#345 adaptation of conda setup procedure

README.md

@@ -4,6 +4,12 @@
 # casa-distro
 Unified development environment for BrainVISA projects.
 
+## Setup development environment
+
+```shell
+sh <(curl -s https://raw.githubusercontent.com/brainvisa/casa-distro/setup/conda/setup) /somewhere```
+```
+
 ## Documentation
 
 * on github, master branch: https://brainvisa.github.io/casa-distro/

setup/conda/bv_maker.cfg

@@ -1,3 +1,6 @@
+[ source $CASA_SRC ]
+  brainvisa $CASA_DISTRO $CASA_BRANCH
+
 [ build $CASA_BUILD ]
   default_steps = configure build
   make_options = -j$NCPU
@@ -8,50 +11,5 @@
   clean_build = ON
   test_ref_data_dir = $CASA_TESTS/ref
   test_run_data_dir = $CASA_TESTS/test
-  # directory $CASA_SRC/3dns-private
-  directory $CASA_SRC/aims-free
-  directory $CASA_SRC/aims-gpl 
-  directory $CASA_SRC/anatomist-free
-  directory $CASA_SRC/anatomist-gpl
-  directory $CASA_SRC/axon
-  # directory $CASA_SRC/bioprocessing
-  # directory $CASA_SRC/brainrat-gpl
-  # directory $CASA_SRC/brainrat-private
-  # directory $CASA_SRC/brainvisa-cmake
-  directory $CASA_SRC/brainvisa-disco
-  directory $CASA_SRC/brainvisa-share
-  directory $CASA_SRC/brainvisa-spm
-  directory $CASA_SRC/brainvisa_freesurfer
-  directory $CASA_SRC/capsul
-  directory $CASA_SRC/casa-distro
-  directory $CASA_SRC/catidb-client
-  directory $CASA_SRC/constellation-gpl
-  directory $CASA_SRC/constellation-nonfree
-  directory $CASA_SRC/cortical_surface-gpl
-  directory $CASA_SRC/cortical_surface-nonfree
-  directory $CASA_SRC/deidentification
-  directory $CASA_SRC/highres-cortex
-  directory $CASA_SRC/longitudinal_pipelines
-  directory $CASA_SRC/morpho-deepsulci
-  directory $CASA_SRC/morphologist
-  directory $CASA_SRC/morphologist-baby
-  directory $CASA_SRC/morphologist-gpl
-  directory $CASA_SRC/morphologist-nonfree
-  directory $CASA_SRC/nuclear_imaging-gpl
-  directory $CASA_SRC/nuclear_imaging-nonfree
-  directory $CASA_SRC/populse_db
-  # directory $CASA_SRC/primatologist-gpl
-  # QualiCATI install fail
-  # directory $CASA_SRC/qualicati
-  # directory $CASA_SRC/rsfmri
-  # directory $CASA_SRC/sacha-gpl
-  # directory $CASA_SRC/sacha-nonfree
-  directory $CASA_SRC/soma-base
-  directory $CASA_SRC/soma-io
-  directory $CASA_SRC/soma-workflow
-  directory $CASA_SRC/sulci-nonfree
-  # Remove web project because it needs bv_env_host to compile
-  # directory $CASA_SRC/web
-  directory $CASA_SRC/whasa-gpl
-  directory $CASA_SRC/whasa-nonfree
 
+  brainvisa $CASA_DISTRO $CASA_BRANCH $CASA_SRC

setup/conda/setup

@@ -0,0 +1,44 @@
+#!/bin/sh
+
+export CASA="$1"
+if [ -z "$CASA" ]; then
+    echo "Missing target directory"
+    exit 1
+fi
+
+export CASA_DISTRO="$2"
+if [ -z "$CASA_DISTRO" ]; then
+    echo "Missing distro"
+    exit 1
+fi
+
+export CONDA="$CASA/conda"
+export CASA_SRC="$CASA/src"
+export CASA_DISTRO_SRC="$CASA_SRC/casa-distro"
+
+set -e
+set -x
+
+if [ ! -e "$CASA_SRC" ]; then
+    mkdir --parents "$CASA_SRC"
+    git -C "$CASA_SRC" clone --branch conda https://github.com/brainvisa/casa-distro
+    git -C "$CASA_SRC" clone --branch conda https://github.com/brainvisa/brainvisa-cmake
+fi
+
+if [ ! -e "$CASA/conf" ]; then
+    mkdir "$CASA/conf"
+    ln -s ../src/casa-distro/setup/conda/bv_maker.cfg "$CASA/conf"
+    cat > "$CASA/conf/environment.sh" << END_OF_FILE
+export CASA_DISTRO=$CASA_DISTRO
+END_OF_FILE
+fi
+
+
+if [ ! -e "$CONDA" ]; then
+    . "$CASA/src/casa-distro/setup/conda/setup_conda"
+    ln -s ../../../../src/casa-distro/setup/conda/casa-distro_activate.sh "$CONDA/etc/conda/activate.d"
+    ln -s ../../../../src/casa-distro/setup/conda/casa-distro_deactivate.sh "$CONDA/etc/conda/deactivate.d"
+    "$CASA/setup_run_conda"
+    "$CASA/setup_run_compiled"
+    "$CASA/setup_dev_conda"
+fi

setup/conda/setup_conda

@@ -12,13 +12,13 @@ fi
 mkdir "$CONDA"
 sh "$CASA/$installer" -u -b -p "$CONDA"
 if [ -e "$CONDA/bin/mamba" ]; then
-    # If mamba is installed, we use conda-forge
+    # If mamba is installed
     export conda="$CONDA/bin/mamba"
     export conda_install="-y"
     # Use most recent glibc ABI (the one used by conda-forge to compile Qt)
     "$conda" install -y sysroot-conda_2_28-x86_64
 else
-    # mamba is not installed, we use anaconda
+    # mamba is not installed
     export conda="$CONDA/bin/conda"
     export conda_install="-y --solver=libmamba"
     # Install packages to use mamba to find packages