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Adds code of conduct for contributing; expands README.md
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Closes #14

+ Adds `CODE_OF_CONDUCT.md`.
+ Adds supported file formats and intended work to `README.md`.
+ Adds basic instructions on contributing to `README.md`.
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103 changes: 103 additions & 0 deletions CODE_OF_CONDUCT.md
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# Contributor Covenant Code of Conduct

## Our Pledge

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.

We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.

## Our Standards

Examples of behavior that contributes to a positive environment for our community include:

* Demonstrating empathy and kindness toward other people
* Being respectful of differing opinions, viewpoints, and experiences
* 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

Examples of unacceptable behavior include:

* 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
* Other conduct which could reasonably be considered inappropriate in a professional setting

## Enforcement Responsibilities

Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take
appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive,
or harmful.

Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits,
issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for
moderation decisions when appropriate.

## Scope

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,
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: [Alice Pyne](mailto:a.l.pyne@sheffield.ac.uk) or [Bob Turner](mailto:r.d.turner@sheffield.ac.uk). All
complaints will be reviewed and investigated promptly and fairly.

All community leaders are obligated to respect the privacy and security of the reporter of any incident.

## Enforcement Guidelines

Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem
in violation of this Code of Conduct:

### 1. Correction

**Community Impact**: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the
community.

**Consequence**: A private, written warning from community leaders, providing clarity around the nature of the violation
and an explanation of why the behavior was inappropriate. A public apology may be requested.

### 2. Warning

**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.

### 3. Temporary Ban

**Community Impact**: A serious violation of community standards, including sustained inappropriate behavior.

**Consequence**: A temporary ban from any sort of interaction or public communication with the community for a specified
period of time. No public or private interaction with the people involved, including unsolicited interaction with those
enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.

### 4. Permanent Ban

**Community Impact**: Demonstrating a pattern of violation of community 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.

## Attribution

This Code of Conduct is adapted from the [Contributor Covenant version
2.0](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).

[Contributor Covenant](https://www.contributor-covenant.org)

For answers to common questions about this code of conduct, see the
[FAQ](https://www.contributor-covenant.org/faq). [Translations](https://www.contributor-covenant.org/translations) are
available.
73 changes: 70 additions & 3 deletions README.md
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# topofileformats

A library for loading various AFM file formats.
<div align="center">

File format support: `.asd`
[![PyPI version](https://badge.fury.io/py/topofileformats.svg)](https://badge.fury.io/py/topofileformats)
![PyPI - Python Version](https://img.shields.io/pypi/pyversions/topofileformats)
[![Code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json))](https://github.com/astral-sh/ruff)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![Code style: flake8](https://img.shields.io/badge/code%20style-flake8-456789.svg)](https://github.com/psf/flake8)
<!-- [![codecov](https://codecov.io/gh/AFM-SPM/topofileformats/branch/dev/graph/badge.svg)]
(https://codecov.io/gh/AFM-SPM/topofileformats) -->
[![pre-commit.ci
status](https://results.pre-commit.ci/badge/github/AFM-SPM/topofileformats/main.svg)](https://results.pre-commit.ci/latest/github/AFM-SPM/topofileformats/main)

</div>

A library for loading various Atomic Force Microscopy (AFM) file formats into Python. This library is primarily intended
for use with [TopoStats](https://github.com/AFM-SPM/TopoStats).

Supported file formats

| File format | Description |
|-------------|----------------|
| `.asd` | High-speed AFM |

Support for the following additional formats is planned. Some of these are already supported in TopoStats and are
awaiting refactoring to move their functionality into topofileformats these are denoted in bold below.

| File format | Description | Status |
|-------------|---------------------------------------------------------|--------------------------------------------|
| `.spm` | [Bruker](https://www.bruker.com/) | TopoStats supported, to be migrated (#16). |
| `.ibw` | [WaveMetrics](https://www.wavemetrics.com/) | TopoStats supported, to be migrated (#17). |
| `.gwy` | [Gwyddion](http://gwyddion.net/) | TopoStats supported, to be migrated (#1). |
| `.nhf` | [Nanosurf](https://www.nanosurf.com/en/) | To Be Implemented. |
| `.aris` | [Imaris Oxford Instruments](https://imaris.oxinst.com/) | To Be Implemented. |
| `.tiff` | [Park Systems](https://www.parksystems.com/) | To Be Implemented. |

## Usage

## .asd
If you wish to process AFM images supported by `topofileformats` it is recommend you use
[TopoStats](https://github.com/AFM-SPM/TopoStats) to do so, however the library can be used on its own.

### .asd

You can open `.asd` files using the `load_asd` function. Just pass in the path to the file and the channel name that you
want to use. (If in doubt use the `"TP"` topography channel).
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frames, pixel_to_nanometre_scaling_factor, metadata = load_asd(file_path="./my_asd_file.asd")
```

## Contributing

Bug reports and feature requests are welcome. Please search for existing issues, if none relating to your bug/feature
are found then feel free to create a new [issue](https://github.com/AFM-SPM/topofileformats/issues/new) detailing what
went wrong or the feature you would like to see implemented.

Pull requests are also welcome, please note that we have a [Code of
Conduct](https://github.com/AFM-SPM/topofileformats/blob/main/CODE_OF_CONDUCT.md).

### Setup

We use [pre-commit](https://pre-commit.com) to apply linting via [ruff](https://github.com/astral-sh/ruff) and
[pylint](https://pylint.pycqa.org/en/latest/index.html) pre-commit hooks and use the
[Black](https://github.com/psf/black) and [Flake8](https://github.com/psf/flake8) code styles. To set yourself up for
contributing after cloning the package and creating a Python virtual environment you should install the development
dependencies and `pre-commit` as shown below.

``` bash
# Activate your virtual environment, this will depend on which system you use e.g. conda or virtualenvwrapper
# Clone the repository
git clone git@github.com:AFM-SPM/topofileformats.git
# Change directories into the newly cloned directory
cd topofileformats
# Install the package along with the optional development (dev) dependencies
pip install -e .[dev]
# Install pre-commit
pre-commit install
```

This will ensure that any commits and pull requests you make will pass the [Pre-commit Continuous
Integration](https://pre-commit.ci). Where possible `ruff` will correct the changes it can, but it may require you to
address some issues manually, before adding any changes and attempting to commit again.

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