gbdraw 0.14.0__py3-none-any.whl

gbdraw/__init__.py

@@ -0,0 +1,58 @@
+"""Public Python interface for gbdraw."""
+
+from .interface import (
+    CircularLayout,
+    CircularOptions,
+    CircularTrackOptions,
+    ComparisonRingOptions,
+    ComparisonRingTrackOptions,
+    ConservationOptions,
+    ConservationTrackOptions,
+    DepthTrackOptions,
+    Diagram,
+    FeatureOptions,
+    LabelOptions,
+    LinearComparisonOptions,
+    LinearLayout,
+    LinearOptions,
+    LinearTrackOptions,
+    Thresholds,
+    TitleOptions,
+    draw_circular,
+    draw_linear,
+    read_genbank,
+    read_gff,
+)
+from .version import __version__
+from .api.requests import RecordDisplayOptions
+from .features.placement import FeaturePlacementOverride, FeaturePlacementTarget
+from .layout.similarity_alignment import SimilarityAlignmentReference
+
+__all__ = [
+    "CircularLayout",
+    "CircularOptions",
+    "CircularTrackOptions",
+    "ComparisonRingOptions",
+    "ComparisonRingTrackOptions",
+    "ConservationOptions",
+    "ConservationTrackOptions",
+    "DepthTrackOptions",
+    "Diagram",
+    "FeatureOptions",
+    "FeaturePlacementOverride",
+    "FeaturePlacementTarget",
+    "LabelOptions",
+    "LinearComparisonOptions",
+    "LinearLayout",
+    "LinearOptions",
+    "LinearTrackOptions",
+    "RecordDisplayOptions",
+    "SimilarityAlignmentReference",
+    "Thresholds",
+    "TitleOptions",
+    "__version__",
+    "draw_circular",
+    "draw_linear",
+    "read_genbank",
+    "read_gff",
+]

gbdraw/_build_support.py

@@ -0,0 +1,261 @@
+from __future__ import annotations
+
+import os
+import re
+import sys
+import zipfile
+from datetime import datetime
+from importlib.util import module_from_spec, spec_from_file_location
+from pathlib import Path
+
+
+REPO_ROOT = Path(__file__).resolve().parents[1]
+PYPROJECT_PATH = REPO_ROOT / "pyproject.toml"
+WEB_ROOT = Path(__file__).resolve().parent / "web"
+CONFIG_PATH = WEB_ROOT / "js" / "config.js"
+
+BROWSER_WHEEL_BUILD_ENV = "GBDRAW_BUILDING_BROWSER_WHEEL"
+
+_PROJECT_VERSION_RE = re.compile(r'^version\s*=\s*"([^"]+)"\s*$', re.MULTILINE)
+_WHEEL_NAME_RE = re.compile(r'^(export const GBDRAW_WHEEL_NAME\s*=\s*")[^"]+(";\s*)$', re.MULTILINE)
+_WHEEL_CACHE_BUST_RE = re.compile(r'^(export const GBDRAW_WHEEL_CACHE_BUST\s*=\s*")[^"]+(";\s*)$', re.MULTILINE)
+
+_PYTHON_RUNTIME_PACKAGE_DATA = [
+    "data/color_palettes.toml",
+    "data/config.toml",
+    "data/losat-release.json",
+    "data/*.ttf",
+    "web/js/services/standalone-interactivity-assets.js",
+]
+
+_WEB_APP_PACKAGE_DATA = [
+    "web/index.html",
+    "web/css/tailwind.css",
+    "web/open-source-notices.html",
+    "web/gallery/palettes/palettes.json",
+    "web/assets/*.ico",
+    "web/assets/*.png",
+    "web/assets/*.svg",
+    "web/js/*.js",
+    "web/js/app/*.js",
+    "web/js/app/*/*.js",
+    "web/js/contracts/*.js",
+    "web/js/workers/*.js",
+    "web/js/services/*.js",
+    "web/js/utils/*.js",
+    "web/js/utils/*/*.js",
+    "web/presets/*.txt",
+    "web/presets/*.tsv",
+    "web/tutorial-data/*.json",
+    "web/tutorial-data/*/*.fna",
+    "web/tutorial-data/*/*.gb",
+    "web/tutorial-data/*/*.gbk",
+    "web/tutorial-data/*/*.gff3",
+    "web/tutorial-data/*/*.tsv",
+    "web/vendor/fonts/*.ttf",
