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| -rw-r--r-- | .SRCINFO | 17 | ||||
| -rw-r--r-- | NEWS.txt | 250 | ||||
| -rw-r--r-- | PKGBUILD | 50 |
3 files changed, 296 insertions, 21 deletions
@@ -1,13 +1,20 @@ pkgbase = python-fastcluster pkgdesc = Fast hierarchical clustering routines for R and Python pkgver = 1.2.6 - pkgrel = 1 + pkgrel = 2 url = https://pypi.org/project/fastcluster - arch = any - license = custom:BSD-2-clause + changelog = NEWS.txt + arch = x86_64 + license = BSD + checkdepends = python-pytest + checkdepends = python-scipy makedepends = python-setuptools + makedepends = python-build + makedepends = python-installer + makedepends = python-oldest-supported-numpy + makedepends = python-wheel depends = python-numpy - source = https://pypi.org/packages/source/f/fastcluster/fastcluster-1.2.6.tar.gz - sha512sums = 94a11ddd80fe219a91f1713230decfde761cd745a6ce0782e5cc0ab7d9818855d031be8c79f97256f0266fd6992a9fa4b0f5e7a30cb42387810fd8baff2a2135 + source = python-fastcluster-1.2.6.tar.gz::https://files.pythonhosted.org/packages/source/f/fastcluster/fastcluster-1.2.6.tar.gz + sha256sums = aab886efa7b6bba7ac124f4498153d053e5a08b822d2254926b7206cdf5a8aa6 pkgname = python-fastcluster diff --git a/NEWS.txt b/NEWS.txt new file mode 100644 index 000000000000..0e277c1ac77e --- /dev/null +++ b/NEWS.txt @@ -0,0 +1,250 @@ +fastcluster: Fast hierarchical clustering routines for R and Python
+
+Copyright:
+ • Until package version 1.1.23: © 2011 Daniel Müllner <http://danifold.net>
+ • All changes from version 1.1.24 on: © Google Inc. <http://google.com>
+
+
+Version history
+‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾
+Version 1.0.0, 03/14/2011:
+
+ • Initial release, dependent on Rcpp. Not available on CRAN.
+
+Version 1.0.1, 03/15/2011:
+
+ • Removed the dependence on Rcpp; only R's original C interface is used.
+
+Version 1.0.2, 03/17/2011:
+
+ • File DESCRIPTION: Fixed a typo
+
+Version 1.0.3, 03/20/2011:
+
+ • File README: Removed the warning about false results from the flashClust
+ package since the new flashClust version 1.01 has this error corrected.
+
+ • Cleaned the test file fastcluster_test.R up. (No dependence on the MASS
+ package any more)
+
+Version 1.0.4, 03/21/2011:
+
+ • Changed the name of the external function from the outdated "Rcpp_linkage"
+ to "fastcluster".
+
+ • Registered the external function "fastcluster" in R.
+
+ • Configured the C header inclusions to work on Fedora (thanks to Peter
+ Langfelder).
+
+Version 1.1.0, 08/21/2011
+
+ • Routines for clustering vector data.
+
+ • Added a User's manual
+
+ • Revision of all files
+
+Version 1.1.1, 10/08/2011
+
+ • Fixed test scripts, which indicated an error on some architectures, even
+ if results were correct. (The assumption was that ties in single linkage
+ clustering are resolved in the same way, both for dissimilarity input and
+ for vector input. This is not necessarily true if the floating point unit
+ uses "excess precision". Now the test scripts are content with arbitrary
+ resolution of ties and do not assume a specific scheme.)
+
+ • Bug fix: uninitialized function pointer in Version 1.1.0
+
+Version 1.1.2, 10/11/2011
+
+ • Fix for Solaris: replaced ssize_t by ptrdiff_t in the C++ code.
+
+ • Removed the NN-chain algorithm for vector input: it was not clear that
+ it would work under all circumstances with the intricacies of floating-
+ point arithmetic. Especially the effects of the excess precision on the
+ x87 are impossible to control in a portable way. Now, the memory-saving
+ routines for the “Ward” linkage use the generic algorithm, as “centroid”
+ and “median” linkage do.
+
+Version 1.1.3, 12/10/2011
+
+ • Replaced ptrdiff_t by std::ptrdiff_t, as GCC 4.6.1 complains about this.
