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[Snyk] Security upgrade werkzeug from 2.2.3 to 3.1.4 - #210

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sdhutchins merged 3 commits into
refactor-phylofrom
snyk-fix-ddd7a33aa00048f4dcf12f7b18ab3c03
Dec 2, 2025
Merged

[Snyk] Security upgrade werkzeug from 2.2.3 to 3.1.4#210
sdhutchins merged 3 commits into
refactor-phylofrom
snyk-fix-ddd7a33aa00048f4dcf12f7b18ab3c03

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@sdhutchins

@sdhutchins sdhutchins commented Nov 30, 2025

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Snyk has created this PR to fix 1 vulnerabilities in the pip dependencies of this project.

Snyk changed the following file(s):

  • requirements.txt
⚠️ Warning 
Flask 1.0 requires Werkzeug, which is not installed.

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  • Max score is 1000. Note that the real score may have changed since the PR was raised.
  • This PR was automatically created by Snyk using the credentials of a real user.
  • Some vulnerabilities couldn't be fully fixed and so Snyk will still find them when the project is tested again. This may be because the vulnerability existed within more than one direct dependency, but not all of the affected dependencies could be upgraded.

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sdhutchins and others added 2 commits August 21, 2020 11:11
@sdhutchins
Merge pull request #155 from datasnakes/dev-master
e207046 
Major updates to database management, ftp, pbs, etc.
@snyk-bot
fix: requirements.txt to reduce vulnerabilities
5a3015f 
The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-WERKZEUG-14151620
@sdhutchins
sdhutchins changed the base branch from master to refactor-phylo December 2, 2025 03:15
@sdhutchins
sdhutchins merged commit 5e9abb7 into refactor-phylo Dec 2, 2025
4 of 5 checks passed
@codecov

codecov Bot commented Dec 2, 2025

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 21.90%. Comparing base (5b564e2) to head (f80222d).
⚠️ Report is 2 commits behind head on refactor-phylo.
✅ All tests successful. No failed tests found.

Additional details and impacted files 
@@               Coverage Diff               @@
##           refactor-phylo     #210   +/-   ##
===============================================
  Coverage           21.90%   21.90%           
===============================================
  Files                  69       69           
  Lines                4364     4364           
===============================================
  Hits                  956      956           
  Misses               3408     3408

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

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sdhutchins added a commit that referenced this pull request Dec 2, 2025
@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 deleted the snyk-fix-ddd7a33aa00048f4dcf12f7b18ab3c03 branch December 2, 2025 04:21
sdhutchins added a commit that referenced this pull request Dec 2, 2025
@sdhutchins @snyk-bot
sdhutchins @dependabot
Add additional tests (#212)
689a074 
* 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>
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
...

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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
...

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* 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.

---------

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* 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.

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

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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
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Shaurita Hutchins <ms.s.hutchins@gmail.com>
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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
...

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

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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>
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* 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>
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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>
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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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@sdhutchins @snyk-bot