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Author SHA1 Message Date
Jiaming Yuan beefd28471 Split up SHAP from RegTree. (#8612) 
* Split up SHAP from `RegTree`.

Simplify the tree interface.
 2023-01-04 18:17:47 +08:00
Jiaming Yuan d308124910 Refactor PySpark tests. (#8605) 
- Convert classifier tests to pytest tests.
- Replace hardcoded tests.
 2023-01-04 17:05:16 +08:00
Jiaming Yuan 6eaddaa9c3 [CI] Fix CI with updated dependencies. (#8631) 
* [CI] Fix CI with updated dependencies.

- Fix jvm package get iris.

* Skip SHAP test for now.

* Revert "Skip SHAP test for now."

This reverts commit 9aa28b4d8aee53fa95d92d2a879c6783ff4b2faa.

* Catch all exceptions.
 2023-01-03 21:04:04 -08:00
Jiaming Yuan 8d545ab2a2 Implement fit stump. (#8607) 2023-01-04 04:14:51 +08:00
Jiaming Yuan c430ae52f3 Fix mypy errors with the latest numpy. (#8617) 2022-12-21 01:42:05 -08:00
Jiaming Yuan c6a8754c62 Define CUDA Context. (#8604) 
We will transition to non-default and non-blocking CUDA stream.
 2022-12-20 15:15:07 +08:00
Jiaming Yuan f6effa1734 Support Series and Python primitives in inplace_predict and QDM (#8547) 2022-12-17 00:15:15 +08:00
Jiaming Yuan a10e4cba4e Fix linalg iterator. (#8603) 2022-12-16 23:05:03 +08:00
Jiaming Yuan 38887a1876 Fix windows build on buildkite. (#8602) 2022-12-16 21:12:24 +08:00
Jiaming Yuan 43a647a4dd Fix inference with categorical feature. (#8591) 2022-12-15 17:57:26 +08:00
Jiaming Yuan 001e663d42 Set enable_categorical to True in predict. (#8592) 2022-12-15 05:27:06 +08:00
Jiaming YuanandPhilip Hyunsu Cho 40343c8ee1 Test dask demos. (#8557) 
Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
 2022-12-13 18:37:31 +08:00
Jiaming Yuan deb3edf562 Support list and tuple for QDM. (#8542) 2022-12-10 01:14:44 +08:00
Jiaming Yuan 8824b40961 Update date in release script. [skip ci] (#8574) 2022-12-09 23:16:10 +08:00
Jiaming Yuan 3e26107a9c Rename and extract Context. (#8528) 
* Rename `GenericParameter` to `Context`.
* Rename header file to reflect the change.
* Rename all references.
 2022-12-07 04:58:54 +08:00
Jiaming Yuan e38fe21e0d Cleanup regression objectives. (#8539) 2022-12-07 01:05:42 +08:00
Jiaming Yuan d99bdd1b1e [CI] Fix github action mismatched glibcxx. (#8551) 
* [CI] Fix github action mismatched glibcxx.

Split up the Linux test to use the toolchain from conda forge.
 2022-12-06 17:42:15 +08:00
Jiaming Yuan 7ac52e674f [doc] Update model schema. (#8538) 
* Update model schema with `num_target`.
 2022-12-06 11:35:07 +08:00
Jiaming Yuan 8afcecc025 [doc] Fix outdated document [skip ci] (#8527) 
* [doc] Fix document around categorical parameters. [skip ci]

* note on validate parameter [skip ci]

* Fix dask doc as well [skip ci]
 2022-12-06 00:56:17 +08:00
Jiaming Yuan e143a4dd7e [pyspark] Refactor local tests. (#8525) 
- Use pytest fixture for spark session.
- Replace hardcoded results.
 2022-12-05 23:49:54 +08:00
Jiaming Yuan e3bf5565ab Extract transform iterator. (#8498) 2022-12-05 21:37:07 +08:00
Jiaming Yuan d8544e4d9e [R] Remove unused assert definition. (#8526) 2022-12-05 20:29:03 +08:00
Jiaming Yuan 157e98edf7 Support half type from cupy. (#8487) 2022-11-30 17:56:42 +08:00
Jiaming Yuan addaa63732 Support null value in CUDA array interface. (#8486) 
* Support null value in CUDA array interface.

