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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>
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #213 +/- ##
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+ Coverage 15.13% 29.68% +14.55%
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Files 67 69 +2
Lines 4182 4345 +163
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+ Hits 633 1290 +657
+ Misses 3549 3055 -494 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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