[PATCH 0/3] Update netcdf.

Done

Details

4 participants

Jonathan Brielmaier
Ludovic Courtès
Christopher Baines
zimoun

Owner: unassigned

Submitted by: Christopher Baines

Severity: normal

Christopher Baines wrote on 25 Oct 2020 11:27

Recipients:(address . guix-patches@gnu.org)(name . Jonathan Brielmaier)(address . jonathan.brielmaier@web.de)

Message-ID:87lffua9ct.fsf@cbaines.net

This fixes an issue building qgis.

Christopher Baines (3):
  gnu: netcdf: Update to 4.7.4.
  gnu: netcdf-fortran: Update to 4.5.3.
  gnu: python2-netcdf4: Remove package.

 gnu/local.mk                                |  1 -
 gnu/packages/maths.scm                      | 22 ++++++++++-----------
 gnu/packages/patches/netcdf-date-time.patch |  6 +++---
 gnu/packages/patches/netcdf-tst_h_par.patch | 21 --------------------
 gnu/packages/python-xyz.scm                 |  3 ---
 5 files changed, 13 insertions(+), 40 deletions(-)
 delete mode 100644 gnu/packages/patches/netcdf-tst_h_par.patch

Christopher Baines wrote on 25 Oct 2020 11:35

[PATCH 3/3] gnu: python2-netcdf4: Remove package.

Recipients:(address . 44208@debbugs.gnu.org)

Message-ID:20201025103508.6845-3-mail@cbaines.net

This fails to build, and as it's the Python 2 variant, I think it can be

removed.

* gnu/packages/python-xyz.scm (python2-netcdf4): Remove variable.

---

gnu/packages/python-xyz.scm | 3 ---

1 file changed, 3 deletions(-)

Toggle diff (16 lines)diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 0fe4703a27..4695869bc9 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -958,9 +958,6 @@ to users of that module.")
     ;; by the Expat license.
     (license (list license:isc license:expat))))
 
-(define-public python2-netcdf4
-  (package-with-python2 python-netcdf4))
-
 (define-public python-license-expression
   (package
     (name "python-license-expression")
-- 
2.28.0

Christopher Baines wrote on 25 Oct 2020 11:35

[PATCH 2/3] gnu: netcdf-fortran: Update to 4.5.3.

Recipients:(address . 44208@debbugs.gnu.org)

Message-ID:20201025103508.6845-2-mail@cbaines.net

This allows the package to build with netcdf 4.7.4.

* gnu/packages/maths.scm (netcdf-fortran): Update to 4.5.3.

---

gnu/packages/maths.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (24 lines)diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index d2631501aa..ba46937f9a 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1619,7 +1619,7 @@ sharing of scientific data.")
 (define-public netcdf-fortran
   (package
     (name "netcdf-fortran")
-    (version "4.4.4")
+    (version "4.5.3")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1627,7 +1627,7 @@ sharing of scientific data.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
+                "0x4acvfhbsx1q79dkkwrwbgfhm0w5ngnp4zj5kk92s1khihmqfhj"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-tests? #f))
-- 
2.28.0

Christopher Baines wrote on 25 Oct 2020 11:35

[PATCH 1/3] gnu: netcdf: Update to 4.7.4.

Recipients:(address . 44208@debbugs.gnu.org)

Message-ID:20201025103508.6845-1-mail@cbaines.net

This will fix an issue building qgis.

* gnu/packages/maths.scm (netcdf): Update to 4.7.4.
[source]: Remove the netcdf-tst_h_par.patch.
[inputs]: Update hdf5 and add curl.
* gnu/packages/patches/netcdf-tst_h_par.patch: Delete.
* gnu/local.mk (dist_patch_DATA): Remove deleted patch.
---
 gnu/local.mk                                |  1 -
 gnu/packages/maths.scm                      | 18 ++++++++----------
 gnu/packages/patches/netcdf-date-time.patch |  6 +++---
 gnu/packages/patches/netcdf-tst_h_par.patch | 21 ---------------------
 4 files changed, 11 insertions(+), 35 deletions(-)
 delete mode 100644 gnu/packages/patches/netcdf-tst_h_par.patch

