seqpro 0.9.0__tar.gz → 0.11.0__tar.gz

seqpro-0.11.0/.claude/skills/zensical-setup/.skillfish.json

@@ -0,0 +1,10 @@
+{
+  "version": 2,
+  "name": "zensical-setup",
+  "owner": "ai-riksarkivet",
+  "repo": "ra-mcp",
+  "path": ".claude/skills/zensical-setup",
+  "branch": "main",
+  "sha": "68889b450a1c796676d02d4eea7649497964d505",
+  "source": "manual"
+}

seqpro-0.11.0/.claude/skills/zensical-setup/SKILL.md

@@ -0,0 +1,662 @@
+---
+name: zensical-setup
+description: >
+  Guide for setting up and configuring Zensical documentation sites.
+  Use when: create documentation site, configure zensical.toml, set up
+  navigation, change theme colors, configure fonts, add analytics,
+  deploy docs site, GitHub Pages, GitLab Pages, mkdocs.yml migration,
+  customize Zensical theme, template overrides, add CSS or JavaScript.
+---
+
+# Zensical Site Setup & Configuration
+
+Zensical is a modern static site generator for project documentation, built by
+the creators of Material for MkDocs. It uses TOML configuration (`zensical.toml`)
+and supports `mkdocs.yml` for migration. This skill covers installation,
+configuration, theming, navigation, deployment, and customization.
+
+## Quick Start
+
+```bash
+# Install
+python3 -m venv .venv && source .venv/bin/activate && pip install zensical
+# Or with uv:
+uv init && uv add --dev zensical
+
+# Create project
+zensical new .
+
+# Preview
+zensical serve
+
+# Build
+zensical build
+```
+
+Generated structure:
+```
+.
+├─ .github/        # GitHub Actions workflow
+├─ docs/
+│  ├─ index.md
+│  └─ markdown.md
+└─ zensical.toml
+```
+
+## Configuration File
+
+Zensical uses `zensical.toml` (recommended) or `mkdocs.yml` (for migration).
+All settings live under the `[project]` scope.
+
+### Essential Settings
+
+```toml
+[project]
+site_name = "My Site"                    # Required
+site_url = "https://example.com"         # Strongly recommended
+site_description = "Project docs"        # For HTML meta
+site_author = "Jane Doe"                 # For HTML meta
+copyright = "© 2025 Jane Doe"       # Footer copyright
+docs_dir = "docs"                        # Source directory (default)
+site_dir = "site"                        # Output directory (default)
+use_directory_urls = true                # Pretty URLs (default)
+dev_addr = "localhost:7860"              # Dev server address (default)
+```
+
+### Theme Variant
+
+Two variants: `modern` (default, fresh design) and `classic` (matches Material for MkDocs).
+
+```toml
+[project.theme]
+variant = "classic"   # Use "classic" for Material for MkDocs look
+```
+
+## Navigation
+
+### Automatic Navigation
+
+By default, Zensical generates navigation from the folder structure.
