lamindb 0.76.10__tar.gz → 0.76.11__tar.gz

{lamindb-0.76.10 → lamindb-0.76.11}/.github/workflows/build.yml

@@ -107,7 +107,7 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.10" # use 3.10, 3.8 and 3.11 give issues
-      - run: pip install -U laminci
+      - run: pip install "laminci@git+https://x-access-token:${{ secrets.LAMIN_BUILD_DOCS }}@github.com/laminlabs/laminci"
       - run: nox -s "install_ci(group='docs')"
       - uses: actions/download-artifact@v4
       - run: nox -s docs

{lamindb-0.76.10 → lamindb-0.76.11}/.gitmodules

@@ -16,3 +16,6 @@
 [submodule "sub/clinicore"]
 	path = sub/clinicore
 	url = https://github.com/laminlabs/clinicore
+[submodule "sub/findrefs"]
+	path = sub/findrefs
+	url = https://github.com/laminlabs/findrefs

{lamindb-0.76.10 → lamindb-0.76.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.76.10
+Version: 0.76.11
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.9
@@ -9,9 +9,9 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Requires-Dist: lnschema_core==0.74.6
-Requires-Dist: lamindb_setup==0.77.6
+Requires-Dist: lamindb_setup==0.77.7
 Requires-Dist: lamin_utils==0.13.6
-Requires-Dist: lamin_cli==0.17.7
+Requires-Dist: lamin_cli==0.17.8
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -23,7 +23,7 @@ Requires-Dist: pandas
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.51.0 ; extra == "bionty"
+Requires-Dist: bionty==0.51.1 ; extra == "bionty"
 Requires-Dist: line_profiler ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"

{lamindb-0.76.10 → lamindb-0.76.11}/docs/api.md

@@ -18,6 +18,8 @@ cli
 lamindb
 bionty
 wetlab
+clinicore
+findrefs
 ```
 
 ```{toctree}

lamindb-0.76.11/docs/clinicore.md

@@ -0,0 +1,5 @@
+# `clinicore`
+
+```{eval-rst}
+.. automodule:: clinicore
+```

{lamindb-0.76.10 → lamindb-0.76.11}/docs/curate-any.ipynb

@@ -24,7 +24,7 @@
     "\n",
     "{class}`~lamindb.core.CanValidate` methods validate against the registries in your LaminDB instance.\n",
     "In {doc}`./bio-registries`, you'll see how to extend standard validation to validation against _public references_ using a `ReferenceTable` ontology object: `public = Record.public()`.\n",
-    "By default, {meth}`~lamindb.core.Record.from_values` considers a match in a public reference a validated value for any {mod}`bionty` entity.\n",
+    "By default, {meth}`~lamindb.core.CanValidate.from_values` considers a match in a public reference a validated value for any {mod}`bionty` entity.\n",
     "\n",
     ":::"
    ]
@@ -131,7 +131,7 @@
    "source": [
     "Following the suggestions to register new labels:\n",
     "\n",
-    "Bulk creating records using {meth}`~lamindb.core.Record.from_values` only returns validated records:\n",
+    "Bulk creating records using {meth}`~lamindb.core.CanValidate.from_values` only returns validated records:\n",
     "\n",
     "Note: Terms validated with public reference are also created with `.from_values`, see {doc}`/bio-registries` for details."
    ]

