Merge pull request #14 from danielnachun/pixi_update2

fix some issues with setup script

bash/pixi/init.sh

@@ -3,6 +3,7 @@
 set -o errexit -o xtrace
 
 # Use sitecustomize.py so that specific Python packages can see python_libs packages
+mkdir -p ${HOME}/.local/lib/python3.12/site-packages
 tee ${HOME}/.local/lib/python3.12/site-packages/sitecustomize.py << EOF
 import sys
 sys.path[0:0] = [
@@ -13,6 +14,9 @@ EOF
 # Use Rprofile.site so that only pixi-installed R can see r_libs packages
 echo ".libPaths('/opt/.pixi/envs/r-base/lib/R/library')" >> ${HOME}/.Rprofile
 
+ln -sf ${HOME}/.pixi/bin/r ${HOME}/.pixi/bin/R
+ln -sf ${HOME}/.pixi/bin/rscript ${HOME}/.pixi/bin/Rscript
+
 # Create config files for rstudio
 mkdir -p ${HOME}/.config/rstudio
 tee ${HOME}/.config/rstudio/database.conf << EOF
@@ -32,7 +36,7 @@ find ${HOME}/.pixi/envs/python/share/jupyter/kernels/ -maxdepth 1 -mindepth 1 -t
     xargs -I % jupyter-kernelspec install --log-level=50 --user %
 find ${HOME}/.pixi/envs/r-base/share/jupyter/kernels/ -maxdepth 1 -mindepth 1 -type d | \
     xargs -I % jupyter-kernelspec install --log-level=50 --user %
-ark --install
+# ark --install
 
 # Jupyter configurations
 mkdir -p $HOME/.jupyter && \

bash/pixi/pixi-mamba.sh

@@ -7,7 +7,7 @@ export MAMBA_ROOT_PREFIX="${HOME}/micromamba"
 curl -fsSL https://raw.githubusercontent.com/gaow/misc/master/bash/pixi/pixi-setup.sh | bash
 
 # Install global packages
-pixi global install <(curl -fsSL https://raw.githubusercontent.com/gaow/misc/master/bash/pixi/envs/global_packages.txt | grep -v "#" | tr '\n' ' ')
+pixi global install $(curl -fsSL https://raw.githubusercontent.com/gaow/misc/master/bash/pixi/envs/global_packages.txt | grep -v "#" | tr '\n' ' ')
 pixi global install r-base=4.3 --expose R=r --expose Rscript=rscript
 pixi global expose remove kill
 pixi global install coreutils
@@ -24,9 +24,9 @@ micromamba shell init --quiet --shell=bash ${HOME}/micromamba
 echo "use_lockfiles: false" >> ${HOME}/.mambarc
 
 echo "Installing recommended R libraries ..."
-pixi global install --environment r-base <(curl -s -O https://raw.githubusercontent.com/gaow/misc/master/bash/pixi/envs/r_packages | grep -v "#" | tr '\n' ' ')
+pixi global install --environment r-base $(curl -fsSL https://raw.githubusercontent.com/gaow/misc/master/bash/pixi/envs/r_packages | grep -v "#" | tr '\n' ' ')
 echo "Installing recommended Python packages ..."
-pixi global install --environment python <(curl -s -O https://raw.githubusercontent.com/gaow/misc/master/bash/pixi/envs/python_packages | grep -v "#" | tr '\n' ' ')
+pixi global install --environment python $(curl -fsSL https://raw.githubusercontent.com/gaow/misc/master/bash/pixi/envs/python_packages | grep -v "#" | tr '\n' ' ')
 pixi clean cache -y
 
 # Install config files