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Adding Bundle Utility Functions #4324

Merged
merged 26 commits into from
May 26, 2022
Merged

Adding Bundle Utility Functions #4324

merged 26 commits into from
May 26, 2022

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ericspod
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Signed-off-by: Eric Kerfoot eric.kerfoot@kcl.ac.uk

Description

This adds a utility function to bundles load_bundle_config which can be used to load the configuration from a bundle without loading the network. This works on a path pointing to a directory or zip file. A init_bundle script function is added to create a basic bundle directory given a name and initial weights file. This can then be filled in by the user but is useful to demonstrate the correct structure of a bundle.

Status

Ready

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • Breaking change (fix or new feature that would cause existing functionality to change).
  • New tests added to cover the changes.
  • Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
  • Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

ericspod and others added 2 commits May 23, 2022 14:50
@ericspod
Adding tests
f444db5 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
22183f5 
for more information, see https://pre-commit.ci
@ericspod ericspod requested review from Nic-Ma and wyli May 24, 2022 10:19
ericspod and others added 2 commits May 24, 2022 11:20
@ericspod
Merge branch 'dev' into bundle_utils
b8150a8
@ericspod
Fix
f0d0632 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
wyli
wyli approved these changes May 24, 2022
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looks good to me, init_bundle provides a warm start... @Nic-Ma could please also review this?

ericspod and others added 4 commits May 24, 2022 11:59
@ericspod
Fix
d17b0ca 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@ericspod
Merge branch 'dev' into bundle_utils
8bfd0a7
@ericspod
Trying to read output from failed process
15ddcb9 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
1e6274e 
for more information, see https://pre-commit.ci
Nic-Ma
Nic-Ma requested changes May 24, 2022
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monai/bundle/utils.py Outdated Show resolved Hide resolved
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@Nic-Ma
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Nic-Ma commented May 24, 2022 •
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Hi @ericspod ,

Thanks for the great enhancement of the bundle user experience!
Put some minor comments inline.

Thanks.

@ericspod
Updates
2e46c01 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
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There's an issue running the init_bundle script with fire not being present when it should be, the test may not work for Windows either.

ericspod added 5 commits May 24, 2022 14:40
@ericspod
Marking bundle_init as excluded
a71e73c 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@ericspod
Marking bundle_init as excluded
df18d75 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@ericspod
Forgot a file
f31f679 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@ericspod
Marking bundle_utils as excluded
a6de05e 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@ericspod
Marking bundle_init as excluded
9d797c1 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
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@Nic-Ma I think I'm waiting on some CI/CD things to be resolved but once that's done could you review again? Thanks!

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Nic-Ma commented May 25, 2022

@Nic-Ma I think I'm waiting on some CI/CD things to be resolved but once that's done could you review again? Thanks!

Sure, I am blocked by some other tasks today, will try to review it again ASAP tonight.

Thanks for your quick update.

ericspod added 3 commits May 25, 2022 13:04
@ericspod
Fix conflict
28b5745 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@ericspod
Merge branch 'ericspod-bundle_utils' into bundle_utils
c420cad
@ericspod
Update
71b93a8 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
Nic-Ma
Nic-Ma approved these changes May 25, 2022
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Hi @ericspod ,

Thanks for your quick update.
It overall looks good to me, put some minor comments inline.

Thanks.

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ericspod and others added 3 commits May 25, 2022 17:55
@ericspod
Merge branch 'dev' into bundle_utils
e53eb99
@ericspod
Updates
ff579fd 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@ericspod
Updates
894572b 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@ericspod ericspod enabled auto-merge (squash) May 25, 2022 19:56
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Nic-Ma commented May 26, 2022

/build

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Nic-Ma commented May 26, 2022

/build

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Nic-Ma commented May 26, 2022

Depends on #4355 to merge first.

Thanks.

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wyli commented May 26, 2022

/build

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wyli commented May 26, 2022

/build

@ericspod ericspod merged commit b892aa5 into Project-MONAI:dev May 26, 2022
@ericspod ericspod deleted the bundle_utils branch May 26, 2022 22:04
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@Nic-Ma Nic-Ma Nic-Ma approved these changes

@wyli wyli wyli approved these changes

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@ericspod @Nic-Ma @wyli