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

Author: sarahmish

.travis.yml

@@ -1,4 +1,5 @@
 # Config file for automatic testing at travis-ci.org
+dist: bionic
 language: python
 python:
   - 3.6
@@ -8,7 +9,7 @@ python:
 install: pip install -U tox-travis
 
 # Command to run tests
-script: tox
+script: travis_wait 30 tox # wait before termination
 
 deploy:
 

HISTORY.md

@@ -1,5 +1,11 @@
 # History
 
-## 0.1.0
+## 0.1.0 - 2020-09-15
 
-* First release on PyPI.
+Release on PyPI: https://pypi.org/project/cardea/
+
+* Analysis notebooks enhancement - [Issue #58](https://github.com/DAI-Lab/Cardea/issues/58) by @sarahmish 
+
+* MIMIC III data loader enhancement - [Issue #57](https://github.com/DAI-Lab/Cardea/issues/57) by @sarahmish
+
+* Freeze package on analysis compatibility - [Issue #55](https://github.com/DAI-Lab/Cardea/issues/55) by @sarahmish

MANIFEST.in

@@ -4,6 +4,8 @@ include HISTORY.md
 include LICENSE
 include README.md
 
+recursive-include cardea *.xml
+
 recursive-include tests *
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]

Makefile

@@ -1,4 +1,3 @@
-.PHONY: clean clean-test clean-pyc clean-build clean-docs docs help
 .DEFAULT_GOAL := help
 
 define BROWSER_PYSCRIPT
@@ -26,68 +25,101 @@ export PRINT_HELP_PYSCRIPT
 
 BROWSER := python -c "$$BROWSER_PYSCRIPT"
 
+.PHONY: help
 help:
 	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
 
 
 # CLEAN TARGETS
 
-
-clean: clean-build clean-pyc clean-coverage clean-test clean-docs ## remove all build, test, coverage, docs and Python artifacts
-
+.PHONY: clean-build
 clean-build: ## remove build artifacts
 	rm -fr build/
 	rm -fr dist/
 	rm -fr .eggs/
 	find . -name '*.egg-info' -exec rm -fr {} +
 	find . -name '*.egg' -exec rm -f {} +
 
+.PHONY: clean-pyc
 clean-pyc: ## remove Python file artifacts
 	find . -name '*.pyc' -exec rm -f {} +
 	find . -name '*.pyo' -exec rm -f {} +
 	find . -name '*~' -exec rm -f {} +
 	find . -name '__pycache__' -exec rm -fr {} +
 
+.PHONY: clean-docs
 clean-docs: ## remove previously built docs
 	rm -f docs/api/*.rst
 	$(MAKE) -C docs clean
 
+.PHONY: clean-coverage
 clean-coverage: ## remove coverage artifacts
 	rm -f .coverage
 	rm -f .coverage.*
 	rm -fr htmlcov/
 
+.PHONY: clean-test
 clean-test: ## remove test and coverage artifacts
 	rm -fr .tox/
 	rm -fr .pytest_cache
 
+.PHONY: clean
+clean: clean-build clean-pyc clean-test clean-coverage clean-docs ## remove all build, test, coverage, docs and Python artifacts
 
-# LINT TARGETS
 
+# INSTALL TARGETS
 
+.PHONY: install
+install: clean-build clean-pyc ## install the package to the active Python's site-packages
+	pip install .
+
+.PHONY: install-test
+install-test: clean-build clean-pyc ## install the package and test dependencies
+	pip install .[test]
+
+.PHONY: install-develop
+install-develop: clean-build clean-pyc ## install the package in editable mode and dependencies for development
+	pip install -e .[dev]
+
+
+# LINT TARGETS
+
+.PHONY: lint
 lint: ## check style with flake8 and isort
 	flake8 cardea tests
 	isort -c --recursive cardea tests
 
+
+
+.PHONY: fix-lint
 fixlint: ## fix lint issues using autoflake, autopep8, and isort
-	find cardea -name '*.py' | xargs autoflake --in-place --remove-all-unused-imports --remove-unused-variables
+	find cardea -name '*.py' | xargs autoflake --in-place --remove-all-unused-imports --remove-unused-variables --ignore-init-module-imports
 	autopep8 --in-place --recursive --aggressive cardea
 	isort --apply --atomic --recursive cardea
 
-	find tests -name '*.py' | xargs autoflake --in-place --remove-all-unused-imports --remove-unused-variables
+	find tests -name '*.py' | xargs autoflake --in-place --remove-all-unused-imports --remove-unused-variables --ignore-init-module-imports
 	autopep8 --in-place --recursive --aggressive tests
 	isort --apply --atomic --recursive tests
 
 
-# TEST TARGETS
 
 
+
+# TEST TARGETS
+
+.PHONY: test
 test: ## run tests quickly with the default Python
 	pytest
 
+.PHONY: test-all
 test-all: ## run tests on every Python version with tox
 	tox
 
+
+
+
+
+.PHONY: coverage
 coverage: clean-coverage ## check code coverage quickly with the default Python
 	coverage run --source cardea -m pytest
 	coverage report -m
@@ -97,42 +129,90 @@ coverage: clean-coverage ## check code coverage quickly with the default Python
 
 # DOCS TARGETS
 
-
+.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
 	$(BROWSER) docs/_build/html/index.html
 
+.PHONY: servedocs
 servedocs: docs ## compile the docs watching for changes
 	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
 
 
 # RELEASE TARGETS
 
-
-release: dist ## package and upload a release
-	twine upload dist/*
-
-test-release: dist ## package and upload a release on TestPyPI
-	twine upload --repository-url https://test.pypi.org/legacy/ dist/*
-
+.PHONY: dist
 dist: clean ## builds source and wheel package
 	python setup.py sdist
 	python setup.py bdist_wheel
 	ls -l dist
 
