Update

README.rst

@@ -20,22 +20,24 @@ This repository contains supplementary material for the reproducibility of compu
 * Jean Peyhardi,
 * Jean-Baptiste Durand.
 
-This article has been submitted to the "arXiv" e-print service.
-Here is the the citation formated as the bibtex standart.
+This `article <https://arxiv.org/abs/1802.02074>`_ has been submitted to the "arXiv" e-print service.
+Here is the the citation formated as the bibtex standard.
 
 .. code-block:: bibtex
 
-  @article{FP17,
-    author    = {},
-    title     = {Splitting distributions for multivariate count data},
-    journal   = {CoRR},
-    volume    = {},
-    year      = {2018},
-    url       = {},
-    timestamp = {},
-    biburl    = {,
-    bibsource = {}
-  }
+   @ARTICLE{2018arXiv180202074F,
+            author = {{Fernique}, P. and {Peyhardi}, J. and {Durand}, J.-B.},
+            title = "{Splitting models for multivariate count data}",
+            journal = {ArXiv e-prints},
+            archivePrefix = "arXiv",
+            eprint = {1802.02074},
+            primaryClass = "math.ST",
+            keywords = {Mathematics - Statistics Theory, Mathematics - Probability},
+            year = 2018,
+            month = feb,
+            adsurl = {http://adsabs.harvard.edu/abs/2018arXiv180202074F},
+            adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+   }
 
 These studies are formatted as pre-executed **Jupyter** `notebooks <https://jupyter.readthedocs.io/en/latest/index.html>`_.
 Refers to the `index.ipynb <share/jupyter/index.ipynb>`_ notebook which presents and references each study.
@@ -52,12 +54,7 @@ Online with **Binder**
 
    Currently, **Binder** does not work with this repository due to timeouts.
 
-To reproduce the studies online, use this `server <https://beta.mybinder.org/v2/gh/statiskit/fpd18/v1.0.0?filepath=share/jupyter/index.ipynb>`_.
-
-.. note::
-
-   This server corresponds to the one used for the article.
-   Most recent server can be runned using this `link <https://beta.mybinder.org/v2/gh/statiskit/fpd18/master?filepath=share/jupyter/index.ipynb>`_.
+To reproduce the studies online, use this `server <https://beta.mybinder.org/v2/gh/statiskit/fpd18/master>`_.
 
 On your computer with **Docker**
 --------------------------------
@@ -69,32 +66,15 @@ After `installing <https://docs.docker.com/engine/installation/>`_ **Docker**, y
 
   .. code-block:: console
 
-    docker run -i -t -p 8888:8888 statiskit/fpd18:v1.0.0-py2k
+    docker run -i -t -p 8888:8888 statiskit/fpd18:latest-py2k
    
 * For the *Python 3* version 
 
   .. code-block:: console
 
-    docker run -i -t -p 8888:8888 statiskit/fpd18:v1.0.0-py3k
+    docker run -i -t -p 8888:8888 statiskit/fpd18:latest-py3k
   
 Then, follow the given instructions.
-
-.. note::
-
-    These images correspond to the ones used for the article.
-    Most recent images can be runned using these commands in a shell:
-
-    * For the *Python 2* version 
-
-      .. code-block:: console
-
-        docker run -i -t -p 8888:8888 statiskit/fpd18:latest-py2k
-   
-    * For the *Python 3* version 
-
-      .. code-block:: console
-
-        docker run -i -t -p 8888:8888 statiskit/fpd18:latest-py3k
 
 Install it !
 ============
@@ -113,26 +93,21 @@ Then, to install the required packages, proceed as as follows:
 
    .. code:: console
    
-     git clone --recursive https://github.com/StatisKit/FP17
+     git clone --recursive https://github.com/StatisKit/FPD18
      
 2. Create a **Conda** environment containing the meta-package :code:`fpd18`,
 
    .. code:: console
 
-       conda create -n fpd18 fpd18=1.0.0 python=2 -c statiskit -c defaults --override-channels
- 
-   .. note::
-
-     This meta-package corresponds to the one used for the article.
-     Most recent meta-package can be installed by replacing :code:`fpd18=1.0.0` by :code:`fpd18` in previous command lines
+       conda create -n fpd18 fpd18 python=2 -c statiskit -c r -c defaults --override-channels
      
 3. Activate the **Conda** environment as advised in your terminal.
 
 4. Enter the directory containing **Jupyter** notebooks,
 
    .. code:: console
    
-     cd FP17
+     cd FPD18
      cd share
      cd jupyter
      
@@ -142,4 +117,4 @@ Then, to install the required packages, proceed as as follows:
 
      jupyter notebook index.ipynb
      
-6. Execute the `index.ipynb <share/jupyter/index.ipynb>`_ notebook to execute all examples or navigate among referenced notebooks to execute them separatly.
+6. Execute the `index.ipynb <share/jupyter/index.ipynb>`_ notebook to execute all examples or navigate among referenced notebooks to execute them separately.

