[bug#56364] [PATCH] gnu: Add glymur

[bug#56364] [PATCH] gnu: Add glymur

[Sharlatan Hellseher]

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Hi Guix team!

This package contains Python interface to OpenJEPEG and LibTIFF which
requires some tweaks to let it find system library.

It's goes as one of the SunPy dependence I've started packing.

> ./pre-inst-env guix build python-glymur --rounds=2 --check
successfully built
/gnu/store/r77vwchzhhfi40xlmffwxyjpa4x8wxzv-python-glymur-0.10.1.drv
successfully built
/gnu/store/r77vwchzhhfi40xlmffwxyjpa4x8wxzv-python-glymur-0.10.1.drv
/gnu/store/nx10j711hps4glkxfw17gx0np1wnz1vh-python-glymur-0.10.1

-- 
… наш разум - превосходная объяснительная машина которая способна
найти смысл почти в чем угодно, истолковать любой феномен, но
совершенно не в состоянии принять мысль о непредсказуемости.

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From 776f0ce0a22c83809d9a3dc4752180580e3632df Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Sat, 2 Jul 2022 21:28:39 +0100
Subject: [PATCH] gnu: Add glymur

* gnu/packages/python-xyz.scm (python-glymur): New variable.
---
 gnu/packages/python-xyz.scm | 74 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 73 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1d43049776..994045645d 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 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2021, 2022 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>
@@ -912,6 +912,78 @@ (define-public python-pyprind
 of a loop structure or other iterative computation.")
     (license license:bsd-3)))
 
+(define-public python-glymur
+  (package
+    (name "python-glymur")
+    (version "0.10.1")
+    (source
+     (origin
+       (method git-fetch)   ; no tests data in PyPi package
+       (uri (git-reference
+             (url "https://github.com/quintusdias/glymur")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1cq9r8vzwvds1kasy5gc2rxw034jh9l43rraps1n739072pfz6qg"))))
+    (build-system python-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-library-locations
+            (lambda _
+              ;; XXX: It's a workaround for Python inability to find the
+              ;; .so libraries with ctypes.util.find_library()
+              (substitute* '("glymur/config.py")
+                (("path = find_library\\(libname\\)")
+                 (string-append
+                  "if libname == \"openjp2\":\n"
+                  "        path = \""
+                  #$(this-package-input "openjpeg") "/lib/libopenjp2.so\"\n"
+                  "    elif libname == \"tiff\":\n"
+                  "        path = \""
+                  #$(this-package-input "libtiff") "/lib/libtiff.so\"\n"
+                  "    elif libname == \"c\":\n"
+                  "        path = \""
+                  #$(this-package-input "glibc") "/lib/libc.so.6\"\n")))))
+          ;; TODO: implement as a feature of python-build-system (PEP-621,
+          ;; PEP-631, PEP-660)
+          (replace 'build
+            (lambda _
+              (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)
+              ;; ZIP does not support timestamps before 1980.
+              (setenv "SOURCE_DATE_EPOCH" "315532800")
+              (invoke "python" "-m" "build" "--wheel" "--no-isolation" ".")))
+          (replace 'install
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let ((whl (car (find-files "dist" "\\.whl$"))))
+                (invoke "pip" "--no-cache-dir" "--no-input"
+                        "install" "--no-deps" "--prefix" #$output whl))))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                ;; Failing test due to inability of
+                ;; ctypes.util.find_library() to determine library path,
+                ;; which is patched above.
+                (delete-file "tests/test_config.py")
+                (invoke "python" "-m" "pytest" "-vv" "tests")))))))
+    (native-inputs
+     (list python-pypa-build python-pytest))
+    (inputs
+     (list openjpeg  ; glymur/lib/openjp2.py
+           libtiff   ; glymur/lib/tiff.py
+           glibc))
+    (propagated-inputs
+     (list python-lxml
+           python-numpy
+           python-packaging))
+    (home-page "https://github.com/quintusdias/glymur")
+    (synopsis "Python interface to OpenJPEG and LibTIFF")
+    (description
+     "This package provides Python interface to the OpenJPEG library which
+allows one to read and write JPEG 2000 files")
+    (license license:expat)))
+
 (define-public python-gphoto2
   (package
     (name "python-gphoto2")
-- 
2.36.1

bug#56364: [PATCH] gnu: Add glymur

[Ludovic Courtès]

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Hi,

Sharlatan Hellseher <sharlatanus@gmail.com> skribis:

> From 776f0ce0a22c83809d9a3dc4752180580e3632df Mon Sep 17 00:00:00 2001
> From: Sharlatan Hellseher <sharlatanus@gmail.com>
> Date: Sat, 2 Jul 2022 21:28:39 +0100
> Subject: [PATCH] gnu: Add glymur
>
> * gnu/packages/python-xyz.scm (python-glymur): New variable.

Applied with the changes below: in this case ‘search-input-file’ is an
improvement IMO because it ensures that the file you’re looking for
(“libopenjp2.so”, etc.) actually exists.  Also it allows us to refer to
the ‘glibc’ package that implicitly provided rather than add a
dependency on an extra ‘glibc’ variant.

Thanks!

Ludo’.


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diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 76491631ae..3f4867ece0 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -931,7 +931,7 @@ (define-public python-glymur
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-library-locations
-            (lambda _
+            (lambda* (#:key inputs #:allow-other-keys)
               ;; XXX: It's a workaround for Python inability to find the
               ;; .so libraries with ctypes.util.find_library()
               (substitute* '("glymur/config.py")
@@ -939,13 +939,13 @@ (define-public python-glymur
                  (string-append
                   "if libname == \"openjp2\":\n"
                   "        path = \""
-                  #$(this-package-input "openjpeg") "/lib/libopenjp2.so\"\n"
+                  (search-input-file inputs "/lib/libopenjp2.so") "\"\n"
                   "    elif libname == \"tiff\":\n"
                   "        path = \""
-                  #$(this-package-input "libtiff") "/lib/libtiff.so\"\n"
+                  (search-input-file inputs "/lib/libtiff.so") "\"\n"
                   "    elif libname == \"c\":\n"
                   "        path = \""
-                  #$(this-package-input "glibc") "/lib/libc.so.6\"\n")))))
+                  (search-input-file inputs "/lib/libc.so.6") "\"\n")))))
           ;; TODO: implement as a feature of python-build-system (PEP-621,
           ;; PEP-631, PEP-660)
           (replace 'build
@@ -971,8 +971,7 @@ (define-public python-glymur
      (list python-pypa-build python-pytest))
     (inputs
      (list openjpeg  ; glymur/lib/openjp2.py
-           libtiff   ; glymur/lib/tiff.py
-           glibc))
+           libtiff)) ; glymur/lib/tiff.py
     (propagated-inputs
      (list python-lxml
            python-numpy