update to 4.3.0

3 files changed, 35 insertions, 129 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 40a1e95f12cd..4fbb910bacdb 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,6 @@
 pkgbase = python-treecorr
 	pkgdesc = Library that efficiently computes 2-point and 3-point correlation functions
-	pkgver = 4.2.9
+	pkgver = 4.3.0
 	pkgrel = 1
 	url = https://github.com/rmjarvis/treecorr
 	changelog = CHANGELOG.rst
@@ -11,14 +11,14 @@ pkgbase = python-treecorr
 	makedepends = python-setuptools
 	makedepends = python-sphinx
 	makedepends = python-wheel
-	depends = python-numpy
-	depends = python-yaml
 	depends = python-cffi
 	depends = python-coord
+	depends = python-numpy
+	depends = python-yaml
 	optdepends = python-fitsio: reads FITS catalogs or writes to FITS output files
 	optdepends = python-pandas: speeds up reading from ASCII catalogs
 	optdepends = python-h5py: reads HDF5 catalogs
-	source = python-treecorr-4.2.9.tar.gz::https://github.com/rmjarvis/treecorr/archive/v4.2.9.tar.gz
-	sha256sums = 59c8ac5e0b4644967917aaa3089e847d7759cd399cee9bc21e733b4558d76c0c
+	source = python-treecorr-4.3.0.tar.gz::https://github.com/rmjarvis/treecorr/archive/v4.3.0.tar.gz
+	sha256sums = 7ede747f29079f7bba083511519164446ee8b56313e33a1ed1dde674c10fc56f
 
 pkgname = python-treecorr
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 1e61c53208e0..3e50393bbf6c 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -1,142 +1,48 @@
-Changes from version 4.1 to 4.2
+Changes from version 4.2 to 4.3
 ===============================
 
-This update mostly involves some improvements to the new patch-based
-computations, in response to feedback from users, who have been trying it out
-in a variety of use cases.  Especially note the new optional ``func`` argument
-to `BinnedCorr2.estimate_cov` and `estimate_multi_cov`, which lets you
-calculate covariances of arbitrary functions of a correlation object or list
-of correlation objects.  See `Covariance of Derived Quantities` for details.
-
-Another big improvement is the ability to correctly perform three-point
-cross-correlations. I still don't have heterogeneous cross correlations like
-NGG or NNG, but now NNN, GGG, and KKK can be done correctly for 2 or 3
-different catalogs.  This update does technically involve an API change,
-since the old code tried to do something when given 3 catalogs, but it
-wasn't really correct, and (consequently) I don't think anyone was actually
-trying to use that feature.
-
 See the listing below for the complete list of new features and changes.
 `Relevant PRs and Issues,
-<https://github.com/rmjarvis/TreeCorr/milestone/7?closed=1>`_
+<https://github.com/rmjarvis/TreeCorr/issues?q=milestone%3A%22Version+4.3%22+is%3Aclosed>`_
 whose issue numbers are listed below for the relevant items.
 
-.. note::
+System Support Changes
+----------------------
+
+- Starting with this version, TreeCorr no longer supports Python 2.7 or 3.6.
+  We currently support Python versions 3.7, 3,8, 3.9, 3.10.
+
+- We now support Windows machines, which we hadn't before this.  Code is now regularly
+  tested on ubuntu, macos and windows. (#136, #143)
 
-    This will be the last (non-bug-fix) TreeCorr release to support Python 2.7.
-    It is becoming harder to continue to support this platform now that it is
-    officially sunsetted, so we encourage all users to switch their code to
-    Python 3.x ASAP.  TreeCorr is currently compatible with Python versions
-    2.7, 3.5, 3.6, 3.7, 3.8, 3.9.  We will probably also drop 3.5 in the next
-    release as well, since that is also retired at this point.
 
 API Changes
 -----------
 
-- Changed the 3pt process function, when given 3 arguments, to accumulate all
-  triangles where points from the three input catalogs can fall into any
-  of the three triangle corners.  If you need the old behavior of keeping
-  track of which catalog goes into which triangle corner, the new
-  ???CrossCorrelation classes do so both more efficiently and more
-  accurately than the previous code. (#115)
-- Changed the `NNNCorrelation.calculateZeta` function to only take
-  RDD and DRR parameters for the cross terms (if desired) rather than all
-  six (DDR, DRD, RDD, DRR, RDR, RRD).  The new cross-correlation behavior of
-  the `NNNCorrelation.process` function now efficiently calculates in RDD what
-  used to be calculated in three calls for DDR, DRD, and RDD.  Likewise the
-  new DRR calculates what used to require DRR, RDR, and RRD. (#122)
+- Many function parameters are now keyword-only.  The old syntax allowing these parameters
+  to be positional still works, but is deprecated. (#129)
+
 
 Performance improvements
 ------------------------
 
-- Only show at most 10 rows with NaNs in cases where there are lots of such
-  rows. (#111)
-- No longer remakes patches and writes them to disk if they are already present
-  on disk.  If you want to force a rewrite for any reason, you can explicitly
-  call `Catalog.write_patches`. (#116)
-- Computing the data/random cross correlations for 3pt are now much faster,
-  since you only need one call for RDD and one for DRR, not all the 6 different
-  permuations. (Specifically, DDR, DRD, RDR, RRD are no longer needed.) (#122)
+- Added ability to compute patch-based covariance matrices using MPI. (#138, #139)
+
 
