lamindb 0.67.1__tar.gz → 0.67.2__tar.gz

{lamindb-0.67.1 → lamindb-0.67.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.67.1
+Version: 0.67.2
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -12,7 +12,7 @@ Classifier: Programming Language :: Python :: 3.11
 Requires-Dist: lnschema_core==0.61.1
 Requires-Dist: lamindb_setup==0.64.2
 Requires-Dist: lamin_utils==0.13.0
-Requires-Dist: lamin_cli==0.6.1
+Requires-Dist: lamin_cli==0.7.0
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0

{lamindb-0.67.1 → lamindb-0.67.2}/docs/changelog.md

@@ -7,10 +7,13 @@
 
 ## 0.67
 
+### 0.67.2 {small}`2024-01-14`
+
+- ✨ Enable staging notebooks & code using the CLI [PR](https://github.com/laminlabs/lamindb/pull/1403) [@falexwolf](https://github.com/falexwolf)
+
 ### 0.67.1 {small}`2024-01-12`
 
 - 🐛 Fix idempotency of `collection.save()` [PR](https://github.com/laminlabs/lamindb/pull/1401) [@falexwolf](https://github.com/falexwolf)
-- 🩹 Also amend run [PR](https://github.com/laminlabs/lamindb/pull/1399) [@falexwolf](https://github.com/falexwolf)
 - 🚸 Disallow bulk-delete for Artifact, Transform & Collection [PR](https://github.com/laminlabs/lamindb/pull/1398) [@falexwolf](https://github.com/falexwolf)
 - 🚸 Init transform versions at 1 [PR](https://github.com/laminlabs/lamindb/pull/1397) [@falexwolf](https://github.com/falexwolf)
 - ✨ Load json and html files [PR](https://github.com/laminlabs/lamindb/pull/1396) [@falexwolf](https://github.com/falexwolf)

{lamindb-0.67.1 → lamindb-0.67.2}/lamindb/__init__.py

@@ -54,7 +54,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.67.1"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.67.2"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 

{lamindb-0.67.1 → lamindb-0.67.2}/noxfile.py

@@ -130,37 +130,41 @@ def docs(session):
         if group in {"tutorial", "guide", "biology"}:
             for path in Path(f"./docs/{group}").glob("*"):
                 path.rename(f"./docs/{path.name}")
-    login_testuser1(session)
     session.run(*"lamin init --storage ./docsbuild --schema bionty".split())
 
     def generate_cli_docs(main_parser):
         page = "# `lamin`\n\nFor a guide, see: {doc}`/setup`.\n\n"
-        commands = [
-            "login",
-            "init",
-            "load",
-            "close",
-            "delete",
-            "track",
-            "info",
-            "migrate",
-            "save",
-            "set",
-            "schema",
-        ]
+        command_groups = {
+            "General": ["login", "info"],
+            "Instances": [
+                "init",
+                "load",
+                "close",
+                "delete",
+                "migrate",
+                "set",
+                "schema",
+            ],
+            "Transforms": ["track", "save", "stage"],
+        }
         for action_group in main_parser._action_groups:
             for group_action in action_group._group_actions:
                 if type(group_action).__name__ == "_SubParsersAction":
-                    for command in commands:
-                        subparser = group_action.choices[command]
-                        # replace the "nox" command with the "lamin" command
-                        help_string = subparser.format_help().replace("nox", "lamin")
-                        page += f"## `lamin {command}`\n\n```\n{help_string}```\n\n"
+                    for command_group, commands in command_groups.items():
+                        page += f"## {command_group}\n\n"
+                        for command in commands:
+                            subparser = group_action.choices[command]
+                            # replace the "nox" command with the "lamin" command
+                            help_string = subparser.format_help().replace(
+                                "nox", "lamin"
+                            )
+                            page += (
+                                f"### `lamin {command}`\n\n```\n{help_string}```\n\n"
+                            )
         Path("./docs/cli.md").write_text(page)
 
     from lamin_cli import __main__
 
     generate_cli_docs(__main__.parser)
-
     build_docs(session, strip_prefix=True, strict=True)
     upload_docs_artifact(aws=True)

{lamindb-0.67.1 → lamindb-0.67.2}/pyproject.toml

@@ -19,7 +19,7 @@ dependencies = [
     "lnschema_core==0.61.1",
     "lamindb_setup==0.64.2",
     "lamin_utils==0.13.0",
-    "lamin_cli==0.6.1",
+    "lamin_cli==0.7.0",
     # others
     "rapidfuzz",
     "pyarrow",

lamindb-0.67.2/sub/lamin-cli/lamin_cli/__init__.py

@@ -0,0 +1,3 @@
+"""Lamin CLI."""
+
+__version__ = "0.7.0"

