various clean-ups

 - adds automated testing
 - updates to install in 2024.10 dev environment
 - text clean-ups

.github/workflows/ci.yml

@@ -0,0 +1,55 @@
+name: Test and lint
+
+on:
+  pull_request:
+    branches: ["main"]
+  push:
+    branches: ["main"]
+
+jobs:
+  build-and-test-qiime2-amplicon-2024-10:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-13]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Conda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        activate-environment: q2-boots-qiime2-amplicon-2024.10
+        environment-file: environments/q2-boots-qiime2-amplicon-2024.10.yml
+        auto-activate-base: false
+
+    - name: Install plugin
+      shell: bash -l {0}
+      run: make install
+
+    - name: Run tests
+      shell: bash -l {0}
+      run: make test
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+    - name: checkout source
+      uses: actions/checkout@v3
+
+    - name: set up python 3.11
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.11
+
+    - name: install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -q https://github.com/qiime2/q2lint/archive/master.zip
+        pip install -q flake8
+
+    - name: run flake8
+      run: flake8
+
+    - name: run q2lint
+      run: q2lint

Makefile

@@ -1,4 +1,4 @@
-.PHONY: all lint test test-cov install dev clean distclean
+.PHONY: all lint test install dev clean distclean
 
 PYTHON ?= python
 
@@ -11,15 +11,12 @@ lint:
 test: all
 	py.test
 
-test-cov: all
-	py.test --cov=q2_feature_table
-
 install: all
-	$(PYTHON) setup.py install
+	pip install .
 
 dev: all
 	pip install -e .
 
 clean: distclean
 
-distclean: ;
+distclean: ;

README.md

@@ -16,38 +16,17 @@ conda update conda
 conda install wget
 ```
 
-### QIIME 2024.2 release version of q2-boots
+### QIIME 2024.10 development version of q2-boots
 
-The most recent release version of q2-boots is the most stable, and is recommended for use in work that you're intending to publish.
-It may not contain all of the most recent feature additions, so if you're at an early experimental phase of your analysis you may prefer to install the development version of q2-boots (see those instructions below).
-
-```shell
-wget https://raw.githubusercontent.com/qiime2/q2-boots/main/environments/q2-boots-qiime2-amplicon-2024.2.yml
-```
-
-```shell
-conda env create -n q2-boots-2024.2 --file ./q2-boots-qiime2-amplicon-2024.2.yml
-```
-
-```shell
-conda activate q2-boots-2024.2
-```
-
-### QIIME 2024.5 development version of q2-boots
-
-Installing the most recent development version of q2-boots allows you to access the most recent functionality, including some that depends on features being introduced in QIIME 2 2024.5.
+Installing the most recent development version of q2-boots allows you to access the most recent functionality, including some that depends on features being introduced in QIIME 2 2024.10.
 It is hard to unambiguously reference development versions of software in publications however, so you'll likely want to re-run your boots analyses with a release version prior to publication.
 
 ```shell
-wget https://raw.githubusercontent.com/qiime2/q2-boots/main/environments/q2-boots-qiime2-amplicon-2024.5.yml
-```
-
-```shell
-conda env create -n q2-boots-2024.5 --file ./q2-boots-qiime2-amplicon-2024.5.yml
+conda env create -n q2-boots-2024.10 -f https://raw.githubusercontent.com/qiime2/q2-boots/main/environments/q2-boots-qiime2-amplicon-2024.10.yml
 ```
 
 ```shell
-conda activate q2-boots-2024.5
+conda activate q2-boots-2024.10
 ```
 
 ## Testing and using `q2-boots`

environments/q2-boots-qiime2-amplicon-2024.10.yml

@@ -0,0 +1,10 @@
+name: q2-boots-qiime2-amplicon-2024.10
+channels:
+- https://packages.qiime2.org/qiime2/2024.10/amplicon/passed
+- conda-forge
+- bioconda
+dependencies:
+  - qiime2-amplicon
+  - pip
+  - pip:
+     - "q2-boots @ git+https://github.com/caporaso-lab/q2-boots.git"

q2_boots/plugin_setup.py

@@ -53,10 +53,13 @@
 plugin = Plugin(
     name='boots',
     version=q2_boots.__version__,
-    website='https://github.com/qiime2/q2-boots',
+    website='https://github.com/caporaso-lab/q2-boots',
     package='q2_boots',
-    short_description='placeholder',
-    description='placeholder'
+    short_description=('Bootstrapped and rarefaction-based diversity '
+                       'analyses.'),
+    description=('A plugin providing bootstrapped and rarefaction-based '
+                 'diversity analyses, designed to mirror the interface of '
+                 'q2-diversity.')
 )
 
 plugin.pipelines.register_function(

setup.py

@@ -10,16 +10,19 @@
 
 import versioneer
 
+description = ('A QIIME 2 plugin supporting bootstrapped and rarefaction-based '
+               'diversity analyses.')
+
 setup(
     name="q2-boots",
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
     license="BSD-3-Clause",
     packages=find_packages(),
     author="Isaiah Raspet",
-    author_email="[email protected]",
-    description="This is a plugin for bootstraping sample data",
-    url="https://github.com/qiime2/q2-boots",
+    author_email="[email protected]",
+    description=description,
+    url="https://github.com/caporaso-lab/q2-boots",
     entry_points={
         "qiime2.plugins": ["q2-boots=q2_boots.plugin_setup:plugin"]
     },