maint: 2021.4 final prep (#506)

source/data-resources.rst

@@ -10,20 +10,21 @@ Taxonomy classifiers for use with q2-feature-classifier
 
 Naive Bayes classifiers trained on:
 
-- `Silva 138 99% OTUs full-length sequences <https://data.qiime2.org/2021.4/common/silva-138-99-nb-classifier.qza>`_ (MD5: ``fddefff8bfa2bbfa08b9cad36bcdf709``)
-- `Silva 138 99% OTUs from 515F/806R region of sequences <https://data.qiime2.org/2021.4/common/silva-138-99-515-806-nb-classifier.qza>`_ (MD5: ``28105eb0f1256bf38b9bb310c701dc4e``)
-- `Greengenes 13_8 99% OTUs full-length sequences <https://data.qiime2.org/2021.4/common/gg-13-8-99-nb-classifier.qza>`_ (MD5: ``03078d15b265f3d2d73ce97661e370b1``)
-- `Greengenes 13_8 99% OTUs from 515F/806R region of sequences <https://data.qiime2.org/2021.4/common/gg-13-8-99-515-806-nb-classifier.qza>`_ (MD5: ``682be39339ef36a622b363b8ee2ff88b``)
+.. TODO: uncomment when ready
+.. - `Silva 138 99% OTUs full-length sequences <https://data.qiime2.org/2021.4/common/silva-138-99-nb-classifier.qza>`_ (MD5: ``TBD``)
+.. - `Silva 138 99% OTUs from 515F/806R region of sequences <https://data.qiime2.org/2021.4/common/silva-138-99-515-806-nb-classifier.qza>`_ (MD5: ``TBD``)
 
+- `Greengenes 13_8 99% OTUs full-length sequences <https://data.qiime2.org/2021.4/common/gg-13-8-99-nb-classifier.qza>`_ (MD5: ``6bbc9b3f2f9b51d663063a7979dd95f1``)
+- `Greengenes 13_8 99% OTUs from 515F/806R region of sequences <https://data.qiime2.org/2021.4/common/gg-13-8-99-515-806-nb-classifier.qza>`_ (MD5: ``9e82e8969303b3a86ac941ceafeeac86``)
+- Silva classifiers coming soon
 
 Please cite the following references if you use any of these pre-trained classifiers:
 
 - Bokulich, N.A., Robeson, M., Dillon, M.R. bokulich-lab/RESCRIPt. Zenodo. http://doi.org/10.5281/zenodo.3891931
 - Bokulich, N.A., Kaehler, B.D., Rideout, J.R. et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6, 90 (2018). https://doi.org/10.1186/s40168-018-0470-z
 - See the `SILVA website <https://www.arb-silva.de/>`_ and the latest `Greengenes publication <https://www.nature.com/articles/ismej2011139>`_ for the latest citation information for these reference databases.
 
-Please note, these classifiers were trained using scikit-learn 0.23.1, and therefore can only be used with scikit-learn 0.23.1. If you observe errors related to scikit-learn version mismatches, please ensure you are using the pretrained-classifiers that were published with the release of QIIME 2 you are using.
-
+Please note, these classifiers were trained using scikit-learn 0.24.1, and therefore can only be used with scikit-learn 0.24.1. If you observe errors related to scikit-learn version mismatches, please ensure you are using the pretrained-classifiers that were published with the release of QIIME 2 you are using.
 
 .. _`marker gene db`:
 

source/install/native.rst

@@ -67,23 +67,23 @@ like for the environment. In this example, we'll name the environment
             </p>
          </div>
          <div id="macOS" class="tab-pane fade">
-            <pre>wget https://data.qiime2.org/distro/core/qiime2-2021.4-py36-osx-conda.yml
-   conda env create -n qiime2-2021.4 --file qiime2-2021.4-py36-osx-conda.yml
+            <pre>wget https://data.qiime2.org/distro/core/qiime2-2021.4-py38-osx-conda.yml
+   conda env create -n qiime2-2021.4 --file qiime2-2021.4-py38-osx-conda.yml
    # OPTIONAL CLEANUP
-   rm qiime2-2021.4-py36-osx-conda.yml</pre>
+   rm qiime2-2021.4-py38-osx-conda.yml</pre>
          </div>
          <div id="linux" class="tab-pane fade">
-            <pre>wget https://data.qiime2.org/distro/core/qiime2-2021.4-py36-linux-conda.yml
-   conda env create -n qiime2-2021.4 --file qiime2-2021.4-py36-linux-conda.yml
+            <pre>wget https://data.qiime2.org/distro/core/qiime2-2021.4-py38-linux-conda.yml
+   conda env create -n qiime2-2021.4 --file qiime2-2021.4-py38-linux-conda.yml
    # OPTIONAL CLEANUP
-   rm qiime2-2021.4-py36-linux-conda.yml</pre>
+   rm qiime2-2021.4-py38-linux-conda.yml</pre>
          </div>
          <div id="wsl" class="tab-pane fade">
             <pre># These instructions are identical to the Linux (64-bit) instructions
-   wget https://data.qiime2.org/distro/core/qiime2-2021.4-py36-linux-conda.yml
-   conda env create -n qiime2-2021.4 --file qiime2-2021.4-py36-linux-conda.yml
+   wget https://data.qiime2.org/distro/core/qiime2-2021.4-py38-linux-conda.yml
+   conda env create -n qiime2-2021.4 --file qiime2-2021.4-py38-linux-conda.yml
    # OPTIONAL CLEANUP
-   rm qiime2-2021.4-py36-linux-conda.yml</pre>
+   rm qiime2-2021.4-py38-linux-conda.yml</pre>
          </div>
       </div>
    </div>