added png to pages bundel and solve docker pb

bcm-uga · Nov 7, 2024 · 3a090ae · 3a090ae
1 parent 08d6c57
commit 3a090ae
Show file tree

Hide file tree

Showing 7 changed files with 82 additions and 6 deletions.
diff --git a/README.md b/README.md
@@ -59,7 +59,7 @@ sudo docker push hombergn/hadaca3_light:latest
 sudo docker push hombergn/hadaca3_pyr:latest
 
 #Single command to build and push. 
-sudo docker build -t hombergn/hadaca3_light .  && sudo docker push hombergn/hadaca3_light:latest
+sudo docker build -t hombergn/hadaca3_pyr .  && sudo docker push hombergn/hadaca3_pyr:latest
 ```
 
 

diff --git a/docker/codabench_hadaca3_pyr/Dockerfile b/docker/codabench_hadaca3_pyr/Dockerfile
@@ -15,6 +15,7 @@ RUN echo 'micromamba activate h3' >> ~/.bashrc
 ENV PATH /opt/conda/bin:$PATH
 
 
+RUN Rscript -e 'install.packages( pkgs = "zip", repos = "https://cloud.r-project.org")'
 RUN Rscript  -e 'BiocManager::install("ComplexHeatmap")'
 RUN Rscript  -e 'BiocManager::install("Biobase")'
 

diff --git a/docker/codabench_hadaca3_pyr/environment/environment-r.yml b/docker/codabench_hadaca3_pyr/environment/environment-r.yml
@@ -7,17 +7,23 @@ dependencies:
   - _openmp_mutex=4.5=2_gnu
   - _r-mutex=1.0.0=anacondar_1
   - _sysroot_linux-64_curr_repodata_hack=3=haa98f57_10
+  - asttokens=2.4.1=pyhd8ed1ab_0
   - binutils_impl_linux-64=2.38=h2a08ee3_1
   - binutils_linux-64=2.38.0=hc2dff05_0
   - blas=1.0=openblas
   - bottleneck=1.3.7=py311hf4808d0_0
   - bwidget=1.9.16=h9eba36c_0
   - bzip2=1.0.8=h5eee18b_6
   - c-ares=1.19.1=h5eee18b_0
-  - ca-certificates=2024.7.2=h06a4308_0
+  - ca-certificates=2024.8.30=hbcca054_0
   - cairo=1.16.0=hb05425b_5
   - cffi=1.16.0=py311h5eee18b_1
+  - comm=0.2.2=pyhd8ed1ab_0
   - curl=8.7.1=hdbd6064_0
+  - debugpy=1.6.7=py311h6a678d5_0
+  - decorator=5.1.1=pyhd8ed1ab_0
+  - exceptiongroup=1.2.2=pyhd8ed1ab_0
+  - executing=2.1.0=pyhd8ed1ab_0
   - expat=2.6.2=h6a678d5_0
   - fontconfig=2.14.1=h4c34cd2_2
   - freetype=2.12.1=h4a9f257_0
@@ -33,8 +39,15 @@ dependencies:
   - gxx_linux-64=11.2.0=hc2dff05_0
   - harfbuzz=4.3.0=hf52aaf7_2
   - icu=73.1=h6a678d5_0
+  - importlib-metadata=8.4.0=pyha770c72_0
+  - importlib_metadata=8.4.0=hd8ed1ab_0
+  - ipykernel=6.29.5=pyh3099207_0
+  - ipython=8.27.0=pyh707e725_0
+  - jedi=0.19.1=pyhd8ed1ab_0
   - jinja2=3.1.4=py311h06a4308_0
   - jpeg=9e=h5eee18b_1
+  - jupyter_client=8.6.2=pyhd8ed1ab_0
+  - jupyter_core=5.7.2=py311h38be061_0
   - kernel-headers_linux-64=3.10.0=h57e8cba_10
   - krb5=1.20.1=h143b758_1
   - ld_impl_linux-64=2.38=h1181459_1
@@ -54,6 +67,7 @@ dependencies:
   - libnghttp2=1.57.0=h2d74bed_0
   - libopenblas=0.3.21=h043d6bf_0
   - libpng=1.6.39=h5eee18b_0
+  - libsodium=1.0.18=h36c2ea0_1
   - libssh2=1.11.0=h251f7ec_0
   - libstdcxx-devel_linux-64=11.2.0=h1234567_1
   - libstdcxx-ng=11.2.0=h1234567_1
@@ -65,24 +79,37 @@ dependencies:
