Merge pull request #1 from weaverba137/pre-0.3

Changes in preparation for version 0.3

.coveragerc

@@ -0,0 +1,25 @@
+[run]
+source = hpsspy
+omit =
+   hpsspy/_version.py
+   hpsspy/conftest*
+   hpsspy/cython_version*
+   hpsspy/setup_package*
+   hpsspy/*/setup_package*
+   hpsspy/*/*/setup_package*
+   hpsspy/test/*
+
+[report]
+exclude_lines =
+   # Have to re-enable the standard pragma
+   pragma: no cover
+
+   # Don't complain about packages we have installed
+   except ImportError
+
+   # Don't complain if tests don't hit assertions
+   raise AssertionError
+   raise NotImplementedError
+
+   # Don't complain about script hooks
+   def main\(.*\):

.gitignore

@@ -1,3 +1,4 @@
+# Compiled files
 *.py[cod]
 
 # C extensions
@@ -13,16 +14,13 @@ parts
 bin
 var
 sdist
+MANIFEST
 develop-eggs
 .installed.cfg
 lib
 lib64
 __pycache__
 
-# Other generated files
-*/version.py
-hpsspy/hpsspy.cfg
-
 # Sphinx
 _build
 _static
@@ -32,6 +30,7 @@ _generated
 pip-log.txt
 
 # Unit test / coverage reports
+htmlcov/
 .coverage
 .tox
 nosetests.xml

.travis.yml

@@ -0,0 +1,81 @@
+#
+# IMPORTANT.  OS X support is so experimental that you have to specifically
+# request to have it enabled, on a per-repository basis.  See
+# http://docs.travis-ci.com/user/multi-os/#Manual-intervention-required
+#
+# This file will still work, without OS X enabled, it just won't run those
+# tests.
+#
+language: python
+
+os:
+    - linux
+    # - osx
+
+# Setting sudo to false opts in to Travis-CI container-based builds.
+sudo: false
+
+# The apt packages below are needed for sphinx builds, which can no longer
+# be installed with sudo apt-get.
+addons:
+    apt:
+        packages:
+            - graphviz
+            - texlive-latex-extra
+            - dvipng
+python:
+    - 2.7
+    - 3.3
+    - 3.4
+    - 3.5
+env:
+    global:
+        # The following versions are the 'default' for tests, unless
+        # overidden underneath. They are defined here in order to save having
+        # to repeat them for all configurations.
+        - MAIN_CMD='python setup.py'
+    matrix:
+        - SETUP_CMD='egg_info'
+        - SETUP_CMD='bdist_egg'
+        - SETUP_CMD='test'
+
+matrix:
+    # Don't wait for allowed failures.
+    fast_finish: true
+
+    # OS X support is still experimental, so don't penalize failuures.
+    allow_failures:
+        - os: osx
+
+    include:
+        # Check for sphinx doc build warnings - we do this first because it
+        # runs for a long time
+        - os: linux
+          python: 3.5
+          env: SETUP_CMD='build_sphinx'
+          # -w is an astropy extension
+
+        # Coverage test, pass the results to coveralls.
+        - os: linux
+          python: 3.5
+          env: MAIN_CMD='coverage' SETUP_CMD='run hpsspy/test/hpsspy_test_suite.py'
+
+        # PEP 8 compliance.
+        - os: linux
+          python: 3.5
+          env: MAIN_CMD='pep8' SETUP_CMD='--count hpsspy'
+
+# before_install:
+#     - curl ipinfo.io
+
+install:
+    - if [[ $MAIN_CMD == 'pep8' ]]; then pip install pep8; fi
+    - if [[ $SETUP_CMD == 'build_sphinx' ]]; then pip install Sphinx; fi
+    - if [[ $MAIN_CMD == 'coverage' ]]; then pip install coverage coveralls; fi
+    # - pip install -r requirements.txt
+
+script:
+    - $MAIN_CMD $SETUP_CMD
+
+after_success:
+    - if [[ $MAIN_CMD == 'coverage' ]]; then coveralls; fi

LICENSE.rst

@@ -1,4 +1,4 @@
-Copyright (c) 2014, Benjamin Alan Weaver <benjamin.weaver@nyu.edu>
+Copyright (c) 2014-2017, Benjamin Alan Weaver <baweaver@lbl.gov>
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification,

MANIFEST.in

@@ -1,7 +1,4 @@
 include LICENSE.rst
 include README.rst
-include ez_setup.py
 
 graft doc
-
-prune doc/_build

README.rst

@@ -1,11 +1,35 @@
 ======
-hpsspy
+HPSSPy
 ======
 
+.. image:: https://img.shields.io/pypi/l/hpsspy.svg
+    :target: https://pypi.python.org/pypi/hpsspy
+    :alt: License
+
+.. image:: https://img.shields.io/pypi/v/hpsspy.svg
+    :target: https://pypi.python.org/pypi/hpsspy
+    :alt: PyPI Badge
+
+.. image:: https://img.shields.io/pypi/dm/hpsspy.svg
+    :target: https://pypi.python.org/pypi/hpsspy
+    :alt: PyPI Downloads
+
+.. image:: https://img.shields.io/travis/weaverba137/hpsspy.svg
+    :target: https://travis-ci.org/weaverba137/hpsspy
+    :alt: Travis Build Status
+
+.. image:: https://coveralls.io/repos/github/weaverba137/hpsspy/badge.svg?branch=pre-0.3
+    :target: https://coveralls.io/github/weaverba137/hpsspy?branch=pre-0.3
+    :alt: Test Coverage Status
+
+.. image:: https://readthedocs.org/projects/hpsspy/badge/?version=pre-0.3
+    :target: http://hpsspy.readthedocs.io/en/latest/?badge=pre-0.3
+    :alt: Documentation Status
+
 Overview
 --------
 
