initial commit

Created from https://github.com/caporaso-lab/cookiecutter-qiime2-plugin. See https://develop.qiime2.org to learn more.

.github/workflows/ci.yml

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+name: Test and lint
+
+on:
+  pull_request:
+    branches: ["main"]
+  push:
+    branches: ["main"]
+
+jobs:
+  build-and-test-qiime2-tiny-2024-5:
+    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: gut-to-soil-manuscript-figures-qiime2-tiny-2024.5
+        environment-file: environments/gut-to-soil-manuscript-figures-qiime2-tiny-2024.5.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

.gitignore

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+# This .gitignore file is derived from:
+# https://github.com/github/gitignore/blob/4488915eec0b3a45b5c63ead28f286819c0917de/Python.gitignore
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# macOS
+.DS_Store

LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2024, Liz Gehret.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

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+include versioneer.py
+include gut_to_soil_manuscript_figures/_version.py

Makefile

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+.PHONY: all lint test install dev clean distclean
+
+PYTHON ?= python
+
+all: ;
+
+lint:
+	q2lint
+	flake8
+
+test: all
+	py.test
+
+install: all
+	pip install .
+
+dev: all
+	pip install -e .
+
+clean: distclean
+
+distclean: ;

README.md

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+# gut-to-soil-manuscript-figures
+
+A [QIIME 2](https://qiime2.org) plugin [developed](https://develop.qiime2.org) by Liz Gehret (elizabeth.gehret@nau.edu). 🔌
+
+## Installation instructions
+
+**The following instructions are intended to be a starting point** and should be replaced when `gut-to-soil-manuscript-figures` is ready to share with others.
+They will enable you to install the most recent *development* version of `gut-to-soil-manuscript-figures`.
+Remember that *release* versions should be used for all "real" work (i.e., where you're not testing or prototyping) - if there aren't instructions for installing a release version of this plugin, it is probably not yet intended for use in practice.
+
+### Install Prerequisites
+
+[Miniconda](https://conda.io/miniconda.html) provides the `conda` environment and package manager, and is currently the only supported way to install QIIME 2.
+Follow the instructions for downloading and installing Miniconda.
+
+After installing Miniconda and opening a new terminal, make sure you're running the latest version of `conda`:
+
+```bash
+conda update conda
+```
+
+###  Install development version of `gut-to-soil-manuscript-figures`
+
+Next, you need to get into the top-level `gut-to-soil-manuscript-figures` directory.
+If you already have this (e.g., because you just created the plugin), this may be as simple as running `cd gut-to-soil-manuscript-figures`.
+If not, you'll need the `gut-to-soil-manuscript-figures` directory on your computer.
+How you do that will differ based on how the package is shared, and ideally the developer will update these instructions to be more specific (remember, these instructions are intended to be a starting point).
+For example, if it's maintained in a GitHub repository, you can achieve this by [cloning the repository](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository).
+Once you have the directory on your computer, change (`cd`) into it.
+
+If you're in a conda environment, deactivate it by running `conda deactivate`.
+
+
+Then, run:
+
+```shell
+conda env create -n gut-to-soil-manuscript-figures-dev --file ./environments/gut-to-soil-manuscript-figures-qiime2-tiny-2024.5.yml
+```
+
+After this completes, activate the new environment you created by running:
+
+```shell
+conda activate gut-to-soil-manuscript-figures-dev
+```
+
+Finally, run:
+
+```shell
+make install
+```
+
+## Testing and using the most recent development version of `gut-to-soil-manuscript-figures`
+
+After completing the install steps above, confirm that everything is working as expected by running:
+
+```shell
+make test
+```
+
+You should get a report that tests were run, and you should see that all tests passed and none failed.
+It's usually ok if some warnings are reported.
+
+If all of the tests pass, you're ready to use the plugin.
+Start by making QIIME 2's command line interface aware of `gut-to-soil-manuscript-figures` by running:
+
+```shell
+qiime dev refresh-cache
+```
+
+You should then see the plugin in the list of available plugins if you run:
+
+```shell
+qiime info
+```
+
+You should be able to review the help text by running:
+
+```shell
+qiime gut-to-soil-manuscript-figures --help
+```
+
+Have fun! 😎
+
+## About
+
+The `gut-to-soil-manuscript-figures` Python package was [created from a template](https://develop.qiime2.org/en/latest/plugins/tutorials/create-from-template.html).
+To learn more about `gut-to-soil-manuscript-figures`, refer to the [project website](https://github.com/caporaso-lab/gut-to-coil-manuscript-figures/).
+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).
+
+`gut-to-soil-manuscript-figures` 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://github.com/caporaso-lab/gut-to-coil-manuscript-figures/).
+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/gut-to-soil-manuscript-figures-qiime2-tiny-2024.5.yml

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+channels:
+- https://packages.qiime2.org/qiime2/2024.5/tiny/passed
+- conda-forge
+- bioconda
+dependencies:
+  - qiime2-tiny
+  # 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.
+  #   - "gut-to-soil-manuscript-figures @ git+https://github.com/REPO-OWNER/gut-to-soil-manuscript-figures.git"