From 384b63aa08e83959549f6bb3e962be90aafa6d4e Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@friendly-machines.com>
Date: Fri, 13 Feb 2026 11:28:48 +0000
Subject: [PATCH] gnu: python-pycifrw: Generate sources from noweb.

* gnu/packages/physics.scm (python-pycifrw)[arguments]<#:phases>{generate-sources}:
New phase.
{check}: Replace.
[native-inputs]: Add latex2html, noweb.

Change-Id: Iaaa77f8c857345ba63a1d07a782d7bf8d086c1c2
---
 gnu/packages/physics.scm | 25 +++++++++++++++++++------
 1 file changed, 19 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/physics.scm b/gnu/packages/physics.scm
index 59ae96a619..78eafa780b 100644
--- a/gnu/packages/physics.scm
+++ b/gnu/packages/physics.scm
@@ -32,10 +32,12 @@
   #:use-module (gnu packages build-tools)
   #:use-module (gnu packages check)
   #:use-module (gnu packages cmake)
+  #:use-module (gnu packages documentation)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages ninja)
+  #:use-module (gnu packages noweb)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-build)
@@ -172,18 +174,29 @@ scattering simulations.")
     (version "4.4.6")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "PyCifRW" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/jamesrhester/pycifrw.git")
+             (commit version)))
        (sha256
-        (base32 "05ggj4l9cir02m593azhl03wfjimx3rvwbznpx01bdqawxsmkgq2"))))
+        (base32 "0xda4vgm6dz6fhhrfv8y6igsc5kznlnv0j3yrwkbcd3qqv16ic6r"))))
     (build-system pyproject-build-system)
     (arguments
-     ;; Tests are not included in the PyPI tarball.
-     (list #:tests? #f))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'generate-sources
+            (lambda _
+              (invoke "make" "-C" "src" "PYTHON=python3" "package")
+              (invoke "make" "-C" "src/drel" "PYTHON=python3" "package")))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "python3" "TestPyCIFRW.py")))))))
     (propagated-inputs
      (list python-numpy python-ply))
     (native-inputs
-     (list python-setuptools))  ; build-backend = setuptools.build_meta
+     (list latex2html noweb python-setuptools))
     (home-page "https://github.com/jamesrhester/pycifrw")
     (synopsis "CIF file reader and writer")
     (description