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[ENH] Creation of singularity image during continuous integration #60

Merged
merged 37 commits into from
Dec 11, 2020
Merged

[ENH] Creation of singularity image during continuous integration #60

merged 37 commits into from
Dec 11, 2020

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sebastientourbier
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This resolves #57.

@sebastientourbier sebastientourbier added the enhancement New feature or request label Dec 8, 2020
@sebastientourbier sebastientourbier linked an issue Dec 8, 2020 that may be closed by this pull request
Build and publish singularity image to SyLabs Cloud in CircleCI #57
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@sebastientourbier sebastientourbier added this to the v2.0.1 milestone Dec 8, 2020
@sebastientourbier sebastientourbier self-assigned this Dec 8, 2020
@sebastientourbier
CI: install singularity in test-singularity job
f755d38
@sebastientourbier
CI: install same singularity version as on the cluster and remove the…
01cf6ca 
… --no-home flag
@sebastientourbier
CI: fix git clone and tag for singularity
a569cb9
@sebastientourbier
CI: review installation of singularity 3.5.1
74b56dd
@sebastientourbier
CI: add --sysconfdir to configuration of singularity installation
fffeaa4
@sebastientourbier
MAINT: code style in .circleci/config.yml [skip ci]
9d65904
@sebastientourbier
CI: remove obsolete packages for singularity
32bd1be
@sebastientourbier
CI: install GO for singularity
e5699b4
@sebastientourbier
CI: add GO to PATH for singularity
41342c7
@sebastientourbier
CI: try to use singularity circleci orb for installation
80e24aa
@sebastientourbier
CI: fix call of commands from singularity cirecleci orb
446387b
@sebastientourbier
CI: update circleci singularity orb
b222f0c
@sebastientourbier
CI: add missing space and add --contain flag in singularity exec comm…
90a6804 
…ands
@sebastientourbier
FIX: removed extra space in shebangs of docker entrypoint scripts
57a9e2f
@sebastientourbier
FIX: removed --contain in singularity exec command
2aed12c
@sebastientourbier
FIX: commented creation of bids_dir and output_dir inside the container
0f72175
@sebastientourbier
DOCKER: Review way content of entrypoint scripts is written
03122f3
@sebastientourbier
DOCKER: add missing && in creation of entrypoint script content
75d9c51
@sebastientourbier
DOCKER: refactoring of entrypoint scripts
4e4c505
@sebastientourbier
MAINT: correct code styles raised by codacy
47a1cbd
sebastientourbier
sebastientourbier commented Dec 10, 2020
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Ready to merge!
@pdedumast @hamzake If you want to review to have an idea of what changes

@sebastientourbier sebastientourbier merged commit e6f97fa into v2.0.1-dev Dec 11, 2020
@sebastientourbier sebastientourbier deleted the 56_singularity_v2.0.1-dev branch December 11, 2020 09:13
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@pdedumast pdedumast pdedumast approved these changes

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@sebastientourbier sebastientourbier

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Build and publish singularity image to SyLabs Cloud in CircleCI
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@sebastientourbier @pdedumast