From 8572ba15d5d1bd21b24c5ae939f036ac12961866 Mon Sep 17 00:00:00 2001 From: Matthew McDermott Date: Mon, 27 May 2024 10:01:36 -0400 Subject: [PATCH 1/4] Update README.md --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index 792fec7..1c2b8ce 100644 --- a/README.md +++ b/README.md @@ -42,6 +42,11 @@ must inherently do a base level of preprocessing over the MEDS data, then will c representation that respects the overall sharding of the raw data. This script uses [Hydra](https://hydra.cc/) to manage configuration, and the configuration file is located at `configs/tabularize.yaml`. +Tabularization will take as input a MEDS dataset in a directory we'll denote `$MEDS_cohort_dir` and will write out a collection of tabularization files to disk in subdirectories of this cohort directory. In particular for a given shard prefix in the raw MEDS cohort (e.g., `train/0`, `held_out/1`, etc.) + 1. In `$MEDS_cohort_dir/tabularized/static/$SHARD_PREFIX.parquet` will be tabularized, wide-format representations of code / value occurrences with null timestamps. In the case that sub-sharding is needed, sub-shards will instead be written as sub-directories of this base directory: `$MEDS_cohort_dir/tabularized/static/$SHARD_PREFIX/$SUB_SHARD.parquet`. This sub-sharding pattern will hold for all files and not be subsequently measured. + 2. In `$MEDS_cohort_dir/tabularized/at_observation/$SHARD_PREFIX.parquet` will be tabularized, wide-format representations of code / value observations for all observations of patient data with a non-null timestamp. + 3. In `$MEDS_cohort_dir/tabularized/over_window/$WINDOW_SIZE/$SHARD_PREFIX.parquet` will be tabularized, wide-format summarization of the code / value occurrences over a window of size `$WINDOW_SIZE` as of the index date at the row's timestamp. + ## AutoML Pipelines # TODOs From 6440485a01c4727c5d1c0711d87d499ba90622d2 Mon Sep 17 00:00:00 2001 From: Teya Bergamaschi Date: Mon, 3 Jun 2024 22:17:29 +0000 Subject: [PATCH 2/4] readthedocs setup --- .readthedocs.yaml | 13 +++ README.md | 65 +++++++------ docs/Makefile | 20 ++++ docs/make.bat | 35 +++++++ docs/source/api.rst | 10 ++ docs/source/conf.py | 93 +++++++++++++++++++ docs/source/generated/scripts.rst | 4 + .../generated/src.MEDS_tabular_automl.rst | 4 + docs/source/generated/src.rst | 30 ++++++ docs/source/generated/tests.rst | 35 +++++++ .../generated/tests.test_saveable_mixin.rst | 23 +++++ .../generated/tests.test_seedable_mixin.rst | 21 +++++ .../tests.test_swapcacheable_mixin.rst | 20 ++++ .../generated/tests.test_tensorable_mixin.rst | 4 + .../generated/tests.test_timeable_mixin.rst | 21 +++++ .../generated/tests.test_tqdmable_mixin.rst | 20 ++++ docs/source/index.rst | 17 ++++ docs/source/installation.rst | 7 ++ docs/source/license.rst | 4 + docs/source/overview.rst | 6 ++ docs/source/usage.rst | 7 ++ 21 files changed, 431 insertions(+), 28 deletions(-) create mode 100644 .readthedocs.yaml create mode 100644 docs/Makefile create mode 100644 docs/make.bat create mode 100644 docs/source/api.rst create mode 100644 docs/source/conf.py create mode 100644 docs/source/generated/scripts.rst create mode 100644 docs/source/generated/src.MEDS_tabular_automl.rst create mode 100644 docs/source/generated/src.rst create mode 100644 docs/source/generated/tests.rst create mode 100644 docs/source/generated/tests.test_saveable_mixin.rst create mode 100644 docs/source/generated/tests.test_seedable_mixin.rst create mode 100644 docs/source/generated/tests.test_swapcacheable_mixin.rst create mode 100644 docs/source/generated/tests.test_tensorable_mixin.rst create mode 100644 docs/source/generated/tests.test_timeable_mixin.rst create mode 100644 docs/source/generated/tests.test_tqdmable_mixin.rst create mode 100644 docs/source/index.rst create mode 100644 docs/source/installation.rst create mode 100644 docs/source/license.rst create mode 100644 docs/source/overview.rst