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3482 add run API for common training, evaluation and inference #3832

Merged
merged 101 commits into from
Mar 11, 2022
Merged

3482 add run API for common training, evaluation and inference #3832

merged 101 commits into from
Mar 11, 2022

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Nic-Ma
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@Nic-Ma Nic-Ma commented Feb 21, 2022 •
edited

Task step 7 of #3482 .

Description

This PR added the run API to execute most common cases of supervised training, evaluation or inference from the config directly.

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.

Nic-Ma and others added 17 commits February 1, 2021 19:15
@Nic-Ma
Merge pull request #19 from Project-MONAI/master
42a45e0 
merge master
@Nic-Ma
Merge pull request #32 from Project-MONAI/master
cd16a13 
merge master
@Nic-Ma
Merge pull request #180 from Project-MONAI/dev
6f87afd 
merge master
@Nic-Ma
Merge pull request #214 from Project-MONAI/dev
f398298 
merge master
@Nic-Ma
Merge pull request #373 from Project-MONAI/dev
85604cf 
merge master
@Nic-Ma
[DLMED] add config parser
a3193ba 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] simplify parse logic
04e3ee7 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] add more function tests
9abb571 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
Merge branch 'dev' into 3482-add-config-parser
32aac56
@Nic-Ma
Merge pull request #374 from Project-MONAI/dev
2ab8fd5 
merge master
@Nic-Ma
[DLMED] fix torchvision tests
fe3f7c2 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] add standard run API
24c4ca1 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
Merge branch 'dev' into 3482-add-config-reader
35dacfb
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
5dc87f0 
for more information, see https://pre-commit.ci
@Nic-Ma
Merge branch 'dev' into 3482-add-config-parser
d4cb4b0
@Nic-Ma
[DLMED] enhance update_config to support multiple items
886b607 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] update API
d7cd6cb 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma Nic-Ma mentioned this pull request Feb 21, 2022
Closed
17 tasks
Nic-Ma and others added 12 commits February 22, 2022 00:11
@Nic-Ma
[DLMED] simplify API
67d19be 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] enhance doc and unit tests
b90b732 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
Merge branch 'dev' into 3482-add-config-parser
9056a9f
@Nic-Ma
Merge branch 'dev' into 3482-add-config-parser
9292450
@Nic-Ma
[DLMED] clear API
bfc74fc 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
Merge branch 'dev' into 3482-add-config-parser
ac3e893
@Nic-Ma
Merge branch 'dev' into 3482-add-config-parser
0551374
@Nic-Ma
[DLMED] simplify usage APIs
362e336 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] support root config
e7559c5 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] fix update reference typo
420346b 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] update usage API
4492a91 
Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
revise APIs and docstrings
3c1205c 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
[DLMED] update according to discussion
d8beeca 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] fix path_id match
81fabd3 
Signed-off-by: Nic Ma <nma@nvidia.com>
wyli and others added 3 commits March 10, 2022 12:36
@wyli
revise according to the comments
c89e3a2 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
[DLMED] update config item
ca16681 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] update patterns
f9cb68a 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] enhance disabled
2aaa23a 
Signed-off-by: Nic Ma <nma@nvidia.com>
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Nic-Ma commented Mar 10, 2022

/black

@Nic-Ma Nic-Ma requested a review from wyli March 10, 2022 16:00
wyli
wyli approved these changes Mar 10, 2022
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thanks @Nic-Ma, this looks nice now and I'll revise and merge it soon.

@wyli
special chars to utils
91dd87f 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
remove circular import
194b113 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
configreader -> configparser following cpython/configparser
056a119 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
printing
fe83f07 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
fixes typing
1403909 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
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wyli commented Mar 10, 2022 •
edited

/black
/build

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Nic-Ma commented Mar 10, 2022

Hi @ericspod @wyli ,

Thanks for your review and updates.
I am trying to unify the _name_ and _path_ key words to _target_, similar to Hydra:
https://github.com/facebookresearch/hydra/blob/main/examples/instantiate/object/conf/db/mysql.yaml#L1

Thanks.

Nic-Ma
Nic-Ma commented Mar 11, 2022
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Hi @wyli ,

Thanks for your update, I put some minor comments inline, others look good to me.

monai/bundle/config_item.py Show resolved Hide resolved
monai/bundle/scripts.py Show resolved Hide resolved
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@Nic-Ma
[DLMED] unify "_name_" and "_path_"
9d4ea6b 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] update to "_target_"
2780530 
Signed-off-by: Nic Ma <nma@nvidia.com>
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Nic-Ma commented Mar 11, 2022

/black
/build

@Nic-Ma Nic-Ma requested a review from wyli March 11, 2022 02:50
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wyli commented Mar 11, 2022

/build

@wyli wyli enabled auto-merge (squash) March 11, 2022 07:15
@wyli
fixes typos
194f21e 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
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wyli commented Mar 11, 2022

/build

@wyli wyli mentioned this pull request Mar 11, 2022
Merged
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@wyli wyli merged commit c319ca8 into Project-MONAI:dev Mar 11, 2022
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@ericspod ericspod ericspod approved these changes

@rijobro rijobro Awaiting requested review from rijobro

@wyli wyli Awaiting requested review from wyli

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