From 81defac6de3d4b4e9c57f456a9430855846bd4e8 Mon Sep 17 00:00:00 2001 From: sapetnioc Date: Tue, 11 Jul 2023 17:58:58 +0200 Subject: [PATCH] #345 conda setup procedure seems to work --- setup/conda/bv_maker.cfg | 1 + setup/conda/setup_repository | 28 ------------------------ setup/conda/setup_run | 18 ---------------- setup/conda/setup_src | 42 ------------------------------------ 4 files changed, 1 insertion(+), 88 deletions(-) delete mode 100755 setup/conda/setup_repository delete mode 100755 setup/conda/setup_run delete mode 100755 setup/conda/setup_src diff --git a/setup/conda/bv_maker.cfg b/setup/conda/bv_maker.cfg index aac093e9..5440cc2f 100644 --- a/setup/conda/bv_maker.cfg +++ b/setup/conda/bv_maker.cfg @@ -1,4 +1,5 @@ [ source $CASA_SRC ] + default_source_dir = {component} brainvisa $CASA_DISTRO $CASA_BRANCH [ build $CASA_BUILD ] diff --git a/setup/conda/setup_repository b/setup/conda/setup_repository deleted file mode 100755 index 221dd029..00000000 --- a/setup/conda/setup_repository +++ /dev/null @@ -1,28 +0,0 @@ -#!/bin/sh - -export CASA=$( dirname $(readlink -f "$0") ) -export CONDA="$CASA/conda" -SRC="$CASA/src" -REPOSITORY="$CASA/repository" - -set -e -set -x - -if [ ! -e "$REPOSITORY" ]; then - mkdir "$REPOSITORY" -fi - -version=5.2.alpha - -cd "$SRC" -components=$( echo * ) -components="soma-base soma-workflow soma-io" -tar Jcf "$REPOSITORY/brainvisa-$version.tar.xz" $components -cd "$REPOSITORY" -sha256=$( sha256sum "$REPOSITORY/brainvisa-$version.tar.xz" | awk '{print $1}' ) -cat > "$CASA/recipe/brainvisa.yaml" << EOF -version: "$version" -sha256: "$sha256" -EOF - -$CASA/conda/bin/mamba build -b--no-anaconda-upload \ No newline at end of file diff --git a/setup/conda/setup_run b/setup/conda/setup_run deleted file mode 100755 index 39fc10bc..00000000 --- a/setup/conda/setup_run +++ /dev/null @@ -1,18 +0,0 @@ -#!/bin/sh - -export CASA=$( dirname $(readlink -f "$0") ) -!/bin/sh - -export CASA=$( dirname $(readlink -f "$0") ) -export CONDA="$CASA/install" - -set -e -set -x - -if [ ! -e "$CONDA" ]; then - . "$CASA/setup_conda" - $CASA/setup_run_conda - export BRAINVISA_INSTALL_PREFIX="$CONDA" - cd "$CASA/build" - "$CASA/bv_env" make install-runtime -fi diff --git a/setup/conda/setup_src b/setup/conda/setup_src deleted file mode 100755 index ac72c200..00000000 --- a/setup/conda/setup_src +++ /dev/null @@ -1,42 +0,0 @@ -# git clone -b master https://bioproj.extra.cea.fr/git/3dns-private "$CASA_SRC/3dns-private" -git clone -b master https://github.com/brainvisa/aims-free.git "$CASA_SRC/aims-free" -git clone -b master https://github.com/brainvisa/aims-gpl.git "$CASA_SRC/aims-gpl" -git clone -b master https://github.com/brainvisa/anatomist-free.git "$CASA_SRC/anatomist-free" -git clone -b master https://github.com/brainvisa/anatomist-gpl.git "$CASA_SRC/anatomist-gpl" -git clone -b master https://github.com/brainvisa/axon.git "$CASA_SRC/axon" -# git clone -b master https://bioproj.extra.cea.fr/git/bioprocessing "$CASA_SRC/bioprocessing" -# git clone -b master https://bioproj.extra.cea.fr/git/brainrat-gpl "$CASA_SRC/brainrat-gpl" -# git clone -b master https://bioproj.extra.cea.fr/git/brainrat-private "$CASA_SRC/brainrat-private" -git clone -b conda https://github.com/brainvisa/brainvisa-cmake.git "$CASA_SRC/brainvisa-cmake" -git clone -b master https://bioproj.extra.cea.fr/git/brainvisa-disco "$CASA_SRC/brainvisa-disco" -git clone -b master https://github.com/brainvisa/brainvisa-share.git "$CASA_SRC/brainvisa-share" -git clone -b master https://github.com/brainvisa/brainvisa-spm.git "$CASA_SRC/brainvisa-spm" -git clone -b master https://github.com/brainvisa/brainvisa_freesurfer.git "$CASA_SRC/brainvisa_freesurfer" -git clone -b master https://github.com/populse/capsul.git "$CASA_SRC/capsul" -git clone -b master https://github.com/brainvisa/casa-distro.git "$CASA_SRC/casa-distro" -git clone -b main https://github.com/cati-neuroimaging/catidb-client.git "$CASA_SRC/catidb-client" -git clone -b master https://github.com/brainvisa/constellation-gpl.git "$CASA_SRC/constellation-gpl" -git clone -b master https://github.com/brainvisa/constellation-nonfree.git "$CASA_SRC/constellation-nonfree" -git clone -b master https://github.com/brainvisa/cortical_surface-gpl.git "$CASA_SRC/cortical_surface-gpl" -git clone -b master https://github.com/brainvisa/cortical_surface-nonfree.git "$CASA_SRC/cortical_surface-nonfree" -git clone -b master https://github.com/cati-neuroimaging/deidentification.git "$CASA_SRC/deidentification" -git clone -b master https://github.com/neurospin/highres-cortex.git "$CASA_SRC/highres-cortex" -git clone -b master https://github.com/cati-neuroimaging/longitudinal_pipelines.git "$CASA_SRC/longitudinal_pipelines" -git clone -b master https://github.com/brainvisa/morpho-deepsulci.git "$CASA_SRC/morpho-deepsulci" -git clone -b master https://github.com/brainvisa/morphologist.git "$CASA_SRC/morphologist" -git clone -b master https://bioproj.extra.cea.fr/git/brainvisa-t1mri/morphologist-baby.git "$CASA_SRC/morphologist-baby" -git clone -b master https://github.com/brainvisa/morphologist-gpl.git "$CASA_SRC/morphologist-gpl" -git clone -b master https://github.com/brainvisa/morphologist-nonfree.git "$CASA_SRC/morphologist-nonfree" -git clone -b master https://github.com/cati-neuroimaging/nuclear_imaging-gpl.git "$CASA_SRC/nuclear_imaging-gpl" -git clone -b master https://github.com/cati-neuroimaging/nuclear_imaging-nonfree.git "$CASA_SRC/nuclear_imaging-nonfree" -git clone -b master https://github.com/populse/populse_db.git "$CASA_SRC/populse_db" -# git clone -b master https://bioproj.extra.cea.fr/git/primatologist-gpl "$CASA_SRC/primatologist-gpl" -# git clone -b master https://github.com/cati-neuroimaging/rsfmri.git "$CASA_SRC/rsfmri" -# git clone -b master https://github.com/cati-neuroimaging/sacha-gpl.git "$CASA_SRC/sacha-gpl" -# git clone -b master https://github.com/cati-neuroimaging/sacha-nonfree.git "$CASA_SRC/sacha-nonfree" -git clone -b master https://github.com/populse/soma-base.git "$CASA_SRC/soma-base" -git clone -b master https://github.com/brainvisa/soma-io.git "$CASA_SRC/soma-io" -git clone -b master https://github.com/populse/soma-workflow.git "$CASA_SRC/soma-workflow" -git clone -b master https://github.com/brainvisa/sulci-nonfree.git "$CASA_SRC/sulci-nonfree" -git clone -b master https://github.com/cati-neuroimaging/whasa-gpl.git "$CASA_SRC/whasa-gpl" -git clone -b master https://github.com/cati-neuroimaging/whasa-nonfree.git "$CASA_SRC/whasa-nonfree"