+
+Version 1.1.4, 02/01/2012
+
+ • Release the GIL in the Python package, so that it can be used efficiently
+ in multithreaded applications.
+
+ • Improved performance for the "Ward" method with vector input.
+
+ • The "members" parameter in the R interface is now treated as a double
+ array, not an integer array as before. This was a slight incompatibility
+ with the stats::hclust function. Thanks to Matthias Studer, University of
+ Geneva, for pointing this out.
+
+Version 1.1.5, 02/14/2012
+
+ • Updated the "members" specification in the User's manual to reflect the
+ recent change.
+
+Version 1.1.6, 03/12/2012
+
+ • Bug fix related to GIL release in the Python wrapper. Thanks to Massimo
+ Di Stefano for the bug report.
+
+ • Small compatibility changes in the Python test scripts (again thanks to
+ Massimo Di Stefano for the report).
+
+Version 1.1.7, 09/17/2012
+
+ • Scipy import is now optional (suggested by Forest Gregg)
+
+ • Compatibility fix for NumPy 1.7. Thanks to Semihcan Doken for the bug
+ report.
+
+Version 1.1.8, 08/28/2012
+
+ • Test for NaN dissimilarity values: Now the algorithms produce an error
+ message instead of silently giving false results. The documentation was
+ updated accordingly. This is the final design as intended: the fastcluster
+ package handles infinity values correctly but complains about NaNs.
+
+ • The Python interface now works with both Python 2 and Python 3.
+
+ • Changed the license to BSD.
+
+Version 1.1.9, 03/15/2013
+
+ • Compatibility fix for the MSVC compilers on Windows.
+
+ • Simplified GIL release in the Python interface.
+
+Version 1.1.10, 05/22/2013
+
+ • Updated citation information (JSS paper).
+
+ • Suppress warnings where applicable. Compilation with GCC should
+ not produce any warning at all, even if all compiler warnings
+ are enabled. (The switch -pedantic still does not work, but this
+ is due to the Python headers.)
+
+ • Optimization: Hidden symbols. Only the interface functions are
+ exported to the symbol table with GCC.
+
+Version 1.1.11, 05/23/2013
+
+ • Compatibility fix for Solaris.
+
+Version 1.1.12, 12/10/2013
+
+ • Tiny maintenance updates: new author web page and e-mail address,
+ new location for R vignette.
+
+Version 1.1.13, 12/17/2013
+
+ • Moved the "python" directory due to CRAN requirements.
+
+Version 1.1.14, 01/02/2015
+
+ • Updated the DESCRIPTION file according to CRAN rules.
+ • Renamed the “ward” method for dissimilarity input to “ward.D” in the R
+ interface and created a new method “ward.D2”, following changes in R's
+ hclust package.
+
+Version 1.1.15, 01/05/2015
+
+ • Fixed the unit test to work with old and new R versions (see the changes
+ in stats::hclust in R 3.1.0).
+
+Version 1.1.16, 01/07/2015
+
+ • Support for large distance matrices (more than 2^31 entries, R's long
+ vector support since version 3.0.0).
+
+Version 1.1.17, 07/03/2015
+
+ • Resolved MSVC compiler warnings.
+
+Version 1.1.18, 07/16/2015
+
+ • Fixed missing NumPy header include path.
+
+Version 1.1.19, 07/19/2015
+
+ • Fixed unit tests. They can be run with "python setup.py test" now.
+
+Version 1.1.20, 07/19/2015
+
+ • New version number due to PyPI upload error.
+
+Version 1.1.21, 09/18/2016
+
+ • Appropiate use of std namespace, as required by CRAN.
+
+Version 1.1.22, 06/12/2016
+
+ • No fenv header usage if software floating-point emulation is used (bug
+ report: NaN test failed on Debian armel).
+
+Version 1.1.23, 03/24/2017
+
+ • setup.py: Late NumPy import for better dependency management.
+
+Version 1.1.24, 08/04/2017
+
+ • R 3.5 corrects the formula for the “Canberra” metric. See
+ https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17285.
+ The formula in the fastcluster package was changed accordingly. This
+ concerns only the R interface. SciPy and fastcluster's Python interface
+ always had the correct formula.
+
+Version 1.1.25, 05/27/2018
+
+ • Removed all “#pragma GCC diagnostic” directives in .cpp files due to changed
+ CRAN requirements (CRAN repository only, not the GitHub repository).
