From 00c1d79a4ce31260315afcb60cbef7edd05edf51 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sat, 3 Dec 2022 12:59:50 -0300 Subject: gnu: python-funcpaserlib: Update to 1.0.1. * gnu/packages/python-xyz.scm (python-funcpaserlib): Update to 1.0.1. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 40c3f9c99c..2292df6037 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -25544,7 +25544,7 @@ (define-public python-fastentrypoints (define-public python-funcparserlib (package (name "python-funcparserlib") - (version "1.0.0") + (version "1.0.1") (source (origin ;; Source tarball on PyPi lacks tests. @@ -25554,7 +25554,7 @@ (define-public python-funcparserlib (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "00pswdys5c4hpqpvfcy5zqv30gyjvjvagi12811jizw57hxrm1cs")))) + (base32 "0dw3i4fyf3j9h1l7xfgs99fc2w2axk6xqk0sdag43k444ss4hkrc")))) (build-system pyproject-build-system) (arguments '(#:phases -- cgit v1.2.3 From 0f89d91411f68fbac0e020fbfe92a6bf880065ac Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Mon, 14 Nov 2022 11:53:06 -0300 Subject: gnu: python-hy: Update to 0.25.0. * gnu/packages/python-xyz.scm (python-hy): Update to 0.25.0. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 2292df6037..0f47e3be4f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14779,7 +14779,7 @@ (define-public python-rply (define-public python-hy (package (name "python-hy") - (version "0.24.0") + (version "0.25.0") (source (origin (method git-fetch) ; no tests in PyPI release @@ -14788,7 +14788,7 @@ (define-public python-hy (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1s458ymd9g3s8k2ccc300jr4w66c7q3vhmhs9z3d3a4qg0xdhs9y")))) + (base32 "1am6z9m0s9svysj0wrfz069rpvbqqimphqll3912q4bvdlz6vrjp")))) (build-system python-build-system) (arguments '(#:phases -- cgit v1.2.3 From f635f725778f86abaa77f674f8f670f74bffd7be Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 6 Dec 2022 11:12:15 +0200 Subject: gnu: vdirsyncer: Update to 0.19.0. * gnu/packages/dav.scm (vdirsyncer): Update to 0.19.0. [arguments]: Remove trailing #t in phases. Remove phase generating the manpage. [native-inputs]: Add python-aioresponses, python-click, python-trustme, python-pytest-asyncio, python-pytest-cov, python-pytest-httpserver. Remove python-pytest-localserver, python-pytest-subtesthack, python-urllib3, python-wsgi-interpreter. [inputs]: Remove field. [propagated-inputs]: Add python-aiohttp, python-aiostream. Remove python-click-threading. * gnu/packages/python-xyz.scm (python-click-5): Remove variable. --- gnu/packages/dav.scm | 39 +++++++++++++++------------------------ gnu/packages/python-xyz.scm | 12 ------------ 2 files changed, 15 insertions(+), 36 deletions(-) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm index 9a336b381e..775a3d9bed 100644 --- a/gnu/packages/dav.scm +++ b/gnu/packages/dav.scm @@ -122,14 +122,13 @@ (define-public xandikos (define-public vdirsyncer (package (name "vdirsyncer") - ;; When updating, check whether python-click-5 can be removed entirely. - (version "0.18.0") + (version "0.19.0") (source (origin (method url-fetch) (uri (pypi-uri name version)) (sha256 (base32 - "00f2bw1a2jbbd1sbci0swnd67kylr341aa9rpbxkajbp3zakxg17")))) + "0995bavlv8s9j0127ncq3yzy5p72lam9qgpswyjfanc6l01q87lf")))) (build-system python-build-system) (arguments `(#:tests? #f ; The test suite is very flakey. @@ -141,38 +140,30 @@ (define-public vdirsyncer (setenv "DAV_SERVER" "radicale") (setenv "REMOTESTORAGE_SERVER" "skip") (if tests? - (invoke "make" "test") - #t))) + (invoke "make" "test")))) (add-after 'unpack 'patch-version-call (lambda _ (substitute* "docs/conf.py" - (("^release.*") (string-append "release = '" ,version "'\n"))) - #t)) - (add-after 'install 'manpage - (lambda* (#:key inputs outputs #:allow-other-keys) - (invoke "make" "--directory=docs/" "man") - (install-file - "docs/_build/man/vdirsyncer.1" - (string-append - (assoc-ref outputs "out") - "/share/man/man1")) - #t))))) + (("^release.