aignostics 0.2.62__tar.gz → 0.2.65__tar.gz

{aignostics-0.2.62 → aignostics-0.2.65}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aignostics
-Version: 0.2.62
+Version: 0.2.65
 Summary: 🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library.
 Project-URL: Homepage, https://aignostics.readthedocs.io/en/latest/
 Project-URL: Documentation, https://aignostics.readthedocs.io/en/latest/
@@ -50,12 +50,12 @@ Classifier: Typing :: Typed
 Requires-Python: <4.0,>=3.11
 Requires-Dist: appdirs>=1.4.4
 Requires-Dist: auth0-python>=4.10.0
-Requires-Dist: boto3>=1.38.36
+Requires-Dist: boto3>=1.38.39
 Requires-Dist: dicom-validator>=0.7.1
 Requires-Dist: dicomweb-client[gcp]>=0.59.2
 Requires-Dist: duckdb<=1.4.0,>=0.10.0
-Requires-Dist: fastapi[all,standard]>=0.115.12
-Requires-Dist: google-cloud-storage>=2.12.0
+Requires-Dist: fastapi[all,standard]>=0.115.13
+Requires-Dist: google-cloud-storage>=3.1.1
 Requires-Dist: google-crc32c>=1.7.1
 Requires-Dist: highdicom>=0.25.1
 Requires-Dist: httpx>=0.28.1
@@ -64,7 +64,7 @@ Requires-Dist: idc-index-data==21.0.0
 Requires-Dist: ijson>=3.4.0
 Requires-Dist: jsf>=0.11.2
 Requires-Dist: jsonschema>=4.24.0
-Requires-Dist: logfire[system-metrics]>=3.19.0
+Requires-Dist: logfire[system-metrics]>=3.21.1
 Requires-Dist: nicegui[native]>=2.20.0
 Requires-Dist: openslide-bin>=4.0.0.8
 Requires-Dist: openslide-python>=1.4.2
@@ -95,13 +95,13 @@ Requires-Dist: show-in-file-manager>=1.1.5
 Requires-Dist: tqdm>=4.67.1
 Requires-Dist: typer>=0.16.0
 Requires-Dist: uptime>=3.0.1
-Requires-Dist: urllib3>=2.2.3
+Requires-Dist: urllib3>=2.5.0
 Requires-Dist: wsidicom>=0.27.1
 Provides-Extra: jupyter
 Requires-Dist: jupyter>=1.1.1; extra == 'jupyter'
 Provides-Extra: marimo
 Requires-Dist: cloudpathlib>=0.21.1; extra == 'marimo'
-Requires-Dist: marimo>=0.13.15; extra == 'marimo'
+Requires-Dist: marimo>=0.14.0; extra == 'marimo'
 Requires-Dist: matplotlib>=3.10.3; extra == 'marimo'
 Requires-Dist: shapely>=2.1.0; extra == 'marimo'
 Provides-Extra: qupath

{aignostics-0.2.62 → aignostics-0.2.65}/examples/notebook.py

@@ -2,7 +2,7 @@
 # requires-python = ">=3.13"
 # dependencies = [
 #     "marimo",
-#     "aignostics==0.2.62",
+#     "aignostics==0.2.65",
 # ]
 # ///
 

{aignostics-0.2.62 → aignostics-0.2.65}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "aignostics"
-version = "0.2.62"
+version = "0.2.65"
 description = "🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library."
 readme = "README.md"
 authors = [
@@ -74,8 +74,8 @@ requires-python = ">=3.11, <4.0"
 
 dependencies = [
     # From Template
-    "fastapi[standard,all]>=0.115.12",
-    "logfire[system-metrics]>=3.19.0",
+    "fastapi[standard,all]>=0.115.13",
+    "logfire[system-metrics]>=3.21.1",
     "nicegui[native]>=2.20.0",
     "opentelemetry-instrumentation-fastapi>=0.53b0",
     "opentelemetry-instrumentation-httpx>=0.53b0",
@@ -94,11 +94,11 @@ dependencies = [
     # Custom
     "appdirs>=1.4.4",
     "auth0-python>=4.10.0",
-    "boto3>=1.38.36",
+    "boto3>=1.38.39",
     "dicom-validator>=0.7.1",
     "dicomweb-client[gcp]>=0.59.2",
     "duckdb>=0.10.0,<=1.4.0",
-    "google-cloud-storage>=2.12.0",
+    "google-cloud-storage>=3.1.1",
     "google-crc32c>=1.7.1",
     "highdicom>=0.25.1",
     "httpx>=0.28.1",
@@ -124,7 +124,7 @@ dependencies = [
     "shapely>=2.1.1",
     "show-in-file-manager>=1.1.5",
     "tqdm>=4.67.1",
-    "urllib3>=2.2.3",
+    "urllib3>=2.5.0",
     "wsidicom>=0.27.1",
 ]
 
