* [bug#41968] [PATCH 0/5] Update python-plotly and python-pandas
@ 2020-06-20 18:22 Pierre Langlois
2020-06-20 18:28 ` [bug#41968] [PATCH 1/5] gnu: deeptools: Deprecate in favor of python-deeptools Pierre Langlois
` (5 more replies)
0 siblings, 6 replies; 9+ messages in thread
From: Pierre Langlois @ 2020-06-20 18:22 UTC (permalink / raw)
To: 41968
Hi Guix!
Recently I wanted to use python-plotly and realized our package could do
with an update, but to do that I also had to update the python-pandas
package otherwise tests wouldn't pass.
So in the end I got 5 patches all together :-).
* gnu: deeptools: Deprecate in favor of python-deeptools.
deeptools and python-deeptools are the same package, I looked at
them since they depend on plotly. I thought I'd merge them as a
drive-by fix.
* gnu: python-pandas: Update to 1.0.5.
I also had to keep versions 0.25 for the python-biom-format package.
* gnu: Add python-retrying.
* gnu: Add python-xarray.
New dependencies.
* gnu: python-plotly: Update to 4.8.1.
I've also had to keep the version 2.4.1 around for the
python-deeptools package.
WDYT?
Thanks,
Pierre
^ permalink raw reply [flat|nested] 9+ messages in thread
* [bug#41968] [PATCH 1/5] gnu: deeptools: Deprecate in favor of python-deeptools.
2020-06-20 18:22 [bug#41968] [PATCH 0/5] Update python-plotly and python-pandas Pierre Langlois
@ 2020-06-20 18:28 ` Pierre Langlois
2020-06-20 18:29 ` [bug#41968] [PATCH 2/5] gnu: python-pandas: Update to 1.0.5 Pierre Langlois
` (4 subsequent siblings)
5 siblings, 0 replies; 9+ messages in thread
From: Pierre Langlois @ 2020-06-20 18:28 UTC (permalink / raw)
To: 41968; +Cc: Pierre Langlois
[-- Attachment #1: 0001-gnu-deeptools-Deprecate-in-favor-of-python-deeptools.patch --]
[-- Type: text/x-patch, Size: 4892 bytes --]
From b46bef2216620ac085bea41762904b16f2c6aec5 Mon Sep 17 00:00:00 2001
From: Pierre Langlois <pierre.langlois@gmx.com>
Date: Sat, 20 Jun 2020 18:42:04 +0200
Subject: [PATCH 1/5] gnu: deeptools: Deprecate in favor of python-deeptools.
And make sure python-deeptools's tests are running.
* gnu/packages/bioinformatics.scm (python-deeptools): Fetch source using git.
[native-inputs]: Add python-mock and python-nose.
(deeptools): Mark as deprecated.
---
gnu/packages/bioinformatics.scm | 61 +++++++--------------------------
1 file changed, 13 insertions(+), 48 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 95f8b16db3..580488fc49 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -17,6 +17,7 @@
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
+;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -53,6 +54,7 @@
#:use-module (guix build-system ruby)
#:use-module (guix build-system scons)
#:use-module (guix build-system trivial)
+ #:use-module (guix deprecation)
#:use-module (gnu packages)
#:use-module (gnu packages autotools)
#:use-module (gnu packages algebra)
@@ -2406,12 +2408,18 @@ interval trees with associated meta-data. It is primarily used by the
(name "python-deeptools")
(version "3.4.3")
(source (origin
- (method url-fetch)
- (uri (pypi-uri "deepTools" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/deeptools/deepTools.git")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "1azgjniss5ff6a90nicdjkxyjwqmi3gzfn09gra42hwlz19hipxb"))))
+ "0l09vyynz6s6w7fnyd94rpys4a6aja6kp4gli64pngdxdz3md1nl"))))
(build-system python-build-system)
+ (native-inputs
+ `(("python-mock" ,python-mock)
+ ("python-nose" ,python-nose)))
(propagated-inputs
`(("python-matplotlib" ,python-matplotlib)
("python-numpy" ,python-numpy)
@@ -2436,6 +2444,8 @@ annotations of the genome.")
;; remainder of the code is licensed under the MIT license.
