5. Authors and history

5.1. PyPop contributors

(Listed in alphabetical order)

Author	ORCiD	Affiliation	Contribution
Karl Kornel	0000-0001-5847-5330	Stanford Research Computing Center	Contributed containerization
Alex Lancaster	0000-0002-0002-9263	Amber Biology LLC, Ronin Institute	Lead developer. Co-designer of Python framework: author of main engine, text file parser, Python extension module framework using SWIG, XML output and XSLT post-processing framework (to generate plain text and HTML output).
Steven J. Mack	0000-0001-9820-9547	University of California, San Francisco	Contributed bug reports, documentation, reviewed PRs.
Michael P. Mariani	0000-0001-5852-0517	Mariani Systems LLC and University of Vermont	Contributed bug reports, documentation, reviewed PRs.
Diogo Meyer	0000-0002-7155-5674	University of São Paulo	Reviewed and tested PyPop, contributed some statistical analysis code.
Mark P. Nelson		University of California, Berkeley	Co-designer of Python framework: implemented and maintained Python modules, particularly the module for Hardy-Weinberg analysis. Updated and maintained XSLT code.
Richard M. Single	0000-0001-6054-6505	University of Vermont	Author of haplotype frequency and linkage disequilibrium analysis module emhaplofreq. Contributed documentation and testing/reviewing PRs.
Vanessa Sochat	0000-0002-4387-3819	Lawrence Livermore National Laboratory	Contributed to the Python 3 port.
Owen Solberg	0000-0003-3060-9709		Implemented filter modules, including conversion to allele name information to sequence data.
Jurriaan H. Spaaks	0000-0002-7064-4069	Netherlands eScience Center	Contributed to Zenodo upload GitHub action
Glenys Thomson	0000-0001-5235-4159	University of California, Berkeley	Principal investigator
Yingssu Tsai	0009-0006-0162-6066	University of California, Berkeley	Implemented prototype of the allele names to sequence conversion filter module.
Gordon Webster	0009-0009-2862-0467	Amber Biology LLC	Contributed documentation and testing framework.

Third-party modules

Included with permission, or via GPL-compatible licenses.

gthwe

The Hardy-Weinberg “exact test” implementation is a modified version of Guo & Thompson’s (Guo and Thompson, 1992) code. Dr. Sun-Wei Guo has kindly allowed us to release the code under the GNU General Public License. Original code available at https://sites.stat.washington.edu/thompson/Genepi/Hardy.shtml

slatkin-exact/monte-carlo.c

Montgomery Slatkin’s implementation of a Monte Carlo approximation of the Ewens-Watterson exact test of neutrality (Slatkin, 1994, Slatkin, 1996). Original code can be found at: http://ib.berkeley.edu/labs/slatkin/monty/Ewens_exact.program.

pval

The code in the ‘pval’ directory (with the exception of ‘pval.c’ the SWIG wrapper, 'pval_wrap.i’ and the Makefile) is part of the R project’s ‘nmath’ numerical library http://www.r-project.org/ and is also licensed under the GNU General Public License (GPL). Minor modifications have been made to allow the module to build correctly.

5.2. PyPop Release History

1.0.2 - 2024-02-24

Bug Fixes

• Synchronize with upstream haplo.stats, fix some redundant checks by @alexlancaster (#196)

Internal

• customize code security scanning for C extensions by @alexlancaster (#195)

• Update numpy requirement from <=1.26.3 to <=1.26.4 by @dependabot (#193)

Documentation

• Documentation updates including security policy by @alexlancaster (#194)

1.0.1 - 2024-02-11

Features

• Add [CustomBinning] filtering unit tests for G and P-codes by @alexlancaster (#186)

Bug Fixes

• switch to scientific notation when frequencies can’t be displayed as decimals by @alexlancaster (#192)

• Port [RandomBinningFilter] to Python 3, include more complex filtering tests by @alexlancaster (#187)

Internal

• Bump the cibuildwheel version from 2.16.4 to 2.16.5: fixes Windows CI builds by @dependabot (#189)

• Bump the version of cibuildwheel from 2.16.2 to 2.16.4 by @dependabot (#188)

• increase test strictness: make test warnings into errors by @alexlancaster (#185)

• Enable wheels on aarch64 architecture by @alexlancaster (#184)

• Update actions/upload-artifact from 3 to 4 in Build on ARM64 by @dependabot (#183)

• Streamline continuous integration: reduce number of wheels, concurrency by @alexlancaster (#182)