+
+### Explicit Navigation
+
+```toml
+[project]
+nav = [
+  { "Home" = "index.md" },
+  { "About" = [
+    "about/index.md",
+    "about/vision.md",
+    "about/team.md"
+  ]},
+  { "GitHub Repo" = "https://github.com/org/repo" }  # External links
+]
+```
+
+### Navigation Features
+
+Enable features under `[project.theme]`:
+
+```toml
+[project.theme]
+features = [
+  # Instant navigation (SPA-like behavior, requires site_url)
+  "navigation.instant",
+  "navigation.instant.prefetch",     # Prefetch on hover
+  "navigation.instant.progress",     # Progress bar on slow connections
+
+  # Navigation structure
+  "navigation.tabs",                 # Top-level sections as tabs
+  "navigation.tabs.sticky",          # Sticky tabs on scroll
+  "navigation.sections",             # Render top-level as groups
+  "navigation.expand",               # Expand all subsections by default
+  "navigation.indexes",              # Section index pages
+  "navigation.path",                 # Breadcrumb navigation
+  "navigation.prune",                # Reduce HTML size ~33%
+  "navigation.top",                  # Back-to-top button
+  "navigation.footer",               # Previous/next page links in footer
+  "navigation.tracking",             # Update URL with active anchor
+
+  # Table of contents
+  "toc.follow",                      # Auto-scroll TOC to active anchor
+  "toc.integrate",                   # TOC in left sidebar (incompatible with navigation.indexes)
+
+  # Instant previews (experimental, headerlinks only)
+  # Configured via markdown extension, see below
+]
+```
+
+**Incompatibilities:**
+- `navigation.prune` ↔ `navigation.expand`
+- `navigation.indexes` ↔ `toc.integrate`
+
+### Instant Previews
+
+```toml
+[project.markdown_extensions.zensical.extensions.preview]
+configurations = [
+  { targets.include = ["setup/extensions/*", "customization.md"] }
+]
+```
+
+### Hiding Sidebars (per page, via front matter)
+
+```yaml
+---
+hide:
+  - navigation
+  - toc
+  - path
+  - footer
+  - tags
+  - feedback
+---
+```
+
+## Colors
+
+### Color Scheme
+
+```toml
+[project.theme.palette]
+scheme = "default"     # Light mode
+# scheme = "slate"     # Dark mode
+primary = "indigo"     # Header/sidebar/links color
+accent = "indigo"      # Interactive elements color
+```
+
+**Available primary colors:** red, pink, purple, deep-purple, indigo, blue,
+light-blue, cyan, teal, green, light-green, lime, yellow, amber, orange,
+deep-orange, brown, grey, blue-grey, black, white, custom.
+
+**Available accent colors:** red, pink, purple, deep-purple, indigo, blue,
+light-blue, cyan, teal, green, light-green, lime, yellow, amber, orange,
+deep-orange.
+
+### Color Palette Toggle (light/dark switch)
+
+```toml
+[[project.theme.palette]]
+scheme = "default"
+toggle.icon = "lucide/sun"
+toggle.name = "Switch to dark mode"
+
+[[project.theme.palette]]
+scheme = "slate"
+toggle.icon = "lucide/moon"
+toggle.name = "Switch to light mode"
+```
+
+### System Preference + Automatic Mode
+
+```toml
+[[project.theme.palette]]
+media = "(prefers-color-scheme)"
+toggle.icon = "lucide/sun-moon"
+toggle.name = "Switch to light mode"
+
+[[project.theme.palette]]
+media = "(prefers-color-scheme: light)"
+scheme = "default"
+toggle.icon = "lucide/sun"
+toggle.name = "Switch to dark mode"
+
+[[project.theme.palette]]
+media = "(prefers-color-scheme: dark)"
+scheme = "slate"
+toggle.icon = "lucide/moon"
+toggle.name = "Switch to system preference"
+```
+
+### Custom Colors via CSS
+
+Set `primary = "custom"` then define CSS variables:
+
+```css
+/* docs/stylesheets/extra.css */
+:root > * {
+  --md-primary-fg-color:        #EE0F0F;
+  --md-primary-fg-color--light: #ECB7B7;
+  --md-primary-fg-color--dark:  #90030C;
+}
+```
+
+### Custom Color Scheme
+
+```css
+[data-md-color-scheme="my-scheme"] {