(license (list license:bsd-3 license:expat))))
+(define-deprecated deeptools python-deeptools)
+
(define-public cutadapt
(package
(name "cutadapt")
@@ -2599,51 +2609,6 @@ trees (phylogenies) and characters.")
with Python.")
(license license:expat)))
-(define-public deeptools
- (package
- (name "deeptools")
- (version "3.1.3")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/deeptools/deepTools.git")
- (commit version)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "1vggnf52g6q2vifdl4cyi7s2fnfqq0ky2zrkj5zv2qfzsc3p3siw"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- ;; This phase fails, but it's not needed.
- (delete 'reset-gzip-timestamps))))
- (inputs
- `(("python-plotly" ,python-plotly)
- ("python-scipy" ,python-scipy)
- ("python-numpy" ,python-numpy)
- ("python-numpydoc" ,python-numpydoc)
- ("python-matplotlib" ,python-matplotlib)
- ("python-pysam" ,python-pysam)
- ("python-py2bit" ,python-py2bit)
- ("python-pybigwig" ,python-pybigwig)))
- (native-inputs
- `(("python-mock" ,python-mock) ;for tests
- ("python-nose" ,python-nose) ;for tests
- ("python-pytz" ,python-pytz))) ;for tests
- (home-page "https://github.com/deeptools/deepTools")
- (synopsis "Tools for normalizing and visualizing deep-sequencing data")
- (description
- "DeepTools addresses the challenge of handling the large amounts of data
-that are now routinely generated from DNA sequencing centers. To do so,
-deepTools contains useful modules to process the mapped reads data to create
-coverage files in standard bedGraph and bigWig file formats. By doing so,
-deepTools allows the creation of normalized coverage files or the comparison
-between two files (for example, treatment and control). Finally, using such
-normalized and standardized files, multiple visualizations can be created to
-identify enrichments with functional annotations of the genome.")
- (license license:gpl3+)))
-
(define-public delly
(package
(name "delly")
--
2.26.2
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [bug#41968] [PATCH 2/5] gnu: python-pandas: Update to 1.0.5.
2020-06-20 18:22 [bug#41968] [PATCH 0/5] Update python-plotly and python-pandas Pierre Langlois
2020-06-20 18:28 ` [bug#41968] [PATCH 1/5] gnu: deeptools: Deprecate in favor of python-deeptools Pierre Langlois
@ 2020-06-20 18:29 ` Pierre Langlois
2020-06-20 18:30 ` [bug#41968] [PATCH 3/5] gnu: Add python-retrying Pierre Langlois
` (3 subsequent siblings)
5 siblings, 0 replies; 9+ messages in thread
From: Pierre Langlois @ 2020-06-20 18:29 UTC (permalink / raw)
To: 41968; +Cc: Pierre Langlois
[-- Attachment #1: 0002-gnu-python-pandas-Update-to-1.0.5.patch --]
[-- Type: text/x-patch, Size: 7568 bytes --]
From 6b7633a973970e0148fa18007a1fd378a6664a6b Mon Sep 17 00:00:00 2001
From: Pierre Langlois <pierre.langlois@gmx.com>
Date: Thu, 18 Jun 2020 00:58:41 +0200
Subject: [PATCH 2/5] gnu: python-pandas: Update to 1.0.5.
But also keep version 0.25.3 around for packages requiring an earlier
versions, as well as version 0.24.2 for a version with python2.
* gnu/packages/python-science.scm (python-pandas): Update to 1.0.5.
[arguments]: Adapt 'patch-which phase. Add new 'prepare-x phase. Do not
delete tests that depend on "moto", they are skipped automatically.
[propagated-inputs]: Add python-jinja2.
[inputs]: Add xsel and xclip.
[native-inputs]: Add xorg-server-for-tests so we can test clipboard support.
(python-pandas-0.24): New variable.
(python2-pandas): Inherit from python-pandas-0.25.
* gnu/packages/bioinformatics.scm (python-biom-format)[propagated-inputs]:
Switch to python-pandas-0.25.
---
gnu/packages/bioinformatics.scm | 4 +-
gnu/packages/python-science.scm | 65 ++++++++++++++++++++++++---------
2 files changed, 50 insertions(+), 19 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 580488fc49..3ee134db77 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -943,7 +943,9 @@ Python.")
("python-future" ,python-future)
("python-click" ,python-click)
("python-h5py" ,python-h5py)
- ("python-pandas" ,python-pandas)))
+ ;; FIXME: Upgrade to pandas 1.0 when
+ ;; https://github.com/biocore/biom-format/issues/837 is resolved.
+ ("python-pandas" ,python-pandas-0.25)))
(native-inputs
`(("python-cython" ,python-cython)
("python-pytest" ,python-pytest)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 2f7516b9f6..55fc1be4f9 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -8,6 +8,7 @@
;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
+;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -37,7 +38,9 @@
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages sphinx)
#:use-module (gnu packages time)
+ #:use-module (gnu packages xdisorg)
#:use-module (gnu packages xml)
+ #:use-module (gnu packages xorg)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix utils)
@@ -231,13 +234,13 @@ Cython.")
(define-public python-pandas
(package
(name "python-pandas")
- (version "0.25.2")
+ (version "1.0.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pandas" version))
(sha256
- (base32 "1gp2pvzdiakvgjmykdzdlzrsfbg4vjm49jjdl9s0ha0a3yfs34fa"))))
+ (base32 "1a2gv3g6jr6vb5ca43fkwjl5xf86wpfz8y3zcy787adjl0hdkib9"))))
(build-system python-build-system)
(arguments
`(#:modules ((guix build utils)
@@ -249,8 +252,15 @@ Cython.")
(lambda* (#:key inputs #:allow-other-keys)
(let ((which (assoc-ref inputs "which")))
(substitute* "pandas/io/clipboard/__init__.py"
- (("^CHECK_CMD = .*")
- (string-append "CHECK_CMD = \"" which "\"\n"))))
+ (("^WHICH_CMD = .*")
+ (string-append "WHICH_CMD = \"" which "\"\n"))))
+ #t))
+ (add-before 'check 'prepare-x
+ (lambda _
+ (system "Xvfb &")
+ (setenv "DISPLAY" ":0")
+ ;; xsel needs to write a log file.
+ (setenv "HOME" "/tmp")
#t))
(replace 'check
(lambda _
@@ -265,25 +275,19 @@ Cython.")
(substitute* "setup.cfg"
(("addopts = --strict-data-files") "addopts = "))
(with-directory-excursion build-directory
- ;; Delete tests that require "moto" which is not yet
- ;; in Guix.
- (for-each delete-file
- '("pandas/tests/io/conftest.py"
- "pandas/tests/io/json/test_compression.py"
- "pandas/tests/io/parser/test_network.py"
- "pandas/tests/io/test_parquet.py"))
(invoke "pytest" "-vv" "pandas" "--skip-slow"
- "--skip-network" "-k"
- ;; XXX: Due to the deleted tests above.
- "not test_read_s3_jsonl"))))))))
+ "--skip-network"))))))))
(propagated-inputs
- `(("python-numpy" ,python-numpy)
+ `(("python-jinja2" ,python-jinja2)
+ ("python-numpy" ,python-numpy)
("python-openpyxl" ,python-openpyxl)
("python-pytz" ,python-pytz)
("python-dateutil" ,python-dateutil)
("python-xlrd" ,python-xlrd)))
(inputs
- `(("which" ,which)))
+ `(("which" ,which)
+ ("xclip" ,xclip)
+ ("xsel" ,xsel)))
(native-inputs
`(("python-cython" ,python-cython)
("python-beautifulsoup4" ,python-beautifulsoup4)
@@ -291,7 +295,9 @@ Cython.")
("python-html5lib" ,python-html5lib)
("python-nose" ,python-nose)
("python-pytest" ,python-pytest)
- ("python-pytest-mock" ,python-pytest-mock)))
+ ("python-pytest-mock" ,python-pytest-mock)
+ ;; Needed to test clipboard support.
+ ("xorg-server" ,xorg-server-for-tests)))
(home-page "https://pandas.pydata.org")
(synopsis "Data structures for data analysis, time series, and statistics")
(description
@@ -303,10 +309,33 @@ doing practical, real world data analysis in Python.")
