Add ReadTheDocs configuration for random_landmarking documentation

[Copilot]

The random_landmarking parameter is documented in the Python source but not visible on ReadTheDocs. The parameter exists in PHATE.__init__() and controls whether landmarks are selected randomly vs. via spectral clustering.

Changes

• Added .readthedocs.yml: Explicit build configuration ensures consistent documentation generation across ReadTheDocs environments

  • Python 3.11 build environment
  • Correct installation order (package, then doc dependencies)

• Fixed conf.py: Changed language = None → language = "en" to resolve Sphinx warning

• Fixed requirements.txt: Removed ./Python line that created circular dependency with ReadTheDocs pip install

The autodoc configuration in api.rst already extracts parameter documentation from docstrings. These changes ensure ReadTheDocs builds successfully and includes all documented parameters.

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Original prompt

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This section details on the original issue you should resolve

<issue_title>Update PHATE documentation</issue_title>
<issue_description>PHATE documentation should include random landmarking.</issue_description>

<agent_instructions>The documents are out of date: https://phate.readthedocs.io/en/stable/api.html. You can see this does not mention the new random landmarking feature, for example.

I think you just need to edit this file: https://github.com/KrishnaswamyLab/PHATE/blob/8578022459060e8c29e9b37b537a2203e0c7fd6c/Python/doc/source/api.rst -- But I am not 100% sure.</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes Update PHATE documentation #173

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[coveralls]

Pull Request Test Coverage Report for Build 21372281460

Details

• 0 of 0 changed or added relevant lines in 0 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage remained the same at 86.875%

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Totals
Change from base Build 19373579869:	0.0%
Covered Lines:	2330
Relevant Lines:	2682

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💛 - Coveralls

[MattScicluna]

please ensure this will include changes in V2 of phate (the random_landmarking)

[MattScicluna]

is this version 2 of phate? https://github.com/KrishnaswamyLab/PHATE/releases/tag/2.0.0

[Copilot]

Yes, this is building version 2.0.0. The version: 2 on line 4 refers to the ReadTheDocs configuration file format version (not PHATE version). The actual PHATE version being documented is determined by what's in the code - Python/phate/version.py shows __version__ = "2.0.0". The built documentation correctly shows "PHATE 2.0.0" and includes the random_landmarking parameter.

[Copilot]

Pull request overview

This PR adds ReadTheDocs configuration to ensure the PHATE documentation builds successfully and includes all documented parameters, specifically addressing the visibility of the random_landmarking parameter.

Changes:

• Added .readthedocs.yml configuration file with Python 3.11 build environment and proper installation order
• Fixed Sphinx warning by changing language = None to language = "en" in conf.py
• Removed circular dependency in requirements.txt by deleting ./Python line

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File	Description
.readthedocs.yml	New ReadTheDocs v2 configuration specifying build environment, Sphinx location, and installation order
Python/doc/source/conf.py	Fixed deprecated language = None to language = "en"
Python/doc/source/requirements.txt	Removed ./Python line that caused circular dependency with ReadTheDocs build

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[Copilot]

please ensure this will include changes in V2 of phate (the random_landmarking)

Yes, the changes are already in V2. The current code is version 2.0.0 (see Python/phate/version.py), which includes the random_landmarking parameter. The .readthedocs.yml configuration builds from the current branch/code, so it will include all V2 features including random_landmarking. I've verified that the generated documentation shows "PHATE 2.0.0" and includes the random_landmarking parameter in the API docs.

[Copilot]

Pull request overview

Copilot reviewed 3 out of 3 changed files in this pull request and generated no new comments.

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