Merge pull request #2 from PixelgenTechnologies/feature/improve-readm…

…e-and-docs

improve README.md for public repo

CONTRIBUTING.md

@@ -60,43 +60,34 @@ Ready to contribute? Here's how to set up ``pixelator`` for local development.
 
     where your `yourgithubuser` is the user/org where you have cloned the repo.
 
-3. Configure your environment.
+3. Configure your environment and install pixelator.
 
    We recommend that you follow the instructions in [DEVELOPERS.md](DEVELOPERS.md).
 
-4. Install pixelator.
-
-   And make sure `fastp` is installed in your system.
-
-    ```shell
-    poetry install
-    fastp -v
-    ```
-
-5. Create a branch for local development.
+4. Create a branch for local development.
 
     ```shell
     git checkout -b name-of-your-bugfix-or-feature
     ```
 
    Now you can make your changes locally.
 
-6. When you're done making changes, check that your changes pass the
+5. When you're done making changes, check that your changes pass the
    tests, including testing other Python versions, with tox:
 
     ```shell
     tox
     ```
 
-7. Commit your changes and push your branch to GitHub:
+6. Commit your changes and push your branch to GitHub:
 
     ```shell
     git add .
     git commit -m "Your detailed description of your changes."
     git push origin name-of-your-bugfix-or-feature
     ```
 
-8. Submit a pull request through the GitHub website.
+7. Submit a pull request through the GitHub website.
 
 ## Testing
 

README.md

@@ -1,58 +1,118 @@
 # Pixelator
 
-Pixelator is a software package to process sequencing FASTQ from Molecular Pixelation (MPX) assays and analyze PXL data (maintained by Pixelgen Technologies AB).
 
-Pixelator is compatible with Python 3.8, 3.9 and 3.10 and has been tested on Linux and macOS x64 machines.
+![python-version](https://img.shields.io/badge/python-3.8%20%7C%203.9%20%7C%203.10-blue)
+[![License: GPL v2](https://img.shields.io/badge/License-GPL_v2-blue.svg)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)
+
+[//]: # (TODO: Enable this once available)
+[//]: # (![conda](https://anaconda.org/bioconda/pixelator/badges/version.svg))
+[//]: # (![pypi](https://img.shields.io/pypi/v/pixelgen-pixelator))
+
+
+[**Documentation**](#documentation) |
+[**Installation**](#installation) |
+[**Contributing**](#contributing) |
+[**Contact**](#contact) |
+[**License**](#license) |
+[**Credits**](#credits)
+
+
+Pixelator is a software package to process sequencing FASTQ from Molecular Pixelation (MPX) assays
+and analyze PXL data.
+
+It provides the `pixelator` commandline tool to process FASTQ files and generate PXL files and reports
+and can be used as a python library for further downstream processing.
+
+
+<p align="center">
+    <img src="https://www.pixelgen.com/wp-content/uploads/2022/12/share-image-pixelgen.png" height=200
+     alt="Pixelgen Technologies" />
+</p>
+<div align="center">© 2023 - Pixelgen Technologies AB</div>
+
+## Documentation
+
+More information about pixelator is available on the [Pixelgen Techologies documentation site](https://software.pixelgen.com/).
 
 ## Installation
 
-### Create a virtual environment using conda/mamba
+### Installation with pip
 
-You will need to [install conda](https://docs.anaconda.com/free/anaconda/install/) to create a dedicated environment.
-We also recommend to install mamba in your base conda environment and use that command instead of conda.
-This will make the installation of the dependencies much faster.
+pixelator is available on pypi as `pixelgen-pixelator` and can be installed with pip.
+It is recommended to install pixelator in a separate virtual environment.
 
 ```shell
-conda activate base
-conda install mamba -c conda-forge
-mamba create -n pixelator python==3.10
-mamba activate pixelator
+pip install pixelgen-pixelator
 ```
 
-### Using pip
+### Installation with conda / mamba
+
+A conda package is available on the bioconda channel and can be installed with conda or mamba.
 
 ```shell
-pip install pixelgen-pixelator
+conda install -c bioconda pixelator
 ```
+or
+```shell
+mamba install -c bioconda pixelator
+```
+
+### Installation from source
 
