lamin_cli 1.10.0__py2.py3-none-any.whl → 1.11.0__py2.py3-none-any.whl

lamin_cli/__init__.py

@@ -6,7 +6,7 @@ The interface is defined in `__main__.py`.
 The root API here is used by LaminR to replicate the CLI functionality.
 """
 
-__version__ = "1.10.0"
+__version__ = "1.11.0"
 
 from lamindb_setup import disconnect, logout
 from lamindb_setup._connect_instance import _connect_cli as connect

lamin_cli/__main__.py

@@ -42,6 +42,10 @@ COMMAND_GROUPS = {
             "name": "Load, save, create & delete data",
             "commands": ["load", "save", "create", "delete"],
         },
+        {
+            "name": "Tracking within shell scripts",
+            "commands": ["track", "finish"],
+        },
         {
             "name": "Describe, annotate & list data",
             "commands": ["describe", "annotate", "list"],
@@ -436,6 +440,41 @@ def save(path: str, key: str, description: str, stem_uid: str, project: str, spa
     if save_(path=path, key=key, description=description, stem_uid=stem_uid, project=project, space=space, branch=branch, registry=registry) is not None:
         sys.exit(1)
 
+@main.command()
+def track():
+    """Start tracking a run of a shell script.
+
+    This command works like {func}`~lamindb.track()` in a Python session. Here is an example script:
+
+    ```
+    # my_script.sh
+    set -e         # exit on error
+    lamin track    # initiate a tracked shell script run
+    lamin load --key raw/file1.txt
+    # do something
+    lamin save processed_file1.txt --key processed/file1.txt
+    lamin finish   # mark the shell script run as finished
+    ```
+
+    If you run that script, it will track the run of the script, and save the input and output artifacts:
+
+    ```
+    sh my_script.sh
+    ```
+    """
+    from lamin_cli._context import track as track_
+    return track_()
+
+
+@main.command()
+def finish():
+    """Finish the current tracked run of a shell script.
+
+    This command works like {func}`~lamindb.finish()` in a Python session.
+    """
+    from lamin_cli._context import finish as finish_
+    return finish_()
+
 
 @main.command()
 @click.argument("entity", type=str, default=None, required=False)

lamin_cli/_context.py

@@ -0,0 +1,76 @@
+import os
+import sys
+from pathlib import Path
+
+import click
+from lamin_utils import logger
+from lamindb_setup.core._settings_store import settings_dir
+
+
+def get_current_run_file() -> Path:
+    """Get the path to the file storing the current run UID."""
+    return settings_dir / "current_shell_run.txt"
+
+
+def is_interactive_shell() -> bool:
+    """Check if running in an interactive terminal."""
+    return sys.stdin.isatty() and sys.stdout.isatty() and os.isatty(0)
+
+
+def get_script_filename() -> Path:
+    """Try to get the filename of the calling shell script."""
+    import psutil
+
+    parent = psutil.Process(os.getppid())
+    cmdline = parent.cmdline()
+
+    # For shells like bash, sh, zsh
+    if parent.name() in ["bash", "sh", "zsh", "dash"]:
+        # cmdline is typically: ['/bin/bash', 'script.sh', ...]
+        if len(cmdline) > 1 and not cmdline[1].startswith("-"):
+            return Path(cmdline[1])
+    raise click.ClickException(
+        "Cannot determine script filename. Please run in an interactive shell."
+    )
+
+
+def track():
+    import lamindb as ln
+
+    if not ln.setup.settings._instance_exists:
+        raise click.ClickException(
+            "Not connected to an instance. Please run: lamin connect account/name"
+        )
+    path = get_script_filename()
+    source_code = path.read_text()
+    transform = ln.Transform(
+        key=path.name, source_code=source_code, type="script"
+    ).save()
+    run = ln.Run(transform=transform).save()
+    current_run_file = get_current_run_file()
+    current_run_file.parent.mkdir(parents=True, exist_ok=True)
+    current_run_file.write_text(run.uid)
+    logger.important(f"started tracking shell run: {run.uid}")
+
+
+def finish():
+    from datetime import datetime, timezone
+
+    import lamindb as ln
+
+    if not ln.setup.settings._instance_exists:
+        raise click.ClickException(
+            "Not connected to an instance. Please run: lamin connect account/name"
+        )
+
+    current_run_file = get_current_run_file()
+    if not current_run_file.exists():
+        raise click.ClickException(
+            "No active run to finish. Please run `lamin track` first."
+        )
+    run = ln.Run.get(uid=current_run_file.read_text().strip())
+    run._status_code = 0
+    run.finished_at = datetime.now(timezone.utc)
+    run.save()
+    current_run_file.unlink()
+    logger.important(f"finished tracking shell run: {run.uid}")

