GitLab

[R-package] enable saving Booster with saveRDS() and loading it with readRDS() (fixes #4296) (#4685)

* idiomatic serialization

* linter

* linter, namespace

* comments, linter, fix failing test

* standardize error messages for null handles

* auto-restore handle in more functions

* linter

* missing declaration

* correct wrong signature

* fix docs

* Update R-package/R/lgb.train.R
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Update R-package/R/lgb.drop_serialized.R
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Update R-package/R/lgb.restore_handle.R
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Update R-package/R/lgb.restore_handle.R
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Update R-package/R/lgb.make_serializable.R
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* move 'restore_handle' from feature importance to dump method

* missing header

* move arguments order, update docs

* linter

* avoid leaving files in working directory

* add test for save_model=NULL

* missing comma

* Update R-package/R/lgb.restore_handle.R
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* Update R-package/src/lightgbm_R.cpp
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* change name of error function

* update comment

* restore old serialization functions but set as deprecated

* Update R-package/R/readRDS.lgb.Booster.R
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* Update R-package/R/saveRDS.lgb.Booster.R
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* update docs

* Update R-package/R/readRDS.lgb.Booster.R
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Update R-package/R/saveRDS.lgb.Booster.R
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Update R-package/tests/testthat/test_basic.R
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Update R-package/R/readRDS.lgb.Booster.R
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* comments

* fix variable name

* restore serialization test for linear models

* Update R-package/R/lightgbm.R
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* update docs

* fix issues with null terminator
Co-authored-by: James Lamb <jaylamb20@gmail.com>
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* add C API function that returns all param names with aliases

* add C API function that returns all param names with aliases

* add R code

* test R code

* remove debug CI

* fix R lint

* refactor

* run CI

* fix R

* fix

* revert CI checks

* revert changes in docs

* Try to make function `const`
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* add `const` in cpp file

* address review comments and sync with `master`
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* [python-package] fix mypy errors in engine.py

* Apply suggestions from code review
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* allow for stdv

* whitespace
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* [python-package] fix mypy errors in sklearn.py

* use ignore comments

* in predict(), respect params set via `set_params()` after fit()

* continue

* add test

* fix return name

* hotfix

* simplify

* fix argument types in custom eval function for Dask estimators

* revert changes to docstrings

* fix argument names in Dask test

* [python-package] fix mypy errors in plotting.py

* empty commit

* [python-package] fix mypy error about missing type hint in dask.py

* list of lists

* use different variable

* use append()

* Update __init__.py

* Update callback.py

* Update sklearn.py

* Update engine.py

* Update sklearn.py

* Update engine.py

* Update basic.py

* Update engine.py

* Update test_plotting.py

* Update dask.py

* Update sklearn.py

* Update test_sklearn.py

* Update basic.py

* Update engine.py

* Update test_engine.py

* Update basic.py

* Update basic.py

* Update engine.py

* update dependencies

* Update DESCRIPTION

* Update .vsts-ci.yml

* Update .vsts-ci.yml

* Update .vsts-ci.yml

* Update .vsts-ci.yml

* Update .vsts-ci.yml

* Try `RD` and `RDscript`

* Update .vsts-ci.yml
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* [R-package] [docs] add intro vignette (#3946)

* add 10 test vignettes

* Revert "add 10 test vignettes"

This reverts commit 40fb2e2f1982402798776ee44e4ec82fc4644d3d.

* Apply suggestions from code review
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>
Co-authored-by: Michael Mayer <mayermichael79@gmail.com>
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* Update get_workflow_status.py

* Update get_workflow_status.py

* add customized parser support

* fix typo of parser_config_file description

* make delimiter as parameter of JoinedLines

* [python] add type hints for custom objective and metric functions in scikit-learn interface

* update type hints

* remote unnecessary input

* Update python-package/lightgbm/sklearn.py
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* remove type hint on objective being callable
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* [c_api] Improve ANSI compatibility by avoiding <stdbool.h>

* fixes in response to CI linting

* inline NOLINT instead of separate test

* moving length declaration to non-ANSI C conditional

* [c_api] Align expected return type in `basic.py` with new c_api type.

