Merge pull request #33 from qpv-research-group/paper_fixes_1

JOSS paper review (1)

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,27 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:.
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Environment (please complete the following information):**
+ - OS: [e.g. macOS, Linux, Windows]
+ - RayFlare version [e.g. 1.0.0]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for RayFlare's functionality
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is; e.g. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/question.md

@@ -0,0 +1,22 @@
+---
+name: Question
+about: Ask a question about RayFlare's functionality, the examples, etc.
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Please, confirm the following:**
+
+- [ ] I have checked [RayFlare’s documentation](http://rayflare.readthedocs.io) and could not find the answer.
+- [ ] I haven’t found any [other issues](https://github.com/qpv-research-group/rayflare/issues?q=) on a related topic.
+
+**What’s the question?**
+Please be concise.
+
+**Additional information**
+Add any other relevant information that could help us answering your question, E.g.:
+- Code of a minimum working example showing what you’re trying to do.
+- Screenshot showing the problem you are talking about.
+- Context in which your question applies

.github/workflows/draft-pdf.yml

@@ -0,0 +1,24 @@
+on: [push]
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: TeX
+        uses: docker://openjournals/paperdraft:latest
+        with:
+          args: paper/paper.md --to=latex --output=paper.tex
+        env:
+          GIT_SHA: $GITHUB_SHA
+          JOURNAL: joss
+      - name: PDF
+        uses: docker://openjournals/paperdraft:latest
+        with:
+          args: paper/paper.md
+        env:
+          GIT_SHA: $GITHUB_SHA
+          JOURNAL: joss
+      - uses: actions/upload-artifact@v2
+        with:
+          path: paper

CODE_OF_CONDUCT.md

@@ -0,0 +1,46 @@
+# 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, gender identity and expression, level of experience, 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 [email protected]. The project team will review and investigate all complaints, and will respond in a way that it deems 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 [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

