Merge branch 'add-contributing-guide' into 'master'

Add contributing guide

See merge request Monash/tupak!179

CONTRIBUTING.md

+
+Contributing to tupak
+=================
+
+This is a short guide to help get you started contributing to tupak.
+
+Getting started
+-------------------
+
+All the code lives in a git repository (for a short introduction to git, see
+[this tutorial](https://docs.gitlab.com/ee/gitlab-basics/start-using-git.html))
+which is hosted here: https://git.ligo.org/Monash/tupak.  If you haven't
+already, you should
+[fork](https://docs.gitlab.com/ee/gitlab-basics/fork-project.html) the repository
+and clone your fork, i.e., on your local machine run
+
+```bash
+$ git clone git@git.ligo.org:albert.einstein/tupak.git
+```
+
+replacing the SSH url to that of your fork. This will create a directory `/tupak`
+containing a local copy of the code. From this directory, you can run
+
+```bash
+$ python setup.py develop
+```
+
+which will install `tupak` and, because we used `develop` instead of `install`
+when you change the code your installed version will automatically be updated.
+
+--- 
+
+#### Removing previously installed versions
+
+If you have previously installed `tupak` using `pip` (or generally find buggy
+behaviour). It may be worthwhile purging your system and reinstalling. To do
+this, first find out where the module is being imported from: from any
+directory that is *not* the source directory, do the following
+
+```bash
+$ python
+>>> import tupak
+>>> print(tupak.__file__)
+/home/user/anaconda2/lib/python2.7/site-packages/tupak-0.2.2-py2.7.egg/tupak/__init__.pyc
+```
+In the example output above, we see that the directory that module is installed
+in. To purge our python installation, run
+
+```bash
+$ rm -r /home/user/anaconda2/lib/python2.7/site-packages/tupak*
+```
+
+You can then verify this was successful by trying to import tupak in the python
+interpreter.
+
+Discussion
+----------
+
+If you've run into behavior you don't understand, or you're
+having trouble working out a good way to apply it to your code, or
+you've found a bug or would like a feature it doesn't have, we want to
+hear from you!
+
+Our main forum for discussion is the project's [GitLab issue
+tracker](https://git.ligo.org/Monash/tupak/issues). This is the right
+place to start a discussion of any of the above or most any other
+topic concerning the project.
+
+#### Code of Conduct
+
+Everyone participating in the tupak community, and in particular in our
+issue tracker, pull requests, and IRC channel, is expected to treat
+other people with respect and more generally to follow the guidelines
+articulated in the [Python Community Code of
+Conduct](https://www.python.org/psf/codeofconduct/).
+
+
+Submitting Changes
+------------------------
+
+All changes to the code base go through the [pull-request
+workflow](https://docs.gitlab.com/ee/user/project/merge_requests/) Anyone may
+review your code and you may expect a few comments and questions.  Once all
+discussions are resolved, core developers will approve the merge request and
+then merge in into master. If you go a few days without a reply, please feel
+free to ping the thread by adding a new comment.
+
+All merge requests should be focused: they should aim to either add one
+feature, solve one bug, or fix some stylistic issues. If multiple changes are
+lumped together it can slow down the process and make it harder to review.
+
+Before you begin: if your change will be a significant amount of work
+to write, we highly recommend starting by opening an issue laying out
+what you want to do.  That lets a conversation happen early in case
+other contributors disagree with what you'd like to do or have ideas
+that will help you do it.
+
+We are keen to maintain a high standard of the code. This makes it easier to
+maintain, develop, and track down buggy behaviour.
+
+All merge requests should also be recorded in the CHANGELOG.md.
+This just requires a short sentence describing describing the change, e.g.,
+"- Enable initial values for emcee to be specified."
+
+ADD DISCUSSION ON CODE QUALITY
+
+Reviewing Changes
+-----------------
+
+If you are reviewing a merge request (either as a core developer or just as an
+interested party) please key these three things in mind
+
+* If you open a discussion, be timely in responding to the submitter. Note, the
+  reverse does not need to apply.
