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Subject: [bug#77371] [PATCH 00/12] Add packages from the scikit-hep project
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This patchset adds some packages from the scikit-hep project [1] (HEP stands for High Energy Physics).

The remaining libraries are a little more difficult to package and tests depend on a large test data package (scikit-hep-testdata) which does not install correctly with a trivial package definition.

[1] https://scikit-hep.org/

Vinicius Monego (12):
  gnu: python-scikit-build-core: Update to 0.11.1.
  gnu: Add python-resample.
  gnu: Add python-boost-histogram.
  gnu: Add python-deflate.
  gnu: Add python-uhi.
  gnu: Add python-histoprint.
  gnu: Add python-hist.
  gnu: Add python-hepunits.
  gnu: Add python-particle.
  gnu: Add python-decaylanguage.
  gnu: Add python-vector.
  gnu: Add python-hepstats.

 gnu/packages/python-compression.scm |  27 +++
 gnu/packages/python-science.scm     | 247 +++++++++++++++++++++++++++-
 gnu/packages/statistics.scm         |  33 ++++
 3 files changed, 305 insertions(+), 2 deletions(-)


base-commit: a3674c059abf16256f549c4d558a0140b9cd8945
-- 
2.49.0

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To: Vinicius Monego <monego@HIDDEN>
Subject: bug#77371: Acknowledgement ([PATCH 00/12] Add packages from the
 scikit-hep project)
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Subject: [bug#77371] [PATCH 01/12] gnu: python-scikit-build-core: Update to 0.11.1.
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* gnu/packages/python-science.scm (python-scikit-build-core): Update to
0.11.1.

Change-Id: I66d04ba5ed89d3a9eb57df1e9491b8170d5b1571
---
 gnu/packages/python-science.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 247ec44629..2471c43d26 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -598,13 +598,13 @@ (define-public python-scikit-allel
 (define-public python-scikit-build-core
   (package
     (name "python-scikit-build-core")
-    (version "0.10.7")
+    (version "0.11.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "scikit_build_core" version))
        (sha256
-        (base32 "1y64d8rl39banfwdkszyd4sbzp795q8lj66yxrz2l84mwygvbjq4"))))
+        (base32 "1dvjmrhhc3549yrdh8dwr61h7xcrr9ijddv7k7dhngykbkgqhnaf"))))
     (build-system pyproject-build-system)
     ;; Tests are aborted with the admonition: "setup.py install is
     ;; deprecated. Use build and pip and other standards-based tools."
-- 
2.49.0

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Subject: [bug#77371] [PATCH 02/12] gnu: Add python-resample.
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* gnu/packages/statistics.scm (python-resample): New variable.

Change-Id: I0bd8ed6c0532c5dba6efd9d15b056da401072fcf
---
 gnu/packages/statistics.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 55b726c66b..48542130a8 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2813,6 +2813,39 @@ (define-public python-openturns
 functionalities needed to treat uncertainties in studies.")
     (license license:lgpl3+)))

+(define-public python-resample
+  (package
+    (name "python-resample")
+    (version "1.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "resample" version))
+       (sha256
+        (base32 "08hbnkfplhyh1pc9ls20pldxslhsp3azb8ibgc4wjg5q801pid2b"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-numpy python-scipy))
+    (native-inputs (list python-pytest python-setuptools python-wheel))
+    (home-page "https://github.com/scikit-hep/resample")
+    (synopsis "Resampling-based inference in Python")
+    (description "This package provides a resampling-based inference based on
+data resampling and permutation.
+
+Features:
+
+@itemize
+@item Bootstrap resampling: ordinary or balanced with optional stratification
+@item Extended bootstrap resampling: also varies sample size
+@item Parametric resampling: Gaussian, Poisson, gamma, etc.)
+@item Jackknife estimates of bias and variance of any estimator
+@item Compute bootstrap confidence intervals (percentile or BCa) for any
+estimator
+@item Permutation-based variants of traditional statistical tests (USP test of
+independence and others)
+@item Tools for working with empirical distributions (CDF, quantile, etc.)
+@end itemize")
+    (license license:bsd-3)))
+
 (define-public r-coda
   (package
     (name "r-coda")
-- 
2.49.0

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* gnu/packages/python-science.scm (python-boost-histogram): New variable.