lamindb-0.76.11/docs/findrefs.md

@@ -0,0 +1,5 @@
+# `findrefs`
+
+```{eval-rst}
+.. automodule:: findrefs
+```

{lamindb-0.76.10 → lamindb-0.76.11}/docs/track.ipynb

@@ -29,7 +29,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Initiate tracking"
+    "## Track data lineage"
    ]
   },
   {
@@ -39,47 +39,20 @@
     "Call {meth}`~lamindb.track` to register a data transformation and start tracking inputs & outputs of a run. You will find your notebook or script in the {class}`~lamindb.Transform` registry along with pipelines & functions. {class}`~lamindb.Run` stores executions."
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "tags": [
-     "hide-output"
-    ]
-   },
-   "outputs": [],
-   "source": [
-    "import lamindb as ln\n",
-    "\n",
-    "# call `ln.track()` to generate a uid that identifies your code\n",
-    "\n",
-    "ln.track(\"9priar0hoE5u0000\")  # call `ln.track(uid)` to track a run with inputs & outputs"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "LaminDB now automatically tracks all input and output data of the current run.\n",
+    "```python\n",
+    "import lamindb as ln\n",
     "\n",
-    "Note: You can access a `requirments.txt` via `ln.context.run.environment`."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Track run report & source code"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "If you want to save the run report & source code for a notebook or script, call:\n",
+    "# --> `ln.track()` generates a uid for your code\n",
+    "# --> `ln.track(uid)` initiates a tracked run\n",
+    "ln.track(\"9priar0hoE5u0000\")\n",
     "\n",
-    "```python\n",
-    "ln.finish()\n",
+    "# your code\n",
+    "\n",
+    "ln.finish()  # mark run as finished, save execution report, source code & environment\n",
     "```"
    ]
   },
@@ -87,7 +60,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Below is how a notebook with run report looks on the hub.\n",
+    "Below is how [a notebook](https://lamin.ai/laminlabs/lamindata/transform/PtTXoc0RbOIq65cN) with run report looks on the hub.\n",
     "\n",
     "<img src=\"https://lamin-site-assets.s3.amazonaws.com/.lamindb/RGXj5wcAf7EAc6J8dJfH.png\" width=\"900px\">"
    ]
@@ -188,6 +161,8 @@
    },
    "outputs": [],
    "source": [
+    "import lamindb as ln\n",
+    "\n",
     "ln.Param(name=\"input_dir\", dtype=\"str\").save()\n",
     "ln.Param(name=\"learning_rate\", dtype=\"float\").save()\n",
     "ln.Param(name=\"downsample\", dtype=\"bool\").save()"

{lamindb-0.76.10 → lamindb-0.76.11}/docs/tutorial.ipynb

@@ -116,9 +116,9 @@
    "source": [
     "import lamindb as ln\n",
     "\n",
-    "# call `ln.track()` to generate a uid that identifies your code\n",
-    "\n",
-    "ln.track(\"NJvdsWWbJlZS0000\")  # call `ln.track(uid)` to track a run with inputs & outputs\n"
+    "# --> `ln.track()` generates a uid for your code\n",
+    "# --> `ln.track(uid)` initiates a tracked run\n",
+    "ln.track(\"NJvdsWWbJlZS0000\")\n"
    ]
   },
   {
@@ -947,7 +947,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.17"
+   "version": "3.10.13"
   },
   "vscode": {
    "interpreter": {

{lamindb-0.76.10 → lamindb-0.76.11}/lamindb/__init__.py

@@ -43,7 +43,7 @@ Modules and settings.
 """
 
 # denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
-__version__ = "0.76.10"
+__version__ = "0.76.11"
 
 import os as _os
 

{lamindb-0.76.10 → lamindb-0.76.11}/lamindb/_finish.py

@@ -35,6 +35,13 @@ def prepare_notebook(
                     if strip_title:
                         lines.pop(i)
                         cell["source"] = "\n".join(lines)
+        # strip resaved finish error if present
+        # this is normally the last cell
+        if cell["cell_type"] == "code" and ".finish(" in cell["source"]:
+            for output in cell["outputs"]:
+                if output.get("ename", None) == "NotebookNotSaved":
+                    cell["outputs"] = []
+                    break
     return None
 
 
@@ -112,7 +119,7 @@ def save_context_core(
         notebook_content = read_notebook(filepath)  # type: ignore
         if not ignore_non_consecutive:  # ignore_non_consecutive is None or False
             is_consecutive = check_consecutiveness(
-                notebook_content, calling_statement=".finish()"
+                notebook_content, calling_statement=".finish("
             )
             if not is_consecutive:
                 response = "n"  # ignore_non_consecutive == False

{lamindb-0.76.10 → lamindb-0.76.11}/lamindb/core/_label_manager.py

@@ -90,10 +90,9 @@ def print_labels(
             # there is a try except block here to deal with schema inconsistencies
             # during transfer between instances
             try:
-                field = get_name_field(self.__class__)
+                field = get_name_field(labels)
                 labels_list = list(labels.values_list(field, flat=True))
                 if len(labels_list) > 0:
-                    get_name_field(labels)
                     print_values = _print_values(labels_list, n=10)
                     type_str = f": {related_model}" if print_types else ""
                     labels_msg += f"    .{related_name}{type_str} = {print_values}\n"

