tfbpshiny 1.0.0__py3-none-any.whl

tfbpshiny/__main__.py

@@ -0,0 +1,215 @@
+from __future__ import annotations
+
+import argparse
+import logging
+import os
+import pathlib
+import sys
+from typing import Literal, cast
+
+from shiny import run_app
+
+from tfbpshiny.configure_logger import LogLevel, configure_logger
+
+_DEFAULT_VIRTUALDB_CONFIG = str(
+    __import__("pathlib").Path(__file__).parent / "brentlab_yeast_collection.yaml"
+)
+
+_DEFAULT_CACHE_DIR = "./tfbpshiny_hf_cache"
+
+
+def _apply_cache_dir(cache_dir: str) -> None:
+    """
+    Set ``HF_CACHE_DIR`` to the resolved absolute path before any HF imports.
+
+    Must be called before importing labretriever or huggingface_hub so that
+    ``snapshot_download`` and ``VirtualDB`` see the overridden path.
+
+    :param cache_dir: Path to the HuggingFace cache directory.
+
+    """
+    os.environ["HF_CACHE_DIR"] = str(pathlib.Path(cache_dir).resolve())
+
+
+def _run_initialize(
+    virtualdb_config: str,
+    hf_token: str | None,
+    log_level: int,
+    log_handler: Literal["console", "file"],
+) -> None:
+    """
+    Download all dataset files into the local HuggingFace cache and verify views.
+
+    Exits the process with code 1 if any download or view-verification step fails.
+
+    :param virtualdb_config: Path to the VirtualDB YAML config file.
+    :param hf_token: Optional HuggingFace token for private repo access.
+    :param log_level: Numeric logging level (e.g. ``logging.INFO``).
+    :param log_handler: Handler type passed to :func:`configure_logger`.
+
+    """
+    from tfbpshiny.utils.vdb_init import initialize_data
+
+    configure_logger("shiny", level=log_level, handler_type=log_handler)
+    logger = logging.getLogger("shiny")
+
+    cache_msg = os.environ.get("HF_CACHE_DIR", "(huggingface default)")
+    logger.info("Downloading all datasets into HuggingFace cache: %s", cache_msg)
+    try:
+        vdb, _ = initialize_data(virtualdb_config, hf_token, local_files_only=False)
+    except Exception:
+        logger.exception("Cache initialization failed.")
+        sys.exit(1)
+
+    logger.info("Verifying all dataset views are readable...")
+    views_df = vdb.query(
+        "SELECT view_name FROM duckdb_views()"
+        " WHERE schema_name = 'main'"
+        "   AND view_name NOT LIKE 'duckdb_%'"
+        "   AND view_name NOT LIKE 'sqlite_%'"
+        "   AND view_name NOT LIKE 'pragma_%'"
+        " ORDER BY view_name"
+    )
+    view_names = views_df["view_name"].tolist()
+    failed: list[str] = []
+    for view_name in view_names:
+        try:
+            df = vdb.query(f'SELECT * FROM "{view_name}" LIMIT 1')
+            logger.info("  OK  %-30s  (%d col(s))", view_name, len(df.columns))
+        except Exception:
+            logger.exception("  FAIL %s", view_name)
+            failed.append(view_name)
+
+    if failed:
+        logger.error("Verification failed for: %s", ", ".join(failed))
+        sys.exit(1)
+
+    logger.info("Cache initialization complete.")
+
+
+def run_launch(args: argparse.Namespace) -> None:
+    """
+    Download the dataset cache (unless ``--skip-initialize`` is set), then start the
+    app.
+
+    By default uses ``./tfbpshiny_hf_cache`` as the HuggingFace cache directory so
+    a plain ``python -m tfbpshiny launch`` is self-contained: it downloads data on
+    first run and serves it on subsequent runs from the same local directory.
+
+    """
+    cache_dir: str = args.cache_dir
+    _apply_cache_dir(cache_dir)
+
+    log_level = LogLevel.from_string(args.log_level)
+    hf_token: str | None = os.getenv("HF_TOKEN")
+
+    if not args.skip_initialize:
+        _run_initialize(
+            virtualdb_config=args.virtualdb_config,
+            hf_token=hf_token,
+            log_level=log_level.value,
+            log_handler=cast(Literal["console", "file"], args.log_handler),
+        )
+
+    # Env vars are the only reliable way to pass config to uvicorn reload workers,
+    # which re-import app.py in a subprocess and cannot see in-process mutations.
