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updated setup and added test data
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@nsylvestertgen
nsylvestertgen committed Aug 9, 2024
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6 changes: 5 additions & 1 deletion .gitignore
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# This .gitignore file is derived from:
# https://github.com/github/gitignore/blob/4488915eec0b3a45b5c63ead28f286819c0917de/Python.gitignore

# Ignore data folder
q2_asap/tests/data/extra_test_files/*
q2_asap/tests/data/extra_test_files

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
Expand Down Expand Up @@ -163,4 +167,4 @@ cython_debug/
#.idea/

# macOS
.DS_Store
.DS_Store
53 changes: 24 additions & 29 deletions LICENSE
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BSD 3-Clause License

Copyright (c) 2024, Nicole Sylvester.
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.
ACADEMIC AND RESEARCH LICENSE
© 2015, The Translational Genomics Research Institute. All rights reserved.

1. License. The Translational Genomics Research Institute (“TGen”) hereby grants you a non-exclusive, non-transferable right to use the ASAP software and any related documentation (collectively, the "Software"), subject to the terms and conditions of this Academic and Research License (“License”). You should carefully read this License before using the Software. YOUR DOWNLOAD AND USE OF THE SOFTWARE INDICATES YOUR ACCEPTANCE OF THIS LICENSE AND ALL OF THE FOLLOWING TERMS AND CONDITIONS.

2. Academic and Research Purposes. This License is limited to, and you may use the Software solely for, your own internal, non-commercial, academic and research purposes, including the right to make modifications or derivatives of the Software. Without limiting the foregoing, you may not use the Software as part of, or in any way in connection with the production, marketing, sale or support of any commercial product or service.

3. Commercial Use. If you desire to use the Software for any commercial purpose whatsoever, you agree to negotiate in good faith to obtain an appropriate license from TGen prior to such commercial use. TGen shall have no obligation to grant such a license to you, and may grant exclusive or non-exclusive licenses to third parties. You agree to notify TGen of any inquiries you may receive regarding commercial use of the Software or any modifications or derivatives thereof. Any inquiries or notices regarding commercial use of the Software should be directed to [email protected].

4. Disclaimer of Warranty. BECAUSE THE SOFTWARE IS LICENSED FREE OF CHARGE, THE SOFTWARE IS LICENSED "AS IS" AND WITHOUT WARRANTIES, REPRESENTATIONS OR GUARANTEES OF ANY KIND OR NATURE, WHETHER WRITTEN OR ORAL, EXPRESS OR IMPLIED, DIRECT OR INDIRECT, BY ESTOPPEL OR OTHERWISE, AND TGEN EXPRESSLY DISCLAIMS ANY AND ALL IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT OF ANY THIRD PARTY PATENT OR OTHER PROPRIETARY RIGHTS. FURTHERMORE, TGEN MAKES NO WARRANTIES, REPRESENTATIONS OR GUARANTEES AS TO THE ACCURACY, RELIABILITY, UTILITY, PERFORMANCE OR EFFECTIVENESS OF THE SOFTWARE, OR ANY DATA OR RESULTS OBTAINED FROM THE USE THEREOF, OR THAT THE USE OF THE SOFTWARE WILL BE ERROR FREE, UNINTERRUPTED, SECURE OR VIRUS-FREE. TO THE EXTENT TGEN MAY NOT AS A MATTER OF LAW DISCLAIM ANY WARRANTY, THE PARTIES AGREE THAT THE SCOPE AND DURATION OF ANY SUCH WARRANTY SHALL BE THE MINIMUM PERMITTED UNDER APPLICABLE LAW. TGen is under no obligation to provide any services, by way of maintenance, updates or otherwise with respect to the Software.

