statsmodels.git
5 years agoMerge version 0.10.2-2+rpi1 and 0.11.1-2 to produce 0.11.1-2+rpi1
Raspbian automatic forward porter [Wed, 13 May 2020 06:48:22 +0000 (07:48 +0100)]
Merge version 0.10.2-2+rpi1 and 0.11.1-2 to produce 0.11.1-2+rpi1

5 years agoMerge statsmodels (0.11.1-2) import into refs/heads/workingbranch
Rebecca N. Palmer [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Merge statsmodels (0.11.1-2) import into refs/heads/workingbranch

5 years agoRemove code from Stack Overflow and wasteful loop
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Remove code from Stack Overflow and wasteful loop

Stack Overflow content is CC-BY-SA licensed,
which this package is not supposed to be.  This snippet may be
too small to be copyrightable, but removing it to be safe.

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name remove_ccbysa_snippet.patch

5 years agoAllow tests to fail if multiprocessing is not available
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Allow tests to fail if multiprocessing is not available

This is currently the case on hurd-i386

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name xfail_no_multiprocessing.patch

5 years agoDynamicFactor test fail on ppc64el
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
DynamicFactor test fail on ppc64el

Warn on use and xfail test

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name xfail_dynamicfactor_ppc64el.patch

5 years agoMarkov* broken on armhf
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Markov* broken on armhf

Warn on use, and xfail tests

I suspect https://github.com/statsmodels/statsmodels/pull/5826
but that improved it enough on amd64 that
reverting it isn't a good solution.

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name xfail_regimeswitching_armhf.patch

5 years agoDon't require warnings that not all arches produce
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Don't require warnings that not all arches produce

numpy 0/0 (in tvalues): armel doesn't
scipy.stats NaN: Upstream already note i386 doesn't,
we find ppc64el and s390x don't either

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/956882
Forwarded: no

Gbp-Pq: Name dont_require_warnings.patch

5 years agoFix typos
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Fix typos

Origin: lintian
Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name spelling.patch

5 years agoUse local requirejs
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Use local requirejs

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name sphinx_local_requirejs.patch

5 years agoAvoid NaN crash in test_structural
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Avoid NaN crash in test_structural

Out-of-range frequency.cycle starting values make untransform_params return NaN,
which crashes summary()

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name fix_test_bounds.patch

5 years agoDon't fail documentation build on examples exceptions
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Don't fail documentation build on examples exceptions

If example code outputs an error when run,
ipython (ipython:: blocks) now fails the whole build by default,
and tools/nbgenerate.py (.ipynb files) now leaves out that file
(leaving a broken link in the examples index).

As some examples use downloaded data and are hence expected to be
unrunnable on a Debian buildd, this instead keeps them
(::ipython with error output, .ipynb without output).

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name sphinx_ignore_errors.patch

5 years agoDon't try to use a theme we don't have
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Don't try to use a theme we don't have

Upstream switched to sphinx_material in
1d7aafad5c3ad634c9ae2122881c1809c2ccbcbe
and Debian doesn't have that theme.

(I haven't investigated packaging it, which might be a better long-term option.)

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed (except maybe the version fix? or is that no longer needed at all?)

Gbp-Pq: Name no_sphinx_material.patch

5 years agoInclude offset and exposure in GEEResults.fittedvalues
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Include offset and exposure in GEEResults.fittedvalues

and remove misleading documentation from GLMResults.fittedvalues

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug: https://github.com/statsmodels/statsmodels/issues/5253
Forwarded: https://github.com/statsmodels/statsmodels/issues/5253#issuecomment-578980169

Gbp-Pq: Name up5253_gee_offset.patch

5 years agoMake the module reference tables appear
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Make the module reference tables appear

Our numpydoc is old enough to still need this manually set

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug: https://github.com/numpy/numpydoc/issues/141
Forwarded: not-needed

Gbp-Pq: Name sphinx_autosummary.patch

5 years agoXfail or loosen tolerances on flaky tests
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Xfail or loosen tolerances on flaky tests

The test_nondiagonal_obs_cov one hasn't yet been seen in Debian
but is known in upstream CI:
https://github.com/statsmodels/statsmodels/pull/6475#issuecomment-581151072

