[bug#68650] [PATCH 0/2] gnu: python-pyamg: Regenerate bundled files.

[bug#68650] [PATCH 0/2] gnu: python-pyamg: Regenerate bundled files.

[Sharlatan Hellseher]

Hi Guix,

It's follow up patch series to cover review suggestion pointed by Vinicius in
https://issues.guix.gnu.org/66930.

Sharlatan Hellseher (2):
  gnu: Add python-cppheaderparser.
  gnu: python-pyamg: Regenerate bundled files.

 gnu/packages/python-science.scm | 50 +++++++++++++++++++++++++++------
 gnu/packages/python-xyz.scm     | 25 ++++++++++++++++-
 2 files changed, 65 insertions(+), 10 deletions(-)


base-commit: d3c3922a8f5d50855165941e19a204d32469006f
-- 
2.41.0

[bug#68650] [PATCH 1/2] gnu: Add python-cppheaderparser.

[Sharlatan Hellseher]

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

Change-Id: I3c57c31a0b63212e43e1ab387b5d329c04ed0e31
---
 gnu/packages/python-xyz.scm | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b23108fbf4..93e7571f78 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -94,7 +94,7 @@
 ;;; Copyright © 2020, 2021 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2020 EuAndreh <eu@euandre.org>
 ;;; Copyright © 2021, 2022 Morgan Smith <Morgan.J.Smith@outlook.com>
-;;; Copyright © 2021-2023 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2021-2024 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2021 Ellis Kenyő <me@elken.dev>
 ;;; Copyright © 2021 LibreMiami <packaging-guix@libremiami.org>
 ;;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz>
@@ -8810,6 +8810,29 @@ (define-public python-cplot
 complex-valued functions.")
     (license license:gpl3+)))
 
+(define-public python-cppheaderparser
+  (package
+    (name "python-cppheaderparser")
+    (version "2.7.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "CppHeaderParser" version))
+       (sha256
+        (base32 "0hncwd9y5ayk8wa6bqhp551mcamcvh84h89ba3labc4mdm0k0arq"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #f))     ;test suite not included in the release
+    (propagated-inputs (list python-ply))
+    (home-page "http://senexcanis.com/open-source/cppheaderparser/")
+    (synopsis
+     "Parse C++ header files and generate a data structure representing the class")
+    (description
+     "CppHeaderParser is a pure python module that will parse C++ header files
+and generate a data structure representing the class.")
+    (license license:bsd-3)))
+
 (define-public python-cppy
   (package
     (name "python-cppy")
-- 
2.41.0

[bug#68650] [PATCH 2/2] gnu: python-pyamg: Regenerate bundled files.

[Sharlatan Hellseher]

* 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.
[desciption]: Improve style, commit implementation details.

Change-Id: I6f68914cd912e6f4592e51c21b129847e73be847
---
 gnu/packages/python-science.scm | 50 +++++++++++++++++++++++++++------
 1 file changed, 41 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index c1be6cde23..4183bd2ea2 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -465,32 +465,64 @@ (define-public python-pyamg
     (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")))
-    (native-inputs (list pybind11 python-pytest python-setuptools-scm))
+      #~(list "--pyargs" "pyamg.tests")
+      #: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.
-
-PyAMG features implementations of:
+(AMG) solvers. It 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
-PyAMG is primarily written in Python with supporting C++ code for
-performance critical operations.")
+@end itemize")
     (license license:expat)))
 
 (define-public python-tspex
-- 
2.41.0

[bug#68650] [PATCH v2 1/2] gnu: Add python-cppheaderparser.

[Sharlatan Hellseher]

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

Change-Id: I3c57c31a0b63212e43e1ab387b5d329c04ed0e31
---
 gnu/packages/python-xyz.scm | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b23108fbf4..93e7571f78 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -94,7 +94,7 @@
 ;;; Copyright © 2020, 2021 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2020 EuAndreh <eu@euandre.org>
 ;;; Copyright © 2021, 2022 Morgan Smith <Morgan.J.Smith@outlook.com>
-;;; Copyright © 2021-2023 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2021-2024 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2021 Ellis Kenyő <me@elken.dev>
 ;;; Copyright © 2021 LibreMiami <packaging-guix@libremiami.org>
 ;;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz>
@@ -8810,6 +8810,29 @@ (define-public python-cplot
 complex-valued functions.")
     (license license:gpl3+)))
 
+(define-public python-cppheaderparser
+  (package
+    (name "python-cppheaderparser")
+    (version "2.7.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "CppHeaderParser" version))
+       (sha256
+        (base32 "0hncwd9y5ayk8wa6bqhp551mcamcvh84h89ba3labc4mdm0k0arq"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #f))     ;test suite not included in the release
+    (propagated-inputs (list python-ply))
+    (home-page "http://senexcanis.com/open-source/cppheaderparser/")
+    (synopsis
+     "Parse C++ header files and generate a data structure representing the class")
+    (description
+     "CppHeaderParser is a pure python module that will parse C++ header files
+and generate a data structure representing the class.")
+    (license license:bsd-3)))
+
 (define-public python-cppy
   (package
     (name "python-cppy")

base-commit: ffc5fefce370f5fc01091869e13fdf525be1e0c0
-- 
2.41.0

[bug#68650] [PATCH v2 2/2] gnu: python-pyamg: Regenerate bundled files.

[Sharlatan Hellseher]

* 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 | 50 +++++++++++++++++++++++++++------
 1 file changed, 41 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index c1be6cde23..4183bd2ea2 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -465,32 +465,64 @@ (define-public python-pyamg
     (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")))
-    (native-inputs (list pybind11 python-pytest python-setuptools-scm))
+      #~(list "--pyargs" "pyamg.tests")
+      #: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.
-
-PyAMG features implementations of:
+(AMG) solvers. It 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
-PyAMG is primarily written in Python with supporting C++ code for
-performance critical operations.")
+@end itemize")
     (license license:expat)))
 
 (define-public python-tspex
-- 
2.41.0

bug#68650: [PATCH 0/2] gnu: python-pyamg: Regenerate bundled files.

[Sharlatan Hellseher]

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Pushed as ae77d94839...77a07a968f to master.

Thanks,
Oleg

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