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Update #1

Merged
merged 88 commits into from
Nov 10, 2020
Merged

Update #1

merged 88 commits into from
Nov 10, 2020

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swethmandava
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What does this PR do?

Fixes # (issue)

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  • Did you make sure your PR does only one thing, instead of bundling different changes together? Otherwise, we ask you to create a separate PR for every change.
  • Did you make sure to update the documentation with your changes?
  • Did you write any new necessary tests?
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  • If you made a notable change (that affects users), did you update the CHANGELOG?

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amogkam and others added 30 commits October 26, 2020 20:24
* fix

* more doc fixes

Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>
Co-authored-by: Adrian Wälchli <aedu.waelchli@gmail.com>
Co-authored-by: chaton <thomas@grid.ai>
* Add geting help message from docstring

* Fix pep8 issue

* Apply suggestions from code review

Co-authored-by: Adrian Wälchli <aedu.waelchli@gmail.com>

* Apply suggestions from code review

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>

Co-authored-by: Adrian Wälchli <aedu.waelchli@gmail.com>
Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>
Co-authored-by: Sean Naren <sean.narenthiran@gmail.com>
Co-authored-by: chaton <thomas@grid.ai>
* allow trainer's profiler param to have a str value

* add tests

* update docs

* update exception message

* Update CHANGELOG

* fix pep8 issues

* cleanup test code

Co-authored-by: Carlos Mocholí <carlossmocholi@gmail.com>

* Add deprecation warning if using bool for profiler

* Add deprecation tests and move deprecated tests

* Remove bool option to profiler from docs

* Deprecate bool args to profiler in CHANGELOG

* fixup! Add deprecation warning if using bool for profiler

* fixup! Add deprecation tests and move deprecated tests

* Apply suggestions from code review

Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>

* Implement suggestions, remove whitespace

* fixup! Implement suggestions, remove whitespace

* Allow bool, str (case insensitive), BaseProfiler

* Add info about bool deprecation to trainer

* fixup! Add info about bool deprecation to trainer

* Move deprecate todo to test_deprecated

* Test wrong profiler type, improve error message

* fixup! Test wrong profiler type, improve error message

* Update pytorch_lightning/trainer/connectors/profiler_connector.py

Co-authored-by: Carlos Mocholí <carlossmocholi@gmail.com>

* Apply suggestions from code review

* Readd bool to profiler types, test cli profiler arg

* Remove extra whitespace in doc

Co-authored-by: Adrian Wälchli <aedu.waelchli@gmail.com>

* Apply suggestions from code review

Co-authored-by: Adrian Wälchli <aedu.waelchli@gmail.com>

* Update deprecation versions

Co-authored-by: Carlos Mocholí <carlossmocholi@gmail.com>
Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>
Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>
Co-authored-by: Adrian Wälchli <aedu.waelchli@gmail.com>
…allel (#4382)

* Update ddp_plugin.py

* Update ddp_plugin.py

* Update ddp_plugin.py

* Update test_ddp_plugin.py

* Update pytorch_lightning/plugins/ddp_plugin.py

* Update pytorch_lightning/plugins/ddp_plugin.py

* Fixed imports, make ddp_kwargs protected

Co-authored-by: SeanNaren <sean.narenthiran@gmail.com>
…4230)

* Fix  COMET_EXPERIMENT_KEY environment variable usage

* Remove unused arg

* Update comet.py

* Add test by Lothiraldan

* remove blank

Co-authored-by: chaton <thomas@grid.ai>
Co-authored-by: Nicki Skafte <skaftenicki@gmail.com>
Co-authored-by: Sean Naren <sean.narenthiran@gmail.com>
* Add key

* Remove unused variables

* Update CHANGELOG [skip ci]

* best_model_monitor -> monitor

Co-authored-by: Sean Naren <sean.narenthiran@gmail.com>
Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>
* Add optimizer hooks in callbacks

