spades: 3.15.5 -> 4.0.0

[bzizou]

Description of changes

Upgrade to Spades 4.0.0

• compilation bug with gcc 13 has been fixed upstream
• copytree.patch suggested and accepted upstream

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/) ---> ./result/bin/spades.py --test
• 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.

[superherointj]

@bzizou I want to mark this as draft until you are ready for review.

Possibilities:

1. Use fetchpatch now. (pinned to commit)
2. Wait for upstream to catch up with patch.

[superherointj]

Can you add:

meta.changelog = "https://github.com/ablab/spades/blob/v${finalAttrs.version}/changelog.md";
meta.downloadPage = "https://github.com/ablab/spades";

[superherointj]

Git commit message body (the second line after title) is missing the release notes:

Release: https://github.com/ablab/spades/releases/tag/v4.0.0

[superherointj]

I have successfully built:

nix build .#pkgsCross.aarch64-multiplatform.spades

Meaning, "aarch64-linux" platform is supported but unlisted.

When adding it, respect alphabetical order.

[superherointj]

pkgsMusl.spades, pkgsStatic.spades are broken.

nix build .#pkgsMusl.spades

Logs: https://termbin.com/sik1

As pkgsMusl.gtest builds fine. Likely problem is the non-Nix vendoring.

A Nix dependency if built independently, will be cached, which de-duplicates builds of this dependency and improve build times for downstream packages. Whenever possible, avoid vendoring and package dependencies as Nix dependencies.

[superherointj]

Please add:

strictDeps = true;

(This is useful in separating kinds of dependencies for cross build. This should be true by default but for legacy reasons it is not)

Then, you can check if python3 (maybe bzip2?) are only needed during build time, hence nativeBuildInputs. Otherwise if needed for final output it's buildInputs.
Also, check if application work as expected. (To confirm these dependencies are not needed at runtime.)

[superherointj]

fetchpatch of copytree.patch is failing at nixpkgs-review

[bzizou]

I agree that redistributing dependencies is dirty... they are numerous: https://github.com/ablab/spades/tree/next/ext/src

I tried to disable some, to replace them by dependencies to nix package but their Cmake files are not ok, and this leads to includes or libraries not found. My knowledge in cmake is probably not sufficient to find some solutions... and I already spent too much time on this. Sorry. So --> broken = stdenv.hostPlatform.isMusl; Maybe should I also add broken = stdenv.hostPlatform.isStatic; ?

Done

[superherointj]

@bzizou LGTM. Only the Darwin build needs to be confirmed.
By any chance, are you able to build this package for Darwin?
If not, we can ping Darwin maintainers for this.

[superherointj]

@toonn Can you post build results for Darwin? Thanks. Sorry for the inconvenience. CI is just unreliable/slow for Darwin?

[superherointj]

I'm approving this despite Darwin build being unknown.

Update: Watching build at:
https://hydra.nixos.org/build/264908242

[bzizou]

@bzizou LGTM. Only the Darwin build needs to be confirmed. By any chance, are you able to build this package for Darwin? If not, we can ping Darwin maintainers for this.

No, I've got no Darwin host

[superherointj]

Darwin build is broken:

https://hydra.nixos.org/build/264908242/nixlog/1

@bzizou Can it be fixed or should we mark it broken for Darwin?