Refactor code. by sdhutchins · Pull Request #177 · datasnakes/OrthoEvolution

sdhutchins · 2022-12-16T03:07:29Z

Mainly a refactoring of phylogenetics.

Copilot

Pull Request Overview

A refactoring of the phylogenetics modules to introduce new, unified wrappers for PhyML and PAML, update documentation, and streamline CI and configuration-loading code.

Introduced PhyML wrapper (phyml.py) and removed the old orthophyml.py
Refactored ETE3PAML and CodemlRun classes, updated their tests and READMEs
Updated CI configs (.travis.yml, GitHub Actions) and improved project-wide task scripts

Reviewed Changes

Copilot reviewed 47 out of 47 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
OrthoEvol/Orthologs/Phylogenetics/Phylip/README.md	Added Phylip usage docs (empty example needs content)
OrthoEvol/Orthologs/Phylogenetics/PhyML/phyml.py	New PhyML wrapper implementation
OrthoEvol/Orthologs/Phylogenetics/PhyML/orthophyml.py	Removed deprecated wrapper
OrthoEvol/Orthologs/Phylogenetics/PhyML/init.py	Updated import to the new wrapper
OrthoEvol/Orthologs/Phylogenetics/PhyML/README.md	Fixed examples and links (typo persists)
OrthoEvol/Manager/db_mana_test.py	Refactored YAML loading; missing imports introduced
OrthoEvol/Cookies/new_website/tasks.py	Streamlined Invoke tasks; missing webbrowser import
.travis.yml	Updated Python versions and added `phyml` install
.github/workflows/ci.yml	Added GitHub Actions CI

Comments suppressed due to low confidence (4)

OrthoEvol/Cookies/new_website/tasks.py:72

webbrowser.open_new_tab is called but webbrowser is not imported at the top of the file. Please add import webbrowser.

if browse:

OrthoEvol/Orthologs/Phylogenetics/PhyML/phyml.py:1

The new PhyML class has no accompanying unit tests. Consider adding tests for _check_exe, _validate_format, and run methods to ensure coverage.

import sys

OrthoEvol/Orthologs/Phylogenetics/PhyML/phyml.py:62

The docstring uses four quotes ("""") instead of triple quotes. Please correct to """Run phyml.""".

""""Run phyml."""

OrthoEvol/Manager/db_mana_test.py:16

resource_filename, yml, and yaml are used but not imported. Add the necessary imports (from pkg_resources import resource_filename, import yaml, etc.) or update references.

file_path = resource_filename(yml.__name__, file_name)

Copilot · 2025-05-30T03:15:21Z

+        """
+        try:
+            AlignIO.read(open(infile), "phylip")
+        except ValueError as e:


If the input file is not valid PHYLIP, _validate_format logs and returns False but the constructor proceeds silently without setting self.infile. Consider raising an exception on invalid format to prevent downstream attribute errors.

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

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>

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>

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>

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>

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>

Copilot

Pull request overview

Copilot reviewed 50 out of 53 changed files in this pull request and generated 17 comments.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

Copilot · 2025-12-02T04:19:08Z


+if __name__ == '__main__':
+    mp = Multiprocess()
+    mp.map2function(phyml, files)


The function name map2function in the README example doesn't match the actual method name map_to_function. This will cause an AttributeError if users follow this example.

Suggested change

mp.map2function(phyml, files)

mp.map_to_function(phyml, files)

Copilot · 2025-12-02T04:19:08Z

 if __name__ == '__main__':
    mp = Multiprocess()
-    mp.map_to_function(printwords, words)
+    mp.map_to_function(printwords, words, processors=8)


The parameter name in the README example uses processors but the actual method parameter is named procs. This inconsistency will cause a TypeError if users follow this documentation.

Copilot · 2025-12-02T04:19:09Z

+    def test_mv(self):
+        # Create a file to move
+        with open("test.txt", "w") as f:
+            f.write("Test content")
+
+        # Create a PyBasher instance
+        pybasher = PyBasher()
+
+        # Move the file
+        pybasher.mv("test.txt", "moved.txt")
+
+        # Check that the file was moved
+        assert not os.path.exists("test.txt")
+        assert os.path.exists("moved.txt")
+
+        # Check that the moved file has the correct contents
+        with open("moved.txt", "r") as f:
+            moved_content = f.read()
+        assert moved_content == "Test content"
+
+        # Clean up
+        os.remove("moved.txt")
+
+    def test_cp(self):
+        # Create a file to copy
+        with open("test.txt", "w") as f:
+            f.write("Test content")
+
+        # Create a PyBasher instance
+        pybasher = PyBasher()
+
+        # Copy the file
+        pybasher.cp("test.txt", "copy.txt")
+
+        # Check that the copy was made
+        assert os.path.exists("copy.txt")
+
+        # Check that the copy has the same contents as the original
+        with open("test.txt", "r") as f:
+            original_content = f.read()
+        with open("copy.txt", "r") as f:
+            copy_content = f.read()
+        assert original_content == copy_content
+
+        # Clean up
+        os.remove("test.txt")
+        os.remove("copy.txt")


The test methods test_mv and test_cp lack proper tearDown cleanup. If the test fails before the cleanup code at the end, it will leave test files behind. Consider using setUp/tearDown or the @contextmanager pattern for better cleanup.