{lamindb-0.67.1 → lamindb-0.67.2}/sub/lamin-cli/lamin_cli/__main__.py

@@ -100,8 +100,12 @@ aa("--pypackage", type=str, metavar="pypackage", default=None, help=pypackage_he
 # save
 save_parser = subparsers.add_parser("save", help="save notebook or script")
 aa = save_parser.add_argument
-filepath_help = "A path to the notebook."
-aa("filepath", type=str, metavar="filepath", help=filepath_help)
+aa("filepath", type=str, metavar="filepath", help="filepath to notebook or script")
+
+# stage
+save_parser = subparsers.add_parser("stage", help="stage a notebook or script")
+aa = save_parser.add_argument
+aa("url", type=str, metavar="url", help="a lamin.ai url")
 
 # login and logout user
 login = subparsers.add_parser("login", help="log in")
@@ -219,6 +223,10 @@ def main():
         from lamin_cli._transform import save
 
         return save(args.filepath)
+    elif args.command == "stage":
+        from lamin_cli._stage import stage
+
+        return stage(args.url)
     elif args.command == "cache":
         from lamindb_setup._cache import clear_cache_dir, get_cache_dir, set_cache_dir
 

lamindb-0.67.2/sub/lamin-cli/lamin_cli/_stage.py

@@ -0,0 +1,29 @@
+from typing import Tuple
+from lamin_utils import logger
+
+
+def decompose_url(url: str) -> Tuple[str, str, str]:
+    assert "Transform" in url
+    uid = url.split("uid=")[1]
+    instance_identifier = "/".join(url.replace("https://lamin.ai/", "").split("/")[:2])
+    return instance_identifier, "transform", uid
+
+
+def stage(identifier: str):
+    import lamindb as ln
+
+    ln.settings.verbosity = "success"
+    if identifier.startswith("https://lamin.ai"):
+        instance_identifier, entity, uid = decompose_url(identifier)
+    else:
+        entity, uid = identifier.split()
+        instance_identifier = ln.setup.settings.instance.identifier
+
+    if entity == "transform":
+        transform = ln.Transform.using(instance_identifier).filter(uid=uid).one()
+        filepath_cache = transform.source_code.stage()
+        target_filename = f"{transform.short_name}.ipynb"
+        filepath_cache.rename(target_filename)
+        logger.success(f"staged source code of transform {uid} as {target_filename}")
+    else:
+        raise NotImplementedError

{lamindb-0.67.1 → lamindb-0.67.2}/sub/lamin-cli/tests/scripts/initialized.py

@@ -1,5 +1,5 @@
 __transform_stem_uid__ = "m5uCHTTpJnjQ"
-__version__ = "0"
+__version__ = "1"
 
 
 import lamindb as ln

{lamindb-0.67.1 → lamindb-0.67.2}/sub/lamin-cli/tests/test_scripts.py

@@ -7,6 +7,7 @@ scripts_dir = Path(__file__).parent.resolve() / "scripts"
 
 print(scripts_dir)
 
+
 def test_initialize():
     filepath = scripts_dir / "not-initialized.py"
     print(scripts_dir)
@@ -19,16 +20,16 @@ def test_initialize():
 
     with open(filepath) as f:
         content = f.read()
-    prepend = f'__transform_stem_uid__ = "'
+    prepend = '__transform_stem_uid__ = "'
     assert content.startswith(prepend)
 
 
-def test_run_and_save():
+def test_run_save_stage():
     env = os.environ
     env["LAMIN_TESTING"] = "true"
-    
+
     filepath = scripts_dir / "initialized.py"
-    # python sub/lamin-cli/tests/scripts/initialized.py     
+    # python sub/lamin-cli/tests/scripts/initialized.py
     result = subprocess.run(
         f"python {str(filepath)}",
         shell=True,
@@ -68,3 +69,11 @@ def test_run_and_save():
     )
     print(result)
     assert result.returncode == 0
+
+    result = subprocess.run(
+        "lamin stage 'transform m5uCHTTpJnjQ5zKv'",
+        shell=True,
+        capture_output=True,
+    )
+    print(result)
+    assert result.returncode == 0

lamindb-0.67.2/sub/lamin-cli/tests/test_stage.py

@@ -0,0 +1,21 @@
+from lamin_cli._stage import decompose_url
+import subprocess
+
+
+def test_decompose_url():
+    url = "https://lamin.ai/laminlabs/arrayloader-benchmarks/record/core/Transform?uid=1GCKs8zLtkc85zKv"  # noqa
+    instance_identifier, entity, uid = decompose_url(url)
+    assert instance_identifier == "laminlabs/arrayloader-benchmarks"
+    assert entity == "transform"
+    assert uid == "1GCKs8zLtkc85zKv"
+
+
+def test_stage():
+    result = subprocess.run(
+        "lamin stage"
+        " 'https://lamin.ai/laminlabs/arrayloader-benchmarks/record/core/Transform?uid=1GCKs8zLtkc85zKv'",  # noqa
+        shell=True,
+        capture_output=True,
+    )
+    print(result)
+    assert result.returncode == 0

