Conversation
…ing with extract_resonance_entrries()
… treatment and spin group numbers
…tFile, and SammyParameterFile
…to sammy/io/card_formats/par10_isotopes.py
…sentation. becuase it was annoying!
Contributor
There was a problem hiding this comment.
Pull Request Overview
Adds support for reading and writing SAMMY parameter files via a new ParManager and migrates isotope parsing to a dedicated Card10 class.
- Replaces legacy
IsotopeCardwithCard10in tests and I/O code - Introduces
ParManagerfor high-level parameter file operations - Updates models for optional isotope information and improves logging
Reviewed Changes
Copilot reviewed 18 out of 18 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/unit/pleiades/sammy/parameters/test_isotope.py | Updated imports/tests to use Card10 instead of IsotopeCard |
| tests/unit/pleiades/sammy/io/test_par_manager.py | Added placeholder file for ParManager unit tests |
| tests/unit/pleiades/sammy/io/card_formats/test_par10_isotopes.py | New unit tests for Card10 parsing of isotope card |
| src/pleiades/sammy/parameters/isotope.py | Removed deprecated IsotopeCard implementation |
| src/pleiades/sammy/parameters/init.py | Dropped import of the removed isotope module |
| src/pleiades/sammy/io/par_manager.py | Added ParManager class for managing SAMMY param file I/O |
| src/pleiades/sammy/io/card_formats/par10_isotopes.py | Introduced Card10 for parsing/writing Card 10 entries |
| src/pleiades/nuclear/models.py | Made isotope_information field optional in IsotopeParameters |
| src/pleiades/nuclear/isotopes/models.py | Removed unused __str__ override |
| src/pleiades/nuclear/isotopes/manager.py | Enhanced logging, fixed prints, and added isotope lookup |
| examples/samexm/ex012/ex012a.inp | Added directive for quantum numbers in example input file |
Comments suppressed due to low confidence (2)
src/pleiades/nuclear/isotopes/manager.py:123
- Method name typo:
get_istotpe_info_from_massshould beget_isotope_info_from_mass.
def get_istotpe_info_from_mass(self, mass: float) -> Optional[IsotopeInfo]:
tests/unit/pleiades/sammy/io/test_par_manager.py:1
- Test file contains no actual test functions—add assertions for
ParManagermethods likeextract_isotopes_and_abundances.
"""Unit tests for SAMMY parameter file classes."""
…ke the pre-commit.ci overlords happy.
…d for pleiades examples.
for more information, see https://pre-commit.ci
…s parameter spin groups by extracting spin group numbers
…inGroupChannels and validate spin group initialization
Collaborator
Author
|
Hey @KedoKudo, I was able to wrap up all the needed pytests for the parameter file io modules. Just submitted it for review. |
Collaborator
Thanks, I will start the review process |
KedoKudo
reviewed
Jul 25, 2025
Collaborator
KedoKudo
left a comment
KedoKudo
left a comment
There was a problem hiding this comment.
Please take a look at the comments. We currently have mixed coding styles in the repo, and we will need to address that at some point (hopefully with 🤖 )
| logger.error(message) | ||
| raise ValueError(message) | ||
|
|
||
| # if fit_config is not an instance of FitConfig, raise an error |
Collaborator
There was a problem hiding this comment.
I think this is a good advice, we only need to check fit_config once.
| for line in content_lines: | ||
| # Check if the line has a continuation marker ("-1") at the end | ||
| # If it does, append the line to the current isotope group | ||
| if line.endswith("-1"): |
Collaborator
There was a problem hiding this comment.
A correctly formatted parameter files should not have white space after -1, but I think maybe adding rstrip() will make it more robust in case an extra space is added accidentally
Comment on lines
+338
to
+339
| if fit_config.nuclear_params.isotopes is None: | ||
| logger.info(f"Isotpe list is empty, creating new isotope with mass {mass}") |
Collaborator
There was a problem hiding this comment.
I recommend accepting this suggestion.
…rd formats. Moved all imports to top of file
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
for more information, see https://pre-commit.ci
…eyword_pairs_to_dict function
Contributor
There was a problem hiding this comment.
Pull Request Overview
This PR implements a comprehensive parameter file manager for SAMMY with complete read/write functionality for handling SAMMY parameter files based on FitConfig objects. The implementation includes reading and writing capabilities for various parameter cards including resonance entries, isotope parameters, radius data, normalization data, background data, particle pair definitions, and spin group definitions.
Key changes include:
- Implementing ParManager class for handling SAMMY parameter file I/O operations
- Creating modular card format parsers for different parameter types (par01-par10, inp04, inp10)
- Replacing the legacy isotope parameter handling with new card-based approach
- Adding comprehensive unit tests for all card formats and the parameter manager
Reviewed Changes
Copilot reviewed 36 out of 38 changed files in this pull request and generated 5 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/unit/pleiades/sammy/test_parfile.py | Removed legacy parameter file test module |
| tests/unit/pleiades/sammy/parameters/test_isotope.py | Updated imports to use new card format classes |
| tests/unit/pleiades/sammy/io/test_par_manager.py | Added comprehensive tests for ParManager functionality |
| tests/unit/pleiades/sammy/io/card_formats/ | Added unit tests for all card format parsers |
| tests/unit/pleiades/nuclear/test_nuclear_models.py | Updated to use new SpinGroups and SpinGroupChannels models |
| src/pleiades/utils/helper.py | Added pseudo-scientific notation parser for SAMMY files |
| src/pleiades/sammy/parameters/ | Removed legacy isotope parameter handling |
| src/pleiades/sammy/io/par_manager.py | Added main ParManager class for parameter file operations |
| src/pleiades/sammy/io/card_formats/ | Added modular card format parsers for different parameter types |
Collaborator
Author
|
All the comments have been resolved and it is ready to either review again or merge into V2.0 |
KedoKudo
approved these changes
Jul 30, 2025
KedoKudo
added a commit
that referenced
this pull request
Oct 3, 2025
* add document to docs for original design * fix name typo * add refactor design document * switch to pep621 format * add boardening card parser * add boradening paramter card * add unused card * add normalization card * add radius parser * add unit test for radii * finished up development for radii card * add parser for data reduction * add unit test for data reduction * add draft orres card * update orres and imp partial unit test * add unit test for LITHI * add unit test for NE110 * add unit test for ChannelParameters * add final integrate test for orres card * expore orrse card at top level * add isotope and unit test * add delta and eta * add finit and gamma card * add Tzero * add siabn * add SELFI * add EFFIC * add DELTE * add DrcapParameters * add NONUN * remove special character * add paramagnetic card * enable checks from v2.0 * add place holder modules for card not used now * enable pre-commit * adjust exclude pattern * safe guard not implemented cards * safe guard resolution card with not implemented errors * safe guard det efficiency card with not implemented error * start with Burst param * add CHANN param * deal with edge cases * update top level import * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add placeholder for the last card * add to_string method for top level * add from string and aux func to top param class * fix unit basic unit tests * fix broadening card str format issue * fixing logic errors in parsing cards * radius card has serious issue, need special attention, disable for now * Fix radius card bug * remove debug print and add usage example notebook * adding ex012 example in notebook format. * fixed bug with reading in isotope header for card 10 in the parfile * added some print statements for errors from_string that prints the actual line you are reading * cut out print statements I added into wrong error message. * added repo map (not complete) * adding notebooks. * deleted notebook * made fudge card optional * updated repo.map * got rid off le=1.0 for abundances in Isotope class. * modified isotope.py to not use extended format and git rid of validate_abundance. * added a fudge factor line * modified print_parameters function. * modified notebook ex012a.ipynb * modified notebook * adding logger for debugging issues * adding os and logger imports to parfile.py * moved _log_and_raise_error() to logger.py * implemented logging in parfile.py for most functions. * adding more logging functionality. * added class and function finder. * reorged radius.py * got rid of logger functionality to find class and function being called * got rid of get_current_class_and_function() * using where_am_i strings for debugging * idk! * debugging default card reading * fixed bug to allow RadiusCard to handle multiple RadiusParameters entries * deleted example. * added attribustes in doc string of ResonanceEntry * finally fixed bugs in radius with printing to file! * expanded print function for parameters * added notes on parameter libraries. * updated debug to info for logging * added loggign * got rid of RadiusParametersContainer class. * adding more detials to parfile_notes.md * updated notebook for example 12. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * got rid of testing abundance validation, since this is no longer true. Deleted extended isotope format since this is unsupported. * Fixed bug in IsotopeCard.is_header_line(). Can now identify both "ISOTO" and "NUCLI" * adjusted functions test_radius.py for new list object for RadiusCard. * adjusted test_full_roundtrip to handle list of radiusParameters * fixed bug in reading in parFile strings. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * using unused variables in RadiusCardKeyword class to make overlord "pre-commit.ci" happy * more making overlord happy * moved helper.py to core/ * adding nuclear params as base class * added additional validator for spin groups in RadiusParameters * moved helper to core, so I needed to change import paths. * I think I broke isotope.py... for now. * Starting to add to physics params * moved helper.py to utils/ * added EnergyParameters, NormalizationParameters, and UserResolutionParameters * updated helper import since moving. * moved fit_params.py to src/pleiades/sammy * added isotope name to IsotopeParameters and created nuclearParameters to have as a list of isotopes. * created PhysicsParameters * made class of AlphanumericOptions. To be used for determining steps in sammy fits. * moved notes to alphanumerics folder. * created class to determine how to treat spin group information and other parameters in SAMMY. Naming based on tables VI A1.1. Also created unit tests. * Adding more detials to notes. * created class pcm_out.py to define the method of output for the parameter covariance matrix, along with unit tests. naming based on Table VI A1.1 in SAMMY manual * create class pcm_in.py to define the prior parameter covariance matrix, along with unit tests. Naming based on Table VI A1.1 in SAMMY