various little updates

book/_config.yml

@@ -54,7 +54,8 @@ html:
 parse:
   myst_substitutions:
     miniconda_url: "[Miniconda](https://conda.io/miniconda.html)"
-    release_epoch: "2024.5"
+    release_epoch: "2024.10"
+    development_epoch: "2025.4"
     tutorial_environment_block: |
       ````{admonition} Reminder
       :class: tip

book/intro.md

@@ -1,11 +1,11 @@
 # *Using QIIME 2*
 
-**Make QIIME 2 work for you.**
+**Your guide to becoming a QIIME 2 Framework power user.**
 
 ```{admonition} Development status of this content
 :class: note
 *Using QIIME 2* is in an early stage of development, and as a result the documentation at https://docs.qiime2.org is still an important source of information for learning to use QIIME 2.
-Over the next few months (as of 10 October 2024), existing content will be migrated and new content will developed.
+Over the next few months (as of 17 January 2025), existing content will be migrated and new content will developed.
 Ultimately https://docs.qiime2.org will be retired.
 While *Using QIIME 2* is in development, some URLs may change.
 
@@ -14,24 +14,24 @@ The canonical URL for this project is https://use.qiime2.org.
 
 ## Goals and development plan for *Using QIIME 2*
 
-As the ecosystem of QIIME 2 {term}`distributions <distribution>` and {term}`plugins <plugin>` continues to grow, it has become necessary to make a split in the documentation between general-purpose information that describes how to use QIIME 2 itself (i.e., "the QIIME 2 framework" 🌳), and how to apply the tools it supports to achieve your data analysis goals.
+As the ecosystem of QIIME 2 {term}`distributions <distribution>` and {term}`plugins <plugin>` continues to grow, it has become necessary to make a split in the documentation between general-purpose information that describes how to use QIIME 2 itself **(i.e., "the QIIME 2 framework" 🌳)**, and how to apply the tools it supports to achieve your data analysis goals.
 We know that you're interested in QIIME 2 primarily for the latter -- to achieve specific analysis goals related to microbiome data science -- so our goal is that *Using QIIME 2* serves primarily as a source for you to refer to when you need to accomplish specific tasks that are general to using the system.
-That includes things like [using `Artifacts` as metadata](metadata-merge), replaying provenance[^replaying-provenance-issue], and [configuring your parallel computing environment](parallel-configuration).
+That includes things like [using `Artifacts` as metadata](metadata-merge), replaying provenance[^replaying-provenance-issue], [creating and using an artifact cache](artifact-cache-tutorial) and [configuring your parallel computing environment](parallel-configuration).
 It will also include explanations that can help you understand the system when you want to go deeper, including things like what QIIME 2 {term}`Artifacts <artifact>` (e.g., {term}`.qza <qza>` files) and {term}`Visualizations <visualization>` (e.g., {term}`.qzv <qzv>` files) are[^result-explanation-issue], and why you need to import your data into `Artifacts` before using QIIME 2[^importing-explanation-issue].
-Generally speaking, **understanding these topics will help you understand what you're doing and empower you to become a QIIME 2 power user, but they aren't strictly necessary to perform simple data analysis.**
+Generally speaking, **understanding these topics will help you understand what you're doing and empower you to become a QIIME 2 Framework power user, but they aren't strictly necessary to perform simple data analysis.**
 
 In addition to *Using QIIME 2*, we are building distribution-specific and plugin-specific documentation.
 **These will be designed to quickly get you started with performing your first data analysis with QIIME 2,** and will fall into a few categories.
 
 ### Distribution-specific documentation
 
 The "old" user documentation at https://docs.qiime2.org serves this purpose for the *amplicon distribution*.
-For example, you can start there to get instructions on how to [install QIIME 2](https://docs.qiime2.org/2024.5/install/), use it to carry out an [analysis of microbiome amplicon data](https://docs.qiime2.org/2024.5/tutorials/moving-pictures-usage/), and [see a reference](https://docs.qiime2.org/2024.5/plugins/) of the {term}`plugins <plugin>` and {term}`actions <action>` that are included in the *amplicon distribution*.