{lamindb-0.76.10 → lamindb-0.76.11}/noxfile.py

@@ -117,7 +117,7 @@ def install_ci(session, group):
         run(session, "uv pip install --system mudata")
         run(
             session,
-            "uv pip install --system --no-deps ./sub/wetlab",
+            "uv pip install --system --no-deps ./sub/wetlab ./sub/findrefs ./sub/clinicore",
         )
     elif group == "cli":
         extras += "jupyter,aws,bionty"
@@ -197,7 +197,10 @@ def docs(session):
         if group in {"tutorial", "guide", "biology"}:
             for path in Path(f"./docs/{group}").glob("*"):
                 path.rename(f"./docs/{path.name}")
-    run(session, "lamin init --storage ./docsbuild --schema bionty,wetlab")
+    run(
+        session,
+        "lamin init --storage ./docsbuild --schema bionty,wetlab,clinicore,findrefs",
+    )
 
     def generate_cli_docs():
         os.environ["NO_RICH"] = "1"

{lamindb-0.76.10 → lamindb-0.76.11}/pyproject.toml

@@ -16,9 +16,9 @@ classifiers = [
 dependencies = [
     # Lamin PINNED packages
     "lnschema_core==0.74.6",
-    "lamindb_setup==0.77.6",
+    "lamindb_setup==0.77.7",
     "lamin_utils==0.13.6",
-    "lamin_cli==0.17.7",
+    "lamin_cli==0.17.8",
     # others
     "rapidfuzz",
     "pyarrow",
@@ -37,7 +37,7 @@ Home = "https://github.com/laminlabs/lamindb"
 
 [project.optional-dependencies]
 bionty = [
-    "bionty==0.51.0",
+    "bionty==0.51.1",
 ]
 aws = [
     "lamindb_setup[aws]",

{lamindb-0.76.10 → lamindb-0.76.11}/sub/bionty/bionty/__init__.py

@@ -145,7 +145,7 @@ Bionty base:
 
 """
 
-__version__ = "0.51.0"
+__version__ = "0.51.1"
 
 from lamindb_setup.core._setup_bionty_sources import (
     load_bionty_sources as _load_bionty_sources,

{lamindb-0.76.10 → lamindb-0.76.11}/sub/bionty/bionty/models.py

@@ -430,7 +430,7 @@ class BioRecord(Record, HasParents, CanValidate):
         Notes:
             For more info, see tutorial :doc:`docs:bionty`
 
-            Bulk create records via :meth:`~docs:lamindb.core.Record.from_values`.
+            Bulk create records via :meth:`~docs:lamindb.core.CanValidate.from_values`.
 
         Examples:
             Create a record by passing a field value:
@@ -474,7 +474,7 @@ class BioRecord(Record, HasParents, CanValidate):
         Notes:
             For more info, see tutorial :doc:`docs:bionty`
 
-            Bulk create records via :meth:`~docs:lamindb.core.Record.from_values`.
+            Bulk create records via :meth:`~docs:lamindb.core.CanValidate.from_values`.
 
         Examples:
             Create a record by passing a field value:
@@ -578,7 +578,7 @@ class Gene(BioRecord, TracksRun, TracksUpdates):
     Notes:
         For more info, see tutorials :doc:`docs:bio-registries` and :doc:`docs:gene`.
 
-        Bulk create Gene records via :meth:`~docs:lamindb.core.Record.from_values`.
+        Bulk create Gene records via :meth:`~docs:lamindb.core.CanValidate.from_values`.
         Map legacy ensembl IDs to current ensembl IDs using :meth:`bionty.base.Gene.map_legacy_ids`.
 
     Examples:
@@ -666,7 +666,7 @@ class Protein(BioRecord, TracksRun, TracksUpdates):
     Notes:
         For more info, see tutorials :doc:`docs:bio-registries` and :doc:`docs:protein`.
 
-        Bulk create records via :meth:`~docs:lamindb.core.Record.from_values`.
+        Bulk create records via :meth:`~docs:lamindb.core.CanValidate.from_values`.
 
     Examples:
         >>> record = bionty.Protein.from_source(name="Synaptotagmin-15B", organism="human")
@@ -749,7 +749,7 @@ class CellMarker(BioRecord, TracksRun, TracksUpdates):
     Notes:
         For more info, see tutorials :doc:`docs:bio-registries` and :doc:`docs:cell_marker`.
 
-        Bulk create CellMarker records via :meth:`~docs:lamindb.core.Record.from_values`.
+        Bulk create CellMarker records via :meth:`~docs:lamindb.core.CanValidate.from_values`.
 