+ • Updated build scripts for Python 3.7 (thanks to Forest Gregg).
+ • Simplified setup.py.
+ • Updated and corrected documentation.
+
+Version 1.1.26, 12/30/2019
+
+• Small updates for Python 3.8.
+
+Version 1.1.27, 01/20/2021
+
+• Updated NumPy dependency for Python 3.9.
+
+Version 1.1.28, 02/03/2021
+
+• Replace deprecated “numpy.bool” and “numpy.int” by “bool” and “int”.
+
+Version 1.2.0, 05/23/2021
+
+• Dropped support for Python 2.
+• Python interface: Updated definition of the Yule distance function, following
+ a change in SciPy 1.6.3.
+
+Version 1.2.1, 05/24/2021
+
+• Documentation update.
+
+Version 1.2.2, 05/24/2021
+
+• Documentation update.
+
+Version 1.2.3, 05/24/2021
+
+• Fixed #pragma in fastcluster.cpp.
+
+Version 1.2.4, 08/21/2021
+
+• Fixed NumPy versions in Travis builds.
+
+Version 1.2.5, 02/26/2022
+
+• Updated pyproject.toml to work with Python 3.10 and future Python versions.
+
+Version 1.2.6, 02/27/2022
+
+• Move to GitHub action for CI. No code changes.
@@ -1,26 +1,44 @@ +# Maintainer: Luis Martinez <luis dot martinez at disroot dot org> # Contributor: Clint Valentine <valentine.clint@gmail.com> # Contributor: Dmitriy Morozov <archlinux@foxcub.org> -_name=fastcluster -pkgname=python-${_name} + +pkgname=python-fastcluster +_pkg="${pkgname#python-}" pkgver=1.2.6 -pkgrel=1 +pkgrel=2 pkgdesc="Fast hierarchical clustering routines for R and Python" -arch=(any) -url="https://pypi.org/project/${_name}" -license=('custom:BSD-2-clause') -depends=(python-numpy) -makedepends=(python-setuptools) -source=(https://pypi.org/packages/source/${_name::1}/${_name}/${_name}-${pkgver}.tar.gz) -sha512sums=('94a11ddd80fe219a91f1713230decfde761cd745a6ce0782e5cc0ab7d9818855d031be8c79f97256f0266fd6992a9fa4b0f5e7a30cb42387810fd8baff2a2135') +arch=('x86_64') +url="https://pypi.org/project/fastcluster" +license=('BSD') +depends=('python-numpy') +makedepends=( + 'python-setuptools' + 'python-build' + 'python-installer' + 'python-oldest-supported-numpy' + 'python-wheel') +checkdepends=('python-pytest' 'python-scipy') +changelog=NEWS.txt +source=("$pkgname-$pkgver.tar.gz::https://files.pythonhosted.org/packages/source/${_pkg::1}/$_pkg/$_pkg-$pkgver.tar.gz") +sha256sums=('aab886efa7b6bba7ac124f4498153d053e5a08b822d2254926b7206cdf5a8aa6') build() { - cd ${_name}-${pkgver} - export PYTHONHASHSEED=0 - python setup.py build + cd "$_pkg-$pkgver" + python -m build --wheel --no-isolation +} + +check() { + cd "$_pkg-$pkgver" + local _py="$(python -c 'import sys; print(".".join(map(str, sys.version_info[:2])))')" + PYTHONPATH="$PWD/build/lib.linux-$CARCH-$_py" python setup.py test } package() { - cd ${_name}-${pkgver} - PYTHONPYCACHEPREFIX="${PWD}/.cache/cpython/" python setup.py install --prefix=/usr --root="${pkgdir}" --optimize=1 --skip-build - install -Dm 644 COPYING.txt -t "${pkgdir}/usr/share/licenses/${pkgname}" + cd "$_pkg-$pkgver" + PYTHONHASHSEED=0 python -m installer --destdir="$pkgdir/" dist/*.whl + local _site="$(python -c 'import site; print(site.getsitepackages()[0])')" + install -d "$pkgdir/usr/share/licenses/$pkgname/" + ln -s \ + "$_site/$_pkg-$pkgver.dist-info/COPYING.txt" \ + "$pkgdir/usr/share/licenses/$pkgname/LICENSE" } |