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>, Graham Inggs
Bug-Debian: https://bugs.debian.org/944054
Forwarded: no

Gbp-Pq: Name 944054_flaky_tests.patch

5 years agoDon't try to write to the source directory
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Don't try to write to the source directory

Not allowed in autopkgtest

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name use_tmp_path.patch

5 years agoUse Python 3 in script shebangs
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Use Python 3 in script shebangs

(Skipping the two .pyx files with #!python - they need to be compiled
with Cython, not directly run with any version of plain Python)

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name python3_shebangs.patch

5 years agoLoosen tolerances on some tests on i386
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Loosen tolerances on some tests on i386

Failure log
https://buildd.debian.org/status/fetch.php?pkg=statsmodels&arch=i386&ver=0.9.0-3&stamp=1567157609&raw=0

As it only fails on i386 (not x32) and isn't far over tolerance,
I suspect different rounding due to x87 excess precision

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/938949
Forwarded: no

Gbp-Pq: Name i386_loosen_test_tolerances.patch

5 years agoUse example data from an R package we have
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Use example data from an R package we have

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name use_available_data.patch

5 years agoKalmanFilter broken on armhf / hppa
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
KalmanFilter broken on armhf / hppa

Warn on use, and xfail the tests

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/924036
Bug-Ubuntu: https://launchpad.net/bugs/1819227
Forwarded: no

Gbp-Pq: Name xfail_kalman_armhf.patch

5 years agoUse intersphinx inventory files from other Debian packages.
Diane Trout [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Use intersphinx inventory files from other Debian packages.

Forwarded: not-needed

Gbp-Pq: Name use-system-inventory

5 years agoto prevent failed test on i386
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
to prevent failed test on i386

Author: Yaroslav Halchenko <debian@onerussian.com>
Bug: https://github.com/statsmodels/statsmodels/issues/1831
Forwarded: upstream consider this probably fixed

Gbp-Pq: Name up_reduce_test_precision

5 years agoUse cached datasets in tests and examples
Debian Science Maintainers [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Use cached datasets in tests and examples

Also remove a download that isn't actually used in that example.

This allows the tests to pass, and at least some of the examples to
be built, in an offline environment such as a Debian buildd.

The cached data is extracted from R packages by debian/datasets/*.

Author: Diane Trout <diane@ghic.org>, Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name use-cached-datasets

5 years agostatsmodels (0.11.1-2) unstable; urgency=medium
Rebecca N. Palmer [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
statsmodels (0.11.1-2) unstable; urgency=medium

  * Tests: don't require a numpy warning that doesn't exist on armel.
Closes: #956882.
  * Tests: allow no-multiprocessing failures (hurd-i386).
  * Remove inconveniently licensed (CC-BY-SA) snippet.

[dgit import unpatched statsmodels 0.11.1-2]

5 years agoImport statsmodels_0.11.1-2.debian.tar.xz
Rebecca N. Palmer [Fri, 24 Apr 2020 14:17:04 +0000 (15:17 +0100)]
Import statsmodels_0.11.1-2.debian.tar.xz

[dgit import tarball statsmodels 0.11.1-2 statsmodels_0.11.1-2.debian.tar.xz]

6 years agoImport statsmodels_0.11.1.orig.tar.gz
Rebecca N. Palmer [Mon, 24 Feb 2020 22:49:06 +0000 (22:49 +0000)]
Import statsmodels_0.11.1.orig.tar.gz

[dgit import orig statsmodels_0.11.1.orig.tar.gz]

6 years agoMerge statsmodels (0.10.2-2+rpi1) import into refs/heads/workingbranch
Peter Michael Green [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Merge statsmodels (0.10.2-2+rpi1) import into refs/heads/workingbranch

6 years agoInclude offset and exposure in GEEResults.fittedvalues
Debian Science Maintainers [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Include offset and exposure in GEEResults.fittedvalues

and remove misleading documentation from GLMResults.fittedvalues

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug: https://github.com/statsmodels/statsmodels/issues/5253
Forwarded: https://github.com/statsmodels/statsmodels/issues/5253#issuecomment-578980169

Gbp-Pq: Name up5253_gee_offset.patch

6 years agoDon't fail documentation build on examples exceptions
Debian Science Maintainers [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Don't fail documentation build on examples exceptions

ipython now fails the whole build by default if anything outputs an error,
which some of ours do when they can't download data.

