[bug#64258] [PATCH 0/2] Add pgmpy library for Bayesian Networks.

[bug#64258] [PATCH 0/2] Add pgmpy library for Bayesian Networks.

[Felix Gruber]

This patchset adds the python-pgmpy library and its dependency
python-daft.

Felix Gruber (2):
  gnu: Add python-daft.
  gnu: Add python-pgmpy.

 gnu/packages/python-xyz.scm | 49 ++++++++++++++++++++++++++++++++++++-
 gnu/packages/statistics.scm | 44 +++++++++++++++++++++++++++++++++
 2 files changed, 92 insertions(+), 1 deletion(-)


base-commit: f25529b08e356f89ca7cecc44295085531a8faba
-- 
2.39.2

[bug#64258] [PATCH 1/2] gnu: Add python-daft.

[Felix Gruber]

* gnu/packages/python-xyz.scm (python-daft): New variable.
---
 gnu/packages/python-xyz.scm | 49 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 48 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b650b71f3b..7ccf2d352b 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -108,7 +108,7 @@
 ;;; Copyright © 2021 Simon Streit <simon@netpanic.org>
 ;;; Copyright © 2021 Daniel Meißner <daniel.meissner-i4k@ruhr-uni-bochum.de>
 ;;; Copyright © 2021, 2022 Pradana Aumars <paumars@courrier.dev>
-;;; Copyright © 2021, 2022 Felix Gruber <felgru@posteo.net>
+;;; Copyright © 2021, 2022, 2023 Felix Gruber <felgru@posteo.net>
 ;;; Copyright © 2021 Sébastien Lerique <sl@eauchat.org>
 ;;; Copyright © 2021 Raphaël Mélotte <raphael.melotte@mind.be>
 ;;; Copyright © 2021 ZmnSCPxj <ZmnSCPxj@protonmail.com>
@@ -3962,6 +3962,53 @@ (define-public python-pomegranate
 Cython for speed.")
     (license license:expat)))
 
+(define-public python-daft
+  (package
+    (name "python-daft")
+    (version "0.1.2")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "daft" version))
+              (sha256
+               (base32
+                "1r8jsfavd624q2q61f863lk6has6mv5csswh39saafd5khwf0xry"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      '(list "-k"
+             (string-append
+               ;; The following tests compare matplotlib output with
+               ;; previously generated images.  They fail due to minor
+               ;; differences in where matplotlib places labels.
+               "not test_bca[png]"
+               " and not test_classic[png]"
+               " and not test_deconvolution[png]"
+               " and not test_exoplanets[png]"
+               " and not test_fixed[png]"
+               " and not test_gaia[png]"
+               " and not test_galex[png]"
+               " and not test_huey_p_newton[png]"
+               " and not test_logo[png]"
+               " and not test_no_circles[png]"
+               " and not test_no_gray[png]"
+               " and not test_recursive[png]"
+               " and not test_thick_lines[png]"
+               " and not test_weaklensing[png]"
+               " and not test_wordy[png]"))))
+    (propagated-inputs (list python-matplotlib python-numpy))
+    (native-inputs (list python-pytest))
+    (home-page "http://daft-pgm.org")
+    (synopsis "PGM rendering library")
+    (description "Daft is a Python package that uses matplotlib to
+render pixel-perfect probabilistic graphical models for publication in
+a journal or on the internet. With a short Python script and an
+intuitive model-building syntax you can design directed (Bayesian
+Networks, directed acyclic graphs) and undirected (Markov random fields)
+models and save them in any formats that matplotlib supports (including
+PDF, PNG, EPS and SVG).")
+    (license license:expat)))
+
 (define-public python-portalocker
   (package
     (name "python-portalocker")
-- 
2.39.2

[bug#64258] [PATCH 2/2] gnu: Add python-pgmpy.

