Copied files from sapetnioc/casaconda project

conda/README.md

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+# Casaconda
+Experimental project to test BrainVISA compilation using a build environment setup using Conda.
+
+## Setup of a build environment using Conda
+
+### From scratch
+
+Install OpenGL dev packages
+```
+sudo apt install libglu1-mesa-dev
+```
+
+Select a directory
+```
+casaconda=/somewhere
+```
+
+Download project with config (and source list)
+```
+git clone https://github.com/sapetnioc/casaconda "$casaconda"
+```
+
+Download sources and setup conda directory
+```
+"$casaconda/setup_dev"
+```
+
+Build everything
+```
+"$casaconda/bv_env" bv_maker
+```
+
+At the time of this writing, documentation building is failing.
+
+### Build a repository for Anatomist
+
+It is necessary to have a complete build environment since the packaging scripts only do packages with `make install...` commands.
+
+Install Conda build
+```
+"$casaconda/conda/bin/mamba" install -y conda-build
+```
+
+Run the package creation recipe
+```
+"$casaconda/conda/bin/mamba" build ~/casaconda/recipe
+```
+
+Publish the resulting repository
+```
+rsync -a --delete "$casaconda/conda/conda-bld/" [email protected]:/var/www/html/brainvisa.info_download/conda/
+```
+
+### Install Anatomist from a repository
+
+One can use the repository located in `https://brainvisa.info/download/conda` but it can be replaced by a local directory too, for instance: `file:///home/me/casaconda/conda/conda-bld`.
+
+Install OpenGL libraries (tested on Ubuntu/Windows-WSL2)
+```
+sudo apt install libgl1-mesa-glx libopengl
+```
+
+Select an install directory:
+```
+conda=/tmp/conda
+```
+
+Install Conda. I recommend installing a version that incorporates Mamba (a really much faster C++ implementation for resolving package dependencies) and that defaults to conda-forge (a very well-maintained community package repository with no legal constraints on use).
+```
+cd /tmp
+wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
+sh Mambaforge-Linux-x86_64.sh -ubp "$conda"
+rm Mambaforge-Linux-x86_64.sh
+```
+
+Install Anatomist. It is possible to substitute the repository located in `https://brainvisa.info/download/conda` by a local directory, for instance: `file:///home/me/casaconda/conda/conda-bld`.
+
+```
+"$conda/bin/mamba" install -c https://brainvisa.info/download/conda -y anatomist
+```
+
+
+Activate the conda repository and use Anatomist, Aims or whatever:
+```
+. "$conda/bin/activate"
+anatomist
+```

conda/bv_maker.cfg

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+[ build $CASA_BUILD ]
+  default_steps = configure build
+  make_options = -j$NCPU
+  cmake_options += -DCONDA=$CASA/conda
+  build_type = Release
+  packaging_thirdparty = OFF
+  clean_config = ON
+  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
+

conda/recipe/brainvisa.yaml

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+version: "5.2.0alpha"
+sha256: "38667670abb2063dadcc85b540e9b5ba45d79560a58c2755d0812ea3ab7c2bdc"

conda/recipe/brainvisa_activate.sh

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+if [ -e "$CONDA_PREFIX/../"]

conda/recipe/casa-distro_activate.sh

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+for i in "$CONDA_PREFIX/../build/bin/bv_env.sh" "$CONDA_PREFIX/../src/brainvisa-cmake/bin/bv_env.sh" "$CONDA_PREFIX/../src/development/brainvisa-cmake/*/bin/bv_env.sh"; do
+    if [ -e "$i" ]; then
+        bv_env_sh="$i"
+        break
+    fi
+done
+if [ -n "$bv_env_sh" ]; then
+    . "$bv_env_sh"
+fi

conda/recipe/casa-distro_deactivate.sh

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+for i in "$CONDA_PREFIX/../build/bin/bv_unenv.sh" "$CONDA_PREFIX/../src/brainvisa-cmake/bin/bv_unenv.sh" "$CONDA_PREFIX/../src/development/brainvisa-cmake/*/bin/bv_unenv.sh"; do
+    if [ -e "$i" ]; then
+        bv_unenv_sh="$i"
+        break
+    fi
+done
+if [ -n "$bv_unenv_sh" ]; then
+    . "$bv_unenv_sh"
+fi

conda/recipe/install_anatomist.sh

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+components="anatomist-free anatomist-gpl"
+
+export CASA=$RECIPE_DIR/..
+export BRAINVISA_INSTALL_PREFIX="$PREFIX"
+cd "$CASA/build"
+for component in $components; do
+    "$CASA/bv_env" make install-$component
+done

conda/recipe/install_brainrat.sh

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+components="brainrat-gpl brainrat-private"
+
+export CASA=$RECIPE_DIR/..
+export BRAINVISA_INSTALL_PREFIX="$PREFIX"
+cd "$CASA/build"
+for component in $components; do
+    make install-$component
+done
+

conda/recipe/install_brainvisa-base.sh

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+components="capsul populse_db soma-base soma-io soma-workflow casa-distro"
+
+export CASA=$RECIPE_DIR/..
+export BRAINVISA_INSTALL_PREFIX="$PREFIX"
+cd "$CASA/build"
+for component in $components; do
+    make install-$component
+done
+

conda/recipe/install_brainvisa-cortical-surface.sh

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+components="cortical_surface-gpl cortical_surface-nonfree"
+
+export CASA=$RECIPE_DIR/..
+export BRAINVISA_INSTALL_PREFIX="$PREFIX"
+cd "$CASA/build"
+for component in $components; do
+    make install-$component
+done
+

conda/recipe/install_brainvisa-data-processing.sh

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+components="aims-free aims-gpl axon brainvisa-share"
+
+export CASA=$RECIPE_DIR/..
+export BRAINVISA_INSTALL_PREFIX="$PREFIX"
+cd "$CASA/build"
+for component in $components; do
+    make install-$component
+done
+

conda/recipe/install_brainvisa-disco.sh

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+components="disco"
+
+export CASA=$RECIPE_DIR/..
+export BRAINVISA_INSTALL_PREFIX="$PREFIX"
+cd "$CASA/build"
+for component in $components; do
+    make install-$component
+done
+

conda/recipe/install_brainvisa-freesurfer.sh

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+components="brainvisa_freesurfer"
+
+export CASA=$RECIPE_DIR/..
+export BRAINVISA_INSTALL_PREFIX="$PREFIX"
+cd "$CASA/build"
+for component in $components; do
+    make install-$component
+done
+

conda/recipe/install_brainvisa-highres-cortex.sh

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+components="highres-cortex"
+
+export CASA=$RECIPE_DIR/..
+export BRAINVISA_INSTALL_PREFIX="$PREFIX"
+cd "$CASA/build"
+for component in $components; do
+    make install-$component
+done
+

conda/recipe/install_brainvisa-spm.sh

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+components="brainvisa-spm"
+
+export CASA=$RECIPE_DIR/..
+export BRAINVISA_INSTALL_PREFIX="$PREFIX"
+cd "$CASA/build"
+for component in $components; do
+    make install-$component
+done
+

conda/recipe/install_morphologist.sh

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+components="morpho-deepsulci morphologist-ui morphologist-gpl morphologist-nonfree sulci-nonfree sulci-models-data"
+
+export CASA=$RECIPE_DIR/..
+export BRAINVISA_INSTALL_PREFIX="$PREFIX"
+cd "$CASA/build"
+for component in $components; do
+    make install-$component
+done
+