From 7be6453e2905417c6ec30c7cf6ef5f4ee7b14d1d Mon Sep 17 00:00:00 2001 From: sapetnioc Date: Tue, 4 Jun 2024 18:09:08 +0200 Subject: [PATCH] #7 redefinition of soma-forge recipes --- soma-forge/recipes/anatomist.yaml | 38 +++----------- soma-forge/recipes/bioprocessing.yaml | 29 +++-------- soma-forge/recipes/brainrat.yaml | 32 ++++-------- soma-forge/recipes/brainvisa.yaml | 19 +++---- soma-forge/recipes/capsul.yaml | 27 +++------- soma-forge/recipes/cati-deidentification.yaml | 31 +++-------- soma-forge/recipes/cati-longitudinal.yaml | 31 +++-------- soma-forge/recipes/cati-rsfmri.yaml | 31 +++-------- soma-forge/recipes/cati-sacha.yaml | 31 +++-------- soma-forge/recipes/cati-whasa.yaml | 32 ++++-------- soma-forge/recipes/cati.yaml | 25 ++++----- soma-forge/recipes/catidb.yaml | 29 ++--------- soma-forge/recipes/constellation.yaml | 30 +++-------- soma-forge/recipes/cortical-surface.yaml | 33 ++++-------- soma-forge/recipes/disco.yaml | 33 ++++-------- soma-forge/recipes/highres-cortex.yaml | 31 +++-------- soma-forge/recipes/morphologist-baby.yaml | 29 +++-------- soma-forge/recipes/morphologist.yaml | 34 +++++-------- soma-forge/recipes/nuclear-imaging.yaml | 33 ++++-------- soma-forge/recipes/populse-db.yaml | 24 ++------- soma-forge/recipes/primatologist.yaml | 43 ++++------------ soma-forge/recipes/qualicati.yaml | 29 +++-------- soma-forge/recipes/soma-freesurfer.yaml | 31 +++-------- soma-forge/recipes/soma-python.yaml | 29 +++-------- soma-forge/recipes/soma-spm.yaml | 31 +++-------- soma-forge/recipes/soma.yaml | 51 +++++++++---------- 26 files changed, 217 insertions(+), 599 deletions(-) diff --git a/soma-forge/recipes/anatomist.yaml b/soma-forge/recipes/anatomist.yaml index 2c30dfc..2a1bae1 100644 --- a/soma-forge/recipes/anatomist.yaml +++ b/soma-forge/recipes/anatomist.yaml @@ -1,23 +1,12 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: anatomist - version: ${{ distro_version }} + name: anatomist + +components: + - anatomist-free + - anatomist-gpl -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in anatomist-free anatomist-gpl; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done +internal-dependencies: + - soma requirements: build: @@ -27,7 +16,6 @@ requirements: - make run: - - soma ==${{ distro_version }} - qwt - matplotlib - virtualgl @@ -36,15 +24,3 @@ requirements: - ipywidgets - ipyevents - notebook - #- xorg-x11-server-xvfb-cos7-x86_64 - -# tests: -# - script: | -# cd "$CASA_BUILD" -# python -m soma_forge test soma -# python -m soma_forge test aims -# python -m soma_forge test axon - -# requirements: -# run: -# - cmake diff --git a/soma-forge/recipes/bioprocessing.yaml b/soma-forge/recipes/bioprocessing.yaml index df93540..ca04d11 100644 --- a/soma-forge/recipes/bioprocessing.yaml +++ b/soma-forge/recipes/bioprocessing.yaml @@ -1,29 +1,16 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: bioprocessing - version: ${{ distro_version }} + name: bioprocessing + +components: + - bioprocessing -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in bioprocessing; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done +internal-dependencies: + - soma + - anatomist requirements: build: - - make + - ${{ compiler('cxx') }} run: - - soma ==${{ distro_version }} - - anatomist ==${{ distro_version }} - scikit-learn diff --git a/soma-forge/recipes/brainrat.yaml b/soma-forge/recipes/brainrat.yaml index 81f2c7c..44432aa 100644 --- a/soma-forge/recipes/brainrat.yaml +++ b/soma-forge/recipes/brainrat.yaml @@ -1,28 +1,14 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: brainrat - version: ${{ distro_version }} + name: brainrat + +components: + - brainrat-private + - brainrat-gpl -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in brainrat-private brainrat-gpl; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done +internal-dependencies: + - soma + - anatomist requirements: build: - - make - - run: - - soma ==${{ distro_version }} - - anatomist ==${{ distro_version }} + - ${{ compiler('cxx') }} diff --git a/soma-forge/recipes/brainvisa.yaml b/soma-forge/recipes/brainvisa.yaml index d7ac689..bb197b8 100644 --- a/soma-forge/recipes/brainvisa.yaml +++ b/soma-forge/recipes/brainvisa.yaml @@ -1,14 +1,9 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: brainvisa - version: ${{ distro_version }} + name: brainvisa -requirements: - run: - - brainrat ==${{ distro_version }} - - disco ==${{ distro_version }} - - highres-cortex ==${{ distro_version }} - - morphologist ==${{ distro_version }} - - primatologist ==${{ distro_version }} +internal-dependencies: + - brainrat + - disco + - highres-cortex + - morphologist + - primatologist diff --git a/soma-forge/recipes/capsul.yaml b/soma-forge/recipes/capsul.yaml index 534002c..da604f9 100644 --- a/soma-forge/recipes/capsul.yaml +++ b/soma-forge/recipes/capsul.yaml @@ -1,30 +1,15 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: capsul + name: capsul version: ${{ distro_version }} -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in capsul; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done +components: + - capsul + +internal-dependencies: + - soma-python requirements: - build: - - make - run: - - soma-python ==${{ distro_version }} - redis-py <4.5.0 - redis-server <7 - pyyaml diff --git a/soma-forge/recipes/cati-deidentification.yaml b/soma-forge/recipes/cati-deidentification.yaml index 97edf4c..f024582 100644 --- a/soma-forge/recipes/cati-deidentification.yaml +++ b/soma-forge/recipes/cati-deidentification.yaml @@ -1,28 +1,9 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: cati-deidentification - version: ${{ distro_version }} - -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in deidentification; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done + name: cati-deidentification -requirements: - build: - - make +components: + - deidentification - run: - - soma ==${{ distro_version }} - - anatomist ==${{ distro_version }} +internal-dependencies: + - soma + - anatomist diff --git a/soma-forge/recipes/cati-longitudinal.yaml b/soma-forge/recipes/cati-longitudinal.yaml index f077068..d6b6010 100644 --- a/soma-forge/recipes/cati-longitudinal.yaml +++ b/soma-forge/recipes/cati-longitudinal.yaml @@ -1,28 +1,13 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: cati-longitudinal - version: ${{ distro_version }} + name: cati-longitudinal + +components: + - longitudinal_pipelines -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in longitudinal_pipelines; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done +internal-dependencies: + - soma + - anatomist requirements: build: - - make - - run: - - soma ==${{ distro_version }} - - anatomist ==${{ distro_version }} + - ${{ compiler('cxx') }} diff --git a/soma-forge/recipes/cati-rsfmri.yaml b/soma-forge/recipes/cati-rsfmri.yaml index f0a2628..08fb3a7 100644 --- a/soma-forge/recipes/cati-rsfmri.yaml +++ b/soma-forge/recipes/cati-rsfmri.yaml @@ -1,28 +1,9 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: cati-rsfmri - version: ${{ distro_version }} - -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in rsfmri; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done + name: cati-rsfmri -requirements: - build: - - make +components: + - rsfmri - run: - - soma ==${{ distro_version }} - - anatomist ==${{ distro_version }} +internal-dependencies: + - soma + - anatomist diff --git a/soma-forge/recipes/cati-sacha.yaml b/soma-forge/recipes/cati-sacha.yaml index ac8174e..f4442af 100644 --- a/soma-forge/recipes/cati-sacha.yaml +++ b/soma-forge/recipes/cati-sacha.yaml @@ -1,28 +1,13 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: cati-sacha - version: ${{ distro_version }} + name: cati-sacha + +components: + - sacha-nonfree sacha-gpl -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in sacha-nonfree sacha-gpl; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done +internal-dependencies: + - soma + - anatomist requirements: build: - - make - - run: - - soma ==${{ distro_version }} - - anatomist ==${{ distro_version }} + - ${{ compiler('cxx') }} diff --git a/soma-forge/recipes/cati-whasa.yaml b/soma-forge/recipes/cati-whasa.yaml index 8f1fefc..cd1fa6b 100644 --- a/soma-forge/recipes/cati-whasa.yaml +++ b/soma-forge/recipes/cati-whasa.yaml @@ -1,28 +1,14 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: cati-whasa - version: ${{ distro_version }} + name: cati-whasa + +components: + - whasa-nonfree + - whasa-gpl -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in whasa-nonfree whasa-gpl; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done +internal-dependencies: + - soma + - anatomist requirements: build: - - make - - run: - - soma ==${{ distro_version }} - - anatomist ==${{ distro_version }} + - ${{ compiler('cxx') }} diff --git a/soma-forge/recipes/cati.yaml b/soma-forge/recipes/cati.yaml index b3ab9bc..fe715cc 100644 --- a/soma-forge/recipes/cati.yaml +++ b/soma-forge/recipes/cati.yaml @@ -1,17 +1,12 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: cati - version: ${{ distro_version }} + name: cati -requirements: - run: - - qualicati ==${{ distro_version }} - - cati-longitudinal ==${{ distro_version }} - - cati-rsfmri ==${{ distro_version }} - - cati-sacha ==${{ distro_version }} - - cati-whasa ==${{ distro_version }} - - cati-deidentification ==${{ distro_version }} - - catidb ==${{ distro_version }} - - nuclear-imaging ==${{ distro_version }} +internal-dependencies: + - qualicati + - cati-longitudinal + - cati-rsfmri + - cati-sacha + - cati-whasa + - cati-deidentification + - catidb + - nuclear-imaging diff --git a/soma-forge/recipes/catidb.yaml b/soma-forge/recipes/catidb.yaml index c33da25..925a50d 100644 --- a/soma-forge/recipes/catidb.yaml +++ b/soma-forge/recipes/catidb.yaml @@ -1,27 +1,8 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: catidb - version: ${{ distro_version }} - -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in catidb-client; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done + name: catidb -requirements: - build: - - make +components: + - catidb-client - run: - - soma ==${{ distro_version }} +internal-dependencies: + - soma diff --git a/soma-forge/recipes/constellation.yaml b/soma-forge/recipes/constellation.yaml index 20a584a..f2d286a 100644 --- a/soma-forge/recipes/constellation.yaml +++ b/soma-forge/recipes/constellation.yaml @@ -1,27 +1,13 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: constellation - version: ${{ distro_version }} + name: constellation + +components: + - constellation-gpl + - constellation-nonfree -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in constellation-gpl constellation-nonfree; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done +internal-dependencies: + - morphologist requirements: build: - - make - - run: - - morphologist ==${{ distro_version }} + - ${{ compiler('cxx') }} diff --git a/soma-forge/recipes/cortical-surface.yaml b/soma-forge/recipes/cortical-surface.yaml index 1897a9f..b13abe5 100644 --- a/soma-forge/recipes/cortical-surface.yaml +++ b/soma-forge/recipes/cortical-surface.yaml @@ -1,29 +1,14 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: cortical-surface - version: ${{ distro_version }} + name: cortical-surface + +components: + - cortical_surface-gpl + - cortical_surface-nonfree -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in cortical_surface-gpl cortical_surface-nonfree; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done +internal-dependencies: + - morphologist + - soma-freesurfer requirements: build: - - make - - run: - - morphologist ==${{ distro_version }} - - soma-freesurfer ==${{ distro_version }} - + - ${{ compiler('cxx') }} diff --git a/soma-forge/recipes/disco.yaml b/soma-forge/recipes/disco.yaml index bb80cf5..c3b8b50 100644 --- a/soma-forge/recipes/disco.yaml +++ b/soma-forge/recipes/disco.yaml @@ -1,29 +1,14 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: disco - version: ${{ distro_version }} + name: disco + +components: + - disco -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in disco; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done +internal-dependencies: + - soma + - anatomist + - soma-spm requirements: build: - - make - - run: - - soma ==${{ distro_version }} - - anatomist ==${{ distro_version }} - - soma-spm ==${{ distro_version }} + - ${{ compiler('cxx') }} diff --git a/soma-forge/recipes/highres-cortex.yaml b/soma-forge/recipes/highres-cortex.yaml index 2c6b74e..34e15af 100644 --- a/soma-forge/recipes/highres-cortex.yaml +++ b/soma-forge/recipes/highres-cortex.yaml @@ -1,28 +1,13 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: highres-cortex - version: ${{ distro_version }} + name: highres-cortex + +components: + - highres-cortex -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in highres-cortex; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done +internal-dependencies: + - soma + - anatomist requirements: build: - - make - - run: - - soma ==${{ distro_version }} - - anatomist ==${{ distro_version }} + - ${{ compiler('cxx') }} diff --git a/soma-forge/recipes/morphologist-baby.yaml b/soma-forge/recipes/morphologist-baby.yaml index 1c9a495..616fab4 100644 --- a/soma-forge/recipes/morphologist-baby.yaml +++ b/soma-forge/recipes/morphologist-baby.yaml @@ -1,27 +1,12 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: morphologist-baby - version: ${{ distro_version }} + name: morphologist-baby + +components: + - morphologist-baby -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in morphologist-baby; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done +internal-dependencies: + - morphologist requirements: build: - - make - - run: - - morphologist ==${{ distro_version }} + - ${{ compiler('cxx') }} diff --git a/soma-forge/recipes/morphologist.yaml b/soma-forge/recipes/morphologist.yaml index ea88133..26a8623 100644 --- a/soma-forge/recipes/morphologist.yaml +++ b/soma-forge/recipes/morphologist.yaml @@ -1,21 +1,19 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: morphologist - version: ${{ distro_version }} + name: morphologist + +components: + - morphologist-nonfree + - morphologist-gpl + - morphologist-ui + - sulci-nonfree + - morpho-deepsulci + +internal-dependencies: + - soma + - anatomist + - soma-spm + - capsul -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in morphologist-nonfree morphologist-gpl morphologist-ui sulci-nonfree morpho-deepsulci; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - done requirements: build: @@ -25,10 +23,6 @@ requirements: - make run: - - soma ==${{ distro_version }} - - anatomist ==${{ distro_version }} - - soma-spm ==${{ distro_version }} - - capsul ==${{ distro_version }} - pytorch - torchvision # dependencies found in deepsulci diff --git a/soma-forge/recipes/nuclear-imaging.yaml b/soma-forge/recipes/nuclear-imaging.yaml index 4a0f058..aa651cf 100644 --- a/soma-forge/recipes/nuclear-imaging.yaml +++ b/soma-forge/recipes/nuclear-imaging.yaml @@ -1,29 +1,14 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: nuclear-imaging - version: ${{ distro_version }} + name: nuclear-imaging + +components: + - nuclear_imaging-gpl + - nuclear_imaging-nonfree -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in nuclear_imaging-gpl nuclear_imaging-nonfree; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done +internal-dependencies: + - soma + - anatomist requirements: build: - - make - - run: - - soma ==${{ distro_version }} - - anatomist ==${{ distro_version }} - + - ${{ compiler('cxx') }} diff --git a/soma-forge/recipes/populse-db.yaml b/soma-forge/recipes/populse-db.yaml index d4beba8..2a381ed 100644 --- a/soma-forge/recipes/populse-db.yaml +++ b/soma-forge/recipes/populse-db.yaml @@ -1,28 +1,10 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: populse-db - version: ${{ distro_version }} + name: populse-db -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in populse-db; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done +components: + - populse-db requirements: - build: - - make - run: - python >3.9 - lark-parser >0.7.0 diff --git a/soma-forge/recipes/primatologist.yaml b/soma-forge/recipes/primatologist.yaml index 9565814..1cd96e1 100644 --- a/soma-forge/recipes/primatologist.yaml +++ b/soma-forge/recipes/primatologist.yaml @@ -1,39 +1,14 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: primatologist - version: ${{ distro_version }} + name: primatologist + +components: + - primatologist-gpl -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in primatologist-gpl; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done +internal-dependencies: + - soma + - anatomist + - soma-freesurfer requirements: build: - - make - - run: - - soma ==${{ distro_version }} - - anatomist ==${{ distro_version }} - - soma-freesurfer ==${{ distro_version }} - -# tests: -# - script: "python -m soma.tests" -# requirements: -# run: -# - pytest -# - script: "python -m soma_workflow.test" -# requirements: -# run: -# - pytest + - ${{ compiler('cxx') }} diff --git a/soma-forge/recipes/qualicati.yaml b/soma-forge/recipes/qualicati.yaml index 5c582dc..ee7810e 100644 --- a/soma-forge/recipes/qualicati.yaml +++ b/soma-forge/recipes/qualicati.yaml @@ -1,31 +1,18 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: qualicati - version: ${{ distro_version }} + name: qualicati + +components: + - qualicati -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in qualicati; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done +internal-dependencies: + - soma + - anatomist requirements: build: - - make + - ${{ compiler('cxx') }} run: - - soma ==${{ distro_version }} - - anatomist ==${{ distro_version }} - nibabel - pydicom - scikit-image diff --git a/soma-forge/recipes/soma-freesurfer.yaml b/soma-forge/recipes/soma-freesurfer.yaml index 1c8c13b..e3c2368 100644 --- a/soma-forge/recipes/soma-freesurfer.yaml +++ b/soma-forge/recipes/soma-freesurfer.yaml @@ -1,28 +1,9 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: soma-freesurfer - version: ${{ distro_version }} - -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in brainvisa_freesurfer; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done + name: soma-freesurfer -requirements: - build: - - make +components: + - brainvisa_freesurfer - run: - - soma ==${{ distro_version }} - - morphologist ==${{ distro_version }} +internal-dependencies: + - soma + - morphologist diff --git a/soma-forge/recipes/soma-python.yaml b/soma-forge/recipes/soma-python.yaml index d42d1bf..ac14fa1 100644 --- a/soma-forge/recipes/soma-python.yaml +++ b/soma-forge/recipes/soma-python.yaml @@ -1,31 +1,16 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: soma-python - version: ${{ distro_version }} + name: soma-python -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in soma-base soma-workflow; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done +components: + - soma-base + - soma-workflow -requirements: - build: - - make +internal-dependencies: + - populse-db +requirements: run: - python >=3.9 - - populse-db ==${{ distro_version }} - pydantic <2 - pyqt - pyqtwebengine diff --git a/soma-forge/recipes/soma-spm.yaml b/soma-forge/recipes/soma-spm.yaml index 8dea5d0..430d895 100644 --- a/soma-forge/recipes/soma-spm.yaml +++ b/soma-forge/recipes/soma-spm.yaml @@ -1,28 +1,9 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: soma-spm - version: ${{ distro_version }} - -build: - number: 0 - script: | - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in brainvisa-spm; do - make install-${component} - make install-${component}-dev - make install-${component}-usrdoc - make install-${component}-devdoc - make install-${component}-devdoc - make install-${component}-devdoc - done + name: soma-spm -requirements: - build: - - make +components: + - brainvisa-spm - run: - - soma ==${{ distro_version }} - - anatomist ==${{ distro_version }} +internal-dependencies: + - soma + - anatomist diff --git a/soma-forge/recipes/soma.yaml b/soma-forge/recipes/soma.yaml index 377646c..a3ce597 100644 --- a/soma-forge/recipes/soma.yaml +++ b/soma-forge/recipes/soma.yaml @@ -1,24 +1,30 @@ -context: - distro_version: ${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/pixi.toml").project.version }} - package: - name: soma - version: ${{ distro_version }} + name: soma + +components: + - soma-io + - aims-free + - aims-gpl + - brainvisa-share + - axon -build: - number: 0 - script: | - cd "$PIXI_PROJECT_ROOT" - pixi run bash << END - cd "$CASA_BUILD" - export BRAINVISA_INSTALL_PREFIX="$PREFIX" - for component in soma-io aims-free aims-gpl brainvisa-share axon; do - make install-\${component} - make install-\${component}-dev - make install-\${component}-usrdoc - make install-\${component}-devdoc - done - END +# build: +# number: 0 +# script: | +# cd "$PIXI_PROJECT_ROOT" +# pixi run bash << END +# cd "$CASA_BUILD" +# export BRAINVISA_INSTALL_PREFIX="$PREFIX" +# for component in soma-io aims-free aims-gpl brainvisa-share axon; do +# make install-\${component} +# make install-\${component}-dev +# make install-\${component}-usrdoc +# make install-\${component}-devdoc +# done +# END + +internal-dependencies: + - soma-python requirements: build: @@ -38,7 +44,6 @@ requirements: - pyyaml - libminc - openjpeg - - soma-python run: - libblitz @@ -50,7 +55,6 @@ requirements: - libminc - openjpeg - pywebp - - python ==${{ load_from_file(env.get("PIXI_PROJECT_ROOT") + "/build/python_version.json").version }} #run_constrained: #- pygltflib @@ -58,11 +62,6 @@ requirements: tests: - script: | - cd "$CASA_BUILD" python -m soma_forge test soma python -m soma_forge test aims python -m soma_forge test axon - - requirements: - run: - - cmake