(properties `((python2-variant . ,(delay python2-pandas))))
(license license:bsd-3)))
+(define-public python-pandas-0.25
+ (package
+ (inherit python-pandas)
+ (version "0.25.3")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "pandas" version))
+ (sha256
+ (base32
+ "191048m6kdc6yfvqs9w412lq60cfvigrsb57y0x116lwibgp9njj"))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments python-pandas)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (replace 'patch-which
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((which (assoc-ref inputs "which")))
+ (substitute* "pandas/io/clipboard/__init__.py"
+ (("^CHECK_CMD = .*")
+ (string-append "CHECK_CMD = \"" which "\"\n"))))
+ #t))
+ (delete 'prepare-x)))))))
+
;; Pandas 0.24.x are the last versions that support Python 2.
(define-public python2-pandas
(let ((pandas (package-with-python2
- (strip-python2-variant python-pandas))))
+ (strip-python2-variant python-pandas-0.25))))
(package
(inherit pandas)
(version "0.24.2")
--
2.26.2
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [bug#41968] [PATCH 3/5] gnu: Add python-retrying.
2020-06-20 18:22 [bug#41968] [PATCH 0/5] Update python-plotly and python-pandas Pierre Langlois
2020-06-20 18:28 ` [bug#41968] [PATCH 1/5] gnu: deeptools: Deprecate in favor of python-deeptools Pierre Langlois
2020-06-20 18:29 ` [bug#41968] [PATCH 2/5] gnu: python-pandas: Update to 1.0.5 Pierre Langlois
@ 2020-06-20 18:30 ` Pierre Langlois
2020-06-20 18:30 ` [bug#41968] [PATCH 4/5] gnu: Add python-xarray Pierre Langlois
` (2 subsequent siblings)
5 siblings, 0 replies; 9+ messages in thread
From: Pierre Langlois @ 2020-06-20 18:30 UTC (permalink / raw)
To: 41968; +Cc: Pierre Langlois
[-- Attachment #1: 0003-gnu-Add-python-retrying.patch --]
[-- Type: text/x-patch, Size: 2562 bytes --]
From f5ab03bda4a872db340349ef837776314501513e Mon Sep 17 00:00:00 2001
From: Pierre Langlois <pierre.langlois@gmx.com>
Date: Thu, 18 Jun 2020 00:57:49 +0200
Subject: [PATCH 3/5] gnu: Add python-retrying.
* gnu/packages/python-xyz.scm (python-retrying): New variable.
---
gnu/packages/python-xyz.scm | 35 ++++++++++++++++++++++++++++++++++-
1 file changed, 34 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e95dec21c2..4a22b42ac2 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -61,7 +61,7 @@
;;; Copyright © 2019 Jack Hill <jackhill@jackhill.us>
;;; Copyright © 2019, 2020 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2019, 2020 Alex Griffin <a@ajgrf.com>
-;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
+;;; Copyright © 2019, 2020 Pierre Langlois <pierre.langlois@gmx.com>
;;; Copyright © 2019 Jacob MacDonald <jaccarmac@gmail.com>
;;; Copyright © 2019, 2020 Giacomo Leidi <goodoldpaul@autistici.org>
;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
@@ -17701,6 +17701,39 @@ on regular expressions.")
`(("python2-enum34" ,python2-enum34)
,@(package-propagated-inputs reparser))))))
+(define-public python-retrying
+ (package
+ (name "python-retrying")
+ (version "1.3.3")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/rholder/retrying.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1kqipkbdaw5s1xg0gi29awm03vp1x8dz24pjidgxagvkvrjpzhi7"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-six" ,python-six)))
+ (home-page "https://github.com/rholder/retrying")
+ (synopsis "Library for adding retry behavior")
+ (description "Retrying is a general-purpose retrying library to simplify
+the task of adding retry behavior to just about anything.
+
+Features:
+
+@itemize
+@item Generic Decorator API.
+@item Specify stop condition (i.e. limit by number of attempts).
+@item Specify wait condition (i.e. exponential backoff sleeping between attempts).
+@item Customize retrying on Exceptions.
+@item Customize retrying on expected returned result.
