Merge pull request #1 from desihub/fleshout

lay out basic directory structure for desigal repository

.gitignore

@@ -2,6 +2,10 @@
 __pycache__/
 *.py[cod]
 *$py.class
+.ipynb_checkpoints
+
+# EMACS backup files
+*~
 
 # C extensions
 *.so

LICENSE.rst

@@ -0,0 +1,25 @@
+Copyright (c) 2014-2017, DESI Collaboration <[email protected]>
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+* Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+* Neither the name of the Astropy Team nor the names of its contributors may be
+  used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

@@ -0,0 +1,12 @@
+include LICENSE.rst
+include README.rst
+include requirements.txt
+
+graft bin
+graft doc
+graft etc
+
+prune build
+prune dist
+prune htmlcov
+prune doc/_build

README.rst

@@ -0,0 +1,76 @@
+=======
+desigal
+=======
+
+.. image:: https://img.shields.io/travis/desihub/desigal.svg
+    :target: https://travis-ci.org/desihub/desigal
+    :alt: Travis Build Status
+.. image:: https://coveralls.io/repos/desihub/desigal/badge.svg?service=github
+    :target: https://coveralls.io/github/desihub/desigal
+    :alt: Test Coverage Status
+.. image:: https://readthedocs.org/projects/desigal/badge/?version=latest
+    :target: http://desigal.readthedocs.org/en/latest/
+    :alt: Documentation Status
+
+Introduction
+============
+
+This repository contains code and documentation for the DESI_ Galaxy and Quasar
+Physics (GQP) Working Group.  For full documentation please visit `desigal on
+Read the Docs`_.
+
+.. _DESI: https://desi.lbl.gov
+.. _`desigal on Read the Docs`: http://desigal.readthedocs.org/en/latest/
+
+Installation
+============
+
+This product is installable using pip_ or it can cloned directly from `Github`_.
+For example, to install the "0.1.0" tag (or release) do
+
+.. code-block:: bash
+
+  pip install git+https://github.com/desihub/[email protected]
+  
+Alternatively, you can clone the master branch from `Github`_ 
+
+.. code-block:: bash
+
+  git clone [email protected]:desihub/desigal.git
+
+and then either install the package to an installation directory of your
+choice
+
+.. code-block:: bash
+
+  python setup.py install --prefix=$INSTALL_DIR  
+
+or explicitly add the code directory to your ``$PYTHONPATH`` environment, e.g. 
+
+.. code-block:: bash
+
+  export PYTHONPATH=/path/to/desigal/py:$PYTHONPATH
+  export PATH=/path/to/desigal/bin:${PATH}
+
+.. _pip: http://pip.readthedocs.org
+.. _Github: https://github.com
+
+Product Contents
+================
+
+bin/
+    Executable scripts.
+doc/
+    High-level documentation (.rst files).
+etc/
+    Small data and configuration files.
+py/
+    Python code.
+
+License
+=======
+
+`desigal`_ is free software licensed under a 3-clause BSD-style license. For
+details see the ``LICENSE.rst`` file.
+
+.. _`desigal`: https://github.com/desihub/desigal

bin/example_script

@@ -0,0 +1,9 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# This is how you call Python code in your package.  Notice how
+# simple it is!
+#
+from sys import exit
+from desigal.main import main
+exit(main())

doc/Makefile

@@ -0,0 +1,179 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+# For macports, use the second line...
+SPHINXBUILD   = sphinx-build
+# SPHINXBUILD   = sphinx-build-2.7
+PAPER         =
+BUILDDIR      = _build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/desispec.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/desispec.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/desispec"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/desispec"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

doc/api.rst

@@ -0,0 +1,13 @@
+===========
+desigal API
+===========
+
+This is used to include docstrings from modules. See `the autodoc documentation`_.
+
+.. _`the autodoc documentation`: http://sphinx-doc.org/ext/autodoc.html?highlight=automodule#directive-automodule
+
+If you're loading a module here, and don't see some functions, try adding the
+``:imported-members:`` option.
+
+.. automodule:: desigal
+   :members:

doc/changes.rst

@@ -0,0 +1,10 @@
+==========
+Change Log
+==========
+
+0.1.0 (2017-05-17)
+------------------
+
+* Initialize repository with `desitemplate`_.
+
+.. _`desitemplate`: https://github.com/desihub/desitemplate