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06/45: gnu: Add aoflagger.


From: guix-commits
Subject: 06/45: gnu: Add aoflagger.
Date: Thu, 4 Aug 2022 06:07:07 -0400 (EDT)

civodul pushed a commit to branch master
in repository guix.

commit cdff1423c0d03e7d3e8445cf14f1123f694468c8
Author: Sharlatan Hellseher <sharlatanus@gmail.com>
AuthorDate: Sun Jun 26 18:34:58 2022 +0100

    gnu: Add aoflagger.
    
    * gnu/packages/astronomy.scm (aoflagger): New variable.
    * gnu/packages/patches/aoflagger-use-system-provided-pybind11.patch:
    New file.
    * gnu/local.mk (dist_patch_DATA): Add it.
    
    Signed-off-by: Ludovic Court├Ęs <ludo@gnu.org>
---
 gnu/local.mk                                       |  1 +
 gnu/packages/astronomy.scm                         | 63 ++++++++++++++++++++++
 .../aoflagger-use-system-provided-pybind11.patch   | 38 +++++++++++++
 3 files changed, 102 insertions(+)

diff --git a/gnu/local.mk b/gnu/local.mk
index 2484320038..cbfe880d6e 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -858,6 +858,7 @@ 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-skip-getservbyname-test.patch       \
   %D%/packages/patches/ark-skip-xar-test.patch                 \
   %D%/packages/patches/aspell-default-dict-dir.patch           \
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 336ef02d66..3c4c92619e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -142,6 +142,69 @@ moment, supported SPICE files are:
 @end itemize\n")
     (license license:cecill)))
 
+(define-public aoflagger
+  (package
+    (name "aoflagger")
+    (version "3.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.com/aroffringa/aoflagger";)
+             (commit (string-append "v" version))))
+       (sha256
+        (base32 "1dcbfrbiybhpbypna2xhddx1wk7yifh38ha2r6p5rzsikzwlsin1"))
+       (patches
+        (search-patches "aoflagger-use-system-provided-pybind11.patch"))
+       (file-name (git-file-name name version))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      ;; XXX: Tests require external files download from
+      ;; https://www.astron.nl/citt/ci_data/aoflagger/
+      ;; FIXME: runtest is not found
+      #:tests? #f
+      #:configure-flags
+      #~(list (string-append "-DCASACORE_ROOT_DIR="
+                             #$(this-package-input "casacore")))
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; aocommon and pybind11 are expected to be found as git submodules,
+          ;; link them before build.
+          (add-after 'unpack 'link-submodule-package
+            (lambda _
+              (rmdir "external/aocommon")
+              (symlink #$(this-package-native-input "aocommon")
+                       (string-append (getcwd) "/external/aocommon")))))))
+    (native-inputs
+     (list aocommon
+           boost
+           pkg-config
+           python
+           pybind11))
+    (inputs
+     (list casacore
+           cfitsio
+           fftw
+           gsl
+           gtkmm-3
+           hdf5
+           lapack
+           libpng
+           libsigc++
+           libxml2
+           lua
+           openblas
+           zlib))
+    (home-page "https://gitlab.com/aroffringa/aoflagger";)
+    (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+)))
+
 (define-public casacore
   (package
     (name "casacore")
diff --git a/gnu/packages/patches/aoflagger-use-system-provided-pybind11.patch 
b/gnu/packages/patches/aoflagger-use-system-provided-pybind11.patch
new file mode 100644
index 0000000000..76bc52a4ba
--- /dev/null
+++ b/gnu/packages/patches/aoflagger-use-system-provided-pybind11.patch
@@ -0,0 +1,38 @@
+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)



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