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gnu: python-seaborn: Update to 0.12.0.

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* gnu/packages/python-xyz.scm (python-seaborn): Update to 0.12.0.
[source]: Remove patches.
[arguments]: Import (ice-9 match) module. Remove patch-more-tests and
start-xserver phases. Replace build and install phases. Fix pytest command in
check phase.
[native-inputs]: Add python-flit-core and python-pypa-build. Remove
xorg-server-for-tests.
* gnu/packages/patches/python-seaborn-2690.patch,
gnu/packages/patches/python-seaborn-kde-test.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Unregister them.
This commit is contained in:
Arun Isaac 2022-10-12 16:49:17 +05:30
parent e074559eda
commit 2d989ad597
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GPG key ID: 2E25EE8B61802BB3
4 changed files with 22 additions and 331 deletions
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2
gnu/local.mk
View file

@ -1759,8 +1759,6 @@ dist_patch_DATA = \
%D%/packages/patches/python-robotframework-atest.patch \ %D%/packages/patches/python-robotframework-atest.patch \
%D%/packages/patches/python-robotframework-source-date-epoch.patch \ %D%/packages/patches/python-robotframework-source-date-epoch.patch \
%D%/packages/patches/python-robotframework-sshlibrary-rf5-compat.patch \ %D%/packages/patches/python-robotframework-sshlibrary-rf5-compat.patch \
%D%/packages/patches/python-seaborn-kde-test.patch \
%D%/packages/patches/python-seaborn-2690.patch \
%D%/packages/patches/python-unittest2-python3-compat.patch \ %D%/packages/patches/python-unittest2-python3-compat.patch \
%D%/packages/patches/python-unittest2-remove-argparse.patch \ %D%/packages/patches/python-unittest2-remove-argparse.patch \
%D%/packages/patches/python-versioneer-guix-support.patch \ %D%/packages/patches/python-versioneer-guix-support.patch \

