lamin_cli 1.6.1__tar.gz → 1.7.0__tar.gz

{lamin_cli-1.6.1 → lamin_cli-1.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamin_cli
-Version: 1.6.1
+Version: 1.7.0
 Summary: Lamin CLI.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Description-Content-Type: text/markdown

lamin_cli-1.7.0/lamin_cli/__init__.py

@@ -0,0 +1,3 @@
+"""Lamin CLI."""
+
+__version__ = "1.7.0"

{lamin_cli-1.6.1 → lamin_cli-1.7.0}/lamin_cli/__main__.py

@@ -19,6 +19,8 @@ from lamindb_setup._init_instance import (
     DOC_STORAGE_ARG,
 )
 
+from .urls import decompose_url
+
 if TYPE_CHECKING:
     from collections.abc import Mapping
 
@@ -114,8 +116,9 @@ def main():
 
 @main.command()
 @click.argument("user", type=str, default=None, required=False)
-@click.option("--key", type=str, default=None, help="The legacy API key.")
+@click.option("--key", type=str, default=None, hidden=True, help="The legacy API key.")
 def login(user: str, key: str | None):
+    # note that the docstring needs to be synced with ln.setup.login()
     """Log into LaminHub.
 
     `lamin login` prompts for your API key unless you set it via environment variable `LAMIN_API_KEY`.
@@ -123,24 +126,12 @@ def login(user: str, key: str | None):
     You can create your API key in your account settings on LaminHub (top right corner).
 
     After authenticating once, you can re-authenticate and switch between accounts via `lamin login myhandle`.
+
+    See also: Login in a Python session via {func}`~lamindb.setup.login`.
     """
     from lamindb_setup._setup_user import login as login_
 
-    if user is None:
-        if "LAMIN_API_KEY" in os.environ:
-            api_key = os.environ["LAMIN_API_KEY"]
-        else:
-            api_key = input("Your API key: ")
-    else:
-        api_key = None
-
-    if key is not None:
-        click.echo(
-            "--key is deprecated and will be removed in the future, "
-            "use `lamin login` and enter your API key."
-        )
-
-    return login_(user, key=key, api_key=api_key)
+    return login_(user, key=key)
 
 
 @main.command()
@@ -175,7 +166,10 @@ def init(
     db: str | None,
     modules: str | None,
 ):
-    """Init an instance."""
+    """Init a LaminDB instance.
+
+    See also: Init in a Python session via {func}`~lamindb.setup.init`.
+    """
     from lamindb_setup._init_instance import init as init_
 
     return init_(storage=storage, db=db, modules=modules, name=name)
@@ -186,15 +180,13 @@ def init(
 @click.argument("instance", type=str)
 # fmt: on
 def connect(instance: str):
-    """Connect to an instance.
+    """Configure default instance for connections.
 
-    Pass a slug (`account/name`) or URL (`https://lamin.ai/account/name`).
+    Python/R sessions and CLI commands will then auto-connect to the configured instance.
 
-    `lamin connect` switches
-    {attr}`~lamindb.setup.core.SetupSettings.auto_connect` to `True` so that you
-    auto-connect in a Python session upon importing `lamindb`.
+    Pass a slug (`account/name`) or URL (`https://lamin.ai/account/name`).
 
-    Alternatively, you can connect in a Python session via {func}`~lamindb.connect`.
+    See also: Connect in a Python session via {func}`~lamindb.connect`.
     """
     from lamindb_setup._connect_instance import _connect_cli
     return _connect_cli(instance)
@@ -202,13 +194,13 @@ def connect(instance: str):
 
 @main.command()
 def disconnect():
-    """Disconnect from an instance.
+    """Clear default instance configuration.
 
-    Is the opposite of connecting to an instance.
+    See also: Disconnect in a Python session via {func}`~lamindb.setup.disconnect`.
     """
-    from lamindb_setup import close as close_
+    from lamindb_setup import disconnect as disconnect_
 
-    return close_()
+    return disconnect_()
 
 
 # fmt: off
@@ -277,7 +269,10 @@ def switch(branch: str | None = None, space: str | None = None):
 @main.command()
 @click.option("--schema", is_flag=True, help="View database schema.")
 def info(schema: bool):
-    """Show info about the environment, instance, branch, space, and user."""
+    """Show info about the environment, instance, branch, space, and user.
+
+    See also: Print the instance settings in a Python session via {func}`~lamindb.setup.settings`.
+    """
     if schema:
         from lamindb_setup._schema import view
 
@@ -300,14 +295,21 @@ def info(schema: bool):
 def delete(entity: str, name: str | None = None, uid: str | None = None, slug: str | None = None, force: bool = False):
     """Delete an entity.
 