+    os.environ["TFBPSHINY_LOG_LEVEL"] = str(log_level.value)
+    os.environ["TFBPSHINY_LOG_HANDLER"] = args.log_handler
+    os.environ["VIRTUALDB_CONFIG"] = args.virtualdb_config
+    os.environ["TFBPSHINY_MATERIALIZE"] = "0" if args.no_materialize else "1"
+
+    kwargs: dict[str, object] = {"port": args.port, "host": args.host}
+    if args.debug:
+        kwargs.update({"reload": True, "reload_dirs": ["tfbpshiny/shiny_app"]})
+    run_app("tfbpshiny.app:app", **kwargs)  # type: ignore
+
+
+def make_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(
+        prog="tfbpshiny",
+        description=(
+            "tfbpshiny — TF Binding and Perturbation Explorer."
+            " Use --help after any command."
+        ),
+        epilog="Use 'tfbpshiny <command> --help' for more info on each command.",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    parser.add_argument(
+        "--log-level",
+        type=str,
+        default="WARNING",
+        choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
+        help="Set logging level.",
+    )
+    parser.add_argument(
+        "--log-handler",
+        type=str,
+        default="console",
+        choices=["console", "file"],
+        help="Set log handler type.",
+    )
+    parser.add_argument(
+        "--virtualdb-config",
+        type=str,
+        default=_DEFAULT_VIRTUALDB_CONFIG,
+        help="Path to the VirtualDB YAML configuration file.",
+    )
+
+    subparsers = parser.add_subparsers(dest="command", required=True)
+
+    launch_parser = subparsers.add_parser(
+        "launch",
+        help="Download the dataset cache (first run) and start the Shiny app.",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    launch_parser.add_argument(
+        "--cache-dir",
+        type=str,
+        default=_DEFAULT_CACHE_DIR,
+        help=(
+            "HuggingFace cache directory. Datasets are downloaded here on first run "
+            "and read from here on subsequent runs. "
+            "Equivalent to setting HF_CACHE_DIR."
+        ),
+    )
+    launch_parser.add_argument(
+        "--skip-initialize",
+        action="store_true",
+        default=False,
+        help=(
+            "Skip the dataset download and verification step. "
+            "Use when the cache is already populated and you want a faster startup."
+        ),
+    )
+    launch_parser.add_argument(
+        "--no-materialize",
+        action="store_true",
+        default=False,
+        help=(
+            "Disable in-memory materialization of dataset views at startup. "
+            "Reduces startup memory at the cost of slower query performance. "
+            "Equivalent to setting TFBPSHINY_MATERIALIZE=0."
+        ),
+    )
+    launch_parser.add_argument(
+        "--port", type=int, default=8000, help="Port to serve the Shiny app on."
+    )
+    launch_parser.add_argument(
+        "--host", type=str, default="127.0.0.1", help="Host to bind the Shiny app."
+    )
+    launch_parser.add_argument(
+        "--debug", action="store_true", help="Enable debug mode with auto-reload."
+    )
+    launch_parser.set_defaults(func=run_launch)
+
+    return parser
+
+
+def main() -> None:
+    parser = make_parser()
+    args = parser.parse_args()
+    args.func(args)
+
+
+if __name__ == "__main__":
+    main()

tfbpshiny/app.css

@@ -0,0 +1,344 @@
+/* --- Custom properties -------------------------------------------------- */
+:root {
+    --color-primary: #2C7A7B;
+    --color-primary-dark: #1A5456;
+    --color-border: #E2E8F0;
+    --color-text: #1A202C;
+
+    --radius-sm: 6px;
+
+    --font-size-label: 0.875rem;
+    --transition-fast: 150ms ease;
+}
+
+/* --- Group headers ------------------------------------------------------ */
+.group-header {
+    font-size: var(--font-size-label);
+    font-weight: 700;
+    letter-spacing: 0.04em;
+    color: var(--color-text);
+    padding: 12px 0 2px;
+    margin-top: 4px;
+    margin-bottom: 12px;
+}
+
+/* --- Empty / instruction state ------------------------------------------ */
+.empty-state {
+    display: flex;
+    flex-direction: column;
+    align-items: center;
+    justify-content: center;
+    padding: 64px 24px;
+    text-align: center;
+    color: var(--color-text);
+}
+
+.empty-state.compact {
+    padding: 20px 12px;
+}
+
+/* --- Selection sidebar -------------------------------------------------- */
+.sidebar-text {
+    color: var(--color-text);
+}
+
+/* Dataset row: grid with toggle+label taking remaining space, filter button
+   pinned to a fixed-width right column so all buttons align vertically. */
+.selection-sidebar .dataset-row {
+    display: grid;
+    grid-template-columns: 1fr 52px;
+    align-items: center;
+    gap: 0.5rem;
+    padding: 0.125rem 0;
+}
+
+.selection-sidebar .dataset-row-label {
+    overflow: hidden;
+    text-overflow: ellipsis;
+    white-space: nowrap;
+}
+
+.selection-sidebar .btn-filter-dataset {
+    width: 100%;
+    font-size: var(--font-size-label);
+    padding: 0.125rem 0.4rem;
+    line-height: 1.4;
+    border-radius: 3px;
+    text-align: center;
+}
+
+.selection-sidebar .btn-filter-dataset.btn-filter-active {
+    color: #fff;
+    background-color: #0d6efd;
+    border-color: #0d6efd;
+}
+
+.selection-sidebar .dataset-list {
+    display: flex;
+    flex-direction: column;
+    gap: 2px;
+}
+
+.btn-apply-pending {
+    display: block;
+    width: calc(100% - 16px);
+    margin: 8px 8px 0 8px;
+    padding: 6px 12px;
+    font-size: 0.85rem;
+    font-weight: 600;
+    color: #fff;
+    background-color: #dc3545;
+    border: none;
+    border-radius: 4px;
+    cursor: pointer;
+    transition: opacity 0.15s ease, background-color 0.15s ease;
+}
+
+.btn-apply-pending:hover {
+    background-color: #bb2d3b;
+}
+
+.btn-apply-pending--idle {
+    opacity: 0.35;
+    pointer-events: none;
+}
+
+
+/* Left cell: toggle + label as an inline flex row */
+.selection-sidebar .dataset-row-left {
+    display: flex;
+    align-items: center;
+    gap: 0.5rem;
+    min-width: 0;
+}
+
+/* Tighten up Shiny's switch input inside dataset rows */
+.selection-sidebar .dataset-row-left .shiny-input-container {
+    margin: 0;
+    width: auto;
+    flex: 0 0 auto;
+}
+
+.selection-sidebar .dataset-row-left .shiny-input-container .form-switch {
+    margin: 0;
+    min-height: 0;
+}
+
+.selection-sidebar .dataset-row-left .shiny-input-container .form-check-input {
+    margin-top: 0;
+}
+
+.selection-sidebar .dataset-row-left .shiny-input-container label {
+    display: none;
+}
+
+/* --- Intersection matrix ------------------------------------------------ */
+.matrix-summary-table {
+    width: 100%;
+    table-layout: fixed;
+    border-spacing: 0;
+    border-collapse: collapse;
+    font-size: var(--font-size-label);
+}
+
+.matrix-summary-table th,
+.matrix-summary-table td {
+    border-bottom: 1px solid #EDF2F7;
+    border-right: 1px solid #EDF2F7;
+}
+
+.matrix-summary-table .matrix-row-header {
+    position: sticky;
+    left: 0;
+    z-index: 2;
+    background: #F8FAFC;
+    text-align: left;
+    width: 20%;
+}
+
+.matrix-summary-table .matrix-col-header {
+    background: #F8FAFC;
+    text-align: center;
+}
+
+.matrix-summary-table .matrix-header-name {
+    font-size: var(--font-size-label);
+    font-weight: 700;
+    color: var(--color-text);
+    white-space: nowrap;
+    text-overflow: ellipsis;
+    overflow: hidden;
+    padding: 8px;
+}
+
+.matrix-summary-table .matrix-row-label {
+    position: sticky;
+    left: 0;
+    z-index: 1;
+    background: #FFFFFF;
+    font-size: var(--font-size-label);
+    font-weight: 600;
+    color: var(--color-text);
+    text-align: left;
+    padding: 10px 12px;
+}
+
+.matrix-summary-table .matrix-cell-empty {
+    background: #F8FAFC;
+}
+
+.matrix-summary-table .matrix-cell-diagonal {
+    background: #EBF8FF;
+    padding: 0;
+}
+
+.matrix-summary-table .matrix-cell-interactive {
+    padding: 0;
+}
+
+.matrix-summary-table .matrix-cell-diagonal:hover,
+.matrix-summary-table .matrix-cell-interactive:hover {
+    background: #4A5568;
+}
+
+.matrix-summary-table .matrix-cell-active {
+    background: #2B4C7E;
+}
+
+.matrix-summary-table .matrix-cell-active:hover {
+    background: #3A6098;
+}
+
+.matrix-summary-table .matrix-cell-active .matrix-cell-button {
+    color: #FFFFFF;
+}
+
+.matrix-summary-table .matrix-cell-pending {
+    background: #7B4F00;
+}
+
+.matrix-summary-table .matrix-cell-pending:hover {
+    background: #9A6300;
+}
+
+.matrix-summary-table .matrix-cell-pending .matrix-cell-button {
+    color: #FFFFFF;
+}
+
+/* --- Pending regulator filter banner ------------------------------------ */
+.pending-regulator-banner {
+    border: 1px solid #9A6300;
+    border-radius: var(--radius-sm);
+    background: #FFF8E7;
+    padding: 10px 14px;
+    margin-bottom: 12px;
+}
+
+.pending-regulator-banner-body {
+    display: flex;
+    align-items: center;
+    justify-content: space-between;
+    gap: 12px;
+    flex-wrap: wrap;
+}
+
+.pending-regulator-banner-text {
+    font-size: var(--font-size-label);
+    color: #5A3800;
+}
+
+.matrix-cell-button {
+    width: 100%;
+    height: 100%;
+    display: block;
+    padding: 10px 8px;
+    border: none;
+    background: transparent;
+    color: var(--color-text);
+    font-size: var(--font-size-label);
+    font-weight: 500;
+    font-variant-numeric: tabular-nums;
+    cursor: pointer;
+    text-align: center;
+    transition: color var(--transition-fast);
+}
+
+.matrix-summary-table .matrix-cell-diagonal:hover .matrix-cell-button,
+.matrix-summary-table .matrix-cell-interactive:hover .matrix-cell-button {
+    color: #FFFFFF;
+}
+
+/* --- GitHub repo badge -------------------------------------------------- */
+.github-badge {
+    display: inline-flex;
+    align-items: center;
+    padding: 4px 6px;
+    color: #fff;
+    font-weight: 500;
+    text-decoration: none;
+    white-space: nowrap;
+    flex-shrink: 0;
+}
+
+.github-badge:hover {
+    text-decoration: none;
+    color: #fff;
+    opacity: 0.85;
+}
+
+.github-badge-version {
+    margin-left: 6px;
+    padding: 1px 6px;
+    border-radius: 10px;
+    background: rgba(255,255,255,0.25);
+    color: #fff;
+    font-size: var(--font-size-label);
+    font-weight: 600;
+}
+
+/* --- Navbar brand title -------------------------------------------------- */
+.navbar-brand {
+    font-size: 1.15rem;
+    font-weight: 700;
+}
+
+/* --- Dataset tooltip ----------------------------------------------------- */
+.tooltip-inner {
+    max-width: 300px;
+    text-align: left;
+}
+
+/* --- Progressive-loading placeholders for comparison cells/tables -------- */
+.cd-cell-loading {
+    display: block;
+    width: 100%;
+    padding: 10px 8px;
+    text-align: center;
+    color: #A0AEC0;
+    font-size: var(--font-size-label);
+    animation: cd-pulse 1.4s ease-in-out infinite;
+}
+
+.cp-table-loading,
+.cm-table-loading {
+    padding: 12px 16px;
+    color: #A0AEC0;
+    font-size: var(--font-size-label);
+    animation: cd-pulse 1.4s ease-in-out infinite;
+}
+
+@keyframes cd-pulse {
+    0%, 100% { opacity: 1; }
+    50%       { opacity: 0.4; }
+}
+
+/* --- Pending-changes banner in binding/perturbation sidebars ------------- */
+.pending-banner {
+    background: #fff3cd;
+    border: 1px solid #ffc107;
+    border-radius: 4px;
+    padding: 0.5rem 0.75rem;
+    margin-bottom: 0.5rem;
+    font-size: 0.85rem;
+    color: #664d03;
+}