From 1009f70fb32d8b379919e02d46e2a3c691b804ec Mon Sep 17 00:00:00 2001
From: Teya Bergamaschi <teya@mit.edu>
Date: Mon, 10 Jun 2024 23:04:28 +0000
Subject: [PATCH] read the docs

---
 docs/source/conf.py                           | 13 ++++-----
 ..._tabular_automl.scripts.describe_codes.rst | 16 +++++++++++
 ..._tabular_automl.scripts.launch_xgboost.rst | 27 +++++++++++++++++++
 .../src.MEDS_tabular_automl.scripts.rst       |  1 -
 ...bular_automl.scripts.tabularize_static.rst | 16 +++++++++++
 ..._automl.scripts.tabularize_time_series.rst | 16 +++++++++++
 docs/source/index.rst                         |  4 +--
 docs/source/license.rst                       |  4 ---
 src/MEDS_tabular_automl/describe_codes.py     |  4 +--
 9 files changed, 86 insertions(+), 15 deletions(-)
 create mode 100644 docs/source/generated/src.MEDS_tabular_automl.scripts.describe_codes.rst
 create mode 100644 docs/source/generated/src.MEDS_tabular_automl.scripts.launch_xgboost.rst
 create mode 100644 docs/source/generated/src.MEDS_tabular_automl.scripts.tabularize_static.rst
 create mode 100644 docs/source/generated/src.MEDS_tabular_automl.scripts.tabularize_time_series.rst
 delete mode 100644 docs/source/license.rst

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):