GNU bug report logs - #59978
[PATCH 0/6] gnu: python-astropy: Unbundle WCSLIB.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 0/6] gnu: python-astropy: Unbundle WCSLIB.
Date: Sun, 11 Dec 2022 22:23:30 +0000

Hi Guix!

This patch series include update of CFITSIO to the latest version which resolve
build faileur on aarch64-linux system reported in
https://issues.guix.gnu.org/59323 with open upstream issue
https://github.com/rwesson/ALFA/issues/29.

CFITSIO is configured with curl support which passed build of WCSLIB
(mentioned as failing before in comments).

PYTHON-ASTROPY has WCSLIB unbundled and passed build.

Rest changes include update child packages to the latest version and making
sure they are pass build on x86_64 and aarch64 systems.

Sharlatan Hellseher (6):
  gnu: cfitsio: Update to 4.2.0.
  gnu: cfitsio: Build with bzip2 support.
  gnu: python-fitsio: Update to 1.1.8.
  gnu: wcslib: Update to 7.12.
  gnu: python-astropy: Update to 5.1.1.
  gnu: indi: Update to 1.9.9.

 gnu/packages/astronomy.scm | 112 +++++++++++++++++++------------------
 1 file changed, 59 insertions(+), 53 deletions(-)


base-commit: c8316c1e47ce2ace5474cbcda03555cf915b4fce
-- 
2.38.1

Message #8 received at 59978 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 59978 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 1/6] gnu: cfitsio: Update to 4.2.0.
Date: Sun, 11 Dec 2022 22:25:40 +0000

Fix build on aarch64-linux as reported in:
- https://issues.guix.gnu.org/59323
- https://github.com/rwesson/ALFA/issues/29

The latest version passed build on aarch64-linux system with curl and
gfortran enabled. wcslib <at> 7.5 passed build with curl enabled (was marked
as failing in cements).

* gnu/packages/astronomy.scm (cfitsio): Update to 4.2.0.
  [arguments]: Use Gexp, enable tests.
  [arguments](phases): Delete check and add post-install-check phases.
  [native-inputs]: Add gfortran.
  [inputs]: Add curl, zlib.
---
 gnu/packages/astronomy.scm | 33 +++++++++++++++++++++------------
 1 file changed, 21 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index c59f4d02a4..8d9cce5158 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -356,7 +356,7 @@ (define-public casacore
 (define-public cfitsio
   (package
     (name "cfitsio")
-    (version "3.49")
+    (version "4.2.0")
     (source
      (origin
        (method url-fetch)
@@ -364,18 +364,27 @@ (define-public cfitsio
              "http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/"
              "cfitsio-" version ".tar.gz"))
        (sha256
-        (base32 "1cyl1qksnkl3cq1fzl4dmjvkd6329b57y9iqyv44wjakbh6s4rav"))))
+        (base32 "128qsv2q0f0g714ahlsixiikvvbwxi9bg9q9pcr5cd3f7wdkv9gb"))))
     (build-system gnu-build-system)
-    ;; XXX Building with curl currently breaks wcslib.  It doesn't use
-    ;; pkg-config and hence won't link with -lcurl.
     (arguments
-     `(#:tests? #f                      ; no tests
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'patch-paths
-           (lambda _
-             (substitute* "Makefile.in" (("/bin/") ""))
-             #t)))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-paths
+            (lambda _
+              (substitute* "Makefile.in" (("/bin/") ""))))
+          (delete 'check)
+          ;; TODO: Testing steps are sourced from docs/fitsio.pdf, implement
+          ;; the logic in Guile in the future.
+          (add-after 'install 'post-install-check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "make" "testprog")
+                (with-output-to-file "testprog.lis" (lambda _(invoke "./testprog")))
+                (invoke "diff" "-r" "testprog.lis" "testprog.out")
+                (invoke "cmp" "-l" "testprog.fit" "testprog.std")))))))
+    (native-inputs (list gfortran))
+    (inputs (list curl zlib))
     (home-page "https://heasarc.gsfc.nasa.gov/fitsio/fitsio.html")
     (synopsis "Library for reading and writing FITS files")
     (description "CFITSIO provides simple high-level routines for reading and
@@ -384,7 +393,7 @@ (define-public cfitsio
 provides many advanced features for manipulating and filtering the information
 in FITS files.")
     (license (license:non-copyleft "file://License.txt"
-                          "See License.txt in the distribution."))))
+                                   "See License.txt in the distribution."))))
 