268
gnu/packages/patches/python-seaborn-2690.patch
View file

@ -1,268 +0,0 @@
This patch was adapted from the upstream pull request 2690.
From ebd6812d48f5b8ed1ebb7d79bda0b2a7b9ae2812 Mon Sep 17 00:00:00 2001
From: Michael Waskom <mwaskom@gmail.com>
Date: Sun, 31 Oct 2021 15:09:27 -0400
Subject: [PATCH 1/4] Update boxplot tests for mpl3.5 compatability
---
seaborn/tests/test_categorical.py | 30 +++++++++++++++++++-----------
1 file changed, 19 insertions(+), 11 deletions(-)
diff --git a/seaborn/tests/test_categorical.py b/seaborn/tests/test_categorical.py
index d4e09b703..488fad2d6 100644
--- a/seaborn/tests/test_categorical.py
+++ b/seaborn/tests/test_categorical.py
@@ -110,6 +110,11 @@ class CategoricalFixture:
df = pd.DataFrame(dict(y=y, g=g, h=h, u=u))
x_df["W"] = g
+ def get_box_artists(self, ax):
+
+ # Exclude labeled patches, which are for the legend
+ return [p for p in ax.patches if not p.get_label()]
+
class TestCategoricalPlotter(CategoricalFixture):
@@ -855,12 +863,12 @@ def test_hue_offsets(self):
def test_axes_data(self):
ax = cat.boxplot(x="g", y="y", data=self.df)
- assert len(ax.artists) == 3
+ assert len(self.get_box_artists(ax)) == 3
plt.close("all")
ax = cat.boxplot(x="g", y="y", hue="h", data=self.df)
- assert len(ax.artists) == 6
+ assert len(self.get_box_artists(ax)) == 6
plt.close("all")
@@ -868,14 +876,14 @@ def test_box_colors(self):
ax = cat.boxplot(x="g", y="y", data=self.df, saturation=1)
pal = palettes.color_palette(n_colors=3)
- for patch, color in zip(ax.artists, pal):
+ for patch, color in zip(self.get_box_artists(ax), pal):
assert patch.get_facecolor()[:3] == color
plt.close("all")
ax = cat.boxplot(x="g", y="y", hue="h", data=self.df, saturation=1)
pal = palettes.color_palette(n_colors=2)
- for patch, color in zip(ax.artists, pal * 2):
+ for patch, color in zip(self.get_box_artists(ax), pal * 2):
assert patch.get_facecolor()[:3] == color
plt.close("all")
@@ -884,7 +892,7 @@ def test_draw_missing_boxes(self):
ax = cat.boxplot(x="g", y="y", data=self.df,
order=["a", "b", "c", "d"])
- assert len(ax.artists) == 3
+ assert len(self.get_box_artists(ax)) == 3
def test_missing_data(self):
@@ -894,13 +902,13 @@ def test_missing_data(self):
y[-2:] = np.nan
ax = cat.boxplot(x=x, y=y)
- assert len(ax.artists) == 3
+ assert len(self.get_box_artists(ax)) == 3
plt.close("all")
y[-1] = 0
ax = cat.boxplot(x=x, y=y, hue=h)
- assert len(ax.artists) == 7
+ assert len(self.get_box_artists(ax)) == 7
plt.close("all")
@@ -2766,11 +2774,11 @@ def test_plot_elements(self):
g = cat.catplot(x="g", y="y", data=self.df, kind="box")
want_artists = self.g.unique().size
- assert len(g.ax.artists) == want_artists
+ assert len(self.get_box_artists(g.ax)) == want_artists
g = cat.catplot(x="g", y="y", hue="h", data=self.df, kind="box")
want_artists = self.g.unique().size * self.h.unique().size
- assert len(g.ax.artists) == want_artists
+ assert len(self.get_box_artists(g.ax)) == want_artists
g = cat.catplot(x="g", y="y", data=self.df,
kind="violin", inner=None)
@@ -3137,14 +3145,14 @@ def test_box_colors(self):
ax = cat.boxenplot(x="g", y="y", data=self.df, saturation=1)
pal = palettes.color_palette(n_colors=3)
- for patch, color in zip(ax.artists, pal):
+ for patch, color in zip(self.get_box_artists(ax), pal):
assert patch.get_facecolor()[:3] == color
plt.close("all")
ax = cat.boxenplot(x="g", y="y", hue="h", data=self.df, saturation=1)
pal = palettes.color_palette(n_colors=2)
- for patch, color in zip(ax.artists, pal * 2):
+ for patch, color in zip(self.get_box_artists(ax), pal * 2):
assert patch.get_facecolor()[:3] == color
plt.close("all")
From ff78ed38817a346e760194ab3b03b28d7ea3ba1b Mon Sep 17 00:00:00 2001
From: Michael Waskom <mwaskom@gmail.com>
Date: Sun, 31 Oct 2021 15:50:54 -0400
Subject: [PATCH 2/4] Update kdeplot tests for mpl3.5 compatability
---
seaborn/tests/test_distributions.py | 53 ++++++++++++++++++++---------
1 file changed, 37 insertions(+), 16 deletions(-)
diff --git a/seaborn/tests/test_distributions.py b/seaborn/tests/test_distributions.py
index d241fd978..466efb69e 100644
--- a/seaborn/tests/test_distributions.py
+++ b/seaborn/tests/test_distributions.py
@@ -39,6 +39,27 @@
)
+def get_contour_coords(c):
+ """Provide compatability for change in contour artist type in mpl3.5."""
+ # See https://github.com/matplotlib/matplotlib/issues/20906
+ if isinstance(c, mpl.collections.LineCollection):
+ return c.get_segments()
+ elif isinstance(c, mpl.collections.PathCollection):
+ return [p.vertices[:np.argmax(p.codes) + 1] for p in c.get_paths()]
+
+
+def get_contour_color(c):
+ """Provide compatability for change in contour artist type in mpl3.5."""
+ # See https://github.com/matplotlib/matplotlib/issues/20906
+ if isinstance(c, mpl.collections.LineCollection):
+ return c.get_color()