+.PHONY: test-publish
+test-publish: dist ## package and upload a release on TestPyPI
+    twine upload --repository-url https://test.pypi.org/legacy/ dist/*
 
-# INSTALL TARGETS
-
-
-install: clean-build clean-pyc ## install the package to the active Python's site-packages
-	pip install .
-
-install-test: clean-build clean-pyc ## install the package and test dependencies
-	pip install .[test]
+.PHONY: publish
+publish: dist ## package and upload a release
+	twine upload dist/*
 
-install-develop: clean-build clean-pyc ## install the package in editable mode and dependencies for development
-	pip install -e .[dev]
+.PHONY: bumpversion-release
+bumpversion-release: ## Merge master to stable and bumpversion release
+	git checkout stable
+	git merge --no-ff master -m"make release-tag: Merge branch 'master' into stable"
+	bumpversion release
+	git push --tags origin stable
+
+.PHONY: bumpversion-patch
+bumpversion-patch: ## Merge stable to master and bumpversion patch
+	git checkout master
+	git merge stable
+	bumpversion --no-tag patch
+	git push
+
+.PHONY: bumpversion-candidate
+bumpversion-candidate: ## Bump the version to the next candidate
+	bumpversion candidate --no-tag
+	
+.PHONY: bumpversion-minor
+bumpversion-minor: ## Bump the version the next minor skipping the release
+	bumpversion --no-tag minor
+
+.PHONY: bumpversion-major
+bumpversion-major: ## Bump the version the next major skipping the release
+	bumpversion --no-tag major
+
+CURRENT_BRANCH := $(shell git rev-parse --abbrev-ref HEAD)
+CHANGELOG_LINES := $(shell git diff HEAD..stable HISTORY.md | wc -l)
+
+.PHONY: check-master
+check-master: ## Check if we are in master branch
+ifneq ($(CURRENT_BRANCH),master)
+	$(error Please make the release from master branch\n)
+endif
+
+.PHONY: check-history
+check-history: ## Check if HISTORY.md has been modified
+ifeq ($(CHANGELOG_LINES),0)
+	$(error Please insert the release notes in HISTORY.md before releasing)
+endif
+
+.PHONY: check-release
+check-release: check-master check-history ## Check if the release can be made
+	@echo "A new release can be made"
+
+.PHONY: release
+release: check-release bumpversion-release publish bumpversion-patch
+
+.PHONY: release-candidate
+release-candidate: check-master publish bumpversion-candidate
+
+.PHONY: release-minor
+release-minor: check-release bumpversion-minor release
+
+.PHONY: release-major
+release-major: check-release bumpversion-major release

README.md

@@ -2,20 +2,20 @@
 <img width=20% src="https://dai.lids.mit.edu/wp-content/uploads/2018/08/cardea.png" alt=“Cardea” />
 </p>
 
-<p align="center"> 
+<p align="left"> 
 <i>Cardea is a machine learning library built on top of FHIR schema. </I>
 </p>
 
-<p align="center"> 
+<p align="left"> 
 <i>An open source project from Data to AI Lab at MIT </I>
 </p>
 
 
 
-
+[![Development Status](https://img.shields.io/badge/Development%20Status-2%20--%20Pre--Alpha-yellow)](https://pypi.org/search/?c=Development+Status+%3A%3A+2+-+Pre-Alpha)
 [![PyPi Shield](https://img.shields.io/pypi/v/cardea.svg)](https://pypi.python.org/pypi/cardea)
-[![Travis CI Shield](https://travis-ci.org/D3-AI/Cardea.svg?branch=master)](https://travis-ci.org/D3-AI/Cardea)
-
+[![Travis CI Shield](https://travis-ci.org/DAI-Lab/Cardea.svg?branch=master)](https://travis-ci.org/DAI-Lab/Cardea)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/DAI-Lab/Cardea/master?filepath=notebooks)
 
 # Cardea
 
@@ -39,4 +39,4 @@ Cardea is a machine learning library built on top of the FHIR data schema. The l
 - Free software: MIT license
 
 ## Documentation
-- Documentation: https://D3-AI.github.io/Cardea
+- Documentation: https://dai-lab.github.io/Cardea

cardea/__init__.py

@@ -3,7 +3,7 @@
 
 __author__ = """MIT Data To AI Lab"""
 __email__ = 'dailabmit@gmail.com'
-__version__ = '0.0.1'
+__version__ = '0.1.0.dev3'
 
 import logging
 

cardea/cardea.py

@@ -162,7 +162,7 @@ def generate_features(self, cutoff):
 
     def execute_model(self, feature_matrix, target, primitives,
                       optimize=False, hyperparameters=None):
-        """Executes and predict all the pipelines.
+        """Executes and predicts all of the pipelines.
 
         This method executes the given pipeline and returns a list for all the pipelines
         with the result of each fold with its associated predicted values and actual values.
@@ -171,7 +171,7 @@ def execute_model(self, feature_matrix, target, primitives,
             data_frame: A dataframe, which encapsulates all the records of that entity.
             primitives_list: A list of the primitives within a pipeline.
             optimize: A boolean value which indicates whether to optimize the model or not.
-            hyperparameters: A dictionary of hyperparameters for each primitives.
+            hyperparameters: A dictionary of hyperparameters for each primitive.
 
         Returns:
             A list for all the executed pipelines and its result.
@@ -182,8 +182,8 @@ def execute_model(self, feature_matrix, target, primitives,
             target=target,
             primitives_list=primitives,
             problem_type=self.chosen_problem.prediction_type,
-            optimize=False,
-            hyperparameters=None
+            optimize=optimize,
+            hyperparameters=hyperparameters
         )
 
     def convert_to_json(dic):