 (define-public python-fitsio
   (package
-- 
2.38.1

Message #11 received at 59978 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 59978 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 2/6] gnu: cfitsio: Build with bzip2 support.
Date: Sun, 11 Dec 2022 22:25:41 +0000

* gnu/packages/astronomy.scm (cfitsio):
  [arguments](configure-flags): Add bzip2 option.
  [inputs]: Add bzip2.
---
 gnu/packages/astronomy.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 8d9cce5158..794e5ca2b9 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -368,6 +368,8 @@ (define-public cfitsio
     (build-system gnu-build-system)
     (arguments
      (list
+      #:configure-flags
+      #~(list (string-append "--with-bzip2=" #$(this-package-input "bzip2")))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-paths
@@ -384,7 +386,7 @@ (define-public cfitsio
                 (invoke "diff" "-r" "testprog.lis" "testprog.out")
                 (invoke "cmp" "-l" "testprog.fit" "testprog.std")))))))
     (native-inputs (list gfortran))
-    (inputs (list curl zlib))
+    (inputs (list bzip2 curl zlib))
     (home-page "https://heasarc.gsfc.nasa.gov/fitsio/fitsio.html")
     (synopsis "Library for reading and writing FITS files")
     (description "CFITSIO provides simple high-level routines for reading and
-- 
2.38.1

Message #14 received at 59978 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 59978 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 3/6] gnu: python-fitsio: Update to 1.1.8.
Date: Sun, 11 Dec 2022 22:25:42 +0000

* gnu/packages/astronomy.scm (python-fitsio): Update to 1.1.8.
  [arguments]{phases}: skip-bzip2-test remove redundant phase as cfitsio
  built with bzip2 support.
  [inputs]: Add curl-minimal.
---
 gnu/packages/astronomy.scm | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 794e5ca2b9..5ce94a1f07 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -400,13 +400,13 @@ (define-public cfitsio
 (define-public python-fitsio
   (package
     (name "python-fitsio")
-    (version "1.1.7")
+    (version "1.1.8")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "fitsio" version))
        (sha256
-        (base32 "0q8siijys9kmjnqvyipjgh6hkhf4fwvr1swhsf4if211i9b0m1xy"))
+        (base32 "1y80hgvlkjz1bijfyb2j03853yc1kc63yrf9ab7as31ad2r6kxb1"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove the bundled cfitsio
@@ -430,13 +430,8 @@ (define-public python-fitsio
                  (("self.system_fitsio_libdir = None") "pass")
                  (("self.use_system_fitsio") "True")
                  (("self.system_fitsio_includedir") includedir)
-                 (("self.system_fitsio_libdir") libdir)))))
-         (add-after 'unpack 'skip-bzip2-test
-           (lambda* (#:key inputs #:allow-other-keys)
-             ;; The bzip2 test fails because Guix' cfitsio
-             ;; is built without bzip2 support.
-             (substitute* "fitsio/test.py"
-               (("'SKIP_BZIP_TEST' in os.environ") "True")))))))
+                 (("self.system_fitsio_libdir") libdir))))))))
+    (inputs (list curl-minimal))
     (propagated-inputs
      (list python-numpy cfitsio))
     (home-page "https://github.com/esheldon/fitsio")
-- 
2.38.1

Message #17 received at 59978 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 59978 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 4/6] gnu: wcslib: Update to 7.12.
Date: Sun, 11 Dec 2022 22:25:43 +0000