     Examples:
         >>> record = bionty.CellMarker.from_source(name="PD1", organism="human")
@@ -830,7 +830,7 @@ class Tissue(BioRecord, TracksRun, TracksUpdates):
     Notes:
         For more info, see tutorials :doc:`docs:bio-registries` :doc:`docs:tissue`.
 
-        Bulk create Tissue records via :meth:`~docs:lamindb.core.Record.from_values`.
+        Bulk create Tissue records via :meth:`~docs:lamindb.core.CanValidate.from_values`.
 
     Examples:
         >>> record = bionty.Tissue.from_source(name="brain")
@@ -902,7 +902,7 @@ class CellType(BioRecord, TracksRun, TracksUpdates):
     Notes:
         For more info, see tutorials :doc:`docs:bio-registries` and :doc:`docs:cell_type`.
 
-        Bulk create CellType records via :meth:`~docs:lamindb.core.Record.from_values`.
+        Bulk create CellType records via :meth:`~docs:lamindb.core.CanValidate.from_values`.
 
     Examples:
         >>> record = bionty.CellType.from_source(name="T cell")
@@ -972,7 +972,7 @@ class Disease(BioRecord, TracksRun, TracksUpdates):
     """Diseases - `Mondo <https://mondo.monarchinitiative.org/>`__, `Human Disease <https://disease-ontology.org/>`__.
 
     Notes:
-        Bulk create Disease records via :meth:`~docs:lamindb.core.Record.from_values`.
+        Bulk create Disease records via :meth:`~docs:lamindb.core.CanValidate.from_values`.
 
         For more info, see tutorials: :doc:`docs:disease`.
 
@@ -1046,7 +1046,7 @@ class CellLine(BioRecord, TracksRun, TracksUpdates):
     Notes:
         For more info, see tutorials :doc:`docs:bio-registries` and :doc:`docs:cell_line`.
 
-        Bulk create CellLine records via :meth:`~docs:lamindb.core.Record.from_values`.
+        Bulk create CellLine records via :meth:`~docs:lamindb.core.CanValidate.from_values`.
 
     Examples:
         >>> standard_name = bionty.CellLine.public().standardize(["K562"])[0]
@@ -1122,7 +1122,7 @@ class Phenotype(BioRecord, TracksRun, TracksUpdates):
     Notes:
         For more info, see tutorials :doc:`docs:bio-registries` and :doc:`docs:phenotype`.
 
-        Bulk create Phenotype records via :meth:`~docs:lamindb.core.Record.from_values`.
+        Bulk create Phenotype records via :meth:`~docs:lamindb.core.CanValidate.from_values`.
 
     Examples:
         >>> record = bionty.Phenotype.from_source(name="Arachnodactyly")
@@ -1196,7 +1196,7 @@ class Pathway(BioRecord, TracksRun, TracksUpdates):
     Notes:
         For more info, see tutorials :doc:`docs:bio-registries` and :doc:`docs:pathway`.
 
-        Bulk create Pathway records via :meth:`~docs:lamindb.core.Record.from_values`.
+        Bulk create Pathway records via :meth:`~docs:lamindb.core.CanValidate.from_values`.
 
     Examples:
         >>> record = bionty.Pathway.from_source(ontology_id="GO:1903353")
@@ -1275,7 +1275,7 @@ class ExperimentalFactor(BioRecord, TracksRun, TracksUpdates):
     Notes:
         For more info, see tutorials :doc:`docs:bio-registries` and :doc:`docs:experimental_factor`.
 
-        Bulk create ExperimentalFactor records via :meth:`~docs:lamindb.core.Record.from_values`.
+        Bulk create ExperimentalFactor records via :meth:`~docs:lamindb.core.CanValidate.from_values`.
 
     Examples:
         >>> standard_name = bionty.ExperimentalFactor.public().standardize(["scRNA-seq"])
@@ -1357,7 +1357,7 @@ class DevelopmentalStage(BioRecord, TracksRun, TracksUpdates):
     Notes:
         For more info, see tutorials :doc:`docs:bio-registries` and :doc:`docs:developmental_stage`.
 
-        Bulk create DevelopmentalStage records via :meth:`~docs:lamindb.core.Record.from_values`.
+        Bulk create DevelopmentalStage records via :meth:`~docs:lamindb.core.CanValidate.from_values`.
 