create mode 100644 docs/source/usage.rst diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..fff2f4b --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,13 @@ +version: "2" + +build: + os: "ubuntu-22.04" + tools: + python: "3.12" + +python: + install: + - requirements: docs/requirements.txt + +sphinx: + configuration: docs/source/conf.py diff --git a/README.md b/README.md index 1c2b8ce..e1fd344 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,10 @@ # Scalable tabularization and tabular feature usage utilities over generic MEDS datasets + This repository provides utilities and scripts to run limited automatic tabular ML pipelines for generic MEDS datasets. #### Q1: What do you mean "tabular pipelines"? Isn't _all_ structured EHR data already tabular? + This is a common misconception. _Tabular_ data refers to data that can be organized in a consistent, logical set of rows/columns such that the entirety of a "sample" or "instance" for modeling or analysis is contained in a single row, and the set of columns possibly observed (there can be missingness) is consistent across all @@ -15,49 +17,56 @@ or future windows in time to produce a single row per patient with a consistent, (though there may still be missingness). #### Q2: Why not other systems? - - [TemporAI](https://github.com/vanderschaarlab/temporai) is the most natural competitor, and already - supports AutoML capabilities. However, TemporAI (as of now) does not support generic MEDS datasets, and it - is not clear if their AutoML systems will scale to the size of datasets we need to support. But, further - investigation is needed, and it may be the case that the best solution here is simply to write a custom - data source for MEDS data within TemporAI and leverage their tools. + +- [TemporAI](https://github.com/vanderschaarlab/temporai) is the most natural competitor, and already + supports AutoML capabilities. However, TemporAI (as of now) does not support generic MEDS datasets, and it + is not clear if their AutoML systems will scale to the size of datasets we need to support. But, further + investigation is needed, and it may be the case that the best solution here is simply to write a custom + data source for MEDS data within TemporAI and leverage their tools. # Installation + Clone this repository and install the requirements by running `pip install .` in the root directory. # Usage + This repository consists of two key pieces: - 1. Construction of and efficient loading of tabular (flat, non-longitudinal) summary features describing - patient records in MEDS over arbitrary time-windows (e.g. 1 year, 6 months, etc.) either backwards or - forwards in time from a given index date. Naturally, only "look-back" windows should be used for - future-event prediction tasks; however, the capability to summarize "look-ahead" windows is also useful - for characterizing and describing the differences between patient populations statistically. - 2. Running basic AutoML pipelines over these tabular features to predict arbitrary binary classification - downstream tasks defined over these datasets. The "AutoML" part of this is not particularly advanced -- - what is more advanced is the efficient construction, storage, and loading of tabular features for the - candidate AutoML models, enabling a far more extensive search over different featurization strategies. + +1. Construction of and efficient loading of tabular (flat, non-longitudinal) summary features describing + patient records in MEDS over arbitrary time-windows (e.g. 1 year, 6 months, etc.) either backwards or + forwards in time from a given index date. Naturally, only "look-back" windows should be used for + future-event prediction tasks; however, the capability to summarize "look-ahead" windows is also useful + for characterizing and describing the differences between patient populations statistically. +2. Running basic