From 629dffbf349f26fdaa0ab05624b5a45b8bfac462 Mon Sep 17 00:00:00 2001 From: Wolfgang Kerzendorf Date: Thu, 21 Jun 2018 10:45:21 +0300 Subject: [PATCH 1/6] restructure landing page to use notebooks --- docs/index.rst | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/docs/index.rst b/docs/index.rst index 37235b3ba67..3e92e1bf3a1 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -37,11 +37,17 @@ Using Tardis * :doc:`Quickstart Guide ` * :doc:`Ejecta Model Setup ` * :doc:`TARDIS Configuration ` -* :doc:`Examples ` * :doc:`Storing simulations to HDF ` * :doc:`Helper Scripts ` * :doc:`Credit & Publication Policies ` +======== +Examples +======== + +.. toctree:: + notebooks/integrator + ====================== Looking under the hood ====================== From 51505d86cbd15c244e2936b5e403484640a958c8 Mon Sep 17 00:00:00 2001 From: Wolfgang Kerzendorf Date: Thu, 21 Jun 2018 11:48:48 +0300 Subject: [PATCH 2/6] add link to notebook --- docs/conf.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 5665f78addc..07c86e3530d 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -59,7 +59,12 @@ 'sphinxcontrib.bibtex'] - +nbsphinx_prolog = """ +This notebook is available at +https://github.com/tardis-sn/tardis/tree/master/docs/notebooks/ +{{ env.doc2path(env.docname, base=None) }} +---- +""" # -- General configuration ---------------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. From 7280043c464644e0b89950f0dfdb45cb6a068144 Mon Sep 17 00:00:00 2001 From: Wolfgang Kerzendorf Date: Thu, 21 Jun 2018 12:10:45 +0300 Subject: [PATCH 3/6] change to toctrees --- docs/changelog.rst | 4 ---- docs/examples/index.rst | 36 +++++++++++++++++++++++++++++++ docs/examples/modelconfig.rst | 13 +++++++----- docs/index.rst | 40 +++++++++++++++++------------------ docs/physics/index.rst | 13 +++++++----- 5 files changed, 72 insertions(+), 34 deletions(-) create mode 100644 docs/examples/index.rst diff --git a/docs/changelog.rst b/docs/changelog.rst index 6a75ddba9b6..76888fe1bf1 100644 --- a/docs/changelog.rst +++ b/docs/changelog.rst @@ -1,7 +1,3 @@ .. _changelog: -********* -Changelog -********* - .. include:: ../CHANGELOG.rst diff --git a/docs/examples/index.rst b/docs/examples/index.rst new file mode 100644 index 00000000000..5382a79bf1c --- /dev/null +++ b/docs/examples/index.rst @@ -0,0 +1,36 @@ +************** +Example Models +************** + +The following provides some example setups for a number of typical TARDIS use +cases. You can use these examples as blueprints for your own TARDIS +applications. + + + +.. toctree:: + :maxdepth: 2 + + modelconfig + tardis_example + +Simple Parametrized Models +========================== + +These setups specify the ejecta solely via the YAML configuration file: + +* :doc:`tardis_example ` + + +API demonstrations +========================= + +An example on how to use the formal integrator with tardis: + +:ref:`notebooks/integrator.ipynb` + + +Detailed Explosion Models +========================= + +Coming soon diff --git a/docs/examples/modelconfig.rst b/docs/examples/modelconfig.rst index 12cd64fe2da..649504f583c 100644 --- a/docs/examples/modelconfig.rst +++ b/docs/examples/modelconfig.rst @@ -17,12 +17,15 @@ The density and composition may be specified independently in the following ways Specifying the density ====================== -* :doc:`using a power-law density profile ` -* :doc:`using an exponential density profile ` -* :doc:`using a custom density profile ` +.. toctree:: + densitypow + densityexp + densitycust + Specifying the composition ========================== -* :doc:`using a uniform composition ` -* :doc:`using a custom stratified composition ` +.. toctree:: + abundanceuni + abundancecust diff --git a/docs/index.rst b/docs/index.rst index 3e92e1bf3a1..e5887434044 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -33,42 +33,42 @@ acknowledge it by citing :cite:`Kerzendorf2014`. Using Tardis ============ -* :doc:`Installation ` -* :doc:`Quickstart Guide ` -* :doc:`Ejecta Model Setup ` -* :doc:`TARDIS Configuration ` -* :doc:`Storing simulations to HDF ` -* :doc:`Helper Scripts ` -* :doc:`Credit & Publication Policies ` - -======== -Examples -======== - .. toctree:: - notebooks/integrator + :maxdepth: 2 + + installation + running + examples/index + scripts/index + credits ====================== Looking under the hood ====================== -* :doc:`Physics behind TARDIS ` -* :doc:`Monte Carlo Primer ` +.. toctree:: + physics/index + montecarlo/index + ================= Developing Tardis ================= -* :doc:`Reporting Issues ` -* :doc:`How to contribute ` -* :doc:`Running tests ` -* :doc:`Changelog ` +.. toctree:: + :maxdepth: 2 + + issues + workflow/development_workflow + runnints_tests + changelog ========== References ========== -* :doc:`Studies using TARDIS and TARDIS references ` +.. toctree:: + zreferences ==== News diff --git a/docs/physics/index.rst b/docs/physics/index.rst index 3f932165171..0a4697f2472 100644 --- a/docs/physics/index.rst +++ b/docs/physics/index.rst @@ -21,7 +21,8 @@ Eventually, information about the following topics will be provided Currently some information are available for -* :doc:`Plasma State Calculation ` +.. toctree:: + new_plasma Old Physics Section of the TARDIS Docu (Outdated) @@ -33,8 +34,10 @@ Old Physics Section of the TARDIS Docu (Outdated) outdated, many basic concepts are still applicable to the current TARDIS version. -* :doc:`physical_quantities` -* :doc:`montecarlo` -* :doc:`new_plasma` -* :doc:`plasma/index` + +.. toctree:: + physical_quantities + montecarlo + new_plasma + plasma/index From 8a8dbed4e9199f25249d3b25fee858f920313a83 Mon Sep 17 00:00:00 2001 From: Wolfgang Kerzendorf Date: Thu, 21 Jun 2018 12:20:10 +0300 Subject: [PATCH 4/6] add more sections to toctree --- docs/atomic/atomic_data.rst | 6 +++--- docs/index.rst | 1 + docs/montecarlo/index.rst | 10 ++++++++++ 3 files changed, 14 insertions(+), 3 deletions(-) diff --git a/docs/atomic/atomic_data.rst b/docs/atomic/atomic_data.rst index 6a30f8f494d..8ac87a7aa72 100644 --- a/docs/atomic/atomic_data.rst +++ b/docs/atomic/atomic_data.rst @@ -4,6 +4,6 @@ Atomic Data for TARDIS ********************** -For a detailed description of the datasets go to :doc:`atomic_data_description` - -.. include:: current_public_table.rst +.. toctree:: + atomic_data_description + current_public_table.rst diff --git a/docs/index.rst b/docs/index.rst index e5887434044..b83a26d1219 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -47,6 +47,7 @@ Looking under the hood ====================== .. toctree:: + atomic physics/index montecarlo/index diff --git a/docs/montecarlo/index.rst b/docs/montecarlo/index.rst index 1e19e5d7bde..3521d665576 100644 --- a/docs/montecarlo/index.rst +++ b/docs/montecarlo/index.rst @@ -9,6 +9,16 @@ can also be found in various papers by L. Lucy and in the main TARDIS publicatio :cite:`Long2002`, :cite:`Lucy2002`, :cite:`Lucy2003`, :cite:`Lucy2005`, :cite:`Kerzendorf2014`) +.. toctree:: + basicprinciples + discretization + propagation + lineinteraction + estimators + virtualpackets + sourceintegration + randomsampling + * :doc:`Basic Principles of Monte Carlo Radiative Transfer ` * :doc:`Monte Carlo discretization ` * :doc:`Propagation of Monte Carlo quanta ` From ca207bb9331b43dd2d7e0d486e97e165800358b2 Mon Sep 17 00:00:00 2001 From: Wolfgang Kerzendorf Date: Mon, 25 Jun 2018 12:00:03 +0300 Subject: [PATCH 5/6] add more documentation --- docs/index.rst | 2 ++ docs/physics/plasma/lte_plasma.rst | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/index.rst b/docs/index.rst index b83a26d1219..2f17219abe8 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -47,6 +47,8 @@ Looking under the hood ====================== .. toctree:: + :maxdepth: 2 + atomic physics/index montecarlo/index diff --git a/docs/physics/plasma/lte_plasma.rst b/docs/physics/plasma/lte_plasma.rst index 6a9597cfdef..8f773b45933 100644 --- a/docs/physics/plasma/lte_plasma.rst +++ b/docs/physics/plasma/lte_plasma.rst @@ -45,6 +45,6 @@ the quantities calculated here. Example Calculations ^^^^^^^^^^^^^^^^^^^^ -.. plot:: physics/plasma/plasma_plots/lte_ionization_balance.py +.. .. plot:: physics/plasma/plasma_plots/lte_ionization_balance.py :include-source: From 125f46d6e19422d1ba39b40d77bcc6083e33c99a Mon Sep 17 00:00:00 2001 From: Wolfgang Kerzendorf Date: Mon, 25 Jun 2018 12:04:32 +0300 Subject: [PATCH 6/6] remove plot directives --- docs/physics/plasma/nebular_plasma.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/physics/plasma/nebular_plasma.rst b/docs/physics/plasma/nebular_plasma.rst index b0f8d2e478a..51c729c26ed 100644 --- a/docs/physics/plasma/nebular_plasma.rst +++ b/docs/physics/plasma/nebular_plasma.rst @@ -84,6 +84,6 @@ the quantities calculated here. Example Calculations ^^^^^^^^^^^^^^^^^^^^ -.. plot:: physics/plasma/plasma_plots/nebular_ionization_balance.py +.. .. plot:: physics/plasma/plasma_plots/nebular_ionization_balance.py :include-source: