Merge pull request tardis-sn#1364 from smithis7/issue_1357_fix

Fixing issue tardis-sn#1357

docs/index.rst

@@ -57,17 +57,20 @@ Mission Statement
     :caption: Using TARDIS
     :hidden:
 
-
-    running/index
+    running/components
+    running/tardis_widgets/index
+    running/interaction/index
 
 
 .. toctree::
     :maxdepth: 2
     :caption: The Physics of TARDIS
     :hidden:
-
-    Physics overview <physics/index>
-    physics/plasma/index
+
+    physics/montecarlo/index
+    physics/new_plasma
+    physics/old_physics
+
 
 .. toctree::
     :maxdepth: 2
@@ -91,8 +94,7 @@ Mission Statement
     :caption: Team & Credits
     :hidden:
 
-    team
-    governance
+    team_and_governance/index
     credits
     Code of Conduct <CODE_OF_CONDUCT.md>
 

docs/physics/new_plasma.rst

@@ -39,3 +39,10 @@ If the necessary Python modules (`PyGraphviz <https://pygraphviz.github.io/>`_ a
 Updating the Plasma
 -------------------
 During each iteration of the main code, TARDIS updates the plasma using the `update_radiationfield` function. This requires, at minimum, new values for `t_rad` (the radiation temperature), `w` (the dilution factor) and `j_blues` (the intensity in the blue part of each line).
+
+
+
+.. toctree::
+    :maxdepth: 2
+
+    plasma/index

docs/physics/old_physics.rst

@@ -0,0 +1,15 @@
+*********************
+Old Physics Section of the TARDIS Docu (Outdated)
+*********************
+
+.. note::
+    The following entries reflects the physics section of the old TARDIS
+    documentation. Even though this section of the documentation is partly
+    outdated, many basic concepts are still applicable to the current TARDIS
+    version.
+
+
+.. toctree::
+    physical_quantities
+    montecarlo_old
+    plasma/index

docs/running/components.rst

@@ -0,0 +1,17 @@
+***********
+Components
+***********
+
+The TARDIS code needs three components to calculate spectra:
+
+
+.. toctree::
+    :maxdepth: 1
+
+    ../configuration/index
+    ../models/index
+    ../atomic/atomic_data
+
+
+A quick start guide to run TARDIS can be found
+`here <../quickstart/quickstart.ipynb>`_.

docs/running/gui.rst

@@ -1,8 +1,6 @@
-.. _gui:
-
-************************
-Graphical User Interface
-************************
+*************************************
+Old Graphical User Interface Section
+*************************************
 
 TARDIS uses the `PyQt5 framework <http://www.riverbankcomputing.com/software/pyqt/download5>`_ for its cross-platform
 interface.

docs/running/interaction/index.rst

@@ -1,15 +1,19 @@
-Interacting with TARDIS
-=======================
+Additional Interactivity
+=========================
 
 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 
 
-    access
+
+    ../commandline
     callback_example
+    ../converters/index
     Custom_TARDIS_Model_Tutorial
+    ../gui
+    access
     init_trad_bug
     integrator
     isotope_pd_subclass

docs/running/tardis_widgets/index.rst

@@ -1,6 +1,8 @@
-**************
-TARDIS Widgets
-**************
+.. _gui:
+
+*************************
+Graphical User Interface
+*************************
 
 A collection of widgets (simple GUIs) that makes it easier for you to explore
 the simulation data within Jupyter Notebooks. 

docs/team_and_governance/alumni.rst

@@ -0,0 +1,30 @@
+**************
+TARDIS Alumni
+**************
+
+The present version of TARDIS would not have been possible if not for the work of these individuals. 
+
+
+Past TARDIS Core Members
+---------------------------
+
+ * Aoife Boyle
+ * Michael Klauser
+ * Stefan Lietzau
+ * Markus Kromer
+ * Ulrich Noebauer
+
+Current and Former GSoC and SOCIS Students
+------------------------------------------
+
+ * Aoife Boyle (GSoC 2015)
+ * Tomas Bylund (SOCIS 2016)
+ * Karan Desai (GSoC 2016)
+ * Vaibhav Gupta (GSoC 2017)
+ * Vytautas Jancauskas (GSoC 2015, 2014)
+ * Stefan Lietzau (GSoC 2017)
+ * Mikhail Mishin (GSoC 2016)
+ * Fotis Tsamis (GSoC 2016)
+ * Ezequiel Passaro (GSoC 2019, 2020)
+ * Jaladh Singhal (GSoC 2019, 2020)
+ * Jordi Eguren Brown (GSoC 2020)

