diff --git a/docs/source/conf.py b/docs/source/conf.py index 298a9c8..34fb932 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -9,16 +9,17 @@ # -- Project information ----------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information -project = "MEDS-TAB" +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" +release = "0.0.1" +version = "0.0.1" # -- 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", @@ -60,8 +61,8 @@ html_static_path = ["_static"] -html_title = f"NEDS-TAB v{version} Documentation" -html_short_title = "MEDS-TAB Documentation" +html_title = f"MEDS-Tab v{version} Documentation" +html_short_title = "MEDS-Tab Documentation" # html_logo = "query-512.png" # html_favicon = "query-16.ico" @@ -70,7 +71,7 @@ html_theme_options = { "dark_mode_code_blocks": False, - # "nav_title": "MEDS-TAB", + # "nav_title": "MEDS-Tab", # "palette": {"primary": "green", "accent": "green"}, # "repo_url": "https://github.com/mmcdermott/MEDS_Tabular_AutoML", # "repo_name": "MEDS_Tabular_AutoML", diff --git a/docs/source/generated/src.MEDS_tabular_automl.scripts.describe_codes.rst b/docs/source/generated/src.MEDS_tabular_automl.scripts.describe_codes.rst new file mode 100644 index 0000000..7b604e6 --- /dev/null +++ b/docs/source/generated/src.MEDS_tabular_automl.scripts.describe_codes.rst @@ -0,0 +1,16 @@ +src.MEDS\_tabular\_automl.scripts.describe\_codes +================================================= + +.. automodule:: src.MEDS_tabular_automl.scripts.describe_codes + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + main diff --git a/docs/source/generated/src.MEDS_tabular_automl.scripts.launch_xgboost.rst b/docs/source/generated/src.MEDS_tabular_automl.scripts.launch_xgboost.rst new file mode 100644 index 0000000..61afb61 --- /dev/null +++ b/docs/source/generated/src.MEDS_tabular_automl.scripts.launch_xgboost.rst @@ -0,0 +1,27 @@ +src.MEDS\_tabular\_automl.scripts.launch\_xgboost +================================================= + +.. automodule:: src.MEDS_tabular_automl.scripts.launch_xgboost + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + main + + + + + + .. rubric:: Classes + + .. autosummary:: + + Iterator + XGBoostModel diff --git a/docs/source/generated/src.MEDS_tabular_automl.scripts.rst b/docs/source/generated/src.MEDS_tabular_automl.scripts.rst index 38c331e..15ca299 100644 --- a/docs/source/generated/src.MEDS_tabular_automl.scripts.rst +++ b/docs/source/generated/src.MEDS_tabular_automl.scripts.rst @@ -30,6 +30,5 @@ src.MEDS\_tabular\_automl.scripts src.MEDS_tabular_automl.scripts.cache_task src.MEDS_tabular_automl.scripts.describe_codes src.MEDS_tabular_automl.scripts.launch_xgboost - src.MEDS_tabular_automl.scripts.sweep_xgboost src.MEDS_tabular_automl.scripts.tabularize_static src.MEDS_tabular_automl.scripts.tabularize_time_series diff --git a/docs/source/generated/src.MEDS_tabular_automl.scripts.tabularize_static.rst b/docs/source/generated/src.MEDS_tabular_automl.scripts.tabularize_static.rst new file mode 100644 index 0000000..61852e0 --- /dev/null +++ b/docs/source/generated/src.MEDS_tabular_automl.scripts.tabularize_static.rst @@ -0,0 +1,16 @@ +src.MEDS\_tabular\_automl.scripts.tabularize\_static +==================================================== + +.. automodule:: src.MEDS_tabular_automl.scripts.tabularize_static + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + main diff --git a/docs/source/generated/src.MEDS_tabular_automl.scripts.tabularize_time_series.rst b/docs/source/generated/src.MEDS_tabular_automl.scripts.tabularize_time_series.rst new file mode 100644 index 0000000..066a968 --- /dev/null +++ b/docs/source/generated/src.MEDS_tabular_automl.scripts.tabularize_time_series.rst @@ -0,0 +1,16 @@ +src.MEDS\_tabular\_automl.scripts.tabularize\_time\_series +========================================================== + +.. automodule:: src.MEDS_tabular_automl.scripts.tabularize_time_series + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + main diff --git a/docs/source/index.rst b/docs/source/index.rst index a3f5247..15737d3 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -3,11 +3,11 @@ 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! +Welcome to MEDS-Tab's documentation! ==================================== .. toctree:: - :maxdepth: 1 + :maxdepth: 2 :caption: Contents: overview diff --git a/docs/source/license.rst b/docs/source/license.rst deleted file mode 100644 index f4954d1..0000000 --- a/docs/source/license.rst +++ /dev/null @@ -1,4 +0,0 @@ -License -======== - -.. include:: ../../LICENSE diff --git a/src/MEDS_tabular_automl/describe_codes.py b/src/MEDS_tabular_automl/describe_codes.py index de70682..fc50139 100644 --- a/src/MEDS_tabular_automl/describe_codes.py +++ b/src/MEDS_tabular_automl/describe_codes.py @@ -1,7 +1,7 @@ from pathlib import Path import polars as pl -from omegaconf import DictConfig, OmegaConf +from omegaconf import DictConfig from MEDS_tabular_automl.utils import DF_T, get_feature_names @@ -118,7 +118,7 @@ def filter_to_codes( return sorted([code for code, freq in code_freqs.items() if freq >= min_code_inclusion_frequency]) -OmegaConf.register_new_resolver("filter_to_codes", filter_to_codes) +# OmegaConf.register_new_resolver("filter_to_codes", filter_to_codes) def clear_code_aggregation_suffix(code):