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name sphinx_ignore_errors.patch

6 years agoMake the module reference tables appear
Debian Science Maintainers [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Make the module reference tables appear

Our numpydoc is old enough to still need this manually set

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug: https://github.com/numpy/numpydoc/issues/141
Forwarded: not-needed

Gbp-Pq: Name sphinx_autosummary.patch

6 years agoXfail or loosen tolerances on flaky tests
Debian Science Maintainers [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Xfail or loosen tolerances on flaky tests

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>, Graham Inggs
Bug-Debian: https://bugs.debian.org/944054
Forwarded: partially https://github.com/statsmodels/statsmodels/pull/6222

Gbp-Pq: Name 944054_flaky_tests.patch

6 years agoUse same Python version for subprocess test
Debian Science Maintainers [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Use same Python version for subprocess test

Avoids a fail due to mismatched extension .so version
when multiple Python 3 versions are available

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name subprocess_use_same_pyver.patch

6 years agoDon't try to write to the source directory
Debian Science Maintainers [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Don't try to write to the source directory

Not allowed in autopkgtest

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name use_tmp_path.patch

6 years agoUse Python 3 in script shebangs
Debian Science Maintainers [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Use Python 3 in script shebangs

(Skipping the two .pyx files with #!python - they need to be compiled
with Cython, not directly run with any version of plain Python)

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name python3_shebangs.patch

6 years agoUse scipy.special not scipy.misc
Debian Science Maintainers [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Use scipy.special not scipy.misc

factorial, comb and logsumexp have been moved: trying to import them
from the old location is an error in scipy 1.3+.
https://ci.debian.net/data/autopkgtest/unstable/amd64/s/statsmodels/2949940/log.gz

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: accepted https://github.com/statsmodels/statsmodels/pull/6164

Gbp-Pq: Name scipy13_compat.patch

6 years agoLoosen tolerances on some tests on i386
Debian Science Maintainers [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Loosen tolerances on some tests on i386

Failure log
https://buildd.debian.org/status/fetch.php?pkg=statsmodels&arch=i386&ver=0.9.0-3&stamp=1567157609&raw=0

As it only fails on i386 (not x32) and isn't far over tolerance,
I suspect different rounding due to x87 excess precision

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/938949
Forwarded: no

Gbp-Pq: Name i386_loosen_test_tolerances.patch

6 years agoWarn that load_pickle() etc are for trusted data only
Debian Science Maintainers [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Warn that load_pickle() etc are for trusted data only

https://docs.python.org/3/library/pickle.html#restricting-globals

Author: Rebecca N. Palmer
Forwarded: https://github.com/statsmodels/statsmodels/pull/6162

Gbp-Pq: Name cache_security.patch

6 years agoUse example data from an R package we have
Debian Science Maintainers [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Use example data from an R package we have

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name use_available_data.patch

6 years agoKalmanFilter broken on armhf / hppa
Debian Science Maintainers [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
KalmanFilter broken on armhf / hppa

Warn on use, and xfail the tests

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/924036
Bug-Ubuntu: https://launchpad.net/bugs/1819227
Forwarded: no

Gbp-Pq: Name xfail_kalman_armhf.patch

6 years agoGive a more useful error if cvxopt is not found
Debian Science Maintainers [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Give a more useful error if cvxopt is not found

message wasn't actually passed to anything, so it previously failed at
statsmodels/base/optimizer.py:13 (_check_method) with
"Unknown fit method l1_cvxopt_cp"

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: accepted https://github.com/statsmodels/statsmodels/pull/6163

Gbp-Pq: Name show_cvxopt_error.patch

6 years agoChange some more links to https
Debian Science Maintainers [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Change some more links to https

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: https://github.com/statsmodels/statsmodels/pull/5937

Gbp-Pq: Name link_security2.patch

6 years agoDon't fetch Twitter logo
Debian Science Maintainers [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Don't fetch Twitter logo

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name privacy.patch

6 years agoUse intersphinx inventory files from other Debian packages.
Diane Trout [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Use intersphinx inventory files from other Debian packages.

