From b3ed3831cd45d884dbd43749c6b2fd9d73ff665b Mon Sep 17 00:00:00 2001 From: Stathis Gennatas Date: Mon, 30 Mar 2026 20:27:26 -0700 Subject: [PATCH] mkdocs + zensical --- python/rtemis_a3/docs/api.md | 31 +++ python/rtemis_a3/docs/index.md | 105 ++++++++++ python/rtemis_a3/mkdocs.yml | 13 ++ python/rtemis_a3/pyproject.toml | 2 + python/rtemis_a3/uv.lock | 330 ++++++++++++++++++++++++++++++++ python/rtemis_a3/zensical.toml | 314 ++++++++++++++++++++++++++++++ 6 files changed, 795 insertions(+) create mode 100644 python/rtemis_a3/docs/api.md create mode 100644 python/rtemis_a3/docs/index.md create mode 100644 python/rtemis_a3/mkdocs.yml create mode 100644 python/rtemis_a3/zensical.toml diff --git a/python/rtemis_a3/docs/api.md b/python/rtemis_a3/docs/api.md new file mode 100644 index 0000000..9fc7f8c --- /dev/null +++ b/python/rtemis_a3/docs/api.md @@ -0,0 +1,31 @@ +# API Reference + +## Functional API + +::: rtemis.a3.create_a3 + +::: rtemis.a3.a3_from_json + +::: rtemis.a3.a3_to_json + +::: rtemis.a3.residue_at + +::: rtemis.a3.variants_at + +## File I/O + +::: rtemis.a3.read_a3json + +::: rtemis.a3.write_a3json + +## Types + +::: rtemis.a3.A3 + +::: rtemis.a3.VariantRecord + +## Errors + +::: rtemis.a3.A3ValidationError + +::: rtemis.a3.A3ParseError diff --git a/python/rtemis_a3/docs/index.md b/python/rtemis_a3/docs/index.md new file mode 100644 index 0000000..08a8190 --- /dev/null +++ b/python/rtemis_a3/docs/index.md @@ -0,0 +1,105 @@ +# rtemis-a3 + +Python implementation of the **Amino Acid Annotation (A3)** format — +a structured JSON format for amino acid sequences with site, region, PTM, +processing, and variant annotations. + +Part of the [rtemis-org/a3](https://github.com/rtemis-org/a3) monorepo, +which provides A3 implementations in Python, TypeScript, R, Julia, and Rust. + +## Installation + +```bash +pip install rtemis-a3 +# or with uv +uv add rtemis-a3 +``` + +## Quick Start + +```python +from rtemis.a3 import create_a3 + +a3 = create_a3( + "MKTAYIAKQR", + site={ + "Active site": {"index": [3, 5], "type": "activeSite"}, + }, + region={ + "Repeat 1": {"index": [[1, 4]], "type": ""}, + }, + ptm={ + "Phosphorylation": {"index": [7], "type": ""}, + }, + variant=[{"position": 3, "from": "K", "to": "R"}], + metadata={ + "uniprot_id": "P12345", + "description": "Example protein", + "organism": "Homo sapiens", + }, +) + +len(a3.sequence) # 10 +``` + +## Parsing JSON + +```python +from rtemis.a3 import a3_from_json, A3ValidationError, A3ParseError + +try: + a3 = a3_from_json(json_string) +except A3ValidationError as e: + print(e.errors) # list of Pydantic error dicts with field paths +except A3ParseError as e: + print(e) # malformed JSON +``` + +## File I/O + +```python +from rtemis.a3 import read_a3json, write_a3json + +a3 = read_a3json("protein.json") +write_a3json(a3, "output.json", indent=2) +``` + +## Serialization + +```python +from rtemis.a3 import a3_to_json + +json_string = a3_to_json(a3) # compact +json_string = a3_to_json(a3, indent=2) # pretty-printed +``` + +## Wire Format + +```json +{ + "sequence": "MKTAYIAKQR", + "annotations": { + "site": { "Active site": { "index": [3, 5], "type": "activeSite" } }, + "region": { "Repeat 1": { "index": [[1, 4]], "type": "" } }, + "ptm": { "Phospho": { "index": [7], "type": "" } }, + "processing": {}, + "variant": [{ "position": 3, "from": "K", "to": "R" }] + }, + "metadata": { + "uniprot_id": "P12345", + "description": "Example protein", + "reference": "", + "organism": "Homo sapiens" + } +} +``` + +All five annotation families are always present in output. Each annotation +entry is `{ index, type }` — bare arrays are rejected. Positions are +1-based, sorted, and deduplicated. Ranges are `[start, end]` pairs +(`start < end`), sorted by start; overlapping ranges are rejected. + +## Canonical Schema + +See the [A3 specification](https://github.com/rtemis-org/a3/blob/main/specs/A3.md) +for the language-agnostic schema definition. diff --git a/python/rtemis_a3/mkdocs.yml b/python/rtemis_a3/mkdocs.yml new file mode 100644 index 0000000..681acba --- /dev/null +++ b/python/rtemis_a3/mkdocs.yml @@ -0,0 +1,13 @@ +site_name: rtemis_a3 + +plugins: + - mkdocstrings: + handlers: + python: + paths: [src] + inventories: + - https://docs.python.org/3/objects.inv + options: + docstring_style: numpy + inherited_members: true + show_source: false \ No newline at end of file diff --git a/python/rtemis_a3/pyproject.toml b/python/rtemis_a3/pyproject.toml index bedbbdd..6529368 100644 --- a/python/rtemis_a3/pyproject.toml +++ b/python/rtemis_a3/pyproject.toml @@ -24,7 +24,9 @@ python = ".venv" [dependency-groups] dev = [ "ipykernel>=7.2.0", + "mkdocstrings-python>=2.0.3", 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The site_description is included in the HTML head and should contain a +# meaningful description of the site content for use by search engines. +# +# Read more: https://zensical.org/docs/setup/basics/#site_description +site_description = "Python implementation of the A3 amino acid annotation format." + +# The site_author attribute. This is used in the HTML head element. +# +# Read more: https://zensical.org/docs/setup/basics/#site_author +site_author = "E.D. Gennatas" + +# The site_url is the canonical URL for your site. When building online +# documentation you should set this. +# Read more: https://zensical.org/docs/setup/basics/#site_url +#site_url = "https://www.example.com/" + +# The copyright notice appears in the page footer and can contain an HTML +# fragment. +# +# Read more: https://zensical.org/docs/setup/basics/#copyright +copyright = """ +Copyright © 2026 EDG +""" + +# Zensical supports both implicit navigation and explicitly defined navigation. +# If you decide not to define a navigation here then Zensical will simply +# derive the navigation structure from the directory structure of your +# "docs_dir". The definition below demonstrates how a navigation structure +# can be defined using TOML syntax. +# +# Read more: https://zensical.org/docs/setup/navigation/ +nav = [ + { "Home" = "index.md" }, + { "API Reference" = "api.md" }, +] + +# With the "extra_css" option you can add your own CSS styling to customize +# your Zensical project according to your needs. You can add any number of +# CSS files. +# +# The path provided should be relative to the "docs_dir". +# +# Read more: https://zensical.org/docs/customization/#additional-css +# +#extra_css = ["stylesheets/extra.css"] + +# With the `extra_javascript` option you can add your own JavaScript to your +# project to customize the behavior according to your needs. +# +# The path provided should be relative to the "docs_dir". +# +# Read more: https://zensical.org/docs/customization/#additional-javascript +#extra_javascript = ["javascripts/extra.js"] + +# ---------------------------------------------------------------------------- +# Section for configuring theme options +# ---------------------------------------------------------------------------- +[project.theme] + +# change this to "classic" to use the traditional Material for MkDocs look. +#variant = "classic" + +# Zensical allows you to override specific blocks, partials, or whole +# templates as well as to define your own templates. To do this, uncomment +# the custom_dir setting below and set it to a directory in which you +# keep your template overrides. +# +# Read more: +# - https://zensical.org/docs/customization/#extending-the-theme +# +#custom_dir = "overrides" + +# With the "favicon" option you can set your own image to use as the icon +# browsers will use in the browser title bar or tab bar. The path provided +# must be relative to the "docs_dir". +# +# Read more: +# - https://zensical.org/docs/setup/logo-and-icons/#favicon +# - https://developer.mozilla.org/en-US/docs/Glossary/Favicon +# +#favicon = "images/favicon.png" + +# Zensical supports more than 60 different languages. This means that the +# labels and tooltips that Zensical's templates produce are translated. +# The "language" option allows you to set the language used. This language +# is also indicated in the HTML head element to help with accessibility +# and guide search engines and translation tools. +# +# The default language is "en" (English). It is possible to create +# sites with multiple languages and configure a language selector. See +# the documentation for details. +# +# Read more: +# - https://zensical.org/docs/setup/language/ +# +language = "en" + +# Zensical provides a number of feature toggles that change the behavior +# of the documentation site. +features = [ + # Zensical includes an announcement bar. This feature allows users to + # dismiss