[Felix Gruber]

* gnu/packages/statistics.scm (python-pgmpy): New variable.
---
 gnu/packages/statistics.scm | 44 +++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index e025653338..dff8f4af6b 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -18,6 +18,7 @@
 ;;; Copyright © 2021 Frank Pursel <frank.pursel@gmail.com>
 ;;; Copyright © 2022 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2023 gemmaro <gemmaro.dev@gmail.com>
+;;; Copyright © 2023 Felix Gruber <felgru@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -81,6 +82,7 @@ (define-module (gnu packages statistics)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages readline)
@@ -7444,3 +7446,45 @@ (define-public ruby-enumerable-statistics
 statistical summary in arrays and enumerables.")
     (home-page "https://github.com/mrkn/enumerable-statistics")
     (license license:expat)))
+
+(define-public python-pgmpy
+  (package
+    (name "python-pgmpy")
+    (version "0.1.22")
+    (source
+     (origin
+       (method git-fetch)  ;pypi package does not include test data
+       (uri (git-reference
+             (url "https://github.com/pgmpy/pgmpy")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "03p8wbac4i4968h6639bqq0z4pg4aynhw3y28iv4l95cimgbr55i"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-daft
+                             python-joblib
+                             python-networkx
+                             python-numpy
+                             python-opt-einsum
+                             python-pandas
+                             python-pyparsing
+                             python-pytorch
+                             python-scikit-learn
+                             python-scipy
+                             python-statsmodels
+                             python-tqdm))
+    (native-inputs (list python-black
+                         python-codecov
+                         python-coverage
+                         python-mock
+                         python-pytest
+                         python-pytest-cov
+                         python-xdoctest))
+    (home-page "https://github.com/pgmpy/pgmpy")
+    (synopsis "Probabilistic Graphical Models library")
+    (description "This package provides a library for Probabilistic
+Graphical Models. It can be used for learning (Structure and Parameter),
+inference (Probabilistic and Causal), and simulations in Bayesian
+Networks.")
+    (license license:expat)))
-- 
2.39.2

[bug#64258] [PATCH v2 0/2] Add pgmpy library for Bayesian Networks.

[Felix Gruber]

I've updated the patchset to pgmpy version 0.1.24.

Felix Gruber (2):
  gnu: Add python-daft.
  gnu: Add python-pgmpy.

 gnu/packages/python-xyz.scm | 49 ++++++++++++++++++++++++++++++++++++-
 gnu/packages/statistics.scm | 43 ++++++++++++++++++++++++++++++++
 2 files changed, 91 insertions(+), 1 deletion(-)


base-commit: 9dcd8802f5bc472579f23a38dcf437f8a9ac976c
-- 
2.42.0

[bug#64258] [PATCH v2 1/2] gnu: Add python-daft.

[Felix Gruber]

* gnu/packages/python-xyz.scm (python-daft): New variable.

Change-Id: I546556c825662e5b8bff46e5a78e7c98c8cc55ed
---
 gnu/packages/python-xyz.scm | 49 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 48 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e521c1580d..1dfaa2480d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -108,7 +108,7 @@
 ;;; Copyright © 2021 Simon Streit <simon@netpanic.org>
 ;;; Copyright © 2021, 2022, 2023 Daniel Meißner <daniel.meissner-i4k@ruhr-uni-bochum.de>
 ;;; Copyright © 2021, 2022 Pradana Aumars <paumars@courrier.dev>
-;;; Copyright © 2021, 2022 Felix Gruber <felgru@posteo.net>
+;;; Copyright © 2021, 2022, 2023 Felix Gruber <felgru@posteo.net>
 ;;; Copyright © 2021 Sébastien Lerique <sl@eauchat.org>
 ;;; Copyright © 2021 Raphaël Mélotte <raphael.melotte@mind.be>
 ;;; Copyright © 2021 ZmnSCPxj <ZmnSCPxj@protonmail.com>
@@ -4157,6 +4157,53 @@ (define-public python-pomegranate
 Cython for speed.")
     (license license:expat)))
 
+(define-public python-daft
+  (package
+    (name "python-daft")
+    (version "0.1.2")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "daft" version))
+              (sha256
+               (base32
+                "1r8jsfavd624q2q61f863lk6has6mv5csswh39saafd5khwf0xry"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      '(list "-k"
+             (string-append
+               ;; The following tests compare matplotlib output with
+               ;; previously generated images.  They fail due to minor
+               ;; differences in where matplotlib places labels.
+               "not test_bca[png]"
+               " and not test_classic[png]"
+               " and not test_deconvolution[png]"
+               " and not test_exoplanets[png]"
+               " and not test_fixed[png]"
+               " and not test_gaia[png]"
+               " and not test_galex[png]"
+               " and not test_huey_p_newton[png]"
+               " and not test_logo[png]"
+               " and not test_no_circles[png]"
+               " and not test_no_gray[png]"
+               " and not test_recursive[png]"
+               " and not test_thick_lines[png]"
+               " and not test_weaklensing[png]"
+               " and not test_wordy[png]"))))
+    (propagated-inputs (list python-matplotlib python-numpy))
+    (native-inputs (list python-pytest))
+    (home-page "http://daft-pgm.org")
+    (synopsis "PGM rendering library")
+    (description "Daft is a Python package that uses matplotlib to
+render pixel-perfect probabilistic graphical models for publication in
+a journal or on the internet. With a short Python script and an
+intuitive model-building syntax you can design directed (Bayesian
+Networks, directed acyclic graphs) and undirected (Markov random fields)
+models and save them in any formats that matplotlib supports (including
+PDF, PNG, EPS and SVG).")
+    (license license:expat)))
+
 (define-public python-portalocker
   (package
     (name "python-portalocker")
-- 
2.42.0

[bug#64258] [PATCH v2 2/2] gnu: Add python-pgmpy.

[Felix Gruber]

* gnu/packages/statistics.scm (python-pgmpy): New variable.

Change-Id: Ic9a42b534500cd1ed98869b8ac4bd3700ee3e2f6
---
 gnu/packages/statistics.scm | 43 +++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index d15732c839..d783464299 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -18,6 +18,7 @@
 ;;; Copyright © 2021 Frank Pursel <frank.pursel@gmail.com>
 ;;; Copyright © 2022 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2023 gemmaro <gemmaro.dev@gmail.com>
+;;; Copyright © 2023 Felix Gruber <felgru@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -7803,3 +7804,45 @@ (define-public ruby-enumerable-statistics
 statistical summary in arrays and enumerables.")
     (home-page "https://github.com/mrkn/enumerable-statistics")
     (license license:expat)))
+
+(define-public python-pgmpy
+  (package
+    (name "python-pgmpy")
+    (version "0.1.24")
+    (source
+     (origin
+       (method git-fetch)  ;pypi package does not include test data
+       (uri (git-reference
+             (url "https://github.com/pgmpy/pgmpy")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0fvzh6v0yhgdryczamvzhfy2ymywkh0ssx4rl47xnfvi43hnij90"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-daft
+                             python-joblib
+                             python-networkx
+                             python-numpy
+                             python-opt-einsum
+                             python-pandas
+                             python-pyparsing
+                             python-pytorch
+                             python-scikit-learn
+                             python-scipy
+                             python-statsmodels
+                             python-tqdm))
+    (native-inputs (list python-black
+                         python-codecov
+                         python-coverage
+                         python-mock
+                         python-pytest
+                         python-pytest-cov
+                         python-xdoctest))
+    (home-page "https://github.com/pgmpy/pgmpy")
+    (synopsis "Probabilistic Graphical Models library")
+    (description "This package provides a library for Probabilistic
+Graphical Models. It can be used for learning (Structure and Parameter),
+inference (Probabilistic and Causal), and simulations in Bayesian
+Networks.")
+    (license license:expat)))
-- 
2.42.0

[bug#64258] [PATCH v3 0/2] Add pgmpy library for Bayesian Networks.

[Felix Gruber]

This version of the patchset fixes guix lint errors and removes
unused native-inputs from the python-pgmpy package.

Felix Gruber (2):
  gnu: Add python-daft.
  gnu: Add python-pgmpy.

 gnu/packages/python-xyz.scm | 47 +++++++++++++++++++++++++++++++++++++
 gnu/packages/statistics.scm | 38 ++++++++++++++++++++++++++++++
 2 files changed, 85 insertions(+)


base-commit: 7722da6fa5422c4fec69d6c8b9536c7d6fc3d326
-- 
2.43.0

[bug#64258] [PATCH v3 1/2] gnu: Add python-daft.

[Felix Gruber]

* gnu/packages/python-xyz.scm (python-daft): New variable.