Change-Id: I91e73a0a3e3a698197b2d309bd5bdf388fd2697a
---
 gnu/packages/python-science.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 2471c43d26..8d245f34e1 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -816,6 +816,33 @@ (define-public python-scikit-misc
 and scientific computing.")
     (license license:bsd-3)))
 
+(define-public python-boost-histogram
+  (package
+    (name "python-boost-histogram")
+    (version "1.5.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "boost_histogram" version))
+       (sha256
+        (base32 "0p2f90p5jwlwrjz3hq2fzaifkmny33g2mpi89nnhi3w41f1jxr2i"))))
+    (build-system pyproject-build-system)
+    ;; This package bundles files from Boost::Histogram and doesn't provide
+    ;; a way to use a system library.
+    (propagated-inputs (list python-numpy))
+    (native-inputs (list cmake-minimal
+                         pybind11-2.13
+                         python-pytest
+                         python-pytest-benchmark
+                         python-scikit-build-core
+                         python-setuptools-scm))
+    (home-page "https://boost-histogram.readthedocs.io/en/latest/")
+    (synopsis "Python bindings for the Boost::Histogram library")
+    (description
+     "This package provides Python bindings for the Boost::Histogram library,
+one of the fastest libraries for histogramming.")
+    (license license:bsd-3)))
+
 (define-public python-scikit-opt
   (package
     (name "python-scikit-opt")
-- 
2.49.0

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* gnu/packages/python-compression.scm (python-deflate): New variable.

Change-Id: I7b04deb2ed291cff1e36422b8e4bf127a0575d08
---
 gnu/packages/python-compression.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm
index 5b994d408f..427d3a7464 100644
--- a/gnu/packages/python-compression.scm
+++ b/gnu/packages/python-compression.scm
@@ -11,6 +11,7 @@
 ;;; Copyright © 2024 TakeV <takev@HIDDEN>
 ;;; Copyright © 2023 Ivan Vilata i Balaguer <ivan@HIDDEN>
 ;;; Copyright © 2024 Maxim Cournoyer <maxim.cournoyer@HIDDEN>
+;;; Copyright © 2025 Vinicius Monego <monego@HIDDEN>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -788,6 +789,32 @@ (define-public python-zipp
 wrapper.  It provides a backport of the @code{Path} object.")
     (license license:expat)))
 
+(define-public python-deflate
+  (package
+    (name "python-deflate")
+    (version "0.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "deflate" version))
+       (sha256
+        (base32 "1vnwyzlq5q73g6qj6gcl95ma1zxdx875zkc1n5aiyy8jjvzyxdfh"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases #~(modify-phases %standard-phases
+                   (add-after 'unpack 'libdeflate-prefix
+                     (lambda _
+                       (setenv "LIBDEFLATE_PREFIX"
+                               #$(this-package-input "libdeflate")))))))
+    (native-inputs (list cmake-minimal python-pytest python-scikit-build-core))
+    (inputs (list libdeflate))
+    (home-page "https://github.com/dcwatson/deflate")
+    (synopsis "Python wrapper for @code{libdeflate}")
+    (description "This packages contains a very thin Python wrapper for
+@code{libdeflate}.")
+    (license license:expat)))
+
 (define-public python-zipstream-ng
   (package
     (name "python-zipstream-ng")
-- 
2.49.0

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* gnu/packages/python-science.scm (python-uhi): New variable.

