Merge pull request #157 from CellProfiling/0.4.0

0.4.0

.coveragerc

@@ -0,0 +1,5 @@
+[report]
+exclude_lines =
+    def __repr__
+    raise AssertionError
+    raise NotImplementedError

.gitignore

@@ -1,13 +1,13 @@
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
+*$py.class
 
 # C extensions
 *.so
 
 # Distribution / packaging
 .Python
-env/
 build/
 develop-eggs/
 dist/
@@ -19,9 +19,13 @@ lib64/
 parts/
 sdist/
 var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
+MANIFEST
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -36,28 +40,97 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
+.nox/
 .coverage
 .coverage.*
 .cache
 nosetests.xml
 coverage.xml
-*,cover
+*.cover
+.hypothesis/
+.pytest_cache/
 
 # Translations
 *.mo
 *.pot
 
 # Django stuff:
 *.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
 
 # Sphinx documentation
 docs/_build/
 
 # PyBuilder
 target/
 
-# imdone
-.imdone/
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# tiffs
+*.tif
+
+# pngs
+*.png
 
-# IPython notebook
-.ipynb_checkpoints/
+# Visual Studio Code
+.vscode/*
+!.vscode/cSpell.json
+!.vscode/extensions.json
+!.vscode/tasks.json

.pre-commit-config.yaml

@@ -0,0 +1,8 @@
+# See https://pre-commit.com/
+# See https://github.com/psf/black#version-control-integration
+repos:
+  - repo: https://github.com/psf/black
+    rev: stable
+    hooks:
+      - id: black
+        language_version: python3.6

.pyup.yml

@@ -0,0 +1,13 @@
+# configure updates globally
+# default: all
+# allowed: all, insecure, False
+update: all
+
+# set the default branch
+# default: empty, the default branch on GitHub
+branch: develop
+
+# update schedule
+# default: empty
+# allowed: "every day", "every week", ..
+schedule: "every month"

.readthedocs.yml

@@ -0,0 +1,20 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: requirements_docs.txt
+    - path: .

.travis.yml

@@ -1,14 +1,24 @@
+dist: xenial
 language: python
+cache: pip
 python:
-  - "2.7"
-virtualenv:
-  system_site_packages: true
-sudo: false
-addons:
-  apt:
-    packages:
-    - python-numpy
-# command to install dependencies
-install: pip install tox-travis
-# command to run tests
+  - "3.6"
+  - "3.7"
+  - "3.8"
+install:
+  - pip install -U tox-travis
+  - pip install -r requirements_tests.txt
+before_script: "./scripts/setup_tests.py"
 script: tox
+deploy:
+  provider: pypi
+  username:
+    secure: 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
+  password:
+    secure: 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
+  edge: true
+  distributions: sdist bdist_wheel
+  skip_existing: true
+  on:
+    tags: true
+    python: "3.6"