manual. * Added class to define which approximation to the R-matrix is to be used for this calculation. Naming based on Table VI A1.1. * fixed bug in rm.py to allow for setting non-default options to true and being mutually_exclusive. Setting default to false. * deleting more options from AlphanumericOptions class as I migrate them. * Added broad.py to determine if broadening is wanted in the sammy fit. * added data class to define the format for the experimental data * updated notes on alphanumeric commands * updated fit_params.py with alphanumerics import * updating alphanumeric notes * added multiple scattering class to define how the multiple scattering corrections are to proceed * updating notes on alphanumeric commands * finally got logic to enforce exclusivity. Starting with data. * updated broad.py with new exclusivity logic. * updated alphanumeric notes * updated dcm.py and unit tests with new mutually exclusive logic. * updated msc and unit test. * updated params and unit tests with new logic for mutually exclusive groups * small edits for readability * updated pcm_in class * updated pcm_out and its unit tests. * updated rm * making coding style in classes and tests more consistent. * fixing casing issue with tests. * cleaning up code * code clean up! * final code clean up * adding lpt option class * created unit tests for lpt option class. * created bayes option class and unit tests. * updated alphanumeric notes * deleteted, since it was refactored. * adding general fit option class. * added some comments * trying to figure out how to implement general fit options into the fit parameters file. * making fit options tests * updating fit_options and unit tests * took out dataTypeOptions * adding comments and example usage. * adding data option file * updated data options. * me make code pretty * moved dataType option to option.py in data dir * adding pint capabilities to data/options.py * reorging fit_params.py * adding a unit class in pleiades utils. * got rid of converting unit functions. * add unit tests for dataParameters in test_options.py * refactor unit options and add unit tests for energy and cross-section conversions * add fit options model and enumerations for SAMMY configuration * add FitConfig and FitOptions models for SAMMY configuration * remove obsolete FitOptions and physics parameters tests * renamed nuclear and experimental libraries * update import paths for nuclear and experimental parameters in fitting config * update import statement for IsotopeParameters to reflect new module structure * add unit tests for FitOptions and FitConfig classes * renamed data to nuclear * more renaming of data to nuclear * renaming to parameters in nuclear dir * renaming to manager in nuclear dir * refactor import path for nuclearParameters in config.py * refactor import path for IsotopeParameters in isotope.py * refactor import paths for NuclearDataManager and nuclearParameters * moved models to nuclear directory * refactor import path for Isotope in transmission.py * refactor import paths for NuclearDataManager in manager.py * moved unit tests for NuclearDataManager and nuclear data models * refactor import path for Mass and UnitType in test_constants.py * refactor import path for models in test_transmissions.py * add example usage for RadiusParameters, ResonanceEntry, IsotopeParameters, and nuclearParameters in parameters.py * add example usage for FitConfig in config.py * refactor get_isotope_info to accept string input and enhance isotope data handling * refactor IsotopeParameters to use NuclearDataManager and make fields optional * add unit tests for RadiusParameters, ResonanceEntry, IsotopeParameters, and nuclearParameters * refactor NuclearDataManager to improve isotope data handling and add abundance/spin setting functionality * refactor IsotopeInfo to rename atomic_mass to mass_data for clarity * adding resonance table * refactor NuclearDataManager to streamline abundance and spin setting, and remove unused cross-section data reading method * refactor IsotopeInfo to make atomic_number and mass_data optional for improved flexibility * refactor IsotopeInfo to add material_number field for enhanced isotope data representation * refactor NuclearDataManager to update isotope parameter type and set atomic_number for improved data handling * refactor IsotopeInfo to remove unused classes and methods for cleaner codebase * refactor NuclearDataManager to remove unused CrossSectionPoint and IsotopeIdentifier imports for cleaner code * refactor IsotopeParameters to replace isotope_name with IsotopeInfo for improved data handling * moved experimental.py to experimental/parameters.py * added fp05 user resolution function. * refactor import paths for PhysicsParameters to align with new directory structure * add working directory structure documentation * update working directory structure documentation with examples and new fitting directories * 45 unit tests (#120) * add README for isotope information files * Deleted *-n.tot files as they are not longer needed. * refactor: rename mass data retrieval method and improve error handling * refactor: update IsotopeParameters to use vary_abundance and remove from_name method * refactor: update isotope handling in nuclearParameters to use isotope objects and improve validation * refactor: simplify isotope tests and enhance IsotopeInfo functionality * refactor: remove unused experimental tests and clean up constants test * feat: add method to download and extract ENDF resonance parameter files * feat: add imports for handling HTTP requests and ZIP file extraction * feat: add isotope manager for handling isotope data files in PLEIADES * feat: add IsotopeInfo and IsotopeMassData models for isotope representation * moved isotope files to isotope/files/ * feat: implement IsotopeManager for managing isotope data files and caching * feat: add documentation and models for isotopic data representation * test: add unit tests for IsotopeManager functionality * test: add unit tests for IsotopeInfo and IsotopeMassData models * migrated classes in parameters.py to models.py * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * migrated several isotope functions from nuclear manager to isotope manager. * refactor: remove obsolete unit tests for nuclear parameters * test: add moved unit tests for RadiusParameters, ResonanceEntry, IsotopeParameters, and NuclearParameters models to test_models.py. Used to be in test_parameters.py * refactor: clean up imports in models.py and fix print statement * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * removing test_parameters.py * feat: add methods