From 4c534c29e905815d3f7231d7fb21fe8669cc508d Mon Sep 17 00:00:00 2001 From: smithis7 Date: Mon, 30 Nov 2020 22:09:41 -0500 Subject: [PATCH 01/10] deleting unused files --- docs/governance.rst | 40 ------------- docs/physics/index.rst | 44 -------------- docs/running/index.rst | 35 ----------- docs/team.rst | 128 ----------------------------------------- 4 files changed, 247 deletions(-) delete mode 100644 docs/governance.rst delete mode 100644 docs/physics/index.rst delete mode 100644 docs/running/index.rst delete mode 100644 docs/team.rst diff --git a/docs/governance.rst b/docs/governance.rst deleted file mode 100644 index a308ce261ca..00000000000 --- a/docs/governance.rst +++ /dev/null @@ -1,40 +0,0 @@ -.. _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. diff --git a/docs/physics/index.rst b/docs/physics/index.rst deleted file mode 100644 index 532a3c4501c..00000000000 --- a/docs/physics/index.rst +++ /dev/null @@ -1,44 +0,0 @@ -***************** -Physics of TARDIS -***************** - -.. warning:: - - This section of the TARDIS documentation is still `incomplete -`_. - -This part of the documentation is dedicated to providing some physical and -astrophysical background for TARDIS. If you do not find the information you are -looking for, consult the official TARDIS publications and the references therein. - -Eventually, information about the following topics will be provided: - -* Spectral Synthesis in SNe Ia ejecta -* Radiative Transfer Primer -* Reference Frames -* Nuclear Decay -* TARDIS Simulation Procedure -* Plasma State Calculation - -Currently some information are available for - -.. toctree:: - new_plasma - montecarlo/index - - -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 - diff --git a/docs/running/index.rst b/docs/running/index.rst deleted file mode 100644 index 1961c777b8d..00000000000 --- a/docs/running/index.rst +++ /dev/null @@ -1,35 +0,0 @@ -************** -Running TARDIS -************** - -The TARDIS code needs three components to calculate spectra: - - -.. toctree:: - :maxdepth: 1 - - ../models/index - ../configuration/index - ../atomic/atomic_data - - -A quick start guide to run TARDIS can be found -`here <../quickstart/quickstart.ipynb>`_. - - -.. toctree:: - :maxdepth: 2 - :caption: Running TARDIS and interactivity - - commandline - gui - interaction/index - custom_source - tardis_widgets/index - to_hdf - using_formal_integral - converters/index - - - - diff --git a/docs/team.rst b/docs/team.rst deleted file mode 100644 index 5deee9f72c2..00000000000 --- a/docs/team.rst +++ /dev/null @@ -1,128 +0,0 @@ -.. _team: - -**** -Team -**** - -TARDIS is developed by a multidisciplinary team. We adhere to our -`code of conduct `_. - -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, 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 - -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) From 82f171e44fc13237a243aa8ebf5e7053a38f723e Mon Sep 17 00:00:00 2001 From: smithis7 Date: Wed, 2 Dec 2020 22:48:16 -0500 Subject: [PATCH 02/10] reorganizing docs/running --- .../Custom_TARDIS_Model_Tutorial.ipynb | 2 +- .../running/{ => interaction}/commandline.rst | 0 .../{ => interaction}/converters/cmfgen.rst | 0 .../{ => interaction}/converters/index.rst | 0 .../converters/mesa.stella.dat | 0 .../converters/stella_to_tardis.ipynb | 0 .../{ => interaction}/custom_source.ipynb | 0 docs/running/interaction/index.rst | 6 +- docs/running/interaction/integrator.ipynb | 62 +++++++++---------- .../interaction/isotope_pd_subclass.ipynb | 2 +- .../{gui.rst => interaction/old_gui.rst} | 0 docs/running/{ => interaction}/to_hdf.rst | 0 .../using_formal_integral.rst | 0 13 files changed, 36 insertions(+), 36 deletions(-) rename docs/running/{ => interaction}/commandline.rst (100%) rename docs/running/{ => interaction}/converters/cmfgen.rst (100%) rename docs/running/{ => interaction}/converters/index.rst (100%) rename docs/running/{ => interaction}/converters/mesa.stella.dat (100%) rename docs/running/{ => interaction}/converters/stella_to_tardis.ipynb (100%) rename docs/running/{ => interaction}/custom_source.ipynb (100%) rename docs/running/{gui.rst => interaction/old_gui.rst} (100%) rename docs/running/{ => interaction}/to_hdf.rst (100%) rename docs/running/{ => interaction}/using_formal_integral.rst (100%) diff --git a/docs/running/interaction/Custom_TARDIS_Model_Tutorial.ipynb b/docs/running/interaction/Custom_TARDIS_Model_Tutorial.ipynb index 1acd79c197c..8fd71e88da4 100644 --- a/docs/running/interaction/Custom_TARDIS_Model_Tutorial.ipynb +++ b/docs/running/interaction/Custom_TARDIS_Model_Tutorial.ipynb @@ -788,7 +788,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.7.8" } }, "nbformat": 4, diff --git a/docs/running/commandline.rst b/docs/running/interaction/commandline.rst similarity index 100% rename from docs/running/commandline.rst rename to docs/running/interaction/commandline.rst diff --git a/docs/running/converters/cmfgen.rst b/docs/running/interaction/converters/cmfgen.rst similarity index 100% rename from docs/running/converters/cmfgen.rst rename to docs/running/interaction/converters/cmfgen.rst diff --git a/docs/running/converters/index.rst b/docs/running/interaction/converters/index.rst similarity index 100% rename from docs/running/converters/index.rst rename to docs/running/interaction/converters/index.rst diff --git a/docs/running/converters/mesa.stella.dat b/docs/running/interaction/converters/mesa.stella.dat similarity index 100% rename from docs/running/converters/mesa.stella.dat rename to docs/running/interaction/converters/mesa.stella.dat diff --git a/docs/running/converters/stella_to_tardis.ipynb b/docs/running/interaction/converters/stella_to_tardis.ipynb similarity index 100% rename from docs/running/converters/stella_to_tardis.ipynb rename to docs/running/interaction/converters/stella_to_tardis.ipynb diff --git a/docs/running/custom_source.ipynb b/docs/running/interaction/custom_source.ipynb similarity index 100% rename from docs/running/custom_source.ipynb rename to docs/running/interaction/custom_source.ipynb diff --git a/docs/running/interaction/index.rst b/docs/running/interaction/index.rst index 8d749e3f835..91e0f138ebc 100644 --- a/docs/running/interaction/index.rst +++ b/docs/running/interaction/index.rst @@ -8,11 +8,11 @@ have full access to the model properties (as described in :ref:`physical_quantit :maxdepth: 1 - ../commandline + commandline callback_example - ../converters/index + converters/index Custom_TARDIS_Model_Tutorial - ../gui + old_gui access init_trad_bug integrator diff --git a/docs/running/interaction/integrator.ipynb b/docs/running/interaction/integrator.ipynb index ea46312380c..9f68e2a9e10 100644 --- a/docs/running/interaction/integrator.ipynb +++ b/docs/running/interaction/integrator.ipynb @@ -60,19 +60,19 @@ "name": "stderr", "output_type": "stream", "text": [ - "[\u001B[1mtardis.plasma.standard_plasmas\u001B[0m][\u001B[1;37mINFO\u001B[0m ] Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5 (\u001B[1mstandard_plasmas.py\u001B[0m:72)\n", - "tardis.plasma.standard_plasmas - \u001B[1;37mINFO\u001B[0m - Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5\n", + "[\u001b[1mtardis.plasma.standard_plasmas\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5 (\u001b[1mstandard_plasmas.py\u001b[0m:72)\n", + "tardis.plasma.standard_plasmas - \u001b[1;37mINFO\u001b[0m - Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5\n", "tardis.atomic - INFO - Read Atom Data with UUID=5ca3035ca8b311e3bb684437e69d75d7 and MD5=21095dd25faa1683f4c90c911a00c3f8\n", - "[\u001B[1mtardis.plasma.base \u001B[0m][\u001B[1;34mDEBUG\u001B[0m ] Updating modules in the following order: (\u001B[1mbase.py\u001B[0m:195)\n", - "tardis.plasma.base - \u001B[1;34mDEBUG\u001B[0m - Updating modules in the following order:\n", - "[\u001B[1mtardis.montecarlo.base\u001B[0m][\u001B[1;34mDEBUG\u001B[0m ] Electron scattering switched on (\u001B[1mbase.py\u001B[0m:411)\n", - "tardis.montecarlo.base - \u001B[1;34mDEBUG\u001B[0m - Electron scattering switched on\n", - "[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m ] Starting iteration 1/1 (\u001B[1mbase.py\u001B[0m:194)\n", - "tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Starting iteration 1/1\n", - "[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m ] Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001B[1mbase.py\u001B[0m:271)\n", - "tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s\n", - "[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m ] Simulation finished in 1 iterations and took 0.90 s (\u001B[1mbase.py\u001B[0m:221)\n", - "tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Simulation finished in 1 iterations and took 0.90 s\n" + "[\u001b[1mtardis.plasma.base \u001b[0m][\u001b[1;34mDEBUG\u001b[0m ] Updating modules in the following order: (\u001b[1mbase.py\u001b[0m:195)\n", + "tardis.plasma.base - \u001b[1;34mDEBUG\u001b[0m - Updating modules in the following order:\n", + "[\u001b[1mtardis.montecarlo.base\u001b[0m][\u001b[1;34mDEBUG\u001b[0m ] Electron scattering switched on (\u001b[1mbase.py\u001b[0m:411)\n", + "tardis.montecarlo.base - \u001b[1;34mDEBUG\u001b[0m - Electron scattering switched on\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 1/1 (\u001b[1mbase.py\u001b[0m:194)\n", + "tardis.simulation.base - 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"tardis.plasma.standard_plasmas - \u001B[1;37mINFO\u001B[0m - Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5\n", + "[\u001b[1mtardis.plasma.standard_plasmas\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5 (\u001b[1mstandard_plasmas.py\u001b[0m:72)\n", + "tardis.plasma.standard_plasmas - \u001b[1;37mINFO\u001b[0m - Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5\n", "tardis.atomic - INFO - Read Atom Data with UUID=5ca3035ca8b311e3bb684437e69d75d7 and MD5=21095dd25faa1683f4c90c911a00c3f8\n", - "[\u001B[1mtardis.plasma.base \u001B[0m][\u001B[1;34mDEBUG\u001B[0m ] Updating modules in the following order: (\u001B[1mbase.py\u001B[0m:195)\n", - "tardis.plasma.base - \u001B[1;34mDEBUG\u001B[0m - Updating modules in the following order:\n", - "[\u001B[1mtardis.montecarlo.base\u001B[0m][\u001B[1;34mDEBUG\u001B[0m ] Electron scattering switched on (\u001B[1mbase.py\u001B[0m:411)\n", - "tardis.montecarlo.base - \u001B[1;34mDEBUG\u001B[0m - Electron scattering switched on\n", - "[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m ] Starting iteration 1/1 (\u001B[1mbase.py\u001B[0m:194)\n", - "tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Starting iteration 1/1\n", + "[\u001b[1mtardis.plasma.base \u001b[0m][\u001b[1;34mDEBUG\u001b[0m ] Updating modules in the following order: (\u001b[1mbase.py\u001b[0m:195)\n", + "tardis.plasma.base - \u001b[1;34mDEBUG\u001b[0m - Updating modules in the following order:\n", + "[\u001b[1mtardis.montecarlo.base\u001b[0m][\u001b[1;34mDEBUG\u001b[0m ] Electron scattering switched on (\u001b[1mbase.py\u001b[0m:411)\n", + "tardis.montecarlo.base - \u001b[1;34mDEBUG\u001b[0m - Electron scattering switched on\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 1/1 (\u001b[1mbase.py\u001b[0m:194)\n", + "tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Starting iteration 1/1\n", "Running with OpenMP - 4 threads\n", - "\u001B[2K\t[100%] Packets(finished/total): 10000/10000\n", - "[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m ] Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001B[1mbase.py\u001B[0m:271)\n", - "tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s\n", - "[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m ] Simulation finished in 1 iterations and took 1.05 s (\u001B[1mbase.py\u001B[0m:221)\n", - "tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Simulation finished in 1 iterations and took 1.05 s\n", + "\u001b[2K\t[100%] Packets(finished/total): 10000/10000\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:271)\n", + "tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Simulation finished in 1 iterations and took 1.05 s (\u001b[1mbase.py\u001b[0m:221)\n", + "tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Simulation finished in 1 iterations and took 1.05 s\n", "Saving the integrated spectrum.