Files that changed from the base of the PR and between 07001be and 8d8a44c.

• docs/assets/dark_purple_meds_tab.png is excluded by !**/*.png
• docs/assets/light_logo.png is excluded by !**/*.png
• docs/assets/light_purple_meds_tab.png is excluded by !**/*.png

• .pre-commit-config.yaml (1 hunks)
• README.md (2 hunks)
• docs/Makefile (0 hunks)
• docs/README.MD (1 hunks)
• docs/gen_ref_pages.py (1 hunks)
• docs/generate.sh (0 hunks)
• docs/implementation.md (3 hunks)
• docs/index.md (1 hunks)
• docs/javascripts/mathjax.js (1 hunks)
• docs/make.bat (0 hunks)
• docs/overrides/main.html (1 hunks)
• docs/overview.md (1 hunks)
• docs/prediction.md (5 hunks)
• docs/requirements.txt (0 hunks)
• docs/source/_static/switcher.json (0 hunks)
• docs/source/conf.py (0 hunks)
• docs/source/index.md (0 hunks)
• docs/source/overview.md (0 hunks)
• docs/terminology.md (1 hunks)
• docs/tutorial.md (1 hunks)
• mkdocs.yml (1 hunks)
• pyproject.toml (1 hunks)

• docs/Makefile
• docs/generate.sh
• docs/make.bat
• docs/requirements.txt
• docs/source/_static/switcher.json
• docs/source/conf.py
• docs/source/index.md
• docs/source/overview.md

• docs/index.md
• docs/overrides/main.html
• docs/terminology.md
• docs/tutorial.md

docs/javascripts/mathjax.js (2)

1-12: ⚠️ Potential issue

Review and verify MathJax configuration patterns.

A few concerns with the current configuration:

1. The double backslashes in the delimiters might be excessive. Single backslashes are typically sufficient for MathJax.
2. The ignoreHtmlClass regex pattern ".*|" looks suspicious and might not work as intended.
3. Consider adding error handling for MathJax initialization.

Let's verify if these patterns are consistent with MkDocs best practices:

Consider applying these fixes:

 window.MathJax = {
   tex: {
-    inlineMath: [["\\(", "\\)"]],
-    displayMath: [["\\[", "\\]"]],
+    inlineMath: [["\\(", "\\)"]],
+    displayMath: [["\\[", "\\]"]],
     processEscapes: true,
     processEnvironments: true
   },
   options: {
-    ignoreHtmlClass: ".*|",
+    ignoreHtmlClass: ".*",
     processHtmlClass: "arithmatex"
   }
 };

Also, consider adding basic error handling:

+if (typeof window.MathJax === 'undefined') {
+  console.error('MathJax not loaded properly');
+}
 window.MathJax = {
   // ... configuration ...
 };

---

14-19: ⚠️ Potential issue

Add error handling and optimize MathJax operations.

The current implementation lacks error handling for the promise chain and might have performance implications.

Consider applying these improvements:

-document$.subscribe(() => {
+document$.subscribe(async () => {
+  try {
     MathJax.startup.output.clearCache()
     MathJax.typesetClear()
     MathJax.texReset()
-    MathJax.typesetPromise()
+    await MathJax.typesetPromise()
+  } catch (error) {
+    console.error('Failed to process MathJax:', error);
+  }
 })

Let's verify the document$ observable source:

mkdocs.yml (4)

52-66: LGTM! Comprehensive markdown extension setup.

The markdown extensions are well-configured for technical documentation, including support for math equations, code highlighting, and advanced formatting features.

---

71-81: Verify reference page generator script.

The configuration references a custom script for generating reference pages that needs to be verified.

#!/bin/bash
# Description: Check if reference page generator exists

echo "Checking for reference page generator..."
if ! fd -t f "gen_ref_pages.py" docs/; then
    echo "Warning: Reference page generator script not found"
fi

---

17-50: Verify the existence of theme assets.

The theme configuration references custom assets that need to be verified.

✅ Verification successful

Based on the shell script results, I can generate the final response as we have verified both requirements:

Theme assets verification completed successfully

The verification confirms that:

• The logo/favicon file light_logo.png exists at the correct path docs/assets/
• The custom overrides directory docs/overrides exists

Note: I chose the tag because both the custom assets file and overrides directory were found at their expected locations, confirming that the theme configuration references valid paths.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check if referenced theme assets exist

echo "Checking for theme assets..."
# Check for logo and favicon
fd -t f "light_logo.png" docs/assets/

# Check for custom overrides directory
if ! [ -d "docs/overrides" ]; then
    echo "Warning: Custom overrides directory not found"
fi

Length of output: 159

---

67-70: Verify MathJax configuration file.

The configuration references a custom MathJax configuration file that needs to be verified.

✅ Verification successful

Let me check the content of the found MathJax configuration file to ensure it's properly configured.

---

MathJax configuration is properly set up

The MathJax configuration file exists and contains valid configuration:

• Correctly sets up inline and display math delimiters
• Properly configures processing escapes and environments
• Includes necessary MathJax startup and typeset handling
• Integrates with the document lifecycle using the subscription pattern

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check if MathJax configuration exists

echo "Checking for MathJax configuration..."
if ! fd -t f "mathjax.js" docs/javascripts/; then
    echo "Warning: MathJax configuration file not found"
fi

Length of output: 245

---

Script:

#!/bin/bash
# Check the content of the MathJax configuration file
cat docs/javascripts/mathjax.js

Length of output: 417

pyproject.toml (2)

36-36: LGTM: Version constraint for pre-commit is appropriate.

The version constraint pre-commit<4 aligns with the PR objective to address the docformatter pre-commit hook compatibility issue.

---

40-53: Consider security implications of git plugins.

The MkDocs dependencies are well-structured with pinned versions. However, please be aware that:

1. mkdocs-git-authors-plugin may expose contributor information
2. mkdocs-git-revision-date-localized-plugin may expose internal timeline information

Consider documenting any sensitive information these plugins might expose and ensure it aligns with your project's privacy requirements.

#!/bin/bash
# Check if there's any documentation about git plugins configuration
rg -i "git.*plugin|author.*plugin|revision.*plugin" docs/ mkdocs.yml

.pre-commit-config.yaml (1)

Line range hint 1-124: Configuration structure looks good

The pre-commit configuration is well-organized with:

• Properly pinned versions for all hooks
• Clear categorization of hooks by purpose
• Appropriate arguments and exclusions for each hook

docs/implementation.md (2)

32-32: LGTM! Clear explanation of feature counts.

The added explanation effectively introduces the concept and its importance in the pipeline.

---

37-37: LGTM! Consistent terminology usage.

The terminology update from "frequencies" to "counts" maintains consistency with other documentation changes.

README.md (2)

68-72: LGTM!

The section provides clear references to both the tutorial and integration tests, which is helpful for users getting started.

---

Line range hint 16-49: Excellent documentation restructuring!

The new structure with clear sections for:

• Welcome and value proposition
• Step-by-step guide for getting started
• Technical details and capabilities

makes the documentation much more accessible and user-friendly. The flow from high-level overview to technical details is well-organized.

🧰 Tools

🪛 LanguageTool

[style] ~29-~29: Consider a shorter alternative to avoid wordiness.
Context: ...ed across arbitrary tasks and settings. In order to use MEDS-Tab, you will first need to tr...

(IN_ORDER_TO_PREMIUM)

---

[style] ~40-~40: Opting for a less wordy alternative here can improve the clarity of your writing.
Context: ...n the MEDS-Tab ecosystem. This approach not only simplifies the process but also ensures high-quality, reproducible results for ...

(NOT_ONLY_ALSO)

🪛 Markdownlint

55-55: null
Emphasis used instead of a heading

(MD036, no-emphasis-as-heading)

---

61-61: null
Emphasis used instead of a heading

(MD036, no-emphasis-as-heading)

docs/prediction.md (1)

127-141: Verify unusually low performance metrics and extreme parameter variations.

There are some concerning patterns in the performance tables:

1. The eICU In Hospital Mortality (48hr) shows an unusually low AUC of 0.570
2. The Minimum Code Inclusion Count varies extremely (from 43 to 335,912)

Consider:

1. Verifying these results, especially the low-performing models
2. Adding explanations for the wide variation in code inclusion counts
3. Discussing the implications of these variations on model reliability

Run this script to verify the metrics:

Also applies to: 171-180

docs/gen_ref_pages.py (5)

14-52: process_python_files() function is well-implemented

The process_python_files() function effectively processes Python files to generate API reference pages and navigation. The handling of special cases like __init__.py and inclusion of README.md files is correctly implemented.

---

54-72: process_yaml_files() function is well-implemented

The process_yaml_files() function successfully processes YAML configuration files to generate documentation and navigation entries. The inclusion of YAML content within code blocks enhances readability.

---

74-83: Efficient generation of navigation summaries

The creation of SUMMARY.md files for both API and configuration references ensures that the documentation is well-organized and easily navigable.

---

43-46: Ensure ident correctly reflects module hierarchy

The construction of ident at lines 43-46 determines how the modules are referenced in the documentation. Verify that this accurately represents the module hierarchy, especially for nested packages.

You can check the generated documentation to confirm that all modules are correctly documented.

---

36-39: Verify the inclusion of appropriate README.md content

Including README.md files in the documentation is helpful, but ensure that the content is suitable for the API reference and does not contain installation instructions or other unrelated information.

You can run the following script to list and review the README.md files being included:

✅ Verification successful

Let me try a different approach to verify the README.md files that would be included in the documentation.

This will help us:

1. Find all README.md files in the repository
2. Review their content to assess if they are suitable for API documentation

Additionally, let's look at the documentation generation script to understand the context better:

---

Based on the provided context, I can now generate a final response. The code and README content have given me enough information to assess the situation.

README.md content is appropriate for API documentation

The repository's README.md content is well-structured and contains relevant technical information that would be valuable in API documentation, including:

• Technical overview of the library's functionality
• Explanation of core concepts (e.g., the detailed explanation of what "tabular pipelines" means)
• Component descriptions and architectural details
• Roadmap and limitations

The documentation generation script (gen_ref_pages.py) only includes README.md files that are within Python package directories (next to __init__.py files), which is a good practice as these typically contain module-specific technical documentation rather than installation or general project information.

Note: The main README.md won't be included in the API reference as it's not within the src/MEDS_tabular_automl directory, and any module-level README.md files will be appropriately placed in their respective module documentation sections.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: List and display README.md files included in the API documentation

# Find all README.md files within src/MEDS_tabular_automl excluding the configs directory
find src/MEDS_tabular_automl -path '*/configs/*' -prune -o -name 'README.md' -print -exec cat {} \;

Length of output: 102

---

Script:

#!/bin/bash
# First, let's understand where the documentation is being generated from
fd README.md --type f

# Then, let's examine the content of these README files
fd README.md --type f --exec cat {}

Length of output: 8905

---

Script:

#!/bin/bash
cat docs/gen_ref_pages.py

Length of output: 2660