lamin_cli 1.4.0__tar.gz → 1.4.2__tar.gz

{lamin_cli-1.4.0 → lamin_cli-1.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamin_cli
-Version: 1.4.0
+Version: 1.4.2
 Summary: Lamin CLI.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Description-Content-Type: text/markdown

lamin_cli-1.4.2/lamin_cli/__init__.py

@@ -0,0 +1,3 @@
+"""Lamin CLI."""
+
+__version__ = "1.4.2"

{lamin_cli-1.4.0 → lamin_cli-1.4.2}/lamin_cli/__main__.py

@@ -314,8 +314,10 @@ def get(entity: str, uid: str | None = None, key: str | None = None):
 @click.option("--description", type=str, default=None, help="A description of the artifact or transform.")
 @click.option("--stem-uid", type=str, default=None, help="The stem uid of the artifact or transform.")
 @click.option("--project", type=str, default=None, help="A valid project name or uid.")
+@click.option("--space", type=str, default=None, help="A valid space name or uid.")
+@click.option("--branch", type=str, default=None, help="A valid branch name or uid.")
 @click.option("--registry", type=str, default=None, help="Either 'artifact' or 'transform'. If not passed, chooses based on path suffix.")
-def save(path: str, key: str, description: str, stem_uid: str, project: str, registry: str):
+def save(path: str, key: str, description: str, stem_uid: str, project: str, space: str, branch: str, registry: str):
     """Save a file or folder.
 
     Example: Given a valid project name "my_project".
@@ -324,13 +326,16 @@ def save(path: str, key: str, description: str, stem_uid: str, project: str, reg
     lamin save my_table.csv --key my_tables/my_table.csv --project my_project
     ```
 
+    By passing a `--project` identifier, the artifact will be labeled with the corresponding project.
+    If you pass a `--space` or `--branch` identifier, you save the artifact in the corresponding {class}`~lamindb.Space` or on the corresponding {class}`~lamindb.Branch`.
+
     Note: Defaults to saving `.py`, `.ipynb`, `.R`, `.Rmd`, and `.qmd` as {class}`~lamindb.Transform` and
     other file types and folders as {class}`~lamindb.Artifact`. You can enforce saving a file as
     an {class}`~lamindb.Artifact` by passing `--registry artifact`.
     """
     from lamin_cli._save import save_from_path_cli
 
-    if save_from_path_cli(path, key, description, stem_uid, project, registry) is not None:
+    if save_from_path_cli(path=path, key=key, description=description, stem_uid=stem_uid, project=project, space=space, branch=branch, registry=registry) is not None:
         sys.exit(1)
 
 

{lamin_cli-1.4.0 → lamin_cli-1.4.2}/lamin_cli/_save.py

@@ -52,6 +52,8 @@ def save_from_path_cli(
     description: str | None,
     stem_uid: str | None,
     project: str | None,
+    space: str | None,
+    branch: str | None,
     registry: str | None,
 ) -> str | None:
     import lamindb_setup as ln_setup
@@ -97,6 +99,20 @@ def save_from_path_cli(
             raise ln.errors.InvalidArgument(
                 f"Project '{project}' not found, either create it with `ln.Project(name='...').save()` or fix typos."
             )
+    if space is not None:
+        space_record = ln.Space.filter(ln.Q(name=space) | ln.Q(uid=space)).one_or_none()
+        if space_record is None:
+            raise ln.errors.InvalidArgument(
+                f"Space '{space}' not found, either create it on LaminHub or fix typos."
+            )
+    if branch is not None:
+        branch_record = ln.Branch.filter(
+            ln.Q(name=branch) | ln.Q(uid=branch)
+        ).one_or_none()
+        if branch_record is None:
+            raise ln.errors.InvalidArgument(
+                f"Branch '{branch}' not found, either create it with `ln.Branch(name='...').save()` or fix typos."
+            )
 
     is_cloud_path = not isinstance(path, LocalPathClasses)
 
@@ -120,9 +136,12 @@ def save_from_path_cli(
             logger.error("Please pass a key or description via --key or --description")
             return "missing-key-or-description"
 
-        artifact = ln.Artifact(
-            path, key=key, description=description, revises=revises
-        ).save()
+        artifact = ln.Artifact(path, key=key, description=description, revises=revises)
+        if space is not None:
+            artifact.space = space_record
+        if branch is not None:
+            artifact.branch = branch_record
+        artifact.save()
         logger.important(f"saved: {artifact}")
         logger.important(f"storage path: {artifact.path}")
         if ln_setup.settings.storage.type == "s3":
@@ -208,7 +227,12 @@ def save_from_path_cli(
                 key=path.name,
                 type="script" if path.suffix in {".R", ".py"} else "notebook",
                 revises=revises,
-            ).save()
+            )
+            if space is not None:
+                transform.space = space_record
+            if branch is not None:
+                transform.branch = branch_record
+            transform.save()
             logger.important(f"created Transform('{transform.uid}')")
         if project is not None:
             transform.projects.add(project_record)

