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@Pandapip1 Pandapip1 commented May 13, 2024

Description of changes

NOTE: Fails due to a broken dependency on python >= 3.12 (#326199)

⚠️ Warning to reviewers: The closure size is 51.55 GiB, due to a large database (metaphlan-db, size 50.7 GiB) that is downloaded as part of the package.

Closes #299219

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:
  • 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/)
  • 24.05 Release Notes (or backporting 23.05 and 23.11 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.

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Result of nixpkgs-review pr 311463 run on x86_64-linux 1

7 packages built:
  • hclust2
  • hclust2.dist
  • metaphlan
  • metaphlan-db
  • metaphlan.dist
  • phylophlan
  • phylophlan.dist

license = licenses.cc0; # These are raw data files not covered under copyright law
maintainers = with maintainers; [ pandapip1 ];
platforms = platforms.all;
hydraPlatforms = []; # Exceeds Hydra's maximum build size
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@Pandapip1 Pandapip1 May 13, 2024

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This particular package is a static database that metaphlan requires in order to function. It's quite large (~30GB built), and isn't terribly well compressed, so for as long as the builder has to keep srcs in storage, it'll effectively have double the storage use.

As this is insanely huge for a Nix package (enough so that hydra can't support it), I have disabled hydra builds for the database.

@ofborg ofborg bot added 8.has: package (new) This PR adds a new package 11.by: package-maintainer This PR was created by a maintainer of all the package it changes. 10.rebuild-darwin: 1-10 This PR causes between 1 and 10 packages to rebuild on Darwin. 10.rebuild-linux: 1-10 This PR causes between 1 and 10 packages to rebuild on Linux. labels May 13, 2024
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The comments for hclust2 partially also apply for the other Python parts in this PR.

@Pandapip1 Pandapip1 force-pushed the init-metaphlan branch 5 times, most recently from 1be6733 to baf8091 Compare May 14, 2024 16:31
@Pandapip1 Pandapip1 requested a review from alyssais as a code owner May 14, 2024 16:31
@github-actions github-actions bot added the 6.topic: lib The Nixpkgs function library label May 14, 2024
@Pandapip1 Pandapip1 requested a review from fabaff May 14, 2024 16:32
@Pandapip1 Pandapip1 force-pushed the init-metaphlan branch 3 times, most recently from 970eca5 to a39b311 Compare May 20, 2024 20:35
@github-actions github-actions bot removed the 6.topic: lib The Nixpkgs function library label May 20, 2024
@Pandapip1 Pandapip1 requested a review from alyssais May 20, 2024 20:35
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Re-requesting review: @fabaff

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@GrahamcOfBorg eval

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Bump

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I've made a couple modifications to save some disk space, format the packages more correctly, and build faster.

@Pandapip1 Pandapip1 requested a review from natsukium as a code owner July 10, 2024 18:26
@github-actions github-actions bot added the 6.topic: python Python is a high-level, general-purpose programming language. label Jul 10, 2024
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Pandapip1 commented Sep 3, 2024

Rebased, since it was getting a lil out of date.

EDIT: Also just removed a with lib;

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Pandapip1 commented Sep 3, 2024

Result of nixpkgs-review pr 311463 run on x86_64-linux 1

4 packages failed to build:
  • python312Packages.metaphlan
  • python312Packages.metaphlan.dist
  • python312Packages.phylophlan
  • python312Packages.phylophlan.dist
9 packages built:
  • metaphlan-db
  • python311Packages.hclust2
  • python311Packages.hclust2.dist
  • python311Packages.metaphlan
  • python311Packages.metaphlan.dist
  • python311Packages.phylophlan
  • python311Packages.phylophlan.dist
  • python312Packages.hclust2
  • python312Packages.hclust2.dist

Blocked on #326199 PR merged, rerunning nixpkgs-review

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Result of nixpkgs-review pr 311463 run on x86_64-linux 1

13 packages built:
  • metaphlan-db
  • python311Packages.hclust2
  • python311Packages.hclust2.dist
  • python311Packages.metaphlan
  • python311Packages.metaphlan.dist
  • python311Packages.phylophlan
  • python311Packages.phylophlan.dist
  • python312Packages.hclust2
  • python312Packages.hclust2.dist
  • python312Packages.metaphlan
  • python312Packages.metaphlan.dist
  • python312Packages.phylophlan
  • python312Packages.phylophlan.dist

@Pandapip1 Pandapip1 changed the title metaphlan: init at 4.1.0 python312Packages.metaphlan: init at 4.1.0 Sep 8, 2024
Gavin John and others added 5 commits September 9, 2024 13:46
Co-authored-by: Fabian Affolter <mail@fabian-affolter.ch>
Co-authored-by: Fabian Affolter <mail@fabian-affolter.ch>
Co-authored-by: Fabian Affolter <mail@fabian-affolter.ch>
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Thanks, changes LGTM and packages build (excluding the big files)

@wegank wegank added the 12.approvals: 1 This PR was reviewed and approved by one person. label Dec 9, 2024
…ages.metaphlan}: transition to fetchurl { tag = ...; ...}
@wegank wegank removed the 12.approvals: 1 This PR was reviewed and approved by one person. label Dec 12, 2024
@wegank wegank added the 2.status: merge conflict This PR has merge conflicts with the target branch label Apr 2, 2025
@nixpkgs-ci nixpkgs-ci bot added 2.status: stale https://github.com/NixOS/nixpkgs/blob/master/.github/STALE-BOT.md 12.approvals: 1 This PR was reviewed and approved by one person. labels Jun 25, 2025
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2.status: merge conflict This PR has merge conflicts with the target branch 2.status: stale https://github.com/NixOS/nixpkgs/blob/master/.github/STALE-BOT.md 6.topic: python Python is a high-level, general-purpose programming language. 8.has: package (new) This PR adds a new package 10.rebuild-darwin: 1-10 This PR causes between 1 and 10 packages to rebuild on Darwin. 10.rebuild-linux: 1-10 This PR causes between 1 and 10 packages to rebuild on Linux. 11.by: package-maintainer This PR was created by a maintainer of all the package it changes. 12.approvals: 1 This PR was reviewed and approved by one person.
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Package request: metaphlan
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