From 629b7e50e78cbc9a790c3e6c8a7cc00a8ca9491c Mon Sep 17 00:00:00 2001 From: Wolf Byttner Date: Sat, 13 Feb 2021 13:27:27 +0000 Subject: [PATCH 1/6] Add initial contributing guide --- contributing.rst | 90 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 90 insertions(+) create mode 100644 contributing.rst diff --git a/contributing.rst b/contributing.rst new file mode 100644 index 00000000..03c03a7b --- /dev/null +++ b/contributing.rst @@ -0,0 +1,90 @@ +Contributing to Traja +===================== + + +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 + +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. + +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 \ No newline at end of file From 6a0ccb8c4c8338f7cd43518654c0a9cdd617813b Mon Sep 17 00:00:00 2001 From: Justin Shenk Date: Wed, 17 Feb 2021 14:01:28 +0100 Subject: [PATCH 2/6] Update contributing.rst fix formatting --- contributing.rst | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/contributing.rst b/contributing.rst index 03c03a7b..93973f3f 100644 --- a/contributing.rst +++ b/contributing.rst @@ -13,26 +13,27 @@ 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 + * 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 + * 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?) + * Uniform + * A shape that works for periodic trajectories (Torus?) * Delay coordinate embeddings - * Persistent homology diagrams of the embeddings + * Persistent homology diagrams of the embeddings * Automatic code formatter * Tutorials - * Find time of day based on activity - * Recover parameters from Pituitary ODE + * Find time of day based on activity + * Recover parameters from Pituitary ODE How to contribute ----------------- @@ -87,4 +88,4 @@ Understanding the parameter space of the pituitary gland ODE (https://www.math.f Style guide ----------- -TODO \ No newline at end of file +TODO From 31a187ff13313820761ec90a3f005bf982903e66 Mon Sep 17 00:00:00 2001 From: Wolf Byttner Date: Sun, 21 Feb 2021 18:23:51 +0000 Subject: [PATCH 3/6] Add test and code quality section to contributors guide --- contributing.rst | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/contributing.rst b/contributing.rst index 93973f3f..71b12982 100644 --- a/contributing.rst +++ b/contributing.rst @@ -42,6 +42,15 @@ 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 ------------------- From 0c22e7f6fa5dc4543bace281406d1b4eb7d3b212 Mon Sep 17 00:00:00 2001 From: Wolf Byttner Date: Mon, 22 Feb 2021 14:34:17 +0000 Subject: [PATCH 4/6] Add intro to contributor's guide --- contributing.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/contributing.rst b/contributing.rst index 71b12982..5477b133 100644 --- a/contributing.rst +++ b/contributing.rst @@ -1,6 +1,10 @@ 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. Current status -------------- From 97e83a9cbcaeb9b6995c219bc067b4c50d686ec3 Mon Sep 17 00:00:00 2001 From: Wolf Byttner Date: Thu, 25 Feb 2021 20:38:15 +0000 Subject: [PATCH 5/6] Improve contributing intro section --- contributing.rst | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/contributing.rst b/contributing.rst index 5477b133..65198bc5 100644 --- a/contributing.rst +++ b/contributing.rst @@ -4,7 +4,9 @@ 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. +open-source contribution models. It is our hope that traja +remains accessible to researchers and help them do higher-quality +research. Current status -------------- From d99d24bce22c17376584fab7ed952253aae8ac09 Mon Sep 17 00:00:00 2001 From: Wolf Byttner Date: Sat, 27 Mar 2021 13:40:39 +0000 Subject: [PATCH 6/6] Add hyperlinks to notebooks (that exist) --- contributing.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/contributing.rst b/contributing.rst index 65198bc5..3130acfc 100644 --- a/contributing.rst +++ b/contributing.rst @@ -39,7 +39,8 @@ The following features are required for feature completeness: * Automatic code formatter * Tutorials * Find time of day based on activity - * Recover parameters from Pituitary ODE + * `Recover parameters from Pituitary ODE `_ + * `Predict stock prices with LSTMs `_ How to contribute -----------------