Don't support 'nan' in data file #1
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rvb
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Feb 14, 2019
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guolinke
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Dec 8, 2020
* Fix LightGBM models locale sensitivity and improve R/W performance.
When Java is used, the default C++ locale is broken. This is true for
Java providers that use the C API or even Python models that require JEP.
This patch solves that issue making the model reads/writes insensitive
to such settings.
To achieve it, within the model read/write codebase:
- C++ streams are imbued with the classic locale
- Calls to functions that are dependent on the locale are replaced
- The default locale is not changed!
This approach means:
- The user's locale is never tampered with, avoiding issues such as
#2979 with the previous
approach #2891
- Datasets can still be read according the user's locale
- The model file has a single format independent of locale
Changes:
- Add CommonC namespace which provides faster locale-independent versions of Common's methods
- Model code makes conversions through CommonC
- Cleanup unused Common methods
- Performance improvements. Use fast libraries for locale-agnostic conversion:
- value->string: https://github.com/fmtlib/fmt
- string->double: https://github.com/lemire/fast_double_parser (10x
faster double parsing according to their benchmark)
Bugfixes:
- #2500
- #2890
- ninia/jep#205 (as it is related to LGBM as well)
* Align CommonC namespace
* Add new external_libs/ to python setup
* Try fast_double_parser fix #1
Testing commit e09e5aad828bcb16bea7ed0ed8322e019112fdbe
If it works it should fix more LGBM builds
* CMake: Attempt to link fmt without explicit PUBLIC tag
* Exclude external_libs from linting
* Add exernal_libs to MANIFEST.in
* Set dynamic linking option for fmt.
* linting issues
* Try to fix lint includes
* Try to pass fPIC with static fmt lib
* Try CMake P_I_C option with fmt library
* [R-package] Add CMake support for R and CRAN
* Cleanup CMakeLists
* Try fmt hack to remove stdout
* Switch to header-only mode
* Add PRIVATE argument to target_link_libraries
* use fmt in header-only mode
* Remove CMakeLists comment
* Change OpenMP to PUBLIC linking in Mac
* Update fmt submodule to 7.1.2
* Use fmt in header-only-mode
* Remove fmt from CMakeLists.txt
* Upgrade fast_double_parser to v0.2.0
* Revert "Add PRIVATE argument to target_link_libraries"
This reverts commit 3dd45dd.
* Address James Lamb's comments
* Update R-package/.Rbuildignore
Co-authored-by: James Lamb <[email protected]>
* Upgrade to fast_double_parser v0.3.0 - Solaris support
* Use legacy code only in Solaris
* Fix lint issues
* Fix comment
* Address StrikerRUS's comments (solaris ifdef).
* Change header guards
Co-authored-by: James Lamb <[email protected]>
StrikerRUS
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Mar 25, 2021
* [docs]Add alt text on images * Update docs/GPU-Windows.rst Co-authored-by: James Lamb <[email protected]> * Update docs/GPU-Windows.rst Co-authored-by: James Lamb <[email protected]> * Apply suggestions from code review Co-authored-by: James Lamb <[email protected]> * Apply suggestions from code review Co-authored-by: James Lamb <[email protected]> * Merge main branch commit updates (#1) * [docs] Add alt text to image in Parameters-Tuning.rst (#4035) * [docs] Add alt text to image in Parameters-Tuning.rst Add alt text to Leaf-wise growth image, as part of #4028 * Update docs/Parameters-Tuning.rst Co-authored-by: James Lamb <[email protected]> Co-authored-by: James Lamb <[email protected]> * [ci] [R-package] upgrade to R 4.0.4 in CI (#4042) * [docs] update description of deterministic parameter (#4027) * update description of deterministic parameter to require using with force_row_wise or force_col_wise * Update include/LightGBM/config.h Co-authored-by: Nikita Titov <[email protected]> * update docs Co-authored-by: Nikita Titov <[email protected]> * [dask] Include support for init_score (#3950) * include support for init_score * use dataframe from init_score and test difference with and without init_score in local model * revert refactoring * initial docs. test between distributed models with and without init_score * remove ranker from tests * test value for root node and change docs * comma * re-include parametrize * fix incorrect merge * use single init_score and