Post-release 2022.12.26 #2182
Merged
Post-release 2022.12.26 #2182
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov Report
@@ Coverage Diff @@
## master #2182 +/- ##
=======================================
Coverage 61.82% 61.82%
=======================================
Files 79 79
Lines 8865 8865
=======================================
Hits 5481 5481
Misses 3384 3384 📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more |
|
*beep* *bop* Hi, human. The Click here to see your results. |
epassaro
added a commit
to epassaro/tardis
that referenced
this pull request
Mar 21, 2023
* Adding rate matrix index (tardis-sn#2132) * adding NlteIndexHelper class * adding nlte_ionization_species to io/schemas/plasma.yml * adding nlte_excitation_species to io/schemas/plasma.yml * added nlte_ionization_species in assemble_plasma * fixed the issue with getting nlte_ionization_species from config * fixed transforming string from config to tuple for nlte ionization species * ran black * attempt of writing tests 1 * ran black * test attempt 2 * black on test_hdf_plasma * experimenting with revert * attempt 3 * reverted tardis/plasma/tests/test_complete_plasmas.py * reverted tardis/plasma/tests/test_hdf_plasma.py * adding cofig for nlte * adding fixture for tardis_cofig_verysimple_nlte * added test_plasma_nlte_section_config * ran black * fixed the issue with the test, ran it locally * ran black on necessary files * updated description in schemas * switching from nlte_ionization to be used from self * ran black * changed nlte_properties_new to nlte_solver_properties * adding nlte_rate_equation_matrix.py * reverting to previous commit * Restructuring NumbaModel (tardis-sn#2136) * Added NumbaRadial1DGeometry * Added to_numba function * Fixed incorrect naming of numba spec * Updated docstring * Updated to_numba docstring * Updated docstring * Updated numba model to contain only time explosion * updated docstring formatting error * Moved geometry to new geometry sub package * Updated all functions where numba model was used * Updated to specify units * converting time_explosion to seconds specifically * Added numba geometry fixture * Updated tests to work with numba geometry * Updated formatting * Fixed issue with geometry initialization * Fixed formatting * Add missing cell to download atom data (tardis-sn#2146) * Possible fix for prerelease workflow (tardis-sn#2127) * Possible fix for prerelease workflow * Fix double @ symbol * Changed to v2 * Pin setuptools_scm to v6 (tardis-sn#2147) * Pin setuptools_scm to v6 * Fix typo * Adding nlte_rate_equation_solver.py (tardis-sn#2140) * added nlte_rate_equation_matrix * adding the rate_equation_matrix * moved rate_matrix into a class NLTERateEquationSolver * fixed a bug in rate_matrix_index, added an example for checking if rate matrix works properly * changed the initial electron density for now * added tests, fixed a small bug * added some doctrings * fixed a typo * added some doctrings * added some doctrings part 2 * added some docstrings part 3 * removed unnecessary import * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * changed how atomic number is created from rate_matrix_index * changed call of a function * got rid of unnecessary if statement in set_nlte_ion_rate * renamed last_row to charge_conservation_row * switched 0, 1 to atomic_number and ion_number to make it more readable * swtihed from rates to coefficients * changed the matrix set up to only keep necessary row for nlte_ion * ran black * fixing some doctrings * swtiched from using numbers to index names * switched the return statement to NotImplementedError * changed groupby from 0, 1 to atomic number, ion number * fixed an issue in the test * ran black Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * Set specific qgrid feedstock version (tardis-sn#2152) * Pre-release 2022.11.17 (tardis-sn#2155) Automated changes for pre-release 2022.11.17 * Post-release 2022.11.17 (tardis-sn#2156) Automated changes for post-release 2022.11.17 * Pre-release 2022.11.20 (tardis-sn#2160) Automated changes for pre-release 2022.11.20 * Fix relativistic packet initialization (tardis-sn#2159) * Fix