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Merge pull request #7 from natashabatalha/dev
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See release notes for explanation of new functionality.
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natashabatalha authored Feb 7, 2020
2 parents 88864bb + d75d5c5 commit 9d02130
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2 changes: 1 addition & 1 deletion .travis.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,8 @@ language: python

matrix:
include:
- python: 3.5
- python: 3.6
- python: 3.7

git:
submodules: true
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182 changes: 11 additions & 171 deletions docs/Makefile
Original file line number Diff line number Diff line change
@@ -1,181 +1,21 @@
# Minimal makefile for Sphinx documentation
#

# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
SPHINXPROJ = picaso
# You can set these variables from the command line, and also
# from the environment for the first two.
SPHINXOPTS ?=
SPHINXBUILD ?= sphinx-build
SOURCEDIR = .
BUILDDIR = ../../picaso-docs
PDFBUILDDIR = /tmp
PDF = ../manual.pdf

# 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

# Put it first so that "make" without argument is like "make help".
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/engine.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/engine.qhc"

devhelp:
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME/.local/share/devhelp/engine"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/engine"
@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) $(PDFBUILDDIR)/latex
@echo "Running LaTeX files through pdflatex..."
make -C $(PDFBUILDDIR)/latex all-pdf
cp $(PDFBUILDDIR)/latex/*.pdf $(PDF)
@echo "pdflatex finished; see $(PDF)"

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 $(BUILDDIR)/linkcheck/output.txt."
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doctest:
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)/doctest/output.txt."
.PHONY: help Makefile

xml:
$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
@echo
@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
# 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)

pseudoxml:
$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
@echo
@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
55 changes: 3 additions & 52 deletions docs/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
# 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('/Users/natashabatalha/Documents/PICASO/picaso/'))
sys.path.insert(0, os.path.abspath('/Users/nbatalh1/Documents/codes/PICASO/picaso/'))


# -- General configuration ------------------------------------------------
Expand Down Expand Up @@ -66,9 +66,9 @@
# built documents.
#
# The short X.Y version.
version = '0.0'
version = '1.0'
# The full version, including alpha/beta/rc tags.
release = '0.0'
release = '1.0'

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
Expand Down Expand Up @@ -116,25 +116,6 @@
htmlhelp_basename = 'picasodoc'


# -- 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',
}

nbsphinx_prolog = """
{% set docname = env.doc2path(env.docname, base=None) %}
Expand All @@ -145,36 +126,6 @@
# This notebook can be downloaded at : https://github.com/natashabatalha/picaso/tree/master/docs/notebooks/{{ docname }}
#

# 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, 'picaso.tex', 'picaso Documentation',
'Natasha E. Batalha', '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, 'picaso', 'picaso 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, 'picaso', 'picaso Documentation',
author, 'picaso', 'One line description of project.',
'Miscellaneous'),
]

def setup(app):
app.add_stylesheet('https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css')
app.add_javascript('https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js')
Expand Down
2 changes: 1 addition & 1 deletion docs/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -94,6 +94,6 @@ Resources
The Derivations <https://natashabatalha.github.io/picaso_dev>
The Code <picaso>
Github <https://github.com/natashabatalha/picaso>
The Paper <picaso>
The Paper <https://arxiv.org/abs/1904.09355>


10 changes: 5 additions & 5 deletions docs/installation.rst
Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ Download and Link Pysynphot Stellar Data

In order to get stellar spectra you will have to download the stellar spectra here from PySynphot:

1) Download the `stellar spectra from here <https://pysynphot.readthedocs.io/en/latest/appendixa.html>_. The Defulat for `PICASO` is `Castelli-Kurucz Atlas: ck04models`.
1) Download the `stellar spectra from here <https://pysynphot.readthedocs.io/en/latest/appendixa.html>`_. The Defulat for `PICASO` is Castelli-Kurucz Atlas: `ck04models <https://archive.stsci.edu/hlsps/reference-atlases/cdbs/grid/ck04models/>`_.

2) Create environment variable

Expand All @@ -61,14 +61,14 @@ Add add this line:

.. code-block:: bash
export PYSYN_CDBS="/path/to/stellar/data/"
export PYSYN_CDBS="/path/to/data/files/grp/hst/cdbs"
Should look something like this

.. code-block:: bash
cd /path/to/stellar/data/
cd /path/to/data/files/grp/hst/cdbs
ls
ck04models phoenix
grid
Where `phoenix` is another stellar database.
Where `grid` contains whatever `pysynphot` data files you have downloaded (e.g. a folder called `ck04models`).
9 changes: 4 additions & 5 deletions docs/make.bat
Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,8 @@ REM Command file for Sphinx documentation
if "%SPHINXBUILD%" == "" (
set SPHINXBUILD=sphinx-build
)
set SOURCEDIR=source
set BUILDDIR=build
set SPHINXPROJ=picaso
set SOURCEDIR=.
set BUILDDIR=_build

if "%1" == "" goto help

Expand All @@ -26,11 +25,11 @@ if errorlevel 9009 (
exit /b 1
)

%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
goto end

:help
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%

:end
popd
7 changes: 0 additions & 7 deletions docs/modules.rst

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