Forwarded: not-needed

Gbp-Pq: Name use-system-inventory

6 years agoto prevent failed test on i386
Debian Science Maintainers [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
to prevent failed test on i386

Author: Yaroslav Halchenko <debian@onerussian.com>
Bug: https://github.com/statsmodels/statsmodels/issues/1831
Forwarded: upstream consider this probably fixed

Gbp-Pq: Name up_reduce_test_precision

6 years agoUse cached datasets for building documentation/examples
Debian Science Maintainers [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Use cached datasets for building documentation/examples

Also remove a download that isn't actually used in that example.

This allows at least some of the examples to be built in an
offline environment such as a Debian buildd.

The cached data is extracted from R packages by debian/datasets/*.

Author: Diane Trout <diane@ghic.org>, Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name use-cached-datasets

6 years agostatsmodels (0.10.2-2+rpi1) bullseye-staging; urgency=medium
Peter Michael Green [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
statsmodels (0.10.2-2+rpi1) bullseye-staging; urgency=medium

  * Disable testsuite.

[dgit import unpatched statsmodels 0.10.2-2+rpi1]

6 years agoImport statsmodels_0.10.2-2+rpi1.debian.tar.xz
Peter Michael Green [Tue, 4 Feb 2020 00:34:03 +0000 (00:34 +0000)]
Import statsmodels_0.10.2-2+rpi1.debian.tar.xz

[dgit import tarball statsmodels 0.10.2-2+rpi1 statsmodels_0.10.2-2+rpi1.debian.tar.xz]

6 years agoMerge statsmodels (0.10.2-2) import into refs/heads/workingbranch
Rebecca N. Palmer [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Merge statsmodels (0.10.2-2) import into refs/heads/workingbranch

6 years agoInclude offset and exposure in GEEResults.fittedvalues
Debian Science Maintainers [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Include offset and exposure in GEEResults.fittedvalues

and remove misleading documentation from GLMResults.fittedvalues

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug: https://github.com/statsmodels/statsmodels/issues/5253
Forwarded: https://github.com/statsmodels/statsmodels/issues/5253#issuecomment-578980169

Gbp-Pq: Name up5253_gee_offset.patch

6 years agoDon't fail documentation build on examples exceptions
Debian Science Maintainers [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Don't fail documentation build on examples exceptions

ipython now fails the whole build by default if anything outputs an error,
which some of ours do when they can't download data.

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name sphinx_ignore_errors.patch

6 years agoMake the module reference tables appear
Debian Science Maintainers [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Make the module reference tables appear

Our numpydoc is old enough to still need this manually set

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug: https://github.com/numpy/numpydoc/issues/141
Forwarded: not-needed

Gbp-Pq: Name sphinx_autosummary.patch

6 years agoXfail or loosen tolerances on flaky tests
Debian Science Maintainers [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Xfail or loosen tolerances on flaky tests

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>, Graham Inggs
Bug-Debian: https://bugs.debian.org/944054
Forwarded: partially https://github.com/statsmodels/statsmodels/pull/6222

Gbp-Pq: Name 944054_flaky_tests.patch

6 years agoUse same Python version for subprocess test
Debian Science Maintainers [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Use same Python version for subprocess test

Avoids a fail due to mismatched extension .so version
when multiple Python 3 versions are available

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name subprocess_use_same_pyver.patch

6 years agoDon't try to write to the source directory
Debian Science Maintainers [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Don't try to write to the source directory

Not allowed in autopkgtest

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name use_tmp_path.patch

6 years agoUse Python 3 in script shebangs
Debian Science Maintainers [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Use Python 3 in script shebangs

(Skipping the two .pyx files with #!python - they need to be compiled
with Cython, not directly run with any version of plain Python)

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name python3_shebangs.patch

6 years agoUse scipy.special not scipy.misc
Debian Science Maintainers [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Use scipy.special not scipy.misc

factorial, comb and logsumexp have been moved: trying to import them
from the old location is an error in scipy 1.3+.
https://ci.debian.net/data/autopkgtest/unstable/amd64/s/statsmodels/2949940/log.gz