• Parallelize wheel builds, re-enable musllinux wheels for Python 3.9+ by @alexlancaster (#181)

• Update lxml requirement from <=5.0.0 to <=5.1.0; disable PyPy 3.7 on Linux by @dependabot (#178)

• Update numpy requirement from <=1.26.2 to <=1.26.3 by @dependabot (#177)

• Update lxml requirement from <=4.9.4 to <=5.0.0 by @dependabot (#174)

• Update lxml requirement from <=4.9.3 to <=4.9.4 by @dependabot (#173)

• update to v4 of download-artifact / upload-artifact by @alexlancaster (#172)

• Bump actions/setup-python from 4 to 5 by @dependabot (#168)

• Update numpy requirement from <=1.26.1 to <=1.26.2 by @dependabot (#167)

Documentation

• Link to new preprint in docs by @alexlancaster (#190)

• Convert bibliography to bibtex by @alexlancaster (#176)

• Convert NEWS.rst to NEWS.md, improve PDF documentation output by @alexlancaster (#175)

1.0.0 - 2023-11-07

PyPop 1.0.0 is the first official release of PyPop using Python 3, and the first release to be included on PyPI. In addition to using modern libraries, there are some new features, such as the new asymmetric LD measures, and better handling of TSV files, along with the typical slew of bug fixes. Many more changes are of an “under the hood” nature, such as a new unit testing and documentation framework, and are detailed below. Many people contributed to this latest release, which has been a while in coming. Thanks especially to all new contributors including Vanessa Sochat, Gordon Webster, Jurriaan H. Spaaks, Karl Kornel and Michael Mariani. Thanks also to all of our bug reporters, and ongoing contributors, especially Richard Single, Owen Solberg and Steve Mack.

New features

• PyPop now fully ported to run under Python 3 (thanks to Vanessa Sochat for major patch)

• Added new asymmetric linkage disequilibrium (ALD) calculations (thanks to Richard Single), see Thomson & Single, 2014 for more details. Added in both the plain text (.txt) as well as the 2-locus-summary.tsv TSV file outputs.

• Improved tab-separated values (TSV) output file handling:

  • old IHWG headers are disabled by default, so the -disable-ihwg option has been replaced by the --enable-ihwg option, which will re-enable them.

  • popmeta: allow TSV files to be put in separate directory with -o/ --outputdir command-lineoption for saving generated files.

  • pypop: renamed --generate-tsv to --enable-tsv

  • dynamic generation of TSV files based on XML input, so the list of files is no longer hard-coded (thanks to Steve Mack for suggestion), this also adds support for haplotypes involving more than 4 loci

• Preliminary support for Genotype List (GL) String (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715123/)

• Added unit-tests using pytest testing framework.

• New documentation system using sphinx, replacing the old DocBook XML, to generate both the website and the PyPop User Guide (HTML and PDF):

  • sphinx-based documentation is now written in ReStructuredText (.rst)

  • improve popmeta and other documentation for command-line programs

  • documentation additions and improvements from Richard Single, Michael Mariani, Gordon Webster and Steve Mack

  • overhaul release process and add a contribution-guide to the PyPop User Guide.

  • update documentation to use new HLA nomenclature throughout

• PyPop now uses numpy in place of the old Numeric library Numpy, and lxml in place of libxml_mod

Bug fixes

• TSV file fixes:

  • fix missing columns in TSV files (thanks to Steve Mack for report)

  • fix headers in 3 and 4 locus TSV files

  • output 2 locus haplotypes in TSV if they are explicitly specified (thanks to Steve Mack)

  • 2-locus-haplo.tsv: fixed missing output in ld.d, ld.dprime, ld.chisq, and exp columns (thanks to Nabil M for the report)

  • rename, remove and add some columns headers, including the new ALD measures:

    • 2-locus-haplo.tsv: rename columns: allele -> haplotype, exp -> haplotype.no-ld.count

    • 2-locus-haplo.tsv: remove obs and obs.freq columns which were duplicative of haplotype.count and haplotype.freq, respectively

    • 2-locus-summary.tsv: add two new ALD measure columns: ald.1_2 and ald.2_1

    • *-locus-summary.tsv: rename columns for multilocus haplotypes for 3 or more loci, allele -> haplotype and locus -> loci

• Fix DigitBinning and CustomBinning filters [Filters] (report from Steve Mack)

• Fix issues with using colons in alleles, and other separation isssues (thanks to Steve Mack)

• Use ~ as the genotype terminator rather than | (fixes some haplotype estimation bugs)

• Round all haplotype frequencies to 5 decimal places to avoid truncation issues (thanks to Steve Mack for report)

• Restore semi-GUI interactive mode by using built-in TkInter file dialog, and use more informative default “placeholder” file names

• Fix warnings generated by numpy and re libraries.

