From 3cbfae1f2f2d22818f76926be013faa00a5336db Mon Sep 17 00:00:00 2001 From: David Meunier Date: Tue, 6 Feb 2024 17:23:11 +0100 Subject: [PATCH] release but without mcr --- .github/workflows/build_on_release.yml | 243 ++++++++++++++++--------- Dockerfile_nomcr | 74 ++++++++ macapype/_version.py | 2 +- 3 files changed, 228 insertions(+), 91 deletions(-) create mode 100644 Dockerfile_nomcr diff --git a/.github/workflows/build_on_release.yml b/.github/workflows/build_on_release.yml index fbc7ea09..4ac4aa5f 100644 --- a/.github/workflows/build_on_release.yml +++ b/.github/workflows/build_on_release.yml @@ -60,13 +60,15 @@ jobs: uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc with: context: . + + file: Dockerfile_nomcr push: true tags: ${{ steps.meta.outputs.tags }} labels: ${{ steps.meta.outputs.labels }} - run-pretest-spm: - name: Running all existing pipelines in macapype_CI.zip (SPM_native) - needs: docker-build + run-pretest-ants-t1-marmo: + name: Running all existing pipelines in macapype_CI.zip (ANTS marmo T1) + needs: docker-build runs-on: ubuntu-latest timeout-minutes: 1440 @@ -78,9 +80,6 @@ jobs: - name: Download dataset run: | - mkdir SPM_native - cd SPM_native - wget --no-check-certificate --content-disposition "https://amubox.univ-amu.fr/public.php?service=files&t=KJ2L5j6L6orPXxM&download" -O macapype_CI.zip unzip -o macapype_CI.zip -d macapype_CI @@ -96,68 +95,75 @@ jobs: ls macapype_CI/marmo-marmobrain echo "" - - name: Running test pipeline macaque_prime-de SPM_native_prep T1 T2 + - name: Running test pipeline marmo-marmobrain ANTS_noseg T1 run: | - docker run -i -v /home/runner/work/macapype/macapype/SPM_native/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de -out /data/macaque_prime-de/results -soft SPM_native_prep -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 T2 - - ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/macaque_prime-de/results/ + docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft ANTS_noseg -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 - ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/macaque_prime-de/results/derivatives/ + ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/ - ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/ + ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/ - ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/sub-032140/ses-001/anat/ + ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/ + ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/sub-Percy/ses-01/anat/ echo "" - - name: Running test pipeline macaque_prime-de SPM_native_noseg T1 T2 - run: | - docker run -i -v /home/runner/work/macapype/macapype/SPM_native/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de -out /data/macaque_prime-de/results -soft SPM_native_noseg -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 T2 + - name: Cleaning dataset + run: + sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/ - ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/sub-032140/ses-001/anat/ - echo "" - - name: Running test pipeline macaque_prime-de SPM_native T1 T2 - run: | - docker run -i -v /home/runner/work/macapype/macapype/SPM_native/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de -out /data/macaque_prime-de/results -soft SPM_native -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 T2 + run-pretest-ants-marmo: + name: Running all existing pipelines in macapype_CI.zip (ANTS marmo) + needs: docker-build + runs-on: ubuntu-latest + timeout-minutes: 1440 - ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/sub-032140/ses-001/anat/ - echo "" + steps: + - name: Pull latest docker image + run: + docker pull macatools/macapype:latest - - name: Running test pipeline marmo-marmobrain SPM_native_prep T1 T2 + - name: Download dataset run: | - docker run -i -v /home/runner/work/macapype/macapype/SPM_native/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft SPM_native_prep -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2 - ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/marmo-marmobrain/results/ - - ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/marmo-marmobrain/results/derivatives/ + wget --no-check-certificate --content-disposition "https://amubox.univ-amu.fr/public.php?service=files&t=KJ2L5j6L6orPXxM&download" -O macapype_CI.zip + unzip -o macapype_CI.zip -d macapype_CI - ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/ + pwd + echo "" - ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/sub-Percy/ses-01/anat/ + ls macapype_CI + echo "" - - name: Running test pipeline marmo-marmobrain SPM_native_noseg T1 T2 - run: | - docker run -i -v /home/runner/work/macapype/macapype/SPM_native/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft SPM_native_noseg -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2 + ls macapype_CI/macaque_prime-de + echo "" - ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/sub-Percy/ses-01/anat/ + ls macapype_CI/marmo-marmobrain echo "" - - name: Running test pipeline marmo-marmobrain SPM_native T1 T2 + - name: Running test pipeline marmo-marmobrain ANTS_noseg T1 T2 run: | - docker run -i -v /home/runner/work/macapype/macapype/SPM_native/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft SPM_native -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2 + docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft ANTS_noseg -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2 - ls /home/runner/work/macapype/macapype/SPM_native/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_spm_t1_t2_native/sub-Percy/ses-01/anat/ + ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/ + + ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/ + + ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/ + + ls /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-Percy/ses-01/anat/ echo "" + - name: Cleaning dataset run: - sudo rm -rf /home/runner/work/macapype/macapype/SPM_native + sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/ - run-pretest: - name: Running all existing pipelines in macapype_CI.zip (ANTS) - needs: docker-build + run-pretest-ants-t1-baboon: + name: Running all existing pipelines in macapype_CI.zip (ANTS T1 baboon) + needs: docker-build runs-on: ubuntu-latest timeout-minutes: 1440 @@ -169,9 +175,6 @@ jobs: - name: Download dataset run: | - mkdir ANTS - cd ANTS - wget --no-check-certificate --content-disposition "https://amubox.univ-amu.fr/public.php?service=files&t=KJ2L5j6L6orPXxM&download" -O macapype_CI.zip unzip -o macapype_CI.zip -d macapype_CI @@ -187,104 +190,164 @@ jobs: ls macapype_CI/marmo-marmobrain echo "" - ls macapype_CI/baboon-cerimed-adrien - echo "" - - - name: Running test pipeline marmo-marmobrain ANTS_noseg T1 + - name: Running test pipeline baboon-cerimed-adrien ANTS_prep T1 run: | - docker run -i -v /home/runner/work/macapype/macapype/ANTS/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft ANTS_noseg -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 + docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/baboon-cerimed-adrien -out /data/baboon-cerimed-adrien/results -soft ANTS_prep -species baboon -sub Fidji -ses 01 -deriv -pad -dt T1 - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/ + ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/ - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/derivatives/ + ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/ - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/ + ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1/ - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/sub-Percy/ses-01/anat/ + ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1/sub-Fidji/ses-01/anat/ echo "" - - name: Running test pipeline marmo-marmobrain ANTS T1 + - name: Cleaning dataset + run: + sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1/ + + + + run-pretest-ants-baboon: + name: Running all existing pipelines in macapype_CI.zip (ANTS baboon) + needs: docker-build + runs-on: ubuntu-latest + timeout-minutes: 1440 + + steps: + - name: Pull latest docker image + run: + docker pull macatools/macapype:latest + + - name: Download dataset run: | - docker run -i -v /home/runner/work/macapype/macapype/ANTS/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft ANTS -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/sub-Percy/ses-01/anat/ + wget --no-check-certificate --content-disposition "https://amubox.univ-amu.fr/public.php?service=files&t=KJ2L5j6L6orPXxM&download" -O macapype_CI.zip + unzip -o macapype_CI.zip -d macapype_CI + + pwd echo "" - - name: Running test pipeline marmo-marmobrain ANTS_noseg T1 T2 - run: | - docker run -i -v /home/runner/work/macapype/macapype/ANTS/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft ANTS_noseg -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2 + ls macapype_CI + echo "" + + ls macapype_CI/macaque_prime-de + echo "" - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-Percy/ses-01/anat/ + ls macapype_CI/marmo-marmobrain echo "" - - name: Running test pipeline marmo-marmobrain ANTS T1 T2 + - name: Running test pipeline baboon-cerimed-adrien ANTS_prep T1 T2 run: | - docker run -i -v /home/runner/work/macapype/macapype/ANTS/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft ANTS -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2 + docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/baboon-cerimed-adrien -out /data/baboon-cerimed-adrien/results -soft ANTS_prep -species baboon -sub Fidji -ses 01 -deriv -pad -dt T1 T2 - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/ + ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/ - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/derivatives/ + ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/ - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/ + ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1_t2/ - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-Percy/ses-01/anat/ + ls /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-Fidji/ses-01/anat/ echo "" - - name: Running test pipeline baboon-cerimed-adrien ANTS_prep T1 + - name: Cleaning dataset + run: + sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1_t2/ + + + + run-pretest-ants-macaque-t1: + name: Running all existing pipelines in macapype_CI.zip (ANTS macaque T1) + needs: docker-build + runs-on: ubuntu-latest + timeout-minutes: 1440 + + + steps: + - name: Pull latest docker image + run: + docker pull macatools/macapype:latest + + - name: Download dataset run: | - docker run -i -v /home/runner/work/macapype/macapype/ANTS/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/baboon-cerimed-adrien -out /data/baboon-cerimed-adrien/results -soft ANTS_prep -species baboon -sub Fidji -ses 01 -deriv -pad -dt T1 - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/baboon-cerimed-adrien/results/ + wget --no-check-certificate --content-disposition "https://amubox.univ-amu.fr/public.php?service=files&t=KJ2L5j6L6orPXxM&download" -O macapype_CI.zip + unzip -o macapype_CI.zip -d macapype_CI - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/baboon-cerimed-adrien/results/derivatives/ + pwd + echo "" - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1/ + ls macapype_CI + echo "" - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1/sub-Fidji/ses-01/anat/ + ls macapype_CI/macaque_prime-de echo "" - - name: Running test pipeline baboon-cerimed-adrien ANTS_prep T1 T2 + ls macapype_CI/marmo-marmobrain + echo "" + + - name: Running test pipeline macaque_prime-de ANTS_prep T1 run: | - docker run -i -v /home/runner/work/macapype/macapype/ANTS/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/baboon-cerimed-adrien -out /data/baboon-cerimed-adrien/results -soft ANTS_prep -species baboon -sub Fidji -ses 01 -deriv -pad -dt T1 T2 + docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de/ -out /data/macaque_prime-de/results -soft ANTS_prep -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/baboon-cerimed-adrien/results/ + ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/ - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/baboon-cerimed-adrien/results/derivatives/ + ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/ - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1_t2/ + ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1/ - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/baboon-cerimed-adrien/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-Fidji/ses-01/anat/ + ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1/sub-032140/ses-001/anat/ echo "" + - name: Cleaning dataset + run: + sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1/ + - - name: Running test pipeline macaque_prime-de ANTS_prep T1 + run-pretest-ants-macaque: + name: Running all existing pipelines in macapype_CI.zip (ANTS macaque) + needs: docker-build + runs-on: ubuntu-latest + timeout-minutes: 1440 + + steps: + - name: Pull latest docker image + run: + docker pull macatools/macapype:latest + + - name: Download dataset run: | - docker run -i -v /home/runner/work/macapype/macapype/ANTS/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de/ -out /data/macaque_prime-de/results -soft ANTS_prep -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/macaque_prime-de/results/ + wget --no-check-certificate --content-disposition "https://amubox.univ-amu.fr/public.php?service=files&t=KJ2L5j6L6orPXxM&download" -O macapype_CI.zip + unzip -o macapype_CI.zip -d macapype_CI - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/macaque_prime-de/results/derivatives/ + pwd + echo "" - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1/ + ls macapype_CI + echo "" - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1/sub-032140/ses-001/anat/ + ls macapype_CI/macaque_prime-de echo "" + ls macapype_CI/marmo-marmobrain + echo "" - name: Running test pipeline macaque_prime-de ANTS_prep T1 T2 run: | - docker run -i -v /home/runner/work/macapype/macapype/ANTS/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de/ -out /data/macaque_prime-de/results -soft ANTS_prep -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 T2 + docker run -i -v /home/runner/work/macapype/macapype/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de/ -out /data/macaque_prime-de/results -soft ANTS_prep -species macaque -sub 032140 -ses 001 -deriv -pad -dt T1 T2 -nprocs 1 - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/macaque_prime-de/results/ + ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/ - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/macaque_prime-de/results/derivatives/ + ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/ - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1_t2/ + ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1_t2/ - ls /home/runner/work/macapype/macapype/ANTS/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-032140/ses-001/anat/ + ls /home/runner/work/macapype/macapype/macapype_CI/macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1_t2/sub-032140/ses-001/anat/ echo "" - name: Cleaning dataset run: - sudo rm -rf /home/runner/work/macapype/macapype/ANTS + sudo rm -rf macaque_prime-de/results/derivatives/macapype_crop_aladin_ants_t1_t2 diff --git a/Dockerfile_nomcr b/Dockerfile_nomcr new file mode 100644 index 00000000..5a7e9f2e --- /dev/null +++ b/Dockerfile_nomcr @@ -0,0 +1,74 @@ +# Generated by: Neurodocker version 0.7.0+15.ga4940e3.dirty +# Latest release: Neurodocker version 0.7.0 +# +# Thank you for using Neurodocker. If you discover any issues +# or ways to improve this software, please submit an issue or +# pull request on our GitHub repository: +# +# https://github.com/ReproNim/neurodocker +# +# Timestamp: 2020/12/02 18:33:44 UTC + +FROM macatools/macapype_env:v0.1.1-nomcr + +USER root + +ARG DEBIAN_FRONTEND="noninteractive" + +MAINTAINER David Meunier "david.meunier@univ-amu.fr" +######################## Python packages + +RUN apt-get update && apt-get install -y git python3-pip libpng-dev libfreetype6-dev libxft-dev libblas-dev liblapack-dev libatlas-base-dev gfortran libxml2-dev libxslt1-dev wget graphviz + +RUN apt-get install -y python3-pil python3-pil.imagetk + + +RUN python3 -m pip install -U pip +RUN python3 -m pip install -U pillow +#RUN pip3 install pillow + +#RUN apt-get install libx11-6 libxext6 libxt6 # matlab +RUN pip3 install xvfbwrapper \ + psutil \ + numpy \ + scipy \ + matplotlib \ + statsmodels \ + pandas \ + networkx\ + mock \ + prov \ + click \ + funcsigs \ + pydotplus \ + pydot \ + rdflib \ + pbr \ + nibabel==3.2.2 \ + packaging \ + pytest \ + install \ + graphviz \ + pybids \ + nipype \ + nilearn \ + scikit-image \ + brain-slam + +############################################# install macapype + +RUN echo $(which python) && \ + echo $(which python3) && \ + ln -s /usr/bin/python3 /usr/bin/python && \ + ln -s /usr/bin/pip3 /usr/bin/pip + +RUN pip install --pre macapype && python -c "import macapype; print(macapype.__version__)" + +################################################## Finishing +RUN apt-get clean \ + && rm -rf /var/lib/apt/lists/* + +RUN rm -rf \ + /tmp/hsperfdata* \ + /var/*/apt/*/partial \ + /var/log/apt/term* diff --git a/macapype/_version.py b/macapype/_version.py index de07881c..5ea569be 100644 --- a/macapype/_version.py +++ b/macapype/_version.py @@ -1,2 +1,2 @@ -__version__ = '0.3.5-rc17' +__version__ = '0.3.5'