+    "web/vendor/*/*.css",
+    "web/vendor/*/*.js",
+    "web/vendor/*/*.json",
+    "web/vendor/*/*.svg",
+    "web/vendor/*/*.ttf",
+    "web/vendor/*/*.whl",
+    "web/vendor/*/*.woff",
+    "web/vendor/*/*.woff2",
+    "web/vendor/*/*/*.css",
+    "web/vendor/*/*/*.js",
+    "web/vendor/*/*/*.json",
+    "web/vendor/*/*/*.mjs",
+    "web/vendor/*/*/*.svg",
+    "web/vendor/*/*/*.ttf",
+    "web/vendor/*/*/*.whl",
+    "web/vendor/*/*/*.woff",
+    "web/vendor/*/*/*.woff2",
+    "web/vendor/*/*/*.zip",
+    "web/vendor/*/*/*.wasm",
+    "web/vendor/*/*/*/*.js",
+    "web/vendor/*/*/*/*.json",
+    "web/vendor/*/*/*/*.mjs",
+    "web/vendor/*/*/*/*.whl",
+    "web/vendor/*/*/*/*.zip",
+    "web/vendor/*/*/*/*.wasm",
+    "web/wasm/*/*.md",
+    "web/wasm/*/*.wasm",
+]
+
+BROWSER_WHEEL_MAX_BYTES = 20 * 1024 * 1024
+
+_BROWSER_WHEEL_FORBIDDEN_PREFIXES = (
+    "gbdraw/bin/",
+    "gbdraw/web/assets/",
+    "gbdraw/web/css/",
+    "gbdraw/web/gallery/",
+    "gbdraw/web/js/",
+    "gbdraw/web/presets/",
+    "gbdraw/web/tutorial-data/",
+    "gbdraw/web/vendor/",
+    "gbdraw/web/wasm/",
+)
+
+_BROWSER_WHEEL_FORBIDDEN_FILES = {
+    "gbdraw/web/index.html",
+    "gbdraw/web/open-source-notices.html",
+}
+
+_BROWSER_WHEEL_ALLOWED_FILES = {
+    "gbdraw/web/js/services/standalone-interactivity-assets.js",
+}
+
+
+def is_browser_wheel_build() -> bool:
+    return os.environ.get(BROWSER_WHEEL_BUILD_ENV) == "1"
+
+
+def get_package_data_patterns(*, include_browser_wheel: bool) -> list[str]:
+    patterns = list(_PYTHON_RUNTIME_PACKAGE_DATA)
+    if not is_browser_wheel_build():
+        patterns.extend(_WEB_APP_PACKAGE_DATA)
+    if include_browser_wheel and not is_browser_wheel_build():
+        patterns.insert(3, f"web/{expected_browser_wheel_name()}")
+    return patterns
+
+
+def get_excluded_package_data_patterns(*, include_browser_wheel: bool) -> list[str]:
+    excluded = ["bin/*/*"]
+    if not include_browser_wheel:
+        excluded.append("web/*.whl")
+    return excluded
+
+
+def read_project_version() -> str:
+    pyproject_text = PYPROJECT_PATH.read_text(encoding="utf-8")
+    match = _PROJECT_VERSION_RE.search(pyproject_text)
+    if match is None:
+        raise RuntimeError(f"Could not determine project version from {PYPROJECT_PATH}")
+    return match.group(1)
+
+
+def expected_browser_wheel_name(version: str | None = None) -> str:
+    if version is None:
+        version = read_project_version()
+    return f"gbdraw-{version}-py3-none-any.whl"
+
+
+def read_browser_wheel_name_from_config() -> str:
+    config_text = CONFIG_PATH.read_text(encoding="utf-8")
+    match = _WHEEL_NAME_RE.search(config_text)
+    if match is None:
+        raise RuntimeError(f"Could not determine GBDRAW_WHEEL_NAME from {CONFIG_PATH}")
+    _, value = match.group(0).split("=", 1)
+    return value.strip().strip(";").strip().strip('"').strip("'")
+
+
+def generate_cache_bust_token() -> str:
+    return datetime.now().strftime("%Y%m%d-%H%M%S")
+
+
+def update_browser_wheel_config(*, wheel_name: str, cache_bust: str | None = None) -> None:
+    config_text = CONFIG_PATH.read_text(encoding="utf-8")
+    updated_text, replacements = _WHEEL_NAME_RE.subn(
+        lambda match: f'{match.group(1)}{wheel_name}{match.group(2)}',