lamin_cli/_io.py

@@ -30,7 +30,7 @@ def io():
 @click.option("--track/--no-track", is_flag=True, help="Whether to track snapshot generation.", default=True)
 # fmt: on
 def snapshot(upload: bool, track: bool) -> None:
-    """Create and optionally upload a SQLite snapshot of the current instance."""
+    """Create a SQLite snapshot of the connected instance."""
     if not ln_setup.settings._instance_exists:
         raise click.ClickException(
             "Not connected to an instance. Please run: lamin connect account/name"
@@ -86,8 +86,8 @@ def snapshot(upload: bool, track: bool) -> None:
                     for table, (orig, clone) in mismatches.items()]
                 )
                 raise click.ClickException(error_msg)
-            except json.JSONDecodeError:
-                error_msg = f"Clone verification failed:\n{result.stderr}"
+            except (json.JSONDecodeError, AttributeError, ValueError, TypeError):
+                raise click.ClickException(f"Clone verification failed:\n{result.stderr}") from None
 
 
         ln_setup.connect(f"{instance_owner}/{instance_name}", use_root_db_user=True)

lamin_cli/_load.py

@@ -6,6 +6,7 @@ from pathlib import Path
 
 from lamin_utils import logger
 
+from ._context import get_current_run_file
 from ._save import infer_registry_from_path, parse_title_r_notebook
 from .urls import decompose_url
 
@@ -48,6 +49,10 @@ def load(
     ln_setup.connect(instance)
     import lamindb as ln
 
+    current_run = None
+    if get_current_run_file().exists():
+        current_run = ln.Run.get(uid=get_current_run_file().read_text().strip())
+
     def script_to_notebook(
         transform: ln.Transform, notebook_path: Path, bump_revision: bool = False
     ) -> None:
@@ -182,7 +187,7 @@ def load(
                 entities = entities.order_by("-created_at")
 
             entity_obj = entities.first()
-            cache_path = entity_obj.cache()
+            cache_path = entity_obj.cache(is_run_input=current_run)
 
             # collection gives us a list of paths
             if isinstance(cache_path, list):

lamin_cli/_save.py

@@ -9,17 +9,23 @@ import lamindb_setup as ln_setup
 from lamin_utils import logger
 from lamindb_setup.core.hashing import hash_file
 
+from lamin_cli._context import get_current_run_file
+
 
 def infer_registry_from_path(path: Path | str) -> str:
     suffixes_transform = {
         "py": {".py", ".ipynb"},
         "R": {".R", ".qmd", ".Rmd"},
+        "sh": {".sh"},
     }
     if isinstance(path, str):
         path = Path(path)
     registry = (
         "transform"
-        if path.suffix in suffixes_transform["py"].union(suffixes_transform["R"])
+        if path.suffix
+        in suffixes_transform["py"]
+        .union(suffixes_transform["R"])
+        .union(suffixes_transform["sh"])
         else "artifact"
     )
     return registry
@@ -42,9 +48,11 @@ def parse_uid_from_code(content: str, suffix: str) -> str | None:
             r'track\(\s*(?:transform\s*=\s*)?([\'"])([a-zA-Z0-9]{12,16})\1'
         )
         uid_pattern = None
+    elif suffix == ".sh":
+        return None
     else:
         raise SystemExit(
-            "Only .py, .ipynb, .R, .qmd, .Rmd files are supported for saving"
+            "Only .py, .ipynb, .R, .qmd, .Rmd, .sh files are supported for saving"
             " transforms."
         )
 
@@ -82,8 +90,13 @@ def save(
 ) -> str | None:
     import lamindb as ln
     from lamindb._finish import save_context_core
+    from lamindb_setup.core._settings_store import settings_dir
     from lamindb_setup.core.upath import LocalPathClasses, UPath, create_path
 
+    current_run = None
+    if get_current_run_file().exists():
+        current_run = ln.Run.get(uid=get_current_run_file().read_text().strip())
+
     # this allows to have the correct treatment of credentials in case of cloud paths
     ppath = create_path(path)
     # isinstance is needed to cast the type of path to UPath
@@ -149,6 +162,7 @@ def save(
             revises=revises,
             branch=branch_record,
             space=space_record,
+            run=current_run,
         ).save()
         logger.important(f"saved: {artifact}")
         logger.important(f"storage path: {artifact.path}")
@@ -219,7 +233,7 @@ def save(
                 if transform is None:
                     uid = f"{stem_uid}0000"
         else:
-            transform_hash, _ = hash_file(ppath)
+            _, transform_hash, _ = hash_file(ppath)
             transform = ln.Transform.filter(hash=transform_hash).first()
             if transform is not None and transform.hash is not None:
                 if transform.hash == transform_hash:
@@ -268,7 +282,7 @@ def save(
                 uid=uid,
                 description=description,
                 key=key,
-                type="script" if ppath.suffix in {".R", ".py"} else "notebook",
+                type="script" if ppath.suffix in {".R", ".py", ".sh"} else "notebook",
                 revises=revises,
             )
             if space is not None:

{lamin_cli-1.10.0.dist-info → lamin_cli-1.11.0.dist-info}/METADATA

@@ -1,10 +1,9 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.3
 Name: lamin_cli
-Version: 1.10.0
+Version: 1.11.0
 Summary: Lamin CLI.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Description-Content-Type: text/markdown
-License-File: LICENSE
 Requires-Dist: rich-click>=1.7
 Project-URL: Home, https://github.com/laminlabs/lamin-cli
 

