting started:
 - [install uv](https://docs.astral.sh/uv/getting-started/installation/)
 - `git clone` the repo and `cd` into the directory
 - run `uv sync` to install all the dependencies in an editable environment
+- run `uv sync --all-packages` to also install `quantem.widget` (optional)
+
+For widget developers (requires [Node.js](https://nodejs.org/)):
+
+- `cd widget && npm install` to install JS dependencies
+- `npm run build` to build the widget
+- `npm run dev` to watch for changes during development
 
 The following will set up the pre-commit and [ruff](https://github.com/astral-sh/ruff) for linting and formatting. These commands only need to be run once when first setting up your dev environment: 
 

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "hatchling.build"
 addopts = [
     "--import-mode=importlib",
 ]
-testpaths = "tests"
+testpaths = ["tests", "widget/tests"]
 
 [tool.ruff.lint]
 select = ["E4","E7","E9","F","I"]
@@ -21,9 +21,15 @@ line-length = 99
 [tool.uv]
 config-settings = { editable_mode = "compat" }
 
+[tool.uv.workspace]
+members = ["widget"]
+
+[tool.uv.sources]
+"quantem.widget" = { workspace = true }
+
 [project]
 name = "quantem"
-version = "0.1.7"
+version = "0.1.8"
 description = "quantitative electron microscopy analysis toolkit."
 keywords = ["EM","TEM","STEM","4DSTEM"]
 readme = "README.md"
@@ -45,9 +51,14 @@ dependencies = [
   "torchvision>=0.22.1",
   "tensorboard>=2.19.0",
   "torchmetrics>=1.7.3",
-  "torchsummary>=1.5.1",
   "optuna>=4.5.0",
   "hdf5plugin>=6.0.0",
+  "torchinfo>=1.8.0",
+]
+
+[project.optional-dependencies]
+widgets = [
+    "quantem.widget",
 ]
 
 [tool.hatch.build.targets.sdist]
@@ -62,6 +73,7 @@ only-include = [
 [dependency-groups]
 test = [
     "pytest>=8.3.5",
+    "pytest-cov>=7.0.0",
 ]
 dev = [
     { include-group = "test" },

src/quantem/__init__.py

@@ -1,6 +1,13 @@
+from pkgutil import extend_path
+__path__ = extend_path(__path__, __name__)
+
+from importlib.metadata import version
+
 from quantem.core import io as io
 from quantem.core import datastructures as datastructures
 from quantem.core import visualization as visualization
 
 from quantem import imaging as imaging
 from quantem import diffractive_imaging as diffractive_imaging
+
+__version__ = version("quantem")