Merge pull request #111 from ExpandingMan/overhaul

massive overhaul

.github/workflows/CompatHelper.yml

@@ -3,14 +3,43 @@ on:
   schedule:
     - cron: 19 22 * * *
   workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
-      - name: Pkg.add("CompatHelper")
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main()
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
-        run: julia -e 'using CompatHelper; CompatHelper.main()'
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.github/workflows/TagBot.yml

@@ -0,0 +1,15 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/ci.yml

@@ -1,42 +1,48 @@
 name: CI
 on:
-  push:
-    branches:
-      - master
-    tags: '*'
   pull_request:
+  push:
+    branches: [main]
+    tags: ['*']
 jobs:
   test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
-    continue-on-error: ${{ matrix.version == 'nightly' }}
     strategy:
+      fail-fast: false
       matrix:
         version:
           - '1.6'
-          - '1'
-          - 'nightly'
+          - '1' # automatically expands to the latest stable 1.x release of Julia
         os:
           - ubuntu-latest
-          - macOS-latest
-          - windows-latest
         arch:
           - x64
-        exclude:
-          # Remove some configurations from the build matrix to reduce CI time.
-          # See https://github.com/marketplace/actions/setup-julia-environment
-          # Don't test on all versions
-          - {os: 'macOS-latest', version: '1.6'}
-          - {os: 'macOS-latest', version: 'nightly'}
-          - {os: 'windows-latest', version: '1.6'}
-          - {os: 'windows-latest', version: 'nightly'}
+        include:
+          - os: windows-latest
+            version: '1'
+            arch: x64
     steps:
-      - uses: actions/checkout@v1
-      - uses: julia-actions/setup-julia@latest
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: julia-actions/julia-buildpkg@latest
-      - uses: julia-actions/julia-runtest@latest
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+        env:
+          JULIA_NUM_THREADS: 4
         with:
           coverage: false
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.gitignore

@@ -3,3 +3,4 @@ deps.jl
 deps
 test/*.buffer
 Manifest.toml
+docs/build

Project.toml

@@ -1,13 +1,17 @@
 name = "XGBoost"
 uuid = "009559a3-9522-5dbb-924b-0b6ed2b22bb9"
-version = "1.5.2"
+version = "2.0.0"
 
 [deps]
-Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
-Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
+CEnum = "fa961155-64e5-5f13-b03f-caf6b980ea82"
+JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
+Term = "22787eb5-b846-44ae-b979-8e399b8463ab"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 XGBoost_jll = "a5c6f535-4255-5ca2-a466-0e519f119c46"
 
@@ -17,8 +21,7 @@ julia = "1.6"
 
 [extras]
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["SparseArrays", "Random", "Test"]
+test = ["Random", "Test"]

README.md

@@ -1,12 +1,12 @@
-XGBoost.jl
-==========
+# XGBoost.jl
 
 [![Build Status](https://github.com/dmlc/XGBoost.jl/workflows/CI/badge.svg)](https://github.com/dmlc/XGBoost.jl/actions)
 [![Latest Version](https://juliahub.com/docs/XGBoost/version.svg)](https://juliahub.com/ui/Packages/XGBoost/rSeEh/)
 [![Pkg Eval](https://juliahub.com/docs/XGBoost/pkgeval.svg)](https://juliahub.com/ui/Packages/XGBoost/rSeEh/)
 [![Dependents](https://juliahub.com/docs/XGBoost/deps.svg)](https://juliahub.com/ui/Packages/XGBoost/rSeEh/?t=2)
+[![docs](https://img.shields.io/badge/docs-latest-blue?style=for-the-badge&logo=julia)](https://dmlc.github.io/XGBoost.jl/)
 
-eXtreme Gradient Boosting in Julia
+eXtreme Gradient Boosting in Julia.
 
 ## Abstract
 This package is a Julia interface of [XGBoost](https://github.com/dmlc/xgboost). 
@@ -17,76 +17,14 @@ gradient boosting packages. It supports various objective functions, including r
 classification and ranking. The package is also made to be extensible, so that users are also
 allowed to define their own objectives easily.
 
-## Features
-* Sparse feature format, it allows easy handling of missing values, and improve computation
-    efficiency.
-* Advanced features, such as customized loss function, cross validation, see [demo folder](demo)
-    for walkthrough examples.
+See the [documentation](https://dmlc.github.io/XGBoost.jl/) for more information.
 
 ## Installation
 ```julia
 ] add XGBoost
 ```
-or
-```julia
-] develop "https://github.com/dmlc/XGBoost.jl.git"
-] build XGBoost
-```
-
-By default, the package installs prebuilt binaries for XGBoost `v0.82.0` on Linux, MacOS and Windows. Only the linux version is built with OpenMP. 
-
-
-## Minimal examples
-
-To show how XGBoost works, here is an example of dataset Mushroom
-
-- Prepare Data
-
-XGBoost support Julia ```Array```, ```SparseMatrixCSC```, libSVM format text and XGBoost binary
-file as input. Here is an example of Mushroom classification. This example will use the function
-```readlibsvm``` in [basic_walkthrough.jl](demo/basic_walkthrough.jl#L5). This function load libsvm
-format text into Julia dense matrix.
-
-```julia
-using XGBoost
-
-train_X, train_Y = readlibsvm("data/agaricus.txt.train", (6513, 126))
-test_X, test_Y = readlibsvm("data/agaricus.txt.test", (1611, 126))
-
-```
-
-- Fit Model
-```julia
-num_round = 2
-bst = xgboost(train_X, num_round, label = train_Y, eta = 1, max_depth = 2)
-```
-
-## Predict
-```julia
-pred = predict(bst, test_X)
-print("test-error=", sum((pred .> 0.5) .!= test_Y) / float(size(pred)[1]), "\n")
-```
-
-## Cross-Validation
-```julia
-nfold = 5
-param = ["max_depth" => 2,
-         "eta" => 1,
-         "objective" => "binary:logistic"]
-metrics = ["auc"]
-nfold_cv(train_X, num_round, nfold, label = train_Y, param = param, metrics = metrics)
-```
-
-## Feature Walkthrough
-Check [demo](https://github.com/antinucleon/XGBoost.jl/blob/master/demo/)
-
-- [Basic walkthrough of features](demo/basic_walkthrough.jl)
-- [Customize loss function, and evaluation metric](demo/custom_objective.jl)
-- [Boosting from existing prediction](demo/boost_from_prediction.jl)
-- [Predicting using first n trees](demo/predict_first_ntree.jl)
-- [Generalized Linear Model](demo/generalized_linear_model.jl)
-- [Cross validation](demo/cross_validation.jl)
-
+This package uses [`xgboost_jll`](https://github.com/JuliaBinaryWrappers/XGBoost_jll.jl) to package
+the `xgboost` binaries (will be installed automatically).
 
-## Model Parameter Setting
-Check [XGBoost Documentation](https://xgboost.readthedocs.io/en/latest/parameter.html)
+## Preview
+![](/assets/xgboost_demo_1.jpg)

assets/data/README.md

@@ -0,0 +1,3 @@
+# Test Data
+This folder contains processed example dataset used for testing.
+Copyright of the dataset belongs to the original copyright holder.