AutoML pipelines over these tabular features to predict arbitrary binary classification + downstream tasks defined over these datasets. The "AutoML" part of this is not particularly advanced -- + what is more advanced is the efficient construction, storage, and loading of tabular features for the + candidate AutoML models, enabling a far more extensive search over different featurization strategies. ## Feature Construction, Storage, and Loading + Tabularization of a (raw) MEDS dataset is done by running the `scripts/data/tabularize.py` script. This script must inherently do a base level of preprocessing over the MEDS data, then will construct a sharded tabular representation that respects the overall sharding of the raw data. This script uses [Hydra](https://hydra.cc/) to manage configuration, and the configuration file is located at `configs/tabularize.yaml`. Tabularization will take as input a MEDS dataset in a directory we'll denote `$MEDS_cohort_dir` and will write out a collection of tabularization files to disk in subdirectories of this cohort directory. In particular for a given shard prefix in the raw MEDS cohort (e.g., `train/0`, `held_out/1`, etc.) - 1. In `$MEDS_cohort_dir/tabularized/static/$SHARD_PREFIX.parquet` will be tabularized, wide-format representations of code / value occurrences with null timestamps. In the case that sub-sharding is needed, sub-shards will instead be written as sub-directories of this base directory: `$MEDS_cohort_dir/tabularized/static/$SHARD_PREFIX/$SUB_SHARD.parquet`. This sub-sharding pattern will hold for all files and not be subsequently measured. - 2. In `$MEDS_cohort_dir/tabularized/at_observation/$SHARD_PREFIX.parquet` will be tabularized, wide-format representations of code / value observations for all observations of patient data with a non-null timestamp. - 3. In `$MEDS_cohort_dir/tabularized/over_window/$WINDOW_SIZE/$SHARD_PREFIX.parquet` will be tabularized, wide-format summarization of the code / value occurrences over a window of size `$WINDOW_SIZE` as of the index date at the row's timestamp. + +1. In `$MEDS_cohort_dir/tabularized/static/$SHARD_PREFIX.parquet` will be tabularized, wide-format representations of code / value occurrences with null timestamps. In the case that sub-sharding is needed, sub-shards will instead be written as sub-directories of this base directory: `$MEDS_cohort_dir/tabularized/static/$SHARD_PREFIX/$SUB_SHARD.parquet`. This sub-sharding pattern will hold for all files and not be subsequently measured. +2. In `$MEDS_cohort_dir/tabularized/at_observation/$SHARD_PREFIX.parquet` will be tabularized, wide-format representations of code / value observations for all observations of patient data with a non-null timestamp. +3. In `$MEDS_cohort_dir/tabularized/over_window/$WINDOW_SIZE/$SHARD_PREFIX.parquet` will be tabularized, wide-format summarization of the code / value occurrences over a window of size `$WINDOW_SIZE` as of the index date at the row's timestamp. ## AutoML Pipelines # TODOs - 1. Leverage the "event bound aggregation" capabilities of [ESGPT Task - Select](https://github.com/justin13601/ESGPTTaskQuerying/) to construct tabular summary features for - event-bound historical windows (e.g., until the prior admission, until the last diagnosis of some type, - etc.). - 2. Support more feature aggregation functions. - 3. Probably rename this repository, as the focus is really more on the tabularization and feature usage - utilities than on the AutoML pipelines themselves. - 4. Import, rather than reimplement, the mapper utilities from the MEDS preprocessing repository. - 5. Investigate the feasibility of using TemporAI for this task. - 6. Consider splitting the feature construction and AutoML pipeline parts of this repository into separate - repositories. + +1. Leverage the "event bound aggregation" capabilities of [ESGPT Task + Select](https://github.com/justin13601/ESGPTTaskQuerying/) to