   - lz4-c=1.9.4=h6a678d5_1
   - make=4.2.1=h1bed415_1
   - markupsafe=2.1.3=py311h5eee18b_0
+  - matplotlib-inline=0.1.7=pyhd8ed1ab_0
   - ncurses=6.4=h6a678d5_0
+  - nest-asyncio=1.6.0=pyhd8ed1ab_0
   - numexpr=2.8.7=py311h812550d_0
   - numpy=1.26.4=py311h24aa872_0
   - numpy-base=1.26.4=py311hbfb1bba_0
-  - openssl=3.0.14=h5eee18b_0
+  - openssl=3.3.1=hb9d3cd8_3
+  - packaging=24.1=pyhd8ed1ab_0
   - pandas=2.2.2=py311ha02d727_0
   - pandoc=2.12=h06a4308_3
   - pango=1.50.7=h05da053_0
+  - parso=0.8.4=pyhd8ed1ab_0
   - pcre2=10.42=hebb0a14_1
+  - pexpect=4.9.0=pyhd8ed1ab_0
+  - pickleshare=0.7.5=py_1003
   - pip=24.0=py311h06a4308_0
   - pixman=0.40.0=h7f8727e_1
+  - platformdirs=4.2.2=pyhd8ed1ab_0
+  - prompt-toolkit=3.0.47=pyha770c72_0
+  - psutil=6.0.0=py311h331c9d8_0
   - pthread-stubs=0.3=h0ce48e5_1
+  - ptyprocess=0.7.0=pyhd3deb0d_0
+  - pure_eval=0.2.3=pyhd8ed1ab_0
   - 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
+  - python_abi=3.11=2_cp311
   - pytz=2024.1=py311h06a4308_0
+  - pyzmq=25.1.2=py311h6a678d5_0
   - r-assertthat=0.2.1=r43h6115d3f_0
   - r-base=4.3.1=h1ae530e_0
   - r-base64enc=0.1_3=r43h76d94ec_4
@@ -187,11 +214,16 @@ dependencies:
   - simplegeneric=0.8.1=py311h06a4308_2
   - six=1.16.0=pyhd3eb1b0_1
   - sqlite=3.45.3=h5eee18b_0
+  - stack_data=0.6.2=pyhd8ed1ab_0
   - sysroot_linux-64=2.17=h57e8cba_10
   - tk=8.6.14=h39e8969_0
   - tktable=2.10=h3d55465_1
+  - tornado=6.4.1=py311h331c9d8_0
+  - traitlets=5.14.3=pyhd8ed1ab_0
+  - typing_extensions=4.12.2=pyha770c72_0
   - tzdata=2024a=h04d1e81_0
   - tzlocal=5.2=py311h06a4308_0
+  - wcwidth=0.2.13=pyhd8ed1ab_0
   - wheel=0.43.0=py311h06a4308_0
   - xorg-kbproto=1.0.7=h7f98852_1002
   - xorg-libx11=1.8.9=hb711507_1
@@ -200,6 +232,28 @@ dependencies:
   - xorg-xextproto=7.3.0=h0b41bf4_1003
   - xorg-xproto=7.0.31=h27cfd23_1007
   - xz=5.4.6=h5eee18b_1
+  - zeromq=4.3.5=h6a678d5_0
+  - zipp=3.20.1=pyhd8ed1ab_0
   - zlib=1.2.13=h5eee18b_1
   - zstd=1.5.5=hc292b87_2
+  - pip:
+      - certifi==2024.8.30
+      - charset-normalizer==3.3.2
+      - colorama==0.4.6
+      - idna==3.8
+      - joblib==1.4.2
+      - kaleido==0.2.1
+      - metrics==0.3.3
+      - pathlib2==2.3.7.post1
+      - pathspec==0.5.5
+      - plotly==5.24.1
+      - pygments==2.2.0
+      - requests==2.32.3
+      - scikit-learn==1.5.1
+      - smgantt==0.0.5
+      - svm==0.1.0
+      - tenacity==9.0.0
+      - threadpoolctl==3.5.0
+      - urllib3==2.2.2
+      - xmltodict==0.13.0
 prefix: /home/nicolashomberg/miniconda3/envs/h3
diff --git a/phase-0-smoothie/bundle/FAQ.md b/phase-0-smoothie/bundle/FAQ.md
@@ -10,14 +10,20 @@ If your submission fails on Codabench, don't panic—review the logs! You can ac
 3. Select the "Logs" tab.
 4. Browse the various types of logs available: `stdout`, `stderr`, `Ingestion stdout`, and `Ingestion stderr`, for both the ingestion and scoring steps.