- Fix for potential null value in array interface.
- Fix incorrect check on mask stride.

* Simple tests.

* Extract mask.
 2022-11-28 17:48:25 -08:00
Jiaming Yuan 3fc1046fd3 Reduce compiler warnings on CPU-only build. (#8483) 2022-11-29 00:04:16 +08:00
Jiaming Yuan d666ba775e Support all pandas nullable integer types. (#8480) 
- Enumerate all pandas integer types.
- Tests for `None`, `nan`, and `pd.NA`
 2022-11-28 22:38:16 +08:00
Jiaming Yuan f2209c1fe4 Don't shuffle columns in categorical tests. (#8446) 2022-11-28 20:28:06 +08:00
Jiaming Yuan 8f97c92541 Support half type for pandas. (#8481) 2022-11-24 12:47:40 +08:00
Jiaming Yuan e07245f110 Take datatable as row major input. (#8472) 
* Take datatable as row major input.

Try to avoid a transform with dense table.
 2022-11-24 09:20:13 +08:00
Jiaming Yuan 284dcf8d22 Add script for change version. (#8443) 
- Replace jvm regex replacement script with mvn command.
- Replace cmake script for python version with python script.
- Automate rest of the manual steps.

The script can handle dev branch, rc release, and formal release version.
 2022-11-24 00:06:39 +08:00
Jiaming Yuan 5f1a6fca0d [R] Use new interface for creating DMatrix from CSR. (#8455) 
* [R] Use new interface for creating DMatrix from CSR.

- CSC is still using the old API.

The old API is not aware of `nthread` parameter, which makes DMatrix to use all available
thread during construction and during transformation lie `SparsePage` -> `CSCPage`.
 2022-11-23 21:36:43 +08:00
Jiaming Yuan 9dd8d70f0e Fix mypy errors. (#8444) 2022-11-09 13:19:11 +08:00
Jiaming YuanandHyunsu Cho 0252d504d8 Fix R package build on CI. (#8445) 
Co-authored-by: Hyunsu Cho <chohyu01@cs.washington.edu>
 2022-11-09 12:18:36 +08:00
Jiaming Yuan a83748eb45 [CI] Revise R tests. (#8430) 
- Use the standard package check (check on the tarball instead of the source tree).
- Run commands in parallel.
- Cleanup dependencies installation.
- Replace makefile.
- Documentation.
- Test using the image from rhub.
 2022-11-09 09:12:13 +08:00
Jiaming YuanandHyunsu Cho ca0f7f2714 [doc] Update C tutorial. [skip ci] (#8436) 
- Use rst references instead of doxygen links.
- Replace deprecated functions.

- Add SaveModel; put free step last [skip ci]

Co-authored-by: Hyunsu Cho <chohyu01@cs.washington.edu>
 2022-11-09 07:14:12 +08:00
Jiaming Yuan 0b36f8fba1 [R] Fix CRAN test notes. (#8428) 
- Limit the number of used CPU cores in examples.
- Add a note for the constraint.
- Bring back the cleanup script.
 2022-11-09 02:03:30 +08:00
Jiaming Yuan 0d3da9869c Require isort on all Python files. (#8420) 2022-11-08 12:59:06 +08:00
Jiaming YuanPhilip Hyunsu ChoRory Mitchell
 		917cbc0699 1.7 release note. [skip ci] (#8374) 
* Draft for 1.7 release note. [skip ci]

* Wording [skip ci]

* Update with backports [skip ci]

* Apply suggestions from code review [skip ci]

* Apply suggestions from code review [skip ci]

Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>

* Update NEWS.md [skip ci]

Co-authored-by: Rory Mitchell <r.a.mitchell.nz@gmail.com>

Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
Co-authored-by: Rory Mitchell <r.a.mitchell.nz@gmail.com>
 2022-10-31 09:32:33 -07:00
Jiaming Yuan 2ed3c29c8a [CI] Cleanup github action tests. (#8397) 
- Merge doxygen build with sphinx.
- Use mamba on non-windows Github Action.
 2022-10-29 06:04:27 +08:00
Jiaming Yuan a408c34558 Update JSON parser demo with categorical feature. (#8401) 
- Parse categorical features in the Python example.
- Add tests.
- Update document.
 2022-10-28 20:57:43 +08:00
Jiaming Yuan cfd2a9f872 Extract dask and spark test into distributed test. (#8395) 
- Move test files.
- Run spark and dask separately to prevent conflicts.
- Gather common code into the testing module.
 2022-10-28 16:24:32 +08:00
Jiaming Yuan f73520bfff Bump development version to 2.0. (#8390) 2022-10-28 15:21:19 +08:00
Jiaming Yuan a2593e60bf Speedup R test on github. (#8388) 2022-10-26 18:02:27 +08:00
Jiaming Yuan 786aa27134 [doc] Additional notes for release [skip ci] (#8367) 2022-10-26 17:55:15 +08:00
Jiaming YuanandHyunsu Philip Cho cf70864fa3 Move Python testing utilities into xgboost module. (#8379) 
- Add typehints.
- Fixes for pylint.

Co-authored-by: Hyunsu Philip Cho <chohyu01@cs.washington.edu>
 2022-10-26 16:56:11 +08:00
Jiaming YuanandPhilip Hyunsu Cho 7e53189e7c [pyspark] Improve tutorial on enabling GPU support. (#8385) 
- Quote the databricks doc on how to manage dependencies.
- Some wording changes.

Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
 2022-10-26 15:45:54 +08:00
Jiaming Yuan d0b99bdd95 [pyspark] Add type hint to basic utilities. (#8375) 2022-10-25 17:26:25 +08:00
Jiaming Yuan 1d2f6de573 remove travis status [skip ci] (#8382) 2022-10-24 14:37:33 +08:00
Jiaming Yuan a3b8bca46a Remove travis configuration file. [skip ci] (#8381) 2022-10-23 02:49:29 +08:00
Jiaming Yuan bb5e18c29c Fix CUDA async stream. (#8380) 2022-10-22 23:13:28 +08:00
Jiaming Yuan 99467f3999 [doc] Cleanup outdated documents for GPU. [skip ci] (#8378) 2022-10-21 20:13:31 +08:00
Jiaming Yuan 28a466ab51 Fixes for R checks. (#8330) 
- Bump configure.ac version.
- Remove amalgamation to reduce the build time for a single object with the added benefit that we can use parallel build during development.
- Fix c function prototype warning.
- Remove Windows automake file generation step to make the build script easier to understand.
 2022-10-20 02:52:54 +08:00
Jiaming Yuan c69af90319 Fix github action r tests. (#8364) 2022-10-20 01:07:18 +08:00
Jiaming Yuan c884b9e888 Validate features for inplace predict. (#8359) 2022-10-19 23:05:36 +08:00
Jiaming Yuan 3901f5d9db [pyspark] Cleanup data processing. (#8344) 
* Enable additional combinations of ctor parameters.
* Unify procedures for QuantileDMatrix and DMatrix.
 2022-10-18 14:56:23 +08:00
Jiaming Yuan 031d66ec27 Configuration for init estimation. (#8343) 
* Configuration for init estimation.