@@ -132,7 +132,7 @@ dependencies = [
 jupyter = ["jupyter>=1.1.1"]
 marimo = [
     "cloudpathlib>=0.21.1",
-    "marimo>=0.13.15",
+    "marimo>=0.14.0",
     "matplotlib>=3.10.3",
     "shapely>=2.1.0",
 ]
@@ -153,10 +153,10 @@ dev = [
     "pip-licenses @ git+https://github.com/neXenio/pip-licenses.git@master", # https://github.com/raimon49/pip-licenses/pull/224
     "pre-commit>=4.1.0",
     "pyinstaller>=6.14.0",
-    "pyright>=1.1.401",
-    "pytest>=8.4.0",
+    "pyright>=1.1.402",
+    "pytest>=8.4.1",
     "pytest-asyncio>=1.0.0",
-    "pytest-cov>=6.1.1",
+    "pytest-cov>=6.2.1",
     "pytest-docker>=3.2.2",
     "pytest-env>=1.1.5",
     "pytest-md-report>=0.7.0",
@@ -167,7 +167,7 @@ dev = [
     "pytest-timeout>=2.4.0",
     "pytest-watcher>=0.4.3",
     "pytest-xdist[psutil]>=3.7.0",
-    "ruff>=0.11.12",
+    "ruff>=0.12.0",
     "scalene>=1.5.51",
     "sphinx>=8.2.3",
     "sphinx-autobuild>=2024.10.3",
@@ -182,7 +182,7 @@ dev = [
     "swagger-plugin-for-sphinx>=5.1.0",
     "tomli>=2.1.0",
     "types-pyyaml>=6.0.12.20250516",
-    "types-requests>=2.32.0.20250602",
+    "types-requests>=2.32.4.20250611",
     "watchdog>=6.0.0",
 ]
 
@@ -215,6 +215,7 @@ override-dependencies = [ # https://github.com/astral-sh/uv/issues/4422
     "h11>=0.16.0",                      # CVE-2025-43859
     "tornado>=6.5.0",                   # CVE-2025-47287
     "jupyter-core>=5.8.1",              # CVE-2025-30167
+    "urllib3>=2.5.0",                   # CVE-2025-50181, CVE-2025-50182
 ]
 
 [tool.ruff]
@@ -352,7 +353,7 @@ source = ["src/"]
 
 
 [tool.bumpversion]
-current_version = "0.2.62"
+current_version = "0.2.65"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"

