working challenge with python and R

docker/codabench_hadaca3_pyr/Dockerfile

@@ -1,5 +1,3 @@
-# Python requirements
-# FROM debian:11.0
 FROM mambaorg/micromamba:1.5.8
 
 # WORKDIR /app
@@ -12,17 +10,78 @@ RUN micromamba env create -f environment-r.yml && micromamba clean --all --yes
 
 SHELL ["micromamba", "run", "-n", "h3", "/bin/bash", "-c"]
 
-# RUN echo 'source /opt/conda/etc/profile.d/conda.sh && micromamba activate h3' >> ~/.bashrc
 RUN echo 'micromamba activate h3' >> ~/.bashrc
 
-
-
 ENV PATH /opt/conda/bin:$PATH
-ENV R_LIBS=/usr/local/lib/R/site-library
 
 
 ENTRYPOINT ["micromamba", "run", "-n", "h3"]
 
 USER root
+RUN apt-get update && apt-get install -y --fix-missing r-base 
 RUN apt-get update && apt-get upgrade -y && apt-get install -y gzip
-# USER 1001
+
+
+
+# # Python requirements
+# FROM debian:11.0
+
+# RUN apt update --fix-missing
+
+# # # Install anaconda
+# # RUN apt-get update --fix-missing && apt-get install -y wget bzip2 ca-certificates \
+# #     libglib2.0-0 libxext6 libsm6 libxrender1 \
+# #     git mercurial subversion
+# # RUN echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
+# #     wget --quiet https://repo.continuum.io/archive/Anaconda3-2022.05-Linux-x86_64.sh && \
+# #     /bin/bash /Anaconda3-2022.05-Linux-x86_64.sh -b -p /opt/conda && \
+# #     rm /Anaconda3-2022.05-Linux-x86_64.sh
+
+# # RUN apt-get install -y curl grep sed dpkg tini
+
+# ENV PATH /opt/conda/bin:$PATH
+# ENV R_LIBS=/usr/local/lib/R/site-library
+
+# # C#, R, etc. requirements
+# RUN apt-get update && apt-get install -y --fix-missing r-base 
+# #mono-runtime libgomp1 libc6
+
+# # Fix for 'xgboost' missing
+# # RUN conda install libgcc
+# #RUN conda install -c conda-forge tensorflow
+
+# # RUN echo "deb http://http.us.debian.org/debian/ testing non-free contrib main" > /etc/apt/sources.list && \
+# #     apt-get update 
+#     # apt-get -y -t testing install python3.9 python3-pip
+
+# RUN apt-get install gzip
+# RUN  apt-get -y install pandoc && apt-get clean && apt-get auto-clean && apt-get -y auto-remove
+
+# # RUN pip3 install \
+# #         theano==1.0.5 \
+# #         Cython==0.29.30 \
+# #         numpy==1.22.4 \
+# #         scipy==1.8.1 \
+# #         scikit-learn==1.1.1 \
+# #         pandas==1.4.2 \
+# #         pyyaml==6.0 \
+# #         imutils==0.5.4 \
+# #         numba==0.55.2 \
+# #         tensorflow==2.9.1
+
+
+# RUN  Rscript -e 'install.packages(pkgs = "BiocManager")'
+
+# RUN  Rscript -e 'BiocManager::install(pkgs = "Biobase")'
+# RUN  Rscript -e 'install.packages(pkgs = "zip")'
+# RUN Rscript -e 'install.packages(pkgs=c("utf8", "farver", "labeling", "munsell", "R6", "viridisLite", "fansi", "pillar", "pkgconfig", "cli", "glue", "lifecycle", "magrittr", "rlang", "stringi", "vctrs", "iterators", "gtable", "isoband", "scales", "tibble", "withr", "plyr", "Rcpp", "registry", "rngtools", "stringr", "digest", "gridBase", "colorspace", "RColorBrewer", "foreach", "doParallel", "ggplot2", "reshape2"))'
+# RUN Rscript -e 'install.packages(pkgs=c("fs", "rappdirs", "base64enc", "cachem", "fastmap", "memoise", "mime", "sass", "highr", "bslib", "evaluate", "fontawesome", "htmltools", "jquerylib", "jsonlite", "knitr", "tinytex", "xfun", "yaml"))'
+# RUN Rscript -e 'install.packages(pkgs=c( "combinat",  "rmarkdown", "clue","infotheo"))'
+
+# RUN  Rscript -e 'install.packages(pkgs = "NMF", repos = "https://cloud.r-project.org")'
+
+# RUN Rscript -e 'install.packages(pkgs=c( "bitops",  "caTools", "gplots","viridis"))'
+
+# COPY environment/requirements.txt .
+
+# RUN pip3 install --no-cache-dir -r requirements.txt

