Merge pull request #6 from molssi-seamm/description

Description

.gitignore

@@ -1,8 +1,85 @@
+# -*- mode: gitignore; -*-
+
+## emacs: https://github.com/github/gitignore/blob/master/Global/Emacs.gitignore
+*~
+\#*\#
+/.emacs.desktop
+/.emacs.desktop.lock
+*.elc
+auto-save-list
+tramp
+.\#*
+
+# Org-mode
+.org-id-locations
+*_archive
+
+# flymake-mode
+*_flymake.*
+
+# eshell files
+/eshell/history
+/eshell/lastdir
+
+# elpa packages
+/elpa/
+
+# reftex files
+*.rel
+
+# AUCTeX auto folder
+/auto/
+
+# cask packages
+.cask/
+dist/
+
+# Flycheck
+flycheck_*.el
+
+# server auth directory
+/server/
+
+# projectiles files
+.projectile
+
+# directory configuration
+.dir-locals.el
+
+# network security
+/network-security.data
+## end of emacs
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
 *$py.class
 
+## macOS useful to ignore https://github.com/github/gitignore/blob/master/Global/macOS.gitignore
+*.DS_Store
+.AppleDouble
+.LSOverride
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+## end of macOS
+
 # C extensions
 *.so
 
@@ -55,8 +132,18 @@ coverage.xml
 # Sphinx documentation
 docs/_build/
 
+# IntelliJ Idea family of suites
+.idea
+*.iml
+## File-based project format:
+*.ipr
+*.iws
+## mpeltonen/sbt-idea plugin
+.idea_modules/
+
 # PyBuilder
 target/
 
-# pyenv python configuration file
-.python-version
+# Cookiecutter
+output/
+python_boilerplate/

.pyup.yml

@@ -0,0 +1,64 @@
+# configure updates globally
+# default: all
+# allowed: all, insecure, False
+update: insecure
+
+# configure dependency pinning globally
+# default: True
+# allowed: True, False
+pin: False
+
+# set the default branch
+# default: empty, the default branch on GitHub
+# branch: dev
+
+# update schedule
+# default: empty
+# allowed: "every day", "every week", ..
+schedule: "every day"
+
+# search for requirement files
+# default: True
+# allowed: True, False
+search: False
+
+# Specify requirement files by hand, default is empty
+# default: empty
+# allowed: list
+requirements:
+  - requirements_install.txt:
+      # update insecure only
+      update: insecure
+      pin: False
+  - requirements.txt:
+      # update all dependencies and pin them
+      update: all
+      pin: True
+  - requirements_dev.txt:
+      # update insecure only
+      update: insecure
+      pin: False
+
+# add a label to pull requests, default is not set
+# requires private repo permissions, even on public repos
+# default: empty
+# label_prs: update
+
+# assign users to pull requests, default is not set
+# requires private repo permissions, even on public repos
+# default: empty
+# assignees:
+#  - carl
+#  - carlsen
+
+# configure the branch prefix the bot is using
+# default: pyup-
+# branch_prefix: pyup/
+
+# set a global prefix for PRs
+# default: empty
+# pr_prefix: "Bug #12345"
+
+# allow to close stale PRs
+# default: True
+close_prs: True

.yapfignore

@@ -0,0 +1,2 @@
+loop_step/_version.py
+loop_step/*_parameters.py

Makefile

@@ -48,14 +48,17 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr .tox/
 	rm -f .coverage
 	rm -fr htmlcov/
+	find . -name '.pytype' -exec rm -fr {} +
 
-lint: ## check style with yapf
+lint: ## check style with flake8
 	flake8 $(MODULE) tests
-#	yapf --diff --recursive $(MODULE) tests
+	yapf --diff --recursive  $(MODULE) tests
 
 format: ## reformat with with yapf and isort
 	yapf --recursive --in-place $(MODULE) tests
-#	isort --recursive --atomic $(MODULE) tests
+
+typing: ## check typing
+	pytype $(MODULE)
 
 test: ## run tests quickly with the default Python
 	py.test

loop_step/__init__.py

@@ -1,10 +1,9 @@
 # -*- coding: utf-8 -*-
 
-"""Top-level package for Loop Step."""
-
-__author__ = """Paul Saxe"""
-__email__ = '[email protected]'
-__version__ = '0.1.0'
+"""
+loop_step
+A step for loops in the SEAMM flowcharts
+"""
 
 # Bring up the classes so that they appear to be directly in
 # the loop_step package.
@@ -13,3 +12,12 @@
 from loop_step.loop_parameters import LoopParameters  # noqa: F401
 from loop_step.loop_step import LoopStep  # noqa: F401
 from loop_step.tk_loop import TkLoop  # noqa: F401
+
+# Handle versioneer
+from ._version import get_versions
+__author__ = """Paul Saxe"""
+__email__ = '[email protected]'
+versions = get_versions()
+__version__ = versions['version']
+__git_revision__ = versions['full-revisionid']
+del get_versions, versions

loop_step/_version.py

@@ -42,7 +42,7 @@ def get_config():
     cfg.style = "pep440"
     cfg.tag_prefix = ""
     cfg.parentdir_prefix = "None"
-    cfg.versionfile_source = "forcefield_step/_version.py"
+    cfg.versionfile_source = "loop_step/_version.py"
     cfg.verbose = False
     return cfg