*") (string-append "release = '" ,version "'\n")))))))) (native-inputs (list python-setuptools-scm python-sphinx ;; Required for testing + python-aioresponses python-hypothesis + python-trustme python-pytest - python-pytest-localserver - python-pytest-subtesthack - python-urllib3 - python-wsgi-intercept + python-pytest-asyncio + python-pytest-cov + python-pytest-httpserver radicale)) - (inputs - (list ;; XXX https://github.com/mitsuhiko/click/issues/200 - python-click-5)) (propagated-inputs - (list python-atomicwrites python-click-log python-click-threading + (list python-aiohttp + python-aiostream + python-atomicwrites + python-click + python-click-log + python-requests python-requests-toolbelt)) (synopsis "Synchronize calendars and contacts") (description "Vdirsyncer synchronizes your calendars and addressbooks diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0f47e3be4f..b74b120510 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3671,18 +3671,6 @@ (define-public python-click-7 (base32 "06kbzd6sjfkqan3miwj9wqyddfxc2b6hi7p5s4dvqjb3gif2bdfj")))) (arguments `()))) -(define-public python-click-5 - (package (inherit python-click) - (name "python-click") - (version "5.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "click" version)) - (sha256 - (base32 "0njsm0wn31l21bi118g5825ma5sa3rwn7v2x4wjd7yiiahkri337")))) - (arguments `()))) - (define-public python-cligj (package (name "python-cligj") -- cgit v1.2.3 From db1c357a788fe38de033ef4f7ad4497d72557898 Mon Sep 17 00:00:00 2001 From: Attila Lendvai Date: Tue, 11 Oct 2022 15:10:00 +0200 Subject: gnu: Add python-simple-rlp. * gnu/packages/python-xyz.scm (python-simple-rlp): New variable. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b74b120510..b0202853d8 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3011,6 +3011,29 @@ (define-public python-simplejson Python 3.3+.") (license license:x11))) +(define-public python-simple-rlp + (package + (name "python-simple-rlp") + (version "0.1.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/SamuelHaidu/simple-rlp") + ;; Upstream doesn't tag the git repo. + (commit "342ea269d84da1ddc4a7630cdebc90159261391c"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1nv92sphpkyrncak4qgj50qmgkmj4ycl2szbnv9c7ihgl5df4div")))) + (build-system python-build-system) + (home-page "https://github.com/SamuelHaidu/simple-rlp") + (synopsis + "Python implementation of RLP (Recursive Length Prefix) encoding") + (description + "@code{simple-rlp} is a python implementation of RLP (Recursive Length \ +Prefix) - Encode and decode data structures.") + (license license:expat))) (define-public python-pyicu (package -- cgit v1.2.3 From 6219491c47f20aef6bc8523110936924e4d3d785 Mon Sep 17 00:00:00 2001 From: Peter Polidoro Date: Thu, 13 Oct 2022 15:42:53 -0400 Subject: gnu: Add python-pint. * gnu/packages/python-xyz.scm (python-pint): New variable. Signed-off-by: Christopher Baines --- gnu/packages/python-xyz.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b0202853d8..b830ade9ca 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -924,6 +924,36 @@ (define-public python-pymdown-extensions Markdown. All extensions are found under the module namespace of pymdownx.") (license license:expat))) +(define-public python-pint + (package + (name "python-pint") + (version "0.19.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "Pint" version)) + (sha256 + (base32 + "1bsbiikm9i4saqc6mc3minkmrgnsgcg734agsvd7icqhyngrim71")))) + (build-system python-build-system) + (native-inputs + (list python-pytest + python-pytest-cov + python-pytest-mpl + python-pytest-subtests + python-setuptools-scm + python-sparse + python-dask + python-xarray + python-distributed)) + (home-page "https://github.com/hgrecco/pint") + (synopsis "Physical quantities module") + (description + "Pint is a Python package to define, operate and manipulate physical +quantities: the product of a numerical value and a unit of measurement. It +allows arithmetic operations between them and conversions from