PyPI - lamindb - Versions diffs - 0.59.1__tar.gz → 0.59.3__tar.gz - Mend

lamindb 0.59.1tar.gz → 0.59.3tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (265) hide show

{lamindb-0.59.1 → lamindb-0.59.3}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.59.1
+Version: 0.59.3
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,8 +9,8 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Requires-Dist: lnschema_core==0.54.0
-Requires-Dist: lamindb_setup==0.57.0
-Requires-Dist: lamin_utils==0.11.5
+Requires-Dist: lamindb_setup==0.57.1
+Requires-Dist: lamin_utils==0.11.7
 Requires-Dist: lamin_cli==0.1.2
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
@@ -20,11 +20,13 @@ Requires-Dist: anndata>=0.8.0,<=0.10.2
 Requires-Dist: fsspec
 Requires-Dist: pandas
 Requires-Dist: graphviz
+Requires-Dist: psycopg2-binary
 Requires-Dist: botocore==1.31.17 ; extra == "aws"
 Requires-Dist: urllib3<2 ; extra == "aws"
 Requires-Dist: boto3==1.28.17 ; extra == "aws"
 Requires-Dist: aiobotocore==2.5.4 ; extra == "aws"
 Requires-Dist: fsspec[s3]==2023.9.0 ; extra == "aws"
+Requires-Dist: s3fs>=2023.1.0 ; extra == "aws"
 Requires-Dist: lnschema_bionty==0.34.0 ; extra == "bionty"
 Requires-Dist: pandas<2 ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
@@ -35,14 +37,13 @@ Requires-Dist: coverage ; extra == "dev"
 Requires-Dist: pytest-cov ; extra == "dev"
 Requires-Dist: nbproject_test>=0.3.0 ; extra == "dev"
 Requires-Dist: faker-biology ; extra == "dev"
+Requires-Dist: lamin_vault ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
 Requires-Dist: readfcs>=1.1.7 ; extra == "fcs"
 Requires-Dist: fsspec[gs]==2023.9.0 ; extra == "gcp"
 Requires-Dist: nbproject==0.9.2 ; extra == "jupyter"
 Requires-Dist: nbstripout ; extra == "jupyter"
 Requires-Dist: nbconvert ; extra == "jupyter"
-Requires-Dist: psycopg2-binary ; extra == "postgres"
-Requires-Dist: lamin_vault ; extra == "postgres"
 Requires-Dist: zarr>=2.16.0 ; extra == "zarr"
 Project-URL: Home, https://github.com/laminlabs/lamindb
 Provides-Extra: aws
@@ -52,7 +53,6 @@ Provides-Extra: erdiagram
 Provides-Extra: fcs
 Provides-Extra: gcp
 Provides-Extra: jupyter
-Provides-Extra: postgres
 Provides-Extra: zarr
 [![Stars](https://img.shields.io/github/stars/laminlabs/lamindb?logo=GitHub&color=yellow)](https://github.com/laminlabs/lamindb)

{lamindb-0.59.1 → lamindb-0.59.3}/docs/changelog.md RENAMED Viewed

@@ -6,9 +6,20 @@
 ## 0.59
+### 0.59.3 {small}`2023-11-04`
+- 💄 Show transform uid in view_flow [PR1280](https://github.com/laminlabs/lamindb/pull/1280) [@sunnyosun](https://github.com/sunnyosun)
+- 🚸 Improve search [PR1279](https://github.com/laminlabs/lamindb/pull/1279) [@sunnyosun](https://github.com/sunnyosun)
+### 0.59.2 {small}`2023-11-04`
+- 🐛 Backed raw subset fix [PR1278](https://github.com/laminlabs/lamindb/pull/1278) [@Koncopd](https://github.com/Koncopd)
+- 🚸 Improve connection stability [PR1277](https://github.com/laminlabs/lamindb/pull/1277) [@falexwolf](https://github.com/falexwolf)
+- 🚸 Improve search [PR1275](https://github.com/laminlabs/lamindb/pull/1275) [@sunnyosun](https://github.com/sunnyosun)
 ### 0.59.1 {small}`2023-11-03`
-- ♻️ Move CLI from lamindb-setup here [PR1264](https://github.com/laminlabs/lamindb/pull/1264) [@falexwolf](https://github.com/falexwolf)
+- ♻️ Move CLI from `lamindb-setup` here [PR1264](https://github.com/laminlabs/lamindb/pull/1264) [@falexwolf](https://github.com/falexwolf)
 - 🐛 `file.replace()` works with virtual keys [PR1265](https://github.com/laminlabs/lamindb/pull/1265) [@Koncopd](https://github.com/Koncopd)
 ### 0.59.0 {small}`2023-10-27`

