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

Author: csala

.gitignore

@@ -64,6 +64,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/api/
 
 # PyBuilder
 target/

HISTORY.md

@@ -1,5 +1,11 @@
 # History
 
+## 0.1.2
+
+* Pin dependency versions to ensure reproducibility
+* Allow S3PipelineExplorer usage without AWS credentials
+* Fix minor bug in S3PipelineExplorer
+
 ## 0.1.1
 
 * Improved documentation

Makefile

@@ -29,6 +29,46 @@ BROWSER := python -c "$$BROWSER_PYSCRIPT"
 help:
 	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
 
+
+# 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
+	rm -f docs/api/*.rst
+	-$(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/
+
+.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 .
@@ -37,23 +77,18 @@ install: clean-build clean-pyc ## install the package to the active Python's sit
 install-test: clean-build clean-pyc ## install the package and test dependencies
 	pip install .[test]
 
-.PHONY: test
-test: ## run tests quickly with the default Python
-	python -m pytest
+.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 piex tests
 	isort -c --recursive piex tests
 
-.PHONY: install-develop
-install-develop: clean-build clean-pyc ## install the package in editable mode and dependencies for development
-	pip install -e .[dev]
-
-.PHONY: test-all
-test-all: ## run tests on every Python version with tox
-	tox
-
 .PHONY: fix-lint
 fix-lint: ## fix lint issues using autoflake, autopep8, and isort
 	find piex -name '*.py' | xargs autoflake --in-place --remove-all-unused-imports --remove-unused-variables
@@ -64,16 +99,30 @@ fix-lint: ## fix lint issues using autoflake, autopep8, and isort
 	autopep8 --in-place --recursive --aggressive tests
 	isort --apply --atomic --recursive tests
 
+
+# TEST TARGETS
+
+.PHONY: test
+test: ## run tests quickly with the default Python
+	python -m pytest
+
+.PHONY: test-all
+test-all: ## run tests on every Python version with tox
+	tox
+
 .PHONY: coverage
 coverage: ## check code coverage quickly with the default Python
 	coverage run --source piex -m pytest
 	coverage report -m
 	coverage html
 	$(BROWSER) htmlcov/index.html
 
+
+# DOCS TARGETS
+
 .PHONY: docs
 docs: clean-docs ## generate Sphinx HTML documentation, including API docs
-	sphinx-apidoc --module-first --separate -o docs/api/ piex
+	sphinx-apidoc --module-first --separate -T -o docs/api/ piex
 	$(MAKE) -C docs html
 
 .PHONY: view-docs
@@ -82,7 +131,10 @@ view-docs: docs ## view docs in browser
 
 .PHONY: serve-docs
 serve-docs: view-docs ## compile the docs watching for changes
-	watchmedo shell-command -W -R -D -p '*.rst;*.md' -c '$(MAKE) -C docs html' .
+	watchmedo shell-command -W -R -D -p '*.rst;*.md' -c '$(MAKE) -C docs html' docs
+
+
+# RELEASE TARGETS
 
 .PHONY: dist
 dist: clean ## builds source and wheel package
@@ -100,7 +152,7 @@ publish: dist ## package and upload a release
 
 .PHONY: bumpversion-release
 bumpversion-release: ## Merge master to stable and bumpversion release
-	git checkout stable
+	git checkout stable || git checkout -b stable
 	git merge --no-ff master -m"make release-tag: Merge branch 'master' into stable"
 	bumpversion release
 	git push --tags origin stable
@@ -120,8 +172,8 @@ bumpversion-minor: ## Bump the version the next minor skipping the release
 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)
+CURRENT_BRANCH := $(shell git rev-parse --abbrev-ref HEAD 2>/dev/null)
+CHANGELOG_LINES := $(shell git diff HEAD..origin/stable HISTORY.md 2>&1 | wc -l)
 
 .PHONY: check-release
 check-release: ## Check if the release can be made
@@ -130,6 +182,8 @@ ifneq ($(CURRENT_BRANCH),master)
 endif
 ifeq ($(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
@@ -140,37 +194,3 @@ release-minor: check-release bumpversion-minor release
 
 .PHONY: release-major
 release-major: check-release bumpversion-major release
-
-.PHONY: clean
-clean: clean-build clean-pyc clean-test clean-coverage 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-coverage
-clean-coverage: ## remove coverage artifacts
-	rm -f .coverage
-	rm -f .coverage.*
-	rm -fr htmlcov/
-
-.PHONY: clean-test
-clean-test: ## remove test artifacts
-	rm -fr .tox/
-	rm -fr .pytest_cache
-
-.PHONY: clean-docs
-clean-docs: ## remove previously built docs
-	rm -f docs/api/*.rst
-	-$(MAKE) -C docs clean 2>/dev/null  # this fails if sphinx is not yet installed

