3482 add `run` API for common training, evaluation and inference by Nic-Ma · Pull Request #3832 · Project-MONAI/MONAI

Nic-Ma · 2022-02-21T13:44:30Z

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.

merge master

Signed-off-by: Nic Ma <[email protected]>

merge master

Signed-off-by: Nic Ma <[email protected]>

for more information, see https://pre-commit.ci

Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Nic Ma <[email protected]>

Nic-Ma · 2022-03-10T15:59:05Z

/black

wyli

thanks @Nic-Ma, this looks nice now and I'll revise and merge it soon.

Signed-off-by: Wenqi Li <[email protected]>

wyli · 2022-03-10T22:06:20Z

/black
/build

Nic-Ma · 2022-03-10T23:59:54Z

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

Hi @wyli ,

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

monai/bundle/config_item.py

monai/bundle/scripts.py

Signed-off-by: Nic Ma <[email protected]>

Nic-Ma · 2022-03-11T02:49:51Z

/black
/build

wyli · 2022-03-11T07:15:29Z

/build

Signed-off-by: Wenqi Li <[email protected]>

wyli · 2022-03-11T07:46:51Z

/build

Nic-Ma and others added 17 commits February 1, 2021 19:15

Merge pull request #19 from Project-MONAI/master

42a45e0

merge master

Merge pull request #32 from Project-MONAI/master

cd16a13

merge master

Merge pull request #180 from Project-MONAI/dev

6f87afd

merge master

Merge pull request #214 from Project-MONAI/dev

f398298

merge master

Merge pull request #373 from Project-MONAI/dev

85604cf

merge master

[DLMED] add config parser

a3193ba

Signed-off-by: Nic Ma <[email protected]>

[DLMED] simplify parse logic

04e3ee7

Signed-off-by: Nic Ma <[email protected]>

[DLMED] add more function tests

9abb571

Signed-off-by: Nic Ma <[email protected]>

Merge branch 'dev' into 3482-add-config-parser

32aac56

Merge pull request #374 from Project-MONAI/dev

2ab8fd5

merge master

[DLMED] fix torchvision tests

fe3f7c2

Signed-off-by: Nic Ma <[email protected]>

[DLMED] add standard run API

24c4ca1

Signed-off-by: Nic Ma <[email protected]>

Merge branch 'dev' into 3482-add-config-reader

35dacfb

[pre-commit.ci] auto fixes from pre-commit.com hooks

5dc87f0

for more information, see https://pre-commit.ci

Merge branch 'dev' into 3482-add-config-parser

d4cb4b0

[DLMED] enhance update_config to support multiple items

886b607

Signed-off-by: Nic Ma <[email protected]>

[DLMED] update API

d7cd6cb

Signed-off-by: Nic Ma <[email protected]>

Nic-Ma mentioned this pull request Feb 21, 2022

Develop MVP of model bundle #3482

Closed

17 tasks

Nic-Ma and others added 12 commits February 22, 2022 00:11

[DLMED] simplify API

67d19be

Signed-off-by: Nic Ma <[email protected]>

[DLMED] enhance doc and unit tests

b90b732

Signed-off-by: Nic Ma <[email protected]>

Merge branch 'dev' into 3482-add-config-parser

9056a9f

Merge branch 'dev' into 3482-add-config-parser

9292450

[DLMED] clear API

bfc74fc

Signed-off-by: Nic Ma <[email protected]>

Merge branch 'dev' into 3482-add-config-parser

ac3e893

Merge branch 'dev' into 3482-add-config-parser

0551374

[DLMED] simplify usage APIs

362e336

Signed-off-by: Nic Ma <[email protected]>

[DLMED] support root config

e7559c5

Signed-off-by: Nic Ma <[email protected]>

[DLMED] fix update reference typo

420346b

Signed-off-by: Nic Ma <[email protected]>

[DLMED] update usage API

4492a91

Signed-off-by: Nic Ma <[email protected]>

revise APIs and docstrings

3c1205c

Signed-off-by: Wenqi Li <[email protected]>

Nic-Ma added 2 commits March 10, 2022 17:55

[DLMED] update according to discussion

d8beeca

Signed-off-by: Nic Ma <[email protected]>

[DLMED] fix path_id match

81fabd3

Signed-off-by: Nic Ma <[email protected]>

Nic-Ma force-pushed the 3482-add-config-reader branch from 4920e06 to 81fabd3 Compare March 10, 2022 11:27

wyli and others added 3 commits March 10, 2022 12:36

revise according to the comments

c89e3a2

Signed-off-by: Wenqi Li <[email protected]>

[DLMED] update config item

ca16681

Signed-off-by: Nic Ma <[email protected]>

[DLMED] update patterns

f9cb68a

Signed-off-by: Nic Ma <[email protected]>

Nic-Ma force-pushed the 3482-add-config-reader branch from e9f5179 to f9cb68a Compare March 10, 2022 15:20

[DLMED] enhance disabled

2aaa23a

Signed-off-by: Nic Ma <[email protected]>

Nic-Ma requested a review from wyli March 10, 2022 16:00

wyli approved these changes Mar 10, 2022

View reviewed changes

wyli added 5 commits March 10, 2022 20:05

special chars to utils

91dd87f

Signed-off-by: Wenqi Li <[email protected]>

remove circular import

194b113

Signed-off-by: Wenqi Li <[email protected]>

configreader -> configparser following cpython/configparser

056a119

Signed-off-by: Wenqi Li <[email protected]>

printing

fe83f07

Signed-off-by: Wenqi Li <[email protected]>

fixes typing

1403909

Signed-off-by: Wenqi Li <[email protected]>

ericspod approved these changes Mar 10, 2022

View reviewed changes

Nic-Ma commented Mar 11, 2022

View reviewed changes

monai/bundle/config_item.py Show resolved Hide resolved

monai/bundle/scripts.py Show resolved Hide resolved

monai/bundle/scripts.py Show resolved Hide resolved

Nic-Ma added 2 commits March 11, 2022 09:53

[DLMED] unify "_name_" and "_path_"

9d4ea6b

Signed-off-by: Nic Ma <[email protected]>

[DLMED] update to "_target_"

2780530

Signed-off-by: Nic Ma <[email protected]>

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

wyli enabled auto-merge (squash) March 11, 2022 07:15

fixes typos

194f21e

Signed-off-by: Wenqi Li <[email protected]>

wyli mentioned this pull request Mar 11, 2022

3922 Make UNETR support torchscript #3923

Merged

7 tasks

wyli merged commit c319ca8 into Project-MONAI:dev Mar 11, 2022

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

3482 add `run` API for common training, evaluation and inference#3832
wyli merged 101 commits intoProject-MONAI:devfrom
Nic-Ma:3482-add-config-reader

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Nic-Ma commented Feb 21, 2022 •

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