{lamindb-0.59.1 → lamindb-0.59.3}/docs/installation.md RENAMED Viewed

@@ -14,8 +14,8 @@ Supported `extras` are:
 ```yaml
 # commonly used
-jupyter   # parse Jupyter notebooks
-bionty    # manage basic biological entities
+jupyter   # parse Jupyter notebook metadata
+bionty    # access basic biological ontologies
 # cloud backends
 aws       # AWS (s3fs, etc.)
 gcp       # Google Cloud (gcfs, etc.)
@@ -23,8 +23,6 @@ gcp       # Google Cloud (gcfs, etc.)
 fcs       # manage FCS files (flow cytometry)
 # storage backends
 zarr      # store & stream arrays with zarr
-# database backends
-postgres  # postgres tools
 # others
 erdiagram # visualize ER diagrams, also needs graphviz
 ```

{lamindb-0.59.1 → lamindb-0.59.3}/docs/introduction.ipynb RENAMED Viewed

@@ -25,7 +25,7 @@
     "```\n",
     ":::\n",
     "\n",
-    "LaminHub Basic is free. Enterprise features, support, integration tests & wetlab plug-ins hosted in your or our infrastructure are available on a [paid plan](https://lamin.ai/pricing): please [reach out](https://lamin.ai/contact)!"
+    "Basic features of LaminHub are free. Enterprise features, support, integration tests & wetlab plug-ins hosted in your or our infrastructure are available on a [paid plan](https://lamin.ai/pricing): please [reach out](https://lamin.ai/contact)!"
    ]
   },
   {
@@ -52,7 +52,7 @@
     "    pip install 'lamindb[jupyter,bionty]'\n",
     "    ```\n",
     "2. [Sign up](https://lamin.ai/signup) for a free account (see more [info](https://lamin.ai/docs/setup)) and copy the API key.\n",
-    "3. Log in on the command line:\n",
+    "3. Log in on the command line (data remains in your infrastructure, with Lamin having no access to it):\n",
     "    ```shell\n",
     "    lamin login <email> --key <API-key>\n",
     "    ```\n",
@@ -77,9 +77,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Because we passed `--schema bionty`, this instance mounted plug-in {mod}`lnschema_bionty`.\n",
-    "\n",
-    "Note that data remains in your infrastructure, with Lamin having no access to it."
+    "Because we passed `--schema bionty`, this instance mounted plug-in {mod}`lnschema_bionty`."
    ]
   },
   {
@@ -614,7 +612,7 @@
     "\n",
     "If you run `lamin save <notebook_path>`, you will save the notebook to your default storage location.\n",
     "\n",
-    "You can explore the notebook report corresponding to the quickstart [here](https://lamin.ai/laminlabs/lamindata/record/core/Transform?id=Hc5AXzibjGg1z8) in LaminHub.\n",
+    "You can explore the notebook report corresponding to the quickstart [here](https://lamin.ai/laminlabs/lamindata/record/core/Transform?id=FPnfDtJz8qbEz8) in LaminHub.\n",
     "\n",
     "### Manage custom schemas\n",
     "\n",

