gmt: fix the build and make the geospatial team adopt it

[autra]

Description of changes

This MR does 2 things:

• it adopts gmt under the geospatial team. Is that ok for you @NixOS/geospatial and @tviti?
• it fixes its build

About the build fix, it seems to be yet another libxml2 fix. For some reason, the error was about libspatialite, but libspatialite package has already the libxml2 fix. netcdf on the other hand, didn't and for some reason, that brought libxml2 without httpSupport for libspatialite too:

/nix/store/81xsp348yfgmaan9r5055mcdjfw7a8wc-binutils-2.42/bin/ld: /nix/store/hfb55givv2afsz93b705hkjd9y98wqam-libspatialite-5.1.0/lib/libspatialite.so.8: undefined reference to `xmlNanoHTTPCleanup@LIBXML2_2.4.30'
collect2: error: ld returned 1 exit status
make[2]: *** [src/CMakeFiles/gmt.dir/build.make:108: src/gmt] Error 1
make[1]: *** [CMakeFiles/Makefile2:601: src/CMakeFiles/gmt.dir/all] Error 2

I don't really understand this (for me libspatialite should get its own libxml2 right?), so please have a look to my fix to ensure it is the correct one.

Another doubt I have: I decided not to patch directly netcdf derivation, but maybe we want this instead (this also fixes the build).

The build failure was discovered when updating geos (#344310)

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
  • sandbox = relaxed
  • sandbox = true
• Tested, as applicable:
  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages
• Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
• Tested basic functionality of all binary files (usually in ./result/bin/)
• 24.11 Release Notes (or backporting 23.11 and 24.05 Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
  • (Module updates) Added a release notes entry if the change is significant
  • (Module addition) Added a release notes entry if adding a new NixOS module
• Fits CONTRIBUTING.md.

---

Add a 👍 reaction to pull requests you find important.

[autra]

Result of nixpkgs-review pr 344941 run on x86_64-linux 1

5 packages built:

• gmt
• python311Packages.pygmt
• python311Packages.pygmt.dist
• python312Packages.pygmt
• python312Packages.pygmt.dist

[autra]

Result of nixpkgs-review pr 344941 run on x86_64-linux 1

5 packages built:

• gmt
• python311Packages.pygmt
• python311Packages.pygmt.dist
• python312Packages.pygmt
• python312Packages.pygmt.dist

[tviti]

This all sounds fine with me! Admittedly, I haven’t been doing as much GIS for my work, and I no longer am using a NixOS machine as a daily driver (just macOS computers w/ nixpkgs installs that I infrequently update), so having more eyes on this than just me is probably better for the community.TaylorOn Sep 27, 2024, at 1:54 PM, Augustin Trancart ***@***.***> wrote: Result of nixpkgs-review pr 344941 run on x86_64-linux 1 5 packages built: gmt python311Packages.pygmt python311Packages.pygmt.dist python312Packages.pygmt python312Packages.pygmt.dist —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: ***@***.***>

[sikmir]

Result of nixpkgs-review pr 344941 run on x86_64-darwin 1

4 packages marked as broken and skipped:

• python311Packages.pygmt
• python311Packages.pygmt.dist
• python312Packages.pygmt
• python312Packages.pygmt.dist

1 package built:

• gmt

[sikmir]

It looks like we can remove it now:

nixpkgs/pkgs/development/python-modules/pygmt/default.nix

Lines 70 to 71 in 240ba84

	# pygmt.exceptions.GMTCLibNotFoundError: Error loading the GMT shared library '/nix/store/r3xnnqgl89vrnq0kzxx0bmjwzks45mz8-gmt-6.1.1/lib/libgmt.dylib'
	broken = stdenv.hostPlatform.isDarwin;

python311Packages.pygmt and python312Packages.pygmt is fine for me on darwin-x86_64.

[autra]

@sikmir updated. I've put the geospatial team as maintainers of pygmt as well, while I was at it.

[autra]

Drafting this until #340707 is merged.

[doronbehar]

@autra would you like to close this? Or perhaps make the PR only be the adoption of the geospation team of the gmt package and related packages?