gnu: aoflagger: Update to 3.4.0-0.b3a459d.

* gnu/packages/astronomy.scm (aoflagger): Update to 3.4.0-0.b3a459d.
[source] <patch>: Remove it as no longer required.

* gnu/packages/patches/aoflagger-use-system-provided-pybind11.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Deregister patch.

Change-Id: I54535150959c5c7ef2c11c1b1541c287b935ed90

gnu/local.mk

@@ -991,7 +991,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/antiword-CVE-2014-8123.patch			\
   %D%/packages/patches/antlr3-3_1-fix-java8-compilation.patch	\
   %D%/packages/patches/antlr3-3_3-fix-java8-compilation.patch	\
-  %D%/packages/patches/aoflagger-use-system-provided-pybind11.patch \
   %D%/packages/patches/apr-fix-atomics.patch			\
   %D%/packages/patches/apr-skip-getservbyname-test.patch	\
   %D%/packages/patches/aria-maestosa-scons-python3.patch	\

gnu/packages/astronomy.scm

@@ -218,65 +218,67 @@ reused in several astronomical applications, such as @code{wsclean},
       (license license:gpl3+))))
 
 (define-public aoflagger
-  (package
+  ;; 3.4.0 was released in 2023, there are a lot of changes and compatibility
-    (name "aoflagger")
+  ;; for EveryBeam.
-    (version "3.4.0")
+  (let ((commit "b3a459df54b35ec18821ae0a392eeef1ca92cdba")
-    (source
+        (revision "0"))
-     (origin
+    (package
-       (method git-fetch)
+      (name "aoflagger")
-       (uri (git-reference
+      (version (git-version "3.4.0" revision commit))
-             (url "https://gitlab.com/aroffringa/aoflagger")
+      (source
-             (commit (string-append "v" version))))
+       (origin
-       (sha256
+         (method git-fetch)
-        (base32 "0dxmcy04cayhs4s2z41wls1dnmg9hkffvlqcmc660idqziffvv1g"))
+         (uri (git-reference
-       (patches
+                (url "https://gitlab.com/aroffringa/aoflagger")
-        (search-patches "aoflagger-use-system-provided-pybind11.patch"))
+                (commit commit)))
-       (file-name (git-file-name name version))))
+         (sha256
-    (build-system cmake-build-system)
+          (base32 "0fgm2svdw52m348hi28pnknxsdy54dkfd7y388b14hwf9z5ransa"))
-    (arguments
+         (file-name (git-file-name name version))))
-     (list
+      (build-system cmake-build-system)
-      ;; Tests require external files download from
+      (arguments
-      ;; https://www.astron.nl/citt/ci_data/aoflagger/
+       (list
-      #:tests? #f
+        ;; Tests require external files download from
-      #:configure-flags
+        ;; https://www.astron.nl/citt/ci_data/aoflagger/
-      #~(list (string-append "-DCASACORE_ROOT_DIR="
+        #:tests? #f
-                             #$(this-package-input "casacore")))
+        #:configure-flags
-      #:phases
+        #~(list (string-append "-DCASACORE_ROOT_DIR="
-      #~(modify-phases %standard-phases
+                               #$(this-package-input "casacore")))
-          ;; aocommon and pybind11 are expected to be found as git submodules,
+        #:phases
-          ;; link them before build.
+        #~(modify-phases %standard-phases
-          (add-after 'unpack 'link-submodule-package
+            ;; aocommon and pybind11 are expected to be found as git submodules,
-            (lambda _
+            ;; link them before build.
-              (rmdir "external/aocommon")
+            (add-after 'unpack 'link-submodule-package
-              (symlink #$(this-package-native-input "aocommon")
+              (lambda _
-                       (string-append (getcwd) "/external/aocommon")))))))
+                (rmdir "external/aocommon")
-    (native-inputs
+                (symlink #$(this-package-native-input "aocommon")
-     (list aocommon
+                         (string-append (getcwd) "/external/aocommon")))))))
-           boost
+      (native-inputs
-           pkg-config
+       (list aocommon
-           python
+             boost
-           pybind11))
+             pkg-config
-    (inputs
+             python
-     (list casacore
+             pybind11))
-           cfitsio
+      (inputs
-           fftw
+       (list casacore
-           gsl
+             cfitsio
-           gtkmm-3
+             fftw
-           hdf5
+             gsl
-           libpng
+             gtkmm-3
-           libsigc++
+             hdf5
-           libxml2
+             libpng
-           lua
+             libsigc++
-           openblas
+             libxml2
-           zlib))
+             lua
-    (home-page "https://gitlab.com/aroffringa/aoflagger")
+             openblas
-    (synopsis "Astronomical tool that can find and remove radio-frequency interference")
+             zlib))
-    (description
+      (home-page "https://gitlab.com/aroffringa/aoflagger")
-     "AOFlagger is a tool that can find and remove radio-frequency
+      (synopsis "Astronomical tool that can find and remove radio-frequency interference")
+      (description
+       "AOFlagger is a tool that can find and remove radio-frequency
 interference (RFI) in radio astronomical observations.  It can make use of Lua
 scripts to make flagging strategies flexible, and the tools are applicable to a
 wide set of telescopes.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public astroterm
   (package

gnu/packages/patches/aoflagger-use-system-provided-pybind11.patch

@@ -1,38 +0,0 @@
-This patch was borrowed from Debian's package:
-https://salsa.debian.org/debian-astro-team/aoflagger/-/blob/0484ef75a663e3e07738550cdade46f433a53dac/debian/patches/Use-system-provided-pybind11.patch
-Description: Use system provided pybind11
-Author: Ole Streicher <olebole@debian.org>
-Origin: Debian
-Last-Update: Mon, 30 Aug 2021 11:05:37 +0200
----
- CMakeLists.txt | 10 +++++-----
- 1 file changed, 5 insertions(+), 5 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 655ea5e..824ee2a 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -62,11 +62,6 @@ foreach(ExternalSubmodule IN LISTS ExternalSubmoduleDirectories)
-   endif()
- endforeach()
- 
--# Include aocommon/pybind11 headers
--include_directories("${CMAKE_SOURCE_DIR}/external/aocommon/include")
--add_subdirectory("${CMAKE_SOURCE_DIR}/external/pybind11")
--include_directories(SYSTEM ${pybind11_INCLUDE_DIR})
--
- find_package(
-   HDF5
-   COMPONENTS C CXX
-@@ -101,6 +96,11 @@ find_package(PythonInterp REQUIRED)
- message(STATUS "Using python version ${PYTHON_VERSION_STRING}")
- include_directories(SYSTEM ${PYTHON_INCLUDE_DIRS})
- 
-+# Include pybind11 headers
-+find_package(pybind11 REQUIRED)
-+include_directories("${CMAKE_SOURCE_DIR}/external/aocommon/include")
-+include_directories(${pybind11_INCLUDE_DIR})
-+
- # boost::alignment requires Boost 1.56
- find_package(Boost 1.56.0 REQUIRED COMPONENTS date_time filesystem system
-                                               unit_test_framework)