setting of full relativity flag * Add relativistic packet source Co-authored-by: Stuart Sim <s.sim@qub.ac.uk> * Fix relativistic vpackets on inner boundary Co-authored-by: Stuart Sim <s.sim@qub.ac.uk> * Fixing typos for nlte ion (tardis-sn#2154) * fixing typos on rate_matrix * changed the np arange to use 0 instead of 0.0 * NLTE jacobian matrix (tardis-sn#2158) * added jacobian matrix and deriv block functions * added doctrings * ran black * switched from df to array * added an initial test * ran black * reorganized the tests * added doctrings * added todo comments for future work * ran black * Kilonova missing zeta (tardis-sn#2150) * solved KN ZetaData issue * KN missing Zeta fixed * mailmap changed * Pre-release 2022.12.11 (tardis-sn#2172) Automated changes for pre-release 2022.12.11 * Post-release 2022.12.12 (tardis-sn#2173) Automated changes for post-release 2022.12.12 * Add missing __init__.py files to transport and geometry subpackages (tardis-sn#2170) * Add missing __init__.py files to transport subpackage * Add missing __init__.py file to geometry subpackage * Pre-release 2022.12.25 (tardis-sn#2180) Automated changes for pre-release 2022.12.25 * Post-release 2022.12.26 (tardis-sn#2182) Automated changes for post-release 2022.12.26 * Pre-release 2023.01.08 (tardis-sn#2186) Automated changes for pre-release 2023.01.08 * Post-release 2023.01.11 (tardis-sn#2188) Automated changes for post-release 2023.01.11 * Downloading nlte_atom_data in ref data (tardis-sn#2187) adding nlte_atom_data to be downloaded * Adding nlte solver (tardis-sn#2171) * adding solver part in the calculate method * adding the objective function * added the solution vector method * final touches for the solver * tests, attempt 1 * ran black * fixed the issue with tests * ran black * added missing doctrings in the nlte_rate_equation_solver.py * added doctrings to tests * changed the test to explicitly calculate the lte solution ion number densities. * ran black * added the atom data file to download_reference_data.sh * fixed download_reference_data.sh * Revert "added the atom data file to download_reference_data.sh" This reverts commit 58ce29e. * got rid of index i, kept only shell * switched DataFrame to pandas.DataFrame in the docstrings * docstring bug fix * got rid of the deepcopy of nlte atomic data file * changed the number of shells to 5 * Update tardis/io/tests/data/tardis_configv1_nlte.yml Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * Update tardis/io/tests/data/tardis_configv1_nlte.yml Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * Update tardis/io/tests/data/tardis_configv1_nlte.yml Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * ran black * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * Update tardis/plasma/tests/test_nlte_solver.py Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * restructured a summary in a docstring for the solution_vector_block * ran black * added the test for w=0 case * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * Update tardis/plasma/properties/nlte_rate_equation_solver.py Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * Update tardis/plasma/tests/test_nlte_solver.py Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * fixed an issue in a docsting * fixed an issue in a docsting * removed a TODO comment Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * Rename T variables to temperature (tardis-sn#2185) * fixes tardis-sn#1600 * fixes tardis-sn#1600 * Update tardis/montecarlo/packet_source.py Co-authored-by: Atharva Arya <55894364+atharva-2001@users.noreply.github.com> * fixes codestyle * improve codestyle * rename the function * Update packet_source.py * improve codequality * add commit * Update packet_source.py Co-authored-by: Atharva Arya <55894364+atharva-2001@users.noreply.github.com> * Fixing test_store_runner_to_hdf (tardis-sn#2198) * checking if the object has the attribute decode * fixed another decode issue * Reading nlte_excitation_species from config (tardis-sn#2195) * implementing nlte_excitation * ran black * fixed a typo * got rid of unnecessary lines * rewrote tests * made a change on assigning the config values to