diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml
index 597df4a4e..38fff23c2 100644
--- a/.github/release-drafter.yml
+++ b/.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'
diff --git a/NEWS.rst b/NEWS.rst
index 8b941bec4..529de5933 100644
--- a/NEWS.rst
+++ b/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.
diff --git a/website/conf.py b/website/conf.py
index abf954fab..7fe4bd610 100644
--- a/website/conf.py
+++ b/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 pypop-genomics
. See README for more detailed instructions.
'
+ "banner_text": 'Release candidates for PyPop are now available via PyPI as package pypop-genomics
. See README for more detailed instructions.
'
}
# Add any paths that contain custom static files (such as style sheets) here,
diff --git a/website/index.rst b/website/index.rst
index 11f32708d..66cd211fd 100644
--- a/website/index.rst
+++ b/website/index.rst
@@ -8,8 +8,7 @@ PyPop: Python for Population Genomics
Please follow the instructions on the GitHub `README.rst
`__ 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:
@@ -17,8 +16,9 @@ PyPop: Python for Population Genomics
.. admonition:: Release summary and news
:class: dropdown, toggle-shown
- - 2023-11-01: release candidate 1 (1.0.0rc1) is now available on
- `PyPI `__.
+ - 2023-11-04: release candidate 2 (1.0.0rc2) is now available on
+ `PyPI `__. 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.