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

Author: csala

CONTRIBUTING.rst

@@ -69,8 +69,7 @@ Ready to contribute? Here's how to set up `Copulas` for local development.
 
     $ mkvirtualenv Copulas
     $ cd Copulas/
-    $ pip install -e .
-    $ pip install -r requirements_dev.txt
+    $ make install-develop
 
 4. Create a branch for local development::
 
@@ -181,14 +180,16 @@ The process of releasing a new version involves several steps combining both ``g
 these changes are committed and available in ``master`` branch.
 Normally this is just a list of the Pull Requests that have been merged since the latest version.
 
-Once this is done, just run the following commands::
+Once this is done, run of the following commands:
+
+1. If you are releasing a patch version::
 
-    git checkout stable
-    git merge --no-ff master    # This creates a merge commit
-    bumpversion release   # This creates a new commit and a TAG
-    git push --tags origin stable
     make release
-    git checkout master
-    git merge stable
-    bumpversion --no-tag patch
-    git push
+
+2. If you are releasing a minor version::
+
+    make release-minor
+
+3. If you are releasing a major version::
+
+    make release-major

HISTORY.md

@@ -1,5 +1,22 @@
 # History
 
+## 0.2.1 - Vine serialization
+
+* Add serialization to Vine copulas.
+* Add `distribution` as argument for the Gaussian Copula.
+* Improve Bivariate Copulas code structure to remove code duplication.
+* Fix bug in Vine Copulas sampling: 'Edge' object has no attribute 'index'
+* Improve code documentation.
+* Improve code style and linting tools configuration.
+
+## 0.2.0 - Unified API
+
+* New API for stats methods.
+* Standarize input and output to `numpy.ndarray`.
+* Increase unittest coverage to 90%.
+* Add methods to load/save copulas.
+* Improve Gaussian copula sampling accuracy.
+
 ## 0.1.1 - Minor Improvements
 
 * Different Copula types separated in subclasses

Makefile

@@ -1,4 +1,3 @@
-.PHONY: clean clean-test clean-pyc clean-build clean-docs docs help
 .DEFAULT_GOAL := help
 
 define BROWSER_PYSCRIPT
@@ -26,38 +25,71 @@ export PRINT_HELP_PYSCRIPT
 
 BROWSER := python -c "$$BROWSER_PYSCRIPT"
 
+.PHONY: help
 help:
 	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
 
-clean: clean-build clean-pyc clean-test clean-docs ## remove all build, test, coverage, docs and Python artifacts
 
+# CLEAN TARGETS
+
+.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
+	-$(MAKE) -C docs clean 2>/dev/null  # this fails if sphinx is not yet installed
+
+.PHONY: clean-coverage
 clean-coverage: ## remove coverage artifacts
 	rm -f .coverage
 	rm -f .coverage.*
 	rm -fr htmlcov/
 
-clean-test: ## remove test and coverage artifacts
+.PHONY: clean-test
+clean-test: ## remove test 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
+
+
+# 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 copulas tests examples
 	isort -c --recursive copulas tests examples
 
-fixlint: ## fix lint issues using autoflake, autopep8, and isort
+.PHONY: fix-lint
+fix-lint: ## fix lint issues using autoflake, autopep8, and isort
 	find copulas -name '*.py' | xargs autoflake --in-place --remove-all-unused-imports --remove-unused-variables
 	autopep8 --in-place --recursive --aggressive copulas
 	isort --apply --atomic --recursive copulas
@@ -70,45 +102,97 @@ fixlint: ## fix lint issues using autoflake, autopep8, and isort
 	autopep8 --in-place --recursive --aggressive examples
 	isort --apply --atomic --recursive examples
 
+# TEST TARGETS
+
+.PHONY: test
 test: ## run tests quickly with the default Python
-	pytest
+	python -m pytest --cov=copulas
 
+.PHONY: test-all
 test-all: ## run tests on every Python version with tox
 	tox
 
-coverage: clean-coverage ## check code coverage quickly with the default Python
+.PHONY: coverage
+coverage: ## check code coverage quickly with the default Python
 	coverage run --source copulas -m pytest
 	coverage report -m
 	coverage html
 	$(BROWSER) htmlcov/index.html
 
-clean-docs: ## remove previously built docs
-	rm -f docs/copulas.rst
-	rm -f docs/copulas.*.rst
-	rm -f docs/modules.rst
-	$(MAKE) -C docs clean
 
+# DOCS TARGETS
+
+.PHONY: docs
 docs: clean-docs ## generate Sphinx HTML documentation, including API docs
-	sphinx-apidoc -o docs/ copulas
 	$(MAKE) -C docs html
 	touch docs/_build/html/.nojekyll
 
-viewdocs: docs ## view docs in browser
+.PHONY: view-docs
+view-docs: docs ## view docs in browser
 	$(BROWSER) docs/_build/html/index.html
 
-servedocs: docs ## compile the docs watching for changes
-	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
+.PHONY: serve-docs
+serve-docs: view-docs ## compile the docs watching for changes
+	watchmedo shell-command -W -R -D -p '*.rst;*.md' -c '$(MAKE) -C docs html' docs
 
-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/*
+# RELEASE TARGETS
 
+.PHONY: dist
 dist: clean ## builds source and wheel package
 	python setup.py sdist
 	python setup.py bdist_wheel
 	ls -l dist
 
