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--- ideas_page [2019/01/28 00:03]
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+++ ideas_page [2019/03/12 00:04] (current)
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 ----
 ==== Expanding the Integration-Testing Framework ====
@@ Line 37: / Line 39: @@
 **Astronomy knowledge needed:** None
-**Mentors:** @orbitfold
+**Mentors:** Vytautas Jancauskas, Ulrich Noebauer
 **Programming skills:** Python
@@ Line 44: / Line 46: @@
 **GSoC Application Tag:** integration-testing
-***TRAVIS*** integration with travis
 **Description:** Testing a scientific code like TARDIS is very important. We need to ensure that the scientific insights we gain using the code are not based on bugs. Open collaboration with GitHub is great, but the more people work on the code the more opportunities there are to introduce bugs. Making sure that the code doesn't change or only changes as we expect it, is thus an important part of TARDIS development.
@@ Line 50: / Line 51: @@
 We have two types of tests: unit tests that verify small portions of the code and full-scale integration tests. Both of these test types are implemented with a framework. But the integration tests are difficult to use.
-  * currently we mainly run the integration tests on an external server. We want to integrate them into our general TRAVIS continuous integration routine. We'd also like to expand that and check also different properties of our model against reference data (e.g. electron densities, ionization fractions, dilution factors)
+  * currently we mainly run the integration tests on an external server. We want to integrate them into our general Azure Pipeline continuous integration routine. We'd also like to expand that and check also different properties of our model against reference data (e.g. electron densities, ionization fractions, dilution factors)
   * hand in hand with expanding the verification process we will improve the reporting process which should contain detailed plots and comparison results. A framework exists but is currently not actively used.
-**Your first objective if you choose to accept the mission:** Mark the TARDIS full test as slow and make it easy to enable it's execution only with a commandline option to `py.test`
+**Your first objective if you choose to accept the mission:** Setup the integration tests to run once a week on Azure pipelines given the examples at https://tardis.readthedocs.io/en/latest/running_tests.html
-?????
 ----
@@ Line 62: / Line 62: @@
 ==== Atomic Datasets ====
-**Difficulty:** Hard
+**Difficulty:** Medium
-**Astronomy knowledge needed:** Medium
+**Astronomy knowledge needed:** Low/None
-**Mentors:** @lukeshingles, @shaching
+**Mentors:** Luke Shingles, Mark Magee
 **Programming skills**: Python, Parsing, Databases, SQLAlchemy
@@ Line 82: / Line 82: @@
 For this project you would help us make parsers for a variety of formats from a collection of atomic data sources (see the TEP) and in the second part put this into a database. The assembled database will not only be very interesting for us, but also for many other fields of astronomy that do rely on atomic data. A useful resource of understanding atomic structure description can be found in http://www.physics.byu.edu/faculty/bergeson/physics571/notes/L27spectnotation.pdf.
-In GSoC 2016 we created a package that compiles all of this information into a database named Carsus (see http://carsus.readthedocs.io/en/latest/). For this year we aim to strengthen the link between Carsus and TARDIS and also include more atomic data into Carsus.
+We created a package that compiles all of this information into a database named Carsus (see http://carsus.readthedocs.io/en/latest/). For this year we aim to strengthen the link between Carsus and TARDIS and also include more atomic data into Carsus.
-**Your first objective if you choose to accept the mission:** Use the script (https://github.com/tardis-sn/carsus-db/blob/master/scripts/create_hdfstore.py) to generate an HDF store - then implement a meta table in the HDF file that stores the units of the columns.
+**Your first objective if you choose to accept the mission:** download the atomic data from http://kookaburra.phyast.pitt.edu/hillier/web/CMFGEN.htm and read in the tabulated data contained in si2_osc_kurucz.
 ----
@@ Line 94: / Line 94: @@
 **Astronomy knowledge needed:** Low/None
-**Mentors:** @unoebauer, @wkerzendorf
+**Mentors:** Yssa Camacho, Stuart Sim
 **Programming skills**: Python
@@ Line 100: / Line 100: @@
 **Related TEP:** [[https://github.com/tardis-sn/tep/blob/master/TEP007_isotopes_decay.rst|TEP007]]
-**GSoC Application Tag:** nuclear decay
+**GSoC Application Tag:** new-model-format
-**Description:** Supernova are powered by the decay of radioactive elements and thus if we want to simulate
+**Description:** The main task that TARDIS accomplishes is to take a model of the exploded star and then simulate the transport of light resulting in a prediction of the observed spectrum. There are currently multiple formats to input the model. For this year, we aim to streamline this process and provide a single format for input. We will also provide converters for the legacy formats.
-supernovae we also need to take this physical process into account. Currently, this is done in a very difficult and
-not easily extensible way in TARDIS. We have thought about adding more support for this and need your help with
-this.
+**Your first objective if you choose to accept the mission:** Combine the functionality from read_cmfgen_density and read_csv_isotope_abundances to read a single files that can interpret columns from both functions (https://github.com/tardis-sn/tardis/blob/master/tardis/io/model_reader.py).
-**Your first objective if you choose to accept the mission:** Make a Pandas DataFrame with columns atomic_number, mass_number, mass - then use [[http://pyne.io/|PYNE]] to write a function that takes this table decays it for 100 days and returns a table with the decayed masses.
+----
+==== Jupyter notebook widget for TARDIS ====
-----
+**Difficulty:** Hard
+**Astronomy knowledge needed:** None
+**Mentors:** Yssa Camacho, Laud Bentil
+**Programming skills:** Python, Jupyter
+**Related TEP:** [[https://github.com/tardis-sn/tep/blob/master/TEP012_gui_overhaul.rst|TEP012]]
+**GSoC Application Tag:** jupyter-widget
+**Description:** Often we need more information about the model and the calculation than the mere spectrum. For example, we frequently need to investigate in detail how a specific spectral line feature forms, which ions and which specific line transitions contribute. For exactly this purpose a Qt-GUI was developed (see [[http://tardis.readthedocs.io/en/latest/gui.html#gui-explanation|here]]). It allows the user to easily analyse TARDIS runs and extract important physical information without knowing the exact inner data structure of TARDIS.