\n", "Doing the formal integral with 4 threads\n", "\n", @@ -1720,23 +1720,23 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 2", + "display_name": "Python 3", "language": "python", - "name": "python2" + "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", - "version": 2 + "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", - "pygments_lexer": "ipython2", - "version": "2.7.12" + "pygments_lexer": "ipython3", + "version": "3.7.8" } }, "nbformat": 4, "nbformat_minor": 1 -} \ No newline at end of file +} diff --git a/docs/running/interaction/isotope_pd_subclass.ipynb b/docs/running/interaction/isotope_pd_subclass.ipynb index d249725a13f..eb2b7f4e5fa 100644 --- a/docs/running/interaction/isotope_pd_subclass.ipynb +++ b/docs/running/interaction/isotope_pd_subclass.ipynb @@ -217,7 +217,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.7.8" } }, "nbformat": 4, diff --git a/docs/running/gui.rst b/docs/running/interaction/old_gui.rst similarity index 100% rename from docs/running/gui.rst rename to docs/running/interaction/old_gui.rst diff --git a/docs/running/to_hdf.rst b/docs/running/interaction/to_hdf.rst similarity index 100% rename from docs/running/to_hdf.rst rename to docs/running/interaction/to_hdf.rst diff --git a/docs/running/using_formal_integral.rst b/docs/running/interaction/using_formal_integral.rst similarity index 100% rename from docs/running/using_formal_integral.rst rename to docs/running/interaction/using_formal_integral.rst From b9a5ef6ffe43186e9f0f4505104b63bbb5267aa1 Mon Sep 17 00:00:00 2001 From: smithis7 Date: Thu, 3 Dec 2020 00:16:46 -0500 Subject: [PATCH 03/10] clarifying which file to use in toctree, as there is a to_hdf.rst and a to_hdf.ipynb --- docs/running/interaction/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/running/interaction/index.rst b/docs/running/interaction/index.rst index 91e0f138ebc..8ea0fdfb3f8 100644 --- a/docs/running/interaction/index.rst +++ b/docs/running/interaction/index.rst @@ -17,7 +17,7 @@ have full access to the model properties (as described in :ref:`physical_quantit init_trad_bug integrator isotope_pd_subclass - to_hdf + to_hdf.rst hdf_writer .. examples/run_simple_example.ipynb From 74d1c1f22a206edf1caba6a082a44640f3deb31c Mon Sep 17 00:00:00 2001 From: smithis7 Date: Fri, 4 Dec 2020 15:48:34 -0500 Subject: [PATCH 04/10] fixing new_plasma toc --- docs/physics/new_plasma.rst | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/docs/physics/new_plasma.rst b/docs/physics/new_plasma.rst index 305ee29e321..3343a2b7275 100644 --- a/docs/physics/new_plasma.rst +++ b/docs/physics/new_plasma.rst @@ -2,6 +2,7 @@ Plasma ****** + The role of the plasma module is to determine the ionisation and excitation states of the elements of the supernova ejecta, given the basic structure, including the elemental abundances, densities and radiation temperature. After the calculation of the plasma state, the :math:`\tau_{\textrm{sobolev}}` values can be calculated. @@ -40,9 +41,9 @@ 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). - - +Plasma Calculations +------------------- .. toctree:: :maxdepth: 2 - plasma/index + plasma/index \ No newline at end of file From 5f3edbc455b8dd30455e2db3980710742dbae60e Mon Sep 17 00:00:00 2001 From: smithis7 Date: Fri, 4 Dec 2020 15:53:55 -0500 Subject: [PATCH 05/10] fixing headers on outdated sections --- docs/physics/old_physics.rst | 6 +++--- docs/running/interaction/old_gui.rst | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/physics/old_physics.rst b/docs/physics/old_physics.rst index 78bf5834795..e78491dd8e8 100644 --- a/docs/physics/old_physics.rst +++ b/docs/physics/old_physics.rst @@ -1,6 +1,6 @@ -********************* -Old Physics Section of the TARDIS Docu (Outdated) -********************* +****************************** +Old Physics Section (Outdated) +****************************** .. note:: The following entries reflects the physics section of the old TARDIS diff --git a/docs/running/interaction/old_gui.rst b/docs/running/interaction/old_gui.rst index 992fb7ffa42..6e14e3672b1 100644 --- a/docs/running/interaction/old_gui.rst +++ b/docs/running/interaction/old_gui.rst @@ -1,6 +1,6 @@ -************************************* -Old Graphical User Interface Section -************************************* +*************************************** +Old Graphical User Interface (Outdated) +*************************************** TARDIS uses the `PyQt5 framework `_ for its cross-platform interface. From 3ff6efae4e722cccc9e16a8ccdfb45c3472ee8b7 Mon Sep 17 00:00:00 2001 From: smithis7 Date: Fri, 4 Dec 2020 16:09:56 -0500 Subject: [PATCH 06/10] adding custom_source and physical_quantities to additional interactivity