Just wondering if it's possible to include an automatic "last updated" date at the top of manuscript following new builds/updates.
Possibly helpful:
https://github.com/mgeier/sphinx-last-updated-by-git/

Bug Description
Instructions for songbird installation on top of the latest QIIME 2 distribution cause errors. It appears the latest version of songbird is at odds with the QIIME 2 environment's Python version.

Steps to reproduce the behavior

1. Install QIIME 2 core distribution (release 2021.8) in conda virtual environment
2. Follow tutorial instructions to install songbird in the environment: conda install songbird -c conda-forge
3. See error screenshot below

Screenshots

Computation Environment

• OS: macOS Big Sur
• QIIME 2 Release 2021.8, in conda environment

Bug Description
In "Taxonomic classification" section the link to ref-seqs for training NaiveBayes classifier is not available anymore. It probably should be replaced by "https://github.com/BenKaehler/readytowear/raw/master/data/gg_13_8/515f-806r/ref-seqs.qza".

Steps to reproduce the behavior

1. Run

wget \
  -O "ref-seqs-v4.qza" \
  "https://github.com/BenKaehler/readytowear/raw/master/data/gg_13_8/515f-806r/ref-seqs-v4.qza"`

2. See ERROR 404: Not Found..

Bug Description
The given command for computing diversity uses an outdated flag --p-n-jobs. The latest release of QIIME 2 (core 2021.8 distribution) renamed this to --p-n-jobs-or-threads.

Steps to reproduce this behavior

1. Follow the tutorial
2. Error out running qiime diversity core-metrics-phylogenetic, found twice in the alpha diversity section

Bug Description
The metadata file in qiita must have been swapped since the last time these docs were built/tested.

The tutorial fails to run now because (most) metadata columns are missing. These are the only columns that I am finding right now in the file 81253_mapping_file.txt:
sample_name platform qiita_prep_id run_prefix

Steps to reproduce the behavior

1. Follow the tutorial
2. The moment you use the metadata file for anything, it fails on missing metadata columns

I am assuming that those columns were once present in the original metadata file, since this tutorial worked previously.