{lamin_cli-1.10.0.dist-info → lamin_cli-1.11.0.dist-info}/RECORD

@@ -1,12 +1,13 @@
-lamin_cli/__init__.py,sha256=EEqwDNhBI_f1OthJACbb7XrDCxzXxoPuIkCP0wbdWdk,605
-lamin_cli/__main__.py,sha256=zGMlXpDgKZpfQqIsedPnk0S8-jy0NEFcF4amtyIOHE0,19721
+lamin_cli/__init__.py,sha256=bd6la8_wxlClB7o8h3FNAjQ6z8HPcZ4QqxvVp4Cvycg,605
+lamin_cli/__main__.py,sha256=DEifHuxyyffXHVpBjn9-LVpVUsuSnRhicxTfsuZ0YUw,20791
 lamin_cli/_annotate.py,sha256=ZD76__K-mQt7UpYqyM1I2lKCs-DraTmnkjsByIHmD-g,1839
 lamin_cli/_cache.py,sha256=oplwE8AcS_9PYptQUZxff2qTIdNFS81clGPkJNWk098,800
+lamin_cli/_context.py,sha256=JLhv98isasX_M_o6tIDkeBWcNH8ryRrl3nk2rmwsuD4,2392
 lamin_cli/_delete.py,sha256=1wp8LQdiWHJznRrm4abxEhApB9derBWEm25ufrzjvIg,1531
-lamin_cli/_io.py,sha256=v103aEmMPegQQJGUfsrAB5rzdLN4NqkN07ZxhglTv7o,4989
-lamin_cli/_load.py,sha256=OqkOJe2Afq4ZrN5abM1ueqaDDvm1psdnQmzhXTTWe1I,8233
+lamin_cli/_io.py,sha256=DboDoecZN5OLCHe5vJzOLuwztW8hxbdRffWj1kmJ9WI,5036
+lamin_cli/_load.py,sha256=v7PCB7sYqGs6jF186aN191lTV2Mr5jdayHKSmdgsw_k,8445
 lamin_cli/_migration.py,sha256=w-TLYC2q6sqcfNtIUewqRW_69_xy_71X3eSV7Ud58jk,1239
-lamin_cli/_save.py,sha256=bysKSkivcvELW1srOoc772udOzREEnFRVPUClBJ9Qac,12084
+lamin_cli/_save.py,sha256=8dM4blz6caKJtbqND-6xJXUMlGIvo2FwvSu1CDcBPig,12517
 lamin_cli/_settings.py,sha256=nqVM8FO9kjL0SXYqP8x-Xfww6Qth4I86HKKeTirsgc4,2657
 lamin_cli/urls.py,sha256=gc72s4SpaAQA8J50CtCIWlr49DWOSL_a6OM9lXfPouM,367
 lamin_cli/clone/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -14,8 +15,8 @@ lamin_cli/clone/_clone_verification.py,sha256=8hRFZt_1Z0i2wMqKBkrioq01RJEjwHy9cY
 lamin_cli/clone/create_sqlite_clone_and_import_db.py,sha256=yv2mLkHdRUao_IkZO_4Swu5w4Nieh1gMrBwPbyn4c1o,1544
 lamin_cli/compute/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 lamin_cli/compute/modal.py,sha256=QnR7GyyvWWWkLnou95HxS9xxSQfw1k-SiefM_qRVnU0,6010
-lamin_cli-1.10.0.dist-info/entry_points.txt,sha256=Qms85i9cZPlu-U7RnVZhFsF7vJ9gaLZUFkCjcGcXTpg,49
-lamin_cli-1.10.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-lamin_cli-1.10.0.dist-info/WHEEL,sha256=Dyt6SBfaasWElUrURkknVFAZDHSTwxg3PaTza7RSbkY,100
-lamin_cli-1.10.0.dist-info/METADATA,sha256=QIppUnCd0P8oMGAcvCSREQo5De9ifM_uomSTgfWdH6k,360
-lamin_cli-1.10.0.dist-info/RECORD,,
+lamin_cli-1.11.0.dist-info/entry_points.txt,sha256=Qms85i9cZPlu-U7RnVZhFsF7vJ9gaLZUFkCjcGcXTpg,49
+lamin_cli-1.11.0.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamin_cli-1.11.0.dist-info/WHEEL,sha256=ssQ84EZ5gH1pCOujd3iW7HClo_O_aDaClUbX4B8bjKY,100
+lamin_cli-1.11.0.dist-info/METADATA,sha256=4TK6hWuABuBxr1PYF_iBpm7KP8xNH7g4LjMWUkHgDKE,338
+lamin_cli-1.11.0.dist-info/RECORD,,

{lamin_cli-1.10.0.dist-info → lamin_cli-1.11.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: flit 3.12.0
+Generator: flit 3.10.1
 Root-Is-Purelib: true
 Tag: py2-none-any
 Tag: py3-none-any