* Update test.sh

* Update test.sh

* Update test.sh

* Update FindLibR.cmake

* Update r_package.yml

* Update FindLibR.cmake

* Update r_package.yml

* Update CMakeLists.txt

* Update CMakeLists.txt

* Update static_analysis.yml

* Update CMakeLists.txt

* Update test.sh

* Update CMakeLists.txt

* Update static_analysis.yml

* Update CMakeLists.txt

* Update cuda.yml

* Update CMakeLists.txt

* Update CMakeLists.txt

* Update cuda.yml

* Update Sanitizer.cmake

* Update FindLibR.cmake

* Update IntegratedOpenCL.cmake

* Update FindLibR.cmake

* Update CMakeLists.txt

* Update FindLibR.cmake

* Update static_analysis.yml

* Update CMakeLists.txt

* Update FindLibR.cmake

* Update IntegratedOpenCL.cmake

* Update static_analysis.yml

* Update CMakeLists.txt

* Update FindLibR.cmake

* add print and summary S3 method

* correct wrong signature

* attempt at bypassing linter

* Update R-package/R/lgb.Booster.R
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Update R-package/src/lightgbm_R.h
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Update include/LightGBM/c_api.h
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* add more tests

* linter

* don't pluralize single tree

* remove duplicated function

* update changed function name

* missing declaration

* Update lightgbm_R.h

* Update R-package/tests/testthat/test_lgb.Booster.R
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* accommodate custom objectives in print

* linter

* linter
Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Faster categorical column names selection (#1)

* Faster categorical column names selection

Change slow and redundant dataframe query by select_dtypes into a dataframe.dtypes list comprehension

* Update compat with CategoricalDtype

* sort imports

* import CategoricalDtype from pandas.api.types

* add categorical import try/except

* Add 'nrounds' as an alias for 'num_iterations'

* Improve tests

* Compare against nrounds directly

* Fix whitespace lints

* initial changes

* initial version

* better handling of cases

* warn only with positive threshold

* remove early_stopping_threshold from high-level functions

* remove remaining early_stopping_threshold

* update test to use callback

* better handling of cases

* rename threshold to min_delta

enhance parameter description

update tests

* Apply suggestions from code review
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* reduce num_boost_round in tests

* Apply suggestions from code review
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* trigger ci
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>
Co-authored-by: Nikita Titov <nekit94-12@hotmail.com>

* respect objective aliases

* Update test_sklearn.py

* revert removal of blank lines

* add argument name which is being overwritten in warning message

* cmake: use object library to avoid duplicate compilation.

* debug: verbose make log for building r package.

* Include /usr/local/include for AppleClang.

* Revert "debug: verbose make log for building r package."

* update cmake comment and fix indentation

* debug cmake USE_DEBUG.

* Revert "debug cmake USt E_DEBUG."

* Add -fPIC for building shared library.

* Always set -fPIC for non MSVC compiler.

* debug: print exception in setup.py

* debug: print cmake output for vs build.

* debug: set opencl related target_xxx on lightgbm_objs.

* Define compile definitions, link libraries on lightgbm_objs.

* Add PUBLIC to target_link_libraries to expose library dependency.

* Use target_link_libraries on object library.

This should propagate usage requirements.

* Fix CUDA linking.

Linking object library (lightgbm_objs) to object library (histograms)
does not linked objects.

* Use PUBLIC link for lightgbm lib.

* Set cuda related properties on final targets.

* Remove debugging changes.

Revert "debug: print exception in setup.py"
Revert "debug: print cmake output for vs build."
etc.

* Remove -D_lightgbm_EXPORTS.

* Revert to add -fPIC only for NOT USE_DEBUG.

* Enable PIC for shared lib.

* Fix enable PIC.

* Use -fPIC for shared lib.

* testlightgbm depends only on object files.

* tweak build for R.

* Try to remove OpenMP related include dir settings.

* link with openmp for capi object library.

* Use PUBLIC for _lightgbm target_link_libraries.

* Try removing exports definition.

* fix typo
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* fix typo
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* Add some comments for cmake code.

* Try to fix cmake warnings CUDA.

* revert accidentally commited R-package path change.

* Try to fix cmake CUDA warnings, set for _lightgbm target.

* Try to fix cmake CUDA warnings, set for lightgbm target.

* empty commit to trigger ci
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* [R-package] parallelize compilation in CMake-based builds

* Apply suggestions from code review
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* working on adding -j

* pass -j through to install.libs.R

* add docs on -j

* use -j4

* Update R-package/README.md
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>