From 42008264d9fff544ee00c3c109093472b8a92bd2 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Fri, 29 Jan 2021 15:17:15 -0500
Subject: gnu: Remove avogadro.

This package fails to build and has been superseded by avogadro2.

* gnu/packages/chemistry.scm (avogadro): Remove variable.
* gnu/packages/patches/avogadro-boost148.patch,
gnu/packages/patches/avogadro-eigen3-update.patch,
gnu/packages/patches/avogadro-python-eigen-lib.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
---
 gnu/packages/chemistry.scm | 85 ----------------------------------------------
 1 file changed, 85 deletions(-)

(limited to 'gnu/packages/chemistry.scm')

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 5351ea596b..e7b061515b 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -52,91 +52,6 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system python))
 
-(define-public avogadro
-  (package
-    (name "avogadro")
-    (version "1.2.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/cryos/avogadro")
-             (commit version)))
-       (sha256
-        (base32 "0258py3lkba85qhs5ynancinyym61vlp0zaq9yrfs3hhnhpzv9n2"))
-       (file-name (git-file-name name version))
-       (patches
-        (search-patches "avogadro-eigen3-update.patch"
-                        "avogadro-python-eigen-lib.patch"
-                        "avogadro-boost148.patch"))))
-    (build-system cmake-build-system)
-    (arguments
-     `(#:tests? #f
-       #:configure-flags
-       (list "-DENABLE_GLSL=ON"
-             (string-append "-DPYTHON_LIBRARIES="
-                            (assoc-ref %build-inputs "python")
-                            "/lib")
-             (string-append "-DPYTHON_INCLUDE_DIRS="
-                            (assoc-ref %build-inputs "python")
-                            "/include/python"
-                            ,(version-major+minor
-                               (package-version python))))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'patch-python-lib-path
-           (lambda* (#:key outputs #:allow-other-keys)
-             ;; This is necessary to install the Python module in the correct
-             ;; directory.
-             (substitute* "libavogadro/src/python/CMakeLists.txt"
-               (("^EXECUTE_PROCESS.*$") "")
-               (("^.*from sys import stdout.*$") "")
-               (("^.*OUTPUT_VARIABLE.*")
-                (string-append "set(PYTHON_LIB_PATH \""
-                               (assoc-ref outputs "out")
-                               "/lib/python"
-                               ,(version-major+minor
-                                  (package-version python))
-                               "/site-packages\")")))
-             #t))
-         (add-after 'install 'wrap-program
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             ;; Make sure 'avogadro' runs with the correct PYTHONPATH.
-             (let* ((out (assoc-ref outputs "out")))
-               (setenv "PYTHONPATH"
-                       (string-append
-                        (assoc-ref outputs "out")
-                        "/lib/python"
-                        ,(version-major+minor
-                           (package-version python))
-                        "/site-packages:"
-                        (getenv "PYTHONPATH")))
-               (wrap-program (string-append out "/bin/avogadro")
-                 `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))))
-             #t)))))
-    (native-inputs
-     `(("doxygen" ,doxygen)
-       ("pkg-config" ,pkg-config)))
-    (inputs
-     `(("boost" ,boost)
-       ("eigen" ,eigen)
-       ("glew" ,glew)
-       ("openbabel" ,openbabel)
-       ("python" ,python-2)
-       ("python-numpy" ,python2-numpy)
-       ("python-pyqt" ,python2-pyqt-4)
-       ("python-sip" ,python2-sip)
-       ("qt" ,qt-4)
-       ("zlib" ,zlib)))
-    (home-page "https://avogadro.cc")
-    (synopsis "Advanced molecule editor")
-    (description
-     "Avogadro is an advanced molecule editor and visualizer designed for use
-in computational chemistry, molecular modeling, bioinformatics, materials
-science, and related areas.  It offers flexible high quality rendering and a
-powerful plugin architecture.")
-    (license license:gpl2+)))
-
 (define-public avogadrolibs
   (package
     (name "avogadrolibs")
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