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Dev refactored - #212

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Dec 2, 2025
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Dev refactored#212
sdhutchins merged 14 commits into
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dev-refactored

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@sdhutchins sdhutchins commented Dec 2, 2025 •
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Improve Test Coverage for OrthoEvolution

Summary

This PR significantly improves test coverage by adding comprehensive test suites for the utilities, Manager, and Tools modules. Also fixes a critical typo in FullUtilities that caused an AttributeError.

Changes Made

Test Coverage Improvements

  • Utilities Module (tests/test_utils.py): Added 20+ test methods for BlastUtils, GenbankUtils, OrthologUtils, ManagerUtils, PackageVersion, and FullUtilities classes (~297 lines)
  • Manager Module (tests/test_manager.py): Added 16 test methods across 6 new test classes covering Management, RepoManagement, UserManagement, WebsiteManagement, ProjectManagement, and BaseDatabaseManagement (~332 lines)
  • Tools Module (tests/test_tools.py): Added 5 test methods for LogIt, PyBasher, NcbiFTPClient, and Multiprocess functionality (~76 lines)

Bug Fixes

  • Fixed typo in OrthoEvol/utilities.py line 951: Ortho0logUtils → OrthologUtils
    • Resolves AttributeError in FullUtilities.__init__()

Impact

  • ~705 lines of new test code significantly increases coverage across three major modules
  • Tests cover initialization, core methods, and edge cases with proper mocking and isolation
  • Fixed critical runtime bug in FullUtilities class

Files Changed

  • tests/test_utils.py (+297 lines)
  • tests/test_manager.py (+332 lines)
  • tests/test_tools.py (+76 lines)
  • OrthoEvol/utilities.py (1 line typo fix)

sdhutchins and others added 5 commits December 15, 2022 21:19
@sdhutchins @snyk-bot
fix: requirements.txt to reduce vulnerabilities (#176)
f75ee85 
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>
@snyk-bot @sdhutchins
fix: requirements.txt to reduce vulnerabilities (#175)
1c9bc89 
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>
@snyk-bot @sdhutchins
fix: requirements.txt to reduce vulnerabilities (#170)
845ba7e 
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>
@snyk-bot @sdhutchins
fix: requirements.txt to reduce vulnerabilities (#179)
b831c0e 
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>
@sdhutchins sdhutchins
@dependabot @snyk-bot
Refactor code. (#177)
3c75a6e 
* 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
...

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>

* 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>
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] <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 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>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

---------

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>
@sdhutchins sdhutchins self-assigned this Dec 2, 2025
@codecov

codecov Bot commented Dec 2, 2025 •
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Codecov Report

❌ Patch coverage is 46.77966% with 157 lines in your changes missing coverage. Please review.
✅ Project coverage is 29.68%. Comparing base (3305c50) to head (1768c93).
⚠️ Report is 4 commits behind head on dev-master.
✅ All tests successful. No failed tests found.

Files with missing lines Patch % Lines
OrthoEvol/Orthologs/Phylogenetics/Phylip/phylip.py 19.69% 53 Missing ⚠️
OrthoEvol/Tools/pybasher/bash.py 45.94% 40 Missing ⚠️
OrthoEvol/Orthologs/Phylogenetics/PAML/ete3paml.py 45.71% 19 Missing ⚠️
OrthoEvol/Orthologs/Phylogenetics/PhyML/phyml.py 59.57% 19 Missing ⚠️
OrthoEvol/Cookies/cookie_jar.py 50.00% 5 Missing ⚠️
OrthoEvol/Orthologs/Align/orthoclustal.py 0.00% 4 Missing ⚠️
OrthoEvol/Pipeline/__init__.py 0.00% 3 Missing ⚠️
OrthoEvol/Pipeline/blastpipeline.py 0.00% 3 Missing ⚠️
OrthoEvol/Orthologs/Blast/blast.py 50.00% 2 Missing ⚠️
OrthoEvol/Orthologs/GenBank/genbank.py 0.00% 2 Missing ⚠️
... and 5 more
Additional details and impacted files 
@@               Coverage Diff               @@
##           dev-master     #212       +/-   ##
===============================================
+ Coverage       15.13%   29.68%   +14.55%     
===============================================
  Files              67       69        +2     
  Lines            4182     4345      +163     
===============================================
+ Hits              633     1290      +657     
+ Misses           3549     3055      -494

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:
  • 📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.

@sdhutchins
sdhutchins merged commit 689a074 into dev-master Dec 2, 2025
9 checks passed
@sdhutchins
sdhutchins deleted the dev-refactored branch December 2, 2025 20:43
sdhutchins added a commit that referenced this pull request Dec 2, 2025
@sdhutchins @snyk-bot
@dependabot sdhutchins
Release 1.0.0b2 (#213)
c4d1395 
* 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
...

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>

* 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>
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] <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 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>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

---------

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>
Co-authored-by: snyk-bot <snyk-bot@snyk.io>
Co-authored-by: Snyk bot <github+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>
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.

---------

Signed-off-by: dependabot[bot] <support@github.com>
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>
@sdhutchins sdhutchins mentioned this pull request Dec 2, 2025
Closed
2 of 5 tasks
sdhutchins added a commit that referenced this pull request Dec 2, 2025
@sdhutchins @snyk-bot
@dependabot sdhutchins
Fix readthedocs build. (#215)
71f413c 
* 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
...

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>

* 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>
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] <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 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>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

---------

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>
Co-authored-by: snyk-bot <snyk-bot@snyk.io>
Co-authored-by: Snyk bot <github+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>
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.

---------

Signed-off-by: dependabot[bot] <support@github.com>
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>
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