Develop (#50)

* add example for hyperparam optimizer use case and debugg allow_multi_dim_metrics

* test json serialization

* Fixed issue with photon registry when multiple registry objects are issued with and without custom elements folder

* Fixed registry test

* dont write json transformer file if save_output = False

* Fixed save_optimum_pipe function

* Added tests for save_optimum_pipe

* fixed save_optimum_pipe loading error

* Fixed save_optimum_pipe bugfix

* Added multiprocessing switch for parallel computing (#53)

* Added multiprocessing switch for parallel computing

* Debugging failing tests: Updated ubuntu and python

* Fixed default multithreading behaviour

* Changed versioning to pbr, resolved circular input errors, moved base… (#52)

* Changed versioning to pbr, resolved circular input errors, moved base elements to __init__

* fixed import

* Added missing pbr dependency

* Fixed relative import

* Removed circular import

* Removed short description

* Added pbr requirement

* Updated GH-Actions

* Fixed inferred versioning from metadata

* Added description file content type

* enabled build on pr and removed generation of version number

* Changed keywords, updated gh actions

* pypi publish action update

* deactivated test pypi build for non master pushes.

* Create dependabot.yml (#54)

* Feature/new imports (#55)

* Added new imports / modified examples

* Added missing __init__ files

* Added self hosted fonts for docs

* gh action for documentation auto-update

* fixed mkdocs path

* removed graph stuff

* Updated readme

* add json serialization for non-native result objects, add warning for imbalanced classes with accuracy

* debug imbalanced data transform unit test

* debug unit tests

* switched to processes for parallelBranch and PermutationTest

* debug

* Adapted gh action to new main branch

* Adapted gh action for new main branch

* refactor photonai output

* removed ugly test results

* added missing import

* [skip ci] Added summary

* Switched to diabetes dataset for sklearn compatibility

* switched python tests from boston_housing to diabetes dataset

* Fixed scikit-learn version due to currently missing support

* Fixed scikit-learn version due to currently missing support

* Fixed np bool

---------

Co-authored-by: Jan Ernsting <[email protected]>

.github/dependabot.yml

@@ -0,0 +1,15 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "daily"
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "daily"

.github/workflows/documentation_build_and_update.yml

@@ -0,0 +1,56 @@
+name: Update documentation
+on: push
+
+jobs:
+  build:
+    name: Build docs
+    runs-on: ubuntu-latest
+    if: ${{ github.ref != 'refs/heads/main' }}
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+
+      - name: Install mkdocs requirements
+        run: pip install mkdocs mkdocs-material pymdown-extensions mkdocstrings-python mkdocs-jupyter jupyter mkdocs-macros-plugin
+
+      - name: Install photonai requirements
+        run: pip install -r requirements.txt
+
+      - name: Install photonai
+        run: pip install .
+
+      - name: Build docs
+        run:  mkdocs build
+  deploy:
+    name: Deploy docs
+    runs-on: ubuntu-latest
+    if: ${{ github.ref == 'refs/heads/main' }}
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+
+      - name: Install mkdocs requirements
+        run: pip install mkdocs mkdocs-material pymdown-extensions mkdocstrings-python mkdocs-jupyter jupyter mkdocs-macros-plugin
+
+      - name: Install photonai requirements
+        run: pip install -r requirements.txt
+
+      - name: Install photonai
+        run: pip install .
+
+      - name: Deploy docs
+        run: mkdocs gh-deploy --force

.github/workflows/python-deploy_to_pypi.yml

@@ -7,17 +7,19 @@ on:
 jobs:
   deploy:
     name: Build and publish to PyPI
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.7.6
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
       with:
-        python-version: 3.7.6
+        fetch-depth: 0
+    - name: Set up Python 3.10.8
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.10.8
     - name: Install pypa/build
-      run: pip install build
+      run: pip install build pbr wheel
     - name: Build a binary wheel and a source tarball
-      run: python -m build --sdist --wheel --outdir dist/ .
+      run: python -m build -n --sdist --wheel --outdir dist/ .
     - name: Publish distribution to Test PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:

.github/workflows/python-test_and_deploy.yml

@@ -5,14 +5,14 @@ name: PHOTONAI test and test deploy
 
 on:
   push:
-    branches: [ master, develop ]
+    branches: [ main, develop ]
   pull_request:
-    branches: [ master, develop ]
+    branches: [ main, develop ]
 
 jobs:
   pytest:
     name: Run PHOTONAI tests and publish test coverage
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
 
     services:
       mongodb:
@@ -21,49 +21,47 @@ jobs:
           - 27017:27017
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.7.6
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10.8
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.7.6
+        python-version: 3.10.8
 #    - name: Install os dependencies
 #      run: | 
 #        sudo apt-get update
 #        sudo apt-get -y install gfortran swig
     - name: Install dependencies
       run: |
-        pip install wheel flake8 
+        pip install wheel flake8 pbr
         python setup.py egg_info
         pip install tensorflow pytest pytest-cov coveralls -r photonai.egg-info/requires.txt -r photonai/optimization/smac/requirements.txt -r photonai/optimization/nevergrad/requirements.txt
     - name: Test with pytest
       run: |
-        PYTHONPATH=./ pytest ./test --cov=./photonai --tb=long
+        PYTHONPATH=./ pytest ./test --cov=./photonai --full-trace
     - name: Coveralls
       run: coveralls
       env: 
         COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   deploy:
     name: Build and publish to TestPyPI
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     needs: pytest
-    if: github.ref == 'refs/heads/master'
+    if: github.ref == 'refs/heads/main'
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.7.6
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
       with:
-        python-version: 3.7.6
-    - name: Replace version number with commit hash
-      run: |
-        dt=$(date '+%Y.%m.%d.%H.%M.%S')
-        sed -i "s/^__version__.*/__version__ = '$dt'/g" setup.py
+        fetch-depth: 0
+    - name: Set up Python 3.10.8
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.10.8
     - name: Install pypa/build
-      run: pip install build
+      run: pip install build pbr wheel
     - name: Build a binary wheel and a source tarball
-      run: python -m build --sdist --wheel --outdir dist/ .
+      run: python -m build -n --sdist --wheel --outdir dist/ .
     - name: Publish distribution to Test PyPI
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.TEST_PYPI_API_TOKEN }}

.gitignore

@@ -181,3 +181,6 @@ tmtagsHistory
 .bundle
 /hyperpipe_results.csv
 /config_history.csv
+
+AUTHORS
+ChangeLog

README.md

@@ -45,8 +45,7 @@ You can setup a full stack machine learning pipeline in a few lines of code:
 from sklearn.datasets import load_breast_cancer
 from sklearn.model_selection import KFold
 
-from photonai.base import Hyperpipe, PipelineElement
-from photonai.optimization import FloatRange, Categorical, IntegerRange
+from photonai import Hyperpipe, PipelineElement, FloatRange, Categorical, IntegerRange
 
 # DESIGN YOUR PIPELINE
 my_pipe = Hyperpipe('basic_svm_pipe',  # the name of your pipeline

documentation/docs/algorithms/algorithms_index.md

@@ -27,7 +27,7 @@ PHOTONAI offers [Grid-Search](../../api/optimization/grid_search), [Random Searc
 
 ## PCA
 ```python
-from photonai.base import PipelineElement
+from photonai import PipelineElement
 PipelineElement('PCA',
                 hyperparameters={'n_components': IntegerRange(5, 20)},
                 test_disabled=True)