Change-Id: I546556c825662e5b8bff46e5a78e7c98c8cc55ed
---
 gnu/packages/python-xyz.scm | 47 +++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index ee689809a3..02ba55d339 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4197,6 +4197,53 @@ (define-public python-pomegranate
 Cython for speed.")
     (license license:expat)))
 
+(define-public python-daft
+  (package
+    (name "python-daft")
+    (version "0.1.2")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "daft" version))
+              (sha256
+               (base32
+                "1r8jsfavd624q2q61f863lk6has6mv5csswh39saafd5khwf0xry"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      '(list "-k"
+             (string-append
+               ;; The following tests compare matplotlib output with
+               ;; previously generated images.  They fail due to minor
+               ;; differences in where matplotlib places labels.
+               "not test_bca[png]"
+               " and not test_classic[png]"
+               " and not test_deconvolution[png]"
+               " and not test_exoplanets[png]"
+               " and not test_fixed[png]"
+               " and not test_gaia[png]"
+               " and not test_galex[png]"
+               " and not test_huey_p_newton[png]"
+               " and not test_logo[png]"
+               " and not test_no_circles[png]"
+               " and not test_no_gray[png]"
+               " and not test_recursive[png]"
+               " and not test_thick_lines[png]"
+               " and not test_weaklensing[png]"
+               " and not test_wordy[png]"))))
+    (propagated-inputs (list python-matplotlib python-numpy))
+    (native-inputs (list python-pytest))
+    (home-page "https://docs.daft-pgm.org/")
+    (synopsis "PGM rendering library")
+    (description "Daft is a Python package that uses matplotlib to
+render pixel-perfect probabilistic graphical models for publication in
+a journal or on the internet.  With a short Python script and an
+intuitive model-building syntax you can design directed (Bayesian
+Networks, directed acyclic graphs) and undirected (Markov random fields)
+models and save them in any formats that matplotlib supports (including
+PDF, PNG, EPS and SVG).")
+    (license license:expat)))
+
 (define-public python-portalocker
   (package
     (name "python-portalocker")
-- 
2.43.0

[bug#64258] [PATCH v3 2/2] gnu: Add python-pgmpy.

[Felix Gruber]

* gnu/packages/statistics.scm (python-pgmpy): New variable.

Change-Id: Ic9a42b534500cd1ed98869b8ac4bd3700ee3e2f6
---
 gnu/packages/statistics.scm | 38 +++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 0c3a560562..5fa19c4217 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -18,6 +18,7 @@
 ;;; Copyright © 2021 Frank Pursel <frank.pursel@gmail.com>
 ;;; Copyright © 2022 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2023 gemmaro <gemmaro.dev@gmail.com>
+;;; Copyright © 2023 Felix Gruber <felgru@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -7667,3 +7668,40 @@ (define-public ruby-enumerable-statistics
 statistical summary in arrays and enumerables.")
     (home-page "https://github.com/mrkn/enumerable-statistics")
     (license license:expat)))
+
+(define-public python-pgmpy
+  (package
+    (name "python-pgmpy")
+    (version "0.1.24")
+    (source
+     (origin
+       (method git-fetch)  ;pypi package does not include test data
+       (uri (git-reference
+             (url "https://github.com/pgmpy/pgmpy")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0fvzh6v0yhgdryczamvzhfy2ymywkh0ssx4rl47xnfvi43hnij90"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-daft
+                             python-joblib
+                             python-networkx
+                             python-numpy
+                             python-opt-einsum
+                             python-pandas
+                             python-pyparsing
+                             python-pytorch
+                             python-scikit-learn
+                             python-scipy
+                             python-statsmodels
+                             python-tqdm))
+    (native-inputs (list python-mock
+                         python-pytest))
+    (home-page "https://github.com/pgmpy/pgmpy")
+    (synopsis "Probabilistic Graphical Models library")
+    (description "This package provides a library for Probabilistic
+Graphical Models.  It can be used for learning (Structure and Parameter),
+inference (Probabilistic and Causal), and simulations in Bayesian
+Networks.")
+    (license license:expat)))
-- 
2.43.0

bug#64258: [PATCH 0/2] Add pgmpy library for Bayesian Networks.

[Sharlatan Hellseher]

[-- Attachment #1: Type: text/plain, Size: 59 bytes --]


Hi,

Pushed as 892b4a9a02..db88f712f8 to master.

--
Oleg

[-- Attachment #2: signature.asc --]
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