appveyor.yml

@@ -12,17 +12,19 @@ platform:
 environment:
   matrix:
     - CONDA_RECIPE: bin\conda\r-statmod
-    - CONDA_RECIPE: bin\conda\r-codetools
-    - CONDA_RECIPE: bin\conda\r-iterators
-    - CONDA_RECIPE: bin\conda\r-doparallel
-    - CONDA_RECIPE: bin\conda\r-foreach
-    - CONDA_RECIPE: bin\conda\r-bpsc
+    # - CONDA_RECIPE: bin\conda\r-codetools
+    # - CONDA_RECIPE: bin\conda\r-iterators
+    # - CONDA_RECIPE: bin\conda\r-doparallel
+    # - CONDA_RECIPE: bin\conda\r-foreach
+    # - CONDA_RECIPE: bin\conda\r-bpsc
     - CONDA_RECIPE: bin\conda\r-mglm
     - CONDA_RECIPE: bin\conda\r-bivpois
-    - CONDA_PACKAGES: fp17
-      JUPYTER_NOTEBOOK:  share\jupyter\comparison.ipynb
-    - CONDA_PACKAGES: fp17
-      JUPYTER_NOTEBOOK:  share\jupyter\application.ipynb
+    - CONDA_RECIPE: bin\conda\fpd18
+    - CONDA_PACKAGES: fpd18
+      JUPYTER_NOTEBOOK:  share\jupyter\comparison_KN05.ipynb
+    - CONDA_PACKAGES: fpd18
+      JUPYTER_NOTEBOOK:  share\jupyter\comparison_ZZ17.ipynb
+    - ANACONDA_RELEASE: true
 
 install:
   - git clone --depth=1 https://github.com/StatisKit/appveyor-ci.git appveyor-ci

bin/docker/linux-64/Dockerfile

@@ -5,7 +5,6 @@ FROM statiskit/linux-64:${GIT_TAG}-py${CONDA_VERSION}k
 COPY README /home/main/README
 RUN rm /home/main/.condarc
 COPY .condarc /home/main/.condarc
-RUN conda install -n $CONDA_DEFAULT_ENV fpd18
 RUN echo "source activate fpd18" >> .bashrc
 RUN echo "cat /home/main/README" >> .bashrc
 

environment.yml

@@ -1,18 +1,6 @@
-name: FPD17
 channels:
   - statiskit
   - r
+  - defaults
 dependencies:
-  - python=2.7
-  - r-essentials
-  - r-mglm
-  - r-bivpois
-  - rpy2
-  - pandas
-  - matplotlib
-  - jupyter
-  - jupyter_contrib_nbextensions
-  - jupyter_nbextensions_configurator
-  - python-statiskit_linalg
-  - python-statiskit_core
-  - python-statiskit_glm
+  - fpd18

postBuild

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+mkdir -p /srv/conda/etc/conda/activate.d
+touch /srv/conda/etc/conda/activate.d/activate-cpu-count.sh
+echo "export CPU_COUNT=1" > /srv/conda/etc/conda/activate.d/activate-cpu-count.sh
+
+mkdir -p /srv/conda/etc/conda/deactivate.d
+touch /srv/conda/etc/conda/activate.d/deactivate-cpu-count.sh
+echo "unset CPU_COUNT" > /srv/conda/etc/conda/deactivate.d/deactivate-cpu-count.sh
+
+export GIT_TAG=`git tag --points-at HEAD`
+if [[ ! "$GIT_TAG" = "" ]]; then
+    GIT_VERSION=`echo $GIT_TAG | tail -c +2`
+    conda install fp17=$GIT_VERSION -c statiskit -c defaults --override-channels
+fi

travis.yml

@@ -16,19 +16,20 @@ services:
 
 env:
   - CONDA_RECIPE=bin/conda/r-statmod
-  - CONDA_RECIPE=bin/conda/r-bpsc
+  # - CONDA_RECIPE=bin/conda/r-bpsc
   - CONDA_RECIPE=bin/conda/r-mglm
   - CONDA_RECIPE=bin/conda/r-bivpois
   - CONDA_RECIPE=bin/conda/fpd18
   - CONDA_PACKAGES=fpd18
-    JUPYTER_NOTEBOOK=share/jupyter/comparison.ipynb
+    JUPYTER_NOTEBOOK=share/jupyter/comparison_KN05.ipynb
   - CONDA_PACKAGES=fpd18
-    JUPYTER_NOTEBOOK=share/jupyter/application.ipynb
+    JUPYTER_NOTEBOOK=share/jupyter/comparison_ZZ17.ipynb
     TRAVIS_WAIT=30
   - DOCKER_CONTEXT=bin/docker/linux-64
     DOCKER_CONTAINER=fpd18
     CONDA_VERSION=2
-
+  - ANACONDA_RELEASE=true
+
 matrix:
   exclude:
   - os: osx