Toggle diff (99 lines)diff --git a/gnu/local.mk b/gnu/local.mk
index 1a01360d72..0ada3b727b 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1355,7 +1355,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/m4-gnulib-libio.patch			\
   %D%/packages/patches/ncompress-fix-softlinks.patch		\
   %D%/packages/patches/netcdf-date-time.patch			\
-  %D%/packages/patches/netcdf-tst_h_par.patch			\
   %D%/packages/patches/netpbm-CVE-2017-2586.patch		\
   %D%/packages/patches/netpbm-CVE-2017-2587.patch		\
   %D%/packages/patches/netsurf-message-timestamp.patch		\
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index f7565dd885..d2631501aa 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1538,17 +1538,17 @@ similar to MATLAB, GNU Octave or SciPy.")
 (define-public netcdf
   (package
     (name "netcdf")
-    (version "4.4.1.1")
+    (version "4.7.4")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
-                           "netcdf-" version ".tar.gz"))
+       (uri (string-append
+             "https://www.unidata.ucar.edu/downloads/netcdf/ftp/"
+             "netcdf-c-" version ".tar.gz"))
        (sha256
         (base32
-         "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
-       (patches (search-patches "netcdf-date-time.patch"
-                                "netcdf-tst_h_par.patch"))))
+         "1a2fpp15a2rl1m50gcvvzd9y6bavl6vjf9zzf63sz5gdmq06yiqf"))
+       (patches (search-patches "netcdf-date-time.patch"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("m4" ,m4)
@@ -1556,10 +1556,8 @@ similar to MATLAB, GNU Octave or SciPy.")
        ("graphviz" ,graphviz)))
     (inputs
      `(("hdf4" ,hdf4-alt)
-
-       ;; XXX: The 'tst_nccopy4.sh' test fails when using hdf5-1.10.
-       ("hdf5" ,hdf5-1.8)
-
+       ("hdf5" ,hdf5)
+       ("curl" ,curl)
        ("zlib" ,zlib)
        ("libjpeg" ,libjpeg-turbo)))
     (arguments
diff --git a/gnu/packages/patches/netcdf-date-time.patch b/gnu/packages/patches/netcdf-date-time.patch
index a4e7925aa1..0bdfc55299 100644
--- a/gnu/packages/patches/netcdf-date-time.patch
+++ b/gnu/packages/patches/netcdf-date-time.patch
@@ -3,9 +3,9 @@
 @@ -13,7 +13,7 @@
  #endif
  
- /* Tell the user the version of netCDF. */
+ /** @internal The version string for the library, used by
+  * nc_inq_libvers(). */
 -static const char nc_libvers[] = PACKAGE_VERSION " of "__DATE__" "__TIME__" $";
-+static const char nc_libvers[] = PACKAGE_VERSION" $";
++static const char nc_libvers[] = PACKAGE_VERSION " $";
  
  /**
- \defgroup lib_version Library Version
diff --git a/gnu/packages/patches/netcdf-tst_h_par.patch b/gnu/packages/patches/netcdf-tst_h_par.patch
deleted file mode 100644
index ac14a4c0a2..0000000000
--- a/gnu/packages/patches/netcdf-tst_h_par.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-From a83702834938b23cc2e843589aa223e2024a7e6f Mon Sep 17 00:00:00 2001
-From: Orion Poplawski <orion@cora.nwra.com>
-Date: Tue, 29 Nov 2016 11:48:01 -0700
-Subject: [PATCH] Add missing #include "err_macros.h" to tst_h_par.c
-
----
- h5_test/tst_h_par.c | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/h5_test/tst_h_par.c b/h5_test/tst_h_par.c
-index c3da7f4..a419d55 100644
---- a/h5_test/tst_h_par.c
-+++ b/h5_test/tst_h_par.c
-@@ -11,6 +11,7 @@
-    $Id: tst_h_par.c,v 1.15 2010/05/25 13:53:04 ed Exp $
- */
- #include <nc_tests.h>
-+#include "err_macros.h"
- #include <hdf5.h>
- 
- /* Defining USE_MPE causes the MPE trace library to be used (and you
-- 
2.28.0

Jonathan Brielmaier wrote on 25 Oct 2020 21:26

Recipients:

Message-ID:dba47c43-a840-e705-dd0e-320c16651729@web.de

On 25.10.20 11:35, Christopher Baines wrote:

Toggle quote (8 lines)> This will fix an issue building qgis.
>
> * gnu/packages/maths.scm (netcdf): Update to 4.7.4.
> [source]: Remove the netcdf-tst_h_par.patch.
> [inputs]: Update hdf5 and add curl.
> * gnu/packages/patches/netcdf-tst_h_par.patch: Delete.
> * gnu/local.mk (dist_patch_DATA): Remove deleted patch.
> ---

[...]

Toggle quote (9 lines)

> (source

> (origin

> (method url-fetch)

> - (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"

> - "netcdf-" version ".tar.gz"))

> + (uri (string-append

> + "https://www.unidata.ucar.edu/downloads/netcdf/ftp/"

> + "netcdf-c-" version ".tar.gz"))

Do we usually mention such changes in the commit message?

Jonathan Brielmaier wrote on 25 Oct 2020 21:28

Re: [PATCH 0/3] Update netcdf.

Recipients:

Message-ID:8244ee4d-00fb-0765-661b-bc66638c9d67@web.de

On 25.10.20 11:27, Christopher Baines wrote:

Toggle quote (3 lines)

> This fixes an issue building qgis.

Indeed it does. Thanks! I only have a minor adjustment in one commit

message, although I don't know if it's a valid one :P

~Jonathan

Ludovic Courtès wrote on 26 Oct 2020 11:52

Re: [bug#44208] [PATCH 1/3] gnu: netcdf: Update to 4.7.4.

Recipients:(name . Christopher Baines)(address . mail@cbaines.net)(address . 44208@debbugs.gnu.org)

Message-ID:87mu09b6np.fsf@gnu.org

Hi,

Christopher Baines <mail@cbaines.net> skribis:

Toggle quote (8 lines)

> This will fix an issue building qgis.

> * gnu/packages/maths.scm (netcdf): Update to 4.7.4.

> [source]: Remove the netcdf-tst_h_par.patch.

> [inputs]: Update hdf5 and add curl.

> * gnu/packages/patches/netcdf-tst_h_par.patch: Delete.

> * gnu/local.mk (dist_patch_DATA): Remove deleted patch.

Great, the whole series LGTM, thanks!

How to find it at https://data.guix-patches.cbaines.net/?

Ludo’.

zimoun wrote on 26 Oct 2020 13:46

Recipients:

Message-ID:86eell5f4n.fsf@gmail.com

Hi,

On Sun, 25 Oct 2020 at 21:26, Jonathan Brielmaier <jonathan.brielmaier@web.de> wrote:

Toggle quote (10 lines)

> On 25.10.20 11:35, Christopher Baines wrote:

>> * gnu/packages/maths.scm (netcdf): Update to 4.7.4.

>> [source]: Remove the netcdf-tst_h_par.patch.

>> [inputs]: Update hdf5 and add curl.

>> * gnu/packages/patches/netcdf-tst_h_par.patch: Delete.

>> * gnu/local.mk (dist_patch_DATA): Remove deleted patch.

> Do we usually mention such changes in the commit message?

Why not? For example, recently I dug in Julia history and these would

have saved some time (read “git log” and not the diff themselves).

Well, my poor opinion. :-)

All the best,

simon

Christopher Baines wrote on 26 Oct 2020 17:04

Recipients:(name . Jonathan Brielmaier)(address . jonathan.brielmaier@web.de)(address . 44208@debbugs.gnu.org)

Message-ID:87o8kpynwv.fsf@cbaines.net

Jonathan Brielmaier <jonathan.brielmaier@web.de> writes:

Toggle quote (21 lines)> On 25.10.20 11:35, Christopher Baines wrote:
>> This will fix an issue building qgis.
>>
>> * gnu/packages/maths.scm (netcdf): Update to 4.7.4.
>> [source]: Remove the netcdf-tst_h_par.patch.
>> [inputs]: Update hdf5 and add curl.
>> * gnu/packages/patches/netcdf-tst_h_par.patch: Delete.
>> * gnu/local.mk (dist_patch_DATA): Remove deleted patch.
>> ---
> [...]
>>      (source
>>       (origin
>>         (method url-fetch)
>> -       (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
>> -                           "netcdf-" version ".tar.gz"))
>> +       (uri (string-append
>> +             "https://www.unidata.ucar.edu/downloads/netcdf/ftp/"
>> +             "netcdf-c-" version ".tar.gz"))
>
> Do we usually mention such changes in the commit message?

Assuming you were referring to the change in name for the source
tarball, I've now added a bit about that in to the commit message. I
don't really have that much information to add though, just that new
releases seem to have a different name.