docker/codabench_hadaca3_pyr/environment/environment-r.yml

@@ -1,9 +1,10 @@
 name: h3
 channels:
+  - conda-forge
   - defaults
 dependencies:
-  - _libgcc_mutex=0.1=main
-  - _openmp_mutex=5.1=1_gnu
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_gnu
   - _r-mutex=1.0.0=anacondar_1
   - _sysroot_linux-64_curr_repodata_hack=3=haa98f57_10
   - binutils_impl_linux-64=2.38=h2a08ee3_1
@@ -44,11 +45,11 @@ dependencies:
   - libev=4.33=h7f8727e_1
   - libffi=3.4.4=h6a678d5_1
   - libgcc-devel_linux-64=11.2.0=h1234567_1
-  - libgcc-ng=11.2.0=h1234567_1
+  - libgcc-ng=14.1.0=h77fa898_0
   - libgfortran-ng=11.2.0=h00389a5_1
   - libgfortran5=11.2.0=h1234567_1
   - libglib=2.78.4=hdc74915_0
-  - libgomp=11.2.0=h1234567_1
+  - libgomp=14.1.0=h77fa898_0
   - libiconv=1.16=h5eee18b_3
   - libnghttp2=1.57.0=h2d74bed_0
   - libopenblas=0.3.21=h043d6bf_0
@@ -59,7 +60,7 @@ dependencies:
   - libtiff=4.5.1=h6a678d5_0
   - libuuid=1.41.5=h5eee18b_0
   - libwebp-base=1.3.2=h5eee18b_0
-  - libxcb=1.15=h7f8727e_0
+  - libxcb=1.16=hd590300_0
   - libxml2=2.10.4=hfdd30dd_2
   - lz4-c=1.9.4=h6a678d5_1
   - make=4.2.1=h1bed415_1
@@ -75,19 +76,21 @@ dependencies:
   - pcre2=10.42=hebb0a14_1
   - pip=24.0=py311h06a4308_0
   - pixman=0.40.0=h7f8727e_1
+  - pthread-stubs=0.3=h0ce48e5_1
   - pybind11-abi=4=hd3eb1b0_1
   - pycparser=2.21=pyhd3eb1b0_0
   - python=3.11.9=h955ad1f_0
   - python-dateutil=2.9.0post0=py311h06a4308_2
   - python-tzdata=2023.3=pyhd3eb1b0_0
   - pytz=2024.1=py311h06a4308_0
   - r-assertthat=0.2.1=r43h6115d3f_0
-  - r-base=4.3.1=h1ae530e_0
+  # - r-base=4.3.1=h1ae530e_0
   - r-base64enc=0.1_3=r43h76d94ec_4
   - r-biocmanager=1.30.22=r43h142f84f_0
   - r-bitops=1.0_7=r43h76d94ec_0
   - r-bslib=0.5.1=r43h6115d3f_0
   - r-cachem=1.0.8=r43h76d94ec_0
+  - r-cairo=1.6_1=r43hec52ca5_0
   - r-catools=1.18.2=r43h884c59f_0
   - r-cli=3.6.1=r43h884c59f_0
   - r-clue=0.3_65=r43h76d94ec_0
@@ -173,6 +176,12 @@ dependencies:
   - tzdata=2024a=h04d1e81_0
   - tzlocal=5.2=py311h06a4308_0
   - wheel=0.43.0=py311h06a4308_0
+  - xorg-kbproto=1.0.7=h7f98852_1002
+  - xorg-libx11=1.8.9=hb711507_1
+  - xorg-libxau=1.0.11=hd590300_0
+  - xorg-libxdmcp=1.1.3=h7f98852_0
+  - xorg-xextproto=7.3.0=h0b41bf4_1003
+  - xorg-xproto=7.0.31=h27cfd23_1007
   - xz=5.4.6=h5eee18b_1
   - zlib=1.2.13=h5eee18b_1
   - zstd=1.5.5=hc292b87_2

scoring_program/detailed_results.Rmd

@@ -8,6 +8,8 @@ output:
     toc_depth: 5
 ---
 
+
+
 ```{r label = "header", echo = FALSE, eval = TRUE}
 knitr::opts_chunk$set(collapse = TRUE, comment = "", echo = FALSE)
 
@@ -21,10 +23,12 @@ remove(list = "package")
 library(package = "ggplot2")
 ```
 
+
 ```{r}
 #read output from prediction
-prediction = readRDS("../input/res/prediction.rds")
-ground_truth = readRDS("../input/ref/ground_truth.rds")
+nb_datasets<- 4
+all_prediction <- readRDS("../input/res/prediction.rds")
+ground_truth <- readRDS("../input/ref/ground_truth.rds")
 
 ```
 ## Summary of the prediction
@@ -34,15 +38,18 @@ ground_truth = readRDS("../input/ref/ground_truth.rds")
 ### Heatmap of the absolute error
 
 ```{r}
-
-colors=viridis::viridis(5)
+colors = viridis::viridis(5)
 cols = colorRampPalette(colors)(50)
 
-dim(prediction)
 
 #image(as.matrix(pred), axes=FALSE, col = cols , ylab = colnames(pred), xlab = rownames(pred))
 
 
+for (dataset_name in 1:nb_datasets){
+
+    prediction <- all_prediction[[dataset_name]]
+    print(dim(prediction) )
+    print(paste0("generating prediction for dataset:",toString(dataset_name) ))
     
     Aerr <- data.frame(
         abserror = as.numeric(
@@ -100,7 +107,7 @@ dim(prediction)
     }
     print(x = p)
     
-
+}
 
 
 ```

scoring_program/scoring.R

@@ -296,6 +296,14 @@ for (dataset_name in 1:nb_datasets){
 # cat(paste0("Time: ", profiling["elapsed"], "\n"), file = output_file, append = TRUE )
 cat(paste0("Time: ", profiling, "\n"), file = output_file, append = TRUE )
 
+rmarkdown::render(
+  input       = paste0(program, .Platform$file.sep, "detailed_results.Rmd")
+  , envir       = parent.frame( )
+  , output_dir  = output
+  # , output_file = "scores.html"
+  , output_file = "detailed_results.html"
+)
+
 print(x = "Output :")
 print(x = list.files(path = output , all.files = TRUE, full.names = TRUE, recursive = TRUE) )
 print(x = "")