docs/team_and_governance/governance.rst

@@ -0,0 +1,40 @@
+.. _governance:
+
+**********
+Governance
+**********
+
+The development of TARDIS and associated software tools are helped through several coordination roles fulfilled by community members (see :ref:`team`). There are several governance rules to ensure scientific excellence, continuity, and transparency. The TARDIS community has matured substantially in recent years and we will revisit these rules as the community evolves. 
+
+Rules for TARDIS-core
+---------------------
+
+New members of TARDIS-core are nominated by current members. All members of TARDIS-core can vote on nominated candidates, who require a 2/3 majority in their favour in order to be approved.
+
+Rules for terms
+---------------
+
+The rule for all roles will be as follows (with the exception of the PI). A single term is limited in time but the number of subsequent terms is not limited. The term limit for all terms is 3 years and is renewable once for another 3 years and then has to be advertised to the wider community. 
+
+Every member of TARDIS-core is allowed to vote and the election will follow an anonymous rank voting system. If this results in a tie the PI will facilitate a discussion with a subsequent run-off election.  
+
+For 6 months the previous position holder will act in an advisory role to the new position holder.
+
+**Term rules for the PI:** The selection of the PI will follow a similar process with the difference that their terms are 5 years (renewable once for another 5 years). A re-election for the role of PI is advertised in TARDIS-core and will be selected from members of this group (unless the group decides on an outsider with 2/3 majority).
+
+
+Science Decisions
+-----------------
+
+Decisions that concern implementation details for TARDIS and related projects that pertain to science questions should be discussed within the TARDIS core team. 
+
+
+Software Decisions
+------------------
+
+Decisions about software architecture and design should take into account consistency over the TARDIS code-base and best-practices. The final decision (after discussion with the rest of the team) rests with the software architect (veto-able by a 2/3 majority).
+
+Financial Decisions
+-------------------
+
+Financial decisions can only be made by the PI but they have to inform TARDIS-core with a reasonable lead time to allow them to raise any objections. The TARDIS-core can veto decisions with a 2/3 majority. 

docs/team_and_governance/index.rst

@@ -0,0 +1,8 @@
+********************
+Team and Governance
+********************
+
+.. toctree::
+    team
+    alumni
+    governance

docs/team_and_governance/team.rst

@@ -0,0 +1,98 @@
+.. _team:
+
+****
+Team
+****
+
+TARDIS is developed by a multidisciplinary team. We adhere to our
+`code of conduct <https://tardis-sn.github.io/tardis/CODE_OF_CONDUCT.html>`_.
+
+The development of TARDIS and associated software tools are made possible through several coordination roles fulfilled by community members. This encompasses a broad scope of responsibilities ranging from direct package development to communication, distribution, and managerial activities.
+
+The roles and their description can be found here: 
+
+* **Principal Investigator**
+  - Wolfgang Kerzendorf
+* **TARDIS CORE** [alphabetical]
+  - Yssavo Camacho-Neves, Andreas Flörs, Andrew Fullard, Alice Harpole, Vytautas Jancauskas, Wolfgang Kerzendorf (founder), Luke Shingles, Stuart Sim (founder), Christian Vogl, Marc Williamson
+* **TARDIS GSoC Coordinators (2020)**
+  Yssavo Camacho-Neves, Alice Harpole, Wolfgang Kerzendorf, Marc Williamson
+* **TARDIS GSoC Mentors (2020)**
+  - Alice Harpole, Andreas Flörs, Christian Vogl, Fionntan Callan, James Gillanders, Luciano G Silvestri, Stuart Sim, Wolfgang Kerzendorf, Yssavo Camacho-Neves, Andrew Fullard, Arjun Savel, Brian Cherinka, Jack O'Brien, Lindsey Kwok, Luke Shingles, Marc Williamson, Mark Magee, Michael Moltenbrey, Vytautas Jancauskas
+* **Ombudsperson**
+  - Michael Zingale (contact info on https://zingale.github.io/)
+* **Software Architect** 
+  - Alice Harpole   
+* **Issues / Pull Request** 
+  - Andreas Flörs
+* **Continuous Integration / Deployment / Testing**
+  - Christian Vogl
+* **Funding / Financial**
+  - Marc Williamson
+* **Science / Science Meeting / Publications**
+  - Yssavo Camacho-Neves
+* **Diversity, Equity, and Inclusion**
+  - Wolfgang Kerzendorf
+
+
+**Principal Investigator**
+
+- Guides the scientific and the educational activities of TARDIS
+- Advised by TARDIS Core
+
+**TARDIS Core**
+
+- Team that oversees the activities and sets the goals for the TARDIS Collaboration
+- Identifies science opportunities that match TARDIS capabilities or coordinates the addition of capabilities
+- Identifies education opportunities such as workshops, lecture development, and outreach opportunities
+
+**TARDIS GSoC Coordinators (2020)**
+
+- Coordinate participation of TARDIS in the Google Summer of Code
+
+**TARDIS GSoC Mentors (2020)**
+
+- Mentors for Google Summer of Code students 
+
+**Ombudsperson**
+
+- Designated person appointed to address the concerns of community members and to uphold the code of conduct
+- Solicit and provide anonymized feedback to the TARDIS CORE team 
+- Assist the TARDIS CORE team with violations of the code of conduct or other ethical concerns
+- **Specifically selected as not being part of the TARDIS collaboration**
+
+**Software Architect**
+
+- Ensure overall design pattern throughout TARDIS
+- Coordinate restructure and rewriting efforts
+- Identify and communicate new technologies relevant to TARDIS
+
+**Issues / Pull Request**
+
+- Monitor open PRs and issues
+- Monitor reviewing is taking place
+- Close abandoned PRs / Issues
+
+**Continuous Integration / Deployment / Testing** 
+
+- Inform team of break in any of the CI/CD pipelines
+- Delegate code maintenance and bug removal
+- Identify new technologies for CI/CD
+
+**Funding / Financial**
+
+- Manage budget for TARDIS
+- Ensure financial transparency 
+- Coordinating with funding organizations
+- Securing funding for parts of the project via discussions and proposals to funding agencies
+
+**Science / Science Meeting / Publications**
+
+- Coordinating work for weekly science meeting
+- Finding publications and collecting TARDIS models
+- Citation guide
+
+**Diversity, Equity, and Inclusion**
+
+- Identify opportunities to use TARDIS to engage members of underrepresented minorities (URM) to coding/STEM
+- Identify papers about engaging URM in coding / science