CONTRIBUTING.md

@@ -0,0 +1,136 @@
+# Contributing to RayFlare
+
+Thanks for your interest in contributing to RayFlare! The following is a set of guidelines for contributing to RayFlare, 
+an open-source, integrated optical modelling of complex stacks. The goal of these 
+guidelines is to make the development of the package efficient and sustainable and to ensure that every commit makes it 
+better, more readable, more robust and better documented. Please feel free suggest changes and improvements. 
+
+(this guide is based on the [Atom editor guide](https://github.com/atom/atom/blob/master/CONTRIBUTING.md))
+
+#### Table Of Contents
+
+[Code of Conduct](#code-of-conduct)
+
+[How Can I Contribute?](#how-can-i-contribute)
+  * [Reporting Bugs](#reporting-bugs)
+  * [Suggesting Enhancements](#suggesting-enhancements)
+  * [Pull Requests](#pull-requests)
+
+[Styleguides](#styleguides)
+  * [Git Commit Messages](#git-commit-messages)
+  * [Documentation Styleguide](#documentation-styleguide)
+
+## Code of Conduct
+
+This project and everyone participating in it is governed by the [RayFlare Code of Conduct](CODE_OF_CONDUCT.md). 
+By participating, you are expected to uphold this code. Please report unacceptable behavior to 
+[the repository Administrator](mailto:[email protected]).
+
+## How Can I Contribute?
+
+### Reporting Bugs
+
+This section guides you through submitting a bug report for RayFlare. Following these guidelines helps maintainers and the 
+community understand your report, reproduce the behavior, and find related reports.
+
+Before creating bug reports, please check [this list](https://github.com/qpv-research-group/rayflare/issues) (including the closed 
+issues) as you might find out that you don't need to create one. When you are creating a bug report, please [include as many details as 
+possible](#how-do-i-submit-a-good-bug-report). 
+
+> **Note:** If you find a **Closed** issue that seems like it is the same thing that you're experiencing, open a new issue 
+>and include a link to the original issue in the body of your new one.
+
+#### How Do I Submit A (Good) Bug Report?
+
+Bugs are tracked as [GitHub issues](https://guides.github.com/features/issues/). Explain the problem and include additional 
+details to help maintainers reproduce the problem:
+
+* **Use a clear and descriptive title** for the issue to identify the problem.
+* **Describe the exact steps which reproduce the problem** in as many details as possible. For example, start by explaining how you installed RayFlare and what you where trying to do.
+* **Provide specific examples to demonstrate the steps**. Include links to files or GitHub projects, or copy/pasteable snippets, which you use in those examples. If you're providing snippets in the issue, use [Markdown code blocks](https://help.github.com/articles/markdown-basics/#multiple-lines).
+* **Describe the behavior you observed after following the steps** and point out what exactly is the problem with that behavior.
+* **Explain which behavior you expected to see instead and why.**
+* **If there is any error output in the temrinal, include that output with your report.**
+
+Provide more context by answering these questions:
+
+* **Did the problem start happening recently** (e.g. after updating to a new version of RayFlare) or was this always a problem?
+* If the problem started happening recently, **can you reproduce the problem in an older version of RayFlare?** What's the most recent version in which the problem doesn't happen? You can download older versions of RayFlare from [the releases page](https://github.com/qpv-research-group/rayflare/releases).
+* **Can you reliably reproduce the issue?** If not, provide details about how often the problem happens and under which conditions it normally happens.
+
+Include details about your configuration and environment:
+
+* **Which version of RayFlare are you using?** 
+* **What's the name and version of the OS you're using**?
+* **Are you running RayFlare in a virtual machine?** If so, which VM software are you using and which operating systems and versions are used for the host and the guest?
+* **If the problem is related with the Poisson-drift-diffusion solver**, which compiler did you use? What were the installation steps you followed?
+
+### Suggesting Enhancements
+
+This section guides you through submitting an enhancement suggestion for RayFlare, including completely new features and minor improvements to existing functionality. Following these guidelines helps maintainers and the community understand your suggestion :pencil: and find related suggestions :mag_right:.
+
+Before creating enhancement suggestions, please check [this list](https://github.com/qpv-research-group/rayflare/issues) (including closed issues) as you might find out that you don't need to create one. When you are creating an enhancement suggestion, please [include as many details as possible](#how-do-i-submit-a-good-enhancement-suggestion).
+
+#### How Do I Submit A (Good) Enhancement Suggestion?
+
+Enhancement suggestions are tracked as [GitHub issues](https://guides.github.com/features/issues/). Create an issue on that repository and provide the following information:
+
+* **Use a clear and descriptive title** for the issue to identify the suggestion.
+* **Provide a step-by-step description of the suggested enhancement** in as many details as possible.
+* **Describe the current behavior** and **explain which behavior you expected to see instead** and why.
+* **Explain why this enhancement would be useful** to most RayFlare users, maybe including some links to scientific papers showing the enhancement in action.
+* **List some other packages or applications where this enhancement exists.**
+* **Specify the name and version of the OS you're using.**
+
+
+### Pull Requests
+
+The process described here has several goals:
+
+- Maintain RayFlare's quality
+- Fix problems that are important to users
+- Engage the community in working toward the best possible RayFlare
+- Enable a sustainable system for RayFlare's maintainers to review contributions
+
+Please follow these steps to have your contribution considered by the maintainers:
+
+1. **Describe clearly what is the purpose of the pull request**. Refer to the relevant issues on [Bugs](#reporting-bugs) or [Enhancements](#suggesting-enhancements). In general, an issue should always be open *prior* to a pull request, to discuss its contents with a maintainer and make sure it makes sense for RayFlare. If the pull request is a work in progress that will take some time to be ready but still you want to discuss it with the community, open a [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/). 
+2. **Include relevant unit tests and integration tests, where needed**. RayFlare's test suite is quite limited at the moment. We are working to improve this and tests as many features as possible, so any new addition to the code must come with its own set of tests to avoid going backwards in this matter.   
+3. **For new features and enhancements, include documentation and examples**. Both in the code, as docstrings in classes, functions and modules, and as proper documentation describing how to use the new feature. 
+4. Follow the [styleguides](#styleguides)
+5. After you submit your pull request, verify that all [status checks](https://help.github.com/articles/about-status-checks/) are passing <details><summary>What if the status checks are failing?</summary>If a status check is failing, and you believe that the failure is unrelated to your change, please leave a comment on the pull request explaining why you believe the failure is unrelated. A maintainer will re-run the status check for you. If we conclude that the failure was a false positive, then we will open an issue to track that problem with our status check suite.</details>
+
+While the prerequisites above must be satisfied prior to having your pull request reviewed, the reviewer(s) may ask you to complete additional design work, tests, or other changes before your pull request can be ultimately accepted.
+
+## Styleguides
+
+### Git Commit Messages
+
+* Use the present tense ("Add feature" not "Added feature")
+* Use the imperative mood ("Move cursor to..." not "Moves cursor to...")
+* Limit the first line to 72 characters or less
+* Reference issues and pull requests liberally after the first line
+* When only changing documentation, include `[ci skip]` in the commit title
+* Consider starting the commit message with an applicable emoji:
+    * :art: `:art:` when improving the format/structure of the code
+    * :racehorse: `:racehorse:` when improving performance
+    * :non-potable_water: `:non-potable_water:` when plugging memory leaks
+    * :memo: `:memo:` when writing docs
+    * :penguin: `:penguin:` when fixing something on Linux
+    * :apple: `:apple:` when fixing something on macOS
+    * :checkered_flag: `:checkered_flag:` when fixing something on Windows
+    * :bug: `:bug:` when fixing a bug
+    * :fire: `:fire:` when removing code or files
+    * :green_heart: `:green_heart:` when fixing the CI build
+    * :white_check_mark: `:white_check_mark:` when adding tests
+    * :lock: `:lock:` when dealing with security
+    * :arrow_up: `:arrow_up:` when upgrading dependencies
+    * :arrow_down: `:arrow_down:` when downgrading dependencies
+
+### Documentation Styleguide
+
+* Use [Markdown](https://daringfireball.net/projects/markdown).
+* Reference methods and classes in markdown with the custom `{}` notation:
+    * Reference classes with `{ClassName}`
+    * Reference instance methods with `{ClassName::methodName}`
+    * Reference class methods with `{ClassName.methodName}`