 New features
 ------------
 
-- Implement patch-based calculations for 3-point correlations.  This enables
-  things like jackknife correlations, low-memory calculations, and MPI execution
-  when doing NNN, KKK, or GGG correlations. (#97, #125)
-- Allow min_rpar and max_rpar for Euclidean metric.  Also Periodic, although
-  I don't know if that's useful. (#101)
-- Added ability to read from hdf5 catalogs.  (#106)
-- Added ability to use named columns in ASCII files if the file has column
-  names. (#108)
-- Added optional initialize=False and finalize=False options to process
-  functions. (#109)
-- Added ability to do 3 point cross-correlations properly, rather than the not
-  exactly correct version that had been implemented.  Not all combinations are
-  implemented.  So far just GGG, KKK, and NNN. (#115)
-- Added ability to read from parquet catalogs.  (#117)
-- Added optional func parameter to estimate_cov and estimate_multi_cov. (#118)
-- Added ability to write output files as hdf5.  (#122)
+- Add `BinnedCorr2.build_cov_design_matrix` and `build_multi_cov_design_matrix` functions (#132)
+- Added ability to write out the full set of pair-wise results in the write commands, and to
+  read them back in.  This allows correlation objects to still be able to correctly calculate
+  the various patch-based covariance matrix estimates after round-tripping through a file.
+  To use this feature, use ``corr.write(..., write_patch_results=True)``. (#141)
+- Allow None as a configuration parameter to be equivalent to not specifying a parameter.
+  E.g. ``bin_size=0.1, min_sep=1., max_sep=100., nbins=None`` is allowed now. (#142)
+
 
 Bug fixes
 ---------
 
-- Fixed a couple problems that could arise in patch-based calculations when
-  one or more of the patches have no objects. (#123)
-
-
-Changes from version 4.2.0 to 4.2.1
-===================================
-
-- Fixed a bug when running NN correlations with MPI.  Thanks to Joe Zuntz for
-  the bug report. (#127)
-
-Changes from version 4.2.1 to 4.2.2
-===================================
-
-- Fixed a build problem with gcc versions 10 and 11.  Thanks to Johannes Lange
-  for reporting the problem.
-
-Changes from version 4.2.2 to 4.2.3
-===================================
-
-- Fixed a bug in the Map^3 calculation when the aperture radii are different.
-  Thanks to Laila Linke for both finding the problem and providing the fix. (#128)
-
-Changes from version 4.2.3 to 4.2.4
-===================================
-
-- Fixed a bug when running the Rlens metric with patches. Thanks to Marina Ricci
-  for the bug report. (#131)
-
-Changes from version 4.2.4 to 4.2.5
-===================================
-
-- Fixed bugs in the shot noise variance estimate for GGG and the propagation of
-  the error to Map3.  Thanks to Lucas Secco for the bug report. (#133)
-
-Changes from version 4.2.5 to 4.2.6
-===================================
-
-- Fixed a numerical bug that could suppress the signal in GG correlations in
-  spherical coordinates if there are multiple objects at the same position.
-  Thanks to Sandra Unruh for the bug report. (#134)
-
-Changes from version 4.2.6 to 4.2.7
-===================================
-
-- Fixed a memory problem when computing patch-based covariance matrix when npatches
-  is moderately large (e.g. 500). Thanks to Joe Zuntz and Judit Prat for finding and
-  reporting the bug. (#137)
-
-Changes from version 4.2.7 to 4.2.8
-===================================
-
-- Fixed a bug in the calculation of jackknife and sample variance when only the second
-  catalog in a cross-correlation uses patches.
-
-Changes from version 4.2.8 to 4.2.9
-===================================
-
-- Fixed a error in the low_mem calculation when ra_units and/or dec_units are not
-  radians. Thanks to Chun-Hao To for the bug report. (#144)
+- Fixed a bug where correlation objects using bin_type=TwoD could not be correctly read back
+  in after being written to a file. (#141)
diff --git a/PKGBUILD b/PKGBUILD
index 729c110f8c47..611fcc60d4b9 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -4,13 +4,13 @@
 
 pkgname=python-treecorr
 _pkg=TreeCorr
-pkgver=4.2.9
+pkgver=4.3.0
 pkgrel=1
 pkgdesc="Library that efficiently computes 2-point and 3-point correlation functions"
 arch=('x86_64')
 url="https://github.com/rmjarvis/treecorr"
 license=('BSD')
-depends=('python-numpy' 'python-yaml' 'python-cffi' 'python-coord')
+depends=('python-cffi' 'python-coord' 'python-numpy' 'python-yaml')
 optdepends=(
 	'python-fitsio: reads FITS catalogs or writes to FITS output files'
 	'python-pandas: speeds up reading from ASCII catalogs'
@@ -19,13 +19,13 @@ makedepends=('python-build' 'python-installer' 'python-setuptools' 'python-sphin
 # checkdepends=('python-fitsio' 'python-pandas' 'python-hdpy' 'python-scipy')
 changelog=CHANGELOG.rst
 source=("$pkgname-$pkgver.tar.gz::$url/archive/v$pkgver.tar.gz")
-sha256sums=('59c8ac5e0b4644967917aaa3089e847d7759cd399cee9bc21e733b4558d76c0c')
+sha256sums=('7ede747f29079f7bba083511519164446ee8b56313e33a1ed1dde674c10fc56f')
 
 build() {
 	cd "$_pkg-$pkgver"
 	python -m build --wheel --no-isolation
-	local _ver="$(python -c 'import sys; print(".".join(map(str, sys.version_info[:2])))')"
-	PYTHONPATH="$PWD/build/lib.linux-$CARCH-$_ver" make -C docs man
+	local _ver="$(python -c 'import sys; print("".join(map(str, sys.version_info[:2])))')"
+	PYTHONPATH="$PWD/build/lib.linux-$CARCH-cpython-$_ver" make -C docs man
 }
 
 package() {