to retrieve isotope information and mass data to isotopeManager class * refactor: update import path for IsotopeInfo and IsotopeMassData; remove unused class methods and docstrings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * bug: fix isotope string matching in get_isotope_info method for case-insensitivity * feat: add tests for isotope information retrieval and mass data validation in test_manager * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * refactor: remove default value for endf_library in IsotopeInfo model. Moved endf_library to nuclear models * refactor: remove endf_library assertion from test_isotope_info_defaults * feat: add EndfLibrary enum and associate it with IsotopeParameters model * feat: implement isotope parameter creation and error handling in NuclearDataManager * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix: correct typo in IsotopeParameters instantiation * fix: correct field names and set default values in IsotopeParameters model * fix: ensure material number is set for isotopes in get_isotope_info method * refactor: remove unused tests and clean up test_create_isotope_parameters methods * fix: correct typo in isotope_information attribute and remove invalid test case * fix: correct typo in isotope_infomation attribute in nuclearParameters validation * refactor: remove obsolete test files for isotope and nuclear data managers * test: add unit tests for IsotopeManager and NuclearDataManager classes * feat: add moved PhysicsParameters and related classes for energy and normalization parameters to models.py * fix: update import path for PhysicsParameters in config.py * fix: update import path for PhysicsParameters in test_fit_config.py * test: add unit tests for EnergyParameters, NormalizationParameters, BroadeningParameters, UserResolutionParameters, and PhysicsParameters * fix: update import path for VaryFlag and helper functions in data_reduction.py * fix: update import path for VaryFlag and helper functions in external_r.py * fix: update import path for VaryFlag in paramagnetic.py * fix: update import path for VaryFlag in radius.py * fix: update import path for VaryFlag in resonance.py * fix: skip tests in TestBackgroundParameters due to non-implementation * fix: skip tests in test_broadening.py due to non-implementation * fix: skip tests in test_data_reduction.py and test_det_efficiency.py due to non-implementation fix: skip tests in test_external_r.py due to non-implementation * fix: skip tests in test_isotope.py, test_last.py, test_misc.py, test_normalization.py, and test_orres.py due to non-implementation * fix: add import for IsotopeParameters in isotope.py * fix: remove skip decorator from TestBackgroundParameters due to non-implementation * fix: remove skip decorators from test functions in test_broadening.py due to implementation * fix: remove skip decorators from test functions in test_data_reduction.py due to implementation * fix: remove skip decorator from TestDetectorEfficiencyParameters as functionality is now implemented * fix: remove skip decorators from TestExternalREntry and TestExternalRFunction as functionality is now implemented * fix: remove skip decorators from test functions in test_last.py, test_misc.py, test_normalization.py, and test_orres.py as functionality is now implemented * fix: update import path for nuclearParameters in config.py * fix: update import path for nuclearParameters in test_fit_config.py * fix: simplify assertions in test_fit_options.py for boolean values * fix: remove transmission.py as it is no longer needed * fix: remove test_transmissions.py as it is no longer needed * fix: remove ex027.ipynb as it is no longer needed * fix: set default values for energy and normalization parameters in models.py * fix: update FitConfig to use Optional for parameters with default None * fix: correct typos in alphanumericOptions.notes * fix: correct typos in working_dir.map for dummy.parfile * fix: correct typos in comments and logging messages in parfile.py * fix: correct typo in options description in lpt.py * fix: correct typo in options description in pcm_in.py --------- Co-authored-by: Alexander Long <alexlong@lanl.gov> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Refactor pyproject.toml for improved configuration and versioning - Updated project metadata including dynamic versioning and license information. - Added project URLs for homepage, repository, documentation, and issues. - Enhanced dependencies with specific version constraints for nova-galaxy. - Configured versioningit for automatic version management. - Streamlined setuptools configuration for package discovery and data inclusion. - Updated pytest configuration with new markers and refined options. - Adjusted ruff configuration for linting with updated line length and exclusions. - Introduced pixi configuration for packaging tasks and dependencies management. - Organized feature dependencies for testing, packaging, development, documentation, and Jupyter integration. * fix deprecated API call issue to nova * Add configuration files for GitHub workflows and update pyproject.toml with new tasks * Update installation instructions and add SAMMY check script * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix typos in documentation and error messages in dcm.py Update exclusion patterns in pre-commit configuration for clarity * Update exclude patterns in pre-commit configuration for consistency * Add global configuration management and unit tests for PleiadesConfig * Implement caching and data retrieval for nuclear data files in NuclearDataManager - Add cache initialization and directory structure for ENDF/JENDL/JEFF data files. - Enhance download functionality with support for IAEA data source. - Introduce DataSource enum for better data source management. - Update tests to cover new caching and downloading features. * Add ENDF data retrieval and caching functionality in NuclearDataManager - Implement filename patterns for ENDF libraries to standardize cache file naming. - Enhance the NuclearDataManager to support both MAT_FIRST and ELEMENT_FIRST patterns. - Update unit tests to validate cache file path generation for different library formats. * update output to match first time running condition * Refactor nuclear data retrieval methods and update related functionality - Renamed DataSource enum to DataRetrievalMethod to better reflect its purpose. - Updated NuclearDataManager to use the new DataRetrievalMethod enum for cache initialization, file path generation, and data retrieval methods. - Modified methods to handle both DIRECT and API retrieval methods, including