-Hpsspy is a Python_ package for interacting with the HPSS_ tape storage
+HPSSPy is a Python_ package for interacting with the HPSS_ tape storage
 system at NERSC_.  It is currently being developed on GitHub_.
 
 .. _Python: http://python.org
@@ -16,13 +40,13 @@ system at NERSC_.  It is currently being developed on GitHub_.
 Requirements
 ------------
 
-Hpsspy assumes that the HPSS utilities `hsi and htar`_ are installed.  You may
+HPSSPy assumes that the HPSS utilities `hsi and htar`_ are installed.  You may
 need a NERSC account to download and install these utilities.
 
 .. _`hsi and htar`: https://www.nersc.gov/users/data-and-file-systems/hpss/storing-and-retrieving-data/software-downloads/
 
 License
 -------
 
-Hpsspy is free software licensed under a 3-clause BSD-style license. For details see
+HPSSPy is free software licensed under a 3-clause BSD-style license. For details see
 the ``LICENSE.rst`` file.

doc/api.rst

@@ -0,0 +1,19 @@
+==========
+HPSSPy API
+==========
+
+.. automodule:: hpsspy
+   :members:
+
+.. automodule:: hpsspy.os
+   :members:
+   :imported-members:
+
+.. automodule:: hpsspy.os.path
+   :members:
+
+.. automodule:: hpsspy.scan
+   :members:
+
+.. automodule:: hpsspy.util
+   :members:

doc/changes.rst

@@ -2,10 +2,11 @@
 Release Notes
 =============
 
-0.2.2 (unreleased)
+0.3.0 (unreleased)
 ------------------
 
-* No changes yet.
+* General refresh of Python code, documentation, test suite.
+* Command-line inputs are no longer rigidly restricted to SDSS or DESI.
 
 0.2.1 (2015-04-22)
 ------------------

doc/conf.py

@@ -14,12 +14,12 @@
 
 import sys
 import os
-import hpsspy
+# import hpsspy
 
 # 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.
-#sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath('..'))
 
 # -- General configuration ------------------------------------------------
 
@@ -31,16 +31,24 @@
 # ones.
 extensions = [
     'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.doctest',
     'sphinx.ext.intersphinx',
     'sphinx.ext.todo',
-    'sphinx.ext.coverage',
     'sphinx.ext.mathjax',
     'sphinx.ext.viewcode',
-    'hpsspy.sphinx.ext.numpydoc'
+    'sphinx.ext.napoleon'
 ]
 
+# Configuration for intersphinx, copied from astropy.
+intersphinx_mapping = {
+    'python': ('http://docs.python.org/', None),
+    # 'python3': ('http://docs.python.org/3/', path.abspath(path.join(path.dirname(__file__), 'local/python3links.inv'))),
+    'numpy': ('http://docs.scipy.org/doc/numpy/', None),
+    'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
+    'matplotlib': ('http://matplotlib.org/', None),
+    'astropy': ('http://docs.astropy.org/en/stable/', None),
+    'h5py': ('http://docs.h5py.org/en/latest/', None)
+    }
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -56,16 +64,19 @@
 # General information about the project.
 project = u'hpsspy'
 author = 'Benjamin Alan Weaver'
-copyright = u'2015, Benjamin Alan Weaver'
+copyright = u'2014-2017, Benjamin Alan Weaver'
 
 # 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.
-#
+
+__import__(project)
+package = sys.modules[project]
+
 # The short X.Y version.
-version = hpsspy.__version__.split('-', 1)[0]
+version = package.__version__.split('-', 1)[0]
 # The full version, including alpha/beta/rc tags.
-release = hpsspy.__version__
+release = package.__version__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -86,7 +97,7 @@
 #default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
@@ -103,16 +114,23 @@
 #modindex_common_prefix = []
 
 # If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
+keep_warnings = False
 
-# Supress warnings about nonexistent documents.
-numpydoc_show_class_members = False
+# Include functions that begin with an underscore, e.g. _private().
+napoleon_include_private_with_doc = True
 
 # -- 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 = 'default'
+#html_theme = 'default'
+#html_theme = 'haiku'
+try:
+    import sphinx_rtd_theme
+    html_theme = 'sphinx_rtd_theme'
+    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+except ImportError:
+    pass
 
 # 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
@@ -270,7 +288,3 @@
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
 #texinfo_no_detailmenu = False
-
-
-# Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'http://docs.python.org/': None}