+        config_text,
+        count=1,
+    )
+    if replacements != 1:
+        raise RuntimeError(f"Could not update GBDRAW_WHEEL_NAME in {CONFIG_PATH}")
+    if cache_bust is not None:
+        updated_text, cache_bust_replacements = _WHEEL_CACHE_BUST_RE.subn(
+            lambda match: f'{match.group(1)}{cache_bust}{match.group(2)}',
+            updated_text,
+            count=1,
+        )
+        if cache_bust_replacements != 1:
+            raise RuntimeError(f"Could not update GBDRAW_WHEEL_CACHE_BUST in {CONFIG_PATH}")
+    if updated_text != config_text:
+        CONFIG_PATH.write_text(updated_text, encoding="utf-8")
+
+
+def refresh_open_source_notices() -> None:
+    generator_path = REPO_ROOT / "tools" / "generate_open_source_notices.py"
+    spec = spec_from_file_location("gbdraw_generate_open_source_notices", generator_path)
+    if spec is None or spec.loader is None:
+        raise RuntimeError(f"Could not load open source notices generator from {generator_path}")
+
+    module = module_from_spec(spec)
+    sys.modules[spec.name] = module
+    spec.loader.exec_module(module)
+    module.write_open_source_notices()
+
+
+def inspect_browser_wheel_payload(path: Path) -> None:
+    if path.stat().st_size > BROWSER_WHEEL_MAX_BYTES:
+        raise RuntimeError(
+            f"Browser wheel {path.relative_to(REPO_ROOT)} is too large: "
+            f"{path.stat().st_size} bytes, expected at most {BROWSER_WHEEL_MAX_BYTES}. "
+            "Run `python tools/prepare_browser_wheel.py`."
+        )
+
+    with zipfile.ZipFile(path) as zf:
+        names = set(zf.namelist())
+
+    forbidden = sorted(
+        name
+        for name in names
+        if name in _BROWSER_WHEEL_FORBIDDEN_FILES
+        or (
+            name not in _BROWSER_WHEEL_ALLOWED_FILES
+            and any(name.startswith(prefix) for prefix in _BROWSER_WHEEL_FORBIDDEN_PREFIXES)
+        )
+        or (name.startswith("gbdraw/web/gbdraw-") and name.endswith(".whl"))
+    )
+    if forbidden:
+        preview = "\n".join(forbidden[:20])
+        if len(forbidden) > 20:
+            preview += f"\n... and {len(forbidden) - 20} more"
+        raise RuntimeError(
+            "Browser wheel contains hosted web assets that should remain outside the "
+            "Pyodide runtime wheel:\n"
+            f"{preview}\n"
+            "Run `python tools/prepare_browser_wheel.py`."
+        )
+
+    required = {
+        "gbdraw/data/color_palettes.toml",
+        "gbdraw/data/config.toml",
+        "gbdraw/web/js/services/standalone-interactivity-assets.js",
+    }
+    missing = sorted(required - names)
+    if missing:
+        raise RuntimeError(
+            "Browser wheel is missing required Python runtime package data:\n"
+            + "\n".join(missing)
+            + "\nRun `python tools/prepare_browser_wheel.py`."
+        )
+
+
+def validate_browser_wheel_prepared() -> Path:
+    expected_name = expected_browser_wheel_name()
+    expected_path = WEB_ROOT / expected_name
+    existing_wheels = sorted(WEB_ROOT.glob("gbdraw-*.whl"))
+
+    if not expected_path.exists():
+        raise FileNotFoundError(
+            f"Missing browser wheel {expected_path.relative_to(REPO_ROOT)}. "
+            "Run `python tools/prepare_browser_wheel.py`."