it when they have read the announcement. + # https://zensical.org/docs/setup/header/#announcement-bar + "announce.dismiss", + + # If you have a repository configured and turn on this feature, Zensical + # will generate an edit button for the page. This works for common + # repository hosting services. + # https://zensical.org/docs/setup/repository/#content-actions + #"content.action.edit", + + # If you have a repository configured and turn on this feature, Zensical + # will generate a button that allows the user to view the Markdown + # code for the current page. + # https://zensical.org/docs/setup/repository/#content-actions + #"content.action.view", + + # Code annotations allow you to add an icon with a tooltip to your + # code blocks to provide explanations at crucial points. + # https://zensical.org/docs/authoring/code-blocks/#code-annotations + "content.code.annotate", + + # This feature turns on a button in code blocks that allow users to + # copy the content to their clipboard without first selecting it. + # https://zensical.org/docs/authoring/code-blocks/#code-copy-button + "content.code.copy", + + # Code blocks can include a button to allow for the selection of line + # ranges by the user. + # https://zensical.org/docs/authoring/code-blocks/#code-selection-button + "content.code.select", + + # Zensical can render footnotes as inline tooltips, so the user can read + # the footnote without leaving the context of the document. + # https://zensical.org/docs/authoring/footnotes/#footnote-tooltips + "content.footnote.tooltips", + + # If you have many content tabs that have the same titles (e.g., "Python", + # "JavaScript", "Cobol"), this feature causes all of them to switch to + # at the same time when the user chooses their language in one. + # https://zensical.org/docs/authoring/content-tabs/#linked-content-tabs + "content.tabs.link", + + # With this feature enabled users can add tooltips to links that will be + # displayed when the mouse pointer hovers the link. + # https://zensical.org/docs/authoring/tooltips/#improved-tooltips + "content.tooltips", + + # With this feature enabled, Zensical will automatically hide parts + # of the header when the user scrolls past a certain point. + # https://zensical.org/docs/setup/header/#automatic-hiding + # "header.autohide", + + # Turn on this feature to expand all collapsible sections in the + # navigation sidebar by default. + # https://zensical.org/docs/setup/navigation/#navigation-expansion + # "navigation.expand", + + # This feature turns on navigation elements in the footer that allow the + # user to navigate to a next or previous page. + # https://zensical.org/docs/setup/footer/#navigation + "navigation.footer", + + # When section index pages are enabled, documents can be directly attached + # to sections, which is particularly useful for providing overview pages. + # https://zensical.org/docs/setup/navigation/#section-index-pages + "navigation.indexes", + + # When instant navigation is enabled, clicks on all internal links will be + # intercepted and dispatched via XHR without fully reloading the page. + # https://zensical.org/docs/setup/navigation/#instant-navigation + "navigation.instant", + + # With instant prefetching, your site will start to fetch a page once the + # user hovers over a link. This will reduce the perceived loading time + # for the user. + # https://zensical.org/docs/setup/navigation/#instant-prefetching + "navigation.instant.prefetch", + + # In order to provide a better user experience on slow connections when + # using instant navigation, a progress indicator can be enabled. + # https://zensical.org/docs/setup/navigation/#progress-indicator + #"navigation.instant.progress", + + # When navigation paths are activated, a breadcrumb navigation is rendered + # above the title of each page + # https://zensical.org/docs/setup/navigation/#navigation-path + "navigation.path", + + # When pruning is enabled, only the visible navigation items are included + # in the rendered HTML, reducing the size of the built site by 33% or more. + # https://zensical.org/docs/setup/navigation/#navigation-pruning + #"navigation.prune", + + # When sections are enabled, top-level sections are rendered as groups in + # the sidebar for viewports above 1220px, but remain as-is on