+@end itemize")
+ (license license:asl2.0)))
+
(define-public python-precis-i18n
(package
(name "python-precis-i18n")
--
2.26.2
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [bug#41968] [PATCH 4/5] gnu: Add python-xarray.
2020-06-20 18:22 [bug#41968] [PATCH 0/5] Update python-plotly and python-pandas Pierre Langlois
` (2 preceding siblings ...)
2020-06-20 18:30 ` [bug#41968] [PATCH 3/5] gnu: Add python-retrying Pierre Langlois
@ 2020-06-20 18:30 ` Pierre Langlois
2020-06-20 18:31 ` [bug#41968] [PATCH 5/5] gnu: python-plotly: Update to 4.8.1 Pierre Langlois
[not found] ` <handler.41968.B.15926773811621.ack@debbugs.gnu.org>
5 siblings, 0 replies; 9+ messages in thread
From: Pierre Langlois @ 2020-06-20 18:30 UTC (permalink / raw)
To: 41968; +Cc: Pierre Langlois
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #1: 0004-gnu-Add-python-xarray.patch --]
[-- Type: text/x-patch, Size: 2247 bytes --]
From 27ec21904f769c1e8114f767972d9037e1e9f68a Mon Sep 17 00:00:00 2001
From: Pierre Langlois <pierre.langlois@gmx.com>
Date: Thu, 18 Jun 2020 00:58:02 +0200
Subject: [PATCH 4/5] gnu: Add python-xarray.
* gnu/package/python-science.scm (python-xarray): New variable.
---
gnu/packages/python-science.scm | 35 +++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 55fc1be4f9..9348894530 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -354,3 +354,38 @@ doing practical, real world data analysis in Python.")
(("if 'NULL byte' in msg:")
"if 'NULL byte' in msg or 'line contains NUL' in msg:"))
#t)))))))
+
+(define-public python-xarray
+ (package
+ (name "python-xarray")
+ (version "0.15.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "xarray" version))
+ (sha256
+ (base32
+ "1yx8j66b7rn10m2l6gmn8yr9cn38pi5cj0x0wwpy4hdnhy6i7qv4"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-setuptools-scm" ,python-setuptools-scm)
+ ("python-pytest" ,python-pytest)))
+ (propagated-inputs
+ `(("python-numpy" ,python-numpy)
+ ("python-pandas" ,python-pandas)))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (invoke "pytest"))))))
+ (home-page "https://github.com/pydata/xarray")
+ (synopsis "N-D labeled arrays and datasets")
+ (description "Xarray (formerly xray) makes working with labelled
+multi-dimensional arrays simple, efficient, and fun!
+
+Xarray introduces labels in the form of dimensions, coordinates and attributes
+on top of raw NumPy-like arrays, which allows for a more intuitive, more
+concise, and less error-prone developer experience. The package includes a
+large and growing library of domain-agnostic functions for advanced analytics
+and visualization with these data structures.")
+ (license license:asl2.0)))
--
2.26.2
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [bug#41968] [PATCH 5/5] gnu: python-plotly: Update to 4.8.1.
2020-06-20 18:22 [bug#41968] [PATCH 0/5] Update python-plotly and python-pandas Pierre Langlois
` (3 preceding siblings ...)
2020-06-20 18:30 ` [bug#41968] [PATCH 4/5] gnu: Add python-xarray Pierre Langlois
@ 2020-06-20 18:31 ` Pierre Langlois
[not found] ` <handler.41968.B.15926773811621.ack@debbugs.gnu.org>
5 siblings, 0 replies; 9+ messages in thread
From: Pierre Langlois @ 2020-06-20 18:31 UTC (permalink / raw)
To: 41968; +Cc: Pierre Langlois
[-- Attachment #1: 0005-gnu-python-plotly-Update-to-4.8.1.patch --]
[-- Type: text/x-patch, Size: 5802 bytes --]
From a1526919f28d8ea4a958ef3b672b3187c8c3bd82 Mon Sep 17 00:00:00 2001
From: Pierre Langlois <pierre.langlois@gmx.com>
Date: Thu, 18 Jun 2020 00:59:09 +0200
Subject: [PATCH 5/5] gnu: python-plotly: Update to 4.8.1.
