[Preview] QIIME 2 2025.4 breaking changes & environment files

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QIIME 2 2025.4 has been released!
Please see the official changelog and breaking changes/environment files posts for more details.

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:exclamation: Important :exclamation:

The following is an early developer preview of all interface & API changes expected in 2025.4, as well as a list of our targeted environment file updates.

Changes will be added up until February 6th, when we will post a formal announcement for our developer community.

Below is the list of guaranteed interface changes, plugin API changes, and environment file updates for the 2025.4 QIIME 2 release. You can use the linked environment files for each distribution to ensure compatibility with any plugin you're developing against the relevant distribution it should be tested/used within. Note that these 'seed' environment files won't change between now and the 2025.4 release, but the full environment files that conda will resolve at any given installation will change. This shouldn't impact your development process, as all of the core dependencies in these 'seed' files will remain the same.

QIIME 2 Library Changes :books:
The QIIME 2 Library has been entirely remade and redesigned by @ebolyen! The site now lists: books & tutorials, videos, workshops, and data resources in addition to the existing plugins.

In addition, the following 3rd party plugins have been added to the library in addition to many plugins from the core QIIME 2 team at the Caporaso Lab and the Bokulich Lab:

QIIME 2 View changes :magnifying_glass_tilted_left:

@Oddant1 added a new Metadata tab to QIIME 2 View that lists all of the Metadata contained within your provenance and provides information about why this metadata may be important.

@Oddant1 added the ability to search provenance for specific keys and key: value pairs on the provenance tab of QIIME 2 View.

@Oddant1 created a vendored version of q2view that will be opened by invoking qiime tools view. See the q2cli section for more details.

Interface Changes :tv:

  • q2cli

    • The --key parameter to qiime tools cache-remove can now be passed multiple times to remove multiple keys.
    • The command qiime tools view can now be given .qza or .qzv files not just .qzvs and will open a fully featured view of the given Result including provenance and citations as if it were opened in q2view. This is done by running a locally hosted Python server when the command is invoked.
    • The command qiime tools view now accepts a --verbose argument that when provided will cause all http requests made to the locally hosted server to be printed to the console (the formatting of the printing often looks a bit goofy so, beware).

  • q2-dada2

    • The pooled option to the --p-chimera-method parameter was removed as it should only be used in tandem with other parameter options that are not available in QIIME2.

Plugin API Changes :electric_plug:

  • qiime2
    • The function get_cache used to get the Artifact Cache currently in use by QIIME 2 has been exposed to plugin developers as importable via qiime2.get_cache

Environment File Changes :card_file_box:

NOTE: The metagenome distribution has been renamed to moshpit!

  • tiny
    • biom-format has been bumped to 2.1.16
    • rnanorm has been pinned at 2.1.0 until our next bump of sklearn (to support API changes)
    • scikit-bio has been bumped to 0.6.2
  • amplicon
    • rpy2 has been added as a new external dependency to support the new ANCOM-BC2 wrapper within q2-composition
    • biom-format has been bumped to 2.1.16
    • fastp 0.24.0 has been added as a new dependency for future functionality in amplicon and moshpit distributions
    • r-vegan has been bumped to 2.6_8
    • rnanorm has been pinned at 2.1.0 until our next bump of sklearn (to support API changes)
    • scikit-bio has been bumped to 0.6.2
  • moshpit
    • q2-alignment has been added as a new QIIME 2 dependency, as RESCRIPt now depends on it.
    • q2-moshpit has been renamed to q2-annotate
    • biom-format has been bumped to 2.1.16
    • fastp 0.24.0 has been added as a new dependency for future functionality in amplicon and moshpit distributions
    • mafft has been pinned at 7.526 due to second order dependencies
    • rnanorm has been pinned at 2.1.0 until our next bump of sklearn (to support API changes)
    • scikit-bio has been bumped to 0.6.2
    • spades has been bumped to 4.0.0
  • pathogenome
    • biom-format has been bumped to 2.1.16
    • mafft has been pinned at 7.526 due to second order dependencies
    • rnanorm has been pinned at 2.1.0 until our next bump of sklearn (to support API changes)
    • scikit-bio has been bumped to 0.6.2
    • spades has been bumped to 4.0.0
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