+ elif isinstance(c, mpl.collections.PathCollection):
+ if c.get_facecolor().size:
+ return c.get_facecolor()
+ else:
+ return c.get_edgecolor()
+
+
class TestDistPlot(object):
rs = np.random.RandomState(0)
@@ -902,7 +923,7 @@ def test_fill_artists(self, long_df):
f, ax = plt.subplots()
kdeplot(data=long_df, x="x", y="y", hue="c", fill=fill)
for c in ax.collections:
- if fill:
+ if fill or Version(mpl.__version__) >= Version("3.5.0b0"):
assert isinstance(c, mpl.collections.PathCollection)
else:
assert isinstance(c, mpl.collections.LineCollection)
@@ -918,8 +939,8 @@ def test_common_norm(self, rng):
kdeplot(x=x, y=y, hue=hue, common_norm=True, ax=ax1)
kdeplot(x=x, y=y, hue=hue, common_norm=False, ax=ax2)
- n_seg_1 = sum([len(c.get_segments()) > 0 for c in ax1.collections])
- n_seg_2 = sum([len(c.get_segments()) > 0 for c in ax2.collections])
+ n_seg_1 = sum([len(get_contour_coords(c)) > 0 for c in ax1.collections])
+ n_seg_2 = sum([len(get_contour_coords(c)) > 0 for c in ax2.collections])
assert n_seg_2 > n_seg_1
def test_log_scale(self, rng):
@@ -946,7 +967,7 @@ def test_log_scale(self, rng):
ax2.contour(10 ** xx, yy, density, levels=levels)
for c1, c2 in zip(ax1.collections, ax2.collections):
- assert_array_equal(c1.get_segments(), c2.get_segments())
+ assert_array_equal(get_contour_coords(c1), get_contour_coords(c2))
def test_bandwidth(self, rng):
@@ -959,7 +980,7 @@ def test_bandwidth(self, rng):
kdeplot(x=x, y=y, bw_adjust=2, ax=ax2)
for c1, c2 in zip(ax1.collections, ax2.collections):
- seg1, seg2 = c1.get_segments(), c2.get_segments()
+ seg1, seg2 = get_contour_coords(c1), get_contour_coords(c2)
if seg1 + seg2:
x1 = seg1[0][:, 0]
x2 = seg2[0][:, 0]
@@ -980,9 +1001,9 @@ def test_weights(self, rng):
kdeplot(x=x, y=y, hue=hue, weights=weights, ax=ax2)
for c1, c2 in zip(ax1.collections, ax2.collections):
- if c1.get_segments() and c2.get_segments():
- seg1 = np.concatenate(c1.get_segments(), axis=0)
- seg2 = np.concatenate(c2.get_segments(), axis=0)
+ if get_contour_coords(c1) and get_contour_coords(c2):
+ seg1 = np.concatenate(get_contour_coords(c1), axis=0)
+ seg2 = np.concatenate(get_contour_coords(c2), axis=0)
assert not np.array_equal(seg1, seg2)
def test_hue_ignores_cmap(self, long_df):
@@ -1030,7 +1051,7 @@ def test_levels_and_thresh(self, long_df):
kdeplot(**plot_kws, levels=np.linspace(thresh, 1, n), ax=ax2)
for c1, c2 in zip(ax1.collections, ax2.collections):
- assert_array_equal(c1.get_segments(), c2.get_segments())
+ assert_array_equal(get_contour_coords(c1), get_contour_coords(c2))
with pytest.raises(ValueError):
kdeplot(**plot_kws, levels=[0, 1, 2])
@@ -1042,7 +1063,7 @@ def test_levels_and_thresh(self, long_df):
kdeplot(**plot_kws, levels=n, thresh=0, ax=ax2)
for c1, c2 in zip(ax1.collections, ax2.collections):
- assert_array_equal(c1.get_segments(), c2.get_segments())
+ assert_array_equal(get_contour_coords(c1), get_contour_coords(c2))
for c1, c2 in zip(ax1.collections, ax2.collections):
assert_array_equal(c1.get_facecolors(), c2.get_facecolors())
@@ -2322,13 +2343,13 @@ def test_bivariate_kde_norm(self, rng):
z = [0] * 80 + [1] * 20
g = displot(x=x, y=y, col=z, kind="kde", levels=10)
- l1 = sum(bool(c.get_segments()) for c in g.axes.flat[0].collections)
- l2 = sum(bool(c.get_segments()) for c in g.axes.flat[1].collections)
+ l1 = sum(bool(get_contour_coords(c)) for c in g.axes.flat[0].collections)
+ l2 = sum(bool(get_contour_coords(c)) for c in g.axes.flat[1].collections)
assert l1 > l2
g = displot(x=x, y=y, col=z, kind="kde", levels=10, common_norm=False)
- l1 = sum(bool(c.get_segments()) for c in g.axes.flat[0].collections)
- l2 = sum(bool(c.get_segments()) for c in g.axes.flat[1].collections)
+ l1 = sum(bool(get_contour_coords(c)) for c in g.axes.flat[0].collections)
+ l2 = sum(bool(get_contour_coords(c)) for c in g.axes.flat[1].collections)
assert l1 == l2
def test_bivariate_hist_norm(self, rng):
From a20ce3fabeb23c97b5827d9fb0c6a96ac109ea64 Mon Sep 17 00:00:00 2001
From: Michael Waskom <mwaskom@gmail.com>
Date: Sun, 31 Oct 2021 16:10:47 -0400
Subject: [PATCH 3/4] Update legend tests for mpl3.5 compatability
---
seaborn/tests/test_distributions.py | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/seaborn/tests/test_distributions.py b/seaborn/tests/test_distributions.py
index 466efb69e..024fe7541 100644
--- a/seaborn/tests/test_distributions.py
+++ b/seaborn/tests/test_distributions.py
@@ -872,7 +872,7 @@ def test_legend(self, long_df):
for label, level in zip(legend_labels, order):
assert label.get_text() == level
- legend_artists = ax.legend_.findobj(mpl.lines.Line2D)[::2]
+ legend_artists = ax.legend_.findobj(mpl.lines.Line2D)
palette = color_palette()
for artist, color in zip(legend_artists, palette):
assert_colors_equal(artist.get_color(), color)