But keep version 2.4.1 around for packages that still need it and for python2
support.
* gnu/packages/graph.scm (python-plotly): Update to 4.8.1.
[source]: Use git-fetch so that tests are also included.
[arguments]: Enable tests.
[home-page]: Follow redirect.
(python-plotly-2.4.1): New variable.
(python2-plotly): Inherit from python-plotly-2.4.1.
* gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Depend on
python-plotly-2.4.1.
---
gnu/packages/bioinformatics.scm | 2 +-
gnu/packages/graph.scm | 74 ++++++++++++++++++++++++++-------
2 files changed, 61 insertions(+), 15 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3ee134db77..ce54c613b0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2431,7 +2431,7 @@ interval trees with associated meta-data. It is primarily used by the
("python-pysam" ,python-pysam)
("python-scipy" ,python-scipy)
("python-deeptoolsintervals" ,python-deeptoolsintervals)
- ("python-plotly" ,python-plotly)))
+ ("python-plotly" ,python-plotly-2.4.1)))
(home-page "https://pypi.org/project/deepTools/")
(synopsis "Useful tools for exploring deep sequencing data")
(description "This package addresses the challenge of handling large amounts
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index dc8f2c64a2..762ee30632 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -5,6 +5,7 @@
;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2020 Alexander Krotov <krotov@iitp.ru>
+;;; Copyright © 2020 Pierre Langlois <pierre.langlos@gmx.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -235,25 +236,49 @@ lines.")
(define-public python-plotly
(package
(name "python-plotly")
- (version "2.4.1")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "plotly" version))
- (sha256
- (base32
- "0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
+ (version "4.8.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/plotly/plotly.py.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "08ab677gr85m10zhixr6dnmlfws8q6sra7nhyb8nf3r8dx1ffqhz"))))
(build-system python-build-system)
(arguments
- '(#:tests? #f)) ; The tests are not distributed in the release
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'chdir
+ (lambda _
+ (chdir "packages/python/plotly")
+ #t))
+ (replace 'check
+ (lambda _
+ (invoke "pytest" "-x" "plotly/tests/test_core")
+ (invoke "pytest" "-x" "plotly/tests/test_io")
+ ;; FIXME: Add optional dependencies and enable their tests.
+ ;; (invoke "pytest" "-x" "plotly/tests/test_optional")
+ (invoke "pytest" "_plotly_utils/tests")))
+ (add-before 'reset-gzip-timestamps 'make-files-writable
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (for-each (lambda (file) (chmod file #o644))
+ (find-files out "\\.gz"))
+ #t))))))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
(propagated-inputs
`(("python-decorator" ,python-decorator)
- ("python-nbformat" ,python-nbformat)
+ ("python-ipywidgets" ,python-ipywidgets)
("python-pandas" ,python-pandas)
- ("python-pytz" ,python-pytz)
("python-requests" ,python-requests)
- ("python-six" ,python-six)))
- (home-page "https://plot.ly/python/")
+ ("python-retrying" ,python-retrying)
+ ("python-six" ,python-six)
+ ("python-statsmodels" ,python-statsmodels)
+ ("python-xarray" ,python-xarray)))
+ (home-page "https://plotly.com/python/")
(synopsis "Interactive plotting library for Python")
(description "Plotly's Python graphing library makes interactive,
publication-quality graphs online. Examples of how to make line plots, scatter
@@ -261,8 +286,29 @@ plots, area charts, bar charts, error bars, box plots, histograms, heatmaps,
subplots, multiple-axes, polar charts, and bubble charts. ")
(license license:expat)))
+(define-public python-plotly-2.4.1
+ (package (inherit python-plotly)
+ (version "2.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "plotly" version))
+ (sha256
+ (base32
+ "0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
+ (native-inputs '())
+ (propagated-inputs
+ `(("python-decorator" ,python-decorator)
+ ("python-nbformat" ,python-nbformat)
+ ("python-pandas" ,python-pandas)
+ ("python-pytz" ,python-pytz)
+ ("python-requests" ,python-requests)
+ ("python-six" ,python-six)))
+ (arguments
+ '(#:tests? #f)))) ; The tests are not distributed in the release
+
(define-public python2-plotly
- (package-with-python2 python-plotly))
+ (package-with-python2 python-plotly-2.4.1))
(define-public python-louvain
(package
--
2.26.2
^ permalink raw reply related [flat|nested] 9+ messages in thread
* bug#41968: Acknowledgement ([PATCH 0/5] Update python-plotly and python-pandas)
[not found] ` <handler.41968.B.15926773811621.ack@debbugs.gnu.org>
@ 2020-06-22 16:44 ` Pierre Langlois
2020-06-24 19:08 ` [bug#41968] " Marius Bakke
0 siblings, 1 reply; 9+ messages in thread
From: Pierre Langlois @ 2020-06-22 16:44 UTC (permalink / raw)
To: 41968-done; +Cc: Pierre Langlois, Ludovic Courtès
Thanks for merging Ludo!
