Fix readthedocs build. (#215)

* fix: requirements.txt to reduce vulnerabilities (#169)

The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-WTFORMS-40581

Co-authored-by: Shaurita Hutchins <ms.s.hutchins@gmail.com>

* Bump jinja2 (#168)

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] <support@github.com>

Co-authored-by: Shaurita Hutchins <ms.s.hutchins@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Add additional tests (#212)

* 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 <snyk-bot@snyk.io>

* 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 <ms.s.hutchins@gmail.com>

* 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 <ms.s.hutchins@gmail.com>

* 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 <ms.s.hutchins@gmail.com>

* 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 <175728472+Copilot@users.noreply.github.com>

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

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* 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
...

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Co-authored-by: Shaurita Hutchins <ms.s.hutchins@gmail.com>
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* 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] <support@github.com>
Co-authored-by: Shaurita Hutchins <ms.s.hutchins@gmail.com>
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* 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
...

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* 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 <snyk-bot@snyk.io>

* 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] <support@github.com>
Co-authored-by: Shaurita Hutchins <ms.s.hutchins@gmail.com>
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---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: sdhutchins <sdhutchins@outlook.com>
Co-authored-by: Shaurita D. Hutchins <shaurita.d.hutchins@gmail.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: snyk-bot <snyk-bot@snyk.io>

* 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] <support@github.com>
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Co-authored-by: Shaurita D. Hutchins <shaurita.d.hutchins@gmail.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Prepare release 1.0.0b2

* Rebuild docs.

* Add action for building docs.

* Fix workflow.

https://github.blog/changelog/2024-04-16-deprecation-notice-v3-of-the-artifact-actions/

* Fix build script.

* Add readthedocs requirements.

* Fix readthe docs yaml.

* Fix badges.

---------

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Co-authored-by: Snyk bot <github+bot@snyk.io>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: snyk-bot <snyk-bot@snyk.io>
Co-authored-by: sdhutchins <sdhutchins@outlook.com>
Co-authored-by: Shaurita D. Hutchins <shaurita.d.hutchins@gmail.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Author: 6 people

.readthedocs.yml

@@ -4,22 +4,22 @@
 version: 2
 
 build:
-  image: latest
-  os: ubuntu-22.04
-  # Pre-build job: Run update_docs.py to regenerate API docs and convert READMEs
-  # This runs before Sphinx builds the documentation
-  commands:
-    - python docs/update_docs.py --skip-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:
-  version: 3.9
   install:
+    - requirements: requirements.txt
+    - requirements: docs/requirements-docs.txt
+    # Install our python package before building the docs
     - method: pip
       path: .
-    - method: pip
-      # Install documentation dependencies
-      pip_install:
-        - sphinx
-        - pypandoc
 
-# Sphinx will be auto-detected from docs/docs/source/conf.py
+sphinx:
+  configuration: docs/docs/source/conf.py

docs/docs/source/index.rst

@@ -1,18 +1,18 @@
 OrthoEvolution
 ====================
 
-.. image:: https://travis-ci.org/datasnakes/OrthoEvolution.svg?branch=master
-    :target: https://travis-ci.org/datasnakes/OrthoEvolution
+.. image:: https://github.com/datasnakes/OrthoEvolution/actions/workflows/ci.yml/badge.svg
+    :target: https://github.com/datasnakes/OrthoEvolution/actions/workflows/ci.yml
 
 .. image:: https://api.codacy.com/project/badge/Grade/25062944794a4d14b5cab274a885ac27
    :target: https://www.codacy.com/app/datasnakes/OrthoEvolution?utm_source=github.com&utm_medium=referral&utm_content=datasnakes/OrthoEvolution&utm_campaign=Badge_Grade
 
-.. image:: https://img.shields.io/badge/chat-on%20gitter-753A88.svg
-   :target: https://gitter.im/datasnakes/OrthoEvolution
-
 .. image:: https://badge.fury.io/py/OrthoEvol.svg
    :target: https://badge.fury.io/py/OrthoEvol
 
+.. image:: https://codecov.io/gh/datasnakes/OrthoEvolution/branch/main/graph/badge.svg
+   :target: https://codecov.io/gh/datasnakes/OrthoEvolution
+
 .. image:: https://readthedocs.org/projects/orthoevolution/badge/?version=latest
    :target: http://orthoevolution.readthedocs.io/en/latest/?badge=latest
 

docs/requirements-docs.txt

@@ -0,0 +1,3 @@
+# Documentation build dependencies for Read the Docs
+sphinx
+pypandoc