Add Climate Data Operators package

Hello Guix,

I would like to contribute a patch to add the Climate Data Operators

package to Guix's geo module. Could you please review it?

Thanks, Roman.

Hi Roman,

NetCDF support isn't working in your patch. The software says this:

"Unsupported file type (library support not compiled in)

To create a CDO application with NetCDF support use:

./configure --with-netcdf=<NetCDF root directory> ..."

So it looks like you will have to modify the configure phase a little.

I don't think you need the expression

`(modules '((guix build utils))`

as you are not using that module in your source expression.

`licenses` doesn't have to be a list unless cdo is dual-licensed.

Please run `guix style` and `guix lint` (using pre-inst-env), which will

help make sure the code style follows the Guix style guidelines.

Thanks,

Antero

Hi Antero,

thanks for your review! Here's an updated version of the patch. I added

--with-netcdf to the configure flags, removed the build utils, added

spaces between sentences and don't use a list for the licence field

anymore.

Could you have another look please?

I'm not sure if I addressed all lint issues, since this command is

failing on my machine recently. Any idea what this could be? Here's the

backtrace of the lint command:

```

[roman@thinkpad guix]$ ./pre-inst-env guix lint cdo

;;; note: source file /home/roman/workspace/guix/gnu/packages/geo.scm

;;; newer than compiled /home/roman/workspace/guix/gnu/packages/geo.go

;;; note: source file /home/roman/workspace/guix/gnu/packages/geo.scm

;;; newer than compiled /home/roman/.cache/guile/ccache/3.0-LE-8-4.5/home/roman/workspace/guix/gnu/packages/geo.scm.go

;;; Failed to autoload html->sxml in (htmlprag):

;;; no code for module (htmlprag)

Backtrace:

In ice-9/boot-9.scm:

1752:10 18 (with-exception-handler _ _ #:unwind? _ # _)

In unknown file:

17 (apply-smob/0 #<thunk 7f3b46a28f60>)

In ice-9/boot-9.scm:

724:2 16 (call-with-prompt _ _ #<procedure default-prompt-handle…>)

In ice-9/eval.scm:

619:8 15 (_ #(#(#<directory (guile-user) 7f3b46a22c80>)))

In guix/ui.scm:

2238:7 14 (run-guix . _)

2201:10 13 (run-guix-command _ . _)

In ice-9/boot-9.scm:

1752:10 12 (with-exception-handler _ _ #:unwind? _ # _)

1752:10 11 (with-exception-handler _ _ #:unwind? _ # _)

In guix/store.scm:

659:37 10 (thunk)

In srfi/srfi-1.scm:

634:9 9 (for-each #<procedure 7f3b4531efa0 at guix/scripts/lin…> …)

In guix/scripts/lint.scm:

65:4 8 (run-checkers _ _ #:store _)

In srfi/srfi-1.scm:

634:9 7 (for-each #<procedure 7f3b31769de0 at guix/scripts/lin…> …)

In guix/scripts/lint.scm:

74:21 6 (_ _)

In guix/lint.scm:

1476:5 5 (check-for-updates #<package cdo@2.0.5 /home/roman/work…>)

811:2 4 (call-with-networking-fail-safe _ _ _)

In ice-9/boot-9.scm:

1752:10 3 (with-exception-handler _ _ #:unwind? _ # _)

1685:16 2 (raise-exception _ #:continuable? _)

1683:16 1 (raise-exception _ #:continuable? _)

1685:16 0 (raise-exception _ #:continuable? _)

ice-9/boot-9.scm:1685:16: In procedure raise-exception:

error: html->sxml: unbound variable

```

Thanks, Roman.

Roman!

Roman Scherer ???

[…]

This is probably solved by running the command above in a guix

shell:

$ guix shell guix -- ./pre-inst-env guix lint cdo

‘pre-inst-env’ sets up some environment (variables) like

GUILE_LOAD_PATH to ensure that Guix can run from your local git

checkout, but nothing more.

Most importantly, it does not create a full Guix profile with the

numerous dependencies of the ‘guix’ package — including the

‘guile-lib’ package that provides HTML->SXML.

That's what the ‘guix shell’ is for. It's a clean alternative to

‘guix install’ing all these guile-* packages into your user

profile. Both work.

Kind regards,

T G-R

Hi Tobias,

thanks for the tip. Unfortunately the command you sent me is not

enough. I still get this error with `guix shell guix`:

```

[roman@thinkpad guix]$ guix shell guix -- ./pre-inst-env guix lint gdal

;;; note: source file /home/roman/workspace/guix/gnu/packages/geo.scm

;;; newer than compiled /home/roman/workspace/guix/gnu/packages/geo.go

;;; note: source file /home/roman/workspace/guix/gnu/packages/geo.scm

;;; newer than compiled /home/roman/.cache/guile/ccache/3.0-LE-8-4.5/home/roman/workspace/guix/gnu/packages/geo.scm.go

;;; Failed to autoload html->sxml in (htmlprag):

;;; no code for module (htmlprag)

Backtrace:

In ice-9/boot-9.scm:

1752:10 18 (with-exception-handler _ _ #:unwind? _ # _)

In unknown file:

17 (apply-smob/0 #<thunk 7f09e3748f60>)

In ice-9/boot-9.scm:

724:2 16 (call-with-prompt _ _ #<procedure default-prompt-handle…>)

In ice-9/eval.scm:

619:8 15 (_ #(#(#<directory (guile-user) 7f09e3742c80>)))

In guix/ui.scm:

2238:7 14 (run-guix . _)

2201:10 13 (run-guix-command _ . _)

In ice-9/boot-9.scm:

1752:10 12 (with-exception-handler _ _ #:unwind? _ # _)

1752:10 11 (with-exception-handler _ _ #:unwind? _ # _)

In guix/store.scm:

659:37 10 (thunk)

In srfi/srfi-1.scm:

634:9 9 (for-each #<procedure 7f09e21bc9e0 at guix/scripts/lin…> …)

In guix/scripts/lint.scm:

65:4 8 (run-checkers _ _ #:store _)

In srfi/srfi-1.scm:

634:9 7 (for-each #<procedure 7f09d2d94c60 at guix/scripts/lin…> …)

In guix/scripts/lint.scm:

74:21 6 (_ _)

In guix/lint.scm:

1476:5 5 (check-for-updates #<package gdal@3.5.0 /home/roman/wor…>)

811:2 4 (call-with-networking-fail-safe _ _ _)

In ice-9/boot-9.scm:

1752:10 3 (with-exception-handler _ _ #:unwind? _ # _)

1685:16 2 (raise-exception _ #:continuable? _)

1683:16 1 (raise-exception _ #:continuable? _)

1685:16 0 (raise-exception _ #:continuable? _)

ice-9/boot-9.scm:1685:16: In procedure raise-exception:

error: html->sxml: unbound variable

```

However, after adding guile-lib to my home profile, it seems to work!

Thanks, Roman.

Tobias Geerinckx-Rice <me@tobias.gr> writes:

Roman,

Roman Scherer ???

That's because I'm an old, who's still used to the (deprecated)

‘guix environment’, but wanted to sound hip by saying ‘guix shell’

instead. A recipe for failure.

The two are semantically equivalent but not identical, so I should

have said

$ guix shell -D guix -- ./pre-inst-env stuff

Note the -D, for --development (‘add P's inputs rather than P

itself’).

Nothing wrong with keeping guile-* packages in your user profile

but the above is a bit cleaner.

Kind regards,

T G-R

Haha, ok. Thanks for the explanation Tobias. I think I leave it in my

home profile, I already have some other guile packages in it.

Tobias Geerinckx-Rice <me@tobias.gr> writes:

Hi,

Roman Scherer <roman.scherer@burningswell.com> skribis:

I tweaked the description and commit log, change #:configure-flags to

use the ‘this-package-input’ idiom, and committed.

Thanks!

Ludo’.

Cool, I didn't know about this-package-input.

Thank you!

Ludovic Courtès <ludo@gnu.org> writes: