guix_mirror_bot pushed a commit to branch astro-updates
in repository guix.
commit b114a0808a25a3e04546a149738e819e4737ab78
Author: Sharlatan Hellseher <sharlata...@gmail.com>
AuthorDate: Thu Sep 18 16:37:59 2025 +0100
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 | 1 -
gnu/packages/astronomy.scm | 114 +++++++++++----------
.../aoflagger-use-system-provided-pybind11.patch | 38 -------
3 files changed, 58 insertions(+), 95 deletions(-)
diff --git a/gnu/local.mk b/gnu/local.mk
index 1ef437c3a8..0e083bec7a 100644
--- a/gnu/local.mk
+++ b/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 \
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index ca467a9f38..1158fd1793 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -218,65 +218,67 @@ reused in several astronomical applications, such as
@code{wsclean},
(license license:gpl3+))))
(define-public aoflagger
- (package
- (name "aoflagger")
- (version "3.4.0")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://gitlab.com/aroffringa/aoflagger";)
- (commit (string-append "v" version))))
- (sha256
- (base32 "0dxmcy04cayhs4s2z41wls1dnmg9hkffvlqcmc660idqziffvv1g"))
- (patches
- (search-patches "aoflagger-use-system-provided-pybind11.patch"))
- (file-name (git-file-name name version))))
- (build-system cmake-build-system)
- (arguments
- (list
- ;; Tests require external files download from
- ;; https://www.astron.nl/citt/ci_data/aoflagger/
- #: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
- 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
+ ;; 3.4.0 was released in 2023, there are a lot of changes and compatibility
+ ;; for EveryBeam.
+ (let ((commit "b3a459df54b35ec18821ae0a392eeef1ca92cdba")
+ (revision "0"))
+ (package
+ (name "aoflagger")
+ (version (git-version "3.4.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.com/aroffringa/aoflagger";)
+ (commit commit)))
+ (sha256
+ (base32 "0fgm2svdw52m348hi28pnknxsdy54dkfd7y388b14hwf9z5ransa"))
+ (file-name (git-file-name name version))))
+ (build-system cmake-build-system)
+ (arguments
+ (list
+ ;; Tests require external files download from
+ ;; https://www.astron.nl/citt/ci_data/aoflagger/
+ #: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
+ 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+)))
+ (license license:gpl3+))))
(define-public astroterm
(package
diff --git a/gnu/packages/patches/aoflagger-use-system-provided-pybind11.patch
b/gnu/packages/patches/aoflagger-use-system-provided-pybind11.patch
deleted file mode 100644
index 76bc52a4ba..0000000000
--- a/gnu/packages/patches/aoflagger-use-system-provided-pybind11.patch
+++ /dev/null
@@ -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 <oleb...@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)