+  --md-primary-fg-color: #EE0F0F;
+  /* ... */
+}
+
+/* Tune dark scheme hue */
+[data-md-color-scheme="slate"] {
+  --md-hue: 210;  /* 0-360 */
+}
+```
+
+## Fonts
+
+```toml
+[project.theme]
+font.text = "Inter"            # Body text (any Google Font)
+font.code = "JetBrains Mono"   # Code blocks (any Google Font)
+# font = false                 # Disable Google Fonts, use system fonts
+```
+
+Custom fonts via CSS:
+```css
+:root {
+  --md-text-font: "My Custom Font";
+  --md-code-font: "My Mono Font";
+}
+```
+
+## Logo & Icons
+
+```toml
+[project.theme]
+logo = "images/logo.png"            # Image file in docs/
+favicon = "images/favicon.png"
+
+[project.theme.icon]
+logo = "lucide/smile"               # Or use a bundled icon
+repo = "fontawesome/brands/github"  # Repository icon
+edit = "material/pencil"            # Edit page button
+view = "material/eye"               # View source button
+previous = "fontawesome/solid/angle-left"
+next = "fontawesome/solid/angle-right"
+
+[project.extra]
+homepage = "https://example.com"    # Override logo link target
+```
+
+### Bundled Icon Sets
+
+- Lucide, Material Design, FontAwesome, Octicons, Simple Icons
+- Over 10,000 icons available
+
+### Adding Custom Icons
+
+Place SVGs in `overrides/.icons/<set-name>/`:
+```toml
+[project.theme]
+custom_dir = "overrides"
+
+[project.markdown_extensions.pymdownx.emoji]
+emoji_index = "zensical.extensions.emoji.twemoji"
+emoji_generator = "zensical.extensions.emoji.to_svg"
+options.custom_icons = ["overrides/.icons"]
+```
+
+## Language
+
+```toml
+[project.theme]
+language = "en"       # 60+ languages supported
+direction = "ltr"     # or "rtl"
+```
+
+### Language Selector
+
+```toml
+[project.extra]
+alternate = [
+  { name = "English", link = "/en/", lang = "en" },
+  { name = "Deutsch", link = "/de/", lang = "de" }
+]
+```
+
+## Repository Integration
+
+```toml
+[project]
+repo_url = "https://github.com/org/repo"
+repo_name = "org/repo"
+edit_uri = "edit/main/docs/"
+
+[project.theme]
+features = [
+  "content.action.edit",   # Edit this page button
+  "content.action.view"    # View source button
+]
+```
+
+## Footer
+
+```toml
+[project]
+copyright = "Copyright &copy; 2025 My Company"
+
+[project.theme]
+features = ["navigation.footer"]
+
+[[project.extra.social]]
+icon = "fontawesome/brands/github"
+link = "https://github.com/org"
+
+[[project.extra.social]]
+icon = "fontawesome/brands/x-twitter"
+link = "https://x.com/handle"
+name = "Company on X"
+
+[project.extra]
+generator = false    # Remove "Made with Zensical" (consider keeping it!)
+```
+
+## Search
+
+Built-in, enabled by default. English only currently.
+
+```toml
+[project.theme]
+features = ["search.highlight"]   # Highlight search terms on result pages
+```
+
+## Header
+
+```toml
+[project.theme]
+features = [
+  "header.autohide",     # Hide header on scroll down
+  "announce.dismiss"     # Dismissable announcement bar
+]
+```
+
+Announcement bar via template override:
+```html
+<!-- overrides/main.html -->
+{% extends "base.html" %}
+{% block announce %}
+  Your announcement here!
+{% endblock %}
+```
+
+## Analytics
+
+```toml
+[project.extra.analytics]
+provider = "google"
+property = "G-XXXXXXXXXX"
+
+[project.extra.analytics.feedback]
+title = "Was this page helpful?"
+
+[[project.extra.analytics.feedback.ratings]]
+icon = "material/emoticon-happy-outline"
+name = "This page was helpful"
+data = 1
+note = "Thanks for your feedback!"
+
+[[project.extra.analytics.feedback.ratings]]
+icon = "material/emoticon-sad-outline"
+name = "This page could be improved"
+data = 0
+note = "Thanks for your feedback!"
+```
+
+## Data Privacy / Cookie Consent
+
+```toml
+[project.extra.consent]
+title = "Cookie consent"
+description = "We use cookies to measure our docs effectiveness."
