Restructure The Repository to Create The Documentation using Sphinx and Sphinx Gallery

.gitignore

@@ -105,3 +105,15 @@ venv.bak/
 
 # Mac OSX
 .DS_Store
+
+# Binary files
+*.pickle
+
+# Sphinx HTML Output
+html/
+
+# Sphinx Gallery output
+*_examples/
+
+# VScode
+.vscode/

2020/2020_williamson_94I/code_comp_setups/16d.yml

@@ -10,8 +10,8 @@ supernova:
   distance: 8.32 Mpc
 
 # standard atomic data base; get it from the tardis-refdata repository
-atom_data: /home/mew488/src/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5
-#atom_data: kurucz_cd23_chianti_H_He.h5
+# atom_data: /home/mew488/src/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5
+atom_data: kurucz_cd23_chianti_H_He.h5
 
 #csvy_model: /Users/marcwilliamson/Research/TARDIS/94I/nomoto_data/hach_fixed/16d.csvy
 csvy_model: hach_exact_csvy_16d.csvy

2020/2020_williamson_94I/code_comp_setups/22d.yml

@@ -9,7 +9,8 @@ supernova:
   distance: 8.32 Mpc
 
 # standard atomic data base; get it from the tardis-refdata repository
-atom_data: /home/mew488/src/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5
+# atom_data: /home/mew488/src/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5
+atom_data: kurucz_cd23_chianti_H_He.h5
 
 #csvy_model: /Users/marcwilliamson/Research/TARDIS/94I/nomoto_data/hach_fixed/22d.csvy
 csvy_model: hach_exact_csvy_22d.csvy

2020/2020_williamson_94I/code_comp_setups/30d.yml

@@ -9,7 +9,8 @@ supernova:
   distance: 8.32 Mpc
 
 # standard atomic data base; get it from the tardis-refdata repository
-atom_data: /home/mew488/src/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5
+# atom_data: /home/mew488/src/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5
+atom_data: kurucz_cd23_chianti_H_He.h5
 
 #csvy_model: /Users/marcwilliamson/Research/TARDIS/94I/nomoto_data/hach_fixed/30d.csvy
 csvy_model: hach_exact_csvy_30d.csvy

2020/2020_williamson_94I/code_comp_setups/40d.yml

@@ -9,7 +9,8 @@ supernova:
   distance: 8.32 Mpc
 
 # standard atomic data base; get it from the tardis-refdata repository
-atom_data: /home/mew488/src/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5
+# atom_data: /home/mew488/src/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5
+atom_data: kurucz_cd23_chianti_H_He.h5
 
 #csvy_model: /Users/marcwilliamson/Research/TARDIS/94I/nomoto_data/hach_fixed/40d.csvy
 csvy_model: hach_exact_csvy_40d.csvy

2020/2020_williamson_94I/he_setups/22d.yml

@@ -9,7 +9,8 @@ supernova:
   distance: 8.32 Mpc
 
 # standard atomic data base; get it from the tardis-refdata repository
-atom_data: /Users/marcwilliamson/Research/TARDIS/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5
+# atom_data: /Users/marcwilliamson/Research/TARDIS/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5
+atom_data: kurucz_cd23_chianti_H_He.h5
 
 #csvy_model: /Users/marcwilliamson/Research/TARDIS/94I/nomoto_data/hach_fixed/22d.csvy
 csvy_model: /Users/marcwilliamson/Research/TARDIS/94I/paper/save/helium/22d/22d_he_3.csvy

2020/2020_williamson_94I/he_setups/22d_he_01.yml

@@ -9,7 +9,8 @@ supernova:
   distance: 8.32 Mpc
 
 # standard atomic data base; get it from the tardis-refdata repository
-atom_data: /home/mew488/src/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5
+# atom_data: /home/mew488/src/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5
+atom_data: kurucz_cd23_chianti_H_He.h5
 
 #csvy_model: /Users/marcwilliamson/Research/TARDIS/94I/nomoto_data/hach_fixed/22d.csvy
 csvy_model: 22d_He_0.01.csvy

2020/2020_williamson_94I/he_setups/22d_he_05.yml

@@ -9,7 +9,8 @@ supernova:
   distance: 8.32 Mpc
 
 # standard atomic data base; get it from the tardis-refdata repository
-atom_data: /home/mew488/src/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5
+# atom_data: /home/mew488/src/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5
+atom_data: kurucz_cd23_chianti_H_He.h5
 
 #csvy_model: /Users/marcwilliamson/Research/TARDIS/94I/nomoto_data/hach_fixed/22d.csvy
 csvy_model: 22d_He_0.05.csvy

2020/2020_williamson_94I/he_setups/22d_he_10.yml

@@ -9,7 +9,8 @@ supernova:
   distance: 8.32 Mpc
 
 # standard atomic data base; get it from the tardis-refdata repository
-atom_data: /home/mew488/src/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5
+# atom_data: /home/mew488/src/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5
+atom_data: kurucz_cd23_chianti_H_He.h5
 
 #csvy_model: /Users/marcwilliamson/Research/TARDIS/94I/nomoto_data/hach_fixed/22d.csvy
 csvy_model: 22d_He_0.10.csvy

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+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/conf.py