Change-Id: I12e802cfc9dd6473cac9657dc477e470238f1bbc
---
 gnu/packages/python-science.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 8d245f34e1..ced52c4b51 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1002,6 +1002,33 @@ (define-public python-scikit-survival
 cross-validation.")
       (license license:gpl3+))))
 
+(define-public python-uhi
+  (package
+    (name "python-uhi")
+    (version "0.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "uhi" version))
+       (sha256
+        (base32 "0753b7yw0zi06g4azafnk3w8i3q6js9i6wwg3pya464gygrbnncm"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-numpy))
+    (native-inputs (list python-boost-histogram
+                         python-fastjsonschema
+                         python-hatch-vcs
+                         python-hatchling
+                         python-pytest))
+    (home-page "https://github.com/scikit-hep/uhi")
+    (synopsis "Universal Histogram Interface")
+    (description "This is a package meant primarily for documenting histogram
+indexing and the PlottableHistogram Protocol and any future cross-library
+standards.  It also contains the code for the PlottableHistogram Protocol, to
+be used in type checking libraries wanting to conform to the protocol. It is
+not usually a runtime dependency, but only a type checking, testing, and/or
+docs dependency in support of other libraries.")
+    (license license:bsd-3)))
+
 (define-public python-tdda
   (package
     (name "python-tdda")
-- 
2.49.0

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* gnu/packages/python-science.scm (python-histoprint): New variable.

Change-Id: I1ace11116c39e2c803afd10849c107c3f232273e
---
 gnu/packages/python-science.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index ced52c4b51..24e1fca1d3 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1029,6 +1029,30 @@ (define-public python-uhi
 docs dependency in support of other libraries.")
     (license license:bsd-3)))
 
+(define-public python-histoprint
+  (package
+    (name "python-histoprint")
+    (version "2.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "histoprint" version))
+       (sha256
+        (base32 "07d2lk64gwhjvw4wccvwks3j4ig7g99q627jjxz4ans5a29p5pz1"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-click python-numpy python-uhi))
+    (native-inputs (list python-awkward
+                         python-boost-histogram
+                         python-hatch-vcs
+                         python-hatchling
+                         python-pytest
+                         python-rich))
+    (home-page "https://github.com/scikit-hep/histoprint")
+    (synopsis "Pretty print histograms to the console")
+    (description "Histoprint uses a mix of terminal color codes and Unicode
+trickery (i.e. combining characters) to plot overlaying histograms.")
+    (license license:bsd-3)))
+
 (define-public python-tdda
   (package
     (name "python-tdda")
-- 
2.49.0

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* gnu/packages/python-science.scm (python-hist): New variable.

Change-Id: Ia3495b6d94a620b797318ffce162aa1d58e79049
---
 gnu/packages/python-science.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 24e1fca1d3..c1fabfa7bd 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1053,6 +1053,31 @@ (define-public python-histoprint
 trickery (i.e. combining characters) to plot overlaying histograms.")
     (license license:bsd-3)))
 
+(define-public python-hist
+  (package
+    (name "python-hist")
+    (version "2.8.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "hist" version))
+       (sha256
+        (base32 "17cd46c0ixq18fr2kgzam09w1sr4qkd9l6nsjdbl4vggw80ck9vx"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-boost-histogram
+                             python-histoprint
+                             python-numpy
+                             python-typing-extensions))
+    (native-inputs (list python-hatch-vcs
+                         python-hatchling
+                         python-pytest
+                         python-pytest-mpl))
+    (home-page "https://hist.readthedocs.io/en/latest/")
+    (synopsis "Hist classes and utilities")
+    (description
+     "Hist is an analyst-friendly front-end for @code{boost-histogram}.")
+    (license license:bsd-3)))
+
 (define-public python-tdda
   (package
     (name "python-tdda")
-- 
2.49.0

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* gnu/packages/python-science.scm (python-hepunits): New variable.

