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@sdhutchins sdhutchins commented Dec 2, 2025

This is a quick fix to ensure ReadTheDocs is building properly.

Simply put, the YAML config needed to be updated properly.

# Read the Docs configuration for OrthoEvolution
# https://docs.readthedocs.io/en/stable/config-file/v2.html

version: 2

build:
  os: "ubuntu-22.04"
  tools:
    python: "3.9"
  jobs:
    pre_build:
      # Pre-build job: Run update_docs.py to regenerate API docs and convert READMEs
      # This runs before Sphinx builds the documentation
      - python docs/update_docs.py --skip-build

python:
  install:
    - requirements: requirements.txt
    - requirements: docs/requirements-docs.txt
    # Install our python package before building the docs
    - method: pip
      path: .

sphinx:
  configuration: docs/docs/source/conf.py

snyk-bot and others added 10 commits February 25, 2022 16:39
The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-WTFORMS-40581

Co-authored-by: Shaurita Hutchins <[email protected]>
Bumps [jinja2](https://github.com/pallets/jinja) from 2.9.6 to 2.11.3.
- [Release notes](https://github.com/pallets/jinja/releases)
- [Changelog](https://github.com/pallets/jinja/blob/master/CHANGES.rst)
- [Commits](pallets/jinja@2.9.6...2.11.3)

Signed-off-by: dependabot[bot] <[email protected]>

Co-authored-by: Shaurita Hutchins <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* fix: requirements.txt to reduce vulnerabilities (#176)

The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-SETUPTOOLS-3113904

Co-authored-by: snyk-bot <[email protected]>

* fix: requirements.txt to reduce vulnerabilities (#175)

The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-PSUTIL-483082

Co-authored-by: Shaurita Hutchins <[email protected]>

* fix: requirements.txt to reduce vulnerabilities (#170)

The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-COOKIECUTTER-2414281

Co-authored-by: Shaurita Hutchins <[email protected]>

* fix: requirements.txt to reduce vulnerabilities (#179)

The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-SETUPTOOLS-3180412

Co-authored-by: Shaurita Hutchins <[email protected]>

* Refactor code. (#177)

* Renamed orthophyl.py to phyml.py

* Renamed orthophylip.py to phylip.py

* Updated import of phylip.py

* Updated import of phyml.py

* Added docstrings for the init of the PhyML class.

* Refactored init in ETE3PAMl to create better API.

* Fixed logging issue.

* Added check_exe function.

* Added new examples to README.

* Added ApplicationError to try/except in run method.

* Added a test for phyml

* Added test data for phyml test.

* Added phyml installation to travis script.

* Added ability for user to choose number of processors.

* Updated README for new api.

* Removed deprecated csvtolist

* Added logging to ETE3PAML

* Added _import_alignment method

* Added a README for the PHYLIP class.

* Added try/except/else/finally for phylip methods

* Removed phylip test from Phylip folder.

* Added docstrings to ETE3PAML class.

* Fixed errors in README.

* Added TODO in codeml.py

* Changed data in test.

* Added missing doctrings.

* Updated example in README.

* Refactored TreeViz api.

* Refactored ncbi-download script

* Added validation function. Extended run api.

* Updated PhyML test data.

* Added ability to capture output for Phylip

* Fixed validate format issue.

* Renamed PhyloTree module to TreeViz

* Added a treeviz test.

* Removed sciluigi. Added matplotlib.

* Removed matplotlib from travis CI pip install line

* Added updated example to readme.

* Added docstrings.

* Removed version of matplotlib

* Corrected path to tree file in test.

* Updated Flask to latest version and removed other flask libraries.

* Corrected paths in tests.

* Additional fix to current directory for tests.

* Changed paths of test output.

* Fixed Phyml tests

* Fix extra lines in code.

* Fix psutil requirement.

* Remove cookiecutter version.

* Remove Flask version requirements.

Flash should be fairly backwards compatible. Fixes will be simpler.

* Drop support for Python < 3.7.

* Fix name for log level to format color.

* Remove version for setuptools.

* Remove incorrect character from travis script.

* Add commands to PyBasher.

* Refactor blastpipeline.

* Remove Flask-User.

* Set _COLORS for logging.

* Deprecate airflow.

* Comment out phyml test.

* Add more test infrastructure.

* Remove luigi version.

* Fix cookies test.

* Test.

* Test.

* Add github action for ci.

* Fix test.