* gnu/packages/astronomy.scm (wcslib): Update to 7.12.
  [arguments]: Use Gexp, enable parallel tests.
---
 gnu/packages/astronomy.scm | 34 +++++++++++++++++-----------------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 5ce94a1f07..1876b0cde0 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -525,7 +525,7 @@ (define-public eye
 (define-public wcslib
   (package
     (name "wcslib")
-    (version "7.5")
+    (version "7.12")
     (source
      (origin
        (method url-fetch)
@@ -533,26 +533,26 @@ (define-public wcslib
              "ftp://ftp.atnf.csiro.au/pub/software/wcslib/wcslib-" version
              ".tar.bz2"))
        (sha256
-        (base32 "1536gmcpm6pckn9xrb6j8s4pm1vryjhzvhfaj9wx3jwxcpbdy0dw"))))
+        (base32 "1m3bx6gh5w3c7vvsqcki0x20mg8lilg13m0i8nh7za89w58dxy4w"))))
     (inputs
      (list cfitsio))
     (build-system gnu-build-system)
     (arguments
-     `(#:configure-flags
-       (list (string-append "--with-cfitsiolib="
-                            (assoc-ref %build-inputs "cfitsio") "/lib")
-             (string-append "--with-cfitsioinc="
-                            (assoc-ref %build-inputs "cfitsio") "/include"))
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'configure 'patch-/bin/sh
-           (lambda _
-             (substitute* "makedefs.in"
-               (("/bin/sh") "sh"))
-             #t))
-         (delete 'install-license-files)) ; installed by ‘make install’
-       ;; Parallel execution of the test suite is not supported.
-       #:parallel-tests? #f))
+     (list
+      #:configure-flags
+      #~(list (string-append "--with-cfitsiolib="
+                             #$(this-package-input "cfitsio") "/lib")
+              (string-append "--with-cfitsioinc="
+                             #$(this-package-input "cfitsio") "/include"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'install-license-files) ; installed by ‘make install’
+          (add-before 'configure 'patch-/bin/sh
+            (lambda _
+              (substitute* "makedefs.in"
+                (("/bin/sh") "sh")))))))
+    ;; TODO: Fix build with gfortran and pack missing optional pgplot.
+    ;; (inputs (list gfortran pgplot))
     (home-page "https://www.atnf.csiro.au/people/mcalabre/WCS")
     (synopsis "Library which implements the FITS WCS standard")
     (description "The FITS \"World Coordinate System\" (@dfn{WCS}) standard
-- 
2.38.1

Message #20 received at 59978 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 59978 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 5/6] gnu: python-astropy: Update to 5.1.1.
Date: Sun, 11 Dec 2022 22:25:44 +0000

* gnu/packages/astronomy.scm (python-astropy): Update to 5.1.1.
  [source]{snippet}: Unbundle wcslib.
  [arguments]{phases}: preparations: Use all system libraries.
  [inputs]: Add wcslib.
---
 gnu/packages/astronomy.scm | 20 ++++++++------------
 1 file changed, 8 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 1876b0cde0..030ae9b4ea 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -982,25 +982,23 @@ (define-public celestia-gtk
 (define-public python-astropy
   (package
     (name "python-astropy")
-    (version "5.1")
+    (version "5.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy" version))
        (sha256
-        (base32 "0zkv3ddzlxx21i796azfbqxrqnsxn83vsczscv577iyzxp3v5c8x"))
+        (base32 "10dxjim60ch4qznqa5s63q936mkvy95p0k26kcwzv43hmybdcjxs"))
        (modules '((guix build utils)))
        (snippet
         '(begin
            ;; Remove Python bundles.
            (with-directory-excursion "astropy/extern"
              (for-each delete-file-recursively '("ply" "configobj")))
-           ;; Remove cextern bundles and leave the wcslib bundle.  Astropy
-           ;; upgrades to different versions of wcslib every few releases
-           ;; and tests break every upgrade.
-           ;; TODO: unbundle wcslib.
+           ;; Remove cextern bundles. Check bundled versions against available
+           ;; in Guix in the future update of astropy.
            (with-directory-excursion "cextern"
-             (for-each delete-file-recursively '("cfitsio" "expat")))
+             (for-each delete-file-recursively '("cfitsio" "expat" "wcslib")))
            #t))))
     (build-system python-build-system)
     (arguments
@@ -1008,10 +1006,8 @@ (define-public python-astropy
        (modify-phases %standard-phases
          (add-after 'unpack 'preparations
            (lambda _
-             ;; Use our own libraries in place of bundles, with the
-             ;; exception of wcslib.
-             (setenv "ASTROPY_USE_SYSTEM_CFITSIO" "1")
-             (setenv "ASTROPY_USE_SYSTEM_EXPAT" "1")
+             ;; Use our own libraries in place of bundles.
+             (setenv "ASTROPY_USE_SYSTEM_ALL" "1")
              ;; Some tests require a writable home.
              (setenv "HOME" "/tmp")
              ;; Relax xfail tests.
@@ -1058,7 +1054,7 @@ (define-public python-astropy
            python-sgp4
            python-skyfield))
     (inputs
-     (list cfitsio expat))
+     (list cfitsio expat wcslib))
     (propagated-inputs
      (list python-configobj
            python-numpy
-- 
2.38.1

