lamindb_setup 1.18.2__py3-none-any.whl → 1.19.1__py3-none-any.whl

lamindb_setup/core/_aws_storage.py

@@ -1,55 +1,57 @@
-from __future__ import annotations
-
-import httpx
-from lamin_utils import logger
-
-
-def get_location(ip="ipinfo.io"):
-    response = httpx.get(f"http://{ip}/json").json()
-    loc = response["loc"].split(",")
-    return {"latitude": float(loc[0]), "longitude": float(loc[1])}
-
-
-def haversine(lat1: float, lon1: float, lat2: float, lon2: float) -> float:
-    import math
-
-    R = 6371  # Radius of the Earth in kilometers
-    dLat = math.radians(lat2 - lat1)
-    dLon = math.radians(lon2 - lon1)
-    a = math.sin(dLat / 2) * math.sin(dLat / 2) + math.cos(
-        math.radians(lat1)
-    ) * math.cos(math.radians(lat2)) * math.sin(dLon / 2) * math.sin(dLon / 2)
-    c = 2 * math.atan2(math.sqrt(a), math.sqrt(1 - a))
-    distance = R * c
-    return distance
-
-
-def find_closest_aws_region() -> str:
-    aws_region_locations = {
-        "us-east-1": {"latitude": 39.0, "longitude": -77.0},  # Northern Virginia
-        "us-east-2": {"latitude": 40.0, "longitude": -83.0},  # Ohio
-        "us-west-1": {"latitude": 37.77, "longitude": -122.41},  # Northern California
-        "us-west-2": {"latitude": 45.52, "longitude": -122.68},  # Oregon
-        "eu-central-1": {"latitude": 50.11, "longitude": 8.68},  # Frankfurt
-        "eu-west-2": {"latitude": 51.51, "longitude": -0.13},  # London, UK
-    }
-    # sometimes get_location fails to obtain coordinates
-    try:
-        your_location = get_location()
-    except Exception as e:
-        logger.warning(f"failed to infer location, using us-east-1: {e}")
-        return "us-east-1"
-
-    closest_region = ""
-    min_distance = float("inf")
-    for region in aws_region_locations:
-        region_location = aws_region_locations[region]
-        distance = haversine(
-            your_location["latitude"],
-            your_location["longitude"],
-            region_location["latitude"],
-            region_location["longitude"],
-        )
-        if distance < min_distance:
-            closest_region, min_distance = region, distance
-    return closest_region
+from __future__ import annotations
+
+from lamin_utils import logger
+
+
+def get_location(ip="ipinfo.io"):
+    # dynamic import to avoid importing the heavy httpx at root
+    import httpx
+
+    response = httpx.get(f"http://{ip}/json").json()
+    loc = response["loc"].split(",")
+    return {"latitude": float(loc[0]), "longitude": float(loc[1])}
+
+
+def haversine(lat1: float, lon1: float, lat2: float, lon2: float) -> float:
+    import math
+
+    R = 6371  # Radius of the Earth in kilometers
+    dLat = math.radians(lat2 - lat1)
+    dLon = math.radians(lon2 - lon1)
+    a = math.sin(dLat / 2) * math.sin(dLat / 2) + math.cos(
+        math.radians(lat1)
+    ) * math.cos(math.radians(lat2)) * math.sin(dLon / 2) * math.sin(dLon / 2)
+    c = 2 * math.atan2(math.sqrt(a), math.sqrt(1 - a))
+    distance = R * c
+    return distance
+
+
+def find_closest_aws_region() -> str:
+    aws_region_locations = {
+        "us-east-1": {"latitude": 39.0, "longitude": -77.0},  # Northern Virginia
+        "us-east-2": {"latitude": 40.0, "longitude": -83.0},  # Ohio
+        "us-west-1": {"latitude": 37.77, "longitude": -122.41},  # Northern California
+        "us-west-2": {"latitude": 45.52, "longitude": -122.68},  # Oregon
+        "eu-central-1": {"latitude": 50.11, "longitude": 8.68},  # Frankfurt
+        "eu-west-2": {"latitude": 51.51, "longitude": -0.13},  # London, UK
+    }
+    # sometimes get_location fails to obtain coordinates
+    try:
+        your_location = get_location()
+    except Exception as e:
+        logger.warning(f"failed to infer location, using us-east-1: {e}")
+        return "us-east-1"
+
+    closest_region = ""
+    min_distance = float("inf")
+    for region in aws_region_locations:
+        region_location = aws_region_locations[region]
+        distance = haversine(
+            your_location["latitude"],
+            your_location["longitude"],
+            region_location["latitude"],
+            region_location["longitude"],
+        )
+        if distance < min_distance:
+            closest_region, min_distance = region, distance
+    return closest_region

