Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Conversation

Nic-Ma
Copy link
Contributor

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

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 <[email protected]>
@Nic-Ma
[DLMED] simplify parse logic
04e3ee7 
Signed-off-by: Nic Ma <[email protected]>
@Nic-Ma
[DLMED] add more function tests
9abb571 
Signed-off-by: Nic Ma <[email protected]>
@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 <[email protected]>
@Nic-Ma
[DLMED] add standard run API
24c4ca1 
Signed-off-by: Nic Ma <[email protected]>
@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 <[email protected]>
@Nic-Ma
[DLMED] update API
d7cd6cb 
Signed-off-by: Nic Ma <[email protected]>
@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 <[email protected]>
@Nic-Ma
[DLMED] enhance doc and unit tests
b90b732 
Signed-off-by: Nic Ma <[email protected]>
@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 <[email protected]>
@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 <[email protected]>
@Nic-Ma
[DLMED] support root config
e7559c5 
Signed-off-by: Nic Ma <[email protected]>
@Nic-Ma
[DLMED] fix update reference typo
420346b 
Signed-off-by: Nic Ma <[email protected]>
@Nic-Ma
[DLMED] update usage API
4492a91 
Signed-off-by: Nic Ma <[email protected]>
@wyli
revise APIs and docstrings
3c1205c 
Signed-off-by: Wenqi Li <[email protected]>
@Nic-Ma 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
@Nic-Ma Nic-Ma force-pushed the 3482-add-config-reader branch from e9f5179 to f9cb68a Compare March 10, 2022 15:20
@Nic-Ma
Copy link
Contributor Author

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
View reviewed changes
Copy link
Contributor

@wyli wyli left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

@wyli
Copy link
Contributor

wyli commented Mar 10, 2022 •
edited
Loading

/black
/build

@Nic-Ma
Copy link
Contributor Author

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
View reviewed changes
Copy link
Contributor Author

@Nic-Ma Nic-Ma left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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
monai/bundle/scripts.py Show resolved Hide resolved
@Nic-Ma
Copy link
Contributor Author

Nic-Ma commented Mar 11, 2022

/black
/build

@Nic-Ma Nic-Ma requested a review from wyli March 11, 2022 02:50
@wyli
Copy link
Contributor

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 <[email protected]>
@wyli
Copy link
Contributor

wyli commented Mar 11, 2022

/build

@wyli wyli mentioned this pull request Mar 11, 2022
Merged
7 tasks
@wyli wyli merged commit c319ca8 into Project-MONAI:dev Mar 11, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@ericspod ericspod ericspod approved these changes

@rijobro rijobro Awaiting requested review from rijobro

@wyli wyli Awaiting requested review from wyli

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@Nic-Ma @wyli @ericspod