+        )
+
+    unexpected_wheels = [path.name for path in existing_wheels if path.name != expected_name]
+    if unexpected_wheels:
+        raise RuntimeError(
+            "Unexpected browser wheel files in gbdraw/web: "
+            f"{', '.join(unexpected_wheels)}. Run `python tools/prepare_browser_wheel.py` to refresh them."
+        )
+
+    configured_name = read_browser_wheel_name_from_config()
+    if configured_name != expected_name:
+        raise RuntimeError(
+            f"gbdraw/web/js/config.js points to {configured_name}, expected {expected_name}. "
+            "Run `python tools/prepare_browser_wheel.py`."
+        )
+
+    inspect_browser_wheel_payload(expected_path)
+    return expected_path

gbdraw/_web_assets.py

@@ -0,0 +1,197 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+from pathlib import Path
+
+
+REPO_ROOT = Path(__file__).resolve().parents[1]
+WEB_ROOT = REPO_ROOT / "gbdraw" / "web"
+VENDOR_ROOT = WEB_ROOT / "vendor"
+PYODIDE_RUNTIME_DIR = VENDOR_ROOT / "pyodide" / "v0.29.0" / "full"
+
+# The Vue build that index.html loads: the global production build, which
+# still contains the template compiler that the in-DOM templates need.
+VUE_RUNTIME_FILE = Path("vendor") / "vue" / "vue.global.prod.js"
+
+ASSET_URLS = {
+    "vue": f"https://unpkg.com/vue@3.5.25/dist/{VUE_RUNTIME_FILE.name}",
+    "pyodide_core": "https://github.com/pyodide/pyodide/releases/download/0.29.0/pyodide-core-0.29.0.tar.bz2",
+    "micropip": "https://cdn.jsdelivr.net/pyodide/v0.29.0/full/micropip-0.11.0-py3-none-any.whl",
+    "tzdata": "https://cdn.jsdelivr.net/pyodide/v0.29.0/full/tzdata-2025.2-py2.py3-none-any.whl",
+    "browser_wasi_shim": "https://registry.npmjs.org/@bjorn3/browser_wasi_shim/-/browser_wasi_shim-0.4.2.tgz",
+    "jspdf": "https://registry.npmjs.org/jspdf/-/jspdf-3.0.3.tgz",
+    "svg2pdf": "https://registry.npmjs.org/svg2pdf.js/-/svg2pdf.js-2.6.0.tgz",
+    "dompurify": "https://registry.npmjs.org/dompurify/-/dompurify-3.2.7.tgz",
+    "phosphor": "https://registry.npmjs.org/@phosphor-icons/web/-/web-2.1.2.tgz",
+    "inter": "https://registry.npmjs.org/@fontsource/inter/-/inter-5.2.8.tgz",
+    "noto_sans_jp": "https://registry.npmjs.org/@fontsource/noto-sans-jp/-/noto-sans-jp-5.2.9.tgz",
+}
+
+PYODIDE_CORE_FILES = {
+    "package.json",
+    "pyodide.asm.js",
+    "pyodide.asm.wasm",
+    "pyodide.js",
+    "pyodide.mjs",
+    "pyodide-lock.json",
+    "python_stdlib.zip",
+}
+
+PYODIDE_RUNTIME_PACKAGE_WHEELS = {
+    "micropip": "micropip-0.11.0-py3-none-any.whl",
+    "tzdata": "tzdata-2025.2-py2.py3-none-any.whl",
+}
+
+PYODIDE_LOCAL_WHEELS = (
+    Path("vendor") / "pyodide-wheels" / "six-1.17.0-py2.py3-none-any.whl",
+    Path("vendor") / "pyodide-wheels" / "python_dateutil-2.9.0.post0-py2.py3-none-any.whl",