the booster_ attribute * use np.float64 instead of float * [ci] ignore untitle Jupyter notebooks in .gitignore (#4047) * [ci] prevent getting incompatible dask and distributed versions (#4054) * [ci] prevent getting incompatible dask and distributed versions * Update .ci/test.sh Co-authored-by: Nikita Titov <[email protected]> * empty commit Co-authored-by: Nikita Titov <[email protected]> * [ci] fix R CMD CHECK note about example timings (fixes #4049) (#4055) * [ci] fix R CMD CHECK note about example timings (fixes #4049) * Apply suggestions from code review Co-authored-by: Nikita Titov <[email protected]> * empty commit Co-authored-by: Nikita Titov <[email protected]> * [ci] add CMake + R 3.6 test back (fixes #3469) (#4053) * [ci] add CMake + R 3.6 test back (fixes #3469) * Apply suggestions from code review Co-authored-by: Nikita Titov <[email protected]> * Update .ci/test_r_package_windows.ps1 * -Wait and remove rtools40 * empty commit Co-authored-by: Nikita Titov <[email protected]> * [dask] include multiclass-classification task in tests (#4048) * include multiclass-classification task and task_to_model_factory dicts * define centers coordinates. flatten init_scores within each partition for multiclass-classification * include issue comment and fix linting error * Update index.rst (#4029) Add alt text to logo image Co-authored-by: James Lamb <[email protected]> * [dask] raise more informative error for duplicates in 'machines' (fixes #4057) (#4059) * [dask] raise more informative error for duplicates in 'machines' * uncomment * avoid test failure * Revert "avoid test failure" This reverts commit 9442bdf. * [dask] add tutorial documentation (fixes #3814, fixes #3838) (#4030) * [dask] add tutorial documentation (fixes #3814, fixes #3838) * add notes on saving the model * quick start examples * add examples * fix timeouts in examples * remove notebook * fill out prediction section * table of contents * add line back * linting * isort * Apply suggestions from code review Co-authored-by: Nikita Titov <[email protected]> * Apply suggestions from code review Co-authored-by: Nikita Titov <[email protected]> * move examples under python-guide * remove unused pickle import Co-authored-by: Nikita Titov <[email protected]> * set 'pending' commit status for R Solaris optional workflow (#4061) * [docs] add Yu Shi to repo maintainers (#4060) * Update FAQ.rst * Update CODEOWNERS * set is_linear_ to false when it is absent from the model file (fix #3778) (#4056) * Add CMake option to enable sanitizers and build gtest (#3555) * Add CMake option to enable sanitizer * Set up gtest * Address reviewer's feedback * Address reviewer's feedback * Update CMakeLists.txt Co-authored-by: Nikita Titov <[email protected]> Co-authored-by: Nikita Titov <[email protected]> * added type hint (#4070) * [ci] run Dask examples on CI (#4064) * Update Parallel-Learning-Guide.rst * Update test.sh * fix path * address review comments * [python-package] add type hints on Booster.set_network() (#4068) * [python-package] add type hints on Booster.set_network() * change behavior * [python-package] Some mypy fixes (#3916) * Some mypy fixes * address James' comments * Re-introduce pass in empty classes * Update compat.py Remove extra lines * [dask] [ci] fix flaky network-setup test (#4071) * [tests][dask] simplify code in Dask tests (#4075) * simplify Dask tests code * enable CI * disable CI * Revert "[ci] prevent getting incompatible dask and distributed versions (#4054)" (#4076) This reverts commit 4e9c976. * Fix parsing of non-finite values (#3942) * Fix index out-of-range exception generated by BaggingHelper on small datasets. Prior to this change, the line "score_t threshold = tmp_gradients[top_k - 1];" would generate an exception, since tmp_gradients would be empty when the cnt input value to the function is zero. * Update goss.hpp * Update goss.hpp * Add API method LGBM_BoosterPredictForMats which runs prediction on a data set given as of array of pointers to rows (as opposed to existing method LGBM_BoosterPredictForMat which requires data given as contiguous array) * Fix incorrect upstream merge * Add link to LightGBM.NET * Fix indenting to 2 spaces * Dummy edit to trigger CI * Dummy edit to trigger CI * remove duplicate functions from merge * Fix parsing of non-finite values. Current implementation silently returns zero when input string is "inf", "-inf", or "nan" when compiled with VS2017, so instead