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Co-authored-by: Jordi Eguren Brown <[email protected]> Co-authored-by: Wolfgang Kerzendorf <[email protected]>
* add pyproject with black settings * black codestyle for all except model, montecarlo * Update tardis/io/atom_data/util.py Co-authored-by: Jaladh Singhal <[email protected]> * Update tardis/io/atom_data/util.py Co-authored-by: Jaladh Singhal <[email protected]> * Update tardis/io/config_reader.py * Update tardis/io/config_reader.py * Update tardis/io/decay.py * Update tardis/io/util.py Co-authored-by: Jaladh Singhal <[email protected]> * Update tardis/plasma/properties/general.py Co-authored-by: Wolfgang Kerzendorf <[email protected]> * Update tardis/plasma/properties/general.py Co-authored-by: Jaladh Singhal <[email protected]> * Update tardis/plasma/properties/nlte.py Co-authored-by: Jaladh Singhal <[email protected]> * Update tardis/plasma/properties/partition_function.py Co-authored-by: Jaladh Singhal <[email protected]> * Update tardis/plasma/properties/partition_function.py Co-authored-by: Wolfgang Kerzendorf <[email protected]> * Delete properties.py * Update tardis/plasma/standard_plasmas.py Co-authored-by: Wolfgang Kerzendorf <[email protected]> * Delete test_montecarlo.py Co-authored-by: Jaladh Singhal <[email protected]>
add code style black badge
* Minor changes to the environment file * Remove old readthedocs files
* removing kwarg from MonteCarloConfiguration, as jitclass does not support them * need to pass enable_full_relativity to configuration_initialize, as removed kwarg in MonteCarloConfiguration * move_r_packet and trace_packet both require montecarlo_configuration arg * r_packet object used in distance calculation in place of r_packet.r value * the full_relativity bool was being passed as a different kwarg * added montecarlo_configuration to args of trace_vpacket_volley and trace_vpacket, so that relativity attribute continues to get passed down * making sure the vpacket funcs that now require montecarlo_configuration get called with this arg * Added random seed; does not work with numba * Changed to numpy random seed * Commented out MonteCarloException block; will test how this impacts output * Need the MonteCarloException block to be run, otherwise large discrepancies between numba branch and master branch * Adding custom seeds to vpackets; few line adjustments * changed from njit to jit to ease debugging * More descriptive montecarloexception, with optional printing beforehand * Changed njit to jit in single_loop to ease debugging * Added single-packet debugging capabilities to MonteCarloRunner. * Removing plotting funcs from montecarlo * Added basic logging capabilities to montecarlo_numba * Generalized logger to *args * Tweaking configuration of logging in module * Logger can now handle kwargs * Renamed logger * Make logging more in line with other TARDIS loggers. * Share global variable DEBUG_MODE across modules with montecarlo init. * No longer calling removed plot_single_packet; also referring to __init__ DEBUG_MODE * Now referring to montecarlo __init__ DEBUG_MODE global * Remove dangling else statement * no longer need plotting in montecarlo_numba base.py * Remove import of function that no longer exists. * No longer holding global variables in montecarlo init * Importing mc_logger for global variables now * Moving log_decorator from base.py * Adding logger to new montecarlo_logger file * Add new logger to, remove print statements from r_packet.py * Ensure that DEBUG_MODE is referenced within the montecarlo_logger file * Allow the function being decorated to take its kwargs. * Apply wraps correctly * Make else block logic more apparent * Get rid of extra blank line * Got rid of a few todos * Add note about why decorator behavior will not change according to config * removing reference to logger in base * Added crude buffer * Increase buffer; check DEBUG_MODE checked during call, not init * Set default buffer in montecarlo logger to stated default * Allow specification of buffer in montecarlo yml * Make sure logger_buffer is passed through to montecarlo logger * Remove todo, question from log_decorator * Adding better docstrings to log_decorator * Add newline at end of montecarlo_logger file * Make logger config happen outside of decorator * Moved print statement to exception; * Added logging to file * No longer profiling calculate_distance_line * Add functionality to profile incomplete packet runs * Rename previous debug mode, as it was not for single packets * Added single packet seed to yml * Propagate single_packet_seed throughout configurations * Reference single packet seed from montecarloconfiguration * Add bool type to single packet seed type * Catch exception better, catch extra random seed * Set whole index, including energies, not just random seed * Change where loop is broken. * Move close_line_threshold check past montecarloexception * Add single-packet debug documentation and script * Add jitclass arg for single packet seed in montecarloconfiguration * Now the default for single_packet_seed cannot be a bool * Added new debug page to developer part of documentation * Now the single_packet_seed has to be not 1, not not False * Pause using log_decorator, remove try/except for nopython * Vpacket jitclass now allows for an int64 index * Exceptions args must be compile-time constants in nopython mode * Allow 0 nu_diff to not throw exception. * v_packets should have the same random seed as their r_packet * Fix MonteCarloException throw * Fix estimator typos * Make sure return is not made before relativity block * Rename esitmators to keep them consistent * Also rename the estimators in montecarlo.pyx * Rename estimators in numba_interface * Clean up estimator typos; change back to njit * Include Doppler factor in energy calculation for full_relativity * Add back not statement * Added relativistic Doppler factor * Add in Doppler factor relativity for interaction * Add angle aberration * add angle aberration to interactions * Update numba version * Remove relativity branching * Logger no longer prints to console if printing to file * Initialize configuration with external module, not jitclass * Remove extra repr of logger.handlers * Ensure the angle aberration is called on vpacket, remove jitclass reference * Convert montecarloconfiguration refs from jitclass to module * Add more references to global module, complete relativistic branching * Pass r_packet.mu to angle aberration calculation * Clarify angle aberration calc, include doppler factor to distance calc * Remove reference to MonteCarloConfiguration * Trying to delete C tests * Remove C montecarlo * Remove references to C module * Alter formal integral tests for python version * Rewrite formal integral in python
* Change `pytestconfig` to `request.config` * Removed docstring by mistake. Fixed.
