lamin_cli 0.21.4__py2.py3-none-any.whl → 1.0a1__py2.py3-none-any.whl

lamin_cli/__init__.py

@@ -1,3 +1,3 @@
 """Lamin CLI."""
 
-__version__ = "0.21.4"
+__version__ = "1.0a1"

lamin_cli/__main__.py

@@ -165,7 +165,7 @@ def connect(instance: str):
     from lamindb_setup import settings as settings_, connect as connect_
 
     settings_.auto_connect = True
-    return connect_(slug=instance)
+    return connect_(slug=instance, _reload_lamindb=False)
 
 
 @main.command()
@@ -239,7 +239,7 @@ def load(entity: str, uid: str = None, key: str = None, with_env: bool = False):
         #     f"! please use: lamin connect {entity}"
         # )
         settings_.auto_connect = True
-        return connect(slug=entity)
+        return connect(slug=entity, _reload_lamindb=False)
     else:
         from lamin_cli._load import load as load_
 

lamin_cli/_load.py

@@ -2,6 +2,7 @@ from __future__ import annotations
 from typing import Tuple
 from lamin_utils import logger
 import shutil
+import re
 from pathlib import Path
 
 
@@ -27,7 +28,7 @@ def load(entity: str, uid: str = None, key: str = None, with_env: bool = False):
         instance = ln_setup.settings.instance.slug
 
     ln_setup.connect(instance)
-    from lnschema_core import models as ln
+    import lamindb as ln
 
     def script_to_notebook(
         transform: ln.Transform, notebook_path: Path, bump_revision: bool = False
@@ -35,16 +36,48 @@ def load(entity: str, uid: str = None, key: str = None, with_env: bool = False):
         import jupytext
         from lamin_utils._base62 import increment_base62
 
-        py_content = transform.source_code.replace(
-            "# # transform.name", f"# # {transform.name}"
-        )
+        if notebook_path.suffix == ".ipynb":
+            # below is backward compat
+            if "# # transform.name" in transform.source_code:
+                new_content = transform.source_code.replace(
+                    "# # transform.name", f"# # {transform.description}"
+                )
+            elif transform.source_code.startswith("# %% [markdown]\n#\n"):
+                new_content = transform.source_code.replace(
+                    "# %% [markdown]\n#\n",
+                    f"# %% [markdown]\n# # {transform.description}\n",
+                )
+        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"fixed title: {current_title} → {transform.description}"
+                    )
         if bump_revision:
             uid = transform.uid
             new_uid = f"{uid[:-4]}{increment_base62(uid[-4:])}"
-            py_content = py_content.replace(uid, new_uid)
+            new_content = new_content.replace(uid, new_uid)
             logger.important(f"updated uid: {uid} → {new_uid}")
-        notebook = jupytext.reads(py_content, fmt="py:percent")
-        jupytext.write(notebook, notebook_path)
+        if notebook_path.suffix == ".ipynb":
+            notebook = jupytext.reads(new_content, fmt="py:percent")
+            jupytext.write(notebook, notebook_path)
+        else:
+            notebook_path.write_text(new_content)
 
     query_by_uid = uid is not None
 
@@ -61,42 +94,36 @@ def load(entity: str, uid: str = None, key: str = None, with_env: bool = False):
             transforms = ln.Transform.objects.filter(key=key, source_code__isnull=False)
 
         if (n_transforms := len(transforms)) == 0:
-            err_msg = (
-                f"uid strating with {uid}"
-                if query_by_uid
-                else f"key={key} and source_code"
-            )
+            err_msg = f"uid {uid}" if query_by_uid else f"key={key} and source_code"
             raise SystemExit(f"Transform with {err_msg} does not exist.")
 
         if n_transforms > 1:
             transforms = transforms.order_by("-created_at")
         transform = transforms.first()
 
-        target_filename = transform.key
-        if Path(target_filename).exists():
-            response = input(f"! {target_filename} exists: replace? (y/n)")
+        target_relpath = Path(transform.key)
+        if len(target_relpath.parents) > 1:
+            logger.important(
+                "preserve the folder structure for versioning:"
+                f" {target_relpath.parent}/"
+            )
+            target_relpath.parent.mkdir(parents=True, exist_ok=True)
+        if target_relpath.exists():
+            response = input(f"! {target_relpath} exists: replace? (y/n)")
             if response != "y":
                 raise SystemExit("Aborted.")
-        if transform._source_code_artifact_id is not None:  # backward compat
-            # need lamindb here to have .cache() available
-            import lamindb as ln
 