and to +different units.") + (license license:bsd-3))) + (define-public python-plotille (package (name "python-plotille") -- cgit v1.2.3 From 2d989ad59793e10c6fef94d9eaa51be91469318a Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Wed, 12 Oct 2022 16:49:17 +0530 Subject: gnu: python-seaborn: Update to 0.12.0. * 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 - gnu/packages/patches/python-seaborn-2690.patch | 268 --------------------- gnu/packages/patches/python-seaborn-kde-test.patch | 36 --- gnu/packages/python-xyz.scm | 51 ++-- 4 files changed, 24 insertions(+), 333 deletions(-) delete mode 100644 gnu/packages/patches/python-seaborn-2690.patch delete mode 100644 gnu/packages/patches/python-seaborn-kde-test.patch (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/local.mk b/gnu/local.mk index af570125bd..6e12f9cdb1 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1759,8 +1759,6 @@ 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 -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 -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 -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 - 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 b830ade9ca..a9b123d4c2 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -10280,40 +10280,37 @@ (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")))) - (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"))))))) + "08vvnp4ps86857imxz2l5xi2vir5xdcdp3apq4badb4b5llifgw9")))) + (build-system python-build-system) + (arguments + (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 -- cgit v1.2.3 From 97cfa1cd7803452977369bc84dc3fc8002ae6541 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Dec 2022 15:13:39 +0100 Subject: gnu: Add python-py4j. * gnu/packages/python-xyz.scm (python-py4j): New variable. --- gnu/packages/python-xyz.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a9b123d4c2..a897bf19f9 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -901,6 +901,24 @@ (define-public python-mkdocs-markdownextradata-plugin variables into the markdown template") (license license:expat))) +(define-public python-py4j + (package + (name "python-py4j") + (version "0.10.9.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "py4j" version)) + (sha256 + (base32 + "1fwdx92cdaiviradksfyygg05g1fpc3x2lf65bv5rnispcam6vhb")))) + (build-system python-build-system) + (home-page "https://www.py4j.org/") + (synopsis "Dynamically access arbitrary Java objects from Python") + (description + "This package enables Python programs to dynamically access arbitrary +Java objects.") + (license license:bsd-3))) + (define-public python-pymdown-extensions (package (name "python-pymdown-extensions") -- cgit v1.2.3 From a88fa1ced73ff320040e3dba58947f91aab6fa02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Dec 2022 18:20:40 +0100 Subject: gnu: Add python-fit-nbinom. * gnu/packages/python-xyz.scm (python-fit-nbinom): New variable. --- gnu/packages/python-xyz.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a897bf19f9..0f0a7ef49f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -565,6 +565,24 @@ (define-public python-fire (home-page "https://github.com/google/python-fire") (license license:asl2.0))) +(define-public python-fit-nbinom + (package + (name "python-fit-nbinom") + (version "1.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "fit_nbinom" version)) + (sha256 + (base32 + "12v8l5i35vjbpvh5i4lw29ys6vpr3z7pysyrx33hxaq09zr015mx")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-numpy python-scipy)) + (home-page "https://github.com/joachimwolff/fit_nbinom") + (synopsis "Negative binomial maximum likelihood estimator") + (description "This package provides an implementation in Python using +scipy and numpy of negative binomial maximum likelihood estimation.") + (license license:gpl3+))) + (define-public python-dotmap (package (name "python-dotmap") -- cgit v1.2.3 From be9e8c3963b45c674a529c7461a4e7933c3efd93 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 11 Dec 2022 13:50:25 +0100 Subject: gnu: Add python-apispec-webframeworks. * gnu/packages/python-xyz.scm (python-apispec-webframeworks): New variable. --- gnu/packages/python-xyz.