construct tabular summary features for + event-bound historical windows (e.g., until the prior admission, until the last diagnosis of some type, + etc.). +2. Support more feature aggregation functions. +3. Probably rename this repository, as the focus is really more on the tabularization and feature usage + utilities than on the AutoML pipelines themselves. +4. Import, rather than reimplement, the mapper utilities from the MEDS preprocessing repository. +5. Investigate the feasibility of using TemporAI for this task. +6. Consider splitting the feature construction and AutoML pipeline parts of this repository into separate + repositories. diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..d0c3cbf --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = source +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..747ffb7 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=source +set BUILDDIR=build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/source/api.rst b/docs/source/api.rst new file mode 100644 index 0000000..4fbf3b9 --- /dev/null +++ b/docs/source/api.rst @@ -0,0 +1,10 @@ +API +==== + +.. autosummary:: + :toctree: generated + :recursive: + + scripts + src + tests diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..c333381 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,93 @@ +import os +import sys + +# Configuration file for the Sphinx documentation builder. +# +# For the full list of built-in configuration values, see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information + +project = "MEDS-TAB" +copyright = "2024, Matthew McDermott, Nassim Oufattole, Teya Bergamaschi" +author = "Matthew McDermott, Nassim Oufattole, Teya Bergamaschi" +release = "0.1.0" +version = "0.1.0" + +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration + + +extensions = [ + "sphinx.ext.duration", + "sphinx.ext.doctest", + "sphinx.ext.autodoc", + "sphinx.ext.autosummary", + "sphinx.ext.intersphinx", + "sphinx.ext.napoleon", + "sphinx_rtd_theme", + "recommonmark", + # "sphinx_immaterial" +] + +source_suffix = { + ".rst": "restructuredtext", + ".txt": "markdown", + ".md": "markdown", +} + +intersphinx_mapping = { + "python": ("https://docs.python.org/3/", None), + "sphinx": ("https://www.sphinx-doc.org/en/master/", None), +} +intersphinx_disabled_domains = ["std"] + +sys.path.insert(0, os.path.abspath("../..")) + +templates_path = ["_templates"] +exclude_patterns = [] + +autosummary_generate = True + +pygments_style = "tango" + + +# -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output + +# html_theme = "sphinx_rtd_theme" +html_theme = "piccolo_theme" +# html_theme = "sphinx_immaterial" +html_static_path = ["_static"] + + +html_title = f"NEDS-TAB v{version} Documentation" +html_short_title = "MEDS-TAB Documentation" + +# html_logo = "query-512.png" +# html_favicon = "query-16.ico" + +# html_sidebars = {"**": ["logo-text.html", "globaltoc.html", "localtoc.html", "searchbox.html"]} + +html_theme_options = { + "dark_mode_code_blocks": False, + # "nav_title": "MEDS-TAB", + # "palette": {"primary": "green", "accent": "green"}, + # "repo_url": "https://github.com/mmcdermott/MEDS_Tabular_AutoML", + # "repo_name": "MEDS_Tabular_AutoML", + # # Visible levels of the global TOC; -1 means unlimited + # "globaltoc_depth": 3, + # If False, expand all TOC entries + "globaltoc_collapse": True, + # If True, show hidden TOC entries + "globaltoc_includehidden": False, +} + + +html_show_copyright = True +htmlhelp_basename = "meds-tab-doc" + + +# -- Options for EPUB output +epub_show_urls = "footnote" diff --git a/docs/source/generated/scripts.rst b/docs/source/generated/scripts.rst new file mode 100644 index 0000000..122deed --- /dev/null +++ b/docs/source/generated/scripts.rst @@ -0,0 +1,4 @@ +scripts +======= + +.. automodule:: scripts diff --git a/docs/source/generated/src.MEDS_tabular_automl.rst