Christopher Baines wrote on 26 Oct 2020 17:06

Recipients:(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 44208-done@debbugs.gnu.org)

Message-ID:87lfftynsc.fsf@cbaines.net

Ludovic Courtès <ludo@gnu.org> writes:

Toggle quote (14 lines)> Hi,
>
> Christopher Baines <mail@cbaines.net> skribis:
>
>> This will fix an issue building qgis.
>>
>> * gnu/packages/maths.scm (netcdf): Update to 4.7.4.
>> [source]: Remove the netcdf-tst_h_par.patch.
>> [inputs]: Update hdf5 and add curl.
>> * gnu/packages/patches/netcdf-tst_h_par.patch: Delete.
>> * gnu/local.mk (dist_patch_DATA): Remove deleted patch.
>
> Great, the whole series LGTM, thanks!

Cool, I've pushed this as 952c62762d3bc8750dfd61a33b13d19ec9d775f7 now.

Toggle quote (2 lines)

> How to find it at https://data.guix-patches.cbaines.net/?

I'd always start at Patchwork, so https://patchwork.cbaines.net/. You
might be able to spot it in the list, but you can also search by
clicking on "Show patches with" in the top left [1].

1: https://patchwork.cbaines.net/project/guix-patches/list/?series=&submitter=&state=&q=44208&archive=&delegate=

There's a few issues with the processing of this series, it was
processed twice, with the first attempt missing a patch. Also, the check
linking to issues.guix.info is broken. I think I've fixed both of the
underlying issues with the relevant scripts now, so these issues should
be fixed for future series.

Closed

Ludovic Courtès wrote on 28 Oct 2020 10:47

Recipients:(name . Christopher Baines)(address . mail@cbaines.net)(address . 44208-done@debbugs.gnu.org)

Message-ID:87h7qe65sc.fsf@gnu.org

Hi,

Christopher Baines <mail@cbaines.net> skribis:

Toggle quote (6 lines)

> I'd always start at Patchwork, so https://patchwork.cbaines.net/. You

> might be able to spot it in the list, but you can also search by

> clicking on "Show patches with" in the top left [1].

> 1: https://patchwork.cbaines.net/project/guix-patches/list/?series=&submitter=&state=&q=44208&archive=&delegate=

OK, this one is now empty, but I guess that’s expected.

Of the 5 “checks” that appear on each page, ‘cbaines/applying patch’ is

really just about applying the patch to ‘master’, right? And

‘cbaines/submitting builds’ is about actually building things?

It’s surprising because when you go the comparison page, sometimes you

can see that builds are scheduled, so we don’t yet whether it has

succeeded. But my understanding is that the Patchwork UI will only

display whether a build has been submitted, not whether it has

succeeded, correct?

We need a hands-on session. :-)

Thanks,

Ludo’.

Closed

Christopher Baines wrote on 31 Oct 2020 17:12

Recipients:(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 44208-done@debbugs.gnu.org)

Message-ID:87v9eqxtl9.fsf@cbaines.net

Ludovic Courtès <ludo@gnu.org> writes:

Toggle quote (16 lines)> Hi,
>
> Christopher Baines <mail@cbaines.net> skribis:
>
>> I'd always start at Patchwork, so https://patchwork.cbaines.net/ . You
>> might be able to spot it in the list, but you can also search by
>> clicking on "Show patches with" in the top left [1].
>>
>> 1: https://patchwork.cbaines.net/project/guix-patches/list/?series=&submitter=&state=&q=44208&archive=&delegate=
>
> OK, this one is now empty, but I guess that’s expected.
>
> Of the 5 “checks” that appear on each page, ‘cbaines/applying patch’ is
> really just about applying the patch to ‘master’, right?  And
> ‘cbaines/submitting builds’ is about actually building things?

Yeah, the applying patch check reflects something about Git's success at
applying the patch, which happens in the Laminar job which is linked
to. Sometimes the check will fail, but a branch is still created, and
sometimes it'll fail and no branch will be created. Applying patches is
a hard problem.

As for the submitting builds check, that's reported by the script that
submits the builds to the coordinator instance being used. So yes, it'll
appear when the builds are submitted, and hopefully it doesn't take too
long for the builds to happen.

Toggle quote (6 lines)

> It’s surprising because when you go the comparison page, sometimes you

> can see that builds are scheduled, so we don’t yet whether it has

> succeeded. But my understanding is that the Patchwork UI will only

> display whether a build has been submitted, not whether it has

> succeeded, correct?