     Examples:
         >>> record = bionty.DevelopmentalStage.from_source(name="neurula stage")
@@ -1432,7 +1432,7 @@ class Ethnicity(BioRecord, TracksRun, TracksUpdates):
     Notes:
         For more info, see tutorials :doc:`docs:bio-registries` and :doc:`docs:ethnicity`.
 
-        Bulk create Ethnicity records via :meth:`~docs:lamindb.core.Record.from_values`.
+        Bulk create Ethnicity records via :meth:`~docs:lamindb.core.CanValidate.from_values`.
 
     Examples:
         >>> record = bionty.Ethnicity.from_source(name="European")

lamindb-0.76.11/sub/clinicore/.github/workflows/build.yml

@@ -0,0 +1,62 @@
+name: build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main, staging]
+
+jobs:
+  build:
+    runs-on: ubuntu-22.04
+    env:
+      GITHUB_EVENT_NAME: ${{ github.event_name }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python: "3.10"
+          - os: ubuntu-latest
+            python: "3.10"
+            pip-flags: "--pre"
+    timeout-minutes: 15
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/checkout@v4
+        with:
+          repository: laminlabs/lndocs
+          ssh-key: ${{ secrets.READ_LNDOCS }}
+          path: lndocs
+          ref: main
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }}
+      - run: pip install "laminci@git+https://x-access-token:${{ secrets.LAMIN_BUILD_DOCS }}@github.com/laminlabs/laminci"
+      # - run: sudo apt-get -y install graphviz
+      - uses: aws-actions/configure-aws-credentials@v4
+        with:
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          aws-region: us-east-1
+      - run: nox -s lint
+      - run: nox -s build
+      - uses: codecov/codecov-action@v2
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+      - uses: cloudflare/pages-action@v1
+        with:
+          apiToken: ${{ secrets.CLOUDFLARE_API_TOKEN }}
+          accountId: 472bdad691b4483dea759eadb37110bd
+          projectName: clinicore
+          directory: "_build/html"
+          gitHubToken: ${{ secrets.GITHUB_TOKEN }}
+          branch: main
+          wranglerVersion: "3"

lamindb-0.76.11/sub/clinicore/.github/workflows/doc-changes.yml

@@ -0,0 +1,23 @@
+name: doc-changes
+
+on:
+  pull_request_target:
+    branches:
+      - main
+    types:
+      - closed
+
+jobs:
+  latest-changes:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - run: pip install "laminci[doc-changes]@git+https://x-access-token:${{ secrets.LAMIN_BUILD_DOCS }}@github.com/laminlabs/laminci"
+      - run: laminci doc-changes
+        env:
+          repo_token: ${{ secrets.GITHUB_TOKEN }}
+          docs_token: ${{ secrets.LAMIN_BUILD_DOCS }}
+          changelog_file: lamin-docs/docs/changelog/soon/usecases.md

lamindb-0.76.11/sub/clinicore/.gitignore

@@ -0,0 +1,109 @@
+# macOS
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# mypy
+.mypy_cache/
+
+# IDE settings
+.vscode/
+.idea/
+
+# Lamin
+_build
+docs/clinicore.*
+lamin_sphinx
+docs/conf.py
+_docs_tmp*
+docs/test-clinicore/

lamindb-0.76.11/sub/clinicore/.pre-commit-config.yaml

@@ -0,0 +1,51 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - commit
+  - push
+minimum_pre_commit_version: 2.12.0
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.4
+    hooks:
+      - id: prettier
+        exclude: |
+          (?x)(
+            docs/changelog.md
+          )
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.6.1
+    hooks:
+      - id: nbstripout
+        exclude: |
+          (?x)(
+              docs/examples/|
+              docs/notes/
+          )
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.7
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+        exclude: |
+          (?x)(
+              .github/workflows/latest-changes.jinja2
+            )
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.7.1
+    hooks:
+      - id: mypy
+        args: [--no-strict-optional, --ignore-missing-imports]
+        additional_dependencies: ["types-requests", "types-attrs"]

lamindb-0.76.11/sub/clinicore/README.md

@@ -0,0 +1,7 @@
+# clinicore: A clinical schema
+
+This schema is focused on the fundamental concepts of clinical data models.
+
+## Contributing
+
+Please run `pre-commit install` and `gitmoji -i` on the CLI before starting to work on this repository!