…ontributing Added better mission statement
* Moved and renamed coverage file * Omit astropy_init from coverage calculation * generalize omit of astropy_init to all file types
* Added roadmap link to main page * Added roadmap page Co-authored-by: Marc Williamson <[email protected]>
* Update team.rst - Add roles and descriptions Added roles and descriptions to the team page * Update team.rst - Added new GSoC students Update GSoC students section * Update team.rst - Added new roles Added new roles and minor style changes * add several nbsphinx related options * restructure the Governance model page * re-enabled nbsphinx * fix issues marked by @yssa Co-authored-by: Yssa Camacho <[email protected]>
* Update team.rst - Add roles and descriptions Added roles and descriptions to the team page * Update team.rst - Added new GSoC students Update GSoC students section * Update team.rst - Added new roles Added new roles and minor style changes * add several nbsphinx related options * restructure the Governance model page * re-enabled nbsphinx * add adapted CoC * ammending code of conduct in the root * add code of conduct * getting upstream/master team.rst Co-authored-by: Yssa Camacho <[email protected]>
* add code_of_conduct_symlink * add code of conduct link
* Added new contributing guidelines * Added symlink of Contributing.md to Contribting to TARDIS section * Fixed sym link * Update CONTRIBUTING.md Co-authored-by: Wolfgang Kerzendorf <[email protected]> * Update CONTRIBUTING.md Co-authored-by: Wolfgang Kerzendorf <[email protected]> Co-authored-by: Marc Williamson <[email protected]> Co-authored-by: Wolfgang Kerzendorf <[email protected]>
* testing mamba installation. Simply install mamba from conda and try to create env * added mamba after conda installation * check if mamba installation succesful * installing mamba before activating * fix syntax errors * Pin mamba to 0.4.0 and make pipelines exit on error with any bash command * move tardis_env.sh into pipelines file * fetch reference data fetching from bash scripts to azure pipelines file * fix syntax error * Added packet data * Adding variable shellopts to check * added shellopts=errexit so that build fails on non-zero error code * testing if pipeline fails * reverting changes, testing succesful * remove unused lines * testing, this should fail the pipeline * Made all single lines where necessary Added a step to fail build on error as suggested by epassaro improved documentation to steps * added back the git lfs pull code * removed git lfs codes * added git lfs to pipelines to make it faster
…tories (tardis-sn#1213) * Added directories to exclude in black configuration file * Added black to tardis environment file * Excluded setup related files from black configuration * Applied black formatting to remaining files
* Add governance document * Update docs/governance.rst Co-authored-by: Christian Vogl <[email protected]> * Added rules for Tardis-core Co-authored-by: Christian Vogl <[email protected]> Co-authored-by: Andreas Flörs <[email protected]>
capitalize TARDIS
add tardis core email
* Unpin packages * Pin numpy to 1.15 again * Pin numba to v0.50 * [skip-ci] Remove Git LFS directive * [skip-ci] (revert) Remove Git LFS directive * Pin pyne to v0.7 * Trying to find problem in macOS env * Trying to find problem in macOS env (2) * Trying to find problem in macOS env (3) * Trying to find problem in macOS env (4) * Remove all the pins * Add some pins * Add some pins (2) * Pin numpy to v1.16 * Pin numpy to v1.17 * Pin numpy to v1.16 and scipy to v1.5 * Pin numba to v0.50 * Pin pyne to v0.7 * [skip-ci] Remove Git LFS directive * [skip-ci] Remove Git LFS directive (2)
Reorganizing files in docs (1/2)
Adding Plasma File in TOC
Reorganizing files in docs (2/2)
Fixing Quickstart Problem
Co-authored-by: Jaladh Singhal <[email protected]>
Co-authored-by: Jaladh Singhal <[email protected]>
…atch Packet logging fixes for visualization
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* Initial commit. Basic line profile * Added documentation sketch * Fixed nuclear abundance readout * [build docs] * Allowed errors in documentation notebook [build docs] * Fixed documentation notebook [build docs] * Fixed documentation notebook [build docs] * Added more profile options, CLI. Improved documentation [build docs] * Fixed wrong import in documentation [build docs] * Fixed wrong import in documentation #2 [build docs] * Cleaned up documentation [build docs] * Cleaned up documentation [build docs] * Fixed plotting error in documentation [build docs] * Added tests [build docs] * Fixed formatting of test [build docs] * [build docs] * Added name to .mailmap * Added name to .mailmap #2 * [build docs] * Fixed typos in docstring * Added propper links to documentation [build docs] * Fixed hyperlink text in documentation [build docs]
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Should be available at epassaro.github.io/tardis.