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tomasstolker · Mar 14, 2019 · 1a4f8ca · 1a4f8ca
1 parent 7a67511
commit 1a4f8ca
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Showing 20 changed files with 25 additions and 19 deletions.
diff --git a/Makefile b/Makefile
@@ -18,7 +18,7 @@ pypi-test:
 
 docs:
 	rm -f docs/species.*rst
-	sphinx-apidoc -o docs species
+	sphinx-apidoc -o docs/source species
 	cd docs/
 	$(MAKE) -C docs clean
 	$(MAKE) -C docs html
@@ -36,7 +36,7 @@ clean:
 	rm -f .coverage
 	rm -f coverage.xml
 	rm -rf .pytest_cache/
-	rm -rf docs/_build
+	rm -rf docs/build
 	rm -rf build/
 	rm -rf dist/
 	rm -rf species.egg-info/

diff --git a/docs/Makefile b/docs/Makefile
@@ -4,8 +4,8 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SOURCEDIR     = .
-BUILDDIR      = _build
+SOURCEDIR     = source
+BUILDDIR      = build
 
 # Put it first so that "make" without argument is like "make help".
 help:

diff --git a/docs/_images/color_mag.png → docs/source/_static/color_mag.png b/docs/_images/color_mag.png → docs/source/_static/color_mag.png
diff --git a/docs/_images/model1.png → docs/source/_static/model1.png b/docs/_images/model1.png → docs/source/_static/model1.png
diff --git a/docs/_images/model2.png → docs/source/_static/model2.png b/docs/_images/model2.png → docs/source/_static/model2.png
diff --git a/docs/_images/photometry.png → docs/source/_static/photometry.png b/docs/_images/photometry.png → docs/source/_static/photometry.png
diff --git a/docs/_images/posterior.png → docs/source/_static/posterior.png b/docs/_images/posterior.png → docs/source/_static/posterior.png
diff --git a/docs/_images/spectrum.png → docs/source/_static/spectrum.png b/docs/_images/spectrum.png → docs/source/_static/spectrum.png
diff --git a/docs/about.rst → docs/source/about.rst b/docs/about.rst → docs/source/about.rst
diff --git a/docs/conf.py → docs/source/conf.py b/docs/conf.py → docs/source/conf.py
@@ -11,11 +11,11 @@
 # 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('.'))
-sys.path.insert(0, os.path.abspath('../species/'))
+
+sys.path.insert(0, os.path.abspath('../../'))
 
 
 # -- Project information -----------------------------------------------------
@@ -25,9 +25,13 @@
 author = 'Tomas Stolker'
 
 # The short X.Y version
-version = ''
+with open('../../species/__init__.py') as initfile:
+    for line in initfile:
+        if '__version__' in line:
+            version = line.split("'")[1]
+
 # The full version, including alpha/beta/rc tags
-release = ''
+release = version
 
 
 # -- General configuration ---------------------------------------------------
@@ -65,7 +69,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = None
@@ -87,7 +91,7 @@
 # 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 = ['_images']
+html_static_path = ['_static']
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.

diff --git a/docs/examples.rst → docs/source/examples.rst b/docs/examples.rst → docs/source/examples.rst
@@ -84,7 +84,7 @@ The following code will download the IRTF spectral library and add the spectra t
                          xlim=(1., 2.5),
                          offset=(-0.08, -0.06))
 
-.. image:: _images/photometry.png
+.. image:: _static/photometry.png
    :width: 80%
    :align: center
 
@@ -116,7 +116,7 @@ Here photometric data of 51 Eri b (Rajan et al. 2017) is added to the database.
                                 output='color_mag.pdf',
                                 legend='upper left')
 
-.. image:: _images/color_mag.png
+.. image:: _static/color_mag.png
    :width: 70%
    :align: center
 
@@ -144,7 +144,7 @@ In the last example, the DRIFT-PHOENIX atmospheric models are added to the datab
                          xlim=(1., 5.),
                          ylim=(0., 1.1e5))
 
-.. image:: _images/model1.png
+.. image:: _static/model1.png
    :width: 80%
    :align: center
 
@@ -159,7 +159,7 @@ Or, a spectrum with the original spectral resolution can be obtained from the (d
                          xlim=(1., 5.),
                          ylim=(0., 2.15e-15))
 
-.. image:: _images/model2.png
+.. image:: _static/model2.png
    :width: 80%
    :align: center
 
@@ -236,10 +236,10 @@ In this example, the 2MASS magnitudes of PZ Tel A are fitted with a IRTF spectru
                          title=r'G6.5V HD 115617 - PZ Tel A',
                          offset=(-0.25, -0.06))
 
-.. image:: _images/posterior.png
+.. image:: _static/posterior.png
    :width: 60%
    :align: center
 
-.. image:: _images/spectrum.png
+.. image:: _static/spectrum.png
    :width: 80%
    :align: center
diff --git a/docs/index.rst → docs/source/index.rst b/docs/index.rst → docs/source/index.rst
diff --git a/docs/installation.rst → docs/source/installation.rst b/docs/installation.rst → docs/source/installation.rst
diff --git a/docs/modules.rst → docs/source/modules.rst b/docs/modules.rst → docs/source/modules.rst
@@ -1,5 +1,7 @@
-species
-=======
+.. _api:
+
+API
+===
 
 .. toctree::
    :maxdepth: 4

diff --git a/docs/species.analysis.rst → docs/source/species.analysis.rst b/docs/species.analysis.rst → docs/source/species.analysis.rst
diff --git a/docs/species.core.rst → docs/source/species.core.rst b/docs/species.core.rst → docs/source/species.core.rst
diff --git a/docs/species.data.rst → docs/source/species.data.rst b/docs/species.data.rst → docs/source/species.data.rst
diff --git a/docs/species.plot.rst → docs/source/species.plot.rst b/docs/species.plot.rst → docs/source/species.plot.rst
diff --git a/docs/species.read.rst → docs/source/species.read.rst b/docs/species.read.rst → docs/source/species.read.rst
diff --git a/docs/species.rst → docs/source/species.rst b/docs/species.rst → docs/source/species.rst