@@ -0,0 +1,64 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# 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('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "tardis-setups"
+copyright = "2022, Wolfgang Kerzendorf"
+author = "Wolfgang Kerzendorf"
+
+
+# -- General configuration ---------------------------------------------------
+
+# 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_gallery.gen_gallery",
+]
+
+sphinx_gallery_conf = {
+    "examples_dirs": [
+        "../tardis-setups/2014",
+        "../tardis-setups/2020",
+    ],  # path to your example scripts
+    "gallery_dirs": [
+        "2014_examples",
+        "2020_examples",
+    ],  # path to where to save gallery generated output
+}
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# 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"]
+
+
+# -- 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 = "sphinx_rtd_theme"
+
+# 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"]

docs/index.rst

@@ -0,0 +1,23 @@
+.. tardis-setups documentation master file, created by
+   sphinx-quickstart on Mon Jun 20 17:55:16 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to tardis-setups's documentation!
+=========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Galleries:
+
+   2014_examples/index
+   2020_examples/index
+
+Indices and tables
+==================
+
+* :ref:`genindex`

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

tardis-setups/2014/README.rst

@@ -0,0 +1,4 @@
+2014 Examples
+==================
+
+Below is a gallery of examples.

tardis-setups/2014/plot_tardis_example.py

@@ -0,0 +1,53 @@
+"""
+Tardis 2014 Example
+==========================
+
+This is the example output
+"""
+
+
+from tardis import run_tardis
+from tardis.io.config_reader import Configuration
+from tardis.io.atom_data.util import download_atom_data
+import matplotlib.pyplot as plt
+
+import sys
+
+sys.path.append("../")
+from setup_utils import config_modifier
+
+# %%
+# Uncomment this line if you need to download the dataset.
+
+
+download_atom_data("kurucz_cd23_chianti_H_He")
+
+# %%
+# Runs the example
+
+conf = Configuration.from_yaml(
+    "../../2014/2014_kerzendorf_sim/appendix_A1/tardis_example.yml"
+)
+conf = config_modifier(conf)
+
+# %%
+sim = run_tardis(conf)
+
+
+# %%
+spectrum = sim.runner.spectrum
+spectrum_virtual = sim.runner.spectrum_virtual
+spectrum_integrated = sim.runner.spectrum_integrated
+
+plt.figure(figsize=(10, 6.5))
+
+spectrum.plot(label="Normal packets")
+spectrum_virtual.plot(label="Virtual packets")
+spectrum_integrated.plot(label="Formal integral")
+
+plt.xlim(500, 9000)
+plt.title("TARDIS example model spectrum")
+plt.xlabel("Wavelength [$\AA$]")
+plt.ylabel("Luminosity density [erg/s/$\AA$]")
+plt.legend()
+plt.show()

tardis-setups/2020/README.rst

@@ -0,0 +1,4 @@
+Year 2020 Results
+==================
+
+Output of configuartion files uploaded in the year 2020.

tardis-setups/2020/plot_16d.py

@@ -0,0 +1,70 @@
+"""
+Williamson et al. (2020) Figure 2 t_explosion=16 days
+==========================
+
+
+Article: Williamson, Marc, Kerzendorf, Wolfgang, Modjaz, Maryam 2021, ApJ,
+“Modeling Type Ic Supernovae with TARDIS: Hidden Helium in SN 1994I?” (`ADS Link`_).
+
+Original Input Files: `YAML`_, `CSVY`_
+
+Original Dataset: Data missing
+
+Original Spectra:
+
+Notes: Please note that the spectra obtained below is obtained by using a slightly
+modified configuration file. This is done to ensure that the spectra can be
+obtained using the computers hosted by us.
+
+.. _ADS Link: https://ui.adsabs.harvard.edu/abs/2021ApJ...908..150W
+.. _YAML: https://github.com/tardis-sn/tardis-setups/blob/master/2020/2020_williamson_94I/code_comp_setups/16d.yml
+.. _CSVY: https://github.com/tardis-sn/tardis-setups/blob/master/2020/2020_williamson_94I/code_comp_setups/hach_exact_csvy_16d.csvy
+"""
+
+
+from tardis import run_tardis
+from tardis.io.config_reader import Configuration
+from tardis.io.atom_data.util import download_atom_data
+import matplotlib.pyplot as plt
+
+import sys
+
+sys.path.append("../")
+from setup_utils import config_modifier
+
+# %%
+# Comment this line if you do not need to download the dataset.
+
+
+download_atom_data("kurucz_cd23_chianti_H_He")
+
+# %%
+conf = Configuration.from_yaml(
+    "../../2020/2020_williamson_94I/code_comp_setups/16d.yml"
+)
+
+# %%
+# Note: Here the configuration is slightly modified to allow
+# the configuration file on a computer with lower configuration.
+
+conf = config_modifier(conf)
+# %%
+sim = run_tardis(conf)
+
+
+spectrum = sim.runner.spectrum
+spectrum_virtual = sim.runner.spectrum_virtual
+spectrum_integrated = sim.runner.spectrum_integrated
+
+plt.figure(figsize=(10, 6.5))
+
+spectrum.plot(label="Normal packets")
+spectrum_virtual.plot(label="Virtual packets")
+spectrum_integrated.plot(label="Formal integral")
+
+plt.xlim(500, 9000)
+plt.title("TARDIS example model spectrum")
+plt.xlabel("Wavelength [$\AA$]")
+plt.ylabel("Luminosity density [erg/s/$\AA$]")
+plt.legend()
+plt.show()