REF: Refector q2-FMT's CI to be a community plugin

.github/workflows/ci.yml

@@ -0,0 +1,55 @@
+name: Test and lint
+
+on:
+  pull_request:
+    branches: ["dev"]
+  push:
+    branches: ["dev"]
+
+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-fmt-qiime2-amplicon-2024.10
+        environment-file: environments/q2-fmt-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
 
@@ -11,11 +11,8 @@ lint:
 test: all
 	py.test
 
-test-cov: all
-	py.test --cov=q2_fmt
-
 install: all
-	$(PYTHON) setup.py install
+	pip install .
 
 dev: all
 	pip install -e .

README.md

@@ -1,6 +1,6 @@
 # q2-fmt (fecal microbiota transplant)
 
-![](https://github.com/qiime2/q2-fmt/actions/workflows/ci-dev.yaml/badge.svg)
+A [QIIME 2](https://qiime2.org) plugin [developed](https://develop.qiime2.org) by Chloe Herman ([email protected]). 🔌
 
 ## Demo
 [![](https://raw.githubusercontent.com/qiime2/q2-fmt/master/demo/screenshot.png)
@@ -122,3 +122,15 @@ qiime stats plot-rainclouds \
   --i-stats stats_baseline0.qza \
   --o-visualization raincloud-baseline0.qzv
 ```
+## About
+
+The `q2-fmt` Python package was [created from template](https://develop.qiime2.org/en/latest/plugins/tutorials/create-from-template.html).
+To learn more about `q2-fmt`, refer to the [project website](https://example.com).
+To learn how to use QIIME 2, refer to the [QIIME 2 User Documentation](https://docs.qiime2.org).
+To learn QIIME 2 plugin development, refer to [*Developing with QIIME 2*](https://develop.qiime2.org).
+
+`q2-fmt` is a QIIME 2 community plugin, meaning that it is not necessarily developed and maintained by the developers of QIIME 2.
+Please be aware that because community plugins are developed by the QIIME 2 developer community, and not necessarily the QIIME 2 developers themselves, some may not be actively maintained or compatible with current release versions of the QIIME 2 distributions.
+More information on development and support for community plugins can be found [here](https://library.qiime2.org).
+If you need help with a community plugin, first refer to the [project website](https://example.com).
+If that page doesn't provide information on how to get help, or you need additional help, head to the [Community Plugins category](https://forum.qiime2.org/c/community-contributions/community-plugins/14) on the QIIME 2 Forum where the QIIME 2 developers will do their best to help you.

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

@@ -0,0 +1,17 @@
+name: q2-fmt-qiime2-amplicon-2024.10
+channels:
+- https://packages.qiime2.org/qiime2/2024.10/amplicon/passed
+- conda-forge
+- bioconda
+dependencies:
+  - qiime2-amplicon
+  # Note 1: Add any additional conda dependencies here.
+  - pip
+  - pip:
+  # Note 2: Add any additional pip dependencies here.
+  #   - # some pip dependency
+  # Note 3: If you host your repository on GitHub, and you uncomment and modify
+  # the following lines to replace REPO-OWNER with the user or organization
+  # name that owns the repository, your installation commands can be updated to
+  # install from this file without additional steps.
+  #   - "q2-fmt @ git+https://github.com/REPO-OWNER/q2-fmt.git"

setup.cfg

@@ -5,3 +5,7 @@ versionfile_source = q2_fmt/_version.py
 versionfile_build = q2_fmt/_version.py
 tag_prefix =
 parentdir_prefix = q2-fmt-
+
+[flake8]
+max-line-length = 80
+extend-ignore = E203

setup.py

@@ -13,6 +13,8 @@
 setup(
     name='q2-fmt',
     version=versioneer.get_version(),
+    cmdclass=versioneer.get_cmdclass(),
+    license="BSD-3-Clause",
     packages=find_packages(),
     package_data={
         'q2_fmt': [
@@ -21,10 +23,9 @@
         'q2_fmt.tests': ['data/*', 'data/peds_dist/*'],
 
     },
-    author='Liz Gehret',
-    author_email='elizabeth.gehret@nau.edu',
+    author='Chloe Herman and Liz Gehret',
+    author_email='crh423@nau.edu',
     description='QIIME 2 Plugin used for FMT analyses.',
-    license='BSD-3-Clause',
     url='https://github.com/qiime2/q2-fmt',
     zip_safe=False,
     entry_points={