5. Limitation of Liability. TGEN SHALL NOT BE LIABLE TO YOU OR TO ANY THIRD PARTY FOR ANY DAMAGES WHATSOEVER, INCLUDING WITHOUT LIMITATION, ACTUAL, DIRECT OR GENERAL DAMAGES, AND SHALL IN NO EVENT BE LIABLE FOR ANY INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, CONSEQUENTIAL OR PUNITIVE DAMAGES (INCLUDING, WITHOUT LIMITATION, DAMAGES RELATING TO THE USE OR INABILITY TO USE THE SOFTWARE, LOSS OF DATA, INACCURATE DATA, PROCUREMENT OF INAPPROPRIATE, SUBSTITUTE OR ALTERNATIVE SOFTWARE, LOSS OF PROFITS, LOSS OF REVENUES, OR BUSINESS INTERRUPTION); IN ALL CASES, HOWEVER CAUSED, RESULTING FROM, RELATED TO OR ARISING OUT OF THE USE OF THE SOFTWARE OR ANY DATA OR RESULTS OBTAINED THEREFROM, REGARDLESS OF FORESEEABILITY AND NOTWITHSTANDING WHETHER YOU OR TGEN HAS BEEN ADVISED OF THE POSSIBILITY OF ANY SUCH DAMAGES, AND REGARDLESS OF THE FORM OF THE CAUSE OF ACTION, WHETHER IN CONTRACT, BREACH OF WARRANTY OR TORT (INCLUDING NEGLIGENCE, GROSS NEGLIGENCE OR STRICT LIABILITY, OR OTHERWISE.

6. No Other Rights Granted. Except as expressly stated herein, this License does not constitute a grant to you, or an intention or commitment to grant to you, any right, title or interest in or to the Software or TGen’s trade secrets or any other intellectual property related to the Software.

7. No Assignment. This License is personal to the person or entity downloading and using the Software pursuant hereto and you may not sell, assign or transfer it to any other party.

8. Use of Names. You may not use the names “The Translational Genomics Research Institute” or “TGen,” or any variations or adaptations thereof, or any marks or symbols related thereto, in any publication, advertising or promotional material of any kind, without the prior written consent from TGen; in each case, which may be granted or withheld in TGen’s sole discretion.

9. Governing Law. This agreement shall be governed by the laws of the State Arizona, without regard to choice of law principles.

10. Termination. This License is effective until terminated. You may terminate this License at any time by destroying all copies of the Software and any documentation or other associated materials in your possession. This License will terminate immediately without notice from TGen if (a) you fail to comply with any of the terms and conditions of this License, or (b) the Software (or any modification or derivative) is found to infringe upon the intellectual property or other proprietary rights of any third party. Upon termination, you must destroy all copies of the Software (including all Software incorporated in any modification or derivative) and any documentation or other associated materials.

Please cite the author in any work or product based on this material.
1 change: 1 addition & 0 deletions MANIFEST.in
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include versioneer.py
include q2_asap/_version.py
include LICENSE
34 changes: 12 additions & 22 deletions README.md
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Expand Up @@ -4,10 +4,6 @@ A [QIIME 2](https://qiime2.org) plugin [developed](https://develop.qiime2.org) b

## Installation instructions

**The following instructions are intended to be a starting point** and should be replaced when `q2-asap` is ready to share with others.
They will enable you to install the most recent *development* version of `q2-asap`.
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.
Expand All @@ -19,13 +15,16 @@ After installing Miniconda and opening a new terminal, make sure you're running
conda update conda
```

[q2-trimmers](https://github.com/TGenNorth/q2-trimmers) provides the trimmer options used by `q2-asap`
[q2-nasp2-types](https://github.com/TGenNorth/q2-nasp2-types) provides custom semantic types and formats used by `q2-asap`
[q2-aligners](https://github.com/TGenNorth/q2-aligners) provides the aligner options used by `q2-asap`

### Install development version of `q2-asap`

Next, you need to get into the top-level `q2-asap` directory.
If you already have this (e.g., because you just created the plugin), this may be as simple as running `cd q2-asap`.
If not, you'll need the `q2-asap` 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).
Since 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`.
Expand All @@ -46,10 +45,10 @@ conda activate q2-asap-dev
Finally, run:

```shell
make install
pip install .
```

## Testing and using the most recent development version of `q2-asap`
## Testing `q2-asap`

After completing the install steps above, confirm that everything is working as expected by running:

Expand All @@ -61,17 +60,6 @@ You should get a report that tests were run, and you should see that all tests p
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 `q2-asap` 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:

Expand All @@ -85,11 +73,13 @@ Have fun! 😎

The `q2-asap` Python package was [created from template](https://develop.qiime2.org/en/latest/plugins/tutorials/create-from-template.html).
To learn more about `q2-asap`, refer to the [project website](https://example.com).
`q2-asap` is a QIIME 2 version of [ASAP] (https://github.com/TGenNorth/ASAP).

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-asap` 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.
`q2-asap` is a QIIME 2 community plugin, meaning that it is not developed and maintained by the developers of QIIME 2.

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.
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.
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