(address . guix-patches@gnu.org)(name . Arun Isaac)(address . arunisaac@systemreboot.net)
20221012122154.12160-1-arunisaac@systemreboot.net
* 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.
---
gnu/local.mk | 2 -
.../patches/python-seaborn-2690.patch | 268 ------------------
.../patches/python-seaborn-kde-test.patch | 36 ---
gnu/packages/python-xyz.scm | 46 ++-
4 files changed, 21 insertions(+), 331 deletions(-)
delete mode 100644 gnu/packages/patches/python-seaborn-2690.patch
delete mode 100644 gnu/packages/patches/python-seaborn-kde-test.patch
Toggle diff (397 lines)
diff --git a/gnu/local.mk b/gnu/local.mk
index 195bbcc40a..bd3eb1d4f0 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1745,8 +1745,6 @@ dist_patch_DATA = \
%D%/packages/patches/python-robotframework-atest.patch \
%D%/packages/patches/python-robotframework-source-date-epoch.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-remove-argparse.patch \
%D%/packages/patches/python-versioneer-guix-support.patch \
diff --git a/gnu/packages/patches/python-seaborn-2690.patch b/gnu/packages/patches/python-seaborn-2690.patch
deleted file mode 100644
index 4662d19c2d..0000000000
--- a/gnu/packages/patches/python-seaborn-2690.patch
+++ /dev/null
@@ -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)
-
diff --git a/gnu/packages/patches/python-seaborn-kde-test.patch b/gnu/packages/patches/python-seaborn-kde-test.patch
deleted file mode 100644
index f300dffc6f..0000000000
--- a/gnu/packages/patches/python-seaborn-kde-test.patch
+++ /dev/null
@@ -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)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 7c647bd42f..593af72575 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -9975,40 +9975,36 @@ (define-public python-pyqrcode
(define-public python-seaborn
(package
(name "python-seaborn")
- (version "0.11.2")
+ (version "0.12.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "seaborn" version))
(sha256
(base32
- "1xpl3zb945sihsiwm9q1yyx84sakk1phcg0fprj6i0j0dllfjifg"))
- (patches (search-patches "python-seaborn-kde-test.patch"
- "python-seaborn-2690.patch"))))
+ "08vvnp4ps86857imxz2l5xi2vir5xdcdp3apq4badb4b5llifgw9"))))
(build-system python-build-system)
(arguments
- `(#:phases (modify-phases %standard-phases
- (add-after 'unpack 'patch-more-tests
- (lambda _
- (substitute* "seaborn/tests/test_distributions.py"
- (("get_contour_color\\(ax\\.collections\\[0\\]\\)")
- "get_contour_color(ax.collections[0])")
- (("c\\.get_color\\(\\)") "get_contour_color(c)")
- (("def test_hue_ignores_cmap")
- "def skip_test_hue_ignores_cmap")
- (("def test_fill_artists")
- "def skip_test_fill_artists")
- (("def test_with_rug") "def skip_test_with_rug"))))
- (add-before 'check 'start-xserver
- (lambda _
- (system "Xvfb :1 &")
- (setenv "DISPLAY" ":1")))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "pytest" "seaborn")))))))
+ (list #:modules '((guix build python-build-system)
+ (guix build utils)
+ (ice-9 match))
+ #:phases #~(modify-phases %standard-phases
+ (replace 'build
+ (lambda _
+ (invoke "python" "-m" "build" "--wheel" "--no-isolation" ".")))
+ (replace 'install
+ (lambda _
+ (match (find-files "dist" "\\.whl$")
+ ((wheel _ ...)
+ (invoke "python" "-m" "pip" "install"
+ (string-append "--prefix=" #$output)
+ wheel)))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "pytest" "-vv")))))))
(propagated-inputs (list python-pandas python-matplotlib python-numpy
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/")
(synopsis "Statistical data visualization")
(description
--
2.37.3