* Check whether the model needs configuration based on const attribute `ModelFitted`
instead of a mutable state.
* Add parameter `boost_from_average` to tell whether the user has specified base score.
* Add tests.
 2022-10-18 01:52:24 +08:00
Jiaming Yuan 2176e511fc Disable pytest-timeout for now. (#8348) 2022-10-17 23:06:10 +08:00
Jiaming Yuan fcddbc9264 FIx incorrect function name. (#8346) 2022-10-17 19:28:20 +08:00
Jiaming Yuan 748d516c50 [pyspark] Enable running GPU tests on variable number of GPUs. (#8335) 2022-10-13 21:03:45 +08:00
Jiaming Yuan 4633b476e9 [doc] Display survival demos in sphinx doc. [skip ci] (#8328) 2022-10-13 20:51:23 +08:00
Jiaming Yuan 3ef1703553 Allow using string view to find JSON value. (#8332) 
- Allow comparison between string and string view.
- Fix compiler warnings.
 2022-10-13 17:10:13 +08:00
Jiaming Yuan 97a5b088a5 [pyspark] Use quantile dmatrix. (#8284) 2022-10-12 20:38:53 +08:00
Jiaming Yuan c68684ff4c Update parameter for categorical feature. (#8285) 2022-10-10 19:48:29 +08:00
Jiaming Yuan 5545c49cfc Require keyword args for data iterator. (#8327) 2022-10-10 17:47:13 +08:00
Jiaming Yuan e1f9f80df2 Use gpu predictor for get csr test. (#8323) 2022-10-10 16:12:37 +08:00
Jiaming Yuan e47b3a3da3 Upgrade mypy. (#8302) 
Some breaking changes were made in mypy.
 2022-10-05 14:31:59 +08:00
Jiaming Yuan 97c3a80a34 Add C document to sphinx, fix arrow. (#8300) 
- Group C API.
- Add C API sphinx doc.
- Consistent use of `OptionalArg` and the parameter name `config`.
- Remove call to deprecated functions in demo.
- Fix some formatting errors.
- Add links to c examples in the document (only visible with doxygen pages)
- Fix arrow.
 2022-10-05 09:52:15 +08:00
Jiaming Yuan 299e5000a4 Fix buildkite label. (#8287) 2022-09-29 17:33:19 -07:00
Jiaming Yuan 55cf24cc32 Obtain CSR matrix from DMatrix. (#8269) 2022-09-29 20:41:43 +08:00
Jiaming Yuan 6925b222e0 Fix mixed types with cuDF. (#8280) 2022-09-29 00:57:52 +08:00
Jiaming Yuan f835368bcf Mark next release as 1.7 instead of 2.0 (#8281) 2022-09-28 14:33:37 +08:00
Jiaming YuanandHyunsu Philip Cho 6d1452074a Remove MGPU cpp tests. (#8276) 
Co-authored-by: Hyunsu Philip Cho <chohyu01@cs.washington.edu>
 2022-09-27 21:18:23 +08:00
Jiaming Yuan fcab51aa82 Support more pandas nullable types (#8262) 
- Float32/64
- Category.
 2022-09-27 01:59:50 +08:00
Jiaming Yuan 4056974e37 Fix sparse threshold warning. (#8268) 2022-09-26 22:22:11 +08:00
Jiaming Yuan 0cd11b893a [doc] Fix sphinx build. (#8270) 2022-09-26 12:33:31 +08:00
Jiaming Yuan 3fd331f8f2 Add checks to C pointer arguments. (#8254) 2022-09-22 19:02:22 +08:00
Jiaming Yuan b791446623 Initial support for IPv6 (#8225) 
- Merge rabit socket into XGBoost.
- Dask interface support.
- Add test to the socket.
 2022-09-21 18:06:50 +08:00
Jiaming Yuan fffb1fca52 Calculate base_score based on input labels for mae. (#8107) 
Fit an intercept as base score for abs loss.
 2022-09-20 20:53:54 +08:00
Jiaming Yuan 2e63af6117 Mitigate flaky data iter test. (#8244) 
- Reduce the number of batches.
- Verify labels.
 2022-09-14 17:54:14 +08:00
Jiaming Yuan bdf265076d Make QuantileDMatrix default to sklearn esitmators. (#8220) 2022-09-13 13:52:19 +08:00
Jiaming Yuan bc818316f2 Prepare for improving Windows networking compatibility. (#8234) 
* Prepare for improving Windows networking compatibility.