* Fix texts for Oven and CookBook.

* Updated utils tests.

* Remove PackageVersion test.

* Fix Cookies tests.

* Remove github action.

* Add ci back. Remove blast tests.

* Change timeout.

* Update OrthoEvol/Orthologs/Phylogenetics/PhyML/README.md

Co-authored-by: Copilot <[email protected]>

* Update OrthoEvol/Orthologs/Phylogenetics/PhyML/phyml.py

Co-authored-by: Copilot <[email protected]>

* Remove travis. Add GH action.

* Upgrade biopython version.

* Fixed tests.

* bump up python versions.

* Bump werkzeug (#211)

Bumps [werkzeug](https://github.com/pallets/werkzeug) from 0.15.3 to 3.1.4.
- [Release notes](https://github.com/pallets/werkzeug/releases)
- [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst)
- [Commits](pallets/werkzeug@0.15.3...3.1.4)

---
updated-dependencies:
- dependency-name: werkzeug
  dependency-version: 3.1.4
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: Shaurita Hutchins <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump jinja2 (#206)

Bumps [jinja2](https://github.com/pallets/jinja) from 2.9.6 to 3.1.6.
- [Release notes](https://github.com/pallets/jinja/releases)
- [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst)
- [Commits](pallets/jinja@2.9.6...3.1.6)

---
updated-dependencies:
- dependency-name: jinja2
  dependency-version: 3.1.6
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: Shaurita Hutchins <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump tqdm from 4.25.0 to 4.66.3 (#208)

Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.25.0 to 4.66.3.
- [Release notes](https://github.com/tqdm/tqdm/releases)
- [Commits](tqdm/tqdm@v4.25.0...v4.66.3)

---
updated-dependencies:
- dependency-name: tqdm
  dependency-version: 4.66.3
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: Shaurita Hutchins <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Add test gpcr dataset.

* Fix utils test.

* Fix issue finding directory.

* Fix manage tests.

* Fix code cov.

* fix: requirements.txt to reduce vulnerabilities (#210)

The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-WERKZEUG-14151620

Co-authored-by: snyk-bot <[email protected]>

* Bump sqlalchemy (#209)

Bumps [sqlalchemy](https://github.com/sqlalchemy/sqlalchemy) from 1.1.9 to 1.2.19.
- [Release notes](https://github.com/sqlalchemy/sqlalchemy/releases)
- [Changelog](https://github.com/sqlalchemy/sqlalchemy/blob/main/CHANGES.rst)
- [Commits](https://github.com/sqlalchemy/sqlalchemy/commits)

---
updated-dependencies:
- dependency-name: sqlalchemy
  dependency-version: 1.2.19
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: Shaurita Hutchins <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: sdhutchins <[email protected]>
Co-authored-by: Shaurita D. Hutchins <[email protected]>
Co-authored-by: Copilot <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: snyk-bot <[email protected]>

* Fix docstrings. Move templates to .github.

* Update examples and python version.

* Update python tasks.

* Add docstring to Orthologs module.

* Fix missing doc strings.

* Added more utils tests.

* Add more tests for manager module.

* Add more tests for tools module.

* Add changelog.

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: snyk-bot <[email protected]>
Co-authored-by: Snyk bot <[email protected]>
Co-authored-by: sdhutchins <[email protected]>
Co-authored-by: Shaurita D. Hutchins <[email protected]>
Co-authored-by: Copilot <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@sdhutchins sdhutchins self-assigned this Dec 2, 2025
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codecov bot commented Dec 2, 2025

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 29.68%. Comparing base (c4d1395) to head (e5b1139).
⚠️ Report is 2 commits behind head on main.
✅ All tests successful. No failed tests found.

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #215   +/-   ##
=======================================
  Coverage   29.68%   29.68%           
=======================================
  Files          69       69           
  Lines        4345     4345           
=======================================
  Hits         1290     1290           
  Misses       3055     3055           

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@sdhutchins sdhutchins changed the title Quick fixes to docs. Fix readthedocs build. Dec 2, 2025
@sdhutchins sdhutchins modified the milestone: Test All Modules Dec 2, 2025
@sdhutchins sdhutchins mentioned this pull request Dec 2, 2025
@sdhutchins sdhutchins merged commit 71f413c into main Dec 2, 2025
11 checks passed
@sdhutchins sdhutchins deleted the dev-master branch December 2, 2025 22:05
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3 participants