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Update boiler plate documents
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53 changes: 29 additions & 24 deletions CODE_OF_CONDUCT.md
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# Contributor Covenant Code of Conduct

## Our Pledge
Expand All @@ -6,8 +7,8 @@ We as members, contributors, and leaders pledge to make participation in our
community a harassment-free experience for everyone, regardless of age, body
size, visible or invisible disability, ethnicity, sex characteristics, gender
identity and expression, level of experience, education, socio-economic status,
nationality, personal appearance, race, religion, or sexual identity
and orientation.
nationality, personal appearance, race, caste, color, religion, or sexual
identity and orientation.

We pledge to act and interact in ways that contribute to an open, welcoming,
diverse, inclusive, and healthy community.
Expand All @@ -22,17 +23,17 @@ community include:
* Giving and gracefully accepting constructive feedback
* Accepting responsibility and apologizing to those affected by our mistakes,
and learning from the experience
* Focusing on what is best not just for us as individuals, but for the
overall community
* Focusing on what is best not just for us as individuals, but for the overall
community

Examples of unacceptable behavior include:

* The use of sexualized language or imagery, and sexual attention or
advances of any kind
* The use of sexualized language or imagery, and sexual attention or advances of
any kind
* Trolling, insulting or derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or email
address, without their explicit permission
* Publishing others' private information, such as a physical or email address,
without their explicit permission
* Other conduct which could reasonably be considered inappropriate in a
professional setting

Expand All @@ -52,14 +53,15 @@ decisions when appropriate.

This Code of Conduct applies within all community spaces, and also applies when
an individual is officially representing the community in public spaces.
Examples of representing our community include using an official e-mail address,
Examples of representing our community include using an official email address,
posting via an official social media account, or acting as an appointed
representative at an online or offline event.

## Enforcement

Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported to the community leaders responsible for enforcement at [email protected].
reported to the community leaders responsible for enforcement at
[email protected].
All complaints will be reviewed and investigated promptly and fairly.

All community leaders are obligated to respect the privacy and security of the
Expand All @@ -81,15 +83,15 @@ behavior was inappropriate. A public apology may be requested.

### 2. Warning

**Community Impact**: A violation through a single incident or series
of actions.
**Community Impact**: A violation through a single incident or series of
actions.

**Consequence**: A warning with consequences for continued behavior. No
interaction with the people involved, including unsolicited interaction with
those enforcing the Code of Conduct, for a specified period of time. This
includes avoiding interactions in community spaces as well as external channels
like social media. Violating these terms may lead to a temporary or
permanent ban.
like social media. Violating these terms may lead to a temporary or permanent
ban.

### 3. Temporary Ban

Expand All @@ -108,21 +110,24 @@ Violating these terms may lead to a permanent ban.
standards, including sustained inappropriate behavior, harassment of an
individual, or aggression toward or disparagement of classes of individuals.

**Consequence**: A permanent ban from any sort of public interaction within
the community.
**Consequence**: A permanent ban from any sort of public interaction within the
community.

## Attribution

This Code of Conduct is adapted from the [Contributor Covenant][homepage],
version 2.0, available at
https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.

Community Impact Guidelines were inspired by [Mozilla's code of conduct
enforcement ladder](https://github.com/mozilla/diversity).
version 2.1, available at
[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].

[homepage]: https://www.contributor-covenant.org
Community Impact Guidelines were inspired by
[Mozilla's code of conduct enforcement ladder][Mozilla CoC].

For answers to common questions about this code of conduct, see the FAQ at
https://www.contributor-covenant.org/faq. Translations are available at
https://www.contributor-covenant.org/translations.
[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
[https://www.contributor-covenant.org/translations][translations].