lamindb_setup/core/_clone.py

@@ -1,50 +1,50 @@
-"""Utilities to work with Postgres Snapshots.
-
-.. autosummary::
-   :toctree:
-
-   upload_sqlite_clone
-"""
-
-import gzip
-import shutil
-from pathlib import Path
-
-from lamindb_setup.core.upath import create_path
-
-
-def upload_sqlite_clone(
-    local_sqlite_path: Path | str | None = None, compress: bool = True
-) -> None:
-    """Uploads the SQLite clone to the default storage.
-
-    Args:
-        local_sqlite_path: Path to the SQLite file.
-            Defaults to the local storage path if not specified.
-        compress: Whether to compress the database with gzip before uploading.
-    """
-    import lamindb_setup as ln_setup
-
-    if local_sqlite_path is None:
-        local_sqlite_path = ln_setup.settings.instance._sqlite_file_local
-    else:
-        local_sqlite_path = Path(local_sqlite_path)
-
-    if not local_sqlite_path.exists():
-        raise FileNotFoundError(f"Database not found at {local_sqlite_path}")
-
-    cloud_db_path = ln_setup.settings.instance._sqlite_file
-
-    if compress:
-        temp_gz_path = local_sqlite_path.with_suffix(".db.gz")
-        with (
-            open(local_sqlite_path, "rb") as f_in,
-            gzip.open(temp_gz_path, "wb") as f_out,
-        ):
-            shutil.copyfileobj(f_in, f_out)
-        cloud_destination = create_path(f"{cloud_db_path}.gz")
-        cloud_destination.upload_from(temp_gz_path, print_progress=True)
-        temp_gz_path.unlink()
-    else:
-        cloud_destination = create_path(cloud_db_path)
-        cloud_destination.upload_from(local_sqlite_path, print_progress=True)
+"""Utilities to work with Postgres Snapshots.
+
+.. autosummary::
+   :toctree:
+
+   upload_sqlite_clone
+"""
+
+import gzip
+import shutil
+from pathlib import Path
+
+from lamindb_setup.core.upath import create_path
+
+
+def upload_sqlite_clone(
+    local_sqlite_path: Path | str | None = None, compress: bool = True
+) -> None:
+    """Uploads the SQLite clone to the default storage.
+
+    Args:
+        local_sqlite_path: Path to the SQLite file.
+            Defaults to the local storage path if not specified.
+        compress: Whether to compress the database with gzip before uploading.
+    """
+    import lamindb_setup as ln_setup
+
+    if local_sqlite_path is None:
+        local_sqlite_path = ln_setup.settings.instance._sqlite_file_local
+    else:
+        local_sqlite_path = Path(local_sqlite_path)
+
+    if not local_sqlite_path.exists():
+        raise FileNotFoundError(f"Database not found at {local_sqlite_path}")
+
+    cloud_db_path = ln_setup.settings.instance._sqlite_file
+
+    if compress:
+        temp_gz_path = local_sqlite_path.with_suffix(".db.gz")
+        with (
+            open(local_sqlite_path, "rb") as f_in,
+            gzip.open(temp_gz_path, "wb") as f_out,
+        ):
+            shutil.copyfileobj(f_in, f_out)
+        cloud_destination = create_path(f"{cloud_db_path}.gz")
+        cloud_destination.upload_from(temp_gz_path, print_progress=True)
+        temp_gz_path.unlink()
+    else:
+        cloud_destination = create_path(cloud_db_path)
+        cloud_destination.upload_from(local_sqlite_path, print_progress=True)