Message #23 received at 59978 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 59978 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 6/6] gnu: indi: Update to 1.9.9.
Date: Sun, 11 Dec 2022 22:25:45 +0000

* gnu/packages/astronomy.scm (indi): Update to 1.9.9.
  [arguments]{tests}: Silent test on aarch64-linux system.
  [inputs]: Add libev.
---
 gnu/packages/astronomy.scm | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 030ae9b4ea..6ddddc358d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -47,6 +47,7 @@ (define-module (gnu packages astronomy)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages image)
   #:use-module (gnu packages image-processing)
+  #:use-module (gnu packages libevent)
   #:use-module (gnu packages libusb)
   #:use-module (gnu packages lua)
   #:use-module (gnu packages maths)
@@ -1978,7 +1979,7 @@ (define-public imppg
 (define-public indi
   (package
     (name "indi")
-    (version "1.9.3")
+    (version "1.9.9")
     (source
      (origin
        (method git-fetch)
@@ -1987,10 +1988,12 @@ (define-public indi
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0c7md288d3g2vf0m1ai6x2l4j4rmlasc4rya92phvd4ynf8vcki2"))))
+        (base32 "1vfcas59nlw8v7n6qhxhcm4isf5wk0crip5rmsallq3bsv3zznfr"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:configure-flags
+     ;; TODO: fix failing tests on aarch64-system.
+     `(#:tests? ,(not (or (%current-target-system) (target-aarch64?)))
+       #:configure-flags
        (let ((out (assoc-ref %outputs "out")))
          (list
           "-DINDI_BUILD_UNITTESTS=ON"
@@ -2015,6 +2018,7 @@ (define-public indi
            curl
            fftw
            gsl
+           libev
            libjpeg-turbo
            libnova
            libtiff
-- 
2.38.1

Message #26 received at 59978 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 59978 <at> debbugs.gnu.org
Date: Sun, 18 Dec 2022 23:16:10 +0000

Hi Guix!

Is anything I need to check for this series?

Regards,
Oleg

-- 
… наш разум - превосходная объяснительная машина которая способна
найти смысл почти в чем угодно, истолковать любой феномен, но
совершенно не в состоянии принять мысль о непредсказуемости.

Message #29 received at 59978 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 59978 <at> debbugs.gnu.org
Cc: Ludovic Courtès <ludo <at> gnu.org>
Subject: Re:
Date: Tue, 27 Dec 2022 18:19:25 +0000

[Message part 1 (text/plain, inline)]

Hi,

I see QA is green and solved some previously failed builds for ARM. I'm
about to complete an update for CASA core package which allows to add
python-casa.

Let me know if I need to change this patch series.

Happy New year!
Oleg


On Sun, 18 Dec 2022, 23:16 Sharlatan Hellseher, <sharlatanus <at> gmail.com>
wrote:

> Hi Guix!
>
> Is anything I need to check for this series?
>
> Regards,
> Oleg
>
> --
> … наш разум - превосходная объяснительная машина которая способна
> найти смысл почти в чем угодно, истолковать любой феномен, но
> совершенно не в состоянии принять мысль о непредсказуемости.
>

[Message part 2 (text/html, inline)]

Message #34 received at 59978-done <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Cc: 59978-done <at> debbugs.gnu.org
Subject: Re: bug#59978: [PATCH 0/6] gnu: python-astropy: Unbundle WCSLIB.
Date: Fri, 06 Jan 2023 23:46:11 +0100

Hi Oleg,

Sharlatan Hellseher <sharlatanus <at> gmail.com> skribis:

>   gnu: cfitsio: Update to 4.2.0.
>   gnu: cfitsio: Build with bzip2 support.
>   gnu: python-fitsio: Update to 1.1.8.
>   gnu: wcslib: Update to 7.12.
>   gnu: python-astropy: Update to 5.1.1.
>   gnu: indi: Update to 1.9.9.

Sorry for taking so long, finally applied!

Thank you & happy new year!

Ludo’.

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