Closing.
Pierre
^ permalink raw reply [flat|nested] 9+ messages in thread
* [bug#41968] Acknowledgement ([PATCH 0/5] Update python-plotly and python-pandas)
2020-06-22 16:44 ` bug#41968: Acknowledgement ([PATCH 0/5] Update python-plotly and python-pandas) Pierre Langlois
@ 2020-06-24 19:08 ` Marius Bakke
2020-06-26 3:20 ` Leo Famulari
0 siblings, 1 reply; 9+ messages in thread
From: Marius Bakke @ 2020-06-24 19:08 UTC (permalink / raw)
To: Pierre Langlois, 41968-done; +Cc: Pierre Langlois, Ludovic Courtès
[-- Attachment #1: Type: text/plain, Size: 212 bytes --]
Pierre Langlois <pierre.langlois@gmx.com> writes:
> Thanks for merging Ludo!
By the way, consider applying for commit access, as you have delivered a
steady stream of quality patches. I'll vouch for you. :-)
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^ permalink raw reply [flat|nested] 9+ messages in thread
* [bug#41968] Acknowledgement ([PATCH 0/5] Update python-plotly and python-pandas)
2020-06-24 19:08 ` [bug#41968] " Marius Bakke
@ 2020-06-26 3:20 ` Leo Famulari
0 siblings, 0 replies; 9+ messages in thread
From: Leo Famulari @ 2020-06-26 3:20 UTC (permalink / raw)
To: Marius Bakke; +Cc: Pierre Langlois, Ludovic Courtès, 41968-done
[-- Attachment #1: Type: text/plain, Size: 309 bytes --]
On Wed, Jun 24, 2020 at 09:08:00PM +0200, Marius Bakke wrote:
> Pierre Langlois <pierre.langlois@gmx.com> writes:
>
> > Thanks for merging Ludo!
>
> By the way, consider applying for commit access, as you have delivered a
> steady stream of quality patches. I'll vouch for you. :-)
Yes, please!
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^ permalink raw reply [flat|nested] 9+ messages in thread
end of thread, other threads:[~2020-06-26 3:22 UTC | newest]
Thread overview: 9+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2020-06-20 18:22 [bug#41968] [PATCH 0/5] Update python-plotly and python-pandas Pierre Langlois
2020-06-20 18:28 ` [bug#41968] [PATCH 1/5] gnu: deeptools: Deprecate in favor of python-deeptools Pierre Langlois
2020-06-20 18:29 ` [bug#41968] [PATCH 2/5] gnu: python-pandas: Update to 1.0.5 Pierre Langlois
2020-06-20 18:30 ` [bug#41968] [PATCH 3/5] gnu: Add python-retrying Pierre Langlois
2020-06-20 18:30 ` [bug#41968] [PATCH 4/5] gnu: Add python-xarray Pierre Langlois
2020-06-20 18:31 ` [bug#41968] [PATCH 5/5] gnu: python-plotly: Update to 4.8.1 Pierre Langlois
[not found] ` <handler.41968.B.15926773811621.ack@debbugs.gnu.org>
2020-06-22 16:44 ` bug#41968: Acknowledgement ([PATCH 0/5] Update python-plotly and python-pandas) Pierre Langlois
2020-06-24 19:08 ` [bug#41968] " Marius Bakke
2020-06-26 3:20 ` Leo Famulari
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