* optimizer param

* update test

Co-authored-by: Nicki Skafte <skaftenicki@gmail.com>
* warning on states

* suggestion

* Update metrics.rst

Co-authored-by: Sean Naren <sean.narenthiran@gmail.com>
* add option to log momentum

* add docstring

* refactor for cleanliness

Co-authored-by: Nicki Skafte <skaftenicki@gmail.com>
* ananyahjha93 and teddykoker to codeowners for metrics

* add Justus

Co-authored-by: Sean Naren <sean.narenthiran@gmail.com>
* feat(wandb): log in sync with Trainer step

* docs: update CHANGELOG

* style(test_wandb): fix formatting

* parentheses

Co-authored-by: Adrian Wälchli <aedu.waelchli@gmail.com>
Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>
* use move_data_to_device instead of to; docstring also allow tuple of Tensor; not supported log error when example_inputs is a dict; commented docstring trace example

* Use isinstance to check if example_inputs is a Mapping, instead of type

Co-authored-by: Justus Schock <12886177+justusschock@users.noreply.github.com>

* import Mapping for isinstance check

* multi-line docstring code to test TorchScript trace()

* Fix PEP8 f-string is missing placeholders

* minor code style improvements

* Use (possibly user overwritten) transfer_batch_to_device instead of move_data_to_device

Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>

* fixed weird comment about trace() log error

* Remove unused import

Co-authored-by: Jeff Yang <ydcjeff@outlook.com>

* Remove logger warning about dict not example_inputs not supported by trace

Co-authored-by: stef-ubuntu <stef@webempath.com>
Co-authored-by: Justus Schock <12886177+justusschock@users.noreply.github.com>
Co-authored-by: Adrian Wälchli <aedu.waelchli@gmail.com>
Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>
Co-authored-by: Jeff Yang <ydcjeff@outlook.com>
Co-authored-by: Jeff Yang <ydcjeff@outlook.com>
* fix: `nb` is set total number of devices, when nb is -1.

 Refs: #4207

* feat: add test code
     1. test combination `auto_select_gpus`, `gpus` options using
Trainer
     2. test `pick_multiple_gpus` function directly

Refs: #4207

* docs: modify contents in `Select GPU devices`

 Refs: #4207

* refactore: reflect the reuslt of review

 Refs: #4207

* refactore: reflect the reuslt of review

 Refs: #4207

* Update CHANGELOG.md

Co-authored-by: chaton <thomas@grid.ai>
Co-authored-by: Roger Shieh <55400948+s-rog@users.noreply.github.com>
Co-authored-by: Nicki Skafte <skaftenicki@gmail.com>
* ddp no-sync

* Update pytorch_lightning/trainer/training_loop.py

Co-authored-by: ananthsub <ananth.subramaniam@gmail.com>

* Update training_loop.py

* factor __enter__ and __exit__ out to separate context manager

* delete _updated_model_last_step

Co-authored-by: justusschock <justusschock@pc125.lfb.rwth-aachen.de>
Co-authored-by: Teddy Koker <teddy.koker@gmail.com>
Co-authored-by: ananthsub <ananth.subramaniam@gmail.com>
Co-authored-by: chaton <thomas@grid.ai>
Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>
* distributed_backend -> accelerator

* distributed_backend -> accelerator

* use_amp -> precision

* format

Co-authored-by: rohitgr7 <rohitgr1998@gmail.com>
…back=...) (#4336)

* first attempt

* update tests

* support multiple

* test bugfix

* changelog

* pep

* pep

* import order

* import

* improve test for resuming

* test

* update test

* add references test

Co-authored-by: Carlos Mocholí <carlossmocholi@gmail.com>

* docstring suggestion deprecation

Co-authored-by: Jeff Yang <ydcjeff@outlook.com>

* paramref

Co-authored-by: Carlos Mocholí <carlossmocholi@gmail.com>
Co-authored-by: Jeff Yang <ydcjeff@outlook.com>
* docs + precision + recall + f_beta + refactor

