Merge branch 'development' into use_new_splitter

Author: eddiebergman

.github/workflows/black_checker.yml

@@ -0,0 +1,33 @@
+name: black-format-check
+
+on: [push, pull_request]
+
+env:
+  #If STRICT is set to true, it will fail on black check fail
+  STRICT: false
+
+jobs:
+
+  black-format-check:
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: Checkout
+      uses: actions/checkout@v2
+      with:
+        submodules: recursive
+
+    - name: Setup Python 3.7
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.7"
+
+    - name: Install black
+      run: |
+        pip install black
+
+    - name: Run Black Check
+      run: |
+        black --check --diff --line-length 100 ./autosklearn || ! $STRICT
+        black --check --diff --line-length 100 ./test || ! $STRICT
+        black --check --diff --line-length 100 ./examples|| ! $STRICT

.github/workflows/dist.yml

@@ -5,25 +5,34 @@ on: [push, pull_request]
 jobs:
   dist:
     runs-on: ubuntu-latest
+
     steps:
-    - uses: actions/checkout@v2
+    - name: Check out the repo
+      uses: actions/checkout@v2
+      with:
+        submodules: recursive
+
     - name: Setup Python
       uses: actions/setup-python@v2
       with:
         python-version: 3.8
+
     - name: Build dist
       run: |
         python setup.py sdist
+
     - name: Twine check
       run: |
         pip install twine
         last_dist=$(ls -t dist/auto-sklearn-*.tar.gz | head -n 1)
         twine_output=`twine check "$last_dist"`
         if [[ "$twine_output" != "Checking $last_dist: PASSED" ]]; then echo $twine_output && exit 1;fi
+
     - name: Install dist
       run: |
         last_dist=$(ls -t dist/auto-sklearn-*.tar.gz | head -n 1)
         pip install $last_dist
+
     - name: PEP 561 Compliance
       run: |
         pip install mypy

.github/workflows/docker-publish.yml

@@ -12,13 +12,18 @@ jobs:
   push_to_registry:
     name: Push Docker image to GitHub Packages
     runs-on: ubuntu-latest
+
     steps:
       - name: Check out the repo
         uses: actions/checkout@v2
+        with:
+          submodules: recursive
+
       - name: Extract branch name
         shell: bash
         run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
         id: extract_branch
+
       - name: Push to GitHub Packages
         uses: docker/build-push-action@v1
         with:
@@ -28,26 +33,32 @@ jobs:
           repository: automl/auto-sklearn/auto-sklearn
           tag_with_ref: true
           tags: ${{ steps.extract_branch.outputs.branch }}
+
       - name: Push to Docker Hub
         uses: docker/build-push-action@v1
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
           repository: mfeurer/auto-sklearn
           tags: ${{ steps.extract_branch.outputs.branch }}
+
       - name: Docker Login
         run: docker login docker.pkg.github.com -u $GITHUB_ACTOR -p $GITHUB_TOKEN
         env:
             GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+
       - name: Pull Docker image
         run: docker pull docker.pkg.github.com/$GITHUB_REPOSITORY/auto-sklearn:$BRANCH
         env:
             BRANCH: ${{ steps.extract_branch.outputs.branch }}
+
       - name: Run image
         run: docker run -i -d --name unittester -v $GITHUB_WORKSPACE:/workspace -w /workspace docker.pkg.github.com/$GITHUB_REPOSITORY/auto-sklearn:$BRANCH
         env:
             BRANCH: ${{ steps.extract_branch.outputs.branch }}
+
       - name: Auto-Sklearn loaded
         run: docker exec  -i unittester python3 -c 'import autosklearn; print(f"Auto-sklearn imported from {autosklearn.__file__}")'
+
       - name: Run unit testing
         run: docker exec  -i unittester python3 -m pytest -v test

.github/workflows/docs.yml

@@ -6,33 +6,42 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
+      with:
+        submodules: recursive
+
     - name: Setup Python
       uses: actions/setup-python@v2
       with:
         python-version: 3.8
+
     - name: Install dependencies
       run: |
-        pip install -e .[docs,examples,examples_unix]
+        pip install -e .[docs,examples]
+
     - name: Make docs
       run: |
         cd doc
         make html
+
     - name: Check links
       run: |
         cd doc
         make linkcheck
+
     - name: Pull latest gh-pages
       if: (contains(github.ref, 'develop') || contains(github.ref, 'master')) && github.event_name == 'push'
       run: |
         cd ..
         git clone https://github.com/automl/auto-sklearn.git --branch gh-pages --single-branch gh-pages
+
     - name: Copy new doc into gh-pages
       if: (contains(github.ref, 'develop') || contains(github.ref, 'master')) && github.event_name == 'push'
       run: |
         branch_name=${GITHUB_REF##*/}
         cd ../gh-pages
         rm -rf $branch_name
         cp -r ../auto-sklearn/doc/build/html $branch_name
+
     - name: Push to gh-pages
       if: (contains(github.ref, 'develop') || contains(github.ref, 'master')) && github.event_name == 'push'
       run: |