-install: clean ## install the package to the active Python's site-packages
-	python setup.py install
+.PHONY: test-publish
+test-publish: dist ## package and upload a release on TestPyPI
+	twine upload --repository-url https://test.pypi.org/legacy/ dist/*
+
+.PHONY: publish
+publish: dist ## package and upload a release
+	twine upload dist/*
+
+.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-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 := $(shell git diff HEAD..stable HISTORY.md | wc -l)
+
+.PHONY: check-release
+check-release: ## Check if the release can be made
+ifneq ($(CURRENT_BRANCH),master)
+	$(error Please make the release from master branch\n)
+endif
+ifeq ($(CHANGELOG_LINES),0)
+	$(error Please insert the release notes in HISTORY.md before releasing)
+else
+	@echo "A new release can be made"
+endif
+
+.PHONY: release
+release: check-release bumpversion-release publish bumpversion-patch
+
+.PHONY: release-minor
+release-minor: check-release bumpversion-minor release
+
+.PHONY: release-major
+release-major: check-release bumpversion-major release

README.md

@@ -1,11 +1,12 @@
-[![][pypi-img]][pypi-url]
-[![][travis-img]][travis-url]
-
 <p align="left">
 <img width=15% src="https://dai.lids.mit.edu/wp-content/uploads/2018/06/Logo_DAI_highres.png" alt=“Copulas” />
 <i>An open source project from Data to AI Lab at MIT.</i>
 </p>
 
+
+[![][pypi-img]][pypi-url]
+[![][travis-img]][travis-url]
+
 # Copulas
 
 [travis-img]: https://travis-ci.org/DAI-Lab/Copulas.svg?branch=master
@@ -80,11 +81,11 @@ a python terminal.
 >>> data = pd.read_csv('data/iris.data.csv')
 >>> data.head()
    feature_01  feature_02  feature_03  feature_04
-   0         5.1         3.5         1.4         0.2
-   1         4.9         3.0         1.4         0.2
-   2         4.7         3.2         1.3         0.2
-   3         4.6         3.1         1.5         0.2
-   4         5.0         3.6         1.4         0.2
+0         5.1         3.5         1.4         0.2
+1         4.9         3.0         1.4         0.2
+2         4.7         3.2         1.3         0.2
+3         4.6         3.1         1.5         0.2
+4         5.0         3.6         1.4         0.2
 ```
 
 Once we have the data, we can pass it into the GaussianUnivariate class.
@@ -95,22 +96,21 @@ Once we have the data, we can pass it into the GaussianUnivariate class.
 >>> gu.fit(feature1)
 >>> print(gu)
 Distribution Type: Gaussian
-mean =  5.843333333333335
-standard deviation =  0.8253012917851409
-max =  7.9
-min =  4.3
+Variable name: feature_01
+Mean: 5.843333333333334
+Standard deviation: 0.8253012917851409
 ```
 
 Once you fit the distribution, you can get the pdf or cdf of data points and you can sample
 from the distribution.
 
 ```python
->>> gu.get_pdf(5)
-0.28678585054723732
->>> gu.get_cdf(5)
-0.15342617720079199
+>>> gu.probability_density(5)
+0.2867858505472377
+>>> gu.cumulative_distribution(5)
+0.15342617720079227
 >>> gu.sample(1)
-array([ 6.14745446])
+array([6.14745446])
 ```
 
 ### Creating a Gaussian Copula
@@ -129,47 +129,27 @@ Distribution Type: Gaussian
 Variable name: feature_01
 Mean: 5.843333333333334
 Standard deviation: 0.8253012917851409
-Max: 7.9
-Min: 4.3
 
 feature_02
 ===============
 Distribution Type: Gaussian
 Variable name: feature_02
 Mean: 3.0540000000000003
 Standard deviation: 0.4321465800705435
-Max: 4.4
-Min: 2.0
 
 feature_03
 ===============
 Distribution Type: Gaussian
 Variable name: feature_03
 Mean: 3.758666666666666
 Standard deviation: 1.7585291834055212
-Max: 6.9
-Min: 1.0
 
 feature_04
 ===============
 Distribution Type: Gaussian
 Variable name: feature_04
 Mean: 1.1986666666666668
 Standard deviation: 0.7606126185881716
-Max: 2.5
-Min: 0.1
-
-Copula Distribution:
-     feature_01  feature_02  feature_03  feature_04
-0     -0.900681    1.032057   -1.341272   -1.312977
-1     -1.143017   -0.124958   -1.341272   -1.312977
-2     -1.385353    0.337848   -1.398138   -1.312977
-3     -1.506521    0.106445   -1.284407   -1.312977
-4     -1.021849    1.263460   -1.341272   -1.312977
-5     -0.537178    1.957669   -1.170675   -1.050031
-...
-
-[150 rows x 4 columns]
 
 Covariance matrix:
 [[ 1.26935536  0.64987728  0.94166734 ... -0.57458312 -0.14548004
@@ -185,10 +165,6 @@ Covariance matrix:
    0.14455133]
  [-0.43589371 -0.21867228 -0.27836438 ...  0.19208669  0.14455133
    0.22229033]]
-
-Means:
-[-3.315866100213801e-16, -7.815970093361102e-16, 2.842170943040401e-16, -2.3684757858670006e-16]
-
 ```
 
 Once you have fit the copula, you can sample from it.