+    Path("vendor") / "pyodide-wheels" / "pytz-2025.2-py2.py3-none-any.whl",
+    Path("vendor") / "pyodide-wheels" / "numpy-2.2.5-cp313-cp313-pyodide_2025_0_wasm32.whl",
+    Path("vendor") / "pyodide-wheels" / "biopython-1.85-cp313-cp313-pyodide_2025_0_wasm32.whl",
+    Path("vendor") / "pyodide-wheels" / "fonttools-4.56.0-py3-none-any.whl",
+    Path("vendor") / "pyodide-wheels" / "svgwrite-1.4.3-py3-none-any.whl",
+    Path("vendor") / "pyodide-wheels" / "bcbio_gff-0.7.1-py3-none-any.whl",
+    Path("vendor") / "pyodide-wheels" / "pandas-2.3.2-cp313-cp313-pyodide_2025_0_wasm32.whl",
+)
+
+PYODIDE_RUNTIME_WHEELS = tuple(
+    Path("vendor") / "pyodide" / "v0.29.0" / "full" / filename
+    for filename in PYODIDE_RUNTIME_PACKAGE_WHEELS.values()
+)
+
+PYODIDE_BUNDLED_WHEELS = PYODIDE_LOCAL_WHEELS + PYODIDE_RUNTIME_WHEELS
+
+UI_FONT_ASSETS = {
+    "inter": (
+        "inter-latin-300-normal.woff2",
+        "inter-latin-400-normal.woff2",
+        "inter-latin-500-normal.woff2",
+        "inter-latin-600-normal.woff2",
+        "inter-latin-700-normal.woff2",
+        "inter-vietnamese-300-normal.woff2",
+        "inter-vietnamese-400-normal.woff2",
+        "inter-vietnamese-500-normal.woff2",
+        "inter-vietnamese-600-normal.woff2",
+        "inter-vietnamese-700-normal.woff2",
+    ),
+    "noto-sans-jp": (
+        "noto-sans-jp-japanese-300-normal.woff2",
+        "noto-sans-jp-japanese-400-normal.woff2",
+        "noto-sans-jp-japanese-500-normal.woff2",
+        "noto-sans-jp-japanese-700-normal.woff2",
+    ),
+}
+
+REQUIRED_UI_FONT_FILES = tuple(
+    Path("vendor") / "fonts" / family / filename
+    for family, filenames in UI_FONT_ASSETS.items()
+    for filename in filenames
+)
+
+
+@dataclass(frozen=True)
+class WebAssetNotice:
+    display_name: str
+    version: str
+    license_expression: str
+    source_url: str
+    bundled_path: str
+    notice: str
+    license_text_anchors: tuple[str, ...] = ()
+
+
+WEB_ASSET_NOTICES = (
+    WebAssetNotice(
+        display_name="Vue.js",
+        version="3.5.25",
+        license_expression="MIT",
+        source_url=ASSET_URLS["vue"],
+        bundled_path=VUE_RUNTIME_FILE.as_posix(),
+        notice="Copyright (c) 2018-present Yuxi (Evan) You and Vue contributors.",
+        license_text_anchors=("license-mit",),
+    ),
+    WebAssetNotice(
+        display_name="Tailwind CSS (generated stylesheet)",
+        version="3.4.17",
+        license_expression="MIT",
+        source_url="https://tailwindcss.com",
+        bundled_path="css/tailwind.css",
+        notice=(
+            "Copyright (c) Tailwind Labs, Inc. The stylesheet is generated with the "
+            "Tailwind CSS compiler and contains its base styles (Preflight)."