.github/workflows/isort_checker.yml

@@ -0,0 +1,31 @@
+name: isort-check
+
+on: [push, pull_request, workflow_dispatch]
+
+env:
+  #If STRICT is set to true, it will fail on isort check fail
+  STRICT: false
+
+jobs:
+
+  black-format-check:
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: Checkout
+      uses: actions/checkout@v2
+      with:
+        submodules: recursive
+
+    - name: Setup Python 3.7
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.7"
+
+    - name: Install isort
+      run: |
+        pip install isort
+
+    - name: Run isort Check
+      run: |
+        isort --check-only autosklearn || ! $STRICT

.github/workflows/pre-commit.yaml

@@ -7,14 +7,19 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
+      with:
+        submodules: recursive
+
     - name: Setup Python 3.7
       uses: actions/setup-python@v2
       with:
         python-version: 3.7
+
     - name: Install pre-commit
       run: |
         pip install pre-commit
         pre-commit install
+
     - name: Run pre-commit
       run: |
         pre-commit run --all-files

.github/workflows/pytest.yml

@@ -3,6 +3,7 @@ name: Tests
 on:
   push:
   pull_request:
+  workflow_dispatch:
   schedule:
     # Every Monday at 7AM UTC
     - cron: '0 07 * * 1'
@@ -13,20 +14,23 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ['3.7', '3.8', '3.9', '3.10']
         use-conda: [true, false]
         use-dist: [false]
         include:
-          - python-version: 3.8
+          - python-version: '3.8'
             code-cov: true
-          - python-version: 3.7
+          - python-version: '3.7'
             use-conda: false
             use-dist: true
       fail-fast: false
 
     steps:
 
     - uses: actions/checkout@v2
+      with:
+        submodules: recursive
+
     - name: Setup Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       # A note on checkout: When checking out the repository that

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "autosklearn/automl_common"]
+	path = autosklearn/automl_common
+	url = https://github.com/automl/automl_common

CONTRIBUTING.md

@@ -30,17 +30,24 @@ Following that we'll tell you about how you can test your changes locally and th
     It's important to work off the latest changes on the **development** branch.
     ```bash
     # With https
-    git clone https://github.com/your-username/auto-sklearn
+    # Note the --recurse-submodules args, we use a submodule autosklearn/automl_common
+    # so it needs to be downloaded too
+    git clone --recurse-submodules https://github.com/your-username/auto-sklearn
 
     # ... or with ssh
-    git clone [email protected]:your-username/auto-sklearn.git
+    git clone --recurse-submodules [email protected]:your-username/auto-sklearn.git
 
     # Navigate into the cloned repo
     cd auto-sklearn
 
     # Create a new branch based off the development one
     git checkout -b my_new_branch development
 
+    # If you missed the --recurse-submodules arg during clone or need to install the
+    # submodule manually, then execute the following line:
+    #
+    # git submodule udate --init --recursive
+
     # ... Alternatively, if you would prefer a more manual method
     # Show all the available branches with a * beside your current one
     git branch
@@ -50,6 +57,11 @@ Following that we'll tell you about how you can test your changes locally and th
 
     # Create a new branch based on the currently active branch
     git checkout -b my_new_branch
+
+    # If you missed the --recurse-submodules arg during clone or need to install the
+    # submodule manually, then execute the following line:
+    #
+    # git submodule udate --init --recursive
     ```
 
     The reason to create a new branch is two fold:
@@ -81,7 +93,7 @@ Following that we'll tell you about how you can test your changes locally and th
     # If you're using shells other than bash you'll need to use
     pip install -e ".[test,examples,doc]"
     ```
-    *   If you're only exposure to using pip is `pip install package_name` then this might be a bit confusing.
+    *   If your only exposure to using pip is `pip install package_name` then this might be a bit confusing.
     *   If we type `pip install -e .` (notice the 'dot'), this tells `pip` to install a package located here, in this directory, `.`.
         The `-e` flag indicates that it should be editable, meaning you will not have to run `pip install .` every time you make a change and want to try it.
     *   Finally the `[test,examples,doc]` tells `pip` that there's some extra optional dependencies that we want to install.
@@ -335,6 +347,9 @@ Lastly, if the feature really is a game changer or you're very proud of it, cons
     cd auto-sklearn
     git checkout -b my_new_branch development
 
+    # Initialize autosklearn/automl_common submodule
+    git submodule update --init --recursive
+
     # Create a virtual environment and activate it so there are no package
     # conflicts
     python -m venv my-virtual-env

MANIFEST.in

@@ -1,9 +1,17 @@
-recursive-include autosklearn/metalearning/files *.arff
-recursive-include autosklearn/metalearning/files *.csv
-recursive-include autosklearn/metalearning/files *.txt
-include autosklearn/util/logging.yaml
+include LICENSE.txt
 include requirements.txt
+include autosklearn/util/logging.yaml
 include autosklearn/requirements.txt
-recursive-include autosklearn/experimental/ *.json
-include autosklearn/experimental/askl2_training_data.json
-include LICENSE.txt
+
+# Meta-data
+recursive-include autosklearn/metalearning/files *.arff *.csv *.txt
+recursive-include autosklearn/experimental *.json
+
+# Remove tests from automl_common
+prune autosklearn/automl_common/test
+exclude autosklearn/automl_common/setup.py
+
+# Include automl_common LICENSE and README
+include autosklearn/automl_common/LICENSE
+include autosklearn/automl_common/README.md
+