diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml old mode 100755 new mode 100644 diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml old mode 100755 new mode 100644 diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml old mode 100755 new mode 100644 index df2fb67..44d75e3 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -10,7 +10,7 @@ jobs: strategy: matrix: os: [ubuntu-latest, windows-latest] - python-version: ['3.8', '3.10', '3.11'] + python-version: ['3.8', '3.10', '3.12'] steps: - uses: actions/checkout@v3 diff --git a/.gitignore b/.gitignore old mode 100755 new mode 100644 diff --git a/DEPENDENCIES.md b/DEPENDENCIES.md deleted file mode 100755 index 7f09ac5..0000000 --- a/DEPENDENCIES.md +++ /dev/null @@ -1,59 +0,0 @@ - -# 3rd-Party Software for [tajimas_d]() - -The following 3rd-party software packages may be used by or distributed with **tajimas_d**. Most of them are developement dependentcies (for testing) as they are not required by the shipped package. - -Any information relevant to third-party vendors listed below are collected using common, reasonable means. - -## Dependencies -### [miniFasta](https://pypi.org/project/miniFasta/) - -#### Declared Licenses -gpl-3.0 - -**Package Homepage**: (https://pypi.org/project/miniFasta/ - -**Dependency Paths**: miniFasta - ---- - -### [mypy (0.930)](http://www.mypy-lang.org/) - -#### Declared Licenses -MIT *OR* Python-2.0 - -### Package Info - -**Package Homepage**: http://www.mypy-lang.org/ - ---- - -### [pytest (7.0.0rc1)](http://pytest.org) - -#### Declared Licenses - -### Package Info - -**Package Homepage**: http://pytest.org - ---- - -### [pytest-cov (3.0.0)](https://github.com/pytest-dev/pytest-cov) - -#### Declared Licenses -MIT - -### Package Info - -**Package Homepage**: https://github.com/pytest-dev/pytest-cov - ---- - -### [tox (4.0.0a9)](https://tox.readthedocs.org/) - -#### Declared Licenses -MIT - -### Package Info - -**Package Homepage**: https://tox.readthedocs.org/ diff --git a/LICENSE b/LICENSE old mode 100755 new mode 100644 diff --git a/README.md b/README.md old mode 100755 new mode 100644 index 2b5b46d..d65b29a --- a/README.md +++ b/README.md @@ -62,6 +62,8 @@ theta_w = watterson_estimator(sequences) ## Standalone version +The standalone version requires `miniFasta>=2.2` to be installed. + ``` usage: tajimas_d [-h] -f PATH [-p] [-t] [-w] @@ -78,8 +80,9 @@ optional arguments: ``` ## License -``` -Copyright (C) 2022 by Jules Kreuer - @not_a_feature + +Copyright (C) 2024 by Jules Kreuer - @not_a_feature + This piece of software is published unter the GNU General Public License v3.0 TLDR: @@ -90,9 +93,5 @@ TLDR: | ✓ Modification | Same license | | | ✓ Patent use | State changes | | | ✓ Private use | | | -``` -Go to [LICENSE.md](https://github.com/not-a-feature/tajimas_d/blob/main/LICENSE) to see the full version. -## Dependencies -In addition to packages included in Python 3, this piece of software uses 3rd-party software packages for development purposes that are not required in the published version. -Go to [DEPENDENCIES.md](https://github.com/not-a-feature/tajimas_d/blob/main/DEPENDENCIES.md) to see all dependencies and licenses. \ No newline at end of file +Go to [LICENSE.md](https://github.com/not-a-feature/tajimas_d/blob/main/LICENSE) to see the full version. diff --git a/dev.py b/dev.py old mode 100755 new mode 100644 diff --git a/pyproject.toml b/pyproject.toml old mode 100755 new mode 100644 diff --git a/requirements_dev.txt b/requirements_dev.txt old mode 100755 new mode 100644 diff --git a/requirements_standalone.txt b/requirements_standalone.txt old mode 100755 new mode 100644 diff --git a/setup.cfg b/setup.cfg old mode 100755 new mode 100644 index f31b613..aca9ff8 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = tajimas_d -version = 2.0.0 +version = 2.0.1 description = Computes Tajimas D, the Pi- or Watterson-Estimator for multiple sequences. long_description = file: README.md long_description_content_type=text/markdown @@ -12,9 +12,6 @@ license_file = LICENSE platforms = unix, linux, osx, cygwin, win32 classifiers = Programming Language :: Python :: 3 - Programming Language :: Python :: 3.8 - Programming Language :: Python :: 3.10 - Programming Language :: Python :: 3.11 [options] packages = diff --git a/setup.py b/setup.py old mode 100755 new mode 100644 diff --git a/tajimas-d.png b/tajimas-d.png old mode 100755 new mode 100644 diff --git a/tox.ini b/tox.ini old mode 100755 new mode 100644