-            ln.settings.track_run_inputs = False
-            filepath_cache = transform._source_code_artifact.cache()
-            if not target_filename.endswith(transform._source_code_artifact.suffix):
-                target_filename += transform._source_code_artifact.suffix
-            shutil.move(filepath_cache, target_filename)
-        elif transform.source_code is not None:
-            if transform.key.endswith(".ipynb"):
-                script_to_notebook(transform, target_filename, bump_revision=True)
+        if transform.source_code is not None:
+            if target_relpath.suffix in (".ipynb", ".Rmd", ".qmd"):
+                script_to_notebook(transform, target_relpath, bump_revision=True)
             else:
-                Path(target_filename).write_text(transform.source_code)
+                target_relpath.write_text(transform.source_code)
         else:
             raise SystemExit("No source code available for this transform.")
-        logger.important(f"{transform.type} is here: {target_filename}")
-        if with_env:
-            import lamindb as ln
 
+        logger.important(f"{transform.type} is here: {target_relpath}")
+
+        if with_env:
             ln.settings.track_run_inputs = False
             if (
                 transform.latest_run is not None
@@ -104,16 +131,15 @@ def load(entity: str, uid: str = None, key: str = None, with_env: bool = False):
             ):
                 filepath_env_cache = transform.latest_run.environment.cache()
                 target_env_filename = (
-                    ".".join(target_filename.split(".")[:-1]) + "__requirements.txt"
+                    target_relpath.parent / f"{target_relpath.stem}__requirements.txt"
                 )
                 shutil.move(filepath_env_cache, target_env_filename)
                 logger.important(f"environment is here: {target_env_filename}")
             else:
                 logger.warning("latest transform run with environment doesn't exist")
-        return target_filename
-    elif entity == "artifact":
-        import lamindb as ln
 
+        return target_relpath
+    elif entity == "artifact":
         ln.settings.track_run_inputs = False
 
         if query_by_uid:
@@ -124,7 +150,7 @@ def load(entity: str, uid: str = None, key: str = None, with_env: bool = False):
             artifacts = ln.Artifact.filter(key=key)
 
         if (n_artifacts := len(artifacts)) == 0:
-            err_msg = f"uid strating with {uid}" if query_by_uid else f"key={key}"
+            err_msg = f"uid={uid}" if query_by_uid else f"key={key}"
             raise SystemExit(f"Artifact with {err_msg} does not exist.")
 
         if n_artifacts > 1:

lamin_cli/_save.py

@@ -1,43 +1,27 @@
 from __future__ import annotations
 from pathlib import Path
 from typing import Union
-import lamindb_setup as ln_setup
 from lamin_utils import logger
 import re
 
 
-def parse_uid_from_code(
-    content: str, suffix: str
-) -> tuple[str | None, str | None, str | None]:
+def parse_uid_from_code(content: str, suffix: str) -> str | None:
     if suffix == ".py":
         track_pattern = re.compile(
             r'ln\.track\(\s*(?:transform\s*=\s*)?(["\'])([a-zA-Z0-9]{16})\1'
         )
-        # backward compat
         uid_pattern = re.compile(r'\.context\.uid\s*=\s*["\']([^"\']+)["\']')
-        stem_uid_pattern = re.compile(
-            r'\.transform\.stem_uid\s*=\s*["\']([^"\']+)["\']'
-        )
-        version_pattern = re.compile(r'\.transform\.version\s*=\s*["\']([^"\']+)["\']')
     elif suffix == ".ipynb":
         track_pattern = re.compile(
             r'ln\.track\(\s*(?:transform\s*=\s*)?(?:\\"|\')([a-zA-Z0-9]{16})(?:\\"|\')'
         )
         # backward compat
         uid_pattern = re.compile(r'\.context\.uid\s*=\s*\\["\']([^"\']+)\\["\']')
-        stem_uid_pattern = re.compile(
-            r'\.transform\.stem_uid\s*=\s*\\["\']([^"\']+)\\["\']'
-        )
-        version_pattern = re.compile(
-            r'\.transform\.version\s*=\s*\\["\']([^"\']+)\\["\']'
-        )
     elif suffix in {".R", ".qmd", ".Rmd"}:
         track_pattern = re.compile(
             r'track\(\s*(?:transform\s*=\s*)?([\'"])([a-zA-Z0-9]{16})\1'
         )
         uid_pattern = None
-        stem_uid_pattern = None
-        version_pattern = None
     else:
         raise SystemExit(
             "Only .py, .ipynb, .R, .qmd, .Rmd files are supported for saving"
@@ -48,26 +32,12 @@ def parse_uid_from_code(
     uid_match = track_pattern.search(content)
     group_index = 1 if suffix == ".ipynb" else 2
     uid = uid_match.group(group_index) if uid_match else None
-    stem_uid = None
-    version = None
 