+        ),
+        license_text_anchors=("license-mit",),
+    ),
+    WebAssetNotice(
+        display_name="Pyodide core runtime",
+        version="0.29.0",
+        license_expression="MPL-2.0",
+        source_url=ASSET_URLS["pyodide_core"],
+        bundled_path="vendor/pyodide/v0.29.0/full/",
+        notice="The local Pyodide package.json declares MPL-2.0.",
+        license_text_anchors=("license-mpl-2.0",),
+    ),
+    WebAssetNotice(
+        display_name="browser_wasi_shim",
+        version="0.4.2",
+        license_expression="MIT OR Apache-2.0",
+        source_url=ASSET_URLS["browser_wasi_shim"],
+        bundled_path="vendor/browser_wasi_shim/dist/",
+        notice="The package metadata identifies the author as bjorn3.",
+        license_text_anchors=("license-mit", "license-apache-2.0"),
+    ),
+    WebAssetNotice(
+        display_name="jsPDF",
+        version="3.0.3",
+        license_expression="MIT",
+        source_url=ASSET_URLS["jspdf"],
+        bundled_path="vendor/jspdf/jspdf.umd.min.js",
+        notice="Copyright (c) 2010-2025 James Hall and contributors.",
+        license_text_anchors=("license-mit",),
+    ),
+    WebAssetNotice(
+        display_name="svg2pdf.js",
+        version="2.6.0",
+        license_expression="MIT",
+        source_url=ASSET_URLS["svg2pdf"],
+        bundled_path="vendor/svg2pdf.js/svg2pdf.umd.min.js",
+        notice="Authored by the yFiles for HTML Support Team at yWorks.",
+        license_text_anchors=("license-mit",),
+    ),
+    WebAssetNotice(
+        display_name="DOMPurify",
+        version="3.2.7",
+        license_expression="MPL-2.0 OR Apache-2.0",
+        source_url=ASSET_URLS["dompurify"],
+        bundled_path="vendor/dompurify/purify.min.js",
+        notice="The distributed header identifies Cure53 and other contributors.",
+        license_text_anchors=("license-mpl-2.0", "license-apache-2.0"),
+    ),
+    WebAssetNotice(
+        display_name="Phosphor Icons Web",
+        version="2.1.2",
+        license_expression="MIT",
+        source_url=ASSET_URLS["phosphor"],
+        bundled_path="vendor/phosphor-icons/regular/",
+        notice="Package author: rektdeckard.",
+        license_text_anchors=("license-mit",),
+    ),
+    WebAssetNotice(
+        display_name="Inter font package",
+        version="Fontsource package 5.2.8",
+        license_expression="OFL-1.1",
+        source_url=ASSET_URLS["inter"],
+        bundled_path="vendor/fonts/inter/",
+        notice="Font package metadata identifies Google Inc. as the author.",
+        license_text_anchors=("license-ofl-1.1",),
+    ),
+    WebAssetNotice(
+        display_name="Noto Sans JP font package",
+        version="Fontsource package 5.2.9",
+        license_expression="OFL-1.1",
+        source_url=ASSET_URLS["noto_sans_jp"],
+        bundled_path="vendor/fonts/noto-sans-jp/",
+        notice="Font package metadata identifies Google Inc. as the author.",
+        license_text_anchors=("license-ofl-1.1",),
+    ),
+)

gbdraw/analysis/__init__.py

@@ -0,0 +1,49 @@
+"""Sequence / genome analysis helpers (internal)."""
+
+from .collinearity import (
+    CollinearityAnchor,
+    CollinearityAnchorMode,
+    CollinearityBlock,
+    CollinearityResult,
+    CollinearitySearchScope,
+    LosslessCollinearityParameters,
+    build_orthogroup_collinearity_blocks,
+    convert_collinearity_blocks_to_comparisons,
+    iter_collinearity_search_pairs,
+    normalize_collinearity_anchor_mode,
+    normalize_collinearity_search_scope,
+)
+from .depth import clear_depth_tsv_cache, depth_df, read_depth_tsv
+from .conservation import (
+    ConservationLoadResult,
+    ConservationSource,
+    ConservationTrack,
+    load_conservation_sources,
+    normalize_conservation_tracks_for_record,
+    resolve_conservation_reference_side,
+)
+
+__all__ = [
+    "CollinearityAnchor",
+    "CollinearityAnchorMode",
+    "CollinearityBlock",
+    "CollinearityResult",
+    "CollinearitySearchScope",
+    "LosslessCollinearityParameters",
+    "build_orthogroup_collinearity_blocks",
+    "convert_collinearity_blocks_to_comparisons",
+    "iter_collinearity_search_pairs",
+    "normalize_collinearity_anchor_mode",
+    "normalize_collinearity_search_scope",
+    "clear_depth_tsv_cache",
+    "ConservationLoadResult",
+    "ConservationSource",
+    "ConservationTrack",
+    "depth_df",
+    "load_conservation_sources",
+    "normalize_conservation_tracks_for_record",
+    "read_depth_tsv",
+    "resolve_conservation_reference_side",
+]
+
+