diff --git a/.gitattribute b/.gitattribute deleted file mode 100644 index f8ade40..0000000 --- a/.gitattribute +++ /dev/null @@ -1 +0,0 @@ -*.1 linguist-documentation \ No newline at end of file diff --git a/Changelog.md b/Changelog.md deleted file mode 100644 index 5cd6849..0000000 --- a/Changelog.md +++ /dev/null @@ -1,71 +0,0 @@ - -# Changelog - - -## [1.2.0] - 2025-03-21 -**New features** -* allow metafounders, defined as “MF_”, in the pedigree file input ({pr}`175`, {user}`RosCraddock`, {user}`XingerTang`) - -* added ``alt_allele_prob_file`` to allow user-inputted alternative allele frequencies for each metafounder and loci. For now, these are restricted to be between 0.01 and 0.99 ({pr}`175`, {user}`RosCraddock`, {user}`XingerTang`) - -* added ``main_metafounder`` to allow user to assign the default metafounder to use where a metafounder has not been assigned to a founder in the pedigree ({pr}`175`, {user}`RosCraddock`, {user}`XingerTang`) - -* added ``update_alt_allele_prob`` to allow the base alternative allele frequencies to be updated after each peeling cycle based on the mean of the founders within the assigned metafounder ({pr}`182`, {user}`RosCraddock`) - -**Bug fixes** -* Fixed bug due to setuptools package being updated for all wheel file naming to follow binary distribution specification (i.e all lower case) and updated documentation ({pr}`182`, {user}`RosCraddock`) - -**Maintenance** -* User-warnings and documentation updates for metafounder implementation and estimation of alternative allele frequency ({pr} `152`, {pr}`175`, {pr}`182`, {user}`RosCraddock`, {user}`XingerTang`) - -* Functional and accuracy tests for metafounder implementation ({pr}`156`, {pr}`182`, {user}`XingerTang`, {user}`RosCraddock`) - -* Updated reference to tinyhouse ({pr}`177`, {user}`XingerTang`) - - -## [1.1.6] - 2024-10-22 -**New features** -* Addition of map file input for non-hybrid mode ({pr}`154`, {user}`XingerTang`) - -**Bug fixes** -* resolved bug to produce output file with ``-hap`` and ``-geno`` ({pr}`157`, {user}`AprilYUZhang`) - -**Maintenance** -* set default hap and geno threshold as 1/3 when calling genotypes ({pr}`157`, {user}`AprilYUZhang`) - -## [1.1.5] - 2023-12-01 -**New features** -* Addition of output options: ``geno``, and ``hap_threshold`` ({pr}`119`, {user}``AprilYuZhang`) - -**Maintenance** -* Updates in option and file names. These include: - - * ``no_dosages`` to ``no_dosage`` - * ``calling_threshold`` to ``geno_threshold`` - * ``call_phase`` to ``hap`` - * ``haps`` to ``phased_geno_prob`` - * ``pedigree`` to ``ped_file`` - * ``genotypes`` to ``geno_file`` - * and more, for all changes please visit: https://github.com/AlphaGenes/AlphaPeel/issues/113#issue-1935197000 ({pr}`105`, {pr}`115`, {pr}`122`, {user}`XingerTang`, {user}`AprilYuZhang`) - -* Updates the documentation and help functions ({pr}`88`, {pr}`119`, {user}`XingerTang`, {user}`AprilYuZhang`). - -* Updates to accuracy and functional tests for new argument names ({pr}`126`, {pr}`130`, {pr}`131`, {user}`XingerTang`). - -## [1.1.4] - 2023-08-25 -**New features** -* Implementation of functional and accuracy testing with pytest ({pr}`53`, {user}`XingerTang`) - -* Implementation of pre-committ protocol through Black and Flake8 ({pr}`40`, {user}`XingerTang`) - -* Implementation of cross-platform tests workflow through github actions ({pr}`59`, {user}`XingerTang`) - -* Added instructions for how to contribute to AlphaPeel ({pr}`27`, {pr}`31`, {user}`XingerTang`) - -**Bug Fixes** -* Fixed bug on the loading of submodule ({pr}`22`, {user}`XingerTang`) - -**Maintenance** -* Update theme for the HTML documentation ({pr}`38`, {user}`XingerTang`) - -* Modified the URL for installation ({pr}`11`, {user}`XingerTang`) diff --git a/docs/source/introduction.rst b/docs/source/introduction.rst index db6286e..eeded7c 100644 --- a/docs/source/introduction.rst +++ b/docs/source/introduction.rst @@ -6,7 +6,7 @@ Introduction Availability ------------ -|Software| is available as open-source from `Github `_ website and can be easily installed using ``pip install AlphaPeel`` (the latest release). +|Software| is available as open-source from `GitHub `_ website and can be easily installed using ``pip install AlphaPeel`` (the latest release). Please report any issues at ``_. diff --git a/pyproject.toml b/pyproject.toml index 51c254c..f1f2f64 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta" name = "AlphaPeel" version = "1.3.0" authors = [ - { name="Andrew Whalen", email="awhalen@roslin.ed.ac.uk" }, + { name="Andrew Whalen", email="alphagenes.dev@gmail.com" }, ] description = "Multilocus and hybrid peeling" # readme corresponds to the long_description