+actions = ["accept", "manage"]
+
+[project.extra.consent.cookies]
+analytics = "Google Analytics"
+custom = "Custom cookie"
+```
+
+Change cookie settings link in footer:
+```toml
+[project]
+copyright = """
+  Copyright &copy; 2025 –
+  <a href="#__consent">Change cookie settings</a>
+"""
+```
+
+## Tags
+
+Tags work by default. Add to pages via front matter:
+```yaml
+---
+tags:
+  - Setup
+  - Getting started
+---
+```
+
+Tag icons:
+```toml
+[project.extra.tags]
+HTML5 = "html"
+
+[project.theme.icon.tag]
+default = "lucide/hash"
+html = "fontawesome/brands/html5"
+```
+
+## Offline Usage
+
+```toml
+[project.plugins.offline]
+# enabled = false  # To disable
+```
+
+Limitations: disable instant navigation, analytics, repo info, comments.
+
+## Custom CSS & JavaScript
+
+```toml
+[project]
+extra_css = ["stylesheets/extra.css"]
+extra_javascript = ["javascripts/extra.js"]
+```
+
+JavaScript modules:
+```toml
+[[project.extra_javascript]]
+path = "javascripts/extra.js"
+type = "module"
+```
+
+Async scripts:
+```toml
+[[project.extra_javascript]]
+path = "javascripts/extra.js"
+async = true
+```
+
+Important: use `document$` observable for instant navigation compatibility:
+```javascript
+document$.subscribe(function() {
+  console.log("Initialize third-party libraries here")
+})
+```
+
+## Template Overrides
+
+```toml
+[project.theme]
+custom_dir = "overrides"
+```
+
+### Override Blocks (recommended)
+
+```html
+<!-- overrides/main.html -->
+{% extends "base.html" %}
+
+{% block htmltitle %}
+  <title>Custom Title</title>
+{% endblock %}
+```
+
+Available blocks: `analytics`, `announce`, `config`, `container`, `content`,
+`extrahead`, `fonts`, `footer`, `header`, `hero`, `htmltitle`, `libs`,
+`outdated`, `scripts`, `site_meta`, `site_nav`, `styles`, `tabs`.
+
+### Override Partials
+
+Place files in `overrides/partials/` matching the theme's partial structure.
+
+### Custom Templates (per page)
+
+```yaml
+---
+template: my_template.html
+---
+```
+
+### Custom 404 Page
+
+Place `404.html` in the overrides directory.
+
+## Markdown Extensions (Default Configuration)
+
+Zensical has sensible defaults. If you need to customize, here is the full
+default expansion you can use as a starting point:
+
+```toml
+[project.markdown_extensions.abbr]
+[project.markdown_extensions.admonition]
+[project.markdown_extensions.attr_list]
+[project.markdown_extensions.def_list]
+[project.markdown_extensions.footnotes]
+[project.markdown_extensions.md_in_html]
+[project.markdown_extensions.toc]
+permalink = true
+[project.markdown_extensions.pymdownx.arithmatex]
+generic = true
+[project.markdown_extensions.pymdownx.betterem]
+smart_enable = "all"
+[project.markdown_extensions.pymdownx.caret]
+[project.markdown_extensions.pymdownx.details]
+[project.markdown_extensions.pymdownx.emoji]
+emoji_generator = "zensical.extensions.emoji.to_svg"
+emoji_index = "zensical.extensions.emoji.twemoji"
+[project.markdown_extensions.pymdownx.highlight]
+[project.markdown_extensions.pymdownx.inlinehilite]
+[project.markdown_extensions.pymdownx.keys]
+[project.markdown_extensions.pymdownx.mark]
+[project.markdown_extensions.pymdownx.smartsymbols]
+[project.markdown_extensions.pymdownx.superfences]
+[project.markdown_extensions.pymdownx.tabbed]
+alternate_style = true
+[project.markdown_extensions.pymdownx.tasklist]
+custom_checkbox = true
+[project.markdown_extensions.pymdownx.tilde]
+```
+
+To reset to MkDocs defaults (no extensions):
+```toml
+[project]
+markdown_extensions = {}
+```
+
+## Deployment
+
+### GitHub Pages (GitHub Actions)
+
+```yaml
+# .github/workflows/docs.yml
+name: Documentation
+on:
+  push:
+    branches: [master, main]
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+jobs:
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/configure-pages@v5
+      - uses: actions/checkout@v5
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - run: pip install zensical
+      - run: zensical build --clean
+      - uses: actions/upload-pages-artifact@v4
+        with:
+          path: site
+      - uses: actions/deploy-pages@v4
+        id: deployment
+```
+
+Site appears at `<username>.github.io/<repository>`.
