gnu: python-pyamg: Regenerate bundled files.

* gnu/packages/python-science.scm (python-pyamg) [source]: Delete
auto-generated files.
[arguments] <#:phases>: Add 'amg-core-bind-them phase to
re-generate *_bind.cpp files deleted in snippet.
[native-inputs]: Add python-cppheaderparser and python-pyyaml.
[description]: Improve style, omit implementation details.

Change-Id: I6f68914cd912e6f4592e51c21b129847e73be847

gnu/packages/python-science.scm

@@ -513,32 +513,64 @@ spheres, cubes, etc.")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "pyamg" version))
+              (modules '((guix build utils)))
+              (snippet
+               ;; Delete autogenerated files, regenerate in a phase.
+               #~(begin
+                   (for-each
+                    (lambda (file)
+                      (delete-file (string-append "pyamg/amg_core/" file)))
+                    '("air_bind.cpp"
+                      "evolution_strength_bind.cpp"
+                      "graph_bind.cpp"
+                      "krylov_bind.cpp"
+                      "linalg_bind.cpp"
+                      "relaxation_bind.cpp"
+                      "ruge_stuben_bind.cpp"
+                      "smoothed_aggregation_bind.cpp"
+                      "tests/bind_examples_bind.cpp"))))
               (sha256
                (base32
                 "0l3dliwynxyjvbgpmi2k8jqvkkw6fc00c8w69h6swhrkfh0ql12z"))))
-    (build-system pyproject-build-system)
     (arguments
      (list
       #:test-flags
       ;; Test installed package in order to find C++ modules.
-      #~(list "--pyargs" "pyamg.tests")))
+      #~(list "--pyargs" "pyamg.tests")
-    (native-inputs (list pybind11 python-pytest python-setuptools-scm))
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; Regenerate the autogenerated files.
+          (add-after 'unpack 'amg-core-bind-them
+            (lambda _
+              ;; bindthem.py heavily depends on location to produce *_bind.cpp
+              ;; file, make it available in tests as well.
+              (copy-file "pyamg/amg_core/bindthem.py"
+                         "pyamg/amg_core/tests/bindthem.py")
+              (with-directory-excursion "pyamg/amg_core"
+                (substitute* "bindthem.py"
+                  (("/usr/bin/env python3") (which "python3")))
+                (invoke "sh" "generate.sh"))
+              (with-directory-excursion "pyamg/amg_core/tests"
+                (invoke "python" "bindthem.py" "bind_examples.h")))))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list pybind11
+           python-cppheaderparser
+           python-pytest
+           python-pyyaml
+           python-setuptools-scm))
     (propagated-inputs (list python-numpy python-scipy))
     (home-page "https://github.com/pyamg/pyamg")
     (synopsis "Algebraic Multigrid Solvers in Python")
     (description "PyAMG is a Python library of Algebraic Multigrid
-(AMG) solvers.
+(AMG) solvers. It features implementations of:
-
-PyAMG features implementations of:
 @itemize
 @item Ruge-Stuben (RS) or Classical AMG
 @item AMG based on Smoothed Aggregation (SA)
 @item Adaptive Smoothed Aggregation (αSA)
 @item Compatible Relaxation (CR)
 @item Krylov methods such as CG, GMRES, FGMRES, BiCGStab, MINRES, etc.
-@end itemize
+@end itemize")
-PyAMG is primarily written in Python with supporting C++ code for
-performance critical operations.")
     (license license:expat)))
 
 (define-public python-tspex