[med-svn] [Git][med-team/python-skbio][master] 5 commits: Versioned Build-Depends: python3-scipy (>= 1.3.3)
Andreas Tille
gitlab at salsa.debian.org
Wed Dec 4 09:08:45 GMT 2019
Andreas Tille pushed to branch master at Debian Med / python-skbio
Commits:
c17b13cf by Andreas Tille at 2019-12-04T08:56:04Z
Versioned Build-Depends: python3-scipy (>= 1.3.3)
- - - - -
80886b86 by Andreas Tille at 2019-12-04T09:00:45Z
Really add upstream patch "Build fixes for pandas 0.25.0 and scipy 1.3.0 (#1665)"
- - - - -
38eb1d56 by Andreas Tille at 2019-12-04T09:01:10Z
debhelper-compat 12
- - - - -
f97c6e58 by Andreas Tille at 2019-12-04T09:01:14Z
Standards-Version: 4.4.1
- - - - -
9230fad6 by Andreas Tille at 2019-12-04T09:01:17Z
Set upstream metadata fields: Repository, Repository-Browse.
Fixes lintian: upstream-metadata-file-is-missing
See https://lintian.debian.org/tags/upstream-metadata-file-is-missing.html for more details.
- - - - -
6 changed files:
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/9c061da7e2746aee403b41621f71b118ce5c52f8.patch
- debian/patches/series
- + debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+python-skbio (0.5.5-3) UNRELEASED; urgency=medium
+
+ * Apply patch from upstream titled
+ "WIP: Build fixes for pandas 0.25.0 and scipy 1.3.0"
+ * Versioned Build-Depends: python3-scipy (>= 1.3.3)
+ * debhelper-compat 12
+ * Standards-Version: 4.4.1
+ * Set upstream metadata fields: Repository, Repository-Browse.
+
+ -- Andreas Tille <tille at debian.org> Thu, 14 Nov 2019 09:31:50 +0100
+
python-skbio (0.5.5-2) unstable; urgency=medium
* Upstream has fixed numpy issue
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12
=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
Kevin Murray <kdmfoss at gmail.com>
Section: python
Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
dh-python,
ipython3,
python3-all-dev,
@@ -22,13 +22,13 @@ Build-Depends: debhelper (>= 12~),
python3-numpy (>= 1:1.9.2),
python3-numpydoc,
python3-pandas (>= 0.19.2),
- python3-scipy,
+ python3-scipy (>= 1.3.3),
python3-setuptools,
python3-sklearn,
python3-sphinx,
python3-sphinx-bootstrap-theme,
libssw-dev
-Standards-Version: 4.3.0
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/python-skbio
Vcs-Git: https://salsa.debian.org/med-team/python-skbio.git
Homepage: https://github.com/biocore/scikit-bio
=====================================
debian/patches/9c061da7e2746aee403b41621f71b118ce5c52f8.patch
=====================================
@@ -0,0 +1,72 @@
+From 9c061da7e2746aee403b41621f71b118ce5c52f8 Mon Sep 17 00:00:00 2001
+From: Daniel McDonald <danielmcdonald at ucsd.edu>
+Date: Mon, 19 Aug 2019 15:27:12 -0700
+Subject: [PATCH] WIP: Build fixes for pandas 0.25.0 and scipy 1.3.0 (#1665)
+
+* Build fixes for pandas 0.25.0 and scipy 1.3.0
+
+* Build fixes for pandas 0.25.0 and scipy 1.3.0
+
+* Build fixes for pandas 0.25.0 and scipy 1.3.0
+---
+ skbio/stats/distance/tests/test_mantel.py | 8 ++++----
+ skbio/stats/evolve/_hommola.py | 4 ++--
+ skbio/stats/power.py | 4 ++--
+ 3 files changed, 8 insertions(+), 8 deletions(-)
+
+--- a/skbio/stats/distance/tests/test_mantel.py
++++ b/skbio/stats/distance/tests/test_mantel.py
+@@ -186,7 +186,7 @@ class MantelTests(MantelTestData):
+ for method in self.methods:
+ obs = mantel(self.minx, self.minx, method=method,
+ alternative='less')
+- self.assertEqual(obs, (1, 1, 3))
++ npt.assert_almost_equal(obs, (1, 1, 3))
+
+ np.random.seed(0)
+
+@@ -247,15 +247,15 @@ class MantelTests(MantelTestData):
+ # distances
+ obs = mantel(self.miny, self.no_variation, method='pearson',
+ alternative=alt)
+- npt.assert_equal(obs, (0.0, 1.0, 3))
++ npt.assert_equal(obs, (np.nan, np.nan, 3))
+
+ obs = mantel(self.no_variation, self.miny, method='pearson',
+ alternative=alt)
+- npt.assert_equal(obs, (0.0, 1.0, 3))
++ npt.assert_equal(obs, (np.nan, np.nan, 3))
+
+ obs = mantel(self.no_variation, self.no_variation,
+ method='pearson', alternative=alt)
+- npt.assert_equal(obs, (1.0, 1.0, 3))
++ npt.assert_equal(obs, (np.nan, np.nan, 3))
+
+ def test_no_variation_spearman(self):
+ exp = (np.nan, np.nan, 3)
+--- a/skbio/stats/evolve/_hommola.py
++++ b/skbio/stats/evolve/_hommola.py
+@@ -126,8 +126,8 @@ def hommola_cospeciation(host_dist, par_
+
+ >>> corr_coeff, p_value, perm_stats = hommola_cospeciation(
+ ... hdist, pdist, interaction, permutations=99)
+- >>> corr_coeff
+- 0.83170965463247903
++ >>> round(corr_coeff, 8)
++ 0.83171097
+
+ In this case, the host distances have a fairly strong positive correlation
+ with the symbiont distances. However, this may also reflect structure
+--- a/skbio/stats/power.py
++++ b/skbio/stats/power.py
+@@ -84,8 +84,8 @@ Now, let's use random sampling to estima
+ the first distribution.
+
+ >>> samples = [ind, dep]
+->>> f(samples)
+-3.6459452596563003e-08
++>>> round(f(samples), 6)
++3.645945e-08
+
+ In `subsample_power`, we can maintain a paired relationship between samples
+ by setting `draw_mode` to "matched". We can also set our critical value, so
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ mathjax-path
0003-Cherry-pick-upstream-fix-for-numpy-transition.patch
no_privacy_breach_logo.patch
6497020.patch
+9c061da7e2746aee403b41621f71b118ce5c52f8.patch
=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,2 @@
+Repository: https://github.com/biocore/scikit-bio
+Repository-Browse: https://github.com/biocore/scikit-bio
View it on GitLab: https://salsa.debian.org/med-team/python-skbio/compare/e6d6590dffe3ec014c11933ca2f37c34ef334c39...9230fad6b37d366b9c9a7aa0987d22dc15d7a36b
--
View it on GitLab: https://salsa.debian.org/med-team/python-skbio/compare/e6d6590dffe3ec014c11933ca2f37c34ef334c39...9230fad6b37d366b9c9a7aa0987d22dc15d7a36b
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