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 <[email protected]> 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 <[email protected]>, Kevin Murray <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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