* Include dmlc filesystem indirectly as dmlc/filesystem.h includes windows.h, which
  conflicts with winsock2.h
* Define `NOMINMAX` conditionally.
* Link the winsock library when mysys32 is used.
* Add config file for read the doc.
 2022-09-10 15:16:49 +08:00
Jiaming Yuan dd44ac91b8 [CI] Use binary R dependencies on Windows. (#8241) 2022-09-09 19:51:15 -07:00
Jiaming Yuan b5eb36f1af Add max_cat_threshold to GPU and handle missing cat values. (#8212) 2022-09-07 00:57:51 +08:00
Jiaming Yuan 441ffc017a Copy data from Ellpack to GHist. (#8215) 2022-09-06 23:05:49 +08:00
Jiaming Yuan ada4a86d1c Fix dask interface with latest cupy. (#8210) 2022-09-03 03:10:43 +08:00
Jiaming Yuan 8dac90a593 Mark parameter validation non-experimental. (#8206) 2022-08-30 15:49:43 +08:00
Jiaming Yuan 9b32e6e2dc Fix release script. (#8187) (#8195) 2022-08-23 15:08:30 +08:00
Jiaming Yuan 16bca5d4a1 Support CPU input for device QuantileDMatrix. (#8136) 
- Copy `GHistIndexMatrix` to `Ellpack` when needed.
 2022-08-11 21:21:26 +08:00
Jiaming Yuan 36e7c5364d [dask] Deterministic rank assignment. (#8018) 2022-08-11 19:17:58 +08:00
Jiaming Yuan d868126c39 [CI] Fix R build on Jenkins. (#8154) 2022-08-11 14:50:03 +08:00
Jiaming Yuan 570f8ae4ba Use black on more Python files. (#8137) 2022-08-11 01:38:11 +08:00
Jiaming Yuan bdb291f1c2 [doc] Clarification for feature importance. (#8151) 2022-08-11 00:30:42 +08:00
Jiaming Yuan 446d536c23 Fix loading DMatrix binary in distributed env. (#8149) 
- Try to load DMatrix binary before trying to parse text input.
- Remove some unmaintained code.
 2022-08-10 22:53:16 +08:00
Jiaming Yuan 8fc60b31bc Update PyPi wheel size limit. (#8150) 2022-08-10 18:49:57 +08:00
Jiaming Yuan 9ae547f994 Use config_context in sklearn interface. (#8141) 2022-08-09 14:48:54 +08:00
Jiaming Yuan bcc8679a05 Update CUDA docker image and NCCL. (#8139) 2022-08-07 16:32:41 +08:00
Jiaming Yuan d87f69215e Quantile DMatrix for CPU. (#8130) 
- Add a new `QuantileDMatrix` that works for both CPU and GPU.
- Deprecate `DeviceQuantileDMatrix`.
 2022-08-02 15:51:23 +08:00
Jiaming Yuan 2cba1d9fcc Fix compatibility with latest cupy. (#8129) 
* Fix compatibility with latest cupy.

* Freeze mypy.
 2022-08-01 15:24:42 +08:00
Jiaming Yuan 2c70751d1e Implement iterative DMatrix for CPU. (#8116) 2022-07-26 22:34:21 +08:00
Jiaming Yuan 546de5efd2 [pyspark] Cleanup data processing. (#8088) 
- Use numpy stack for handling list of arrays.
- Reuse concat function from dask.
- Prepare for `QuantileDMatrix`.
- Remove unused code.
- Use iterator for prediction to avoid initializing xgboost model
 2022-07-26 15:00:52 +08:00