     if uid_pattern is not None and uid is None:
         uid_match = uid_pattern.search(content)
         uid = uid_match.group(1) if uid_match else None
-    if stem_uid_pattern is not None:
-        stem_uid_match = stem_uid_pattern.search(content)
-        stem_uid = stem_uid_match.group(1) if stem_uid_match else None
-    if version_pattern is not None:
-        version_match = version_pattern.search(content)
-        version = version_match.group(1) if version_match else None
-
-    if uid is None and (stem_uid is None or version is None):
-        target = "script" if suffix in {".py", ".R"} else "notebook"
-        raise SystemExit(
-            f"Cannot infer transform uid. Did you run `ln.track()` in your {target}?"
-        )
 
-    return uid, stem_uid, version
+    return uid
 
 
 def save_from_filepath_cli(
@@ -76,6 +46,8 @@ def save_from_filepath_cli(
     description: str | None,
     registry: str | None,
 ) -> str | None:
+    import lamindb_setup as ln_setup
+
     if not isinstance(filepath, Path):
         filepath = Path(filepath)
 
@@ -94,14 +66,23 @@ def save_from_filepath_cli(
         "R": set([".R", ".qmd", ".Rmd"]),
     }
 
-    if (
-        filepath.suffix in {".qmd", ".Rmd"}
-        and not filepath.with_suffix(".html").exists()
-    ):
-        raise SystemExit(
-            f"Please export your {filepath.suffix} file as an html file here"
-            f" {filepath.with_suffix('.html')}"
-        )
+    if filepath.suffix in {".qmd", ".Rmd"}:
+        if not (
+            filepath.with_suffix(".html").exists()
+            or filepath.with_suffix(".nb.html").exists()
+        ):
+            raise SystemExit(
+                f"Please export your {filepath.suffix} file as an html file here"
+                f" {filepath.with_suffix('.html')}"
+            )
+        if (
+            filepath.with_suffix(".html").exists()
+            and filepath.with_suffix(".nb.html").exists()
+        ):
+            raise SystemExit(
+                f'Please delete one of\n - {filepath.with_suffix(".html")}\n -'
+                f' {filepath.with_suffix(".nb.html")}'
+            )
 
     if registry is None:
         registry = (
@@ -128,9 +109,9 @@ def save_from_filepath_cli(
     elif registry == "transform":
         with open(filepath) as file:
             content = file.read()
-        uid, stem_uid, version = parse_uid_from_code(content, filepath.suffix)
-        logger.important(f"mapped '{filepath}' on uid '{uid}'")
+        uid = parse_uid_from_code(content, filepath.suffix)
         if uid is not None:
+            logger.important(f"mapped '{filepath}' on uid '{uid}'")
             transform = ln.Transform.filter(uid=uid).one_or_none()
             if transform is None:
                 logger.error(
@@ -139,10 +120,17 @@ def save_from_filepath_cli(
                 )
                 return "not-tracked-in-transform-registry"
         else:
-            transform = ln.Transform.get(uid__startswith=stem_uid, version=version)
+            transform = ln.Transform.filter(key=filepath.name).one_or_none()
+            if transform is None:
+                transform = ln.Transform(
+                    name=filepath.name,
+                    key=filepath.name,
+                    type="script" if filepath.suffix in {".R", ".py"} else "notebook",
+                ).save()
+                logger.important(f"created Transform('{transform.uid}')")
         # latest run of this transform by user
         run = ln.Run.filter(transform=transform).order_by("-started_at").first()
-        if run.created_by.id != ln_setup.settings.user.id:
+        if run is not None and run.created_by.id != ln_setup.settings.user.id:
             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?"
@@ -156,16 +144,6 @@ def save_from_filepath_cli(
             filepath=filepath,
             from_cli=True,
         )
-        if filepath.suffix in {".qmd", ".Rmd"}:
-            report_file = ln.Artifact(
-                filepath.with_suffix(".html"),  # validated at the top that this exists
-                description=f"Report of run {run.uid}",
-                visibility=0,  # hidden file
-                run=False,
-            )
-            report_file.save(upload=True, print_progress=False)
-            run.report = report_file
-            run.save()
         return return_code
     else:
         raise SystemExit("Allowed values for '--registry' are: 'artifact', 'transform'")