plasma properties * fixed the tests * Update tardis/io/tests/test_config_reader.py Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> --------- Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> * Fix config reader tests (tardis-sn#2200) Fix config tests * Pre-release 2023.02.05 (tardis-sn#2205) Automated changes for pre-release 2023.02.05 * Post-release 2023.02.06 (tardis-sn#2206) Automated changes for post-release 2023.02.06 * Add version tag to simulation objects (tardis-sn#2190) * Add test for versioning info * Add version string to simulation objects * Add name to mailmap * Add another alias to mailmap * Pre-release 2023.02.12 (tardis-sn#2208) Automated changes for pre-release 2023.02.12 * Post-release 2023.02.16 (tardis-sn#2210) Automated changes for post-release 2023.02.16 * Pre-release 2023.02.19 (tardis-sn#2211) Automated changes for pre-release 2023.02.19 * Cache LFS objects in the tests workflow (tardis-sn#2194) * Cache LFS objects (actions/checkout#165) * Delete steps to see file size Delete commented step which used to download LFS objects using the bash script * Add lfs:false flag * Add my username to .mailmap * Cache hit and allow pytest to run all tests * Do git lfs checkout if the cache key is found * Post-release 2023.02.20 (tardis-sn#2213) Automated changes for post-release 2023.02.20 * Correct the description of 'no_of_packets' in Monte Carlo Configuration (tardis-sn#2214) * Correct the description of 'no_of_packets' in Monte Carlo Configuration * Added a simple description * Pre-release 2023.02.26 (tardis-sn#2222) Automated changes for pre-release 2023.02.26 * Post-release 2023.02.27 (tardis-sn#2223) Automated changes for post-release 2023.02.27 * Add docstrings to subpackages (tardis-sn#2204) * add docstring to subpackage grid * Add docstrings to subpackages * Change comments to docstrings * add docstrings to subpackages * rename gui/__init__.py * Reformat using black * add contributor infos to mailmap file * add extended summary to docstrings * Add extended summary to plasma/properties * Update tardis/io/parsers/__init__.py Co-authored-by: Sona Chitchyan <chitchyan.sona@gmail.com> --------- Co-authored-by: kim <kim@tg-lingemann.de> Co-authored-by: Sona Chitchyan <chitchyan.sona@gmail.com> * Docs Fix: Download Atom Data in rpacket_tracking.ipynb (tardis-sn#2236) Download atom data from the function * Fix for automerge (tardis-sn#2242) Use gh CLI to approve pull requests; use new token * Fix for release dates (tardis-sn#2243) * MonteCarlo packet progress bar completes to 100% (tardis-sn#2237) * Refresh packet progress bar after every iteration * Udpdated .mailmap * Reformatted with black * Fix team reviewers on workflows (tardis-sn#2246) * Pre-release 2023.03.20 (tardis-sn#2247) Automated changes for pre-release 2023.03.20 * Post-release 2023.03.20 (tardis-sn#2248) Automated changes for post-release 2023.03.20 * Create new workflow * Patch for arepo tests * Restore deleted parameter * Black format; Add missing skip reason * Fix typo in comment * Add more comments * Create slash command dispatcher * Changes to dispatcher * Black format --------- Co-authored-by: Sona Chitchyan <chitchyan.sona@gmail.com> Co-authored-by: Satwik Kambham <satwik.kambham@gmail.com> Co-authored-by: Andrew <andrewgfullard@gmail.com> Co-authored-by: Christian Vogl <cvogl@mpa-garching.mpg.de> Co-authored-by: tardis-bot <60989672+tardis-bot@users.noreply.github.com> Co-authored-by: Stuart Sim <s.sim@qub.ac.uk> Co-authored-by: gleck97 <86471143+gleck97@users.noreply.github.com> Co-authored-by: ABHISHEK PATIDAR <95904102+1e9abhi1e10@users.noreply.github.com> Co-authored-by: Atharva Arya <55894364+atharva-2001@users.noreply.github.com> Co-authored-by: Kim <44905449+kimsina@users.noreply.github.com> Co-authored-by: Abhishek Patidar <1e9abhi1e10@gmail.com> Co-authored-by: Le Truong <43793681+PommesFrittes@users.noreply.github.com> Co-authored-by: kim <kim@tg-lingemann.de> Co-authored-by: Shreyas Singh <125031481+shreyas3156@users.noreply.github.com>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
*beep* *bop*
Hi, human.
These are the changes required after the latest TARDIS release.