-### Using conda
+Pixelator can be installed from source by cloning the repository.
 
 ```shell
-conda install -c bioconda pixelgen-pixelator
+git clone https://github.com/pixelgentechnologies/pixelator.git
+cd pixelator
+pip install .
 ```
 
-### Using mamba
+### Using docker
+
+The pixelator commandline tool can be run with docker images available on
+the [GitHub container registry](https://github.com/PixelgenTechnologies/pixelator/pkgs/container/pixelator).
 
 ```shell
-mamba install -c bioconda pixelgen-pixelator
+docker pull ghcr.io/pixelgentechnologies/pixelator:latest
+docker run ghcr.io/pixelgentechnologies/pixelator:latest pixelator --help
 ```
 
-### Using docker
+## Contributing
+
+Contribution are welcome!
+Please check out the [contributing guidelines](./CONTRIBUTING.md) for more information.
+
+## Contact
+
+For feature requests or bug reports, please use the GitHub issues.
+For questions, comments, or suggestions you can use the GitHub discussions.
+
+You can also email the development team at [[email protected]](mailto:[email protected]).
+
+## License
+
+Pixelator is licensed under the [GPL-2.0](./LICENSE) license.
+
+## Credits
+
+Pixelator is developed and maintained by the [developers](https://github.com/PixelgenTechnologies) at [Pixelgen Technologies](https://pixelgen.com).
 
-You can also [use Pixelator from our distributed docker images](./USAGE.md#pixelator-docker-images).
+When using pixelator in your research, please cite the following publication:
 
-## How to use Pixelator
+> Karlsson, Filip, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, et al. “Molecular Pixelation: Single Cell Spatial Proteomics by Sequencing.” bioRxiv, June 8, 2023. https://doi.org/10.1101/2023.06.05.543770.
 
-See [USAGE.md](./USAGE.md)
 
-## How to develop
+Main development happened thanks to:
 
-See [DEVELOPERS.md](./DEVELOPERS.md)
+- Jose Fernandez Navarro ([@jfnavarro](https://github.com/jfnavarro))
+- Alvaro Martinez Barrio ([@ambarrio](https://github.com/ambarrio))
+- Johan Dahlberg ([@johandahlberg](https://github.com/johandahlberg))
+- Florian De Temmerman ([@fbdtemme](https://github.com/fbdtemme))
 
-## How to contribute
+A huge thank you to all [code contributors](https://github.com/PixelgenTechnologies/pixelator/graphs/contributors)!
 
-See [CONTRIBUTING.md](./CONTRIBUTING.md)
+A non-exhaustive list of contributors follows:
 
-## Contact and credits
+- Filip Karlsson ([@fika-pixelgen](https://github.com/fika-pixelgen))
+- Max Karlsson ([@maxkarlsson](https://github.com/maxkarlsson))
 
-See [AUTHORS.md](./AUTHORS.md)

pyproject.toml

@@ -1,19 +1,24 @@
 [tool]
 [tool.poetry]
-name = "pixelator"
+name = "pixelgen-pixelator"
 version = "0.0.0"
 homepage = "https://github.com/PixelgenTechnologies/pixelator"
 repository = "https://github.com/PixelgenTechnologies/pixelator"
 documentation = ""
 description = "Software package to process sequencing FASTQ from Molecular Pixelation (MPX) assays"
-authors = ["Pixelgen Technologies Developers <[email protected]>",]
+authors = ["Pixelgen Technologies AB <[email protected]>",]
+maintainers = [
+    "Alvaro Martinez Barrio <[email protected]>"
+]
 readme = "README.md"
-license =  "MIT"
+license =  "GPL-2.0-only"
 keywords = ["protein", "single-cell", "molecular-pixelation", "spatial", "proteomics"]
 classifiers=[
-    'Development Status :: 3 - Alpha',
+    'Development Status :: 4 - Beta',
     'Intended Audience :: Developers',
-    'License :: OSI Approved :: MIT Software License',
+    'Intended Audience :: Science/Research',
+    'Topic :: Scientific/Engineering :: Bio-Informatics',
+    'License :: OSI Approved :: GNU General Public License v2 (GPLv2)',
     'Natural Language :: English',
     'Programming Language :: Python :: 3.8',
     'Programming Language :: Python :: 3.9',