Move the Extract-represent-validate-notebook to here (#53)

* update notebook title * update notebook * try without uv for build * no uv * more lenient build * Update .readthedocs.yaml Co-authored-by: Philipp A. <[email protected]> * no lamin to make rtd work? * updated notebook * less dependencies doc? * remove use of lamindb docs temp * add lamin again * try slim vitessce for docs * revert change * revert more settings * no ln.setup.init in conf.py * no ln.setup.init in conf.p * fix warnings doc build * remove info lamin * slight comment improvement * remove commented code conf.py; simpler image display notebook * removed some comments --------- Co-authored-by: Philipp A. <[email protected]>
theislab · Oct 16, 2024 · 2518294 · 2518294
1 parent a2b8215
commit 2518294
Show file tree

Hide file tree

Showing 9 changed files with 1,988 additions and 1,148 deletions.
diff --git a/docs/_static/tutorial_images/laminhub_screenshot.png b/docs/_static/tutorial_images/laminhub_screenshot.png
diff --git a/docs/_static/tutorial_images/vitessce_screenshot.png b/docs/_static/tutorial_images/vitessce_screenshot.png
diff --git a/docs/api.md b/docs/api.md
@@ -20,6 +20,9 @@
 .. autosummary::
     :toctree: generated
 
+    io.omop.setup_obs
+    io.omop.setup_variables
+    io.omop.get_time_interval_table
     io.omop.load
     io.omop.extract_person
     io.omop.extract_observation_period

diff --git a/docs/conf.py b/docs/conf.py
@@ -7,15 +7,14 @@
 from __future__ import annotations
 
 # -- Path setup --------------------------------------------------------------
-from contextlib import suppress
 import sys
 from datetime import datetime
 from importlib.metadata import metadata
 from pathlib import Path
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
-    from sphinx.application import Sphinx
+    pass
 
 
 HERE = Path(__file__).parent
@@ -146,18 +145,12 @@
     ("py:class", "duckdb.duckdb.DuckDBPyConnection"),
     # Is documented as a py:attribute instead
     ("py:class", "numpy.int64"),
+    # For now not in public facing API
+    ("py:class", "awkward.highlevel.Array"),
 ]
 
 # Redirect broken parameter annotation classes
 qualname_overrides = {
     "zarr._storage.store.Store": "zarr.storage.MemoryStore",
     "lnschema_core.models.Artifact": "lamindb.Artifact",
 }
-
-
-def setup(app: Sphinx) -> None:
-    """Setup lamindb for CI."""
-    import lamindb as ln
-
-    with suppress(RuntimeError):
-        ln.setup.init(storage="/tmp/lamindb")
diff --git a/docs/index.md b/docs/index.md
@@ -11,8 +11,8 @@ changelog.md
 contributing.md
 references.md
 
+notebooks/tutorial_omop_visualization
 notebooks/omop_tables_tutorial
-notebooks/tutorial_ehrdata_omop
 notebooks/cohort_definition
 notebooks/study_design_example_omop_cdm
 notebooks/indwelling_arterial_catheters