 
-## Cannot create your submissions ? Try our conda environnement:  (Especially useful for python user !)
+## Cannot create your submissions ? Try interactive docker or conda environnement:  (Especially useful for python user !)
 
 A conda evnironnement is provided follow this steps to install and activate it: 
 - retrieve the file environment-r.yml from github : [environment-r.yml](https://github.com/bcm-uga/hadaca3/blob/main/docker/codabench_hadaca3_pyr/environment/environment-r.yml) : 
 - `wget https://raw.githubusercontent.com/bcm-uga/hadaca3/main/docker/codabench_hadaca3_pyr/environment/environment-r.yml`
 - and run: `conda env create -f environment-r.yml && conda activate h3`
 
 
+To run the docker interactively you can run either R with : 
+ - `sudo docker run -it -v .:/hadaca3 -w /hadaca3 hombergn/hadaca3_pyr R`  and then `source("submission_script.R")` for the R version
+ - `sudo docker run -it -v .:/hadaca3 -w /hadaca3 hombergn/hadaca3_pyr python` and then `import submission_script` for the python version 
+
+Beware that Mac users with M1 processors might encounter problems. 
+
 
 ## Running Submissions ingestion and scoring locally with Docker
 

diff --git a/phase-0-smoothie/bundle/aim-of-the-challenge.md b/phase-0-smoothie/bundle/aim-of-the-challenge.md
@@ -1 +1,4 @@
 The objective of this challenge is to estimate the fruit composition of different smoothies (mixtures to be deconvoluted) based on the vitamin composition of the smoothie, using the exact vitamin composition of each fruit (reference profile).
+
+
+<img title="Exemple of decovolution" alt="Exemple of decovolution" src="https://raw.githubusercontent.com/bcm-uga/hadaca3/08d6c575e1c157ce9d67319487e6c64ffef8700a/phase-0-smoothie/bundle/decovo_intro.png" width="800" >
diff --git a/phase-0-smoothie/generate_bundle_smoothie.sh b/phase-0-smoothie/generate_bundle_smoothie.sh
@@ -30,7 +30,7 @@ cp "$path_data"reference_fruits.rds input_data/reference_fruits.rds
 
 
 mkdir starting_kit
-rm -r starting_kit/*
+rm -rf starting_kit/*
 cp -r input_data/* starting_kit/
 # sh generate_data.sh $1
 # sh generate_data.sh real

diff --git a/templates/template_starter_kit/template_submission_script.R b/templates/template_starter_kit/template_submission_script.R
@@ -70,8 +70,20 @@ validate_pred <- function(pred, nb_samples = ncol(mixes_data) , nb_cells= ncol(r
 ###############################
 ### Code submission mode
 
+print("")
+for (package in c("zip") ) {
+  if ( !{ package %in% installed.packages( ) } ) {
+        print(x = paste("Installation of ", package, sep = "") )
+        install.packages(
+            pkgs = "zip"
+          , repos = "https://cloud.r-project.org"
+        )
+    } 
+}
+
+
 # we generate a zip file with the 'program' source code
-print()
+print(x='')
 if ( !dir.exists(paths = "submissions") ) {
     dir.create(path = "submissions")
 }
Original file line number	Diff line number	Diff line change
		@@ -1 +1,4 @@
		The objective of this challenge is to estimate the fruit composition of different smoothies (mixtures to be deconvoluted) based on the vitamin composition of the smoothie, using the exact vitamin composition of each fruit (reference profile).


		<img title="Exemple of decovolution" alt="Exemple of decovolution" src="https://raw.githubusercontent.com/bcm-uga/hadaca3/08d6c575e1c157ce9d67319487e6c64ffef8700a/phase-0-smoothie/bundle/decovo_intro.png" width="800" >