Copilot · 2025-12-02T04:19:09Z

+    def test_mv(self):
+        # Create a file to move
+        with open("test.txt", "w") as f:
+            f.write("Test content")
+
+        # Create a PyBasher instance
+        pybasher = PyBasher()
+
+        # Move the file
+        pybasher.mv("test.txt", "moved.txt")
+
+        # Check that the file was moved
+        assert not os.path.exists("test.txt")
+        assert os.path.exists("moved.txt")
+
+        # Check that the moved file has the correct contents
+        with open("moved.txt", "r") as f:
+            moved_content = f.read()
+        assert moved_content == "Test content"
+
+        # Clean up
+        os.remove("moved.txt")
+
+    def test_cp(self):
+        # Create a file to copy
+        with open("test.txt", "w") as f:
+            f.write("Test content")
+
+        # Create a PyBasher instance
+        pybasher = PyBasher()
+
+        # Copy the file
+        pybasher.cp("test.txt", "copy.txt")
+
+        # Check that the copy was made
+        assert os.path.exists("copy.txt")
+
+        # Check that the copy has the same contents as the original
+        with open("test.txt", "r") as f:
+            original_content = f.read()
+        with open("copy.txt", "r") as f:
+            copy_content = f.read()
+        assert original_content == copy_content
+
+        # Clean up
+        os.remove("test.txt")
+        os.remove("copy.txt")


[nitpick] The test uses bare assert statements instead of unittest assertion methods (e.g., self.assertFalse, self.assertTrue). While this works, it's inconsistent with the rest of the test class and doesn't provide as helpful error messages on failure.

Copilot · 2025-12-02T04:19:09Z

+        """Generate a maximum likelihoood tree using dnapaml.
+
+        :param outfile:  Standard output filename.
+        :param outtree:  Name of maximum likelihoood tree.


Typo in the docstring: "likelihoood" should be "likelihood".

Suggested change

"""Generate a maximum likelihoood tree using dnapaml.

:param outfile: Standard output filename.

:param outtree: Name of maximum likelihoood tree.

"""Generate a maximum likelihood tree using dnapaml.

:param outfile: Standard output filename.

:param outtree: Name of maximum likelihood tree.

Copilot · 2025-12-02T04:19:12Z

+import warnings
+
+from Bio import Phylo
+from ete3 import Tree


Import of 'Tree' is not used.

Copilot · 2025-12-02T04:19:12Z

+                            shutil.rmtree(item)
+                        else:
+                            item.unlink()
+                    except (OSError, PermissionError):


'except' clause does nothing but pass and there is no explanatory comment.

Copilot · 2025-12-02T04:19:12Z

+                # Try to remove the directory again
+                try:
+                    self.test_dir.rmdir()
+                except (OSError, PermissionError):


'except' clause does nothing but pass and there is no explanatory comment.

Copilot · 2025-12-02T04:19:13Z

+        if test_repo.exists():
+            try:
+                shutil.rmtree(test_repo)
+            except (OSError, PermissionError):


'except' clause does nothing but pass and there is no explanatory comment.

Copilot · 2025-12-02T04:19:13Z

+        if project_path.exists():
+            try:
+                rmtree(project_path)
+            except (OSError, PermissionError):


'except' clause does nothing but pass and there is no explanatory comment.

* 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>

* 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>

* 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>

sdhutchins and others added 30 commits July 31, 2019 15:58

Renamed orthophyl.py to phyml.py

dc1529c

Renamed orthophylip.py to phylip.py

68be622

Updated import of phylip.py

6ff9dcd

Updated import of phyml.py

3c9edcc

Added docstrings for the init of the PhyML class.

68608e5

Refactored init in ETE3PAMl to create better API.

7bf7740

Fixed logging issue.

0d6b792

Added check_exe function.

4b267b3

Added new examples to README.

dfaf2f3

Added ApplicationError to try/except in run method.

c7d08cc

Added a test for phyml

7c420b9

Added test data for phyml test.

01b458c

Added phyml installation to travis script.

f4edaf7

Added ability for user to choose number of processors.

7ee4e7b

Updated README for new api.

a2214ea

Removed deprecated csvtolist

73261f2

Added logging to ETE3PAML

215a24d

Added _import_alignment method

2734fc7

Added a README for the PHYLIP class.

2feab29

Added try/except/else/finally for phylip methods

5e75f38

Removed phylip test from Phylip folder.

1d47901

Added docstrings to ETE3PAML class.

a584164

Fixed errors in README.

eb5914d

Added TODO in codeml.py

32676ae

Changed data in test.

f86847a

Added missing doctrings.

2a718e3

Updated example in README.

8a27d3b

Refactored TreeViz api.

a764257

Refactored ncbi-download script

9cbfc28

Added validation function. Extended run api.

073f272

sdhutchins requested a review from Copilot May 30, 2025 03:12

sdhutchins marked this pull request as ready for review May 30, 2025 03:12

sdhutchins removed the request for review from a team May 30, 2025 03:12

sdhutchins self-assigned this May 30, 2025

Copilot AI reviewed May 30, 2025

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sdhutchins and others added 16 commits May 29, 2025 22:17

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

f3b8b01

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

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

1097583

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

Remove travis. Add GH action.

415080e

Upgrade biopython version.

b04c3cf

Fixed tests.

2eb0d73

bump up python versions.

e946cc3

Add test gpcr dataset.

65b3a83

Fix utils test.

ced3cae

Fix issue finding directory.

bd414d3

Fix manage tests.

9ad5d59

Fix code cov.

5b564e2

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

5e9abb7

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>

sdhutchins requested a review from Copilot December 2, 2025 04:14

Copilot started reviewing on behalf of sdhutchins December 2, 2025 04:15 View session

Copilot finished reviewing on behalf of sdhutchins December 2, 2025 04:16

Copilot AI reviewed Dec 2, 2025

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sdhutchins merged commit 3c75a6e into dev-refactored Dec 2, 2025
15 of 16 checks passed

sdhutchins deleted the refactor-phylo branch December 2, 2025 04:21

	mp.map2function(phyml, files)
	mp.map_to_function(phyml, files)

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