gnu: python-pymol: Update to 3.1.0.

* gnu/packages/chemistry.scm (python-pymol): Update to 3.1.0.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:tests?>: Disable them.
<#:phases>: Refresh them.  Delete 'build phase.
[native-inputs]: Add cmake-minimal, python-pytest, python-setuptools.
[propagated-inputs]: Add python-numpy.
[description]: Improve style.

Change-Id: Ida6105297f294e3fda060d8c8b938fe743faf6e6
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu/packages/chemistry.scm

@@ -720,7 +720,7 @@ quantum chemistry (and molecular mechanics) softwares.")
 (define-public python-pymol
   (package
     (name "python-pymol")
-    (version "2.5.0")
+    (version "3.1.0")
     (source
      (origin
        (method git-fetch)
@@ -729,54 +729,61 @@ quantum chemistry (and molecular mechanics) softwares.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "08zmfgclkbjkqjpq8xs1mphs1i8rpqj76mcw7m2mrhvma5qj1nr5"))))
-    (build-system python-build-system)
+        (base32 "199zhpdljsvfjnvs7h7q17ib7ajnjiwg790rg8xxhaszjd968byq"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:configure-flags
-       (list "--glut" "--testing")
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'make-reproducible
-           (lambda _
-             (substitute* "create_shadertext.py"
-               (("time\\.time\\(\\)") "0"))))
-         (add-after 'unpack 'add-include-directories
-           (lambda* (#:key inputs #:allow-other-keys)
-             (setenv "CPLUS_INCLUDE_PATH"
-                     (string-append (assoc-ref inputs "freetype")
-                                    "/include/freetype2:"
-                                    (assoc-ref inputs "libxml2")
-                                    "/include/libxml2:"
-                                    (getenv "CPLUS_INCLUDE_PATH")))))
-         ;; Prevent deleting the leading / in the __init__.py path in the
-         ;; launch script.
-         (add-after 'unpack 'disable-unchroot
-           (lambda _
-             (substitute* "setup.py"
-               (("self\\.unchroot") ""))))
-         ;; The setup.py script does not support one of the Python build
-         ;; system's default flags, "--single-version-externally-managed".
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (invoke "python" "setup.py" "install"
-                     (string-append "--prefix=" (assoc-ref outputs "out"))
-                     "--root=/"))))))
-    (inputs
-     (list freetype
-           libpng
-           freeglut
-           glew
-           libxml2
-           mmtf-cpp
-           python-pyqt
-           glm
-           netcdf))
-    (native-inputs (list catch2))
+     (list
+      ;; XXX: Most tests fail with import errors.
+      #:tests? #f
+      #:configure-flags
+      #~(list "--glut" "--testing")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'make-reproducible
+            (lambda _
+              (substitute* "create_shadertext.py"
+                (("time\\.time\\(\\)")
+                 "0"))))
+          (add-after 'unpack 'add-include-directories
+            (lambda* (#:key inputs #:allow-other-keys)
+              (setenv "CPLUS_INCLUDE_PATH"
+                      (string-join
+                       (list
+                        (search-input-directory inputs "/include/freetype2")
+                        (search-input-directory inputs "/include/libxml2")
+                        (getenv "CPLUS_INCLUDE_PATH"))
+                       ":"))))
+          ;; Prevent deleting the leading / in the __init__.py path in the
+          ;; launch script.
+          (add-after 'unpack 'disable-unchroot
+            (lambda _
+              (substitute* "setup.py"
+                (("self\\.unchroot")
+                 ""))))
+          ;; The setup.py script does not support one of the Python build
+          ;; system's default flags, "--single-version-externally-managed".
+          (delete 'build)
+          (replace 'install
+            (lambda _
+              (invoke "python" "setup.py" "install"
+                      (string-append "--prefix=" #$output) "--root=/"))))))
+    (inputs (list freetype
+                  libpng
+                  freeglut
+                  glew
+                  libxml2
+                  mmtf-cpp
+                  python-pyqt
+                  glm
+                  netcdf))
+    (native-inputs (list cmake-minimal catch2 python-pytest python-setuptools))
+    (propagated-inputs (list python-numpy))
     (home-page "https://pymol.org")
     (synopsis "Molecular visualization system")
-    (description "PyMOL is a capable molecular viewer and renderer.  It can be
-used to prepare publication-quality figures, to share interactive results with
-your colleagues, or to generate pre-rendered animations.")
+    (description
+     "PyMOL is a capable molecular viewer and renderer.  It can be used to
+prepare publication-quality figures, to share interactive results with your
+colleagues, or to generate pre-rendered animations.")
     (license license:bsd-3)))
 
 (define-public python-pyscf