Merge pull request #98 from JannisHoch/dev

v0.0.5

CODE_OF_CONDUCT.md

@@ -0,0 +1,76 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, 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.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers 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, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at j.m.hoch@uu.nl. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

CONTRIBUTING.md

@@ -0,0 +1,38 @@
+# How to contribute
+
+This python-package is a first outcome of an interdisciplinary project aimed at understanding the complex interplay between conflict and climate and environment.
+As such, the presented code and functionalities can only be seen as a first step towards a fully-fledged model.
+We therefore strongly encourage other users to contribute to this project!
+
+## General notes
+
+When contributing to this repository, please first discuss the change you wish to make via issue, email, or any other method with the owners of this repository before making a change.
+
+Please note we have a code of conduct, please follow it in all your interactions with the project, the project owners, and users of the project.
+
+## Getting Started
+
+* Make sure you have a GitHub account.
+* Fork the repository on GitHub.
+
+## Making Changes
+
+* Create a topic branch from where you want to base your work.
+  * This is usually the dev branch.
+  * Only target release branches if you are certain your fix must be on that
+    branch.
+  * To quickly create a topic branch based on master, run `git checkout -b
+    fix/dev/my_contribution master`. Please avoid working directly on the
+    `dev` (or `master`) branch.
+* Make commits of logical and atomic units. Write a [good commit message][commit]!
+* Make sure you have added the necessary tests for your changes.
+
+## Submitting Changes
+
+* Push your changes to a topic branch in your fork of the repository.
+* Submit a pull request to the repository.
+* The core team looks at pull requests as soon as possible, but no maximum waiting time can be given here.
+* After feedback has been given we expect responses within two weeks. After two
+  weeks we may close the pull request if it isn't showing any activity.
+
+[commit]: http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html

README.rst

@@ -2,54 +2,63 @@
 Overview
 ===============
 
-The conflict_model
+CoPro
 ----------------
-(Machine learning) model for mapping environmental drivers of conflict risk.
 
-.. image:: https://travis-ci.com/JannisHoch/conflict_model.svg?token=BnX1oxxHRbyd1dPyXAp2&branch=dev
+Welcome to CoPro, a machine-learning tool for conflict risk projections based on climate, environmental, and societal drivers.
+
+.. image:: https://travis-ci.com/JannisHoch/conflict_model.svg?branch=dev
     :target: https://travis-ci.com/JannisHoch/conflict_model
 
 .. image:: https://img.shields.io/badge/License-MIT-blue.svg
-    :target: https://github.com/JannisHoch/conflict_model/blob/dev/LICENSE
+    :target: https://github.com/JannisHoch/copro/blob/dev/LICENSE
+
+.. image:: https://readthedocs.org/projects/copro/badge/?version=latest
+    :target: https://copro.readthedocs.io/en/latest/?badge=latest
 
-.. image:: https://readthedocs.org/projects/conflict-model/badge/?version=dev
-    :target: https://conflict-model.readthedocs.io/en/dev/?badge=dev
+.. image:: https://img.shields.io/github/v/release/JannisHoch/copro
+    :target: https://github.com/JannisHoch/copro/releases/tag/v0.0.5-pre
 
-.. image:: https://img.shields.io/github/v/release/JannisHoch/conflict_model
-    :target: https://github.com/JannisHoch/conflict_model/releases/tag/v0.0.3
+.. image:: https://zenodo.org/badge/254407279.svg
+    :target: https://zenodo.org/badge/latestdoi/254407279
 
 .. image:: https://badges.frapsoft.com/os/v2/open-source.svg?v=103
     :target: https://github.com/ellerbrock/open-source-badges/
 
 Installation
 ----------------
 
-To install the conflict model, first clone the code from GitHub. It is advised to create an individual python environment first. 
+To install copro, first clone the code from GitHub. It is advised to create an individual python environment first. 
 You can then install the model package into this environment.
 
 .. code-block:: console
 
-    $ git clone https://github.com/JannisHoch/conflict_model.git
-    $ cd path/to/conflict_model
+    $ git clone https://github.com/JannisHoch/copro.git
+    $ cd path/to/copro
     $ conda env create -f environment.yml
-    $ conda activate conflict_model
+    $ conda activate copro
     $ python setup.py develop
 
 Execution
 ----------------
 
+To be able to run the model, the conda environment has to be activated first.
+
+.. code-block:: console
+
+    $ conda activate copro
+
 Example notebook
 ^^^^^^^^^^^^^^^^^^
 
-To run the example jupyter notebook, follow these instructions
+There are jupyter notebooks available to guide you through the model application process.
+They can all be run and converted to htmls by executing the provided shell-script.
 
 .. code-block:: console
 
-    $ cd path/to/conflict_model/example
+    $ cd path/to/copro/example
     $ sh run.sh
 
-This automatically executes the notebook and converts it to a html-file, also stored in the example folder.
-
 It is of course also possible to execute the notebook cell by cell using jupyter notebook.
 
 Runner script
@@ -60,16 +69,26 @@ All data and settings are retrieved from the settings-file which needs to be pro
 
 .. code-block:: console
 
-    $ cd path/to/conflict_model/scripts
-    $ python runner.py path/to/conflict_model/data/run_setting.cfg
+    $ cd path/to/copro/scripts
+    $ python runner.py ../example/example_settings.cfg
 
 By default, output is stored to the output directory specified in the settings-file. 
 
+Documentation
+---------------
+
+Model documentation including model API can be found at http://copro.rtfd.io/
+
+Code of conduct and Contributing
+---------------------------------
+
+Please find the relevant information on our Code of Conduct and how to contribute to this package in the relevant files.
+
 Authors
 ----------------
 
 * Jannis M. Hoch (Utrecht University)
 * Sophie de Bruin (Utrecht University, PBL)
 * Niko Wanders (Utrecht University)
 
-Corrosponding author: Jannis M. Hoch (j.m.hoch@uu.nl)
+Corrosponding author: Jannis M. Hoch (j.m.hoch@uu.nl)