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: accepted https://github.com/statsmodels/statsmodels/pull/6164

Gbp-Pq: Name scipy13_compat.patch

6 years agoLoosen tolerances on some tests on i386
Debian Science Maintainers [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Loosen tolerances on some tests on i386

Failure log
https://buildd.debian.org/status/fetch.php?pkg=statsmodels&arch=i386&ver=0.9.0-3&stamp=1567157609&raw=0

As it only fails on i386 (not x32) and isn't far over tolerance,
I suspect different rounding due to x87 excess precision

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/938949
Forwarded: no

Gbp-Pq: Name i386_loosen_test_tolerances.patch

6 years agoWarn that load_pickle() etc are for trusted data only
Debian Science Maintainers [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Warn that load_pickle() etc are for trusted data only

https://docs.python.org/3/library/pickle.html#restricting-globals

Author: Rebecca N. Palmer
Forwarded: https://github.com/statsmodels/statsmodels/pull/6162

Gbp-Pq: Name cache_security.patch

6 years agoUse example data from an R package we have
Debian Science Maintainers [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Use example data from an R package we have

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name use_available_data.patch

6 years agoKalmanFilter broken on armhf / hppa
Debian Science Maintainers [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
KalmanFilter broken on armhf / hppa

Warn on use, and xfail the tests

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/924036
Bug-Ubuntu: https://launchpad.net/bugs/1819227
Forwarded: no

Gbp-Pq: Name xfail_kalman_armhf.patch

6 years agoGive a more useful error if cvxopt is not found
Debian Science Maintainers [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Give a more useful error if cvxopt is not found

message wasn't actually passed to anything, so it previously failed at
statsmodels/base/optimizer.py:13 (_check_method) with
"Unknown fit method l1_cvxopt_cp"

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: accepted https://github.com/statsmodels/statsmodels/pull/6163

Gbp-Pq: Name show_cvxopt_error.patch

6 years agoChange some more links to https
Debian Science Maintainers [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Change some more links to https

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: https://github.com/statsmodels/statsmodels/pull/5937

Gbp-Pq: Name link_security2.patch

6 years agoDon't fetch Twitter logo
Debian Science Maintainers [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Don't fetch Twitter logo

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name privacy.patch

6 years agoUse intersphinx inventory files from other Debian packages.
Diane Trout [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Use intersphinx inventory files from other Debian packages.

Forwarded: not-needed

Gbp-Pq: Name use-system-inventory

6 years agoto prevent failed test on i386
Debian Science Maintainers [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
to prevent failed test on i386

Author: Yaroslav Halchenko <debian@onerussian.com>
Bug: https://github.com/statsmodels/statsmodels/issues/1831
Forwarded: upstream consider this probably fixed

Gbp-Pq: Name up_reduce_test_precision

6 years agoUse cached datasets for building documentation/examples
Debian Science Maintainers [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Use cached datasets for building documentation/examples

Also remove a download that isn't actually used in that example.

This allows at least some of the examples to be built in an
offline environment such as a Debian buildd.

The cached data is extracted from R packages by debian/datasets/*.

Author: Diane Trout <diane@ghic.org>, Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed

Gbp-Pq: Name use-cached-datasets

6 years agostatsmodels (0.10.2-2) unstable; urgency=medium
Rebecca N. Palmer [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
statsmodels (0.10.2-2) unstable; urgency=medium

  * Docs: don't fail the build on no-network exceptions.  Closes: #950087.
  * Remove #945501 cleanup code: not worth the risk in (future) stable.
  * Bump Standards-Version to 4.5.0 (no changes needed).
  * Include offset and exposure in GEE fittedvalues (upstream bug 5253).

[dgit import unpatched statsmodels 0.10.2-2]

6 years agoImport statsmodels_0.10.2-2.debian.tar.xz
Rebecca N. Palmer [Tue, 28 Jan 2020 22:29:29 +0000 (22:29 +0000)]
Import statsmodels_0.10.2-2.debian.tar.xz

[dgit import tarball statsmodels 0.10.2-2 statsmodels_0.10.2-2.debian.tar.xz]

6 years agoImport statsmodels_0.10.2.orig.tar.gz
Rebecca N. Palmer [Tue, 3 Dec 2019 21:23:04 +0000 (21:23 +0000)]
Import statsmodels_0.10.2.orig.tar.gz

[dgit import orig statsmodels_0.10.2.orig.tar.gz]

7 years agoMerge statsmodels (0.8.0-9) import into refs/heads/workingbranch
Rebecca N. Palmer [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Merge statsmodels (0.8.0-9) import into refs/heads/workingbranch

7 years agoFix indexing errors in KaplanMeier
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Fix indexing errors in KaplanMeier

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Bug-Debian: https://bugs.debian.org/860449
Forwarded: not-needed (affected code no longer in upstream)

Gbp-Pq: Name kaplan_meier_860449.patch

7 years agoStop using no-longer-existing pd.ols
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Stop using no-longer-existing pd.ols

Fixes
module 'pandas' has no attribute 'ols'
e.g. in the vector_ar documentation examples.

Origin: upstream https://github.com/statsmodels/statsmodels/commit/4d76116c9c3f47c629503837b3db91bec4d22a5a
Author: Kevin "bashtage" Sheppard
Forwarded: not-needed

Gbp-Pq: Name vector_ar_window_ols.patch

7 years agoFix errors in examples
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Fix errors in examples

Be compatible with current pandas
https://github.com/statsmodels/statsmodels/commit/66a4f98d0ac86ea957fa6f8168cc2df178c64630
https://github.com/statsmodels/statsmodels/commit/67415ad8d4c04dc1dd9ea9ebb1e059af92646c7b
https://github.com/statsmodels/statsmodels/commit/572d507dfa28044166cf4f183177a046f90934ae

and with one dataset layout change within statsmodels, based on
https://github.com/statsmodels/statsmodels/commit/31ec838d1eab2ec559ab69d42151085bdf9f18e1

Look in the correct path for star_diagram.png
(using this fix instead of
https://github.com/statsmodels/statsmodels/commit/3363ce1dc41b1717db5b6779a2a9cbf8f72a0294
to be minimally risky during freeze)

Author: Kevin "bashtage" Sheppard, Rebecca N. Palmer <rebecca_palmer@zoho.com>
Origin: upstream (mostly)
Forwarded: not-needed

Gbp-Pq: Name examples_fixes.patch

7 years agoDon't use np.genfromtxt on non-ASCII data
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Don't use np.genfromtxt on non-ASCII data

Fixes UnicodeDecodeError on file e6.dat

Author: Peter "thequackdaddy" Quackenbush, Rebecca N. Palmer <rebecca_palmer@zoho.com>
Origin: upstream
Forwarded: not-needed

Gbp-Pq: Name lutkepohl_data_load.patch

7 years agoCreate a normal array, not an array of 1x1 arrays
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Create a normal array, not an array of 1x1 arrays

Fixes "object arrays are not supported".

Author: Kevin "bashtage" Sheppard
Origin: upstream https://github.com/statsmodels/statsmodels/pull/4911/commits/18dcceefbfed61b0d11ae5884a9f4cea82c2edb5
Forwarded: not-needed

Gbp-Pq: Name unconstrain_stationary_multivariate.patch

7 years agoMake tests compatible with current numpy/scipy/pandas
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Make tests compatible with current numpy/scipy/pandas

These issues are all within test code, i.e. should not affect users.

https://github.com/statsmodels/statsmodels/commit/bb8fba9d4d9883be2991b43b29bfa3a9c3fb325a
https://github.com/statsmodels/statsmodels/commit/310f91da9f07d9483965d624d76dbb7abebbd67f
https://github.com/statsmodels/statsmodels/pull/4911/commits/18dcceefbfed61b0d11ae5884a9f4cea82c2edb5
https://github.com/statsmodels/statsmodels/commit/f1d5eddd44d61099a9f8f90c40c35716a8346cf7

and one new fix only needed on 32 bit Python 2 (integer data loads as
int64, which gets converted to long producing factor names like
C(agecat)[T.4L], which does not match C(agecat)[T.4])

