Documentation formatting #9
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* try to force python>=3.8 * undo - try to force python>=3.8; install pickle5 * install pickle5 (via pip) * try to patch pickle version * blackify
And http->https for GH links
* remove pytest mark for skipping the tests * set overwrite option to True * empty commit to rerun tests
* added base workflow file * added branch specific preview generation * added condition to skip job in main repo * added conditional check for commit message * removed path and branch conditions * added condition to check for branch name * changed workflow name * minor changes [build docs] * add branch subfolder [build docs] * changes to documentation [build docs] * fix typo * set fetch depth 0 to checkout step Co-authored-by: Ezequiel Pássaro <epassaro15@gmail.com>
* string formatting done * Update conf.py * Update widgets.py * Update atom_web_download.py * Update base.py * Update base.py * Update util.py * Update blondin_toymodel.py * Update config_internal.py * Update config_validator.py * Update decay.py * Update model_reader.py * Update density.py * Update spectrum.py * Update atomic.py * Update base.py * Update ion_population.py * Update nlte.py * Update test_complete_plasmas.py * Update base.py * Update exceptions.py * Update base.py * Update atom_data.py * Update conftest.py * Update plot_helpers.py * Update report.py * Update runner.py * Update test_integration.py * Update test_tardis_full.py * Update test_tardis_full_formal_integral.py * Update base.py * Update shell_info.py * Update analysis.py * Delete tempCodeRunnerFile.py * Delete tempCodeRunnerFile.py * Delete tempCodeRunnerFile.py * Delete tempCodeRunnerFile.py * Delete tempCodeRunnerFile.py * Delete tempCodeRunnerFile.py * Update config_internal.py * Applied black formatting Co-authored-by: Himanshu <addyjeridiq@gmail.com> Co-authored-by: Andrew Fullard <andrewgfullard@gmail.com>
* Add catch for missing elements The elements coloured in the plot are determined via the absorption and emission. It's possible however, that these elements are not the same, e.g. if you specify a limited wavelength range. This could give an error if you try to plot an element not in the emission dataframe, for example. This adds a try statement to catch this case * Fixed typo * Black formatting * Fixed typo * Add species column to packet df Added a new column to the packet dataframe that gives the species id. This combines the atomic and ion numbers into a unique id that will be used to group species later. * Added species list parser Added parser to convert request species list into ids to be used by plotter * Implement parser call Call species list parser function * Fixed parser Rearranged parser so it didn't crash if species_list was none * Implement MPL ion contributions Added in the ion contribution stuff for the mpl plotting. Also added a new function to get the colorbar labels. This is necessary to determine how many unique colours there should be * Changed order of functions * Implement plotly ion contributions Added colouring for ion contributions in plotly figures * Remove print statements * Fixed df bug and added comments Fixed bug in the absorption and emission df calculations. Now they elements should be handled correctly so there won't be errors if a species appears in emission and not absorption, and vice versa Added comments throughout * Black formatting * Added colour function Added a new function to work out what colours will be plotted. This was originally repeated multiple times in the code, but now it's a single function that's called multiple times Also fixed a bug in the absorption luminosities dataframe * Address review comments Change name of some variables and fixed some typos. * Change print to logger * Black formatting * Updated variable names and string formatting * Black formatting
* First restructure * Clean up imports * Fixed looping import * Fix for numba_config import
* Readded the numba formal integral changes * Update base.py to match main * Reverted formal integral instantiation to be more similar to the original C version for consistency * Moved numba implimentation to the montecarlo_numba folder since this is a numba implementation * Removed extra ravel * Added back old formal integral for testing * Added test for function in the numba formal integral * Changed the way the shell size is computed, should be correct now * nevermind * Moved numba formal integral tests so that paths work out for testing framework * Moved pointer incrementation to the end of the loop * Fixed typo * Switched tests to use numba models * numba models instantiate with proper data types now * Fixed numba_formal_integral tests to instantiate numba models with numba compatable types * Added a couple docstrings with some notes about future improvements * Streamlined the interface slightly to better catch bugs * Added some debug statements to watch array sizes in tests * Changed way size_line and size_shell are created using tau_sobolevs * Changed the most inner for-loop to be more similar to the C code and updated the njit dict to no longer use fastmath * Added back in the check for interpolate shells * Added back in old code for interpolate shells and now computes over the interpolated shells * Fixed interpolate shells function and made sure dataframes are properly returned when computing the intergral * Fixed bug in counter for Jred_lu pointer * More explicit about typing. the value for SIGMA_THOMSON now comes from the numba config (which is should have in the past). Should now match C code within test criteria * Finished tests for the numba formal integral helper functions * Added some docstrings and removed some commented out code * Removed old import of C formal integral * Removed deprecated formal integral import * Changed test to generate a new numba model as to not interfere with other tests * removed old C interface * Updated tests and environment to exclude compilers and Cython * Reformatted conftest so black doesn't complain * Removed commented out lines, made cleaner * Added back montecarlo tests since it apepars some r_packet tests are at least set up here. Also, readded the setup_package.py file * Removed commented out packages from the environment file * Slight optimization and readability improvements * Further optimization, now pre-computes indices of next resonance point * Removed old binary search, made formatting fixed Co-authored-by: Andrew Fullard <andrewgfullard@gmail.com> Co-authored-by: Wolfgang Kerzendorf <wkerzendorf@gmail.com>
…le (tardis-sn#1554) * Adding Config Validation for Uniform Abundance via Schema * Adding Validation for time_explosion * Validating based on different sections * Fixing CSVY Tests Implementation * Added Configuration Validation Tests * Added Docstrings for the validation tests
* create update refdata pipeline [skip ci] * update refdata pipeline (tardis-sn#1435) * test gh comment * remove basic pipeline * minor changes (tardis-sn#1436) * final changes for update refdata pipeline (tardis-sn#1439) * set pr trigger for all branches * change fail message * add disabled push step * add comment about manual trigger * add comment * final changes
* added symlinks for tardis_example.yml * updating symlinks * symlink corrections * updating quickstart
* better handling of pickle5 backport * blackify * move pickle5 to I/O section * remove duplicated dep
* incorporating old_physics * Update documentation-build.yml * unfinished changes * more unfinished changes and adding in animation * more content changes and working on some hyperlinks * rough draft * rough draft retry * first draft for PR * removing something I do not want to merge * retry on fixing mistake * fixing typos * making changes * fixing equation * addressing more comments * fixing animation * addressing Dr. Kerzendorf's comments * hopefully final changes
…sn#1559) * added support to pass config objects in run_tardis * updated docstrings * added tests for the feature * added docstrings
…is-sn#1551)" (tardis-sn#1574) This reverts commit 5166037.
* changed example according to new feature * [build docs]
* move bokeh step * use exact python version
* Fix jitclass * update numba version to not be fixed * Move pickle5 to pip section * Move pickle5 back to conda-forge * Pin numba version to latest stable * Leading 0
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…nk_fix Fixing `Team` Link redirection in Code Of Conduct
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