debian/changelog

+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@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

-12

debian/control

@@ -5,7 +5,7 @@ Uploaders: Tim Booth <tbooth@ceh.ac.uk>,
            Kevin Murray <kdmfoss@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

+From 9c061da7e2746aee403b41621f71b118ce5c52f8 Mon Sep 17 00:00:00 2001
+From: Daniel McDonald <danielmcdonald@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

+Repository: https://github.com/biocore/scikit-bio
+Repository-Browse: https://github.com/biocore/scikit-bio