-    Currently supported: `branch`, `artifact`, and `instance`.
+    Currently supported: `branch`, `artifact`, `transform`, `collection`, and `instance`. For example:
 
     ```
-    lamin delete instance --slug account/name
+    lamin delete https://lamin.ai/account/instance/artifact/e2G7k9EVul4JbfsEYAy5
     lamin delete branch --name my_branch
+    lamin delete instance --slug account/name
     ```
     """
-    from lamindb_setup._delete import delete
+    from lamindb_setup import connect, delete
+
+    # TODO: refactor to abstract getting and deleting across entities
+    if entity.startswith("https://") and "lamin" in entity:
+        url = entity
+        instance, entity, uid = decompose_url(url)
+        connect(instance)
 
     if entity == "branch":
         assert name is not None, "You have to pass a name for deleting a branch."
@@ -319,6 +321,16 @@ def delete(entity: str, name: str | None = None, uid: str | None = None, slug: s
         from lamindb import Artifact
 
         Artifact.get(uid).delete()
+    elif entity == "transform":
+        assert uid is not None, "You have to pass a uid for deleting an transform."
+        from lamindb import Transform
+
+        Transform.get(uid).delete()
+    elif entity == "collection":
+        assert uid is not None, "You have to pass a uid for deleting an collection."
+        from lamindb import Collection
+
+        Collection.get(uid).delete()
     elif entity == "instance":
         return delete(slug, force=force)
     else:  # backwars compatibility
@@ -387,10 +399,14 @@ def _describe(entity: str = "artifact", uid: str | None = None, key: str | None
 def describe(entity: str = "artifact", uid: str | None = None, key: str | None = None):
     """Describe an artifact.
 