{lamin_cli-0.21.4.dist-info → lamin_cli-1.0a1.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: lamin_cli
-Version: 0.21.4
+Version: 1.0a1
 Summary: Lamin CLI.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Description-Content-Type: text/markdown

lamin_cli-1.0a1.dist-info/RECORD

@@ -0,0 +1,12 @@
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+lamin_cli/__main__.py,sha256=CnwhcWeSJwLdq4esnewNKc6Z-T4AuZ8EMDmILfpBZF0,9946
+lamin_cli/_cache.py,sha256=kW8rqlMwQeOngm9uq2gjzPVl3EBrwh6W2F2AvyBFABY,799
+lamin_cli/_load.py,sha256=I2UGifZdIbbLm0JBOsuoR2CZeq5_uQR1BwIujDq8WfA,6694
+lamin_cli/_migration.py,sha256=xTbad6aDUwuK0QvWCmDW3f8-xaqwisS-Cqf-LbD1WRI,1071
+lamin_cli/_save.py,sha256=PrvZSL02jU1BWLUEVTTQsn2MLi942RKOyN3Qd3qfl6s,5677
+lamin_cli/_settings.py,sha256=iS37mcQUHKRWxi2sHnAojEI6sWk3w232qwG-GeY2_Qc,1141
+lamin_cli-1.0a1.dist-info/entry_points.txt,sha256=Qms85i9cZPlu-U7RnVZhFsF7vJ9gaLZUFkCjcGcXTpg,49
+lamin_cli-1.0a1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamin_cli-1.0a1.dist-info/WHEEL,sha256=ssQ84EZ5gH1pCOujd3iW7HClo_O_aDaClUbX4B8bjKY,100
+lamin_cli-1.0a1.dist-info/METADATA,sha256=4t0BVXkfQyWzahzefrlFl2vG0MRyYmxfNoT6rvQdcJg,337
+lamin_cli-1.0a1.dist-info/RECORD,,

{lamin_cli-0.21.4.dist-info → lamin_cli-1.0a1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: flit 3.9.0
+Generator: flit 3.10.1
 Root-Is-Purelib: true
 Tag: py2-none-any
 Tag: py3-none-any

lamin_cli-0.21.4.dist-info/RECORD

@@ -1,12 +0,0 @@
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-lamin_cli/__main__.py,sha256=-QAfgrYKcPjl0qkiWr8Tfm5wRaaZ99rW2atjIBnBn9Y,9900
-lamin_cli/_cache.py,sha256=kW8rqlMwQeOngm9uq2gjzPVl3EBrwh6W2F2AvyBFABY,799
-lamin_cli/_load.py,sha256=n0_qHTCXsZQIUy87rVdPvT89fx60N-KZgn_dL8nsvEA,5523
-lamin_cli/_migration.py,sha256=xTbad6aDUwuK0QvWCmDW3f8-xaqwisS-Cqf-LbD1WRI,1071
-lamin_cli/_save.py,sha256=X5Rn1rmvtoKz10oZXWWDK3XmNchFhruQ_is-sE8Q-BM,6575
-lamin_cli/_settings.py,sha256=iS37mcQUHKRWxi2sHnAojEI6sWk3w232qwG-GeY2_Qc,1141
-lamin_cli-0.21.4.dist-info/entry_points.txt,sha256=Qms85i9cZPlu-U7RnVZhFsF7vJ9gaLZUFkCjcGcXTpg,49
-lamin_cli-0.21.4.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-lamin_cli-0.21.4.dist-info/WHEEL,sha256=Sgu64hAMa6g5FdzHxXv9Xdse9yxpGGMeagVtPMWpJQY,99
-lamin_cli-0.21.4.dist-info/METADATA,sha256=tWTkIflVJ0CM_3pwig0RnfF0eddeR6LntJKyf2_GI5c,338
-lamin_cli-0.21.4.dist-info/RECORD,,