Prepare for 4.0 release (#528)

* Remove deprecated functions (#496)

* Remove deprecated functions

* Remove Java from CI

* Fix tests

* More fix

* Update C API doc

* Fix CI

* Fix CMake example

* Fix temp dir on Windows

* Creat tmpdir

* Remove unused code (#497)

* Remove unused code

* Remove treelite::optional, since it's not used

* Remove unused imports

* typo

* Remove deprecated functions from doc (#498)

* Set up formatting check via pre-commit (#500)

* Set up pre-commit

* Use f-strings

* Fix typo

* Replace setup.py with pyproject.toml (#501)

* Replace setup.py with pyproject.toml

* Replace setup.py with pyproject.toml

* Add script to change version

* Convert pathlib to str before passing it to LoadLibrary

* Fix visibility on Linux

* Fix MacOS wheel build

* Use Mamba to speed up Python env setup

* Move ContiguousArray and TaskType to separate headers (#502)

* Document current v3 serialization format (#504)

* Document current v3 serialization format

* Add missing description

* Clean up serialization logic (#507)

* Clean up serialization logic

* Add missing header

* Add missing header

* Add missing header

* Fix compatibility test

* Add extra check for num_nodes

* Add missing header

* Add missing std::

* Use shared_ptr<> to store ref to mixin

* Don't store iterator in mixin

* Remove stray &

* Document proposed v4 serialization format (#505)

* Document current v3 serialization format

* Add missing description

* Document proposed v4 serialization format

* Fix typo

* Update

* Apply suggestions from code review

* Update docs/serialization/v4.rst

* Update docs/serialization/v4.rst

* Use std::variant in treelite::Model (#508)

* Fix loading from XGBoost 2.0 dev (#509)

* Removed deprecated parameter size_leaf_vector

* Handle iteration_indptr field in JSON

* Add additional metadata for trees (#510)

* Add additional metadata for trees

* Use class_id

* Fix formatting

* Simplify task_type

* Update v4.rst

* Fix serializer test (#512)

* Fix serializer test

* Fix typo

* Use C++ headers from Conda env

* Fix compiler warnings (#513)

* Fix warnings from Visual Studio

* Fix warnings from GCC

* Fix unused parameter warning

* Use std:: prefix for uint32_t and size_t

* Clean up unused parameter warnings

* Refactor sklearn importer to use mix-in classes (#516)

* Minor formatting fixes

* Move sklearn importers to sklearn namespace

* Refactor sklearn importer to use mix-in classes

* Divide tests into multiple files

* Revise v4 spec (#518)

Also simplify doc build

* Fix typo in doc

* Rename NodeType -> TreeNodeType

* Clarify behavior of node stats field

* Name a nameless field

* [Doc] Clarify leaf_vector_shape

* Fix doc build

* Use signed integers for some metadata types, to avoid programming errors

* Clarify the meaning of average_tree_output

* Rename pred_transform -> postprocessor

* Clarify num_class

* Implement Treelite v4 specification (#524)

* Bring in treelite-ng

* Apply linting to CMake files

* Fix CMakeLists.txt

* Fix C++ app example

* Fix build on MacOS

* Fix build on MacOS

* Fix scripts

* Use MacOS 10.15+

* Fix test on MacOS: size_t != uint64_t on MacOS

* Install latest XGBoost in CI

* Don't install if TEST_COVERAGE

* Don't install fmt

* Don't use O0 for test coverage

* Use latest MacOS and Windows workers

* Require MSVC 2022

* Use latest Windows

* Ensure that we use positive int for seeding rng

* Fix build with USE_OPENMP=OFF

* Fix flaky test

* Add back LightGBM

* Install XGBoost from the source

* Fix tests

* [Doc] various fixes (#525)

* [Doc] various fixes

* Update docstring

* Update docstrings

* Add submodules

* Doc fix

* [sklearn] Use more stable interface to get base_scores (#526)

