Add reference to JMLR paper

doc/index.rst

@@ -189,22 +189,30 @@ KeOps provides core routines for the following packages:
 
 
 
-Licensing, academic use
+Licensing, citation, academic use
 -----------------------
 
 This library is licensed under the permissive `MIT license <https://en.wikipedia.org/wiki/MIT_License>`_,
 which is fully compatible with both **academic** and **commercial** applications.
-If you use this code in a research paper, **please cite**:
+
+If you use this code in a research paper, **please cite** our 
+`original publication <https://jmlr.org/papers/v22/20-275.html>`_:
 
 .. code-block:: bibtex
 
-    @article{charlier2020kernel,
-        title={Kernel operations on the {GPU}, with autodiff, without memory overflows},
-        author={Charlier, Benjamin and Feydy, Jean and Glaun{\`e}s, Joan Alexis and Collin, Fran{\c{c}}ois-David and Durif, Ghislain},
-        journal={arXiv preprint arXiv:2004.11127},
-        year={2020}
+    @article{JMLR:v22:20-275,
+      author  = {Benjamin Charlier and Jean Feydy and Joan Alexis Glaunès and François-David Collin and Ghislain Durif},
+      title   = {Kernel Operations on the GPU, with Autodiff, without Memory Overflows},
+      journal = {Journal of Machine Learning Research},
+      year    = {2021},
+      volume  = {22},
+      number  = {74},
+      pages   = {1-6},
+      url     = {http://jmlr.org/papers/v22/20-275.html}
     }
 
+.. note:: Charlier, B., Feydy, J., Glaunès, J. A., Collin, F.-D. & Durif, G. Kernel Operations on the GPU, with Autodiff, without Memory Overflows. Journal of Machine Learning Research 22, 1–6 (2021).
+
 
 For applications to **geometric (deep) learning**, 
 you may also consider our `NeurIPS 2020 paper <https://www.jeanfeydy.com/Papers/KeOps_NeurIPS_2020.pdf>`_:
@@ -243,7 +251,7 @@ a report on our `GitHub issue tracker <https://github.com/getkeops/keops/issues>
 - `Mauricio Diaz <https://github.com/mdiazmel>`_, from the University of Montpellier: CI setup.
 - `Benoît Martin <https://github.com/benoitmartin88>`_, from the Aramis Inria team: multi-GPU support.
 - `Francis Williams <https://www.fwilliams.info>`_, from New York University: maths operations.
-- `Kshiteej Kalambarkar <https://www.linkedin.com/in/kshiteejkalambarkar/>`_, from Quansight: maths operations.
+- `Kshiteej Kalambarkar <https://github.com/kshitij12345>`_, from Quansight: maths operations.
 - `D. J. Sutherland <https://djsutherland.ml>`_, from the TTI-Chicago: bug fix in the Python package.
 - `David Völgyes <https://scholar.google.no/citations?user=ngT2GvMAAAAJ&hl=en>`_, from the Norwegian Institute of Science and Technology: bug fix in the formula parser.
 

licence.txt

@@ -1,4 +1,8 @@
-Copyright (c) 2018-2020 B. Charlier, J. Feydy, J. Glaunès, G. Durif, F.-D. Collin
+The MIT License (MIT)
+
+Copyright (c) 2015-2019 Daniel Frey (included C++ library 'sequences')
+
+Copyright (c) 2018-2021 B. Charlier, J. Feydy, J. Glaunès, G. Durif, F.-D. Collin (KeOps/PyKeOps/KeOpslab/RKeOps)
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

readme.md

@@ -184,18 +184,26 @@ KeOps provides core routines for the following projects and libraries:
   [Shapes toolbox](https://plmlab.math.cnrs.fr/jeanfeydy/shapes_toolbox),
   two research-oriented [LDDMM](https://en.wikipedia.org/wiki/Large_deformation_diffeomorphic_metric_mapping) toolkits.
 