36
gnu/packages/patches/python-seaborn-kde-test.patch
View file

@ -1,36 +0,0 @@
This patch is an excerpt of this upstream commit:
commit 0a24478a550132f1882e5be5f5dbc0fc446a8a6c
Author: Michael Waskom <mwaskom@users.noreply.github.com>
Date: Mon Dec 21 18:44:58 2020 -0500
Raise minimal supported Python to 3.7 and bump requirements (#2396)
It fixes the failure of 'test_weights'.
--- a/seaborn/tests/test_distributions.py
+++ b/seaborn/tests/test_distributions.py
@@ -709,21 +708,17 @@ class TestKDEPlotUnivariate:
integral = integrate.trapz(ydata, np.log10(xdata))
assert integral == pytest.approx(1)
- @pytest.mark.skipif(
- LooseVersion(scipy.__version__) < "1.2.0",
- reason="Weights require scipy >= 1.2.0"
- )
def test_weights(self):
x = [1, 2]
weights = [2, 1]
- ax = kdeplot(x=x, weights=weights)
+ ax = kdeplot(x=x, weights=weights, bw_method=.1)
xdata, ydata = ax.lines[0].get_xydata().T
- y1 = ydata[np.argwhere(np.abs(xdata - 1).min())]
- y2 = ydata[np.argwhere(np.abs(xdata - 2).min())]
+ y1 = ydata[np.abs(xdata - 1).argmin()]
+ y2 = ydata[np.abs(xdata - 2).argmin()]
assert y1 == pytest.approx(2 * y2)

47
gnu/packages/python-xyz.scm
View file

@ -10280,40 +10280,37 @@ (define-public python-pyqrcode
(define-public python-seaborn (define-public python-seaborn
(package (package
(name "python-seaborn") (name "python-seaborn")
(version "0.11.2") (version "0.12.0")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (pypi-uri "seaborn" version)) (uri (pypi-uri "seaborn" version))
(sha256 (sha256
(base32 (base32
"1xpl3zb945sihsiwm9q1yyx84sakk1phcg0fprj6i0j0dllfjifg")) "08vvnp4ps86857imxz2l5xi2vir5xdcdp3apq4badb4b5llifgw9"))))
(patches (search-patches "python-seaborn-kde-test.patch"
"python-seaborn-2690.patch"))))
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(#:phases (modify-phases %standard-phases (list #:modules '((guix build python-build-system)
(add-after 'unpack 'patch-more-tests (guix build utils)
(lambda _ (ice-9 match))
(substitute* "seaborn/tests/test_distributions.py" #:phases #~(modify-phases %standard-phases
(("get_contour_color\\(ax\\.collections\\[0\\]\\)") (replace 'build
"get_contour_color(ax.collections[0])") (lambda _
(("c\\.get_color\\(\\)") "get_contour_color(c)") (invoke "python" "-m" "build" "--wheel"
(("def test_hue_ignores_cmap") "--no-isolation" ".")))
"def skip_test_hue_ignores_cmap") (replace 'install
(("def test_fill_artists") (lambda _
"def skip_test_fill_artists") (match (find-files "dist" "\\.whl$")
(("def test_with_rug") "def skip_test_with_rug")))) ((wheel _ ...)
(add-before 'check 'start-xserver (invoke "python" "-m" "pip" "install"
(lambda _ (string-append "--prefix=" #$output)
(system "Xvfb :1 &") wheel)))))
(setenv "DISPLAY" ":1"))) (replace 'check
(replace 'check (lambda* (#:key tests? #:allow-other-keys)
(lambda* (#:key tests? #:allow-other-keys) (when tests?
(when tests? (invoke "pytest" "-vv")))))))
(invoke "pytest" "seaborn")))))))
(propagated-inputs (list python-pandas python-matplotlib python-numpy (propagated-inputs (list python-pandas python-matplotlib python-numpy
python-scipy)) python-scipy))
(native-inputs (list python-pytest xorg-server-for-tests)) (native-inputs (list python-flit-core python-pypa-build python-pytest))
(home-page "https://seaborn.pydata.org/") (home-page "https://seaborn.pydata.org/")
(synopsis "Statistical data visualization") (synopsis "Statistical data visualization")
(description (description