Author: Kevin "bashtage" Sheppard, Peter "thequackdaddy" Quackenbush, Matthew Brett, Rebecca N. Palmer <rebecca_palmer@zoho.com>
Origin: upstream (mostly)
Forwarded: no

Gbp-Pq: Name test_fixes.patch

7 years agoAllow loading the CO2 dataset in pandas >= 0.23
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Allow loading the CO2 dataset in pandas >= 0.23

Fixes __new__() got an unexpected keyword argument 'format'

Author: Matthew Brett
Origin: upstream https://github.com/statsmodels/statsmodels/commit/bd2985d781484c2a2ce47a3db107690bbe688acd
Forwarded: not-needed

Gbp-Pq: Name co2_dataset_load.patch

7 years agoDon't use gammaln on complex input
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Don't use gammaln on complex input

In scipy >= 1.0, it rejects such input with
TypeError: ufunc 'gammaln' not supported for the input types, and the
inputs could not be safely coerced to any supported types according
to the casting rule ''safe''

Author: Kevin "bashtage" Sheppard, Rebecca N. Palmer <rebecca_palmer@zoho.com>
Origin: upstream https://github.com/statsmodels/statsmodels/pull/3964/commits/c11c6242ff81a0f83d3e7fd83a8105397d3cbc1d
Forwarded: not-needed

Gbp-Pq: Name gammaln_complex.patch

7 years agoFix shape mismatch errors in MICE imputation
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Fix shape mismatch errors in MICE imputation

numpy/pandas no longer allows assigning an nx1 2D value at a 1D index

Author: Peter "thequackdaddy" Quackenbush, Josef "josef-pkt" Perktold
Origin: upstream https://github.com/statsmodels/statsmodels/commit/df92bde1a85c238db9561304a196dbc618cfeaa1 https://github.com/statsmodels/statsmodels/commit/0871eba510e7ebe8aa9323f4f3ee50226576ed29
Forwarded: not-needed

Gbp-Pq: Name imputation_broadcasting.patch

7 years agoStop using no-longer-existing chisqprob
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Stop using no-longer-existing chisqprob

Needed for compatibility with scipy >= 1.0

Author: Kevin "bashtage" Sheppard
Origin: upstream https://github.com/statsmodels/statsmodels/commit/575fc69257171e1dbc86461b510eb818a63c5fab
Forwarded: not-needed

Gbp-Pq: Name chisqprob.patch

7 years agoMake the datasets cache work in Python 3
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Make the datasets cache work in Python 3

Fixes URLError messages appearing in the built documentation

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed (upstream fixed this in _cache_it instead)

Gbp-Pq: Name python3_dataset_caching.patch

7 years agoDon't fetch Twitter logo
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Don't fetch Twitter logo

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no

Gbp-Pq: Name privacy.patch

7 years agoFix spelling
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Fix spelling

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Origin: lintian (partly)
Forwarded: https://github.com/statsmodels/statsmodels/pull/5513

Gbp-Pq: Name spelling.patch

7 years agoUse mathjax instead of no-longer-existing pngmath
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Use mathjax instead of no-longer-existing pngmath

Either imgmath or mathjax fixes the FTBFS;
mathjax also makes TeX display as equations, i.e. fixes #687301

Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: not-needed (mathjax is already the upstream default)

Gbp-Pq: Name no-sphinx-pngmath.patch

7 years agoDo not try to access remote locations on buildtime test
Andreas Tille tille@debian.org, Rebecca N. Palmer [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Do not try to access remote locations on buildtime test

Bug-Debian: https://bugs.debian.org/882641

Gbp-Pq: Name prevent_online_access_in_buildtime_tests.patch

7 years agoUse intersphinx inventory files from other Debian packages.
Diane Trout [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Use intersphinx inventory files from other Debian packages.