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0f0a7ef49f..d429a4a734 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20975,6 +20975,34 @@ (define-public python-apispec as Swagger.") (license license:expat))) +(define-public python-apispec-webframeworks + (package + (name "python-apispec-webframeworks") + (version "0.5.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "apispec-webframeworks" version)) + (sha256 + (base32 + "1wyw30402xq2a8icrsjmy9v43jyvawcjd85ccb2zicqlg4k5pcqd")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-apispec)) + (native-inputs + (list python-bottle + python-flake8 + python-flake8-bugbear + python-flask + python-mock + python-pre-commit + python-pytest + python-tornado + python-tox)) + (home-page "https://github.com/marshmallow-code/apispec-webframeworks") + (synopsis "Web framework plugins for apispec") + (description "This package provides plugins for using @code{apispec} with +web frameworks.") + (license license:expat))) + (define-public python-flasgger (package (name "python-flasgger") -- cgit v1.2.3 From bc47a1bf02e9071743d56243ba5aabf4b764afc5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 11 Dec 2022 15:47:18 +0100 Subject: gnu: Add python-pygtrie. * gnu/packages/python-xyz.scm (python-pygtrie): New variable. --- gnu/packages/python-xyz.scm | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index d429a4a734..4298fd4c40 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4978,6 +4978,23 @@ (define-public python-pygments-github-lexers (description "This package installs Github custom lexers to Pygments.") (license license:bsd-3))) +(define-public python-pygtrie + (package + (name "python-pygtrie") + (version "2.5.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "pygtrie" version)) + (sha256 + (base32 + "1qm4xdmzd4q5pc9h5gjdpr5m7lg06k8dvqnjn7d07d3fhani8d90")))) + (build-system pyproject-build-system) + (home-page "https://github.com/mina86/pygtrie") + (synopsis "Pure Python trie data structure implementation") + (description + "This package provides a pure Python trie data structure implementation.") + (license license:asl2.0))) + (define-public python-bump2version (package (name "python-bump2version") -- cgit v1.2.3 From 94e9651241b3e827531779717952d386535801f3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 12 Dec 2022 11:12:27 +0100 Subject: gnu: Add python-pomegranate. * gnu/packages/python-xyz.scm (python-pomegranate): New variable. --- gnu/packages/python-xyz.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu/packages/python-xyz.scm') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4298fd4c40..8591423116 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3320,6 +3320,46 @@ (define-public python-polling2 a certain expected condition.") (license license:expat))) +(define-public python-pomegranate + (package + (name "python-pomegranate") + (version "0.14.8") + (source (origin + (method url-fetch) + (uri (pypi-uri "pomegranate" version)) + (sha256 + (base32 + "0gb9srkbxzlkjyfizvxkw5y0bvnfcyiaxapz0hrdaba8j096b5i2")) + (modules '((guix build utils))) + ;; Delete generated Cython C files. + (snippet + '(for-each delete-file (find-files "." "\\.c$"))))) + (build-system python-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "setup.py" "test"))))))) + (propagated-inputs + (list python-joblib + python-networkx + python-numpy + python-pyyaml + python-scipy)) + (native-inputs + (list python-cython + python-nose + python-pandas)) + (home-page "https://pypi.python.org/pypi/pomegranate/") + (synopsis "Graphical models library for Python") + (description + "Pomegranate is a graphical models library for Python, implemented in +Cython for speed.") + (license license:expat))) + (define-public python-poyo (package (name "python-poyo") -- cgit v1.2.3