b/docs/source/generated/src.MEDS_tabular_automl.rst new file mode 100644 index 0000000..7ad2ae1 --- /dev/null +++ b/docs/source/generated/src.MEDS_tabular_automl.rst @@ -0,0 +1,4 @@ +src.MEDS\_tabular\_automl +========================= + +.. automodule:: src.MEDS_tabular_automl diff --git a/docs/source/generated/src.rst b/docs/source/generated/src.rst new file mode 100644 index 0000000..b9f0096 --- /dev/null +++ b/docs/source/generated/src.rst @@ -0,0 +1,30 @@ +src +=== + +.. automodule:: src + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + src.MEDS_tabular_automl diff --git a/docs/source/generated/tests.rst b/docs/source/generated/tests.rst new file mode 100644 index 0000000..4a46c63 --- /dev/null +++ b/docs/source/generated/tests.rst @@ -0,0 +1,35 @@ +tests +===== + +.. automodule:: tests + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + tests.test_saveable_mixin + tests.test_seedable_mixin + tests.test_swapcacheable_mixin + tests.test_tensorable_mixin + tests.test_timeable_mixin + tests.test_tqdmable_mixin diff --git a/docs/source/generated/tests.test_saveable_mixin.rst b/docs/source/generated/tests.test_saveable_mixin.rst new file mode 100644 index 0000000..080bdb4 --- /dev/null +++ b/docs/source/generated/tests.test_saveable_mixin.rst @@ -0,0 +1,23 @@ +tests.test\_saveable\_mixin +=========================== + +.. automodule:: tests.test_saveable_mixin + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + BadDerived + Derived + DillDerived + TestSaveableMixin diff --git a/docs/source/generated/tests.test_seedable_mixin.rst b/docs/source/generated/tests.test_seedable_mixin.rst new file mode 100644 index 0000000..2bbc5b0 --- /dev/null +++ b/docs/source/generated/tests.test_seedable_mixin.rst @@ -0,0 +1,21 @@ +tests.test\_seedable\_mixin +=========================== + +.. automodule:: tests.test_seedable_mixin + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + SeedableDerived + TestSeedableMixin diff --git a/docs/source/generated/tests.test_swapcacheable_mixin.rst b/docs/source/generated/tests.test_swapcacheable_mixin.rst new file mode 100644 index 0000000..803635c --- /dev/null +++ b/docs/source/generated/tests.test_swapcacheable_mixin.rst @@ -0,0 +1,20 @@ +tests.test\_swapcacheable\_mixin +================================ + +.. automodule:: tests.test_swapcacheable_mixin + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + TestSwapcacheableMixin diff --git a/docs/source/generated/tests.test_tensorable_mixin.rst b/docs/source/generated/tests.test_tensorable_mixin.rst new file mode 100644 index 0000000..b6d3329 --- /dev/null +++ b/docs/source/generated/tests.test_tensorable_mixin.rst @@ -0,0 +1,4 @@ +tests.test\_tensorable\_mixin +============================= + +.. automodule:: tests.test_tensorable_mixin diff --git a/docs/source/generated/tests.test_timeable_mixin.rst b/docs/source/generated/tests.test_timeable_mixin.rst new file mode 100644 index 0000000..f9aeef5 --- /dev/null +++ b/docs/source/generated/tests.test_timeable_mixin.rst @@ -0,0 +1,21 @@ +tests.test\_timeable\_mixin +=========================== + +.. automodule:: tests.test_timeable_mixin + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + TestTimeableMixin + TimeableDerived diff --git a/docs/source/generated/tests.test_tqdmable_mixin.rst b/docs/source/generated/tests.test_tqdmable_mixin.rst new file mode 100644 index 0000000..6fd1a78 --- /dev/null +++ b/docs/source/generated/tests.test_tqdmable_mixin.rst @@ -0,0 +1,20 @@ +tests.test\_tqdmable\_mixin +=========================== + +.. automodule:: tests.test_tqdmable_mixin + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + TestTQDMableMixin diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 0000000..7d014d7 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,17 @@ +.. MEDS-TAB documentation master file, created by + sphinx-quickstart on Mon Jun 3 20:41:52 2024. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to MEDS-TAB's documentation! +==================================== + +.. toctree:: + :maxdepth: 1 + :caption: Contents: + + overview + installation + usage + api + license diff --git a/docs/source/installation.rst b/docs/source/installation.rst new file mode 100644 index 0000000..fe44a54 --- /dev/null +++ b/docs/source/installation.rst @@ -0,0 +1,7 @@ +Installation +============ + +.. include:: ../../README.md + :parser: markdown + :start-after: Installation + :end-before: Usage diff --git a/docs/source/license.rst b/docs/source/license.rst new file mode 100644 index 0000000..f4954d1 --- /dev/null +++ b/docs/source/license.rst @@ -0,0 +1,4 @@ +License +======== + +.. include:: ../../LICENSE diff --git a/docs/source/overview.rst b/docs/source/overview.rst new file mode 100644 index 0000000..c19436c --- /dev/null +++ b/docs/source/overview.rst @@ -0,0 +1,6 @@ +Overview +======== + +.. include:: ../../README.md + :parser: markdown + :end-before: Installation diff --git a/docs/source/usage.rst b/docs/source/usage.rst new file mode 100644 index 0000000..752bc51 --- /dev/null +++ b/docs/source/usage.rst @@ -0,0 +1,7 @@ +Usage +====== + +.. include:: ../../README.md + :parser: markdown + :start-after: Usage + :end-before: TODOs From f8bdd18213ef51be62862a6d8cd0e33ccfa52cb4 Mon Sep 17 00:00:00 2001 From: Teya Bergamaschi Date: Mon, 3 Jun 2024 22:33:55 +0000 Subject: [PATCH 3/4] requirements for readthedocs --- docs/requirements.txt | 15 +++++++++++++++ docs/source/index.rst | 3 +++ 2 files changed, 18 insertions(+) create mode 100644 docs/requirements.txt diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..85aba40 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,15 @@ +sphinx==7.1.2 +sphinx-rtd-theme==1.3.0rc1 +sphinx-collections +recommonmark +piccolo_theme +sphinx_subfigure +nbsphinx +myst_parser +pypandoc +linkify-it-py +ipykernel +omegaconf +ipywidgets +ipykernel +ipython diff --git a/docs/source/index.rst b/docs/source/index.rst index 7d014d7..77ec646 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -5,6 +5,9 @@ Welcome to MEDS-TAB's documentation! ==================================== +.. image:: https://readthedocs.org/projects/meds-tabular-automl/badge/?version=latest + :target: https://meds-tabular-automl.readthedocs.io/en/latest/?badge=latest + :alt: Documentation Status .. toctree:: :maxdepth: 1 From 6240c8af59e9d573e524fc31dbad7e6bcd058f8f Mon Sep 17 00:00:00 2001 From: Teya Bergamaschi Date: Mon, 3 Jun 2024 22:45:15 +0000 Subject: [PATCH 4/4] fix read the docs --- docs/source/api.rst | 2 -- docs/source/conf.py | 4 +-- docs/source/generated/scripts.rst | 4 --- docs/source/generated/tests.rst | 35 ------------------- .../generated/tests.test_saveable_mixin.rst | 23 ------------ .../generated/tests.test_seedable_mixin.rst | 21 ----------- .../tests.test_swapcacheable_mixin.rst | 20 ----------- .../generated/tests.test_tensorable_mixin.rst | 4 --- .../generated/tests.test_timeable_mixin.rst | 21 ----------- .../generated/tests.test_tqdmable_mixin.rst | 20 ----------- 10 files changed, 1 insertion(+), 153 deletions(-) delete mode 100644 docs/source/generated/scripts.rst delete mode 100644 docs/source/generated/tests.rst delete mode 100644 docs/source/generated/tests.test_saveable_mixin.rst delete mode 100644 docs/source/generated/tests.test_seedable_mixin.rst delete mode 100644 docs/source/generated/tests.test_swapcacheable_mixin.rst delete mode 100644 docs/source/generated/tests.test_tensorable_mixin.rst delete mode 100644 docs/source/generated/tests.test_timeable_mixin.rst delete mode 100644 docs/source/generated/tests.test_tqdmable_mixin.rst diff --git a/docs/source/api.rst b/docs/source/api.rst index 4fbf3b9..463c193 100644 --- a/docs/source/api.rst +++ b/docs/source/api.rst @@ -5,6 +5,4 @@ API :toctree: generated :recursive: - scripts src - tests diff --git a/docs/source/conf.py