new feature: torch dataset (#71)

* towards first ehrdataloader

* use of escapechar % caused concept table L2231 to fail, too many columns

* refactor multiple unit to con instead of tensor; add test multiple unit warning

* refactor time interval writing sql query

* activate keyword-only in setup_variables again

* updates and ehrdataset notebook

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* torch optional dependency

* fix typo

* add torch do doc dependencies

* fix doc warning w/ broken link

* fix doc warning w/ 2nd broken link

* add omop_ml to index.md

* fix display of links

* add new things to api doc

* fill placeholders w/ links

* fix 1 more link

* remove mimicii for now from api

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

CHANGELOG.md

@@ -12,4 +12,4 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
--   Basic tool, preprocessing and plotting functions
+- Basic tool, preprocessing and plotting functions

docs/api.md

@@ -37,7 +37,19 @@
     dt.mimic_iv_omop
     dt.gibleed_omop
     dt.synthea27nj_omop
-    dt.mimic_ii
+    dt.physionet2012
+```
+
+## Tools
+
+```{eval-rst}
+.. module:: ehrdata.tl
+.. currentmodule:: ehrdata
+
+.. autosummary::
+    :toctree: generated
+
+    tl.omop.EHRDataset
 ```
 
 ## Plotting

docs/contributing.md

@@ -155,11 +155,11 @@ This will automatically create a git tag and trigger a Github workflow that crea
 Please write documentation for new or changed features and use-cases.
 This project uses [sphinx][] with the following features:
 
--   The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
--   [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
--   Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
--   [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
--   Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
+- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
+- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
+- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
+- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
+- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
 
 See scanpy’s {doc}`scanpy:dev/documentation` for more information on how to write your own.
 
@@ -183,10 +183,10 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu
 
 #### Hints
 
--   If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`.
-    Only if you do so can sphinx automatically create a link to the external documentation.
--   If building the documentation fails because of a missing link that is outside your control,
-    you can add an entry to the `nitpick_ignore` list in `docs/conf.py`
+- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`.
+  Only if you do so can sphinx automatically create a link to the external documentation.
+- If building the documentation fails because of a missing link that is outside your control,
+  you can add an entry to the `nitpick_ignore` list in `docs/conf.py`
 
 (docs-building)=
 

docs/index.md

@@ -17,4 +17,5 @@ notebooks/cohort_definition
 notebooks/study_design_example_omop_cdm
 notebooks/indwelling_arterial_catheters
 notebooks/tutorial_time_series_with_pypots
+notebooks/omop_ml
 ```