lamindb 0.76.7__py3-none-any.whl → 0.76.8__py3-none-any.whl

lamindb/core/datasets/_fake.py

@@ -1,36 +1,36 @@
-from __future__ import annotations
-
-
-def fake_bio_notebook_titles(n=100) -> list[str]:
-    """A fake collection of study titles."""
-    from faker import Faker
-
-    fake = Faker()
-
-    from faker_biology.mol_biol import Antibody
-    from faker_biology.physiology import CellType, Organ, Organelle
-
-    fake.add_provider(CellType)
-    fake.add_provider(Organ)
-    fake.add_provider(Organelle)
-    fake.add_provider(Antibody)
-
-    my_words = [
-        "study",
-        "investigate",
-        "research",
-        "result",
-        "cluster",
-        "rank",
-        "candidate",
-        "visualize",
-        "efficiency",
-        "classify",
-    ]
-    my_words += [fake.organ() for i in range(5)] + ["intestine", "intestinal"]
-    my_words += [fake.celltype() for i in range(10)]
-    my_words += [fake.antibody_isotype() for i in range(20)]
-
-    my_notebook_titles = [fake.sentence(ext_word_list=my_words) for i in range(n)]
-
-    return my_notebook_titles
+from __future__ import annotations
+
+
+def fake_bio_notebook_titles(n=100) -> list[str]:
+    """A fake collection of study titles."""
+    from faker import Faker
+
+    fake = Faker()
+
+    from faker_biology.mol_biol import Antibody
+    from faker_biology.physiology import CellType, Organ, Organelle
+
+    fake.add_provider(CellType)
+    fake.add_provider(Organ)
+    fake.add_provider(Organelle)
+    fake.add_provider(Antibody)
+
+    my_words = [
+        "study",
+        "investigate",
+        "research",
+        "result",
+        "cluster",
+        "rank",
+        "candidate",
+        "visualize",
+        "efficiency",
+        "classify",
+    ]
+    my_words += [fake.organ() for i in range(5)] + ["intestine", "intestinal"]
+    my_words += [fake.celltype() for i in range(10)]
+    my_words += [fake.antibody_isotype() for i in range(20)]
+
+    my_notebook_titles = [fake.sentence(ext_word_list=my_words) for i in range(n)]
+
+    return my_notebook_titles

lamindb/core/exceptions.py

@@ -1,77 +1,90 @@
-"""Exceptions.
-
-The registry base class:
-
-.. autosummary::
-   :toctree: .
-
-   DoesNotExist
-   ValidationError
-   NotebookNotSavedError
-   NoTitleError
-   MissingContextUID
-   UpdateContext
-   IntegrityError
-
-"""
-
-
-class TrackNotCalled(SystemExit):
-    pass
-
-
-class NotebookNotSaved(SystemExit):
-    pass
-
-
-class ValidationError(SystemExit):
-    """Validation error: not mapped in registry."""
-
-    pass
-
-
-# inspired by Django's DoesNotExist
-# equivalent to SQLAlchemy's NoResultFound
-class DoesNotExist(Exception):
-    """No record found."""
-
-    pass
-
-
-# -------------------------------------------------------------------------------------
-# ln.context.track() AKA context
-# -------------------------------------------------------------------------------------
-
-
-class IntegrityError(Exception):
-    """Integrity error.
-
-    For instance, it's not allowed to delete artifacts outside managed storage
-    locations.
-    """
-
-    pass
-
-
-class NotebookNotSavedError(Exception):
-    """Notebook wasn't saved."""
-
-    pass
-
-
-class NoTitleError(Exception):
-    """Notebook has no title."""
-
-    pass
-
-
-class MissingContextUID(SystemExit):
-    """User didn't define transform settings."""
-
-    pass
-
-
-class UpdateContext(SystemExit):
-    """Transform settings require update."""
-
-    pass
+"""Exceptions.
+
+.. autosummary::
+   :toctree: .
+
+   InvalidArgument
+   DoesNotExist
+   ValidationError
+   NotebookNotSavedError
+   NoTitleError
+   MissingContextUID
+   UpdateContext
+   IntegrityError
+
+"""
+
+# inheriting from SystemExit has the sole purpose of suppressing
+# the traceback - this isn't optimal but the current best solution
+# https://laminlabs.slack.com/archives/C04A0RMA0SC/p1726856875597489
+
+
+class InvalidArgument(SystemExit):
+    """Invalid method or function argument."""
+
+    pass
+
+
+class TrackNotCalled(SystemExit):
+    """ln.context.track() wasn't called."""
+
+    pass
+
+
+class NotebookNotSaved(SystemExit):
+    """Notebook wasn't saved."""
+
+    pass
+
+
+class ValidationError(SystemExit):
+    """Validation error: not mapped in registry."""
+
+    pass
+
+
+# inspired by Django's DoesNotExist
+# equivalent to SQLAlchemy's NoResultFound
+class DoesNotExist(Exception):
+    """No record found."""
+
+    pass
+
+
+# -------------------------------------------------------------------------------------
+# ln.context.track() AKA context
+# -------------------------------------------------------------------------------------
+
+
+class IntegrityError(Exception):
+    """Integrity error.
+
+    For instance, it's not allowed to delete artifacts outside managed storage
+    locations.
+    """
+
+    pass
+
+
+class NotebookNotSavedError(Exception):
+    """Notebook wasn't saved."""
+
+    pass
+
+
+class NoTitleError(Exception):
+    """Notebook has no title."""
+
+    pass
+
+
+class MissingContextUID(SystemExit):
+    """User didn't define transform settings."""
+
+    pass
+
+
+class UpdateContext(SystemExit):
+    """Transform settings require update."""
+
+    pass

lamindb/core/fields.py

@@ -1,12 +1,12 @@
-"""Fields.
-
-The field accessor of a :class:`~lamindb.core.Record`:
-
-.. autosummary::
-   :toctree: .
-
-   FieldAttr
-
-"""
-
-from lnschema_core.types import FieldAttr
+"""Fields.
+
+The field accessor of a :class:`~lamindb.core.Record`:
+
+.. autosummary::
+   :toctree: .
+
+   FieldAttr
+
+"""
+
+from lnschema_core.types import FieldAttr