changes to file naming conventions based on the method used. - Updated PleiadesConfig to reflect the new retrieval methods and their corresponding URLs. - Refactored unit tests to accommodate changes in the data retrieval methods, ensuring proper coverage for both DIRECT and API methods. - Removed references to the NNDC data source as it is not yet implemented. * Migrate logging from Python's native logging to Loguru and update logger configuration * 117 physics examples (#126) * moved notebook to examples/notebooks * adding data files to build examples around * moved ipynb file to examples/notebooks. * adding all the silicon example files from sammy to pleiades examples. * remove ex012a notebook and parameter file from samexm examples * Adding example ex027 from sammy to pleiades examples * Made python notebook based on ex012. * Wrapped up initial parts of notebook. Need to implement results and plotting classes before moving forward. * Add SAMMY Exercise EX027 notebook for generating parameter files from ENDF files * Fix execution count and ensure working directories are created in the SAMMY exercise notebook * Update examples/Notebooks/pleiades_Si_transmission.ipynb Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * had to modify example 027 naming scheme * got rid of unneeded commands in input file * Use relative paths for input, parameter, and data files in SAMMY command execution * Remove obsolete symlink for ex027.dat in examples/samexm/ex027/endf * Update SAMMY_OUTPUT_FILES to reflect correct output file names * Refactor SAMMY exercise notebook to use persistent working directories and improve output handling * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Correcting error in name of notebook * Format SAMMY_OUTPUT_FILES for consistency * IDK why my edits were written over. rewriting them * got rid of timestamp * Modified working_dir to be in ./workspaces * adding endf_dummy.dat file for example 027. * Update data file reference in SAMMY example to use endf_dummy.dat * Update SAMMY example notebook to include endf_dummy.dat and enhance output logging * Enhance mock_sammy_files fixture to copy test input files to a temporary directory for path safety * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Change script shebang from csh to bash for compatibility --------- Co-authored-by: Alexander Long <alexlong@lanl.gov> Co-authored-by: Chen Zhang <zhangc@ornl.gov> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Loguru migration (#127) * Migrate logging from Python's native logging to Loguru across multiple modules * Migrate logging from Python's native logging to Loguru in manager and factory modules; add loguru log capture fixture for testing * Migrate logging from Python's native logging to Loguru in multiple parameter files; update logger configuration and debug statements * Migrate logging from Python's native logging to Loguru in misc.py; update warning and info logging statements * update notebook to use loguru for console logging * Update logging configuration to create log files in a dedicated directory; enhance logger initialization across multiple modules * Add PLEIADES Logging System Tutorial Notebook. * Update src/pleiades/sammy/parameters/external_r.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * fix incorrect shebang --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Sammy files handle update (#129) * update deps * Implement file management in SammyFiles: add move_to_working_dir and cleanup_working_files methods with tests * Update src/pleiades/sammy/backends/local.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Add shlex import for command line parsing in local backend * update endf example notebook and fix sammyFile handler * update Si transmission notebook --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * 93 result visualization 1 (#130) * Add data models for isotope abundance and results mapping * Porting plotting functions for LST files from v1.0 to v2.0 * moved last remaining notebook to examples/notebooks/ * Add LstData class for loading and validating SAMMY .LST files * Enhance PLEIADES tutorial by adding SAMMY result loading and plotting sections * Working on adding capabilties to read .LPT files * Updated directory structure in repo.map to reflect current repo structure * renamed file for data models for isotope abundance and results mapping. Used to be results_maps.py * Add FitResults and RunResults models for SAMMY data aggregation * Implement LPT file processing and block splitting functionality * Add function to extract results from LPT block strings, or fit iterations, and return FitResults object * Refactor FitResults and RunResults models to use default_factory for data initialization and improve method organization * Add method to append isotopes to nuclear parameters and log the action * Refactor ResultsManager class to encapsulate fit result management. * Move lpt.py to lpt_manager.py and added class for managing and extracting results from SAMMY LPT files * Remove unused method get_single_fit_results from RunResults class * Refactor ResultsManager to initialize with file paths and manage LPT files * Add comments to clarify initialization of managers in ResultsManager * Refactor LptManager to initialize with file path and process LPT files on instantiation * Refactor LptManager to streamline processing of LPT file blocks by removing debug print statement * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix IsotopeParameters to set default value for isotope_infomation field * Refactor IsotopeMassData and IsotopeInfo models to use Optional fields with default values * Refactor LptManager to enhance isotope extraction with regex matching and improve data handling * Refactor RadiusParameters to use Optional fields with default values for improved flexibility * Refactor LptManager to enhance isotope and radius extraction, and add broadening parameter handling * Add extract_normalizations_info method to LptManager for normalization data extraction * Refactor LptManager to enhance broadening parameter extraction with varied flag handling * Refactor LptManager to improve broadening and normalization parameter extraction, enhance initialization with RunResults, and add utility functions for value parsing. * Refactor ResultsManager to enhance LptManager initialization with RunResults and remove unused parameters. * Refactor FitResults to integrate chi-squared calculations and enhance initialization with default values. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Refactor LptManager to remove debug print statements and standardize value extraction using split_lpt_values. * Remove commented expectation for number of values in background line parsing * Add chi-squared extraction to LptManager for enhanced result analysis * Rename Chi2Results to ChiSquaredResults and update related attributes for consistency * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Enhance LptManager class documentation and update attribute names for clarity * Implement LstManager class to manage and extract results from SAMMY LST files * Implement LstManager initialization in ResultsManager and add print_results_data method for improved data output * Initialize fit_results list and LstData container in RunResults class * Update LstData column names for clarity and consistency with SAMMY output * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Refactor LstData class to update column names for SAMMY LPT files and improve data loading logic * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Refactor sammyData class to improve data handling and update data_file type to Optional[Path] * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Refactor LstManager to use sammyData instead of LstData and update type annotations for improved clarity * Refactor ResultsManager to use Path for file paths and improve type handling * Refactor RunResults to use sammyData instead of LstData for improved data handling * Refactor ResultsManager to streamline initialization and enhance fit result logging * Add plotting methods for transmission and cross-section data in ResultsManager and sammyData * Remove unnecessary import of matplotlib in plot_cross_section method of sammyData * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Enhance transmission data plotting in sammyData to optionally show differences * Refactor plot_transmission method to enhance visualization and add residuals plotting * Enhance plot_transmission and plot_cross_section methods to support optional parameters for showing differences and plotting uncertainty * Update SAMMY results loading and visualization in pleiades_Si_transmission notebook * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Refactor tests to replace dataParameters with sammyData and update assertions for default and custom values * Refactor test_fit_config to replace dataParameters with sammyData for consistency and clarity * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Refactor FitConfig to replace dataParameters with sammyData for consistency * Remove data_file parameter from sammyData in test_fit_config_custom_values for consistency * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Remove data_file parameter from test_sammy_data_custom_values for consistency * Add unit tests for FitResults and RunResults initialization and updates * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Improve error handling in print_fit_result and print_results_data methods * Add unit tests for ResultsManager methods and logging integration * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * run example notebook and keep results * Fix class name casing for SammyData in options.py * Fix typo in isotope_information field name in IsotopeParameters model * Fix typo in isotope_information field name in create_isotope_parameters_from_string method * Fix class name casing for SammyData in multiple files * Fix typo in isotope_information field name in test cases * Fix typo in isotope_information field name in nuclearParameters class * Refactor property accessors in SammyData to use get() for safer data retrieval * Add logger initialization to options.py for improved logging * Add plot_transmission function for visualizing run results with optional residuals * Moved all sammy plotting functionality to sammy/results/plotter.py. This plotting.py file will be used for more image plotting with pleiades * Updated Si Notebook for new plotting routines. --------- Co-authored-by: Alexander M. Long <alexlong@lanl.gov> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Chen Zhang <chenzhang8722@gmail.com> * SAMMY inp module (#131) * Add RMatrixOptions class and corresponding unit tests * Add CrossSectionOptions class and unit tests for option validation * Add ENDFOptions class and unit tests for option validation and dependencies * Add BayesSolutionOptions class and unit tests for option validation and exclusivity * Add BroadeningOptions class and unit tests for option validation and exclusivity * Add alphanumeric data input options and tests for covariance matrix and multiple scattering corrections - Implemented `CovarianceMatrixOptions` class for covariance matrix data input control. - Added `ExperimentalDataInputOptions` class for experimental data input control. - Created `MultipleScatteringCorrectionsOptions` class for handling multiple scattering corrections. - Developed unit tests for each of the new options classes to ensure correct behavior and mutual exclusivity. - Added test cases for valid and invalid combinations of options to validate the functionality. * Add covariance matrix output options and associated tests - Implement CovarianceMatrixOutputOptions class for managing output options related to covariance matrices. - Introduce validation to ensure mutually exclusive options are handled correctly. - Create unit tests for CovarianceMatrixOutputOptions to verify default values, valid combinations, and error handling for mutually exclusive options. Add unit tests for cross section options - Implement tests for CrossSectionOptions to validate default settings, individual option handling, and mutually exclusive options. - Ensure comprehensive coverage of all possible configurations and expected behaviors. Add unit tests for LPT output options - Create tests for LPTOutputOptions to check default values, valid combinations, and error handling for mutually exclusive options. - Validate the correct generation of alphanumeric commands based on selected options. Add unit tests for quantum numbers options - Implement tests for QuantumNumbersOptions to verify default settings, valid combinations, and mutually exclusive options. - Ensure accurate command generation based on selected options. Add unit tests for covariance matrix input options - Create tests for CovarianceMatrixOptions to validate default values, individual option handling, and mutually exclusive options. - Ensure comprehensive coverage of all possible configurations and expected behaviors. Add unit tests for R-matrix options - Implement tests for RMatrixOptions to verify default settings, valid combinations, and mutually exclusive options. - Validate the correct generation of alphanumeric commands based on