+    Examples:
+
     ```
     lamin describe --key example_datasets/mini_immuno/dataset1.h5ad
     lamin describe https://lamin.ai/laminlabs/lamin-site-assets/artifact/6sofuDVvTANB0f48
     ```
+
+    See also: Describe an artifact in a Python session via {func}`~lamindb.Artifact.describe`.
     """
     _describe(entity=entity, uid=uid, key=key)
 
@@ -402,7 +418,7 @@ def describe(entity: str = "artifact", uid: str | None = None, key: str | None =
 def get(entity: str = "artifact", uid: str | None = None, key: str | None = None):
     """Query metadata about an entity.
 
-    Currently still equivalent to `lamin describe`.
+    Currently equivalent to `lamin describe`.
     """
     logger.warning("please use `lamin describe` instead of `lamin get` to describe")
     _describe(entity=entity, uid=uid, key=key)
@@ -420,7 +436,7 @@ def get(entity: str = "artifact", uid: str | None = None, key: str | None = None
 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".
+    Example: Given a valid project name "my_project",
 
     ```
     lamin save my_table.csv --key my_tables/my_table.csv --project my_project
@@ -448,7 +464,7 @@ def save(path: str, key: str, description: str, stem_uid: str, project: str, spa
 def annotate(key: str, uid: str, project: str, registry: str, features: tuple):
     """Annotate an artifact or a transform.
 
-    You can annotate with projects and valid features & values.
+    You can annotate with projects and valid features & values. For example,
 
     ```
     lamin annotate --key raw/sample.fastq --project "My Project"
@@ -511,7 +527,7 @@ def run(filepath: str, project: str, image_url: str, packages: str, cpu: int, gp
 
     This is an EXPERIMENTAL feature that enables to run a script on Modal.
 
-    Example: Given a valid project name "my_project".
+    Example: Given a valid project name "my_project",
 
     ```
     lamin run my_script.py --project my_project

{lamin_cli-1.6.1 → lamin_cli-1.7.0}/lamin_cli/_load.py

@@ -6,15 +6,8 @@ from pathlib import Path
 
 from lamin_utils import logger
 
-
-def decompose_url(url: str) -> tuple[str, str, str]:
-    assert any(keyword in url for keyword in ["transform", "artifact", "collection"])
-    for entity in ["transform", "artifact", "collection"]:
-        if entity in url:
-            break
-    uid = url.split(f"{entity}/")[1]
-    instance_slug = "/".join(url.split("/")[3:5])
-    return instance_slug, entity, uid
+from ._save import parse_title_r_notebook
+from .urls import decompose_url
 
 
 def load(
@@ -55,27 +48,21 @@ def load(
             else:
                 new_content = transform.source_code
         else:  # R notebook
-            # Pattern to match title only within YAML header section
-            title_pattern = r'^---\n.*?title:\s*"([^"]*)".*?---'
-            title_match = re.search(
-                title_pattern, transform.source_code, flags=re.DOTALL | re.MULTILINE
-            )
             new_content = transform.source_code
-            if title_match:
-                current_title = title_match.group(1)
-                if current_title != transform.description:
-                    pattern = r'^(---\n.*?title:\s*)"([^"]*)"(.*?---)'
-                    replacement = f'\\1"{transform.description}"\\3'
-                    new_content = re.sub(
-                        pattern,
-                        replacement,
-                        new_content,
-                        flags=re.DOTALL | re.MULTILINE,
-                    )
-                    logger.important(
-                        f"updated title to match description: {current_title} →"
-                        f" {transform.description}"
-                    )
+            current_title = parse_title_r_notebook(new_content)
+            if current_title is not None and current_title != transform.description:
+                pattern = r'^(---\n.*?title:\s*)"([^"]*)"(.*?---)'
+                replacement = f'\\1"{transform.description}"\\3'
+                new_content = re.sub(
+                    pattern,
+                    replacement,
+                    new_content,
+                    flags=re.DOTALL | re.MULTILINE,
+                )
+                logger.important(
+                    f"updated title to match description: {current_title} →"
+                    f" {transform.description}"
+                )
         if bump_revision:
             uid = transform.uid
             if (

{lamin_cli-1.6.1 → lamin_cli-1.7.0}/lamin_cli/_save.py

@@ -61,6 +61,16 @@ def parse_uid_from_code(content: str, suffix: str) -> str | None:
     return uid
 
 
+def parse_title_r_notebook(content: str) -> str | None:
+    # Pattern to match title only within YAML header section
+    title_pattern = r'^---\n.*?title:\s*"([^"]*)".*?---'
+    title_match = re.search(title_pattern, content, flags=re.DOTALL | re.MULTILINE)
+    if title_match:
+        return title_match.group(1)
+    else:
+        return None
+
+
 def save_from_path_cli(
     path: Path | str,
     key: str | None,
@@ -187,8 +197,7 @@ def save_from_path_cli(
                 )
                 return "delete-html-or-nb-html"
 
-        with path.open() as file:
-            content = file.read()
+        content = path.read_text()
         uid = parse_uid_from_code(content, path.suffix)
 
         if uid is not None:
@@ -217,10 +226,18 @@ def save_from_path_cli(
             transform = ln.Transform.filter(key=path.name, is_latest=True).one_or_none()
             if transform is not None and transform.hash is not None:
                 if transform.hash == transform_hash:
-                    logger.important(
-                        f"found existing Transform('{uid}') with matching hash"
-                    )
-                    return None
+                    if transform.type != "notebook":
+                        return None
+                    if os.getenv("LAMIN_TESTING") == "true":
+                        response = "y"
+                    else:
+                        response = input(
+                            f"Found an existing Transform('{transform.uid}') "
+                            "with matching source code hash.\n"
+                            "Do you want to update it? (y/n) "
+                        )
+                    if response != "y":
+                        return None
                 else:
                     # we need to create a new version
                     stem_uid = transform.uid[:12]
@@ -241,6 +258,8 @@ def save_from_path_cli(
 
                 nb = read_notebook(path)
                 description = get_title(nb)
+            elif path.suffix in {".qmd", ".Rmd"}:
+                description = parse_title_r_notebook(content)
             else:
                 description = None
             transform = ln.Transform(
@@ -262,17 +281,17 @@ def save_from_path_cli(
         # latest run of this transform by user
         run = ln.Run.filter(transform=transform).order_by("-started_at").first()
         if run is not None and run.created_by.id != ln_setup.settings.user.id:
-            if os.environ.get("LAMIN_TESTING") == "true":
+            if os.getenv("LAMIN_TESTING") == "true":
                 response = "y"
             else:
                 response = input(
                     "You are trying to save a transform created by another user: Source"
                     " and report files will be tagged with *your* user id. Proceed?"
-                    " (y/n)"
+                    " (y/n) "
                 )
             if response != "y":
                 return "aborted-save-notebook-created-by-different-user"
-        if run is None and transform.key.endswith(".ipynb"):
+        if run is None and transform.type == "notebook":
             run = ln.Run(transform=transform).save()
             logger.important(
                 f"found no run, creating Run('{run.uid}') to display the html"

lamin_cli-1.7.0/lamin_cli/urls.py

@@ -0,0 +1,8 @@
+def decompose_url(url: str) -> tuple[str, str, str]:
+    assert any(keyword in url for keyword in ["transform", "artifact", "collection"])
+    for entity in ["transform", "artifact", "collection"]:
+        if entity in url:
+            break
+    uid = url.split(f"{entity}/")[1]
+    instance_slug = "/".join(url.split("/")[3:5])
+    return instance_slug, entity, uid

lamin_cli-1.6.1/lamin_cli/__init__.py

@@ -1,3 +0,0 @@
-"""Lamin CLI."""
-
-__version__ = "1.6.1"