lamindb/core/loaders.py

@@ -1,164 +1,164 @@
-"""Loaders in :class:`lamindb.Artifact.load`.
-
-.. autosummary::
-   :toctree: .
-
-   SUPPORTED_SUFFIXES
-   load_fcs
-   load_tsv
-   load_h5ad
-   load_h5mu
-   load_html
-   load_json
-   load_image
-   load_svg
-
-"""
-
-from __future__ import annotations
-
-import builtins
-import re
-from pathlib import Path
-from typing import TYPE_CHECKING
-
-import anndata as ad
-import pandas as pd
-from lamindb_setup.core.upath import (
-    create_path,
-    infer_filesystem,
-)
-
-from lamindb.core._settings import settings
-
-if TYPE_CHECKING:
-    import mudata as md
-    from lamindb_setup.core.types import UPathStr
-
-try:
-    from .storage._zarr import load_anndata_zarr
-except ImportError:
-
-    def load_anndata_zarr(storepath):  # type: ignore
-        raise ImportError("Please install zarr: pip install zarr")
-
-
-is_run_from_ipython = getattr(builtins, "__IPYTHON__", False)
-
-
-# tested in lamin-usecases
-def load_fcs(*args, **kwargs) -> ad.AnnData:
-    """Load an `.fcs` file to `AnnData`."""
-    try:
-        import readfcs
-    except ImportError:  # pragma: no cover
-        raise ImportError("Please install readfcs: pip install readfcs") from None
-    return readfcs.read(*args, **kwargs)
-
-
-def load_tsv(path: UPathStr, **kwargs) -> pd.DataFrame:
-    """Load `.tsv` file to `DataFrame`."""
-    path_sanitized = Path(path)
-    return pd.read_csv(path_sanitized, sep="\t", **kwargs)
-
-
-def load_h5ad(filepath, **kwargs) -> ad.AnnData:
-    """Load an `.h5ad` file to `AnnData`."""
-    fs, filepath = infer_filesystem(filepath)
-
-    with fs.open(filepath, mode="rb") as file:
-        adata = ad.read_h5ad(file, backed=False, **kwargs)
-        return adata
-
-
-def load_h5mu(filepath: UPathStr, **kwargs):
-    """Load an `.h5mu` file to `MuData`."""
-    import mudata as md
-
-    path_sanitized = Path(filepath)
-    return md.read_h5mu(path_sanitized, **kwargs)
-
-
-def load_html(path: UPathStr):
-    """Display `.html` in ipython, otherwise return path."""
-    if is_run_from_ipython:
-        with open(path, encoding="utf-8") as f:
-            html_content = f.read()
-        # Extract the body content using regular expressions
-        body_content = re.findall(
-            r"<body(?:.*?)>(?:.*?)</body>", html_content, re.DOTALL
-        )
-        # Remove any empty body tags
-        if body_content:
-            body_content = body_content[0]
-            body_content = body_content.strip()  # type: ignore
-        from IPython.display import HTML, display
-
-        display(HTML(data=body_content))
-    else:
-        return path
-
-
-def load_json(path: UPathStr) -> dict:
-    """Load `.json` to `dict`."""
-    import json
-
-    with open(path) as f:
-        data = json.load(f)
-    return data
-
-
-def load_image(path: UPathStr):
-    """Display `.svg` in ipython, otherwise return path."""
-    if is_run_from_ipython:
-        from IPython.display import Image, display
-
-        display(Image(filename=path))
-    else:
-        return path
-
-
-def load_svg(path: UPathStr) -> None | Path:
-    """Display `.svg` in ipython, otherwise return path."""
-    if is_run_from_ipython:
-        from IPython.display import SVG, display
-
-        display(SVG(filename=path))
-        return None
-    else:
-        return path
-
-
-FILE_LOADERS = {
-    ".csv": pd.read_csv,
-    ".tsv": load_tsv,
-    ".h5ad": load_h5ad,
-    ".parquet": pd.read_parquet,
-    ".fcs": load_fcs,
-    ".zarr": load_anndata_zarr,
-    ".html": load_html,
-    ".json": load_json,
-    ".h5mu": load_h5mu,
-    ".jpg": load_image,
-    ".png": load_image,
-    ".svg": load_svg,
-}
-
-SUPPORTED_SUFFIXES = list(FILE_LOADERS.keys())
-"""Suffixes with defined artifact loaders."""
-
-
-def load_to_memory(filepath: UPathStr, **kwargs):
-    """Load a file into memory.
-
-    Returns the filepath if no in-memory form is found.
-    """
-    filepath = create_path(filepath)
-
-    filepath = settings._storage_settings.cloud_to_local(filepath, print_progress=True)
-
-    loader = FILE_LOADERS.get(filepath.suffix)
-    if loader is None:
-        return filepath
-    else:
-        return loader(filepath, **kwargs)
+"""Loaders in :class:`lamindb.Artifact.load`.
+
+.. autosummary::
+   :toctree: .
+
+   SUPPORTED_SUFFIXES
+   load_fcs
+   load_tsv
+   load_h5ad
+   load_h5mu
+   load_html
+   load_json
+   load_image
+   load_svg
+
+"""
+
+from __future__ import annotations
+
+import builtins
+import re
+from pathlib import Path
+from typing import TYPE_CHECKING
+
+import anndata as ad
+import pandas as pd
+from lamindb_setup.core.upath import (
+    create_path,
+    infer_filesystem,
+)
+
+from lamindb.core._settings import settings
+
+if TYPE_CHECKING:
+    import mudata as md
+    from lamindb_setup.core.types import UPathStr
+
+try:
+    from .storage._zarr import load_anndata_zarr
+except ImportError:
+
+    def load_anndata_zarr(storepath):  # type: ignore
+        raise ImportError("Please install zarr: pip install zarr")
+
+
+is_run_from_ipython = getattr(builtins, "__IPYTHON__", False)
+
+
+# tested in lamin-usecases
+def load_fcs(*args, **kwargs) -> ad.AnnData:
+    """Load an `.fcs` file to `AnnData`."""
+    try:
+        import readfcs
+    except ImportError:  # pragma: no cover
+        raise ImportError("Please install readfcs: pip install readfcs") from None
+    return readfcs.read(*args, **kwargs)
+
+
+def load_tsv(path: UPathStr, **kwargs) -> pd.DataFrame:
+    """Load `.tsv` file to `DataFrame`."""
+    path_sanitized = Path(path)
+    return pd.read_csv(path_sanitized, sep="\t", **kwargs)
+
+
+def load_h5ad(filepath, **kwargs) -> ad.AnnData:
+    """Load an `.h5ad` file to `AnnData`."""
+    fs, filepath = infer_filesystem(filepath)
+
+    with fs.open(filepath, mode="rb") as file:
+        adata = ad.read_h5ad(file, backed=False, **kwargs)
+        return adata
+
+
+def load_h5mu(filepath: UPathStr, **kwargs):
+    """Load an `.h5mu` file to `MuData`."""
+    import mudata as md
+
+    path_sanitized = Path(filepath)
+    return md.read_h5mu(path_sanitized, **kwargs)
+
+
+def load_html(path: UPathStr):
+    """Display `.html` in ipython, otherwise return path."""
+    if is_run_from_ipython:
+        with open(path, encoding="utf-8") as f:
+            html_content = f.read()
+        # Extract the body content using regular expressions
+        body_content = re.findall(
+            r"<body(?:.*?)>(?:.*?)</body>", html_content, re.DOTALL
+        )
+        # Remove any empty body tags
+        if body_content:
+            body_content = body_content[0]
+            body_content = body_content.strip()  # type: ignore
+        from IPython.display import HTML, display
+
+        display(HTML(data=body_content))
+    else:
+        return path
+
+
+def load_json(path: UPathStr) -> dict:
+    """Load `.json` to `dict`."""
+    import json
+
+    with open(path) as f:
+        data = json.load(f)
+    return data
+
+
+def load_image(path: UPathStr):
+    """Display `.svg` in ipython, otherwise return path."""
+    if is_run_from_ipython:
+        from IPython.display import Image, display
+
+        display(Image(filename=path))
+    else:
+        return path
+
+
+def load_svg(path: UPathStr) -> None | Path:
+    """Display `.svg` in ipython, otherwise return path."""
+    if is_run_from_ipython:
+        from IPython.display import SVG, display
+
+        display(SVG(filename=path))
+        return None
+    else:
+        return path
+
+
+FILE_LOADERS = {
+    ".csv": pd.read_csv,
+    ".tsv": load_tsv,
+    ".h5ad": load_h5ad,
+    ".parquet": pd.read_parquet,
+    ".fcs": load_fcs,
+    ".zarr": load_anndata_zarr,
+    ".html": load_html,
+    ".json": load_json,
+    ".h5mu": load_h5mu,
+    ".jpg": load_image,
+    ".png": load_image,
+    ".svg": load_svg,
+}
+
+SUPPORTED_SUFFIXES = list(FILE_LOADERS.keys())
+"""Suffixes with defined artifact loaders."""
+
+
+def load_to_memory(filepath: UPathStr, **kwargs):
+    """Load a file into memory.
+
+    Returns the filepath if no in-memory form is found.
+    """
+    filepath = create_path(filepath)
+
+    filepath = settings._storage_settings.cloud_to_local(filepath, print_progress=True)
+
+    loader = FILE_LOADERS.get(filepath.suffix)
+    if loader is None:
+        return filepath
+    else:
+        return loader(filepath, **kwargs)