+QT for this type of application is no longer the ideal framework. Many applications now work with Jupyter notebook and we want to have a functional GUI that acts as a Jupyter widget. Once this is implemented, we would like to have several example notebooks that exist within the documentation so that it is easy for users to try it out themselves.
+**Your first objective if you choose to accept the mission:** Make a Jupyter notebook and embed it in the documentation that showcases the current way of running TARDIS and plots a spectrum.
+----
-=== Jupyter notebook widget for TARDIS ====
+==== Distribution of TARDIS via conda ====
 **Difficulty:** Medium
@@ Line 123: / Line 136: @@
 **Astronomy knowledge needed:** None
-**Mentors:** @wkerzendorf, @unoebauer
+**Mentors:** Wolfgang Kerzendorf, Vytautas Jancauskas
-**Programming skills:** Python
+**Programming skills:** Python, conda
-**Related TEP:** [[https://github.com/tardis-sn/tep/blob/master/TEP012_gui_overhaul.rst|TEP012]]
-**GSoC Application Tag:** gui
+**GSoC Application Tag:** conda
-**Description:** Often we need more information about the model and the calculation than the mere spectrum. For example, we frequently need to investigate in detail how a specific spectral line feature forms, which ions and which specific line transitions contribute. For exactly this purpose a Qt-GUI was developed (see [[http://tardis.readthedocs.io/en/latest/gui.html#gui-explanation|here]]). It allows the user to easily analyse TARDIS runs and extract important physical information without knowing the exact inner data structure of TARDIS.
+**Description:** TARDIS is a tool to analyze transient phenomenon like supernovae. It is important for researchers to quickly install this tool to react to newly observed objects. Anaconda offers a quick and easy way to install python packages and its dependencies. For this project, we want to make it easy to install TARDIS via Anaconda.
-During GSoC 2019 we want to update and improve this GUI. As a first step, the GUI has to be made compatible with the current design of TARDIS, i.e. able to work with simulation objects. After this preparatory step, the GUI should be extended to contain the analysis tools which currently reside in the [[https://github.com/tardis-sn/tardisanalysis|tardisanalysis]] repository. Finally, an addon scheme should be developed/implemented which enables the user to easily add more analysis tools.
+**Your first objective if you choose to accept the mission:** Make a conda packages for TARDIS following the instructions on https://conda.io/projects/conda-build/en/latest/source/recipe.html.
-**Your first objective if you choose to accept the mission:**
-At the moment, the GUI is incompatible with the current version of TARDIS and can't be started (Issue [[https://github.com/tardis-sn/tardis/issues/690|#690]]). Make a PR that implements the necessary minimal changes in the GUI to start with the current version of TARDIS. In this first task, it is not necessary to fix all potentially broken features but that the main GUI window can be started without errors.
+----
-=== Distribution of TARDIS via conda ====
+==== Enable the Dask framework for parallel execution for TARDIS ====
-**Difficulty:** Medium
+**Difficulty:** Hard
 **Astronomy knowledge needed:** None
-**Mentors:** @wkerzendorf, @unoebauer
+**Mentors:** Tyler Pritchard, Christian Vogl
-**Programming skills:** Python
+**Programming skills:** Python, dask
+**GSoC Application Tag:** dask
+**Description:** Exploring different simulations of supernovae and comparing them with observations is one of the important tasks of TARDIS. This means that TARDIS needs to be run many tens of thousand times with different inputs. The Dask framework will allow TARDIS to be excecuted on multi-core systems and super-computers. This project aims to combine TARDIS with dask to make it easy to run many iterations of TARDIS.
+**Your first objective if you choose to accept the mission:** Use dask to run distributed TARDIS instances in parallel on your system. Use http://distributed.dask.org/en/latest/client.html as a guide to make a simple example.
+----
+==== Improve the C/Python interface ====
+**Difficulty:** Hard
+**Astronomy knowledge needed:** None
+**Mentors:** Wolfgang Kerzendorf, Christian Vogl
+**Programming skills:** python, cython
+**GSoC Application Tag:**c_interface
+**Description:** TARDIS is a hybrid code built on C/Cython/Python. Currently, there is a lot of interface code to port the python data structures from Python via Cython to C. This makes the code cumbersome to test and try out new things. There are now several new ways that promise to make this easier. We want to try to use cFFI and Apache Arrow to do this.
+**Your first objective if you choose to accept the mission:** use cFFI to provide an automatic interface for testing the parts in the montecarlo package instead of ctypes.
+----
+==== Profile TARDIS ====
+**Difficulty:** Easy/Moderate
+**Astronomy knowledge needed:** None
+**Mentors:** Wolfgang Kerzendorf
+**Programming skills:** python, cython
+**GSoC Application Tag:**asv
+**Description:** TARDIS is a code that prides itself on being relatively fast to compute a synthetic spectrum. We are also continuously adding additional microphysics in the code which sometimes requires additional calculation. It is important to understand how much this microphyiscs adds to the runtime of the code. For this we want to implement a benchmark in asv (airspeed velocity) that can automatically generate a report for us.
+**Your first objective if you choose to accept the mission:** implement a simple benchmark in asv.
-**Related TEP:** [[https://github.com/tardis-sn/tep/blob/master/TEP012_gui_overhaul.rst|TEP012]]
-**GSoC Application Tag:** gui

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