• Windows fixes:

  • Emhaplofreq will now give identical results on Windows as all other platform (needed to port POSIX-version of drand48() to Windows).

  • Fixed CustomBinning filters that were failing on Windows.

  • Enable all unit tests for Windows.

Internal

• Replace old getopt with argparse library

• Major code refactoring, including moving code into src directory, and using packages in setup.py

• Added continuous integration via GitHub Actions for releases and website updates

• Prepare package for inclusion in PyPI

• Add code examples used in documentation as unit tests

• Create GitHub action for upload to Zenodo (thanks to Jurriaan H. Spaaks)

• Support for arm64 builds on MacOS, e.g. M1-based Macs (thanks to Owen Solberg for report and extensive testing).

• Remove dependency on psutil, rarely needed.

• Only build wheels on platforms for which binary wheels are available for all dependencies.

0.7.0 - 2008-09-09

New features

• makeNewPopFile option has been changed. This option allows user to generate intermediate output of filtered files. Now option should be of the format: type:order where type is one of separate-loci or all-loci so that the user can specify whether a separate file should be generated for each locus (separate-loci) or a single file with all loci (all-loci). order should be the order in the filtering chain where the matrix is generated, there is no default, for example, for generating files after the first filter operation use 1.

• New command-line option --generate-tsv, will generate the .dat tab-separated values (TSV) files on the the generated -out.xml files (aka “popmeta”) directly from pypop without needing to run additional script. Now output from pypop can be directly read into spreadsheet.

• New feature: add individual genotype tests to Hardy-Weinberg module (gthwe), now computes statistics based on individual genotypes in the HWP table. The [HardyWeinbergGuoThompson] or [HardyWeinbergGuoThompsonMonteCarlo] options must be enabled in the configuration “.ini” file in order for these tests to be carried out.

• Major improvements to custom and random binning filters (Owen Solberg).

• New feature: generate homozygosity values using the Ewens-Watterson test for all pairwise loci, or all sites within a gene for sequence data ([homozygosityEWSlatkinExactPairwise] in .ini file). Note: this really only works for sequence data where the phase for sites within an allele are known.

• Haplotype and LD estimation module emhaplofreq improvements

  • improved memory usage and speed for emhaplofreq module.

  • maximum sample size for emhaplofreq module increased from 1023 to 5000 individuals.

  • maximum length of allele names increased to 20

Bug fixes

• Support Python 2.4 on GCC 4.0 platforms.

• Add missing initialisation for non-sequence data when processing haplotypes. Thanks to Jill Hollenbach for the report.

• Fix memory leak in xslt translation.

• Various fixes relating to parsing XML output.

• Fixed an incorrect parameter name.

• Handle some missing sections in .ini better. Thanks to Owen Solberg for report.

• Various build and installation fixes (SWIG, compilation flags)

• Make name of source package be lowercase “pypop”.

• Change data directory: /usr/share/pypop/ to /usr/share/PyPop/

• Print out warning when maximum length of allele exceeded, rather than crashing. Thanks to Steve Mack for report.

Other issues

• Sequence filter

  • In the Sequence filter, add special case for Anthony Nolan HLA data: mark null alleles ending in “N” (e.g. HLA-B*5127N) as “missing data” (****).

  • Also in Sequence, keep track of unsequenced sites separately (via unsequencedSites variable) from “untyped” (aka “missing data”). Treat unsequencedSite as a unique allele to make sure that those sites don’t get treated as having a consensus sequence if only one of the sequences in the the set of matches is typed.

  • If no matching sequence is found in the MSF files, then return a sequence of * symbols (ie, will be treated as truly missing data, not untyped alleles.

  • Add another special case for HLA data: test for 7 digits in allele names (e.g. if 2402101 is not found insert a zero after the first 4 digits to form 24020101, and check for that). This is to cope with yet-another HLA nomenclature change.

• Change semantics of batchsize, make “0” (default) process files separately if only R dat files is enabled. If batchsize not set explicitly (and therefore 0) set batchsize to 1 is PHYLIP mode is enabled.

0.6.0 - 2005-04-13

New features

• Allow for odd allele counts when processing an allele count data (i.e “semi”-typing). When PyPop is dealing with data that is originally genotyped, the current default is preserved i.e. we dis-allow individuals that are typed at only allele, and set allowSemiTyped to false.