README.md

@@ -1,4 +1,10 @@
 
+<p align="left">
+<img width=15% src="https://dai.lids.mit.edu/wp-content/uploads/2018/06/Logo_DAI_highres.png" alt=“DAI-Lab” />
+<i>An open source project from Data to AI Lab at MIT.</i>
+</p>
+
+
 [![PyPI Shield](https://img.shields.io/pypi/v/piex.svg)](https://pypi.python.org/pypi/piex)
 [![Travis CI Shield](https://travis-ci.org/HDI-Project/piex.svg?branch=master)](https://travis-ci.org/HDI-Project/piex)
 
@@ -108,8 +114,8 @@ Each dataset was split using a holdout method in two parts, training and testing
 used respectively to find and fit the optimal pipeline for each dataset, and to later on
 evaluate the goodness-of-fit of each pipeline against a specific metric for each dataset.
 
-Each dataset is stored in Amazon S3 in the [D3M format](https://github.com/mitll/d3m-schema),
-including the training and testing partitioning, and available for download using piex.
+This collection of datasets is stored in an Amazon S3 Bucket in the [D3M format](https://github.com/mitll/d3m-schema),
+including the training and testing partitioning, and can be downloaded both using piex or a web browser following this link: https://d3m-data-dai.s3.amazonaws.com/index.html
 
 ### What is an experiment/test?
 

docs/conf.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# piex documentation build configuration file, created by
+# PiEx documentation build configuration file, created by
 # sphinx-quickstart on Fri Jun  9 13:47:02 2017.
 #
 # This file is execfile()d with the current directory set to its
@@ -17,14 +17,9 @@
 # directory, add these directories to sys.path here. If the directory is
 # relative to the documentation root, use os.path.abspath to make it
 # absolute, like shown here.
-#
-import os
-import sys
 
 import sphinx_rtd_theme # For read the docs theme
 
-sys.path.insert(0, os.path.abspath('..'))
-
 import piex
 
 # -- General configuration ---------------------------------------------
@@ -54,9 +49,13 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'D3M Pipeline Explorer'
-copyright = u'2018, MIT Data To AI Lab'
-author = u'MIT Data To AI Lab'
+project = 'PiEx'
+slug = 'piex'
+title = project + ' Documentation',
+copyright = '2018, MIT Data To AI Lab'
+author = 'MIT Data To AI Lab'
+description = 'Pipeline Explorer.'
+user = 'HDI-Project'
 
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
@@ -77,15 +76,14 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ['.py', '_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
-
 # -- Options for HTML output -------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -97,8 +95,8 @@
 # Readthedocs additions
 html_context = {
     'display_github': True,
-    'github_user': 'HDI-Project',
-    'github_repo': 'piex',
+    'github_user': user,
+    'github_repo': project,
     'github_version': 'master',
     'conf_py_path': '/docs/',
 }
@@ -114,13 +112,22 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+# html_static_path = ['_static']
+
+# The name of an image file (relative to this directory) to use as a favicon of
+# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+# html_favicon = 'images/favicon.ico'
 
+# If given, this must be the name of an image file (path relative to the
+# configuration directory) that is the logo of the docs. It is placed at
+# the top of the sidebar; its width should therefore not exceed 200 pixels.
+# html_logo = 'images/dai-logo.png'
 
 # -- Options for HTMLHelp output ---------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'piexdoc'
+htmlhelp_basename = slug + 'doc'
 
 
 # -- Options for LaTeX output ------------------------------------------
@@ -146,34 +153,39 @@
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass
 # [howto, manual, or own class]).
-latex_documents = [
-    (master_doc, 'piex.tex',
-     u'D3M Pipeline Explorer Documentation',
-     u'MIT Data To AI Lab', 'manual'),
-]
+latex_documents = [(
+    master_doc,
+    slug + '.tex',
+    title,
+    author,
+    'manual'
+)]
 
 
 # -- Options for manual page output ------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'piex',
-     u'D3M Pipeline Explorer Documentation',
-     [author], 1)
-]
+man_pages = [(
+    master_doc,
+    slug,
+    title,
+    [author],
+    1
+)]
 
 
 # -- Options for Texinfo output ----------------------------------------
 
 # Grouping the document tree into Texinfo files. List of tuples
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
-texinfo_documents = [
-    (master_doc, 'piex',
-     u'D3M Pipeline Explorer Documentation',
-     author,
-     'piex',
-     'One line description of project.',
-     'Miscellaneous'),
-]
+texinfo_documents = [(
+    master_doc,
+    slug,
+    title,
+    author,
+    slug,
+    description,
+    'Miscellaneous'
+)]

piex/__init__.py

@@ -4,4 +4,4 @@
 
 __author__ = """MIT Data To AI Lab"""
 __email__ = '[email protected]'
-__version__ = '0.1.1'
+__version__ = '0.1.2-dev'