Co-authored-by: Teddy Koker <teddy.koker@gmail.com>

* rebase

Co-authored-by: Teddy Koker <teddy.koker@gmail.com>

* fixes

Co-authored-by: Teddy Koker <teddy.koker@gmail.com>

* added missing file

* docs

* docs

* extra import

* add confusion matrix

* add to docs

* add test

* pep8 + isort

* update tests

* move util function

* unify functional and class

* add to init

* remove old implementation

* update tests

* pep8

* add duplicate

* fix doctest

* Update pytorch_lightning/metrics/classification/confusion_matrix.py

Co-authored-by: Justus Schock <12886177+justusschock@users.noreply.github.com>

* changelog

* bullet point args

* bullet docs

* bullet docs

Co-authored-by: ananyahjha93 <ananya@pytorchlightning.ai>
Co-authored-by: Teddy Koker <teddy.koker@gmail.com>
Co-authored-by: Justus Schock <12886177+justusschock@users.noreply.github.com>
Co-authored-by: chaton <thomas@grid.ai>
Co-authored-by: Roger Shieh <55400948+s-rog@users.noreply.github.com>
Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>
* changelog 1.0.4

* changelog 1.0.4
* prepare for 1.7 support [ci skip]

* tpu [ci skip]

* test run 1.7

* all 1.7, needs to fix tests

* couple with torchvision

* windows try

* remove windows

* 1.7 is here

* on purpose fail [ci skip]

* return [ci skip]

* 1.7 docker

* back to normal [ci skip]

* change to some_val [ci skip]

* add seed [ci skip]

* 4 places [ci skip]

* fail on purpose [ci skip]

* verbose=True [ci skip]

* use filename to track

* use filename to track

* monitor epoch + changelog

* Update tests/checkpointing/test_model_checkpoint.py

Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>

Co-authored-by: Sean Naren <sean.narenthiran@gmail.com>
Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>
* Add functional multiclass AUROC metric

* Add multiclass_auroc tests

* fixup! Add functional multiclass AUROC metric

* fixup! fixup! Add functional multiclass AUROC metric

* Add multiclass_auroc doc reference

* Update CHANGELOG

* formatting

* Shorter error message regex match in tests

* Set num classes as pytest parameter

* formatting

* Update CHANGELOG

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>
Co-authored-by: Nicki Skafte <skaftenicki@gmail.com>
* lock cuda version

* back to normal
Co-authored-by: Jeff Yang <ydcjeff@outlook.com>
* timeout for tpu check

* added tests

* updated CHANGELOG.md

* fixed windows tests

* Update pytorch_lightning/utilities/xla_device_utils.py

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>

* requested changes

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>
Co-authored-by: Adrian Wälchli <aedu.waelchli@gmail.com>
* docs update

* update callbacks docs

* docs

* notebook examples

* warning

* line lenght

* update deprecation

Co-authored-by: Sean Naren <sean.narenthiran@gmail.com>
Co-authored-by: Roger Shieh <55400948+s-rog@users.noreply.github.com>
tchaton and others added 29 commits November 5, 2020 22:27
* update logging

* solve more bugs

* replace Mapping by Dict

* update on comments

* resolve pep8

* Apply suggestions from code review

Co-authored-by: ananthsub <ananth.subramaniam@gmail.com>

* Update pytorch_lightning/trainer/connectors/logger_connector/epoch_result_store.py

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>

* update on comments

* typo

* update for coverage

* update test

* update

* Update tests/models/test_hooks.py

Co-authored-by: Sean Naren <sean.narenthiran@gmail.com>

* Update tests/models/test_hooks.py

Co-authored-by: Sean Naren <sean.narenthiran@gmail.com>

* update on comments

* remove deepcopy

* remove useless look for

* another small optim

* extra optim

* remove lastest optim, can be source of bug

* resolve bug

* add docstring

* optimize coverage

* Update pytorch_lightning/trainer/connectors/logger_connector/epoch_result_store.py

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>

* Update pytorch_lightning/trainer/connectors/logger_connector/epoch_result_store.py