• New command-line option -f (long version --filelist) which accepts a file containing a list of files (one per line) to process (note that this is mutually exclusive with supplying INPUTFILEs, and will abort with an error message if you supply both simultaneously).

• In batch version, handle multiple INPUTFILEs supplied as command-line arguments and support Unix shell-globbing syntax (e.g. pypop.py -c config.ini *.pop). (NOTE: This is supported only in batch version, not in the interactive version, which expects one and only one file supplied by user.

• Allele count files can now be filtered through the filter apparatus (particularly the Sequence and AnthonyNolan) in the same was as genotype files transparently. [This has been enabled via a code refactor that treats allele count files as pseudo-genotype files for the purpose of filtering]. This change also resulted in the removal of the obsolete lookup-table-based homozygosity test.

• Add --disable-ihwg option to popmeta script to disable hardcoded generation of the IHWG header output, and use the output as defined in the header in the original .pop input text file. This is disabled by default to preserve backwards compatibility.

• Add --batchsize (-b short version) option for popmeta. Does the processing in “batches”. If set and greater than one, list of XML files is split into batchsize group. For example, if there are 20 XML files and option is via using (“-b 2” or “–batchsize=2”) then the files will be processed in two batches, each consisting of 10 files. If the number does not divide evenly, the last list will contain all the “left-over” files. This option is particularly useful with large XML files that may not fit in memory all at once. Note this option is mutually exclusive with the --enable-PHYLIP option because the PHYLIP output needs to calculate allele frequencies across all populations before generating files.

• New .ini file option: [HardyWeinbergGuoThompsonMonteCarlo]: add a plain Monte-Carlo (randomization, without the Markov chain test) test for the HardyWeinberg “exact test”. Add code for Guo & Thompson test to distribution (now under GNU GPL).

Bug fixes

• HardyWeinbergGuoThompson overall p-value test was numerically unstable because it attempted to check for equality in greater than or equal to constructs (“<=”) which is not reliable in C. Replaced this with a GNU Scientific Library (GSL) function gsl_fcmp() which compares floats to within an EPSILON (defaults to 1e-6).

• Allow HardyWeinbergGuoThompson test to be run if at least two alleles present (test was originally failing with a too-few-alleles message if there were not at least 3 alleles). Thanks to Kristie Mather for the report.

• Checks to see if a locus is monomorphic, if it is, it generates an allele summary report, but skips the rest of the single locus analyses which do not make sense for monomorphic locus. Thanks to Steve Mack and Owen Solberg for the bug report(s).

• Now builds against recent versions of SWIG (no longer stuck at version 1.3.9), should be compatible with versions of SWIG > 1.3.10. (Tested against SWIG 1.3.21).

• Homozygosity module: Prevent math errors by in Slatkin’s exact test by forcing the homozygosity to be positive (only a problem for rare cases, when the result is so close to zero that the floating point algorithms cause a negative result.)

0.5.2 (public beta) - 2004-03-09

Bug fixes

• Add missing RandomBinning.py file to source distribution Thanks to Hazael Maldonado Torres for the bug report.

• Fixed line endings for .bat scripts for Win32 so they work under Windows 98 thanks to Wendy Hartogensis for the bug report.

0.5.1 (public beta) - 2004-02-26

Changes

• New parameter numInitCond, number of initial conditions by the haplotype estimation and LD algorithm used before performing permutations. Defaults to 50.

• Remove some LOG messages/diagnostics that were erroneously implying an error to the user (if nothing is wrong, don’t say anything). Add some more useful messages for what is being done in haplo/LD estimation step.

• Add popmeta.py to the distribution: this is undocumented and unsupported as yet, it is at alpha stage only, use at your own risk!

Bug fixes

• Remember to output plaintext version of LD for specified loci.

0.5 (public beta) - 2003-12-31

Changes

• All Linux wrapper scripts no longer have .sh file suffixes for consistency with DOS (all DOS bat files can be executed without specifying the .bat extension).

Bug fixes

• Add wrapper scripts for interactive and batch mode for both DOS and Linux so that correct shared libraries are called.

• Pause and wait for user to press a key at end of DOS .bat file so that output can be viewed before window close.

• Set PYTHONHOME in wrapper scripts to prevent messages about missing <prefix> being displayed.

0.4.3beta

Bug fixes

• Fixed bug in processing of popname field. Thanks to Richard Single for the report.