{lamindb-0.59.1 → lamindb-0.59.3}/docs/tutorial.ipynb RENAMED Viewed

@@ -829,7 +829,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This will enable you to query the report and source code via `transform.latest_report` and `transform.source_file` and see it in the hub, e.g., [here](https://lamin.ai/laminlabs/lamindata/record/core/Transform?id=NJvdsWWbJlZSz8).\n",
+    "This will enable you to query the report and source code via `transform.latest_report` and `transform.source_file` and see it in the hub, e.g., [here](https://lamin.ai/laminlabs/lamindata/record/core/Transform?uid=NJvdsWWbJlZSz8).\n",
     "\n",
     "<img src=\"https://lamin-site-assets.s3.amazonaws.com/.lamindb/RGXj5wcAf7EAc6J8aBoM.png\" width=\"700px\">"
    ]

{lamindb-0.59.1 → lamindb-0.59.3}/lamindb/__init__.py RENAMED Viewed

@@ -53,7 +53,7 @@ Static classes & modules:
 """
-__version__ = "0.59.1"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.59.3"  # denote a release candidate for 0.1.0 with 0.1rc1
 import os as _os

{lamindb-0.59.1 → lamindb-0.59.3}/lamindb/_parents.py RENAMED Viewed

@@ -277,7 +277,7 @@ def _record_label(record: Registry, field: Optional[str] = None):
         name = f'{record.transform.name.replace("&", "&amp;")}'
         return (
             rf'<{TRANSFORM_EMOJIS.get(str(record.transform.type), "💫")} {name}<BR/><FONT COLOR="GREY" POINT-SIZE="10"'  # noqa
-            rf' FACE="Monospace">uid={record.uid}<BR/>type={record.transform.type},'
+            rf' FACE="Monospace">uid={record.transform.uid}<BR/>type={record.transform.type},'  # noqa
             rf" user={record.created_by.name}<BR/>run_at={format_field_value(record.run_at)}</FONT>>"  # noqa
         )
     elif isinstance(record, Transform):

{lamindb-0.59.1 → lamindb-0.59.3}/lamindb/dev/storage/_backed_access.py RENAMED Viewed

@@ -547,7 +547,7 @@ class AnnDataAccessorSubset(_AnnDataAttrsMixin):
         prepare_indices = None
         if self.indices is not None:
             oidx = self.indices[0]
-            if oidx != slice(None):
+            if isinstance(oidx, np.ndarray) or oidx != slice(None):
                 prepare_indices = oidx, slice(None)
         return AnnDataRawAccessor(
             self.storage["raw"],
@@ -575,7 +575,7 @@ class AnnDataRawAccessor(AnnDataAccessorSubset):
         if attrs_keys is None:
             attrs_keys = {}
-            if isinstance(var_raw, (h5py.Dataset, zarr.Array)):
+            if isinstance(var_raw, ArrayTypes):
                 attrs_keys["var"] = list(var_raw.dtype.fields.keys())
             else:
                 # for some reason list(var_raw.keys()) is very slow for zarr

{lamindb-0.59.1 → lamindb-0.59.3}/pyproject.toml RENAMED Viewed

@@ -16,18 +16,19 @@ classifiers = [
 dependencies = [
     # Lamin PINNED packages
     "lnschema_core==0.54.0",
-    "lamindb_setup==0.57.0",
-    "lamin_utils==0.11.5",
+    "lamindb_setup==0.57.1",
+    "lamin_utils==0.11.7",
     "lamin_cli==0.1.2",
     # others
     "rapidfuzz",
     "pyarrow",
     "typing_extensions!=4.6.0",
     "python-dateutil",
-    "anndata>=0.8.0,<=0.10.2",  # we're using anndata internals
+    "anndata>=0.8.0,<=0.10.2",  # will upgrade to new anndata releases
     "fsspec",
     "pandas",
     "graphviz",
+    "psycopg2-binary",
 ]
 [project.urls]
@@ -37,16 +38,13 @@ Home = "https://github.com/laminlabs/lamindb"
 bionty = [
     "lnschema_bionty==0.34.0",
 ]
-postgres = [
-    "psycopg2-binary",
-    "lamin_vault",  # only used for secrets management
-]
 aws = [
     "botocore==1.31.17",  # for aiobotocore inside s3fs, to fix deps resolution
     "urllib3<2", # for botocore
     "boto3==1.28.17", # to avoid conflicts arising due to the pin on botocore
     "aiobotocore==2.5.4",
-    "fsspec[s3]==2023.9.0"
+    "fsspec[s3]==2023.9.0",
+    "s3fs>=2023.1.0",  # very old versions of s3fs don't work
 ]
 gcp = [
     "fsspec[gs]==2023.9.0"
@@ -79,6 +77,8 @@ dev = [
     "nbproject_test>=0.3.0",
     # biology
     "faker-biology",
+    # vault
+    "lamin_vault",
 ]
 [tool.black]