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>

* Update tests/trainer/logging_tests/test_distributed_logging.py

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>

* Update pytorch_lightning/trainer/evaluation_loop.py

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>

* Update tests/trainer/logging/test_logger_connector.py

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>

* Update tests/trainer/logging_tests/test_train_loop_logging_1_0.py

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>

* update on comments

* update

* update on comments

* update parity speed

* get it down to 0.65

* update

* 0.8 max_dif

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>
Co-authored-by: ananthsub <ananth.subramaniam@gmail.com>
Co-authored-by: Sean Naren <sean.narenthiran@gmail.com>
Co-authored-by: William Falcon <waf2107@columbia.edu>
Co-authored-by: chaton <thomas@grid.ai>
Co-authored-by: Adrian Wälchli <aedu.waelchli@gmail.com>
* add MNIST DALI example, update README.md

* Fix PEP8 warnings

* reformatted using black

* add mnist_dali to test_examples.py

* Add documentation as docstrings

* add nvidia-pyindex and nvidia-dali-cuda100

* replace nvidia-pyindex with --extra-index-url

* mark mnist_dali test as Linux and GPU only

* adjust CUDA docker and examples.txt, fix import error in test_examples.py

* adjust the GPU check

* Exit when DALI is not available

* remove requirements-examples.txt and DALI pip install

* Refactored example, moved to new logging api, added runtime check for test and dali script

* Patch to reflect the mnist example module

* add req.

* Apply suggestions from code review

* Removed requirement as it breaks CPU install, added note in README to install DALI

* add DALI to Drone

* test examples

* Apply suggestions from code review

* imports

* ABC

* cuda

* cuda

* pip DALI

* Move build into init function

Co-authored-by: SeanNaren <sean@grid.ai>
Co-authored-by: Jirka Borovec <jirka@pytorchlightning.ai>
Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>
Co-authored-by: Sean Naren <sean.narenthiran@gmail.com>
* add congratulations at the end of our notebooks

* udpate image
* added log_dir shortcut to trainer properties for writing logs

* added log_dir shortcut

* added log_dir shortcut

* added log_dir shortcut

* added log_dir shortcut

* added log_dir shortcut

* added log_dir shortcut

* added log_dir shortcut

* added log_dir shortcut
* ref: unify slurm and TE under backendPlugin

* ref: unify slurm and TE under backendPlugin
* ref: unify slurm and TE under backendPlugin 4/n

* ref: unify slurm and TE under backendPlugin 5/n
* accelerator docs

* accelerator docs
* note

* Update docs/source/metrics.rst

Co-authored-by: chaton <thomas@grid.ai>
Co-authored-by: Sean Naren <sean.narenthiran@gmail.com>
Co-authored-by: Jeff Yang <ydcjeff@outlook.com>
PyTorch Forecasting is a new library that is designed for time series forecasting practitioners and researchers alike.
It is based on the awesome work on PyTorch Lightning. Thanks a lot for creating such an asset!

Have a look at the documentation for more information.

Co-authored-by: chaton <thomas@grid.ai>
Co-authored-by: Jeff Yang <ydcjeff@outlook.com>
Co-authored-by: Jeff Yang <ydcjeff@outlook.com>
Co-authored-by: stef-ubuntu <stef@webempath.com>
Co-authored-by: Jeff Yang <ydcjeff@outlook.com>
Co-authored-by: Nicki Skafte <skaftenicki@gmail.com>
* [dockers] install nvidia-dali-cuda100

* Apply suggestions from code review

* build DALI

* build DALI

* build DALI

* dali from source

* dali from source

* use binaries

* qq

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>
Co-authored-by: Jirka Borovec <jirka@pytorchlightning.ai>
Co-authored-by: Sean Naren <sean.narenthiran@gmail.com>
* Add missing load functionality in hpc

* Add general file load for hpc

* Add mark in CHANGELOG

* Fix Typo Li**hg**tning

Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>

* Refactor line separation

Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>

* Fix entangled fixation commit

* Fix naming of restore_model_states

* Fix amp restore place

Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>
Co-authored-by: chaton <thomas@grid.ai>
* skip on fast dev