Indeed. It's possible to feed information about the build results back

in to Patchwork, but that'll require polling/watching the build results

as they're fed back to the Guix Data Service, I'm also not sure how

flexible Patchwork checks are.

Toggle quote (2 lines)

> We need a hands-on session. :-)

Yeah, next on my list of things is to actually send an email out about

the recent changes, but I can hopefully do more with this patch review

stuff over the next month or two.

My innovation for today is including some indication of build statuses

on the package derivation comparision page, and excitingly builds are

starting to happen for patches that I'm looking at (like [1] and [2]).

1: https://data.guix-patches.cbaines.net/compare/package-derivations?base_commit=c15509682f931f8afbe2d71ccdef278454c53774&target_commit=d9a510a2b972b90f8efed9172608f8e0d22768d1&locale=en_US.UTF-8

2: https://data.guix-patches.cbaines.net/compare/package-derivations?base_commit=1c6d98533153bc8e0e36236e7fbcf1eb5e178d26&target_commit=8335d68660ce8813b6bbf515e40ed01cae4e7fb7&locale=en_US.UTF-8

Closed

Ludovic Courtès wrote on 2 Nov 2020 16:38

Recipients:(name . Christopher Baines)(address . mail@cbaines.net)(address . 44208-done@debbugs.gnu.org)

Message-ID:87eelbkbvj.fsf@gnu.org

Hi!

Christopher Baines <mail@cbaines.net> skribis:

Toggle quote (4 lines)

> Yeah, next on my list of things is to actually send an email out about

> the recent changes, but I can hopefully do more with this patch review

> stuff over the next month or two.

Neat.

Toggle quote (7 lines)

> My innovation for today is including some indication of build statuses

> on the package derivation comparision page, and excitingly builds are

> starting to happen for patches that I'm looking at (like [1] and [2]).

> 1: https://data.guix-patches.cbaines.net/compare/package-derivations?base_commit=c15509682f931f8afbe2d71ccdef278454c53774&target_commit=d9a510a2b972b90f8efed9172608f8e0d22768d1&locale=en_US.UTF-8

> 2: https://data.guix-patches.cbaines.net/compare/package-derivations?base_commit=1c6d98533153bc8e0e36236e7fbcf1eb5e178d26&target_commit=8335d68660ce8813b6bbf515e40ed01cae4e7fb7&locale=en_US.UTF-8

Very nice! #2 is giving me “unknown commit”, maybe because the branch

has now vanished or something?

Thanks,

Ludo’.

Closed

Christopher Baines wrote on 3 Nov 2020 00:43

Recipients:(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 44208-done@debbugs.gnu.org)

Message-ID:87eelbqq9i.fsf@cbaines.net

Ludovic Courtès <ludo@gnu.org> writes:

Toggle quote (20 lines)> Hi!
>
> Christopher Baines <mail@cbaines.net> skribis:
>
>> Yeah, next on my list of things is to actually send an email out about
>> the recent changes, but I can hopefully do more with this patch review
>> stuff over the next month or two.
>
> Neat.
>
>> My innovation for today is including some indication of build statuses
>> on the package derivation comparision page, and excitingly builds are
>> starting to happen for patches that I'm looking at (like [1] and [2]).
>>
>> 1: https://data.guix-patches.cbaines.net/compare/package-derivations?base_commit=c15509682f931f8afbe2d71ccdef278454c53774&target_commit=d9a510a2b972b90f8efed9172608f8e0d22768d1&locale=en_US.UTF-8
>> 2: https://data.guix-patches.cbaines.net/compare/package-derivations?base_commit=1c6d98533153bc8e0e36236e7fbcf1eb5e178d26&target_commit=8335d68660ce8813b6bbf515e40ed01cae4e7fb7&locale=en_US.UTF-8
>
> Very nice!  #2 is giving me “unknown commit”, maybe because the branch
> has now vanished or something?

Yeah, to try and keep the Guix Data Service database from growing
indefinitely, the branches for patches are automatically deleted when
the Debbugs issue is closed, and then there's some code to remove the
relevant data from the Guix Data Service. The last bit still needs some
more work to happen automatically, and I realised yesterday that I may
need to also automate cancelling builds to coincide with the derivations
being removed from the Guix Data Service (otherwise when the build comes
around, the agents can't fetch the derivation, also it's probably good
not to waste time on these builds).

Closed

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