Merge remote-tracking branch 'origin/main' into HEAD

Author: nikosavola

.github/.markdownlint-cli2.yaml

@@ -8,6 +8,9 @@ config:
     code_block_line_length: 120
   # Allow punctuation in headings (useful for project names with versions)
   MD026: false
+  # Allow duplicate headings as long as they are not siblings (e.g., "Added" under different versions)
+  MD024:
+    siblings_only: true
   # Disable first-line-h1 rule for docs files that use includes
   MD041: false
 # Ignore specific files or patterns

.github/CODEOWNERS

@@ -1 +1 @@
-* @joamatab @ThomasPluck @nikosavola
+* @joamatab @ThomasPluck @nikosavola @Alex-l-r

.github/dependabot.yml

@@ -8,6 +8,7 @@ updates:
       default-days: 7
     ignore:
       - dependency-name: "doplaydo/*"
+      - dependency-name: "jupyter-book"
   - package-ecosystem: github-actions
     directory: /
     schedule:

.github/workflows/claude-pr-review.yml

@@ -0,0 +1,16 @@
+name: Claude PR Review
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+  issue_comment:
+    types: [created]
+permissions:
+  contents: read
+  pull-requests: write
+  issues: write
+  id-token: write
+jobs:
+  review:
+    uses: doplaydo/pdk-ci-workflow/.github/workflows/claude-pr-review.yml@main
+    secrets:
+      ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}

.github/workflows/pages.yml

@@ -3,70 +3,12 @@ permissions:
   contents: read
 on:
   pull_request:
-  workflow_run:
-    workflows: ["Test"]
-    types: [completed]
+  push:
     branches:
       - main
-  merge_group:
   workflow_dispatch:
+  merge_group:
 jobs:
-  get-python-versions:
-    uses: ./.github/workflows/get-python-versions.yml
-  build-docs:
-    needs: get-python-versions
-    runs-on: ubuntu-latest
-    name: Build HTML docs
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ${{ fromJson(needs.get-python-versions.outputs.python-versions) }}
-    steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
-        with:
-          lfs: true
-      - name: Install uv
-        uses: astral-sh/setup-uv@cec208311dfd045dd5311c1add060b2062131d57 # v7.0.0
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install just
-        uses: extractions/setup-just@53165ef7e734c5c07cb06b3c8e7b647c5aa16db3 # v3.0.0
-      - name: Install Computer Modern Unicode fonts
-        run: sudo apt-get install -y fonts-cmu
-      - run: uv sync --all-extras --no-extra gdsfactoryplus
-      - run: just docs
-      - uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7.0.0
-        with:
-          name: html-docs-${{ matrix.python-version }}
-          path: "./docs/_build/html/"
-  build-docs-result:
-    runs-on: ubuntu-latest
-    name: Build docs result
-    needs: build-docs
-    if: always()
-    steps:
-      - name: Check build-docs matrix results
-        run: |
-          if [[ "${{ needs.build-docs.result }}" == "success" ]]; then
-            echo "All build-docs jobs succeeded"
-            exit 0
-          else
-            echo "One or more build-docs jobs failed"
-            exit 1
-          fi
-  get-latest-python:
-    needs: get-python-versions
-    runs-on: ubuntu-latest
-    outputs:
-      latest-python: ${{ steps.get-latest.outputs.latest-python }}
-    steps:
-      - name: Get latest Python version
-        id: get-latest
-        run: |
-          versions='${{ needs.get-python-versions.outputs.python-versions }}'
-          latest=$(echo "$versions" | jq -r '.[-1]')
-          echo "latest-python=$latest" >> "$GITHUB_OUTPUT"
-          echo "Latest Python version: $latest"
   build-docs-pdf:
     runs-on: ubuntu-latest
     name: Build PDF docs
@@ -113,40 +55,13 @@ jobs:
         with:
           name: pdf-docs
           path: "./docs/_build/latex/qpdk.pdf"
-  deploy-docs:
-    runs-on: ubuntu-latest
-    name: Deploy to GitHub Pages
-    needs: [build-docs, build-docs-pdf, get-latest-python]
-    if: >
-      (github.event_name == 'workflow_run' && github.event.workflow_run.conclusion == 'success') || (github.event_name == 'workflow_dispatch' && github.ref == 'refs/heads/main')
-
+  pages:
+    needs: build-docs-pdf
     permissions:
+      actions: read
       pages: write
       id-token: write
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
-    steps:
-      - name: Download HTML artifact (latest Python)
-        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.0
-        with:
-          name: html-docs-${{ needs.get-latest-python.outputs.latest-python }}
-          path: _site
-      - name: Download PDF artifact
-        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.0
-        with:
-          name: pdf-docs
-          path: _site
-      - name: Download coverage report
-        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.0
-        continue-on-error: true
-        with:
-          name: coverage-report-${{ needs.get-latest-python.outputs.latest-python }}
-          path: _site/reports/coverage
-          run-id: ${{ github.event.workflow_run.id || github.run_id }}
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-      - name: Upload merged pages artifact
-        uses: actions/upload-pages-artifact@7b1f4a764d45c48632c6b24a0339c27f5614fb0b # v4.0.0
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@cd2ce8fcbc39b97be8ca5fce6e763baed58fa128 # v5.0.0
+    uses: doplaydo/pdk-ci-workflow/.github/workflows/pages.yml@main # zizmor: ignore[unpinned-uses, secrets-inherit]
+    secrets:
+      GFP_API_KEY: ${{ secrets.GFP_API_KEY }}
+      SIMCLOUD_APIKEY: ${{ secrets.SIMCLOUD_APIKEY }}

.github/zizmor.yml

@@ -1,6 +1,13 @@
 rules:
   unpinned-uses:
-    disable: false
+    ignore:
+      - "claude-pr-review.yml"
+  excessive-permissions:
+    ignore:
+      - "claude-pr-review.yml"
+  secrets-inherit:
+    ignore:
+      - "claude-pr-review.yml"
   dangerous-triggers:
     ignore:
       - "pages.yml"

.pre-commit-config.yaml

@@ -5,6 +5,37 @@ exclude: ^uv\.lock$
 # 30: Global end-of-file-fixer
 # 40: Global trailing-whitespace cleanup
 repos:
+  - repo: https://github.com/doplaydo/pdk-ci-workflow
+    rev: 6d46a20ed995ac59e898c16e0eea8f3216c1f147
+    hooks:
+      - id: check-required-files
+        priority: 10
+      - id: check-pyproject-sections
+        priority: 10
+      - id: check-package-init
+        priority: 10
+      - id: check-cells-structure
+        priority: 10
+      - id: check-tech-structure
+        priority: 10
+      - id: check-pdk-object
+        priority: 10
+      - id: check-test-structure
+        priority: 10
+      - id: check-makefile-targets
+        priority: 10
+      - id: check-workflows
+        priority: 10
+      - id: check-multi-band
+        priority: 10
+      - id: check-no-raw-layers
+        priority: 10
+      - id: check-no-main-in-cells
+        priority: 10
+      - id: check-precommit-config
+        priority: 10
+      - id: check-version-sync
+        priority: 10
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
@@ -106,13 +137,13 @@ repos:
       - id: hadolint
         priority: 10
   - repo: https://github.com/checkmake/checkmake.git
-    rev: 0.2.2
+    rev: v0.3.2
     hooks:
       - id: checkmake
         priority: 20
         args: ['--config=.github/.checkmake.ini']
   - repo: https://github.com/EbodShojaei/bake
-    rev: v1.4.4
+    rev: v1.4.6
     hooks:
       - id: mbake-validate
         priority: 20