* Doc fix

* Add legacy model builder (#527)

* Add legacy model builder

* Use bysource order

.clang-format

@@ -0,0 +1,59 @@
+---
+Language: Cpp
+Standard: c++17
+BasedOnStyle: Google
+TabWidth: 2
+IndentWidth: 2
+ColumnLimit: 100
+UseTab: Never
+
+AccessModifierOffset: -1
+AlignAfterOpenBracket: DontAlign
+AlignConsecutiveAssignments: None
+AlignConsecutiveDeclarations: None
+AlignEscapedNewlines: Left
+AlignTrailingComments: false
+AllowAllArgumentsOnNextLine: true
+AllowAllConstructorInitializersOnNextLine: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: Empty
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Empty
+AllowShortIfStatementsOnASingleLine: Never
+AllowShortLambdasOnASingleLine: All
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakTemplateDeclarations: Yes
+BinPackArguments: true
+BinPackParameters: true
+BreakBeforeBinaryOperators: All
+BreakBeforeBraces: Attach
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializers: BeforeColon
+BreakInheritanceList: AfterColon
+BreakStringLiterals: true
+CompactNamespaces: false
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+IndentWrappedFunctionNames: false
+InsertBraces: true
+IndentCaseLabels: false
+KeepEmptyLinesAtTheStartOfBlocks: false
+NamespaceIndentation: None
+PointerAlignment: Left
+ReflowComments: true
+SortIncludes: CaseInsensitive
+SpaceAfterCStyleCast: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyParentheses: false
+SpacesInAngles: false
+SpacesInCStyleCastParentheses: false
+SpacesInContainerLiterals: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+QualifierAlignment: Right

.flake8

@@ -0,0 +1,30 @@
+[flake8]
+filename = *.py, *.pyx, *.pxd
+exclude =
+   *.egg,
+   .git,
+   __pycache__,
+   build/,
+   cpp,
+   docs,
+   tests/cython/
+
+# Cython Rules ignored:
+# E999: invalid syntax (works for Python, not Cython)
+# E225: Missing whitespace around operators (breaks cython casting syntax like <int>)
+# E226: Missing whitespace around arithmetic operators (breaks cython pointer syntax like int*)
+# E227: Missing whitespace around bitwise or shift operator (Can also break casting syntax)
+# W503: line break before binary operator (breaks lines that start with a pointer)
+# W504: line break after binary operator (breaks lines that end with a pointer)
+
+extend-ignore =
+    # handled by black
+    E501, W503, E203
+    # imported but unused
+    F401
+    # redefinition of unused
+    F811
+    extend-ignore =
+    # E203 whitespace before ':'
+    # https://github.com/psf/black/issues/315
+    E203

.github/workflows/coverage-tests.yml

@@ -41,7 +41,7 @@ jobs:
         bash ops/cpp-python-coverage.sh
   win-python-coverage:
     name: Run Python and C++ tests with test coverage (Windows)
-    runs-on: windows-2019
+    runs-on: windows-latest
     steps:
     - uses: actions/checkout@v2
       with:
@@ -63,7 +63,7 @@ jobs:
         call ops/win-python-coverage.bat
   macos-python-coverage:
     name: Run Python and C++ tests with test coverage (MacOS)
-    runs-on: macos-11
+    runs-on: macos-latest
     steps:
     - uses: actions/checkout@v2
       with:
@@ -83,29 +83,3 @@ jobs:
       shell: bash -l {0}
       run: |
         bash ops/macos-python-coverage.sh
-  java-coverage:
-    name: Run Java tests with test coverage
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-      with:
-        submodules: 'true'
-    - uses: mamba-org/provision-with-micromamba@v14
-      with:
-        cache-downloads: true
-        cache-env: true
-        environment-name: dev
-        environment-file: ops/conda_env/dev.yml
-    - uses: actions/setup-java@v1
-      with:
-        java-version: 1.8
-    - name: Cache Maven packages
-      uses: actions/cache@v2
-      with:
-        path: ~/.m2
-        key: treelite4j-${{ runner.os }}-m2-${{ hashFiles('./runtime/java/treelite4j/pom.xml') }}
-        restore-keys: treelite4j-${{ runner.os }}-m2
-    - name: Run tests with test coverage computation
-      shell: bash -l {0}
-      run: |
-        bash ops/java-coverage.sh