+For example, you can start there to get instructions on how to [install QIIME 2](https://docs.qiime2.org/2024.10/install/), use it to carry out an [analysis of microbiome amplicon data](https://docs.qiime2.org/2024.10/tutorials/moving-pictures-usage/), and [see a reference](https://docs.qiime2.org/2024.10/plugins/) of the {term}`plugins <plugin>` and {term}`actions <action>` that are included in the *amplicon distribution*.
 That user documentation predates the diverse distributions and plugins that now exist in the ecosystem - it therefore mixes distribution-specific information with the general purpose information that is currently being transitioned to *Using QIIME 2*.
 
 ### Plugin-specific documentation
 
-Stand-alone plugins (i.e., those not included in existing distributions), like [q2-boots](https://github.com/caporaso-lab/q2-boots), will provide their own documentation linked from the new QIIME 2 Library[^new-library-not-live].
+Stand-alone plugins (i.e., those not included in existing distributions), like [q2-boots](https://github.com/caporaso-lab/q2-boots), will provide their own documentation linked from [the new QIIME 2 Library](https://library.qiime2.org)[^new-library-wip].
 For now, you can refer to the [q2-boots documentation here](https://q2-boots.readthedocs.io/en/latest/), as an example of where we're going.
 
 ### Data-set specific documentation
@@ -94,6 +94,7 @@ Initial support for the development of QIIME 2 was provided through a [grant](ht
  <p xmlns:cc="http://creativecommons.org/ns#" xmlns:dct="http://purl.org/dc/terms/"><a property="dct:title" rel="cc:attributionURL" href="https://use.qiime2.org">Using QIIME 2</a> led by <a rel="cc:attributionURL dct:creator" property="cc:attributionName" href="https://cap-lab.bio">Greg Caporaso</a> is licensed under <a href="https://creativecommons.org/licenses/by-nc-nd/4.0/?ref=chooser-v1" target="_blank" rel="license noopener noreferrer" style="display:inline-block;">CC BY-NC-ND 4.0 <img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/cc.svg?ref=chooser-v1" alt=""><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/by.svg?ref=chooser-v1" alt=""><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/nc.svg?ref=chooser-v1" alt=""><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/nd.svg?ref=chooser-v1" alt=""></a>.</p>
 
 [^replaying-provenance-issue]: See [here](https://github.com/caporaso-lab/using-qiime2/issues/13).
- [^new-library-not-live]: The new QIIME 2 Library is not yet live, but will be soon (as of 10 October 2024).
- [^result-explanation-issue]: See [here](https://github.com/caporaso-lab/using-qiime2/issues/11).
- [^importing-explanation-issue]: See [here](https://github.com/caporaso-lab/using-qiime2/issues/12).
+[^new-library-wip]: The new QIIME 2 Library is in the early stages of development (as of 17 January 2025) - a lot of exciting new functionality for both users and developers is currently in progress!
+For the time-being, you can still find the old QIIME 2 Library at https://old-library.qiime2.org.
+[^result-explanation-issue]: See [here](https://github.com/caporaso-lab/using-qiime2/issues/11).
+[^importing-explanation-issue]: See [here](https://github.com/caporaso-lab/using-qiime2/issues/12).

book/tutorials/intro.md

@@ -27,36 +27,36 @@ conda update conda
 ## Install the QIIME 2 "Tiny Distribution"
 
 The QIIME 2 "Tiny Distribution" is a minimal set of QIIME 2 functionality for building and using plugins through the QIIME 2 command line or Python 3 API.
-Here's we'll install the most recent release version of QIIME 2, QIIME 2 {{ release_epoch }}.
+Here's we'll install the most recent development version of QIIME 2, QIIME 2 {{ development_epoch }}.
 
-% Unfortunately we can't use MyST substitutions in literals, so including `{{ release_epoch }}` in the following install commands won't work.
+% Unfortunately we can't use MyST substitutions in literals, so including `{{ development_epoch }}` in the following install commands won't work.
 % We need to figure out how we want to address this in the future to automatically update these commands on new releases.
 % Options are having a `latest` URL for release versions, or running a pre-processing script to update these docs before building them.
 