CHANGELOG.md

@@ -0,0 +1,82 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to
+[Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.3.6] - 2026-04-14
+
+### Fixed
+
+- Initial pre-commit hook fixes.
+- Resolved circular imports and implemented lazy-loading for model dependencies.
+- Fixed import redundancy issues ("Module is imported with 'import' and 'import from'").
+
+### Added
+
+- Added fluxonium qubit layout with superinductor and Josephson junction.
+- Introduced Monte Carlo CPW tolerance analysis for resonator simulations.
+- Added component tags and improved svgbob ASCII art diagrams for docstrings.
+- Enabled Google Colab support for notebooks.
+
+### Changed
+
+- Refactored waveguide models to use `sax[rf]`.
+- Switched PyPI publishing to OIDC Trusted Publisher.
+
+## [0.3.5] - 2026-03-29
+
+### Added
+
+- Implemented unimon qubit layout, SAX model, and Hamiltonian.
+- Added `just show` command for interactive component visualization.
+- Added lumped-element resonator with meander inductor.
+
+### Fixed
+
+- Fixed `M1_ETCH` overlap with `M1_DRAW` in `half_circle_coupler`.
+- Resolved LaTeX PDF documentation build warnings and errors.
+
+### Changed
+
+- Increased test coverage from 86% to 93%.
+- Upgraded `pyrefly` to 0.58.0 for stricter type checking.
+
+## [0.3.4] - 2026-03-25
+
+### Added
+
+- Added pulse-level simulation notebook with JAX backend via `qutip-qip`.
+- Introduced NetKet transmon qubit design notebook.
+- Added a component designer agent for quantum device visualization.
+
+### Changed
+
+- Removed `scikit-rf` dependency in favor of consolidated CPW models.
+- Refactored resonator length optimization to utilize Optax and JAX.
+- Migrated documentation from Jupyter Book to pure Sphinx.
+
+## [0.3.3] - 2026-03-12
+
+### Added
+
+- Added HFSS simulation support via PyAEDT and Q2D impedance extraction helpers.
+- Enabled collision checking for CPW route bundles.
+
+### Changed
+
+- Standardized logging using `gf.logger` across the library.
+- Refactored AEDT simulation utilities into a class-based structure.
+
+## [0.3.0] - 2026-03-09
+
+### Added
+
+- Replaced `scikit-rf` backend with JAX-native transmission line models.
+- Added `pymablock` dispersive shift notebook and perturbation theory helpers.
+
+### Changed
+
+- Enhanced models for airbridge physics and SQUID junctions.
+- Optimized cell layouts using `gf.pack`.

Makefile

@@ -1,4 +1,4 @@
-.PHONY: docs build dev
+.PHONY: docs build install dev test
 
 # Makefile — compatibility shim for gdsfactory PDK CI tooling
 #
@@ -10,13 +10,32 @@
 JUST_CMD := uvx --from rust-just just
 
 docs:
+	@if [ "$$GITHUB_ACTIONS" = "true" ]; then sudo apt-get update -y && sudo apt-get install -y fonts-cmu; fi
 	@$(JUST_CMD) docs
+	@if [ "$$GITHUB_ACTIONS" = "true" ]; then \
+		TOKEN=$${GH_TOKEN:-$${GITHUB_TOKEN:-$$(git config --get http.https://github.com/.extraheader | cut -d ' ' -f 3 | base64 -d | cut -d ':' -f 2 2>/dev/null)}}; \
+		if [ -n "$$TOKEN" ]; then \
+			GH_TOKEN=$$TOKEN gh run download $$GITHUB_RUN_ID -n pdf-docs -D docs/_build/html || echo "PDF artifact not found, skipping…"; \
+		else \
+			echo "GH_TOKEN not set and could not be extracted from git, skipping PDF download…"; \
+		fi; \
+	fi
 
 build:
 	@$(JUST_CMD) build
 
-dev:
-	@$(JUST_CMD) install
+install:
+	@if [ "$$GITHUB_ACTIONS" = "true" ]; then \
+		$(JUST_CMD) install "--all-extras --no-extra gdsfactoryplus"; \
+	else \
+		$(JUST_CMD) install; \
+	fi
+
+dev: install
+	@$(JUST_CMD) install-pre
+
+test:
+	@$(JUST_CMD) test
 
 # Any target not explicitly defined above is forwarded to just.
 %:

docs/docs.just

@@ -80,12 +80,12 @@ docs-prerequisites: write-cells write-models write-justfile-help copy-sample-not
 
 # Build the HTML documentation
 [group('docs')]
-docs: docs-prerequisites setup-ipython-config-temporary-before
+docs: check-lfs docs-prerequisites setup-ipython-config-temporary-before
     @trap 'just setup-ipython-config-temporary-after' EXIT INT TERM; uv run --group docs sphinx-build -b html docs docs/_build/html
 
 # Setup LaTeX for PDF documentation
 [group('docs')]
-docs-latex: docs-prerequisites setup-ipython-config-temporary-before
+docs-latex: check-lfs docs-prerequisites setup-ipython-config-temporary-before
     @trap 'just setup-ipython-config-temporary-after' EXIT INT TERM; uv run --group docs sphinx-build -b latex docs docs/_build/latex
 
 # Build PDF documentation (requires a TeXLive installation)