GNU bug report logs - #49541
[PATCH 0/2] Add python-pingouin

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Arun Isaac <arunisaac <at> systemreboot.net>
To: guix-patches <at> gnu.org
Cc: "Bonface Munyoki K ." <me <at> bonfacemunyoki.com>,
 Arun Isaac <arunisaac <at> systemreboot.net>
Subject: [PATCH 0/2] Add python-pingouin
Date: Tue, 13 Jul 2021 15:12:40 +0530

Hi,

This patchset adds python-pingouin.

Off list, Bonface expressed interest in reviewing these patches. So, CCing
them here.

Regards,
Arun

Arun Isaac (2):
  gnu: Add python-pandas-flavor.
  gnu: Add python-pingouin.

 gnu/packages/python-science.scm | 102 ++++++++++++++++++++++++++++++++
 1 file changed, 102 insertions(+)

-- 
2.32.0

Message #8 received at 49541 <at> debbugs.gnu.org (full text, mbox):

From: Arun Isaac <arunisaac <at> systemreboot.net>
To: 49541 <at> debbugs.gnu.org
Cc: "Bonface Munyoki K ." <me <at> bonfacemunyoki.com>,
 Arun Isaac <arunisaac <at> systemreboot.net>
Subject: [PATCH 1/2] gnu: Add python-pandas-flavor.
Date: Tue, 13 Jul 2021 15:19:50 +0530

* gnu/packages/python-science.scm (python-pandas-flavor): New variable.
---
 gnu/packages/python-science.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index d2c4caac3a..1292781f2b 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -13,6 +13,7 @@
 ;;; Copyright © 2021 Greg Hogan <code <at> greghogan.com>
 ;;; Copyright © 2021 Roel Janssen <roel <at> gnu.org>
 ;;; Copyright © 2021 Paul Garlick <pgarlick <at> tourbillion-technology.com>
+;;; Copyright © 2021 Arun Isaac <arunisaac <at> systemreboot.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -733,3 +734,30 @@ dependencies.")
                    license:silofl1.1
                    license:cc0
                    license:public-domain))))
+
+(define-public python-pandas-flavor
+  (package
+    (name "python-pandas-flavor")
+    (version "0.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pandas_flavor" version))
+       (sha256
+        (base32
+         "12g4av8gpl6l83yza3h97j3f2jblqv69frlidrvdq8ny2rc6awbq"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-pandas" ,python-pandas)
+       ("python-xarray" ,python-xarray)))
+    (home-page "https://github.com/Zsailer/pandas_flavor")
+    (synopsis "Write your own flavor of Pandas")
+    (description "Pandas 0.23 added a simple API for registering accessors
+with Pandas objects.  Pandas-flavor extends Pandas' extension API by
+
+@itemize
+@item adding support for registering methods as well
+@item making each of these functions backwards compatible with older versions
+of Pandas
+@end itemize")
+    (license license:expat)))
-- 
2.32.0

Message #11 received at 49541 <at> debbugs.gnu.org (full text, mbox):

From: Arun Isaac <arunisaac <at> systemreboot.net>
To: 49541 <at> debbugs.gnu.org
Cc: "Bonface Munyoki K ." <me <at> bonfacemunyoki.com>,
 Arun Isaac <arunisaac <at> systemreboot.net>
Subject: [PATCH 2/2] gnu: Add python-pingouin.
Date: Tue, 13 Jul 2021 15:19:51 +0530

* gnu/packages/python-science.scm (python-pingouin): New variable.
---
 gnu/packages/python-science.scm | 74 +++++++++++++++++++++++++++++++++
 1 file changed, 74 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 1292781f2b..6fce8d2319 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -37,6 +37,7 @@
   #:use-module (gnu packages check)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages image-processing)
+  #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages perl)
@@ -48,6 +49,7 @@
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages simulation)
   #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages statistics)
   #:use-module (gnu packages time)
   #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages xml)
@@ -761,3 +763,75 @@ with Pandas objects.  Pandas-flavor extends Pandas' extension API by
 of Pandas
 @end itemize")
     (license license:expat)))
+
+(define-public python-pingouin
+  (package
+    (name "python-pingouin")
+    (version "0.3.12")
+    (source
+     ;; The PyPI tarball does not contain the tests.
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/raphaelvallat/pingouin")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1ap29x54kdr19vi8qxj9g6cz2r1q4f0z7dcf6g77zwav7hf7r61a"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; On loading, Pingouin uses the outdated package to check if a newer
+         ;; version is available on PyPI. This check adds an extra dependency
+         ;; and is irrelevant to Guix users. So, disable it.
+         (add-after 'unpack 'remove-outdated-check
+           (lambda _
+             (substitute* "setup.py"
+               (("'outdated',") ""))
+             (substitute* "pingouin/__init__.py"
+               (("^from outdated[^\n]*") "")
+               (("^warn_if_outdated[^\n]*") ""))))
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "pytest")))))))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)))
+    (propagated-inputs
+     `(("python-matplotlib" ,python-matplotlib)
+       ("python-mpmath" ,python-mpmath)
+       ("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-pandas-flavor" ,python-pandas-flavor)
+       ("python-scikit-learn" ,python-scikit-learn)
+       ("python-scipy" ,python-scipy)
+       ("python-seaborn" ,python-seaborn)
+       ("python-statsmodels" ,python-statsmodels)
+       ("python-tabulate" ,python-tabulate)))
+    (home-page "https://pingouin-stats.org/")
+    (synopsis "Statistical package for Python")
+    (description "Pingouin is a statistical package written in Python 3 and
+based mostly on Pandas and NumPy.  Its features include
+
+@itemize
+@item ANOVAs: N-ways, repeated measures, mixed, ancova
+@item Pairwise post-hocs tests (parametric and non-parametric) and pairwise
+correlations
+@item Robust, partial, distance and repeated measures correlations
+@item Linear/logistic regression and mediation analysis
+@item Bayes Factors
+@item Multivariate tests
+@item Reliability and consistency
+@item Effect sizes and power analysis
+@item Parametric/bootstrapped confidence intervals around an effect size or a
+correlation coefficient
+@item Circular statistics
+@item Chi-squared tests
+@item Plotting: Bland-Altman plot, Q-Q plot, paired plot, robust correlation,
+and more
+@end itemize")
+    (license license:gpl3)))
+
-- 
2.32.0

Message #14 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Bonface Munyoki K. <me <at> bonfacemunyoki.com>
To: Arun Isaac <arunisaac <at> systemreboot.net>
Cc: guix-patches <at> gnu.org
Subject: Re: [PATCH 0/2] Add python-pingouin
Date: Tue, 13 Jul 2021 13:21:36 +0300

[Message part 1 (text/plain, inline)]

Ola o/

Arun Isaac <arunisaac <at> systemreboot.net> anaandika:

> Hi,
>
> This patchset adds python-pingouin.
>
> Off list, Bonface expressed interest in reviewing these patches. So, CCing
> them here.
>

Thanks for tagging me! LGTM; Both packages build
for me. Thanks for packaging these.

> Regards,
> Arun
>
> Arun Isaac (2):
>   gnu: Add python-pandas-flavor.
>   gnu: Add python-pingouin.
>
>  gnu/packages/python-science.scm | 102 ++++++++++++++++++++++++++++++++
>  1 file changed, 102 insertions(+)

-- 
Bonface M. K. D4F09EB110177E03C28E2FE1F5BBAE1E0392253F
Free Software Activist
Humble GNU Emacs User | Bearer of scheme-y parens
Curator: <https://upbookclub.com> | Twitter: @BonfaceKilz

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Message #19 received at 49541-done <at> debbugs.gnu.org (full text, mbox):

From: Arun Isaac <arunisaac <at> systemreboot.net>
To: "Bonface Munyoki K." <me <at> bonfacemunyoki.com>
Cc: 49541-done <at> debbugs.gnu.org
Subject: Re: [PATCH 0/2] Add python-pingouin
Date: Tue, 13 Jul 2021 17:16:18 +0530

[Message part 1 (text/plain, inline)]

Thanks for the review. Pushed to master!

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