[homepage]: https://www.contributor-covenant.org
[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
[Mozilla CoC]: https://github.com/mozilla/diversity
[FAQ]: https://www.contributor-covenant.org/faq
[translations]: https://www.contributor-covenant.org/translations
29 changes: 7 additions & 22 deletions LICENSE
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Copyright (c) 2018-2020, Michael P. Howard
Copyright (c) 2021-2022, Auburn University
Copyright (c) 2021-2024, Auburn University

All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

* 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.
2. 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.

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 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.
3. 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.
81 changes: 22 additions & 59 deletions README.md
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# azplugins

azplugins is a component (plugin) for [HOOMD-blue](http://glotzerlab.engin.umich.edu/hoomd-blue)
which expands its functionality for tackling a variety of problems in soft matter physics.
Currently, azplugins is tested against v2.6.0 of HOOMD-blue. See [CHANGELOG.rst](CHANGELOG.rst) for
a list of recent development. If you are interested in adding new code, please refer to the
[guidelines](SourceConventions.md).
azplugins is a component for [HOOMD-blue][1] which expands its functionality for
tackling a variety of problems in soft matter physics. Currently, azplugins is
tested against v4.7.0 of HOOMD-blue. See [CHANGELOG.rst](CHANGELOG.rst) for a
list of recent development.

## Compiling azplugins

azplugins can be built using either of the standard [plugin build methods](http://hoomd-blue.readthedocs.io/en/stable/developer.html).
To build azplugins **internally** to HOOMD-blue, add a symlink to the code into the `hoomd-blue/hoomd`:

```bash
cd hoomd-blue/hoomd
ln -s /path/to/azplugins/azplugins azplugins
cd ../build && make install
```

azplugins is now available as a component of HOOMD-blue:

```python
import hoomd
from hoomd import azplugins
```

To build azplugins **externally** to HOOMD-blue, ensure that the `hoomd` module is on your Python path
(or hint to its location using `HOOMD_ROOT`), and install to an appropriate location:

```bash
cd /path/to/azplugins
mkdir build && cd build
cmake ..
make install
```

You must make sure that your installation location is on your `PYTHONPATH`, and then `azplugins` can
be imported as usual

```python
import hoomd
import azplugins
```

### Prerequisites

azplugins requires the same dependencies used to build HOOMD-blue. Typically, this means a modern
Python installation with numpy, a reasonably recent version of CMake, and a C++11 capable compiler.
To get good performance, you probably also want a recent CUDA toolkit and an MPI library.
azplugins follows the [standard component template][2]. It has the same
dependencies used to build HOOMD-blue, and you can follow the [directions][3]
listed in the HOOMD-blue documentation to build an external component.

### Testing

All code is unittested at the Python level. If azplugins has been built as an internal HOOMD-blue component,
it is automatically included into the testing tree. To run only the `azplugins` tests out of your build
directory, use ctest:
To be added.

```bash
ctest -R azplugins-*
```
## Contributing

If azplugins has been built as an external Python package, all CTest options are available to you.
To run all tests out of your build directory,

```bash
make test
```
Contributions are welcomed and appreciated! Fork and create a pull request on
[GitHub][4]. Be sure to follow the [HOOMD-blue guidelines for developers][5]! We
value the input and experiences all users and contributors bring to
`relentless`.

## History

azplugins began as a collection of code shared between students and postdocs at Princeton University (2016-2018).
It is named for their research advisor, Prof. Athanassios (Thanos) Z. Panagiotopoulos, whose group has made several
contributions to HOOMD-blue and frequently uses it in their work.
azplugins began as a collection of code shared between students and postdocs at
Princeton University (2016-2018). It is named for their research advisor, Prof.
Athanassios (Thanos) Z. Panagiotopoulos.

[1]: http://glotzerlab.engin.umich.edu/hoomd-blue
[2]: https://hoomd-blue.readthedocs.io/en/latest/components.html
[3]: https://hoomd-blue.readthedocs.io/en/latest/components.html
[4]: https://github.com/mphowardlab/azplugins
[5]: https://hoomd-blue.readthedocs.io/en/latest/developers.html
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