lamindb_setup/core/_deprecated.py

@@ -1,62 +1,62 @@
-from __future__ import annotations
-
-# BSD 3-Clause License
-# Copyright (c) 2017-2018 P. Angerer, F. Alexander Wolf, Theis Lab
-# All rights reserved.
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-# * Redistributions of source code must retain the above copyright notice, this
-#   list of conditions and the following disclaimer.
-# * Redistributions in binary form must reproduce the above copyright notice,
-#   this list of conditions and the following disclaimer in the documentation
-#   and/or other materials provided with the distribution.
-# * Neither the name of the copyright holder nor the names of its
-#   contributors may be used to endorse or promote products derived from
-#   this software without specific prior written permission.
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-import warnings
-from functools import wraps
-
-
-def deprecated(new_name: str):
-    """Deprecated.
-
-    This is a decorator which can be used to mark functions, methods and properties
-    as deprecated. It will result in a warning being emitted
-    when the function is used.
-
-    It will also hide the function from the docs.
-
-    Example::
-
-        @property
-        @deprecated("n_files")
-        def n_objects(self) -> int:
-            return self.n_files
-
-    """
-
-    def decorator(func):
-        @wraps(func)
-        def new_func(*args, **kwargs):
-            warnings.warn(
-                f"Use {new_name} instead of {func.__name__}, "
-                f"{func.__name__} will be removed in the future.",
-                category=DeprecationWarning,
-                stacklevel=2,
-            )
-            return func(*args, **kwargs)
-
-        setattr(new_func, "__deprecated", True)
-        return new_func
-
-    return decorator
+from __future__ import annotations
+
+# BSD 3-Clause License
+# Copyright (c) 2017-2018 P. Angerer, F. Alexander Wolf, Theis Lab
+# All rights reserved.
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
+# * Neither the name of the copyright holder nor the names of its
+#   contributors may be used to endorse or promote products derived from
+#   this software without specific prior written permission.
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+import warnings
+from functools import wraps
+
+
+def deprecated(new_name: str):
+    """Deprecated.
+
+    This is a decorator which can be used to mark functions, methods and properties
+    as deprecated. It will result in a warning being emitted
+    when the function is used.
+
+    It will also hide the function from the docs.
+
+    Example::
+
+        @property
+        @deprecated("n_files")
+        def n_objects(self) -> int:
+            return self.n_files
+
+    """
+
+    def decorator(func):
+        @wraps(func)
+        def new_func(*args, **kwargs):
+            warnings.warn(
+                f"Use {new_name} instead of {func.__name__}, "
+                f"{func.__name__} will be removed in the future.",
+                category=DeprecationWarning,
+                stacklevel=2,
+            )
+            return func(*args, **kwargs)
+
+        setattr(new_func, "__deprecated", True)
+        return new_func
+
+    return decorator

lamindb_setup/core/_docs.py

@@ -1,14 +1,14 @@
-from __future__ import annotations
-
-from textwrap import dedent
-
-
-def doc_args(*args):
-    """Pass arguments to docstrings."""
-
-    def dec(obj):
-        obj.__orig_doc__ = obj.__doc__
-        obj.__doc__ = dedent(obj.__doc__).format(*args)
-        return obj
-
-    return dec
+from __future__ import annotations
+
+from textwrap import dedent
+
+
+def doc_args(*args):
+    """Pass arguments to docstrings."""
+
+    def dec(obj):
+        obj.__orig_doc__ = obj.__doc__
+        obj.__doc__ = dedent(obj.__doc__).format(*args)
+        return obj
+
+    return dec