Forwarded: not-needed

Gbp-Pq: Name use-system-inventory

7 years agoUse Python3 to create documentation
Diane Trout [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Use Python3 to create documentation

Bug: https://github.com/statsmodels/statsmodels/pull/5348

Gbp-Pq: Name use-python3-for-doc-build

7 years agofix_numpydoc_issue
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
fix_numpydoc_issue

Author; Denis Laxalde <denis@laxalde.org>
Last-Update: Thu, 17 Aug 2017 22:06:46 +0200
Description:  Fix numpy doc input

Gbp-Pq: Name fix_numpydoc_issue.patch

7 years agoSeems the tests are failing due to some problem in pandas
Andreas Tille [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Seems the tests are failing due to some problem in pandas

Last-Update: Thu, 17 Aug 2017 12:47:48 +0200
Bug-Debian: https://bugs.debian.org/868977

which we can not fix here.  Ignore the issue for the moment to be able
to drop severity of bug #868977 from serious to important

Gbp-Pq: Name skip_tests_failing_due_to_panda_issue.patch

7 years agodeb_skip_test_ons390
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
deb_skip_test_ons390

Gbp-Pq: Name deb_skip_test_ons390

7 years agoto prevent failed test on i386
Yaroslav Halchenko [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
to prevent failed test on i386

Bug: https://github.com/statsmodels/statsmodels/issues/1831
Last-Update: 2014-07-16

Gbp-Pq: Name up_reduce_test_precision

7 years agoUse Debian packaged IPhythonSphinx extensions
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Use Debian packaged IPhythonSphinx extensions

Last-Update: Wed, 13 Feb 2019 08:43:05 +0100

Also drop matplotlib.sphinxext.only_directives which fail with
python3-matplotlib and are not used

Gbp-Pq: Name deb_use_internal_ipythonsphinx_extensions

7 years agoUse cached datasets for building documentation/examples
Debian Science Maintainers [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Use cached datasets for building documentation/examples

Also remove a download that isn't actually used in that example.

This allows at least some of the examples to be built in an
offline environment such as a Debian buildd.

See debian/README.source for more information about the cached datasets.

Author: Diane Trout <diane@ghic.org>, Rebecca N. Palmer <rebecca_palmer@zoho.com>

Gbp-Pq: Name use-cached-datasets

7 years agostatsmodels (0.8.0-9) unstable; urgency=medium
Rebecca N. Palmer [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
statsmodels (0.8.0-9) unstable; urgency=medium

  * Team upload.
  * Disable KalmanFilter on armhf, as it gives wrong results
    (and probably always has).

[dgit import unpatched statsmodels 0.8.0-9]

7 years agoImport statsmodels_0.8.0-9.debian.tar.xz
Rebecca N. Palmer [Sat, 2 Mar 2019 14:59:35 +0000 (14:59 +0000)]
Import statsmodels_0.8.0-9.debian.tar.xz

[dgit import tarball statsmodels 0.8.0-9 statsmodels_0.8.0-9.debian.tar.xz]

9 years agoImport statsmodels_0.8.0.orig.tar.gz
Yaroslav Halchenko [Wed, 8 Feb 2017 18:08:38 +0000 (18:08 +0000)]
Import statsmodels_0.8.0.orig.tar.gz

[dgit import orig statsmodels_0.8.0.orig.tar.gz]

9 years ago[PATCH] MAINT: test_anova.py fails on pandas 0.19.0 because stringio closes after...
thequackdaddy [Tue, 20 Dec 2016 16:10:22 +0000 (10:10 -0600)]
[PATCH] MAINT: test_anova.py fails on pandas 0.19.0 because stringio closes after read_table. Make read_table global to fix.

Gbp-Pq: Name workaround_panda_readtable_bug.patch

9 years agofix_wrong_index_type
Ole Streicher [Mon, 26 Dec 2016 17:33:56 +0000 (17:33 +0000)]
fix_wrong_index_type

Descrption: Fix index type in `reshape` to be integer.

This will avoid FTBFS with numpy >= 1.12 beta

Gbp-Pq: Name fix_wrong_index_type.patch

9 years ago[PATCH] Simplified commit
thequackdaddy [Wed, 16 Nov 2016 20:25:19 +0000 (14:25 -0600)]
[PATCH] Simplified commit

Gbp-Pq: Name up_3239.patch

9 years agodeb_no_nbformat_for_now
Debian Science Maintainers [Mon, 26 Dec 2016 17:33:56 +0000 (17:33 +0000)]
deb_no_nbformat_for_now

Gbp-Pq: Name deb_no_nbformat_for_now