🚚 Move transform settings into settings (#1498)

docs/annotate.ipynb

@@ -60,8 +60,8 @@
    "source": [
     "bt.settings.auto_save_parents = False  # ignores ontological hierarchy\n",
     "ln.settings.verbosity = \"info\"\n",
-    "ln.transform.stem_uid = \"sU0y1kF3igep\"\n",
-    "ln.transform.version = \"0\""
+    "ln.settings.transform.stem_uid = \"sU0y1kF3igep\"\n",
+    "ln.settings.transform.version = \"0\""
    ]
   },
   {

docs/faq/key.ipynb

@@ -125,8 +125,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.transform.stem_uid = \"WIwaNDvlEkwS\"\n",
-    "ln.transform.version = \"1\"\n",
+    "ln.settings.transform.stem_uid = \"WIwaNDvlEkwS\"\n",
+    "ln.settings.transform.version = \"1\"\n",
     "ln.track()"
    ]
   },

docs/faq/setup.ipynb

@@ -84,8 +84,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.transform.stem_uid = \"2lhqA4uTKSFP\"\n",
-    "ln.transform.version = \"0\"\n",
+    "ln.settings.transform.stem_uid = \"2lhqA4uTKSFP\"\n",
+    "ln.settings.transform.version = \"0\"\n",
     "ln.track()"
    ]
   },

docs/faq/track-run-inputs.ipynb

@@ -78,8 +78,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.transform.stem_uid = \"Rx2s9aPTMQLY\"\n",
-    "ln.transform.version = \"1\"\n",
+    "ln.settings.transform.stem_uid = \"Rx2s9aPTMQLY\"\n",
+    "ln.settings.transform.version = \"1\"\n",
     "ln.track()"
    ]
   },

docs/introduction.ipynb

@@ -71,8 +71,8 @@
     "ln.setup.init(schema=\"bionty\", storage=\"./lamin-intro\")\n",
     "\n",
     "# tag your code with auto-generated identifiers for a script or notebook\n",
-    "ln.transform.stem_uid = \"FPnfDtJz8qbE\"\n",
-    "ln.transform.version = \"1\"\n",
+    "ln.settings.transform.stem_uid = \"FPnfDtJz8qbE\"\n",
+    "ln.settings.transform.version = \"1\"\n",
     "\n",
     "# track the execution of a transform with a global run context\n",
     "ln.track()"

docs/meta.ipynb

@@ -67,8 +67,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.transform.stem_uid = \"vldHzF3aTAiW\"\n",
-    "ln.transform.version = \"1\"\n",
+    "ln.settings.transform.stem_uid = \"vldHzF3aTAiW\"\n",
+    "ln.settings.transform.version = \"1\"\n",
     "ln.track()"
    ]
   },

docs/track.ipynb

@@ -67,8 +67,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.transform.stem_uid = \"9priar0hoE5u\"\n",
-    "ln.transform.version = \"0\"\n",
+    "ln.settings.transform.stem_uid = \"9priar0hoE5u\"\n",
+    "ln.settings.transform.version = \"0\"\n",
     "ln.track()"
    ]
   },

docs/transfer.ipynb

@@ -48,8 +48,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.transform.stem_uid = \"ITeOtm7bhtdq\"\n",
-    "ln.transform.version = \"1\"\n",
+    "ln.settings.transform.stem_uid = \"ITeOtm7bhtdq\"\n",
+    "ln.settings.transform.version = \"1\"\n",
     "ln.track()"
    ]
   },

docs/tutorial.ipynb

@@ -118,8 +118,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.transform.stem_uid = \"NJvdsWWbJlZS\"\n",
-    "ln.transform.version = \"0\"\n",
+    "ln.settings.transform.stem_uid = \"NJvdsWWbJlZS\"\n",
+    "ln.settings.transform.version = \"0\"\n",
     "ln.track()"
    ]
   },

docs/tutorial2.ipynb

@@ -703,8 +703,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.transform.stem_uid = \"dMtrt8YMSdl6\"\n",
-    "ln.transform.version = \"1\"\n",
+    "ln.settings.transform.stem_uid = \"dMtrt8YMSdl6\"\n",
+    "ln.settings.transform.version = \"1\"\n",
     "\n",
     "ln.track()"
    ]

lamindb/__init__.py

@@ -107,7 +107,7 @@ def __getattr__(name):
     from ._view import view
     from .core._run_context import run_context
     from .core._settings import settings
-    from .core._transform_settings import transform_settings as transform
+    from .core._transform_settings import transform  # backward compat
 
     # schema modules
     if not _os.environ.get("LAMINDB_MULTI_INSTANCE") == "true":

lamindb/core/_run_context.py

@@ -16,7 +16,7 @@
 from lnschema_core.types import TransformType
 from lnschema_core.users import current_user_id
 
-from lamindb.core._transform_settings import transform_settings
+from lamindb.core._transform_settings import transform as transform_settings
 
 from ._settings import settings
 from ._sync_git import get_transform_reference_from_git_repo
@@ -77,7 +77,7 @@ def get_stem_uid_and_version_from_file(file_path: str) -> Tuple[str, str]:
 
     if stem_uid is None or version is None:
         raise SystemExit(
-            f"ln.transform.stem_uid and ln.transform.version aren't set in {file_path}\n"
+            f"ln.settings.transform.stem_uid and ln.settings.transform.version aren't set in {file_path}\n"
             "Call ln.track() and copy/paste the output into the notebook"
         )
     return stem_uid, version
@@ -124,7 +124,7 @@ def update_stem_uid_or_version(
         updated = new_version != version
     if updated:
         new_metadata = (
-            f'ln.transform.stem_uid = "{new_stem_uid}"\nln.transform.version ='
+            f'ln.settings.transform.stem_uid = "{new_stem_uid}"\nln.settings.transform.version ='
             f' "{new_version}"\n'
         )
         raise SystemExit(
@@ -167,8 +167,8 @@ def get_notebook_name_colab() -> str:
 
