#345 setup_conda script automatization

brainvisa · May 17, 2023 · 90d1515 · 90d1515
1 parent 1d9730a
commit 90d1515
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Showing 3 changed files with 9 additions and 12 deletions.
diff --git a/conda/setup_conda b/conda/setup_conda
@@ -30,8 +30,7 @@ root_apptainer="apptainer run --writable --fakeroot --containall -B $casaconda:/
 
 if [ ! -e "$system_image" ]; then
     apptainer build --sandbox "$casaconda/system" "$script_dir/apptainer.def"
-    cp -a "$script_dir/setup_run_apt" "$casaconda"
-    $root_apptainer /casa/setup_run_apt
+    $root_apptainer /casa/src/casa-distro/conda/setup_run_apt
 fi
 
 if [ ! -e "$casaconda/Miniforge3-Linux-x86_64.sh" ]; then
@@ -43,15 +42,13 @@ conda="$apptainer /casa/conda/bin/conda"
 if [ ! -e "$casaconda/conda" ]; then
     mkdir "$casaconda/conda"
     $apptainer sh "/casa/Miniforge3-Linux-x86_64.sh" -u -b -p "/casa/conda"
-    $conda update conda -y
-    cp -a "$script_dir/setup_run_conda" "$casaconda"
-    $apptainer /casa/setup_run_conda
-    cp -a "$script_dir/setup_dev_conda" "$casaconda"
-    $apptainer /casa/setup_dev_conda
+#    $conda update conda -y
+    $conda install -y mamba
+    $apptainer /casa/src/casa-distro/conda/setup_run_conda
+    $apptainer /casa/src/casa-distro/conda/setup_dev_conda
 fi
 
-cp -a "$script_dir/setup_run_compiled" "$casaconda"
-$root_apptainer /casa/setup_run_compiled
+$root_apptainer /casa/src/casa-distro/conda/setup_run_compiled
 
 if [ ! -e "$casaconda/src" ]; then
     $apptainer git clone https://github.com/sapetnioc/brainvisa-submodules /casa/src

diff --git a/conda/setup_dev_conda b/conda/setup_dev_conda
@@ -7,7 +7,7 @@
 set -x
 set -e
 
-conda=/casa/conda/bin/conda
+conda=/casa/conda/bin/mamba
 
 if [ -e /casa/conda/bin/gdb ]; then
     # if gdb is installed, we assume that this script has already been
@@ -106,7 +106,7 @@ brainvisa_standard_dev_dependencies=(
     libpng #? was libpng-dev
     #! libqt5x11extras5-dev
     #! libqwt-qt5-dev
-    libsigcpp<3 #? was libsigc++-2.0-dev
+    'libsigcpp<3' #? was libsigc++-2.0-dev
     #! libspnav-dev
     libsvm #? was libsvm-dev
     libtiff #? was libtiff-dev

diff --git a/conda/setup_run_conda b/conda/setup_run_conda
@@ -14,7 +14,7 @@ if [ -e /casa/conda/bin/git ]; then
     exit 0
 fi
 
-conda=/casa/conda/bin/conda
+conda=/casa/conda/bin/mamba
 
 build_dependencies=(
     # General build dependencies (notably useful for pip-compiled packages)