lamin_cli 0.21.3__tar.gz → 0.22.0__tar.gz

{lamin_cli-0.21.3 → lamin_cli-0.22.0}/PKG-INFO

@@ -1,10 +1,9 @@
 Metadata-Version: 2.1
 Name: lamin_cli
-Version: 0.21.3
+Version: 0.22.0
 Summary: Lamin CLI.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Description-Content-Type: text/markdown
-Requires-Dist: lamindb_setup==0.81.1
 Requires-Dist: rich-click>=1.7
 Project-URL: Home, https://github.com/laminlabs/lamin-cli
 

lamin_cli-0.22.0/lamin_cli/__init__.py

@@ -0,0 +1,3 @@
+"""Lamin CLI."""
+
+__version__ = "0.22.0"

{lamin_cli-0.21.3 → lamin_cli-0.22.0}/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
 
 
@@ -35,16 +36,39 @@ 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":
+            new_content = transform.source_code.replace(
+                "# # transform.name", f"# # {transform.name}"
+            )
+        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.name:
+                    pattern = r'^(---\n.*?title:\s*)"([^"]*)"(.*?---)'
+                    replacement = f'\\1"{transform.name}"\\3'
+                    new_content = re.sub(
+                        pattern,
+                        replacement,
+                        new_content,
+                        flags=re.DOTALL | re.MULTILINE,
+                    )
+                    logger.important(f"fixed title: {current_title} → {transform.name}")
         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
 
@@ -61,11 +85,7 @@ 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:
@@ -87,8 +107,8 @@ def load(entity: str, uid: str = None, key: str = None, with_env: bool = False):
                 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.key.endswith((".ipynb", ".Rmd", ".qmd")):
+                script_to_notebook(transform, Path(target_filename), bump_revision=True)
             else:
                 Path(target_filename).write_text(transform.source_code)
         else:

{lamin_cli-0.21.3 → lamin_cli-0.22.0}/lamin_cli/_save.py

@@ -94,14 +94,23 @@ 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 = (
@@ -156,16 +165,6 @@ 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-0.21.3 → lamin_cli-0.22.0}/pyproject.toml

@@ -8,9 +8,6 @@ authors = [{name = "Lamin Labs", email = "open-source@lamin.ai"}]
 readme = "README.md"
 dynamic = ["version", "description"]
 dependencies = [
-    # lamindb-setup is only pinned here
-    # NOT in lamindb
-    "lamindb_setup==0.81.1",
     "rich-click>=1.7",
 ]
 

{lamin_cli-0.21.3 → lamin_cli-0.22.0}/tests/test_save_scripts.py

@@ -54,7 +54,6 @@ def test_run_save_cache():
     assert "loaded Transform" in result.stdout.decode()
     assert "m5uCHTTp" in result.stdout.decode()
     assert "started Run" in result.stdout.decode()
-    assert "source code is already saved" in result.stdout.decode()
 
     # you can re-save the script
     result = subprocess.run(
@@ -66,7 +65,6 @@ def test_run_save_cache():
     # print(result.stdout.decode())
     # print(result.stderr.decode())
     assert result.returncode == 0
-    assert "source code is already saved" in result.stdout.decode()
     assert "run.environment is already saved" in result.stdout.decode()
 
     # edit the script
@@ -204,7 +202,6 @@ def test_run_save_with_params():
     print(result.stdout.decode())
     print(result.stderr.decode())
     assert result.returncode == 0
-    assert "source code is already saved" in result.stdout.decode()
     assert (
         "run-track-with-params.py' on uid 'JjRF4mACd9m00000'" in result.stdout.decode()
     )

lamin_cli-0.21.3/lamin_cli/__init__.py

@@ -1,3 +0,0 @@
-"""Lamin CLI."""
-
-__version__ = "0.21.3"