Merge pull request #23 from QCDIS/22-add-r-packages-for-waddenzee-flavor

22 add r packages for waddenzee flavor

flavors/lter-life-wadden/environment.yaml

@@ -0,0 +1,16 @@
+name: lter-life-wadden
+channels:
+  - conda-forge
+dependencies:
+  - ipykernel
+  - minio
+  - webdavclient3
+  - r-irkernel
+  - r-jsonlite
+  - r-optparse
+  - r-fme
+  - r-desolve
+  - r-plot3d
+  - r-sf
+  - r-ncdf4
+  - r-tidyverse

flavors/lter-life-wadden/flavor_config.yaml

@@ -0,0 +1,3 @@
+flavor_name: lter-life-wadden
+build_jupyter: True
+free_disk_space: True

flavors/lter-life-wadden-py/naavre-jupyter.Dockerfile → flavors/lter-life-wadden/naavre-jupyter.Dockerfile

@@ -10,8 +10,8 @@ RUN \
     git clone --depth 1 https://github.com/acolite/acolite.git && \
     # Acolite doesn't run on Python 3.12 yet
     sed -i 's/- python=3$/- python<=3.11/' acolite/environment.yml && \
-    mamba env update --name lter-life-wadden-py --file ./acolite/environment.yml && \
-    site_package_dir="$(/opt/conda/envs/lter-life-wadden-py/bin/python -c  "import site; print(''.join(site.getsitepackages()))")" && \
+    mamba env update --name lter-life-wadden --file ./acolite/environment.yml && \
+    site_package_dir="$(/opt/conda/envs/lter-life-wadden/bin/python -c  "import site; print(''.join(site.getsitepackages()))")" && \
     cp ./acolite/acolite -r "$site_package_dir" && \
     cp ./acolite/config -r "$site_package_dir" && \
     cp ./acolite/data -r "$site_package_dir"

flavors/lter-life-wadden/tests/test_import.R

@@ -0,0 +1,9 @@
+library(optparse)
+library(jsonlite)
+
+library(FME)
+library(deSolve)
+library(plot3D)
+library(sf)
+library(ncdf4)
+library(tidyverse)

flavors/lter-life-wadden-py/tests/tests.sh → flavors/lter-life-wadden/tests/tests.sh

@@ -3,3 +3,4 @@ set -e
 source /venv/bin/activate
 dir="${0%/*}"
 find "$dir" -name "*.py" -print0 | xargs --null -I "{}" python "{}"
+find "$dir" -name "*.R" -print0 | xargs --null -I "{}" Rscript "{}"