Merge remote-tracking branch 'origin/main' into replace_pval_extensio…

…n_with_scipyl

.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: 'PyPop $RESOLVED_VERSION'
-tag-template: 'v$RESOLVED_VERSION'
+name-template: 'PyPop 1.0.0rc3'
+tag-template: 'v1.0.0-rc3'
 prerelease: true
 include-pre-releases: true
 prerelease-identifier: 'rc'

NEWS.rst

@@ -3,9 +3,9 @@ PyPop Release History
 
 .. _news-start:
 
-Release Notes for PyPop 1.0.0rc1
+Release Notes for PyPop 1.0.0rc2
 --------------------------------
-(2023-11-01)
+(2023-11-04)
 
 PyPop 1.0.0 is the first official release of PyPop using Python 3, and
 the first release to be included on `PyPI
@@ -18,8 +18,8 @@ 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
-ongoing contributors and bug reporters, Richard Single, Owen Solberg
-and Steve Mack.
+all of our bug reporters, and ongoing contributors, especially Richard
+Single, Owen Solberg and Steve Mack.
 
 
 New features
@@ -28,7 +28,8 @@ New features
   Sochat for major patch)
 * Added new assymetric linkage disequilibrium (ALD) calculations
   (thanks to Richard Single), see [Thomson:Single:2014]_ for more
-  details.
+  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``
@@ -71,6 +72,22 @@ Bug fixes
   * 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)
@@ -240,7 +257,7 @@ Bug fixes
   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
+* 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.

website/conf.py

@@ -128,7 +128,7 @@
 #
 html_theme_options = { # these are both piccolo theme-specific
     "source_url": 'https://github.com/alexlancaster/pypop/',
-    "banner_text": 'A release candidate for PyPop (1.0.0rc1) is now available via PyPI as package <code>pypop-genomics</code>. See <a href="https://github.com/alexlancaster/pypop#readme">README</a> for more detailed instructions.<br/>'
+    "banner_text": 'Release candidates for PyPop are now available via PyPI as package <code>pypop-genomics</code>. See <a href="https://github.com/alexlancaster/pypop#readme">README</a> for more detailed instructions.<br/>'
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,

website/index.rst

@@ -8,17 +8,17 @@ PyPop: Python for Population Genomics
 
     Please follow the instructions on the GitHub `README.rst
     <https://github.com/alexlancaster/pypop#readme>`__ for how to
-    install 1.0.0 release candidate 1 from PyPI (or build PyPop from
-    source on a modern Python 3 system).  A formal 1.0.0 release will
+    install a 1.0.0 release candidate from PyPI. A formal 1.0.0 release will
     be made soon.
 
 .. _news:
 
 .. admonition:: Release summary and news
   :class: dropdown, toggle-shown
 
-  - 2023-11-01: release candidate 1 (1.0.0rc1) is now available on
-    `PyPI <https://pypi.org/project/pypop-genomics/>`__.
+  - 2023-11-04: release candidate 2 (1.0.0rc2) is now available on
+    `PyPI <https://pypi.org/project/pypop-genomics/>`__. Fixes some missing TSV output.
+  - 2023-11-01: release candidate 1 (1.0.0rc1) released.
   - 2023-10-27: seventh beta pre-release 1.0.0b7,  Previous ``arm64``
     issues have been resolved. Thanks to Owen Solberg for extensive
     testing and debugging.