Docs

.travis.yml

@@ -1,3 +1,5 @@
+# use http://lint.travis-ci.org/ to check the file.
+
 language: python
 
 sudo: required
@@ -8,6 +10,10 @@ cache:
   directories:
     - $HOME/miniconda
 
+env:
+  global:
+    - secure:` "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"
+
 # Removing the directory will remove the env but leave the cached packages
 # at $HOME/miniconda/pkgs. That is a win-win because when re-creating the
 # env we will download only the new packages.
@@ -48,6 +54,8 @@ matrix:
     env: TEST_TARGET=default
   - python: 2.7
     env: TEST_TARGET=coding_standards
+  - python: 3.6
+    env: TEST_TARGET=docs
   allow_failures:
   - python: 2.7
     env: TEST_TARGET=coding_standards
@@ -72,6 +80,7 @@ before_install:
   - export PATH="$HOME/miniconda/bin:$PATH"
   - conda config --set always_yes yes --set changeps1 no --set show_channel_urls true
   - conda update conda
+  - conda config --add channels conda-forge --force
   - conda config --add channels odm2 --force
   - conda create --name TEST python=$TRAVIS_PYTHON_VERSION --file requirements.txt --file requirements-dev.txt
   - source activate TEST
@@ -89,3 +98,17 @@ script:
   - if [[ $TEST_TARGET == 'coding_standards' ]]; then
       find . -type f -name "*.py" ! -name 'conf.py' | xargs flake8 --max-line-length=100 ;
     fi
+
+  - if [[ $TEST_TARGET == 'docs' ]]; then
+      set -e ;
+      conda install doctr ;
+      pushd docs ;
+      make clean html linkcheck ;
+      popd ;
+      python -m doctr deploy --sync .;
+      python -m doctr deploy --sync --no-require-master  --built-docs docs/build/html "docs-$TRAVIS_BRANCH" ;
+    fi
+
+doctr:
+  require-master: true
+  sync: False

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = ODM2PythonAPI
+SOURCEDIR     = source
+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/source/conf.py

@@ -0,0 +1,177 @@
+# -*- coding: utf-8 -*-
+#
+# ODM2PythonAPI documentation build configuration file, created by
+# sphinx-quickstart on Thu Sep 28 11:03:57 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('.'))
+
+
+# -- 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'ODM2PythonAPI'
+copyright = u'2017, Stephanie Reeder'
+author = u'Stephanie Reeder'
+
+# 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.
+
+from odm2api._version import get_versions
+version = release = get_versions()['version']
+del get_versions
+
+# 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 = []
+
+# 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 = {
+    'logo': 'logo.png',
+    'logo_name': 'ODM2',
+    'github_user': 'ODM2',
+    'github_repo': 'ODM2PythonAPI',
+    'github_banner': True,
+    'travis_button': True,
+    'fixed_sidebar': True,
+}
+
+# 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']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+        'donate.html',
+    ]
+}
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'ODM2PythonAPIdoc'
+
+
+# -- 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, 'ODM2PythonAPI.tex', u'ODM2PythonAPI Documentation',
+     u'Stephanie Reeder', '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, 'odm2pythonapi', u'ODM2PythonAPI 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, 'ODM2PythonAPI', u'ODM2PythonAPI Documentation',
+     author, 'ODM2PythonAPI', 'One line description of project.',
+     'Miscellaneous'),
+]

docs/source/credits.rst

@@ -0,0 +1,10 @@
+Credits
+-------
+
+This work was supported by National Science Foundation Grants
+`EAR-1224638 <https://www.nsf.gov/awardsearch/showAward?AWD_ID=1224638>`__
+and
+`ACI-1339834 <https://www.nsf.gov/awardsearch/showAward?AWD_ID=1339834>`__.
+Any opinions, findings, and conclusions or recommendations expressed in
+this material are those of the author(s) and do not necessarily reflect
+the views of the National Science Foundation.

docs/source/index.rst

@@ -0,0 +1,19 @@
+ODM2 Python API
+===============
+
+A Python-based application programmer's interface for the `Observations Data Model 2 (ODM2) <http://www.odm2.org>`__.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   installing
+   modules
+   credits
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/installing.rst

@@ -0,0 +1,62 @@
+Installation
+------------
+
+The easiest and most reliable way to install the ODM2 Python API
+(``odm2api``) is using the `Conda package management
+system <https://conda.io/docs/>`__ via either
+`Anaconda <https://www.anaconda.com/download/>`__ or
+`Miniconda <https://conda.io/miniconda.html>`__. To start using
+conda (if it's not your system default), add conda to the PATH; on
+OS X and Linux, it's something like
+``export PATH=$HOME/miniconda3/bin:$PATH``, but the exact path may vary.
+
+To activate a conda environment, say, "myenv":
+
+.. code:: bash
+
+    activate myenv  # On Windows
+    source activate myenv  # On MacOSX or Linux
+
+**Note:** ``odm2api`` currently is only tested on Python 2.7. Some
+changes have been made to support Python 3.x, but they haven't been
+tested thoroughly.
+
+Latest release, from ODM2 anaconda.org channel
+----------------------------------------------
+
+The `latest release <https://github.com/ODM2/ODM2PythonAPI/releases>`__ is available
+on the `ODM2 anaconda.org channel <https://anaconda.org/odm2/odm2api>`__
+for all major OS platforms (linux, OS X, win32/win64). To install it on
+an existing conda environment:
+
+::
+
+    conda install odm2api --channel odm2
+
+All dependencies are installed, including Pandas and its dependencies
+(numpy, etc).
+
+To create a new environment "myenv" with the ``odm2api`` package:
+
+::
+
+    conda create -n myenv -c odm2 python=2.7 odm2api
+
+
+Installing the development version
+----------------------------------
+
+To create a new environment "myenv" with ``odm2api``, first clone the repository.
+Then, on a terminal shell:
+
+.. code:: bash
+
+    conda create --name myenv python=2.7 --file requirements.txt --file requirements-dev.txt -c odm2
+
+Activate the new environment, then install ``odm2api`` into the
+environment:
+
+.. code:: bash
+
+    activate myenv  # On Windows
+    source activate myenv  # On OS X or Linux

docs/source/modules.rst

@@ -0,0 +1,7 @@
+:mod:`ODMconnection`
+---------------------
+
+.. automodule:: odm2api.ODMconnection
+   :members:
+   :undoc-members:
+   :show-inheritance:

github_deploy_key.enc

@@ -0,0 +1 @@
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requirements-dev.txt

@@ -1,9 +1,19 @@
+alabaster
 flake8
+flake8-builtins
+flake8-comprehensions
+flake8-import-order
+flake8-mutable
+flake8-print
+flake8-quotes
 mock
+nbsphinx
 psycopg2
+pycodestyle
 pymysql
 pytest
 pytest-cov
+sphinx
 # FIXME: I am not sure these are needed.
 # pysqlite
 # sqlite