Change-Id: I174495c4fdacd21491e9e7d5abdd7d5dd0e5ffe8
---
 gnu/packages/python-science.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index c1fabfa7bd..876c68912a 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1124,6 +1124,25 @@ (define-public python-tdda
 of regular expressions from text data and automatic test generation.")
     (license license:expat))) ; MIT License
 
+(define-public python-hepunits
+  (package
+    (name "python-hepunits")
+    (version "2.3.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "hepunits" version))
+       (sha256
+        (base32 "1n1nf2rz2d86qzjmcwykbc16jzsqb45vs8lyksg98b3jd8nwsd4l"))))
+    (build-system pyproject-build-system)
+    (native-inputs (list python-hatch-vcs python-hatchling python-pytest))
+    (home-page "https://github.com/scikit-hep/hepunits")
+    (synopsis "Units and constants in the HEP system of units")
+    (description "@code{hepunits} collects the most commonly used units and
+constants in the HEP System of Units, as derived from the basic units
+originally defined by the CLHEP project.")
+    (license license:bsd-3)))
+
 (define-public python-trimesh
   (package
     (name "python-trimesh")
-- 
2.49.0

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* gnu/packages/python-science.scm (python-particle): New variable.

Change-Id: Ib2462e25aadba797532c005a3b4d4e4a238a611e
---
 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 876c68912a..b17c543619 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1143,6 +1143,34 @@ (define-public python-hepunits
 originally defined by the CLHEP project.")
     (license license:bsd-3)))
 
+(define-public python-particle
+  (package
+    (name "python-particle")
+    (version "0.25.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "particle" version))
+       (sha256
+        (base32 "1sb19sdng47ymh10r8b553xf8p0cqfs7j9qblh4fzsmz73pbp90z"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-attrs
+                             python-hepunits
+                             python-typing-extensions))
+    (native-inputs (list python-hatch-vcs
+                         python-hatchling
+                         python-pandas
+                         python-pytest
+                         python-pytest-benchmark
+                         python-tabulate))
+    (home-page "https://github.com/scikit-hep/particle")
+    (synopsis "Extended PDG particle data and MC identification codes")
+    (description
+     "@code{Particle} provides a pythonic interface to the Particle Data Group
+(PDG) particle data tables and particle identification codes, with extended
+particle information and extra goodies.")
+    (license license:bsd-3)))
+
 (define-public python-trimesh
   (package
     (name "python-trimesh")
-- 
2.49.0

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* gnu/packages/python-science.scm (python-decaylanguage): New variable.

Change-Id: I5c709016f80b19cef22105bff42ca62b8f384f1b
---
 gnu/packages/python-science.scm | 36 +++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index b17c543619..c2f23c8d55 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -61,6 +61,7 @@ (define-module (gnu packages python-science)
   #:use-module (gnu packages digest)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages geo)
+  #:use-module (gnu packages graphviz)
   #:use-module (gnu packages image)
   #:use-module (gnu packages image-processing)
   #:use-module (gnu packages machine-learning)
@@ -1171,6 +1172,41 @@ (define-public python-particle
 particle information and extra goodies.")
     (license license:bsd-3)))
 
+(define-public python-decaylanguage
+  (package
+    (name "python-decaylanguage")
+    (version "0.18.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "decaylanguage" version))
+       (sha256
+        (base32 "0kc9i9k51kg2zv8dwywpigiipxzmyxpzb101imjsvv1licip7b8v"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; This file fails to be collected with "DeprecationWarning: setDaemon()
+      ;; is deprecated, set the daemon attribute instead".
+      #:test-flags #~(list "--ignore" "tests/test_convert.py")))
+    (propagated-inputs (list python-attrs
+                             python-graphviz
+                             python-hepunits
+                             python-lark-parser
+                             python-numpy
+                             python-pandas
+                             python-particle
+                             python-plumbum))
+    (native-inputs (list python-hatch-vcs
+                         python-hatchling
+                         python-pytest))
+    (home-page "https://decaylanguage.readthedocs.io/en/latest/")
+    (synopsis "Language to describe, manipulate and convert particle decays")
+    (description "DecayLanguage implements a language to describe and convert
+particle decays between digital representations, effectively making it
+possible to interoperate several fitting programs.  Particular interest is
+given to programs dedicated to amplitude analyses.")
+    (license license:bsd-3)))
+
 (define-public python-trimesh
   (package
     (name "python-trimesh")
-- 
2.49.0

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* gnu/packages/python-science.scm (python-vector): New variable.