 `````{tab-set}
 ````{tab-item} macOS
 ```bash
-conda env create -n using-qiime2 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.5-py39-osx-conda.yml
+conda env create -n using-qiime2 --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-macos-latest-conda.yml
 ```
 ````
 
 ````{tab-item} Linux
 ```bash
-conda env create -n using-qiime2 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.5-py39-linux-conda.yml
+conda env create -n using-qiime2 --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-ubuntu-latest-conda.yml
 ```
 ````
 
 ````{tab-item} macOS (Apple Silicon)
 ```bash
-CONDA_SUBDIR=osx-64 conda env create -n using-qiime2 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.5-py39-osx-conda.yml
+CONDA_SUBDIR=osx-64 conda env create -n using-qiime2 --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-macos-latest-conda.yml
 conda activate using-qiime2
 conda config --env --set subdir osx-64
 ```
 ````
 
 ````{tab-item} Windows (via WSL)
 ```bash
-conda env create -n using-qiime2 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.5-py39-linux-conda.yml
+conda env create -n using-qiime2 --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-ubuntu-latest-conda.yml
 ```
 ````
 
@@ -80,19 +80,16 @@ You should see something like the following, though the version numbers you'll s
 
 ```
 System versions
-Python version: 3.9.19
-QIIME 2 release: 2024.5
-QIIME 2 version: 2024.5.1
-q2cli version: 2024.5.0
+Python version: 3.10.14
+QIIME 2 release: 2025.4
+QIIME 2 version: 2025.4.0.dev0+11.g85975ad
+q2cli version: 2025.4.0.dev0+8.g63d82cb
 
 Installed plugins
-types: 2024.5.0
+metadata: 2025.4.0.dev0+5.g7af916f
+types: 2025.4.0.dev0+6.g11e14d8
 
-Application config directory
-/Users/jgc/miniconda3/envs/using-qiime2/var/q2cli
-
-Getting help
-To get help with QIIME 2, visit https://qiime2.org
+...
 ```
 
 At this stage you have a working QIIME 2 environment, but it doesn't do a whole lot.
@@ -113,20 +110,17 @@ If you run `qiime info` again, you should now see a new plugin, `dwq2`, in the l
 
 ```
 System versions
-Python version: 3.9.19
-QIIME 2 release: 2024.5
-QIIME 2 version: 2024.5.1
-q2cli version: 2024.5.0
+Python version: 3.10.14
+QIIME 2 release: 2025.4
+QIIME 2 version: 2025.4.0.dev0+11.g85975ad
+q2cli version: 2025.4.0.dev0+8.g63d82cb
 
 Installed plugins
 dwq2: 0+unknown
-types: 2024.5.0
-
-Application config directory
-/Users/jgc/miniconda3/envs/using-qiime2/var/q2cli
+metadata: 2025.4.0.dev0+5.g7af916f
+types: 2025.4.0.dev0+6.g11e14d8
 
-Getting help
-To get help with QIIME 2, visit https://qiime2.org
+...
 ```
 
 ## Exploring the available functionality

book/tutorials/use-the-artifact-cache.md

@@ -1,7 +1,7 @@
 (artifact-cache-tutorial)=
 # Using an Artifact Cache
 
-The artifact cache allows users to have finer control over where and how QIIME 2 {term}`Results <Result>` are stored on disk.
+An artifact cache allows users to have finer control over where and how QIIME 2 {term}`Results <Result>` are stored on disk.
 
 Artifact caches serve two primary purposes:
 1. Providing the user with control over where QIIME 2 stores its working (temporary) files.

environment.yml

@@ -1,4 +1,4 @@
-name: using-qiime2
+name: using-qiime2-dev
 channels:
 - https://packages.qiime2.org/qiime2/2024.10/tiny/passed
 - conda-forge