{lamindb-0.67.1 → lamindb-0.67.2}/sub/lamindb-setup/docs/changelog.md

@@ -3,6 +3,8 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+🐛 Fix option inheritance in create_path and add tests | [617](https://github.com/laminlabs/lamindb-setup/pull/617) | [Koncopd](https://github.com/Koncopd) | 2024-01-12 |
+✅ Update tests relying on laminhub-rest | [616](https://github.com/laminlabs/lamindb-setup/pull/616) | [fredericenard](https://github.com/fredericenard) | 2024-01-12 |
 🚚 Rename .bionty to .public | [615](https://github.com/laminlabs/lamindb-setup/pull/615) | [sunnyosun](https://github.com/sunnyosun) | 2024-01-10 | 0.64.2
 🚸 Fix connection timeout | [611](https://github.com/laminlabs/lamindb-setup/pull/611) | [falexwolf](https://github.com/falexwolf) | 2024-01-08 | 0.64.1
 🚸 Add anonymous access (now works without login) | [610](https://github.com/laminlabs/lamindb-setup/pull/610) | [falexwolf](https://github.com/falexwolf) | 2024-01-06 | 0.64.0

{lamindb-0.67.1 → lamindb-0.67.2}/sub/lamindb-setup/lamindb_setup/dev/upath.py

@@ -412,8 +412,9 @@ def create_path(pathlike: Union[str, Path, UPath]) -> UPath:
     else:
         raise ValueError("pathlike should be of type Union[str, Path, UPath]")
 
-    # ensures there's no trailing slash for directories
-    path = UPath(path.as_posix().rstrip("/"))
+    # remove trailing slash
+    if path._parts[-1] == "":
+        path._parts = path._parts[:-1]
 
     if isinstance(path, S3Path):
         path = UPath(path, cache_regions=True)

lamindb-0.67.2/sub/lamindb-setup/tests/prod-only/test_upath.py

@@ -0,0 +1,18 @@
+from lamindb_setup.dev.upath import UPath, create_path
+
+
+def test_create_path():
+    upath = UPath("s3://lndb-setup-ci/xyz/", default_fill_cache=False)
+    assert "default_fill_cache" in upath._kwargs
+
+    upath = create_path(upath)
+    # test option inheritance
+    assert "default_fill_cache" in upath._kwargs
+    # test cache_regions setting for s3
+    assert "cache_regions" in upath._kwargs
+    # test removal of training slash
+    assert upath.as_posix()[-1] != "/"
+    assert (
+        UPath("s3://lndb-setup-ci/xyz").as_posix()
+        == create_path("s3://lndb-setup-ci/xyz/").as_posix()
+    )

{lamindb-0.67.1 → lamindb-0.67.2}/sub/lamindb-setup/tests/prod-staging/test_load_instance.py

@@ -1,8 +1,8 @@
 import os
 
 import pytest
-from laminhub_rest.routers.collaborator import delete_collaborator
-from laminhub_rest.routers.instance import add_collaborator
+from laminhub_rest.core.collaborator._add_collaborator import add_collaborator
+from laminhub_rest.core.collaborator._delete_collaborator import delete_collaborator
 
 import lamindb_setup as ln_setup
 from lamindb_setup.dev._hub_client import connect_hub_with_auth
@@ -29,13 +29,13 @@ def test_load_after_revoked_access():
         ln_setup.login(
             "static-testuser1@lamin.ai", password="static-testuser1-password"
         )
-        admin_token = ln_setup.settings.user.access_token
+        admin_hub = connect_hub_with_auth()
         add_collaborator(
             "static-testuser2",
             "laminlabs",
             "static-testinstance1",
             "write",
-            f"Bearer {admin_token}",
+            admin_hub,
         )
         ln_setup.login(
             "static-testuser2@lamin.ai", password="static-testuser2-password"
@@ -46,7 +46,7 @@ def test_load_after_revoked_access():
             "laminlabs",
             "static-testinstance1",
             ln_setup.settings.user.uuid,
-            f"Bearer {admin_token}",
+            admin_hub,
         )
         with pytest.raises(RuntimeError) as error:
             ln_setup.load("https://lamin.ai/laminlabs/static-testinstance1", _test=True)

lamindb-0.67.1/sub/lamin-cli/lamin_cli/__init__.py

@@ -1,3 +0,0 @@
-"""Lamin CLI."""
-
-__version__ = "0.6.1"