Merge pull request #73 from traja-team/contributing

Add initial contributing guide

contributing.rst

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+Contributing to Traja
+=====================
+
+Traja is a research library. Functionality must therefore be both
+cutting-edge and reliable. Traja is part of a wider project to
+increase collaboration in research, through the adoption of
+open-source contribution models. It is our hope that traja
+remains accessible to researchers and help them do higher-quality
+research.
+
+Current status
+--------------
+
+Traja is currently undergoing active development with approximately
+60 % of features present. Significant interface changes are still
+possible, however we avoid these unless absolutely necessary.
+
+The work is currently focussed on reaching version 1.0 with feature
+completeness and 95 % test coverage.
+
+The following features are required for feature completeness:
+
+* Latent space visualisers
+   * Eigenspace-based
+   * Colour-coded to visualise evolution over time
+   * Delay coordinate embeddings
+* State-space visualisers
+* Additional encoder and decoder options in AE and VAE models
+   * MLP
+   * 1d convolution
+* Pituitary gland example dataset
+* Regression output visualisers
+* VAE GAN models
+* Additional VAE latent-space shapes
+   * Uniform
+   * A shape that works for periodic trajectories (Torus?)
+* Delay coordinate embeddings
+   * Persistent homology diagrams of the embeddings
+* Automatic code formatter
+* Tutorials
+   * Find time of day based on activity
+   * `Recover parameters from Pituitary ODE <https://colab.research.google.com/drive/1Fc8Z6LtjMBk20QPPzJt8uDAxWu5dz_1Y?usp=sharing>`_
+   * `Predict stock prices with LSTMs <https://colab.research.google.com/drive/1TAW9Lv0Sm9g8YRgYXaiHIZBqnGtGQn1H?usp=sharing>`_
+
+How to contribute
+-----------------
+
+Traja welcomes contributions! To get started, pick up any issue
+labeled with `good first issue`! Alternatively you can read some
+background material or try a tutorial.
+
+Testing and code quality
+------------------------
+
+Since Traja is a library, we strive for sensible tests achieving a
+high level of code coverage. Future commits are required to maintain
+or improve code quality, test coverage. To aid in this, Travis runs
+automated tests on each pull request. Additionally, we run codecov
+on PRs.
+
+Background material
+-------------------
+
+This is a collection of papers and resources that explain the
+main problems we are working on with Traja.
+
+Analysis of mice that have suffered a stroke:
+
+    @article{10.3389/fnins.2020.00518,
+      author={Justin Shenk and
+              Klara J. Lohkamp and
+              Maximilian Wiesmann and
+              Amanda J. Kiliaan},
+      title={Automated Analysis of Stroke Mouse Trajectory Data With Traja},
+      journal={Frontiers in Neuroscience},
+      volume={14},
+      pages={518},
+      year={2020},
+      url={https://www.frontiersin.org/article/10.3389/fnins.2020.00518},
+      doi={10.3389/fnins.2020.00518},
+      issn={1662-453X},
+    }
+
+
+Understanding the parameter space of the pituitary gland ODE (https://www.math.fsu.edu/~bertram/papers/bursting/JCNS_16.pdf):
+
+
+    @article{10.1007/s10827-016-0600-1,
+      author = {Fletcher, Patrick and Bertram, Richard and Tabak, Joel},
+      title = {From Global to Local: Exploring the Relationship between Parameters and Behaviors in Models of Electrical Excitability},
+      year = {2016},
+      publisher = {Springer-Verlag},
+      address = {Berlin, Heidelberg},
+      volume = {40},
+      number = {3},
+      issn = {0929-5313},
+      url = {https://doi.org/10.1007/s10827-016-0600-1},
+      doi = {10.1007/s10827-016-0600-1},
+      journal = {J. Comput. Neurosci.},
+      month = June,
+      pages = {331–345},
+    }
+
+
+Style guide
+-----------
+TODO