aignostics-0.2.65/src/aignostics/application/_gui/assets/.gitignore

@@ -0,0 +1 @@
+orig

aignostics-0.2.65/src/aignostics/bucket/_cli.py

@@ -0,0 +1,324 @@
+"""CLI of bucket module."""
+
+from __future__ import annotations
+
+import datetime
+import json
+import sys
+from pathlib import Path  # noqa: TC003
+from typing import Annotated
+
+import humanize
+import typer
+
+from aignostics.utils import console, get_logger, get_user_data_directory
+
+from ._service import DownloadProgress, Service
+
+MESSAGE_NOT_YET_IMPLEMENTED = "NOT YET IMPLEMENTED"
+
+logger = get_logger(__name__)
+
+
+cli = typer.Typer(
+    name="bucket",
+    help="Operations on cloud bucket on Aignostics Platform.",
+)
+
+
+@cli.command()
+def upload(
+    source: Annotated[
+        Path,
+        typer.Argument(
+            help="Source file or directory to upload",
+            exists=True,
+            file_okay=True,
+            dir_okay=True,
+            writable=False,
+            readable=True,
+            resolve_path=False,
+        ),
+    ],
+    destination_prefix: Annotated[
+        str,
+        typer.Option(
+            help="Destination layout. Supports {username}, {timestamp}. "
+            'E.g. you might want to use "{username}/myproject/"'
+        ),
+    ] = "{username}",
+) -> None:
+    """Upload file or directory to bucket in Aignostics platform."""
+    import psutil  # noqa: PLC0415
+    from rich.progress import (  # noqa: PLC0415
+        BarColumn,
+        FileSizeColumn,
+        Progress,
+        TaskProgressColumn,
+        TextColumn,
+        TimeRemainingColumn,
+        TotalFileSizeColumn,
+        TransferSpeedColumn,
+    )
+
+    console.print(f"Uploading {source} to bucket...")
+
+    total_bytes = 0
+    files_count = 0
+
+    if source.is_file():
+        total_bytes = source.stat().st_size
+        files_count = 1
+    else:
+        for file_path in source.glob("**/*"):
+            if file_path.is_file():
+                total_bytes += file_path.stat().st_size
+                files_count += 1
+
+    console.print(f"Found {files_count} files with total size of {humanize.naturalsize(total_bytes)}")
+
+    username = psutil.Process().username()
+    timestamp = datetime.datetime.now(tz=datetime.UTC).strftime("%Y%m%d_%H%M%S")
+    base_prefix = destination_prefix.format(username=username, timestamp=timestamp)
+    base_prefix = base_prefix.strip("/")
+
+    with Progress(
+        TextColumn(
+            f"[progress.description]Uploading from {source.name} to "
+            f"{Service().get_bucket_protocol()}:/{Service().get_bucket_name()}/{base_prefix}"
+        ),
+        BarColumn(),
+        TaskProgressColumn(),
+        TimeRemainingColumn(),
+        FileSizeColumn(),
+        TotalFileSizeColumn(),
+        TransferSpeedColumn(),
+        TextColumn("[progress.description]{task.description}"),
+    ) as progress:
+        task = progress.add_task(f"Uploading to {base_prefix}/...", total=total_bytes)
+
+        def update_progress(bytes_uploaded: int, file: Path) -> None:
+            relpath = file.relative_to(source)
+            progress.update(task, advance=bytes_uploaded, description=f"{relpath}")
+
+        results = Service().upload(source, base_prefix, update_progress)
+
+    if results["success"]:
+        console.print(f"[green]Successfully uploaded {len(results['success'])} files:[/green]")
+        for key in results["success"]:
+            console.print(f"  [green]- {key}[/green]")
+
+    if results["failed"]:
+        console.print(f"[red]Failed to upload {len(results['failed'])} files:[/red]")
+        for key in results["failed"]:
+            console.print(f"  [red]- {key}[/red]")
+
+    if not results["failed"]:
+        console.print("[green]All files uploaded successfully![/green]")
+
+
+@cli.command()
+def find(
+    what: Annotated[
+        list[str] | None,
+        typer.Argument(help="Patterns or keys to match object keys against - all if not specified."),
+    ] = None,
+    what_is_key: Annotated[
+        bool,
+        typer.Option(
+            help="Specify if 'what' is a single object key. If not specified, 'what' is treated as a regex pattern.",
+        ),
+    ] = False,
+    detail: Annotated[bool, typer.Option(help="Show details")] = False,
+    signed_urls: Annotated[bool, typer.Option("--signed-urls", help="Include signed download URLs")] = False,
+) -> None:
+    """Find objects in bucket on Aignostics Platform."""
+    try:
+        result = Service().find(what, what_is_key, detail, signed_urls)
+        console.print_json(json=json.dumps(result, default=str))
+    except ValueError as e:
+        msg = f"Failed to find objects matching {what or 'all'}: {e!s}"
+        logger.exception(msg)
+        console.print(f"[red]Error:[/red] {e}")
+        sys.exit(2)
+
+
+@cli.command()
+def download(
+    what: Annotated[
+        list[str] | None,
+        typer.Argument(help="Patterns or keys to match object keys against - all if not specified."),
+    ] = None,
+    what_is_key: Annotated[
+        bool,
+        typer.Option(
+            help="Specify if 'what' is a single object key. If not specified, 'what' is treated as a regex pattern.",
+        ),
+    ] = False,
+    destination: Annotated[
+        Path,
+        typer.Option(
+            help="Destination directory to download the matching objects to.",
+            exists=False,
+            file_okay=False,
+            dir_okay=True,
+            writable=True,
+            readable=True,
+            resolve_path=True,
+        ),
+    ] = get_user_data_directory("bucket_downloads"),  # noqa: B008
+) -> None:
+    """Download objects from bucket in Aignostics platform to local directory."""
