Code

Prepare version 5.0 release#176

Code

Merged

mmore500 merged 107 commits intojeetsukumaran:mainjeetsukumaran/DendroPy:mainfrom connoryang1:release-5.0connoryang1/DendroPy:release-5.0Copy head branch name to clipboardMay 22, 2024

+1,963-477

Commits

Commits on Oct 9, 2023

• Restructure tests folder for separate unit and smoke tests

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Commits on Oct 22, 2023

• Create smoke tests for popgenism.py

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• Add pytest compatability through pytest-runner

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• Add init files in other test folders for Python2 support

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Commits on Oct 24, 2023

• Merge remote-tracking branch 'playground/smoke_tests'

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Commits on Oct 27, 2023

• Create symlink to src/dendropy for both testing directories

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• Drop 2.7 and 3.5 support in CI

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• Create smoke tests for coalescent.py

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• Remove line to fix ci

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Commits on Oct 29, 2023

• Edit CI to be compatible with pytest and new file structure

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• Change python3 to python

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• Force pytest 7.0.0

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Commits on Oct 31, 2023

• Add requirements.txt

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• Change cov to tests/unittests

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• Update requirements.txt to work with python3.6

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• Remove .eggs

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• Add .eggs to .gitignore

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• Prepare for merge

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• Remove extra comment from test_popgenism.py

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• Fix error in test case

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Commits on Nov 1, 2023

• Merge pull request #1 from Nephrain/add-smoke-tests

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  9f012ab

Commits on Nov 10, 2023

• Add more smoke tests

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Commits on Nov 11, 2023

• Fix some tests and variable names

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• Format

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Commits on Nov 14, 2023

• Add more smoke tests

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• Format

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• Merge pull request #2 from Nephrain/add-smoke-tests

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  connoryang1

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  833efde

• Protect against root node

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• Fix Latex

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  27b7ac5

• Fix copy paste kwarg in docs

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• Check if domain_taxa exists

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• Test node age fix

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Commits on Nov 17, 2023

• Update docstring to specify correct type

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  24045c8

• Fix typo in newick string formatting

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  dae496f

• Fix typo

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• Delete extra newline

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• Add NoneType checking to log()

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• Try simpler session implementation

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• fixup! Try simpler session implementation

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  ea1a9cc

• Make processio unit test

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  bec0b7b

• Remove tests covered by new unit test

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  bd066bb

• Fix tests and add missing asserts

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  6e6d0ca

• Fix tests

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  23c37ee

• Clean up tests, add missing asserts

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  9590f38

• Add missing asserts to tests

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  7a62e47

• Change variable names, remove TODO

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Commits on Nov 28, 2023

• Fix LaTex

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  65f0648

• Deprecate factorial

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• Deprecate gcd

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• Replace internal use of deprecated functions

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• Add is_mutable to docstring

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• Make parameter docstring more specific

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  6fac698

• Deprecate old arguments

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• Add deprecation warning if neither arguments provided

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  705a85a

• Fix typo

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Commits on Dec 1, 2023

• Update src/dendropy/model/coalescent.py

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  connoryang1

  and

  mmore500

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  3528fe7

• Update src/dendropy/model/parsimony.py

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  connoryang1

  and

  mmore500

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  348bc86

• Delete leftover asserts

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  bcb6b47

• Delete dead code

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  7d872d5

• Delete redundant smoke test

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  eb51c8e

• Delete leftover debugging code

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  0f3db80

• Change file variable names

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  84d6c40

• Change getter and setters to use decorators

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  b56c3d2

• Add else condition to set contained_trees to an empty TreeList

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  ebf6455

• Delete leftover code

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  f5dee3f

• Merge branch 'add-smoke-tests' of github.com:Nephrain/DendroPy into add-smoke-tests

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  d18ab4a

• Merge pull request #3 from Nephrain/add-smoke-tests

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  connoryang1

  authored
  9a1f42a

• Delete asdf.xyz

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  7ed0b65

Commits on Dec 8, 2023

• Deprecate bibtex.py

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Commits on Dec 10, 2023

• Create default setup.cfg for pytest

  connoryang1

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Commits on May 17, 2024

• Revise deprecation notice text

  mmore500

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  40e55c4

• Merge pull request #4 from Nephrain/remove-bibtex

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  mmore500

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  b8fdea9

• Merge branch 'main' into release-5.0

  mmore500

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• Merge branch 'main' into release-5.0

  mmore500

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  77caf57

Commits on May 18, 2024

• Remove duplicated kwarg

  mmore500

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• Strip trailing whitespace

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• Fix Python versions tested/supported

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  c925f10

• Deprecate PatristicDistanceMatrix

  mmore500

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• Drop special cases for python < 3.4

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• Drop more special cases for Python <3.4

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• Drop special-case StringIO handling for old python

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  a4da42d

• Drop unused imports

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• Drop more Python2 legacy support

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• Add smoke test for fast_birth_death_tree

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• Strip trailing whitespace

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  5fb2d63

• Deprecate unused kwargs

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  783334a

• fixup! Deprecate unused kwargs

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  c606632

• Add missing docstrings

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  8fb6a03

• Fix typo in test file name

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  1d1f995

• Fix taxon namespace conflicts

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  0977e95

• Track seqgen wrapper API change

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  c33938c

• Workaround bipartition mutability error

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  b06e049

• Fix minor typos in docstring

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  ae6bc5f

• Workaround mutability for bipartition frozenset

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  8e4b564

• Fix consensus tree smoke test

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• Warn broken examples

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• Warn on MRCA for unrooted tree

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  ef2c39c

• Don't depend on deprecated distutils strtobool

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  c405985

• Fix minor typo in docs

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  c29bd5d

• Use full Newick formatter for __str__

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• Drop docstring entries for nonexistant kwargs

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• Fix docstring typo

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Commits on May 19, 2024

• Merge branch 'main' of https://github.com/jeetsukumaran/DendroPy into release-5.0

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  committed
  74bc901

• fixup! Warn broken examples

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  committed
  ceeba59

• Fix test to track new str behavior

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  bf87518

• fixup! Warn broken examples

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  committed
  77dc3e7

Commits on May 22, 2024

• Merge branch 'main' into release-5.0

  mmore500

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