{lamin_cli-1.4.0 → lamin_cli-1.4.2}/tests/core/conftest.py

@@ -7,13 +7,13 @@ from lamin_utils import logger
 
 def pytest_sessionstart(session: pytest.Session):
     ln.setup.init(
-        storage="./default_storage_ci",
-        name="laminci-unit-tests",
+        storage="./default_storage_cli",
+        name="lamin-cli-unit-tests",
     )
     ln.setup.settings.auto_connect = True
 
 
 def pytest_sessionfinish(session: pytest.Session):
     logger.set_verbosity(1)
-    shutil.rmtree("./default_storage_ci")
-    ln.setup.delete("laminci-unit-tests", force=True)
+    shutil.rmtree("./default_storage_cli")
+    ln.setup.delete("lamin-cli-unit-tests", force=True)

{lamin_cli-1.4.0 → lamin_cli-1.4.2}/tests/core/test_migrate.py

@@ -5,9 +5,9 @@ import os
 # import lamindb_setup as ln_setup
 
 
-def test_migrate_create():
-    exit_status = os.system("lamin migrate create")
-    assert exit_status == 0
+# def test_migrate_create():
+#     exit_status = os.system("lamin migrate create")
+#     assert exit_status == 0
 
 
 def test_migrate_deploy():

{lamin_cli-1.4.0 → lamin_cli-1.4.2}/tests/core/test_save_files.py

@@ -24,10 +24,12 @@ def test_save_local_file():
     )
     assert result.returncode == 1
 
-    ln.Project(name="test_project").save()
+    project = ln.Project(name="test_project").save()
+    # cannot define Space with regular user, is defined in lamindb/tests/permissions
+    branch = ln.Branch(name="contrib1").save()
 
     result = subprocess.run(
-        f"lamin save {filepath} --key mytest --project test_project",
+        f"lamin save {filepath} --key mytest --project test_project --branch contrib1",
         shell=True,
         capture_output=True,
     )
@@ -38,6 +40,10 @@ def test_save_local_file():
     assert "labeled with project: test_project" in result.stdout.decode()
     assert result.returncode == 0
 
+    artifact = ln.Artifact.get(key="mytest")
+    assert artifact.branch == branch
+    assert project in artifact.projects.all()
+
     # test passing the registry and saving the same file
     result = subprocess.run(
         f"lamin save {filepath} --key mytest --registry artifact",
@@ -69,14 +75,14 @@ def test_save_local_file():
 def test_save_cloud_file():
     # should be no key for cloud paths
     result = subprocess.run(
-        "lamin save s3://lamindb-ci/lndb-storage/testfile.hdf5 --key filekey.h5ad",
+        "lamin save s3://cellxgene-data-public/cell-census/2024-07-01/h5ads/fe1a73ab-a203-45fd-84e9-0f7fd19efcbd.h5ad --key wrongkey.h5ad",
         shell=True,
         check=False,
     )
     assert result.returncode == 1
 
     result = subprocess.run(
-        "lamin save s3://lamindb-ci/lndb-storage/testfile.hdf5",
+        "lamin save s3://cellxgene-data-public/cell-census/2024-07-01/h5ads/fe1a73ab-a203-45fd-84e9-0f7fd19efcbd.h5ad",
         shell=True,
         check=True,
     )

{lamin_cli-1.4.0 → lamin_cli-1.4.2}/tests/core/test_save_notebooks.py

@@ -196,7 +196,7 @@ print("my consecutive cell")
     # get the the source code via command line
     result = subprocess.run(
         "yes | lamin load"
-        f" https://lamin.ai/{ln.setup.settings.user.handle}/laminci-unit-tests/transform/hlsFXswrJjtt0001",
+        f" https://lamin.ai/{ln.setup.settings.user.handle}/lamin-cli-unit-tests/transform/hlsFXswrJjtt0001",
         shell=True,
         capture_output=True,
     )

{lamin_cli-1.4.0 → lamin_cli-1.4.2}/tests/core/test_save_scripts.py

@@ -187,7 +187,7 @@ if __name__ == "__main__":
     # try to get the source code via command line
     result = subprocess.run(
         "yes | lamin load"
-        f" https://lamin.ai/{settings.user.handle}/laminci-unit-tests/transform/m5uCHTTpJnjQ0000",
+        f" https://lamin.ai/{settings.user.handle}/lamin-cli-unit-tests/transform/m5uCHTTpJnjQ0000",
         shell=True,
         capture_output=True,
     )

lamin_cli-1.4.0/lamin_cli/__init__.py

@@ -1,3 +0,0 @@
-"""Lamin CLI."""
-
-__version__ = "1.4.0"