selected options. * Add AveragesOptions and URROptions classes with validation and command generation methods * Add plot file and special analysis options with validation and tests - Implemented PlotFileOptions class for managing plot file configurations, including energy units, ODF file options, plot generation, and theoretical uncertainties. - Added SpecialAnalysisOptions class for special analysis configurations, including cross section reconstruction, uncertainty multipliers, and matrix generation. - Introduced validation for mutually exclusive options in both classes to ensure correct configurations. - Developed comprehensive unit tests for both PlotFileOptions and SpecialAnalysisOptions to verify default values, option exclusivity, and command generation. - Created test cases for physical constants and angular distribution options to ensure functionality and correctness. * Refactor code structure for improved readability and maintainability * Add P-Covariance Matrix Output, Physical Constants, Plot File, R-Matrix, and Special Analysis Options * Refactor FitOptions class to integrate alphanumerics modules and enhance validation; update tests for default and custom configurations * Add InpManager class for managing SAMMY input files with FitOptions integration; include tests for initialization, command generation, and file writing * Enhance InpManager class to support additional parameters and generate corresponding sections; update tests for initialization and content generation * add viztracer for future performance benchmark * add example usage for inp_manager in notebooks * 50.1 parameter workflow (#133) * Add .scratch/ to .gitignore to ignore any testing or drafting files * Implement ParManager class for SAMMY parameter file management. Starting with extract_resonance_entrries() * Added notes on the SAMMY parameter file based on SAMMY manual. * Add SAMMY output list file with column descriptions for results plotting * Created notes for SAMMY input files. * Fixed error in doc string of IsotopeParameters * Fix formatting in SAMMY parameter file notes for clarity on abundance treatment and spin group numbers * Remove unused import of IsotopeCard from parameters initialization * Refactor tests to use Card10 instead of IsotopeCard for isotope data handling * Add Card10 class for handling isotope parameter card sets with format definitions * Add logging and new method for extracting isotope info from mass data * Enhance Card10 class with comprehensive parsing and validation for isotope parameters * Add missing instruction for quantum numbers in example input file * Remove legacy notes files for Pleiades, SammyInputFile, SammyOutputLstFile, and SammyParameterFile * Moved IsotopeCard class and associated parsing logic from isotope.py to sammy/io/card_formats/par10_isotopes.py * Remove __str__ method from IsotopeInfo class to simplify string representation. becuase it was annoying! * Add unit tests for Card10 class to validate isotopes and abundances parsing * Refactor ParManager to extract isotopes and abundances from SAMMY parameter files * placeholder for unit tests for SAMMY parameter file classes * Fix parameter naming convention in SammyParameterFile.notes for to make the pre-commit.ci overlords happy. * adding examples of parameter files from SAMMY runs. These will be used for pleiades examples. * Added append isotope functionality to the FitConfig class. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added more detialed docstrings * Added card headers and moved resonance parsing to par01_resonances.py * create Card01 class to read, parse, and process resonance data from parFiles. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Process Card 10 first in ParManager to extract isotope data before other cards. Added extract_resonance_entries for card01 * Refactor Card01 class to improve resonance parsing and error handling; added fix_pseudo_scientific function for scientific notation correction. * Enhance resonance extraction in ParManager to handle presence or absence of headers; ensure Card 1 is always included in detected cards. * Added placeholder for to_lines method in Card01 class; currenly raises NotImplementedError for output conversion. * Update src/pleiades/sammy/io/par_manager.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Refactor to_lines method in Card01 and Card10 classes to accept FitConfig parameter; update docstrings for clarity. * Add extract_radii_parameters method to ParManager for processing radius data from Card 7 * Change log level from debug to info for header line detection in Card01 class * Add initial implementation of Card07 class for radii processing * Implement Card07 class with from_lines method for parsing isotope parameter cards * Update radius parameter handling in ParManager to support key-word format * Add warning log for missing isotopes in fit_config when creating default UNKN isotope * Refine Card07 class docstring for clarity and detail * Implement Card07a class for parsing radii parameters in SAMMY format * Abundances are initially allowed to be negative in SAMMY, so getting rid of ge=0 in the abundance field of IsotopeParameters. Also got rid of unused where_am_I variables * Moved check_pseudo_scientific() to helper.py * added check_pseudo_scientific() to readin resonance fields in parFile * Add normalization parameter extraction to ParManager for Card 6 * Implement Card06 class for parsing normalization parameters in SAMMY format * Fix attribute name for physics parameters in Card06 class * Add string representation method to NormalizationParameters class * Add string representation method to RadiusParameters class for improved debugging * Implement Card04 class for parsing broadening parameters in SAMMY format * Add string representation method to BroadeningParameters class for improved readability * Add string representation methods for RadiusParameters, ResonanceEntry, and IsotopeParameters classes for improved debugging and readability * Add method to extract broadening parameters from SAMMY parameter files * Refactor logging in Card07a class to use info level for isotope and radius parameter assignments * Add methods to generate and write SAMMY parameter file sections * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add default particle information to nuclearParameters class * Add ParticlePair model to represent pairs of particles in nuclear reaction channels * Enhance ParticlePair class with string representation and add method to append particle pairs in IsotopeParameters * Add particle pair extraction and section generation to ParManager * Add Card04 