mobile. + # https://zensical.org/docs/setup/navigation/#navigation-sections + "navigation.sections", + + # When tabs are enabled, top-level sections are rendered in a menu layer + # below the header for viewports above 1220px, but remain as-is on mobile. + # https://zensical.org/docs/setup/navigation/#navigation-tabs + #"navigation.tabs", + + # When sticky tabs are enabled, navigation tabs will lock below the header + # and always remain visible when scrolling down. + # https://zensical.org/docs/setup/navigation/#sticky-navigation-tabs + #"navigation.tabs.sticky", + + # A back-to-top button can be shown when the user, after scrolling down, + # starts to scroll up again. + # https://zensical.org/docs/setup/navigation/#back-to-top-button + "navigation.top", + + # When anchor tracking is enabled, the URL in the address bar is + # automatically updated with the active anchor as highlighted in the table + # of contents. + # https://zensical.org/docs/setup/navigation/#anchor-tracking + "navigation.tracking", + + # When search highlighting is enabled and a user clicks on a search result, + # Zensical will highlight all occurrences after following the link. + # https://zensical.org/docs/setup/search/#search-highlighting + "search.highlight", + + # When anchor following for the table of contents is enabled, the sidebar + # is automatically scrolled so that the active anchor is always visible. + # https://zensical.org/docs/setup/navigation/#anchor-following + # "toc.follow", + + # When navigation integration for the table of contents is enabled, it is + # always rendered as part of the navigation sidebar on the left. + # https://zensical.org/docs/setup/navigation/#navigation-integration + #"toc.integrate", +] + +# ---------------------------------------------------------------------------- +# You can configure your own logo to be shown in the header using the "logo" +# option in the "theme" subsection. The logo must be a relative path to a file +# in your "docs_dir", e.g., to use `docs/assets/logo.png` you would set: +# ---------------------------------------------------------------------------- +#logo = "assets/logo.png" + +# ---------------------------------------------------------------------------- +# If you don't have a dedicated project logo, you can use a built-in icon from +# the icon sets shipped in Zensical. Please note that the setting lives in a +# different subsection, and that the above take precedence over the icon. +# +# Read more: +# - https://zensical.org/docs/setup/logo-and-icons +# - https://github.com/zensical/ui/tree/master/dist/.icons +# ---------------------------------------------------------------------------- +#[project.theme.icon] +#logo = "lucide/smile" + +# ---------------------------------------------------------------------------- +# In the "font" subsection you can configure the fonts used. By default, fonts +# are loaded from Google Fonts, giving you a wide range of choices from a set +# of suitably licensed fonts. There are options for a normal text font and for +# a monospaced font used in code blocks. +# ---------------------------------------------------------------------------- +#[project.theme.font] +#text = "Inter" +#code = "Jetbrains Mono" + +# ---------------------------------------------------------------------------- +# In the "palette" subsection you can configure options for the color scheme. +# You can configure different color schemes, e.g., to turn on dark mode, +# that the user can switch between. Each color scheme can be further +# customized. +# +# Read more: +# - https://zensical.org/docs/setup/colors/ +# ---------------------------------------------------------------------------- +[[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" + +# ---------------------------------------------------------------------------- +# The "extra" section contains miscellaneous settings. +# ---------------------------------------------------------------------------- +#[[project.extra.social]] +#icon = "fontawesome/brands/github" +#link = "https://github.com/user/repo" + +[project.plugins.mkdocstrings.handlers.python] +inventories = ["https://docs.python.org/3/objects.inv"] +paths = ["src"] + +[project.plugins.mkdocstrings.handlers.python.options] +docstring_style = "numpy" +inherited_members = true +show_source = false \ No newline at end of file