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Add bundle root directory to Python search directories automatically #6910

Merged
merged 19 commits into from
Aug 31, 2023
Merged

Add bundle root directory to Python search directories automatically #6910

merged 19 commits into from
Aug 31, 2023

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KumoLiu
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@KumoLiu KumoLiu commented Aug 29, 2023

Fixes #6722 .

Description

Add scripts directory to Python search directories automatically in the run function in ConfigWorkflow.

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.

@KumoLiu
fix Project-MONAI#6722
623c58e 
Signed-off-by: KumoLiu <yunl@nvidia.com>
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KumoLiu commented Aug 29, 2023

Hi @ericspod, could you please help review whether this one can help fix #6722? I added the scripts folder in the sys.path before running. This one should be merged after #6835.
cc @wyli @Nic-Ma

@wyli wyli requested review from ericspod and Nic-Ma August 29, 2023 09:43
ericspod
ericspod reviewed Aug 29, 2023
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monai/bundle/workflows.py Outdated Show resolved Hide resolved
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This looks in the right direction. We should have a test for it which creates a bundle with a scripts directory containing __init__.py with a single function definition. The bundle would call this function which would just print something to stdout and we'd check that value appears in the output. This test should use subprocess to run the bundle as a command line program to ensure a new Python runtime is created which has its own isolated environment.

@KumoLiu
directly add bundle root path
e4efa53 
Signed-off-by: KumoLiu <yunl@nvidia.com>
@KumoLiu
fix Project-MONAI#6911
9fca72e 
Signed-off-by: KumoLiu <yunl@nvidia.com>
@KumoLiu
Revert "fix Project-MONAI#6911"
1eb0d8c 
This reverts commit 9fca72e.
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KumoLiu commented Aug 29, 2023

This looks in the right direction. We should have a test for it which creates a bundle with a scripts directory containing __init__.py with a single function definition. The bundle would call this function which would just print something to stdout and we'd check that value appears in the output. This test should use subprocess to run the bundle as a command line program to ensure a new Python runtime is created which has its own isolated environment.

Agreed, will add the test ASAP, thanks!

KumoLiu and others added 12 commits August 30, 2023 22:19
@KumoLiu
Merge branch 'dev' of https://github.com/Project-MONAI/MONAI into add…
5cd9c1f 
…_scripts
@KumoLiu
fix Project-MONAI#6722
bd3364b 
Signed-off-by: KumoLiu <yunl@nvidia.com>
@KumoLiu
directly add bundle root path
ea2afe1 
Signed-off-by: KumoLiu <yunl@nvidia.com>
@KumoLiu
fix Project-MONAI#6911
644ca99 
Signed-off-by: KumoLiu <yunl@nvidia.com>
@KumoLiu
Revert "fix Project-MONAI#6911"
604628e 
This reverts commit 9fca72e.

Signed-off-by: KumoLiu <yunl@nvidia.com>
@anudeepadi @monai-bot @KumoLiu
Mask usernames in print_config function (Project-MONAI#6471) (Project…
5c0ccca 
…-MONAI#6913)

Fixes Project-MONAI#6471 

### Description

A few sentences describing the changes proposed in this pull request.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] 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.

---------

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>
Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
Signed-off-by: KumoLiu <yunl@nvidia.com>
@KumoLiu
Fix Spacing (Project-MONAI#6912)
82d6234 
Fixes Project-MONAI#6911.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] 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).
- [x] 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.

---------

Signed-off-by: KumoLiu <yunl@nvidia.com>
@KumoLiu
6834 Add MetaProterties and update load API (Project-MONAI#6835)
c0e2b52 
Fixes Project-MONAI#6834.

### Description
This PR introduces the idea of `BundleManager`, with `get` as one of the
methods, to avoid repeatedly instantiating `ConfigWorkflow`.

**usage**
```
bundle = BundleManager("spleen_ct_segmentation")
bundle.get("network_data_format")

or

bundle.get(property="train_preprocessing")
```

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] 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.

---------

Signed-off-by: KumoLiu <yunl@nvidia.com>
@KumoLiu
add unittests
0ac8542 
Signed-off-by: KumoLiu <yunl@nvidia.com>
@KumoLiu
Merge branch 'add_scripts' of https://github.com/KumoLiu/MONAI into a…
7feb8b7 
…dd_scripts

Signed-off-by: KumoLiu <yunl@nvidia.com>
@KumoLiu
DCO Remediation Commit for KumoLiu <yunl@nvidia.com>
272d2f7 
I, KumoLiu <yunl@nvidia.com>, hereby add my Signed-off-by to this commit: 1eb0d8c

Signed-off-by: KumoLiu <yunl@nvidia.com>
@KumoLiu
fix flake8
000a370 
Signed-off-by: KumoLiu <yunl@nvidia.com>
@KumoLiu KumoLiu marked this pull request as ready for review August 30, 2023 14:50
@KumoLiu
remove unused line
b004a8d 
Signed-off-by: KumoLiu <yunl@nvidia.com>
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KumoLiu commented Aug 30, 2023

Hi @ericspod, and @wyli, I have added unit tests for this PR, could you please help review it again? Thanks in advance!
cc @Nic-Ma

@KumoLiu KumoLiu requested review from ericspod and wyli August 30, 2023 14:56
@KumoLiu
fix flake8
1638a25 
Signed-off-by: KumoLiu <yunl@nvidia.com>
wyli
wyli reviewed Aug 30, 2023
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monai/bundle/workflows.py Outdated Show resolved Hide resolved
@KumoLiu KumoLiu changed the title Add scripts directory to Python search directories automatically Add bundle root directory to Python search directories automatically Aug 31, 2023
@KumoLiu
address comments
94998da 
Signed-off-by: KumoLiu <yunl@nvidia.com>
@wyli
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wyli commented Aug 31, 2023

/build

wyli
wyli approved these changes Aug 31, 2023
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Thanks, it looks good to me.

@wyli wyli enabled auto-merge (squash) August 31, 2023 06:25
@wyli wyli merged commit be4e1f5 into Project-MONAI:dev Aug 31, 2023
37 checks passed
@KumoLiu KumoLiu deleted the add_scripts branch August 31, 2023 10:16
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@wyli wyli wyli approved these changes

@Nic-Ma Nic-Ma Awaiting requested review from Nic-Ma

@ericspod ericspod Awaiting requested review from ericspod

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Add scripts directory to Python search directories automatically and avoid using PYTHONPATH
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@KumoLiu @ericspod @wyli @anudeepadi