Remove outdated or cookie-cutter generated files

Makefile

-.PHONY: clean clean-test clean-pyc clean-build docs help
-.DEFAULT_GOAL := help
-
-define BROWSER_PYSCRIPT
-import os, webbrowser, sys
-
-try:
-	from urllib import pathname2url
-except:
-	from urllib.request import pathname2url
-
-webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
-endef
-export BROWSER_PYSCRIPT
-
-define PRINT_HELP_PYSCRIPT
-import re, sys
-
-for line in sys.stdin:
-	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
-	if match:
-		target, help = match.groups()
-		print("%-20s %s" % (target, help))
-endef
-export PRINT_HELP_PYSCRIPT
-
-BROWSER := python -c "$$BROWSER_PYSCRIPT"
-
-help:
-	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
-
-clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
-
-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 {} +
-
-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 {} +
-
-clean-test: ## remove test and coverage artifacts
-	rm -fr .tox/
-	rm -f .coverage
-	rm -fr htmlcov/
-	rm -fr .pytest_cache
-
-lint: ## check style with flake8
-	flake8 nexus tests
-
-test: ## run tests quickly with the default Python
-	python setup.py test
-
-
-test-all: ## run tests on every Python version with tox
-	tox
-
-coverage: ## check code coverage quickly with the default Python
-	coverage run --source nexus setup.py test
-	coverage report -m
-	coverage html
-	$(BROWSER) htmlcov/index.html
-
-docs: ## generate Sphinx HTML documentation, including API docs
-	rm -f docs/nexus.rst
-	rm -f docs/modules.rst
-	sphinx-apidoc -o docs/ nexus
-	$(MAKE) -C docs clean
-	$(MAKE) -C docs html
-	$(BROWSER) docs/_build/html/index.html
-
-servedocs: docs ## compile the docs watching for changes
-	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
-
-release: dist ## package and upload a release
-	twine upload 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

docs/Makefile

-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = python -msphinx
-SPHINXPROJ    = nexus
-SOURCEDIR     = .
-BUILDDIR      = _build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/authors.rst

-.. include:: ../AUTHORS.rst

docs/conf.py

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# nexus 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
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-# If extensions (or modules to document with autodoc) are in another
-# 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
-sys.path.insert(0, os.path.abspath('..'))
-
-import nexus
-
-# -- General configuration ---------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#
-# needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode']
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-#
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = u'nexus'
-copyright = u"2018, IRIS PASSCAL"
-author = u"IRIS PASSCAL"
-
-# The version info for the project you're documenting, acts as replacement
-# for |version| and |release|, also used in various other places throughout
-# the built documents.
-#
-# The short X.Y version.
-version = nexus.__version__
-# The full version, including alpha/beta/rc tags.
-release = nexus.__version__
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
-
-# 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']
-
-# 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
-# a list of builtin themes.
-#
-html_theme = 'alabaster'
-
-# Theme options are theme-specific and customize the look and feel of a
-# theme further.  For a list of options available for each theme, see the
-# documentation.
-#
-# html_theme_options = {}
-
-# 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']
-
-
-# -- Options for HTMLHelp output ---------------------------------------
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'nexusdoc'
-
-
-# -- Options for LaTeX output ------------------------------------------
-
-latex_elements = {
-    # The paper size ('letterpaper' or 'a4paper').
-    #
-    # 'papersize': 'letterpaper',
-
-    # The font size ('10pt', '11pt' or '12pt').
-    #
-    # 'pointsize': '10pt',
-
-    # Additional stuff for the LaTeX preamble.
-    #
-    # 'preamble': '',
-
-    # Latex figure (float) alignment
-    #
-    # 'figure_align': 'htbp',
-}
-
-# 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, 'nexus.tex',
-     u'nexus Documentation',
-     u'IRIS PASSCAL', '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, 'nexus',
-     u'nexus Documentation',
-     [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, 'nexus',
-     u'nexus Documentation',
-     author,
-     'nexus',
-     'One line description of project.',
-     'Miscellaneous'),
-]
-
-
-

docs/contributing.rst

-.. include:: ../CONTRIBUTING.rst

docs/history.rst

-.. include:: ../HISTORY.rst

docs/index.rst

-Welcome to nexus's documentation!
-======================================
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-
-   readme
-   installation
-   usage
-   modules
-   contributing
-   authors
-   history
-
-Indices and tables
-==================
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

docs/installation.rst

-.. highlight:: shell
-
-============
-Installation
-============
-
-
-Stable release
---------------
-
-To install nexus, run this command in your terminal:
-
-.. code-block:: console
-
-    $ pip install nexus
-
-This is the preferred method to install nexus, as it will always install the most recent stable release.
-
-If you don't have `pip`_ installed, this `Python installation guide`_ can guide
-you through the process.
-
-.. _pip: https://pip.pypa.io
-.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
-
-
-From sources
-------------
-
-The sources for nexus can be downloaded from the `Github repo`_.
-
-You can either clone the public repository:
-
-.. code-block:: console
-
-    $ git clone https://git.passcal.nmt.edu/passoft/nexus
-
-Or download the `tarball`_:
-
-.. code-block:: console
-
-    $ curl  -OL https://git.passcal.nmt.edu/passoft/nexus/tarball/master
-
-Once you have a copy of the source, you can install it with:
-
-.. code-block:: console
-
-    $ python setup.py install
-
-
-.. _Github repo: https://git.passcal.nmt.edu/passoft/nexus
-.. _tarball: https://git.passcal.nmt.edu/passoft/nexus/tarball/master

docs/make.bat

-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=python -msphinx
-)
-set SOURCEDIR=.
-set BUILDDIR=_build
-set SPHINXPROJ=nexus
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The Sphinx module was not found. Make sure you have Sphinx installed,
-	echo.then set the SPHINXBUILD environment variable to point to the full
-	echo.path of the 'sphinx-build' executable. Alternatively you may add the
-	echo.Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-
-:end
-popd

docs/readme.rst

-.. include:: ../README.rst

docs/usage.rst

-=====
-Usage
-=====
-
-To use nexus in a project::
-
-    import nexus

pyinstaller.sh

-pyinstaller -d -y --clean debug_nexus --log-level DEBUG\
-	--add-data '/Users/lloyd/code/obspy/obspy/imaging/data/*.npz:obspy/imaging/data/'
-#pyinstaller -d -y --clean debug_nexus --log-level DEBUG\

run_nexus

-#!/usr/bin/env python
-'''
-Launch nexus in a similar way as entry_point console_scripts.
-For testing, don't use
-'''
-from nexus import nexus
-
-nexus.main()