-# Licensing, academic use
+# Licensing, citation, academic use
 
 This library is licensed under the permissive [MIT license](https://en.wikipedia.org/wiki/MIT_License),
 which is fully compatible with both **academic** and **commercial** applications.
-If you use this code in a research paper, **please cite**:
+
+If you use this code in a research paper, **please cite** our 
+[original publication](https://jmlr.org/papers/v22/20-275.html):
+
+> Charlier, B., Feydy, J., Glaunès, J. A., Collin, F.-D. & Durif, G. Kernel Operations on the GPU, with Autodiff, without Memory Overflows. Journal of Machine Learning Research 22, 1–6 (2021).
 
 ```tex
-@article{charlier2020kernel,
-    title={Kernel operations on the {GPU}, with autodiff, without memory overflows},
-    author={Charlier, Benjamin and Feydy, Jean and Glaun{\`e}s, Joan Alexis and Collin, Fran{\c{c}}ois-David and Durif, Ghislain},
-    journal={arXiv preprint arXiv:2004.11127},
-    year={2020}
+@article{JMLR:v22:20-275,
+  author  = {Benjamin Charlier and Jean Feydy and Joan Alexis Glaunès and François-David Collin and Ghislain Durif},
+  title   = {Kernel Operations on the GPU, with Autodiff, without Memory Overflows},
+  journal = {Journal of Machine Learning Research},
+  year    = {2021},
+  volume  = {22},
+  number  = {74},
+  pages   = {1-6},
+  url     = {http://jmlr.org/papers/v22/20-275.html}
 }
 ```
 
@@ -234,7 +242,7 @@ a report on our [GitHub issue tracker](https://github.com/getkeops/keops/issues)
 - [Mauricio Diaz](https://github.com/mdiazmel), from the University of Montpellier: CI setup.
 - [Benoît Martin](https://github.com/benoitmartin88), from the Aramis Inria team: multi-GPU support.
 - [Francis Williams](https://www.fwilliams.info), from New York University: maths operations.
-- [Kshiteej Kalambarkar](https://www.linkedin.com/in/kshiteejkalambarkar/), from Quansight: maths operations.
+- [Kshiteej Kalambarkar](https://github.com/kshitij12345), from Quansight: maths operations.
 - [D. J. Sutherland](https://djsutherland.ml), from the TTI-Chicago: bug fix in the Python package.
 - [David Völgyes](https://scholar.google.no/citations?user=ngT2GvMAAAAJ&hl=en), from the Norwegian Institute of Science and Technology: bug fix in the formula parser.
 

rkeops/DESCRIPTION

@@ -38,7 +38,8 @@ Imports:
     Rcpp (>= 1.0.1), 
     RhpcBLASctl, 
     openssl (>= 1.3), 
-    stringr (>= 1.4.0)
+    stringr (>= 1.4.0),
+    Rdpack
 Suggests: 
     testthat (>= 2.1.0),
     knitr,
@@ -53,3 +54,4 @@ LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.1
 VignetteBuilder: knitr
+RdMacros: Rdpack

rkeops/LICENSE

@@ -1,2 +1,7 @@
-YEAR: 2015-2020
-COPYRIGHT HOLDER: Benjamin Charlier, Jean Feydy, Joan A. Glaunès, Ghislain Durif, François-David Collin (KeOps/RKeOps), Daniel Frey (included C++ library 'sequences'), see included file COPYRIGHTS for details.
+YEAR: 2015-2019
+COPYRIGHT HOLDER: Daniel Frey (included C++ library 'sequences')
+
+YEAR: 2018-2021
+COPYRIGHT HOLDER: Benjamin Charlier, Jean Feydy, Joan A. Glaunès, Ghislain Durif, François-David Collin (KeOps/RKeOps)
+
+See included file COPYRIGHTS for details.

rkeops/NAMESPACE

@@ -38,6 +38,7 @@ export(use_cpu)
 export(use_gpu)
 import(Rcpp)
 importFrom(Rcpp,sourceCpp)
+importFrom(Rdpack,reprompt)
 importFrom(RhpcBLASctl,omp_set_num_threads)
 importFrom(openssl,sha256)
 importFrom(parallel,detectCores)

rkeops/R/rkeops-package.R

@@ -32,9 +32,13 @@
 #' (`browseVignettes("rkeops")`) and visit 
 #' https://www.kernel-operations.io/.
 #' 
+#' @references
+#' \insertRef{JMLR:v22:20-275}{rkeops}
+#' 
 #' @import Rcpp
 #' @importFrom Rcpp sourceCpp
 #' @importFrom utils head packageVersion
+#' @importFrom Rdpack reprompt
 #' @useDynLib rkeops, .registration = TRUE
 #' 
 NULL

rkeops/ci/prepare_ci.R

@@ -1,4 +1,4 @@
 pkg_list <- c("devtools", "openssl", "knitr", "Rcpp", "RcppEigen", 
               "RhpcBLASctl", "rmarkdown", 
-              "roxygen2", "stringr", "testthat")
+              "roxygen2", "stringr", "testthat", "Rdpack")
 install_pkg(pkg_list) # function defined in local .Rprofile