make release-tag: Merge branch 'master' into stable

Author: sarahmish

.github/workflows/docs.yml

@@ -0,0 +1,29 @@
+name: Generate Docs
+
+on:
+  push:
+    branches: [ master ]
+
+jobs:
+
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.6
+
+    - name: Build
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .[dev]
+        make docs
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{secrets.GITHUB_TOKEN}}
+        publish_dir: docs/_build/html
+        

.github/workflows/tests.yml

@@ -0,0 +1,60 @@
+name: Run Tests
+
+on:
+  push:
+    branches: [ '*' ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  devel:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7]
+        os: [ubuntu-latest, macos-latest]
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install package
+      run: pip install .[dev]
+    - name: make test-devel
+      run: make test-devel
+      
+  unit:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7]
+        os: [ubuntu-latest, macos-latest]
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install package and dependencies
+      run: pip install .[test]
+    - name: Test with pytest
+      run: make test
+
+  readme:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7]
+        os: [ubuntu-latest, macos-latest]
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install package and dependencies
+      run: pip install rundoc .
+    - name: make test-readme
+      run: make test-readme
+

.travis.yml

@@ -1,26 +1,45 @@
 # History
 
+## 0.1.2 - 2021-02-19
+
+New Modeler component
+
+* Invalid default metric name - [Issue #82](https://github.com/MLBazaar/Cardea/issues/82) by @ChengFR
+
+* Parameter 'presort' in 'sklearn.ensemble.GradientBoostingClassifier' has been deprecated since sklearn v0.22 - [Issue #80](https://github.com/MLBazaar/Cardea/issues/80) by @ChengFR
+
+* Loading demo data in either FHIR or MIMIC format - [Issue #79](https://github.com/MLBazaar/Cardea/issues/79) by @sarahmish
+
+* Fix a customized primitive: Categorizer - [Issue #75](https://github.com/MLBazaar/Cardea/issues/75) by @ChengFR
+
+* Update Cardea Class - [Issue #73](https://github.com/MLBazaar/Cardea/issues/73) by @sarahmish
+
+* Clean up the modeler - [Issue #71](https://github.com/MLBazaar/Cardea/issues/71) by @ChengFR
+
+* Update and clean up the dependencies - [Issue #70](https://github.com/MLBazaar/Cardea/issues/70) by @ChengFR
+
+
 ## 0.1.1 - 2020-12-11
 
 Benchmark framework
 
-* Link google colab to Cardea and add badge README.md - [Issue #67](https://github.com/DAI-Lab/Cardea/issues/67) by @sarahmish
+* Link google colab to Cardea and add badge README.md - [Issue #67](https://github.com/MLBazaar/Cardea/issues/67) by @sarahmish
 
-* Modeler load pipelines instead of lists of primitives enhancement - [Issue #65](https://github.com/DAI-Lab/Cardea/issues/65) by @ChengFR
+* Modeler load pipelines instead of lists of primitives enhancement - [Issue #65](https://github.com/MLBazaar/Cardea/issues/65) by @ChengFR
 
-* Benchmark testing apis enhancement - [Issue #64](https://github.com/DAI-Lab/Cardea/issues/64) by @ChengFR
+* Benchmark testing apis enhancement - [Issue #64](https://github.com/MLBazaar/Cardea/issues/64) by @ChengFR
 
-* Update documentation theme enhancement - [Issue #62](https://github.com/DAI-Lab/Cardea/issues/62) by @sarahmish
+* Update documentation theme enhancement - [Issue #62](https://github.com/MLBazaar/Cardea/issues/62) by @sarahmish
 
-* Primitive setup enhancement - [Issue #61](https://github.com/DAI-Lab/Cardea/issues/61) by @sarahmish & @ChengFR
+* Primitive setup enhancement - [Issue #61](https://github.com/MLBazaar/Cardea/issues/61) by @sarahmish & @ChengFR
 
 
 ## 0.1.0 - 2020-09-15
 
 Release on PyPI: https://pypi.org/project/cardea/
 
-* Analysis notebooks enhancement - [Issue #58](https://github.com/DAI-Lab/Cardea/issues/58) by @sarahmish 
+* Analysis notebooks enhancement - [Issue #58](https://github.com/MLBazaar/Cardea/issues/58) by @sarahmish 
 
-* MIMIC III data loader enhancement - [Issue #57](https://github.com/DAI-Lab/Cardea/issues/57) by @sarahmish
+* MIMIC III data loader enhancement - [Issue #57](https://github.com/MLBazaar/Cardea/issues/57) by @sarahmish
 
-* Freeze package on analysis compatibility - [Issue #55](https://github.com/DAI-Lab/Cardea/issues/55) by @sarahmish
+* Freeze package on analysis compatibility - [Issue #55](https://github.com/MLBazaar/Cardea/issues/55) by @sarahmish

HISTORY.md

@@ -115,8 +115,17 @@ test: ## run tests quickly with the default Python
 test-all: ## run tests on every Python version with tox
 	tox
 
+.PHONY: test-readme
+test-readme: ## run the readme snippets
+	rundoc run --single-session python3 -t python3 README.md
 
 
+.PHONY: check-dependencies
+check-dependencies: ## test if there are any broken dependencies
+	pip check
+
+.PHONY: test-devel
+test-devel: check-dependencies lint docs ## test everything that needs development dependencies
 
 
 .PHONY: coverage
@@ -131,16 +140,14 @@ coverage: clean-coverage ## check code coverage quickly with the default Python
 
 .PHONY: docs
 docs: clean-docs ## generate Sphinx HTML documentation, including API docs
-	sphinx-apidoc --module-first --separate --no-toc --output-dir docs/api/ cardea
 	$(MAKE) -C docs html
-	touch docs/_build/html/.nojekyll
 
 .PHONY: viewdocs
-viewdocs: docs ## view docs in browser
+viewdocs: ## view the docs in a browser
 	$(BROWSER) docs/_build/html/index.html
 
 .PHONY: servedocs
-servedocs: docs ## compile the docs watching for changes
+servedocs: ## compile the docs watching for changes
 	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .