large cleanup operation

working apidoc
tardis-sn · Jul 22, 2019 · 0149d89 · 0149d89
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Showing 13 changed files with 49 additions and 45 deletions.
diff --git a/docs/conf.py b/docs/conf.py
@@ -47,11 +47,12 @@
     'sphinx.ext.todo',
     'sphinx.ext.mathjax',
     'sphinx.ext.graphviz',
+    'sphinx.ext.viewcode',
     'numpydoc',
     'nbsphinx',
-    'sphinx.ext.autodoc',
     'sphinx-jsonschema',
-    'recommonmark'
+    'recommonmark',
+    'sphinxcontrib.apidoc'
 ]
 
 source_suffix = {
@@ -105,6 +106,12 @@
 release = tardis.__version__
 
 
+# -- APIDoc configuration -----------------------------------------------------
+apidoc_module_dir = '../tardis'
+apidoc_output_dir = 'api'
+apidoc_excluded_paths = ['*tests*', '*setup_package*']
+apidoc_separate_modules = True
+
 # -- Options for HTML output ---------------------------------------------------
 
 # A NOTE ON HTML THEMES

diff --git a/docs/development/running_tests.rst b/docs/development/running_tests.rst
@@ -52,7 +52,7 @@ or generate new ones.
 
 Both of of these require a configuration file for the integration tests:
 
-.. literalinclude:: yml_files/integration.yml
+.. literalinclude:: integration.yml
     :language: yaml
 
 Inside the atomic data directory there needs to be atomic data for each of

diff --git a/docs/index.rst b/docs/index.rst
@@ -19,7 +19,7 @@ TARDIS is an open-source Monte Carlo radiative-transfer spectral synthesis code
 for 1D models of supernova ejecta. It is designed for rapid spectral modelling
 of supernovae. It is developed and maintained by a :ref:`multi-disciplinary team <team>`
 including software engineers, computer scientists, statisticians,
-and astrophysicists .
+and astrophysicists. `--- dsfjsdlkfjsdlf`
 
 If you use this code for any publications or presentations please follow our
 citation guidelines in :ref:`tardiscredits`
@@ -42,17 +42,12 @@ assistance.
 
 
 .. toctree::
-    :maxdepth: 2
+    :maxdepth: 3
     :caption: Using TARDIS
     :hidden:
 
 
     running/index
-    running/configuration/configuration
-    atomic/atomic_data
-    models/index
-    examples/index
-    scripts/index
 
 
 .. toctree::
@@ -90,6 +85,14 @@ assistance.
     development/index
     CHANGELOG.md
 
+.. toctree::
+    :maxdepth: 2
+    :caption: API
+    :hidden:
+
+    api/modules
+
+
 
 .. toctree::
     :caption: References

diff --git a/docs/graphics/optical_depth_summation.png → ...ecarlo/images/optical_depth_summation.png b/docs/graphics/optical_depth_summation.png → ...ecarlo/images/optical_depth_summation.png
diff --git a/docs/graphics/scatter_downbranch_ma.png → ...ntecarlo/images/scatter_downbranch_ma.png b/docs/graphics/scatter_downbranch_ma.png → ...ntecarlo/images/scatter_downbranch_ma.png
diff --git a/docs/graphics/spherical_symmetry.png → .../montecarlo/images/spherical_symmetry.png b/docs/graphics/spherical_symmetry.png → .../montecarlo/images/spherical_symmetry.png
diff --git a/docs/physics/montecarlo/lineinteraction.rst b/docs/physics/montecarlo/lineinteraction.rst
@@ -94,5 +94,5 @@ shows the situation in the resonant scatter mode, the middle one for the
 downbranching scheme and the right one the macro atom results.
 
 .. image::
-    ../graphics/scatter_downbranch_ma.png
+    images/scatter_downbranch_ma.png
     :width: 700
diff --git a/docs/physics/montecarlo/propagation.rst b/docs/physics/montecarlo/propagation.rst
@@ -58,7 +58,7 @@ following sketch (taken from :cite:`Noebauer2014`):
 
 
 .. image::
-    ../graphics/spherical_symmetry.png
+    images/spherical_symmetry.png
     :width: 400
 
 
@@ -182,7 +182,7 @@ the sketch below (taken from :cite:`Noebauer2014`, adapted from
 :cite:`Mazzali1993`):
 
 .. image::
-    ../graphics/optical_depth_summation.png
+    images/optical_depth_summation.png
     :width: 400
 
 Three possible cases are highlighted. In the first case, the drawn optical

diff --git a/docs/physics/plasma/plasma.rst b/docs/physics/plasma/plasma.rst
@@ -55,19 +55,13 @@ Here's an example how to instantiate a simple base plasma::
                28                0.5  513016973.936
                26                0.5  539183641.472
 
-
-
-
-
-
-
 Plasma Types
 ------------
 .. toctree::
     :maxdepth: 0
 
-    plasma_doc/lte_plasma.rst
-    plasma_doc/nebular_plasma.rst
+    lte_plasma.rst
+    nebular_plasma.rst
 
 
 .. _tau_sobolev:
@@ -90,9 +84,11 @@ This function calculates the Sobolev optical depth :math:`\tau_\textrm{Sobolev}`
 
 
 
+.. toctree::
+    :maxdepth: 1
 
-.. include:: plasma_doc/macroatom.rst
-.. include:: plasma_doc/nlte.rst
+    macroatom.rst
+    nlte.rst
 
 
 .. .. automodapi:: tardis.plasma_array

diff --git a/docs/running/index.rst b/docs/running/index.rst
@@ -9,9 +9,9 @@ The TARDIS code needs three components to calculate spectra:
     :maxdepth: 1
     :numbered:
 
-    ../models/index.rst
-    ../configuration/index.rst
-    3. Atom Database <https://tardis-sn.github.io/carsus/>
+    ../models/index
+    ../configuration/index
+    ../atomic/atomic_data
 
 
 A quick start guide to run TARDIS can be found
@@ -26,21 +26,6 @@ A quick start guide to run TARDIS can be found
     gui
     notebooks/index.rst
 
-.. _quickstart:
-
-
-Running TARDIS interactively in a Jupyter notebook (recommended)
-================================================================
-
-To get more information from each run of TARDIS one can run it interactively and
-have full access to the model properties (as described in :ref:`physical_quantities`)
-
-.. toctree::
-    :maxdepth: 1
-
-    examples/run_simple_example.ipynb
-
-
 
 
 
diff --git a/docs/running/notebooks/index.rst b/docs/running/notebooks/index.rst
@@ -1,4 +1,7 @@
-Interactive TARDIS runs
-=======================
+TARDIS interactive runs
+==================================================
 
-xxx
+To get more information from each run of TARDIS one can run it interactively and
+have full access to the model properties (as described in :ref:`physical_quantities`)
+
+..    examples/run_simple_example.ipynb
diff --git a/setup.cfg b/setup.cfg
@@ -36,7 +36,7 @@ author = TARDIS Collaboration
 author_email = wkerzendorf@gmail.com
 license = BSD (3 clause)
 url = http://tardis.readthedocs.org/
-edit_on_github = False
+edit_on_github = True
 github_project = tardis-sn/tardis
 version = 3.0.dev
 minimum_python_version = 3.6

diff --git a/tardis/io/atom_data/atom_web_download.py b/tardis/io/atom_data/atom_web_download.py
@@ -8,13 +8,23 @@
 logger = logging.getLogger(__name__)
 
 def get_atomic_repo_config():
+    """
+    Get the repo configuration dictionary for the atomic data
+
+    Returns
+    -------
+        : dict
+
+    """
+
     atomic_repo_fname = get_internal_data_path('atomic_data_repo.yml')
     return yaml.load(open(atomic_repo_fname))
 
 
 def download_atom_data(atomic_data_name=None):
     """
     Download the atomic data from the repository
+
     Parameters
     ----------
     atomic_data_name: str