 MESSAGE = """To track this {transform_type}, set the following two global variables:
 
-ln.transform.stem_uid = "{stem_uid}"
-ln.transform.version = "{version}"
+ln.settings.transform.stem_uid = "{stem_uid}"
+ln.settings.transform.version = "{version}"
 """
 
 

lamindb/core/_settings.py

@@ -8,6 +8,8 @@
 from lamindb_setup.core._settings_instance import sanitize_git_repo_url
 from upath import UPath
 
+from ._transform_settings import TransformSettings, transform
+
 VERBOSITY_TO_INT = {
     "error": 0,  # 40
     "warning": 1,  # 30
@@ -91,6 +93,11 @@ def _storage_settings(self) -> ln_setup.dev.StorageSettings:
             storage_settings = ln_setup.dev.StorageSettings(root=self._using_storage)
         return storage_settings
 
+    @property
+    def transform(self) -> TransformSettings:
+        """Transform settings."""
+        return transform
+
     @property
     def sync_git_repo(self) -> Optional[str]:
         """Sync transforms with scripts in git repository.

lamindb/core/_sync_git.py

@@ -9,6 +9,10 @@
 from ._settings import sanitize_git_repo_url, settings
 
 
+class BlobHashNotFound(SystemExit):
+    pass
+
+
 def get_git_repo_from_remote() -> Path:
     repo_url = settings.sync_git_repo
     repo_dir = setup_settings.storage.cache_dir / repo_url.split("/")[-1]
@@ -27,14 +31,25 @@ def get_git_repo_from_remote() -> Path:
     return repo_dir
 
 
-def check_remote_git_url_matches_setting():
+def check_local_git_repo() -> bool:
     result = subprocess.run(
         "git config --get remote.origin.url",
         shell=True,
         capture_output=True,
     )
-    remote_url = sanitize_git_repo_url(result.stdout.decode().strip())
-    assert remote_url == settings.sync_git_repo
+    result_str = result.stdout.decode().strip()
+    if result_str == "":
+        # running-not-in-a-git-repo
+        return False
+    else:
+        remote_url = sanitize_git_repo_url(result_str)
+        if remote_url == settings.sync_git_repo:
+            # running-in-correct-git-repo
+            return True
+        else:
+            # running-in-wrong-git-repo
+            logger.warning("running in wrong git repo")
+            return False
 
 
 def get_git_commit_hash(
@@ -91,18 +106,19 @@ def get_filepath_within_git_repo(
 
 def get_transform_reference_from_git_repo(path: Path) -> str:
     blob_hash = hash_code(path).hexdigest()
-    commit_hash = get_git_commit_hash(blob_hash)
-    if commit_hash is not None:
-        logger.warning("found script in local repository")
-        check_remote_git_url_matches_setting()
+    commit_hash = None
+    if check_local_git_repo():
         repo_dir = None
     else:
         repo_dir = get_git_repo_from_remote()
-        commit_hash = get_git_commit_hash(blob_hash, repo_dir=repo_dir)
-        if commit_hash is None:
-            raise RuntimeError(
-                f"Did not find blob hash {blob_hash} of {path} in git repo {repo_dir}"
-            )
+    commit_hash = get_git_commit_hash(blob_hash, repo_dir=repo_dir)
+    if commit_hash is None:
+        if repo_dir is None:
+            repo_dir = Path.cwd()
+        raise BlobHashNotFound(
+            f"❌ Did not find blob hash {blob_hash} in git repo ({settings.sync_git_repo}) {repo_dir}\n"
+            f"Did you commit the script? -> {path}"
+        )
     gitpath = get_filepath_within_git_repo(commit_hash, blob_hash, repo_dir)
     reference = f"{settings.sync_git_repo}/blob/{commit_hash}/{gitpath}"
     return reference

lamindb/core/_transform_settings.py

@@ -1,11 +1,9 @@
 from typing import Optional
 
 
-# user-facing name
-class transform:
+class TransformSettings:
     stem_uid: Optional[None] = None
     version: Optional[None] = None
 
 
-# internal name
-transform_settings = transform
+transform = TransformSettings()

tests/notebooks/no-title.ipynb

@@ -27,8 +27,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.transform.stem_uid = \"Irn3xQyQ40GU\"\n",
-    "ln.transform.version = \"1\"\n",
+    "ln.settings.transform.stem_uid = \"Irn3xQyQ40GU\"\n",
+    "ln.settings.transform.version = \"1\"\n",
     "\n",
     "with pytest.raises(NoTitleError):\n",
     "    ln.track()"

tests/test_run_context.py

@@ -103,6 +103,6 @@ def test_sync_git_repo():
     transform = ln.Transform.filter(name="initialized.py").one()
     assert (
         transform.reference
-        == "https://github.com/laminlabs/lamin-cli/blob/39fb29b1b3ccc891a025b5a631d6294413b6ee45/tests/scripts/initialized.py"
+        == "https://github.com/laminlabs/lamin-cli/blob/4244dadaf8e189549d614c54d49c78e35b00da85/tests/scripts/initialized.py"
     )
     assert transform.reference_type == "url"