lamindb-0.59.3/sub/lamin-cli/lamin_cli/__init__.py ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ """Lamin CLI."""
2	+ __version__ = "0.1.2"

{lamindb-0.59.1 → lamindb-0.59.3}/sub/lamin-cli/lamin_cli/_notebook.py RENAMED Viewed

@@ -125,7 +125,11 @@ def save(notebook_path: str) -> Optional[str]:
     # convert the notebook file to html
     notebook_path_html = notebook_path.replace(".ipynb", ".html")
     logger.info(f"exporting notebook as html {notebook_path_html}")
-    result = subprocess.run(f"jupyter nbconvert --to html {notebook_path}", shell=True)
+    # log_level is set to 40 to silence the nbconvert logging
+    result = subprocess.run(
+        f"jupyter nbconvert --to html {notebook_path} --Application.log_level=40",
+        shell=True,
+    )
     assert result.returncode == 0
     # copy the notebook file to a temporary file
     notebook_path_stripped = notebook_path.replace(".ipynb", "_stripped.ipynb")
@@ -204,6 +208,7 @@ def save(notebook_path: str) -> Optional[str]:
     )
     report_file.save()
     run.report = report_file
+    run.is_consecutive = is_consecutive
     run.save()
     # annotate transform
     transform.source_file = source_file

lamindb-0.59.3/sub/lamindb-setup/.pre-commit-config.yaml ADDED Viewed

@@ -0,0 +1,64 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+        exclude: |
+          (?x)(
+              .github/workflows/latest-changes.jinja2
+          )
+      - id: check-yaml
+      - id: check-added-large-files
+  - repo: https://github.com/psf/black
+    rev: 22.6.0
+    hooks:
+      - id: black-jupyter
+  - repo: https://github.com/pycqa/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        additional_dependencies:
+          - flake8-black==0.3.3
+          - flake8-typing-imports==1.10.0
+        language_version: python3
+        args:
+          - --max-line-length=88
+          - --ignore=E203,W503,BLK100,TYP001
+        exclude: |
+          (?x)(
+              __init__.py
+          )
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v2.6.2
+    hooks:
+      - id: prettier
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.3.9
+    hooks:
+      - id: nbstripout
+        exclude: |
+          (?x)(
+              docs/examples/|
+              docs/notes/|
+              tests
+          )
+  - repo: https://github.com/Lucas-C/pre-commit-hooks
+    rev: v1.1.9
+    hooks:
+      - id: forbid-crlf
+      - id: remove-crlf
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.940
+    hooks:
+      - id: mypy
+        exclude: |
+          (?x)(
+              tests/hub-local/conftest.py
+          )
+  - repo: https://github.com/pycqa/pydocstyle
+    rev: 6.1.1
+    hooks:
+      - id: pydocstyle
+        args: # google style + __init__, see http://www.pydocstyle.org/en/stable/error_codes.html
+          - --ignore=D100,D101,D102,D103,D104,D106,D107,D203,D204,D213,D215,D400,D401,D403,D404,D406,D407,D408,D409,D412,D413

{lamindb-0.59.1 → lamindb-0.59.3}/sub/lamindb-setup/docs/changelog.md RENAMED Viewed

@@ -3,6 +3,7 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+🚸 Lower `conn_mag_age` | [573](https://github.com/laminlabs/lamindb-setup/pull/573) | [falexwolf](https://github.com/falexwolf) | 2023-11-04 | 0.57.1
 🚚 Move CLI to lamindb | [572](https://github.com/laminlabs/lamindb-setup/pull/572) | [falexwolf](https://github.com/falexwolf) | 2023-10-30 | 0.57.0
 ♻️ Also enable to read db from env variable | [571](https://github.com/laminlabs/lamindb-setup/pull/571) | [falexwolf](https://github.com/falexwolf) | 2023-10-26 | 0.56.4
 ♻️ Enable to pre-define the instance id | [570](https://github.com/laminlabs/lamindb-setup/pull/570) | [falexwolf](https://github.com/falexwolf) | 2023-10-26 | 0.56.3

{lamindb-0.59.1 → lamindb-0.59.3}/sub/lamindb-setup/lamindb_setup/__init__.py RENAMED Viewed

@@ -44,7 +44,7 @@ Developer API.
 """
-__version__ = "0.57.0"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.57.1"  # denote a release candidate for 0.1.0 with 0.1rc1
 import sys
 from os import name as _os_name

{lamindb-0.59.1 → lamindb-0.59.3}/sub/lamindb-setup/lamindb_setup/dev/django.py RENAMED Viewed

@@ -55,7 +55,9 @@ def setup_django(
     if not settings.configured:
         default_db = dj_database_url.config(
             default=isettings.db,
-            conn_max_age=600,
+            # https://laminlabs.slack.com/archives/C04FPE8V01W/p1698239551460289
+            # assuming postgres terminates a connection after 299s
+            conn_max_age=299,
             conn_health_checks=True,
         )
         DATABASES = {

{lamindb-0.59.1 → lamindb-0.59.3}/sub/lamindb-setup/noxfile.py RENAMED Viewed

@@ -29,10 +29,8 @@ def install(session: nox.Session, group: str) -> None:
         session.run(*"pip install ./laminhub-rest[server]".split())
         session.run(*"pip install -e .[aws,dev]".split())
         # need for CLI, but this is bad because it's downstream
-        session.run(
-            *"git clone --branch cli https://github.com/laminlabs/lamindb".split()
-        )
-        session.run(*"pip install lamindb/sub/lamin-cli".split())
+        session.run(*"git clone https://github.com/laminlabs/lamin-cli".split())
+        session.run(*"pip install lamin-cli".split())
     elif group == "noaws":
         session.run(*"pip install -e .[aws,dev]".split())
     elif group == "vault":
@@ -43,10 +41,8 @@ def install(session: nox.Session, group: str) -> None:
         )
         session.run(*"pip install -e .[aws,dev]".split())
         # need for CLI, but this is bad because it's downstream
-        session.run(
-            *"git clone --branch cli https://github.com/laminlabs/lamindb".split()
-        )
-        session.run(*"pip install lamindb/sub/lamin-cli".split())
+        session.run(*"git clone https://github.com/laminlabs/lamin-cli".split())
+        session.run(*"pip install lamin-cli".split())
     elif group == "hub-local":
         session.run(*"pip install -e .[aws,dev,hub]".split())
         session.run(*"pip install ./laminhub-rest[server]".split())

{lamindb-0.59.1 → lamindb-0.59.3}/tests/test_storage.py RENAMED Viewed

@@ -1,6 +1,7 @@
 import shutil
 import h5py
+import numpy as np
 import pandas as pd
 import pytest
 import zarr
@@ -106,6 +107,12 @@ def test_backed_access(adata_format):
     obs_sub = ["TCAATCACCCTTCG-8", "CGTTATACAGTACC-8", "TGCCAAGATTGTGG-7"]
     sub = access[obs_sub]
     assert sub.obs_names.tolist() == obs_sub
+    assert sub.to_memory().shape == (3, 200)
+    idx = np.array([1, 2, 5])
+    sub = access[idx]
+    assert sub.raw.shape == (3, 100)
+    assert sub.to_memory().shape == (3, 200)
     var_sub = ["SSU72", "PARK7", "RBP7"]
     sub = access[:, var_sub]