.github/workflows/macos-wheel-builder.yml

@@ -25,7 +25,7 @@ env:
 jobs:
   macos-wheel-builder:
     name: Build and test Python wheels (MacOS)
-    runs-on: macos-11
+    runs-on: macos-latest
     strategy:
       fail-fast: false
       matrix:

.github/workflows/misc-tests.yml

@@ -48,7 +48,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-11]
+        os: [ubuntu-latest, macos-latest]
     steps:
     - uses: actions/checkout@v2
       with:
@@ -72,7 +72,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-11]
+        os: [ubuntu-latest, macos-latest]
     steps:
     - uses: actions/checkout@v2
       with:

.github/workflows/pre-commit.yml

@@ -0,0 +1,11 @@
+name: pre-commit
+
+on: [push, pull_request]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - uses: pre-commit/action@v3.0.0

.github/workflows/windows-wheel-builder.yml

@@ -25,7 +25,7 @@ env:
 jobs:
   windows-wheel-builder:
     name: Build and test Python wheels (Windows)
-    runs-on: windows-2019
+    runs-on: windows-latest
     steps:
     - uses: actions/checkout@v2
       with:

.isort.cfg

@@ -1,3 +1,3 @@
 [settings]
 profile=black
-known_first_party=treelite,treelite_runtime
+known_first_party=treelite

.pre-commit-config.yaml

@@ -0,0 +1,66 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v3.2.0
+  hooks:
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+  - id: check-yaml
+  - id: check-added-large-files
+    args: ["--maxkb=4000"]
+- repo: https://github.com/psf/black
+  rev: 23.1.0
+  hooks:
+  - id: black
+- repo: https://github.com/pycqa/isort
+  rev: 5.12.0
+  hooks:
+  - id: isort
+    args: ["--profile", "black", "--filter-files"]
+- repo: https://github.com/MarcoGorelli/cython-lint
+  rev: v0.15.0
+  hooks:
+  - id: cython-lint
+  - id: double-quote-cython-strings
+- repo: https://github.com/PyCQA/flake8
+  rev: 5.0.4
+  hooks:
+  - id: flake8
+    args: [--config=.flake8]
+    files: .*$
+    types: [file]
+    types_or: [python]
+    additional_dependencies: [flake8-force]
+- repo: local
+  hooks:
+    - id: pylint
+      name: pylint
+      entry: python dev/run_pylint.py
+      language: python
+      types: [python]
+      additional_dependencies: [
+        pylint, hatchling, pytest, scikit-learn, hypothesis, pandas, treelite,
+        lightgbm, xgboost, tqdm
+      ]
+- repo: https://github.com/pocc/pre-commit-hooks
+  rev: v1.3.5
+  hooks:
+    - id: clang-format
+      args: ["-i", "--style=file:.clang-format"]
+      language: python
+      additional_dependencies: [clang-format>=15.0]
+      types_or: [c, c++]
+    - id: cpplint
+      language: python
+      args: [
+        "--linelength=100", "--recursive",
+        "--filter=-build/c++11,-build/include,-build/namespaces_literals,-runtime/references,-build/include_order,+build/include_what_you_use",
+        "--root=include"]
+      additional_dependencies: [cpplint]
+      types_or: [c++]
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v1.2.0
+  hooks:
+    - id: mypy
+      additional_dependencies: [types-setuptools, numpy]

.readthedocs.yaml

@@ -28,4 +28,3 @@ sphinx:
 python:
   install:
    - requirements: docs/requirements.txt
-  system_packages: true