just explicitly check for these values and fail if there is no match. No attempt to optimise string allocations in this implementation since it is usually rarely invoked. * Dummy commit to trigger CI * Also handle -nan in double parsing method * Update include/LightGBM/utils/common.h Remove trailing whitespace to pass linting tests Co-authored-by: Nikita Titov <[email protected]> Co-authored-by: matthew-peacock <[email protected]> Co-authored-by: Guolin Ke <[email protected]> Co-authored-by: Nikita Titov <[email protected]> * [dask] remove unused imports from typing (#4079) * Range check for DCG position discount lookup (#4069) * Add check to prevent out of index lookup in the position discount table. Add debug logging to report number of queries found in the data. * Change debug logging location so that we can print the data file name as well. * Revert "Change debug logging location so that we can print the data file name as well." This reverts commit 3981b34. * Add data file name to debug logging. * Move log line to a place where it is output even when query IDs are read from a separate file. * Also add the out-of-range check to rank metrics. * Perform check after number of queries is initialized. * Update * [ci] upgrade R CI scripts to work on Ubuntu 20.04 (#4084) * [ci] install additional LaTeX packages in R CI jobs * update autoconf version * bump upper limit on package size to 100 * [SWIG] Add streaming data support + cpp tests (#3997) * [feature] Add ChunkedArray to SWIG * Add ChunkedArray * Add ChunkedArray_API_extensions.i * Add SWIG class wrappers * Address some review comments * Fix linting issues * Move test to tests/test_ChunkedArray_manually.cpp * Add test note * Move ChunkedArray to include/LightGBM/utils/ * Declare more explicit types of ChunkedArray in the SWIG API. * Port ChunkedArray tests to googletest * Please C++ linter * Address StrikerRUS' review comments * Update SWIG doc & disable ChunkedArray<int64_t> * Use CHECK_EQ instead of assert * Change include order (linting) * Rename ChunkedArray -> chunked_array files * Change header guards * Address last comments from StrikerRUS * store all CMake files in one place (#4087) * v3.2.0 release (#3872) * Update VERSION.txt * update appveyor.yml and configure * fix Appveyor builds Co-authored-by: James Lamb <[email protected]> Co-authored-by: Nikita Titov <[email protected]> Co-authored-by: StrikerRUS <[email protected]> * [ci] Bump version for development (#4094) * Update .appveyor.yml * Update cran-comments.md * Update VERSION.txt * update configure Co-authored-by: James Lamb <[email protected]> * [ci] fix flaky Azure Pipelines jobs (#4095) * Update test.sh * Update setup.sh * Update .vsts-ci.yml * Update test.sh * Update setup.sh * Update .vsts-ci.yml * Update setup.sh * Update setup.sh Co-authored-by: Subham Agrawal <[email protected]> Co-authored-by: James Lamb <[email protected]> Co-authored-by: shiyu1994 <[email protected]> Co-authored-by: Nikita Titov <[email protected]> Co-authored-by: jmoralez <[email protected]> Co-authored-by: marcelonieva7 <[email protected]> Co-authored-by: Philip Hyunsu Cho <[email protected]> Co-authored-by: Deddy Jobson <[email protected]> Co-authored-by: Alberto Ferreira <[email protected]> Co-authored-by: mjmckp <[email protected]> Co-authored-by: matthew-peacock <[email protected]> Co-authored-by: Guolin Ke <[email protected]> Co-authored-by: ashok-ponnuswami-msft <[email protected]> Co-authored-by: StrikerRUS <[email protected]> * Apply suggestions from code review Co-authored-by: Nikita Titov <[email protected]> Co-authored-by: James Lamb <[email protected]> Co-authored-by: Subham Agrawal <[email protected]> Co-authored-by: shiyu1994 <[email protected]> Co-authored-by: Nikita Titov <[email protected]> Co-authored-by: jmoralez <[email protected]> Co-authored-by: marcelonieva7 <[email protected]> Co-authored-by: Philip Hyunsu Cho <[email protected]> Co-authored-by: Deddy Jobson <[email protected]> Co-authored-by: Alberto Ferreira <[email protected]> Co-authored-by: mjmckp <[email protected]> Co-authored-by: matthew-peacock <[email protected]> Co-authored-by: Guolin Ke <[email protected]> Co-authored-by: ashok-ponnuswami-msft <[email protected]> Co-authored-by: StrikerRUS <[email protected]>
shiyu1994
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Nov 12, 2021
* 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
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