From 792bb9b404f0586bed17295974ac01bcfb92a3b6 Mon Sep 17 00:00:00 2001 From: Didier <Didier.Gemmerle@univ-lorraine.fr> Date: Mon, 27 May 2024 16:19:00 +0200 Subject: [PATCH] adding README --- README.md | 134 +++++++++++++++++++++++++++--------------------------- 1 file changed, 68 insertions(+), 66 deletions(-) diff --git a/README.md b/README.md index 59d232a..686093a 100644 --- a/README.md +++ b/README.md @@ -1,92 +1,94 @@ # DRlib -DRlib is a C++ library for modeling, simulation and inference of marked point processes +DRlib is a C++ library for modeling, simulation and inference of marked +point processes. -## Getting started +The aim is to complete existing tools such as spatstat library in R [1] with reliable and efficient C++ code allowing intensive Bayesian MCMC based inference for marked Gibbs point processes. This proposal has its roots in the MPPLIB library developed mainly by [2,3] where exact simulation algorithms for marked point processes were translated into C++ in order to perform +massive simulation studies. -To make it easy for you to get started with GitLab, here's a list of recommended next steps. - -Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)! - -## Add your files - -- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files -- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command: +The current version of the library is freely available at the following address https://gitlab.univ-lorraine.fr/labos/iecl/drlib. +## To start quickly and test +To get a local copy of the library: ``` -cd existing_repo -git remote add origin https://gitlab.univ-lorraine.fr/labos/iecl/DRlib.git -git branch -M main -git push -uf origin main +mkdir Installation_directory +cd Installation_directory +git clone https://gitlab.univ-lorraine.fr/labos/iecl/drlib.git ``` -## Integrate with your tools - -- [ ] [Set up project integrations](https://gitlab.univ-lorraine.fr/labos/iecl/DRlib/-/settings/integrations) - -## Collaborate with your team - -- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/) -- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html) -- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically) -- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/) -- [ ] [Automatically merge when pipeline succeeds](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html) - -## Test and Deploy - -Use the built-in continuous integration in GitLab. - -- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html) -- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/) -- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html) -- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/) -- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html) +The library currently has 2 main directories, *main* and *python*. -*** +``` +cd drlib +ls -1 + main + python +``` -# Editing this README +The *main* directory contains some examples of using of the DRlib library: +``` +- Fixed-AreaInt : process Poisson+Area Interaction with fixed radius +- Fixed-Strauss : process Poisson+Strauss with fixed radius +- Fixed-Strauss-AreaInt : process Poisson+Strauss+Area Interaction + with fixed radius +- Generic : process with possibility of any combinaison in Poisson, + Area Interaction with fixed radius, Area Interaction + with random radius, Strauss with fixed radius and + Strauss with random radius +- Function-FGJK : F, G, J, K functions with envelopes computations +``` -When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template. +Each directories has the following structure: +``` +- C++ + - SRC : source files and Makefile + - EXEC : executable programs + - PARAMS : parameters files + - RESULTS : results files +- R + a set of useful programs to visualize the results + ``` -## Suggestions for a good README -Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information. -## Name -Choose a self-explaining name for your project. +The *python* directory contains some examples of using of the DRlib library: -## Description -Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors. -## Badges -On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge. +Compilation and test +``` +cd C++/SRC +make clean +make +cd ../EXEC +and run the corresponding .bat program -## Visuals -Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method. +WARNING : the unix rights on .bat programs with git could be wrong. + To solve this chmod 555 *.bat +````` -## Installation -Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection. +## Documentation +The documentation is currently being written, and a link will be added when a version will be available. In the meantime, the source programs are extensively commented. -## Usage -Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README. +In short, the idea of the library is to assemble a set of *components* to express the energy function. This set is currently made up of Poisson, Area Interaction with a fixed and random radius, Strauss with a fixed and random radius and of soon component with a convex envelope, and only needs to be completed... -## Support -Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc. +## Authors and acknowledgment +Authors : Didier Gemmerlé, Radu-Stefan Stoica, Chistophe Reype and Nathan Gillot. -## Roadmap -If you have ideas for releases in the future, it is a good idea to list them in the README. +Contributor : Pierre Auburtin and Diego Astaburuaga. -## Contributing -State if you are open to contributions and what your requirements are for accepting them. +## References -For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self. +[1] A. J. Baddeley, E. Rubak, and R. Turner. Spatial Point Patterns: +Methodology and Applications with R. London: Chapman and +Hall/CRC Press, 2016. -You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser. +[2] M. N. M. van Lieshout and R. S. Stoica. “Perfect simulation for +marked point processes”. In: Computational Statistics and Data +Analysis 51 (2006), pp. 679–698. -## Authors and acknowledgment -Show your appreciation to those who have contributed to the project. +[3] R. S. Stoica, M. Deaconu, A. Philippe and L. Hurtado-Gil. “Shadow Simulated Annealing: a new algorithm for +approximate Bayesian inference of Gibbs point processes”. In: Spatial +Statistics 43 (2021), pp. 1–21 -## License -For open source projects, say how it is licensed. +[4] R. S. Stoica, A. Philippe, P. Gregori and J. Mateu. "ABC Shadow algorithm: a tool for statistical +analysis of spatial patterns". In: Statistics and Computing 27, (2017), pp. 1225–1238 -## Project status -If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers. -- GitLab