+    service = Service()
+
+    try:
+        matched_objects = service.find(what, what_is_key)
+        if not matched_objects:
+            console.print(f"[warning]No objects found matching {what or 'all'}[/warning]")
+            return
+    except ValueError as e:
+        msg = f"Failed to find objects matching {what or 'all'} on download to {destination}: {e!s}"
+        logger.exception(msg)
+        console.print(f"[red]Error:[/red] {e}")
+        sys.exit(2)
+
+    from rich.console import Group  # noqa: PLC0415
+    from rich.live import Live  # noqa: PLC0415
+    from rich.panel import Panel  # noqa: PLC0415
+    from rich.progress import (  # noqa: PLC0415
+        BarColumn,
+        FileSizeColumn,
+        Progress,
+        TaskID,
+        TaskProgressColumn,
+        TextColumn,
+        TimeElapsedColumn,
+        TimeRemainingColumn,
+        TotalFileSizeColumn,
+        TransferSpeedColumn,
+    )
+
+    main_progress = Progress(
+        BarColumn(),
+        TaskProgressColumn(),
+        TimeElapsedColumn(),
+        TextColumn("[progress.description]{task.description}"),
+    )
+
+    file_progress = Progress(
+        BarColumn(),
+        TaskProgressColumn(),
+        TimeElapsedColumn(),
+        TimeRemainingColumn(),
+        FileSizeColumn(),
+        TotalFileSizeColumn(),
+        TransferSpeedColumn(),
+        TextColumn("[progress.description]{task.description}"),
+    )
+
+    progress_group = Panel(
+        Group(main_progress, file_progress),
+        title=f"Download objects matching {what or 'all'}",
+        subtitle=f"Destination '{destination}'",
+    )
+
+    current_file_task: TaskID | None = None
+    main_task = main_progress.add_task("", total=len(matched_objects))
+
+    def progress_callback(progress: DownloadProgress) -> None:
+        nonlocal current_file_task
+        main_progress.update(
+            main_task,
+            completed=progress.overall_processed,
+            description=f"Object {progress.overall_current} of {progress.overall_total}",
+        )
+
+        if progress.current_file_key:
+            file_description = f"{progress.current_file_key}"
+            if current_file_task is None:
+                current_file_task = file_progress.add_task(file_description, total=progress.current_file_size)
+            file_progress.update(
+                current_file_task,
+                completed=progress.current_file_downloaded,
+                total=progress.current_file_size,
+                description=file_description,
+            )
+        elif current_file_task is not None:
+            file_progress.remove_task(current_file_task)
+            current_file_task = None
+
+    try:
+        with Live(progress_group, console=console, refresh_per_second=10, transient=True):
+            result = service.download(what, destination, what_is_key, progress_callback)
+    except ValueError as e:
+        msg = f"Failed to download objects matching {what or 'all'} to {destination}: {e!s}"
+        logger.exception(msg)
+        console.print(f"[red]Error:[/red] {e!s}")
+        sys.exit(2)
+
+    for downloaded_path in result.downloaded:
+        console.print(f"[green]✓[/green] Downloaded: {downloaded_path.name}")
+
+    for failed_key in result.failed:
+        console.print(f"[red]✗[/red] Failed: {failed_key}")
+
+    console.print(
+        f"[bold]Summary:[/bold] [success]{result.downloaded_count}[/success] downloaded, "
+        f"[error]{result.failed_count}[/error] failed, [info]{result.total_count}[/info] total"
+    )
+
+
+@cli.command()
+def delete(
+    what: Annotated[
+        list[str],
+        typer.Argument(help="Patterns or keys to match object keys against."),
+    ],
+    what_is_key: Annotated[
+        bool,
+        typer.Option(
+            help="Specify if 'what' is a single object key. If not specified, 'what' is treated as a regex pattern.",
+        ),
+    ] = False,
+    dry_run: Annotated[
+        bool,
+        typer.Option(
+            help="If set, only determines number of items that would be deleted, without actually deleting.",
+        ),
+    ] = True,
+) -> None:
+    """Delete objects in bucket on Aignostics Platform."""
+    try:
+        deleted_count = Service().delete(what, what_is_key, dry_run)
+        if deleted_count > 0:
+            action = "Would delete" if dry_run else "Deleted"
+            console.print(f"[green]✓[/green] {action} {deleted_count} object(s) matching {what}")
+        else:
+            console.print(f"[yellow]⚠[/yellow] No objects found matching pattern {what}")
+    except ValueError as e:
+        msg = f"Failed to delete objects matching {what}: {e!s}"
+        logger.exception(msg)
+        console.print(f"[red]Error:[/red] {e}")
+        sys.exit(2)
+
+
+@cli.command()
+def purge(
+    dry_run: Annotated[
+        bool,
+        typer.Option(help="If set, only determines number of items that would be deleted, without actually deleting."),
+    ] = True,
+) -> None:
+    """Purge all objects in bucket on Aignostics Platform."""
+    try:
+        deleted_count = Service().delete(what=None, what_is_key=False, dry_run=dry_run)
+        if deleted_count > 0:
+            action = "Would purge bucket by deleting" if dry_run else "Purged bucket by deleting"
+            console.print(f"[green]✓[/green] {action} {deleted_count} object(s)")
+        else:
+            console.print("[yellow]⚠[/yellow] No objects found to purge.")
+    except ValueError as e:
+        msg = f"Failed to purge bucket: {e!s}"
+        logger.exception(msg)
+        console.print(f"[red]Error:[/red] {e}")
+        sys.exit(2)