+
+### GitLab Pages
+
+```yaml
+# .gitlab-ci.yml
+pages:
+  stage: deploy
+  image: python:latest
+  script:
+    - pip install zensical
+    - zensical build --clean
+  pages:
+    publish: public
+  rules:
+    - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH'
+```
+
+**Important:** Set `site_dir = "public"` for GitLab Pages.
+
+Site appears at `<username>.gitlab.io/<repository>`.
+
+## Content Area Width
+
+```css
+/* docs/stylesheets/extra.css */
+.md-grid {
+  max-width: 1440px;
+  /* Or: max-width: initial; for full width */
+}
+```
+
+## mkdocstrings (API docs)
+
+```bash
+pip install mkdocstrings-python
+```
+
+```toml
+[project.plugins.mkdocstrings.handlers.python]
+paths = ["src"]
+inventories = ["https://docs.python.org/3/objects.inv"]
+
+[project.plugins.mkdocstrings.handlers.python.options]
+docstring_style = "google"
+inherited_members = true
+show_source = false
+```
+
+## Comment System (Giscus example)
+
+Override `partials/comments.html` with the Giscus script, then enable per page:
+```yaml
+---
+comments: true
+---
+```
+
+## CLI Reference
+
+| Command | Purpose |
+|---------|---------|
+| `zensical new <dir>` | Create new project |
+| `zensical serve` | Preview with live reload |
+| `zensical serve -o` | Preview and open browser |
+| `zensical serve -a localhost:3000` | Custom address |
+| `zensical build` | Build static site |
+| `zensical build --clean` | Build with cache cleaning |
+| `zensical build -f path/to/config` | Use specific config file |

seqpro-0.11.0/.github/workflows/bump.yaml

@@ -0,0 +1,49 @@
+name: Bump version
+
+on:
+  workflow_dispatch:
+
+jobs:
+  bump:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          token: "${{ secrets.GH_TOKEN }}"
+
+      - name: Install commitizen
+        run: pip install commitizen --quiet
+
+      - name: Detect partial bump
+        id: detect
+        run: |
+          PROJECT_VERSION=$(cz version --project)
+          # Only match tags in the current format (no 'v' prefix) to avoid false
+          # positives from legacy v-prefixed tags.
+          LATEST_TAG=$(git tag --sort=-version:refname | grep -E '^[0-9]+\.[0-9]+\.[0-9]+$' | head -1)
+          if [ -n "$LATEST_TAG" ] && [ "$LATEST_TAG" != "$PROJECT_VERSION" ]; then
+            echo "partial=true" >> $GITHUB_OUTPUT
+            echo "tag=$LATEST_TAG" >> $GITHUB_OUTPUT
+          else
+            echo "partial=false" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Bump version
+        if: steps.detect.outputs.partial != 'true'
+        uses: commitizen-tools/commitizen-action@master
+        with:
+          github_token: ${{ secrets.GH_TOKEN }}
+
+      - name: Fix partial bump (tag exists on remote, update files only)
+        if: steps.detect.outputs.partial == 'true'
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          NEW_VERSION="${{ steps.detect.outputs.tag }}"
+          cz bump --files-only --yes
+          BUMPED_VERSION=$(cz version --project)
+          git add pyproject.toml CHANGELOG.md
+          git commit -m "bump: version $NEW_VERSION"
+          git push origin main
+          git push origin "$BUMPED_VERSION"