section --- docs/running/interaction/index.rst | 2 ++ docs/{physics => running/interaction}/physical_quantities.ipynb | 0 2 files changed, 2 insertions(+) rename docs/{physics => running/interaction}/physical_quantities.ipynb (100%) diff --git a/docs/running/interaction/index.rst b/docs/running/interaction/index.rst index 8ea0fdfb3f8..407febe3baf 100644 --- a/docs/running/interaction/index.rst +++ b/docs/running/interaction/index.rst @@ -12,6 +12,7 @@ have full access to the model properties (as described in :ref:`physical_quantit callback_example converters/index Custom_TARDIS_Model_Tutorial + custom_source old_gui access init_trad_bug @@ -19,6 +20,7 @@ have full access to the model properties (as described in :ref:`physical_quantit isotope_pd_subclass to_hdf.rst hdf_writer + physical_quantities .. examples/run_simple_example.ipynb diff --git a/docs/physics/physical_quantities.ipynb b/docs/running/interaction/physical_quantities.ipynb similarity index 100% rename from docs/physics/physical_quantities.ipynb rename to docs/running/interaction/physical_quantities.ipynb From 84d0e1c23a4cf5054fd75d9ac307b1fb1ebb5937 Mon Sep 17 00:00:00 2001 From: smithis7 Date: Fri, 4 Dec 2020 16:11:48 -0500 Subject: [PATCH 07/10] removing physical_quantities from old_physics --- docs/physics/old_physics.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/physics/old_physics.rst b/docs/physics/old_physics.rst index e78491dd8e8..09588d3f53d 100644 --- a/docs/physics/old_physics.rst +++ b/docs/physics/old_physics.rst @@ -10,6 +10,5 @@ Old Physics Section (Outdated) .. toctree:: - physical_quantities montecarlo_old plasma/index \ No newline at end of file From 3d299597e21fb4acd3bf51fefd3b0409558785df Mon Sep 17 00:00:00 2001 From: smithis7 Date: Sat, 5 Dec 2020 22:40:17 -0500 Subject: [PATCH 08/10] fixing heading on CONTRIBUTING.md --- CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 4065b91c7b9..868e48b336d 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,4 +1,4 @@ -# Contributing to TARDIS +# Contribution Guidelines So you are wondering how can you contribute to TARDIS? Congrats, you've landed on the right page! From ac98ba860c6907219254470fb224733d0e6e26b5 Mon Sep 17 00:00:00 2001 From: smithis7 Date: Sun, 6 Dec 2020 14:40:28 -0500 Subject: [PATCH 09/10] adding using_formal_integral --- docs/running/interaction/index.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/running/interaction/index.rst b/docs/running/interaction/index.rst index 407febe3baf..38c9d7cff93 100644 --- a/docs/running/interaction/index.rst +++ b/docs/running/interaction/index.rst @@ -21,6 +21,7 @@ have full access to the model properties (as described in :ref:`physical_quantit to_hdf.rst hdf_writer physical_quantities + using_formal_integral .. examples/run_simple_example.ipynb From 28e161a06ecb4bebc0e0be6c9faf297332a5c836 Mon Sep 17 00:00:00 2001 From: smithis7 Date: Tue, 8 Dec 2020 15:54:43 -0500 Subject: [PATCH 10/10] doing Jaladh's suggestions --- docs/physics/{new_plasma.rst => plasma.rst} | 8 ++++++-- docs/physics/plasma/{plasma.rst => old_plasma.rst} | 6 +++--- 2 files changed, 9 insertions(+), 5 deletions(-) rename docs/physics/{new_plasma.rst => plasma.rst} (97%) rename docs/physics/plasma/{plasma.rst => old_plasma.rst} (98%) diff --git a/docs/physics/new_plasma.rst b/docs/physics/plasma.rst similarity index 97% rename from docs/physics/new_plasma.rst rename to docs/physics/plasma.rst index 3343a2b7275..154d9ea3542 100644 --- a/docs/physics/new_plasma.rst +++ b/docs/physics/plasma.rst @@ -45,5 +45,9 @@ Plasma Calculations ------------------- .. toctree:: :maxdepth: 2 - - plasma/index \ No newline at end of file + + plasma/lte_plasma + plasma/nebular_plasma + plasma/macroatom + plasma/nlte + plasma/helium_nlte \ No newline at end of file diff --git a/docs/physics/plasma/plasma.rst b/docs/physics/plasma/old_plasma.rst similarity index 98% rename from docs/physics/plasma/plasma.rst rename to docs/physics/plasma/old_plasma.rst index 9d2379016ac..f2b0b6e541e 100644 --- a/docs/physics/plasma/plasma.rst +++ b/docs/physics/plasma/old_plasma.rst @@ -1,8 +1,8 @@ .. _plasmas: -****** -Plasma -****** +***************** +Plasma (Outdated) +***************** .. currentmodule:: tardis.plasma_array