* fix error

* changelog

* fix recursive issue

* combine tests

* pep8

* move logic to base funcs

* fix mistake

* Update pytorch_lightning/tuner/lr_finder.py

Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>

* pep

Co-authored-by: William Falcon <waf2107@columbia.edu>
Co-authored-by: Nicki Skafte <nugginea@gmail.com>
Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>
Co-authored-by: chaton <thomas@grid.ai>
* changes

* fix spelling

* small note

* trying to fix ddp test

* fix ddp

* fix for test

* suggestion

* CHANGELOG

* Update pytorch_lightning/metrics/metric.py

Co-authored-by: chaton <thomas@grid.ai>
Co-authored-by: Sean Naren <sean.narenthiran@gmail.com>
Co-authored-by: Sean Naren <sean@grid.ai>
…allback (#4560)

* replace MisconfigurationException with warning

* update test

* check raising UserWarning

Co-authored-by: chaton <thomas@grid.ai>
Co-authored-by: Nicki Skafte <skaftenicki@gmail.com>
Co-authored-by: Nicki Skafte <skaftenicki@gmail.com>
* [#4411] fix gpu_log_memory with mlflow logger

* sanitize parenthesis instead of removing for all loggers

* apply regex for mlflow key sanitization

* replace ',' with '.' typo

* add single warning and test

Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>
Co-authored-by: chaton <thomas@grid.ai>
…4347)

* search for attribute in datamodule if not found elsewhere

* add test for datamodule

* add lightning_getattr test for datamodule

* Apply suggestions from code review

Co-authored-by: Adrian Wälchli <aedu.waelchli@gmail.com>

* Update CHANGELOG.md

* Update CHANGELOG.md

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>
Co-authored-by: Nicki Skafte <skaftenicki@gmail.com>
Co-authored-by: Adrian Wälchli <aedu.waelchli@gmail.com>
Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>
* fix mock pkgs in docs

* sphinx

* CI

Co-authored-by: chaton <thomas@grid.ai>
* resolve bug

* add self._running_manual_optim

* update

* update tests

* update lightning module

* resolve bug

* update tests

* update

* resolve pep8

* update

* replace by `ddp_spawn`

* temporary fix

* update

* update

* move update to training_loop

* make both ddp_spawn

* introduce `manual_optimizer_step`

* update changelog

* added changelog wrong place

* add force_optimizer_step

* update docstring for tests

* update optimizer_step

* update zero_grad

* resolve flake8

* move update into manual_optimizer_step

* add zero_grad

* remove zero_grad tests

* remove manual_backward in AMP, it doesn't help

* update

* loosen tests

* update

* update doc

* add TODO

* Removed unnecessary get model from native amp

* Remove try except with pytest raise

* Add seed, clean up imports, remove try catch to reproduce error

* update code

* update test

* revert back

* formatting

* Update pytorch_lightning/core/lightning.py

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>

Co-authored-by: SeanNaren <sean@grid.ai>
Co-authored-by: Sean Naren <sean.narenthiran@gmail.com>
Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>
* move value to cpu to save memory

* update

* move to cpu

* try something

* update

* update

* add back out_dict.update({k: v})

* add move_metrics_to_cpu

* update

* Update pytorch_lightning/utilities/memory.py

Co-authored-by: Justus Schock <12886177+justusschock@users.noreply.github.com>

* resolve comments

* Update pytorch_lightning/core/step_result.py

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>

* Update pytorch_lightning/trainer/connectors/logger_connector/logger_connector.py

Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>

Co-authored-by: Justus Schock <12886177+justusschock@users.noreply.github.com>
Co-authored-by: Jirka Borovec <Borda@users.noreply.github.com>
Co-authored-by: Sean Naren <sean.narenthiran@gmail.com>
@swethmandava swethmandava merged commit 282ce57 into swethmandava:master Nov 10, 2020
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