Change-Id: I77d72b0c18a0bc215cb2198ce5447e587b13d0fe
---
 gnu/packages/python-science.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index c2f23c8d55..41504b457e 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1207,6 +1207,35 @@ (define-public python-decaylanguage
 given to programs dedicated to amplitude analyses.")
     (license license:bsd-3)))
 
+(define-public python-vector
+  (package
+    (name "python-vector")
+    (version "1.6.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "vector" version))
+       (sha256
+        (base32 "1r6ncbdnak75nvyhn9rkmgg08l6ggxyvb5ikqrv5zlskwl62v62r"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; This file requires python-papermill (not yet packaged).
+      #:test-flags #~(list "--ignore" "tests/test_notebooks.py")))
+    (propagated-inputs (list python-numpy python-packaging))
+    (native-inputs (list python-awkward
+                         python-hatch-vcs
+                         python-hatchling
+                         python-pytest
+                         python-sympy))
+    (home-page "https://github.com/scikit-hep/vector")
+    (synopsis "Arrays of 2D, 3D, and Lorentz vectors")
+    (description "Vector is a Python library for 2D and 3D spatial vectors, as
+well as 4D space-time vectors.  It is especially intended for performing
+geometric calculations on arrays of vectors, rather than one vector at a time
+in a Python @code{for} loop.")
+    (license license:bsd-3)))
+
 (define-public python-trimesh
   (package
     (name "python-trimesh")
-- 
2.49.0

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Subject: [bug#77371] [PATCH 12/12] gnu: Add python-hepstats.
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* gnu/packages/python-science.scm (python-hepstats): New variable.

Change-Id: I0fc06ac9cde4443d2ec973f25985b5161d4ee33c
---
 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 41504b457e..ca684fbadc 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -46,6 +46,7 @@
 (define-module (gnu packages python-science)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gnu packages)
+  #:use-module (gnu packages astronomy)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bioinformatics)
   #:use-module (gnu packages boost)
@@ -1236,6 +1237,33 @@ (define-public python-vector
 in a Python @code{for} loop.")
     (license license:bsd-3)))
 
+(define-public python-hepstats
+  (package
+    (name "python-hepstats")
+    (version "0.9.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "hepstats" version))
+       (sha256
+        (base32 "1rvvc3r83p41c5mpsy5l02r97zrylamgm1gmxs988csysiqri4ng"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-asdf
+                             python-numpy
+                             python-pandas
+                             python-scipy
+                             python-tqdm
+                             python-uhi))
+    (native-inputs (list python-hatch-vcs
+                         python-hatchling
+                         python-pytest
+                         python-pytest-runner))
+    (home-page "https://github.com/scikit-hep/hepstats")
+    (synopsis "Statistics tools and utilities")
+    (description "@code{hepstats} is a library for statistical inference
+aiming to cover the needs of High Energy Physics.")
+    (license license:bsd-3)))
+
 (define-public python-trimesh
   (package
     (name "python-trimesh")
-- 
2.49.0

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Subject: [bug#77371] [PATCH 00/12] Add packages from the scikit-hep project
Resent-From: Andreas Enge <andreas@HIDDEN>
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Hello Vinicius,

your patch series shows some lint warnings in QA:
   https://qa.guix.gnu.org/issue/77371
and one failing package (python-hepstats) on aarch64.

Maybe you can correct the lint problems and push everything not
dependent on the failing package?

Andreas

Last modified: Tue, 8 Apr 2025 10:30:02 UTC

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