+* Keep your questions/comments focussed on the scope of the merge request. If
+  while reviewing the code you notice other things which could be improved, open
+  a new issue.
+* Be supportive - merge requests represent a lot of hard work and effort and
+  should be encouraged.
+
+Core developer guidelines
+-------------------------
+
+Core developers should follow these rules when processing pull requests:
+
+* Always wait for tests to pass before merging PRs.
+* Delete branches for merged PRs (by core devs pushing to the main repo).
+* Make sure related issues are linked and (if appropriate) closed.
+* Squash commits
+
+
+Issue-tracker conventions
+-------------------------
+
+#### Bug reporting
+
+If you notice any bugs in the code, please let us know!
+
+Issues reporting bugs should include:
+* A brief description of the issue.
+* A full error trace (if applicable).
+* A minimal example to reproduce the issue.
+
+#### Feature requests
+
+If there's any additional functionality you'd like to see in the code open an
+issue describing the desired feature.
+
+In order to maximise the likelihood that feature requests will be fulfilled
+you should:
+* Make the feature request as specific as possible, vague requests are
+  unlikely to be taken on by users.
+* If possible break down the feature into small chunks which can be
+  marked off on a checklist.
+
+
+
+## Code overview
+
+In this section, we'll give an overview of how the code is structured. This is intended to help orient users and make it easier to contribute. The layout is intended to define the logic of the code and new merge requests should aim to fit within this logic (unless there is a good argument to change it). For example, code which adds a new sampler should not effect the gravitational-wave specific parts of the code. Note that this document is not programatically generated and so may get out of date with time. If you notice something wrong, please open an issue. 
+
+### Top level
+
+At the top level, the code is split into three modules containing the core, gravitational-wave specific, and hyper-parameter specific functionality. New changes should always respect this  
+
+```mermaid
+graph TD
+tupak[tupak] --> core[.core]
+tupak --> gw[.gw]
+tupak --> hyper[.hyper]
+```
+
+### Core
+The core module contains the core inference logic - methods to define a prior, likelihood, and run Bayesian inference.
+
+```mermaid
+graph TD
+core[tupak.core] --> prior[.prior] 
+core --> likelihood[.likelihood] 
+core --> result[.result] 
+core --> sampler[.sampler] 
+core --> utils[.utils]
+
+prior --> Prior[".Prior()"]
+style Prior fill:#D7BDE2
+prior --> Normal[".Normal(Prior)"]
+style Normal fill:#D7BDE2
+prior --> Uniform[".Uniform(Prior)"]
+style Uniform fill:#D7BDE2
+
+likelihood --> Likelihood(".Likelihood()")
+style Likelihood fill:#D7BDE2
+likelihood --> GaussianLikelihood(".GaussianLikelihood()")
+style GaussianLikelihood fill:#D7BDE2
+
+result --> Result(".Result()")
+style Result fill:#D7BDE2
+
+sampler --> run_sampler("run_sampler()")
+style run_sampler fill:#5499C7
+```
+
+Note this layout is not comprehensive, for example only a few example "Priors" are shown.
+
+### Gravitational-wave specific
+
+```mermaid
+graph TD
+gw[tupak.gw] --> gw_likelihood[.likelihood]
+gw --> gw_prior[.prior]
+gw --> gw_source[.source]
+gw --> gw_waveform_generator[.waveform_generator]
+gw --> gw_utils[.utils]
+gw --> gw_conversion[.conversion]
+
+gw_likelihood --> GravitationalWaveTransient(".GravitationalWaveTransient()")
+style GravitationalWaveTransient fill:#D7BDE2
+gw_source --> lal_bbh(".lal_binary_black_hole()")
+style lal_bbh fill:#5499C7
+gw_waveform_generator--> WaveformGenerator(".WaveformGenerator()")
+style WaveformGenerator fill:#D7BDE2
+```
+### Legend of flow diagrams
+To show a module we use a grey box. A nested module is indicated as such
+```mermaid
+graph LR
+module[module] --> A[.other_module </br>]
+```
+i.e., in python, `module.other_module`. Meanwhile, a class,  `MyClass` living in module `my_module`  is indicated by
+```mermaid
+graph LR 
+ my_module[my_module] --> Class[".MyClass(parent)"]
+ style Class fill:#D7BDE2
+```
+where the `(Parent)` indicates the parent class from which this class inherits. Finally, we define a function living in a module as
+```mermaid
+graph LR 
+ my_module[my_module] --> function[".function()"]
+ style function fill:#5499C7
+```
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