b/docs/source/conf.py index c333381..298a9c8 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -18,7 +18,7 @@ # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration - +sys.path.insert(0, os.path.abspath("../..")) extensions = [ "sphinx.ext.duration", "sphinx.ext.doctest", @@ -43,8 +43,6 @@ } intersphinx_disabled_domains = ["std"] -sys.path.insert(0, os.path.abspath("../..")) - templates_path = ["_templates"] exclude_patterns = [] diff --git a/docs/source/generated/scripts.rst b/docs/source/generated/scripts.rst deleted file mode 100644 index 122deed..0000000 --- a/docs/source/generated/scripts.rst +++ /dev/null @@ -1,4 +0,0 @@ -scripts -======= - -.. automodule:: scripts diff --git a/docs/source/generated/tests.rst b/docs/source/generated/tests.rst deleted file mode 100644 index 4a46c63..0000000 --- a/docs/source/generated/tests.rst +++ /dev/null @@ -1,35 +0,0 @@ -tests -===== - -.. automodule:: tests - - - - - - - - - - - - - - - - - - - -.. rubric:: Modules - -.. autosummary:: - :toctree: - :recursive: - - tests.test_saveable_mixin - tests.test_seedable_mixin - tests.test_swapcacheable_mixin - tests.test_tensorable_mixin - tests.test_timeable_mixin - tests.test_tqdmable_mixin diff --git a/docs/source/generated/tests.test_saveable_mixin.rst b/docs/source/generated/tests.test_saveable_mixin.rst deleted file mode 100644 index 080bdb4..0000000 --- a/docs/source/generated/tests.test_saveable_mixin.rst +++ /dev/null @@ -1,23 +0,0 @@ -tests.test\_saveable\_mixin -=========================== - -.. automodule:: tests.test_saveable_mixin - - - - - - - - - - - - .. rubric:: Classes - - .. autosummary:: - - BadDerived - Derived - DillDerived - TestSaveableMixin diff --git a/docs/source/generated/tests.test_seedable_mixin.rst b/docs/source/generated/tests.test_seedable_mixin.rst deleted file mode 100644 index 2bbc5b0..0000000 --- a/docs/source/generated/tests.test_seedable_mixin.rst +++ /dev/null @@ -1,21 +0,0 @@ -tests.test\_seedable\_mixin -=========================== - -.. automodule:: tests.test_seedable_mixin - - - - - - - - - - - - .. rubric:: Classes - - .. autosummary:: - - SeedableDerived - TestSeedableMixin diff --git a/docs/source/generated/tests.test_swapcacheable_mixin.rst b/docs/source/generated/tests.test_swapcacheable_mixin.rst deleted file mode 100644 index 803635c..0000000 --- a/docs/source/generated/tests.test_swapcacheable_mixin.rst +++ /dev/null @@ -1,20 +0,0 @@ -tests.test\_swapcacheable\_mixin -================================ - -.. automodule:: tests.test_swapcacheable_mixin - - - - - - - - - - - - .. rubric:: Classes - - .. autosummary:: - - TestSwapcacheableMixin diff --git a/docs/source/generated/tests.test_tensorable_mixin.rst b/docs/source/generated/tests.test_tensorable_mixin.rst deleted file mode 100644 index b6d3329..0000000 --- a/docs/source/generated/tests.test_tensorable_mixin.rst +++ /dev/null @@ -1,4 +0,0 @@ -tests.test\_tensorable\_mixin -============================= - -.. automodule:: tests.test_tensorable_mixin diff --git a/docs/source/generated/tests.test_timeable_mixin.rst b/docs/source/generated/tests.test_timeable_mixin.rst deleted file mode 100644 index f9aeef5..0000000 --- a/docs/source/generated/tests.test_timeable_mixin.rst +++ /dev/null @@ -1,21 +0,0 @@ -tests.test\_timeable\_mixin -=========================== - -.. automodule:: tests.test_timeable_mixin - - - - - - - - - - - - .. rubric:: Classes - - .. autosummary:: - - TestTimeableMixin - TimeableDerived diff --git a/docs/source/generated/tests.test_tqdmable_mixin.rst b/docs/source/generated/tests.test_tqdmable_mixin.rst deleted file mode 100644 index 6fd1a78..0000000 --- a/docs/source/generated/tests.test_tqdmable_mixin.rst +++ /dev/null @@ -1,20 +0,0 @@ -tests.test\_tqdmable\_mixin -=========================== - -.. automodule:: tests.test_tqdmable_mixin - - - - - - - - - - - - .. rubric:: Classes - - .. autosummary:: - - TestTQDMableMixin