class for parsing and generating particle pair definitions * Refactor ParticlePair class by removing phase shift calculation and adding Q value and threshold energy fields * Enhance Card04 class to support flexible Q and Threshold parsing, including optional float handling and improved line processing for particle pair definitions. * Add unit tests for Card04 particle pair parsing and validation * Add validation to ParticlePair to ensure q_value and threshold are not set simultaneously * Refactor Card04 class to improve keyword normalization and logging, and enhance particle pair handling for isotopes. * Refactor test suite for Card04 to simplify FitConfig setup and enhance particle pair validation across fixtures * Add SpinGroupChannelInfo and SpinGroups classes for enhanced spin group modeling * Add method to extract spin group definitions from SAMMY parameter files * Add Card10p2 model for INP10 card format to handle spin groups * Enhance Card10 class to support spin group handling and improve to_lines method for formatting * Add blank line termination to Card10 output for improved formatting * Remove obsolete backslash from Card Set 9 description in SammyInputFile.notes * Add string representation methods for SpinGroupChannelInfo and SpinGroups classes for improved debugging and display * Enhance Card10p2 class to improve parsing of spin groups and channel information in INP10 card format * Implement to_lines method in Card01 class for converting fit_config to Card 1 format * Remove commented-out logger info for isotope spin groups in Card07a class * Enhance ParManager to log spin group extraction and update to_lines method for Card classes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add method to generate Input Card 10.2 section in ParManager * Refactor Card10p2 to enhance spin group handling and improve to_lines method for better output formatting * Enhance Card01 to improve spin group handling and output formatting, adding validation for isotopes and refining resonance line generation * Refactor ResonanceEntry __str__ method for improved output formatting, using aligned columns and simplified flag representation * Add empty line at the end of to_lines method in Card10p2 for improved output formatting * Fix Card 10 condition check and adjust section filtering in ParManager for improved data handling * Add to_lines method to Card07a for converting radius parameters to output lines * Refactor Card07a to improve radius parameter handling and output formatting, including enhanced flag conversion and isotope processing * Add generate_par_card7a_section method to ParManager for Card 7a output generation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add to_lines method to Card06 for generating formatted output lines * Uncomment generate_par_card6_section method call in ParManager for improved section generation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update IsotopeInfo model to enforce non-negative mass number and atomic number * Refactor particle pair tests for clarity and consistency; enhance attribute checks and remove unused tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix spin group number validation in IsotopeParameters; ensure correct attribute access and logging * Remove unnecessary warning log for multiple isotopes in Card07a class * debugging spin groups still * adding unit tests. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * still debugging.... * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Working on channel validation. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix bug in get_line_type() * add method to append spin groups in IsotopeParameters * refactor spin group handling in Card10p2 to improve isotope matching and logging * enhance tests for Card10p2: add validation for empty input, bad fit_config, and round-trip serialization * refactor Card01: update isotope handling to use IsotopeParameters for default isotope creation * add unit tests for Card01: implement tests for resonance blocks and header validation * validate fit_config type in Card10p2: ensure it is an instance of FitConfig * add unit tests for Card04: implement tests for broadening parameters and validation * implement to_lines method in Card04: format and return broadening parameters for output * add unit tests for Card06: implement tests for normalization parameters and validation * add unit tests for Card10: implement round-trip tests for standard and extended formats * refactor Card07a: added better radii handling for scenarios with empty isotope lists * add SpinGroupChannels class: implement validation and string representation for spin groups and their channels * refactor Card07a: integrate SpinGroupChannels for improved handling of spin groups and channels * add unit tests for Card07a: implement tests for radii blocks and validation of spin groups and channels * add unit tests for ParManager: implement tests for parameter file reading, extraction methods, and data consistency * refactor IsotopeParameters: improve validation of resonance and radius parameter spin groups by extracting spin group numbers * refactor test_nuclear_models: update RadiusParameters tests to use SpinGroupChannels and validate spin group initialization * delete test_parfile: remove obsolete unit tests for SAMMY parameter file parsing * refactor ParManager: replace direct imports with alias imports for card formats. Moved all imports to top of file * Update src/pleiades/utils/helper.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update src/pleiades/sammy/io/card_formats/par10_isotopes.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update src/pleiades/sammy/io/card_formats/par10_isotopes.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update src/pleiades/sammy/io/card_formats/par01_resonances.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add column ranges for parsing resonance data in Card01 class * Update unit test docstrings for Card 1, Card 4, Card 6, Card 7a, and Card 10 classes * Update parameter documentation from 'Parameters' to 'Args' in parse_keyword_pairs_to_dict function * Remove unnecessary comment in Card10 class to improve code clarity * Remove commented-out assertions in TestNuclearParameters to enhance code clarity * Clarify comment on trailing blank lines handling in Card07a class --------- Co-authored-by: Alexander Long <alexlong@lanl.gov> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * 57 normalization good (#134) * started signature for normalization. this refs #57 * Definition of the input parameters. Checking validity. Listing most dominant files. this refs #57 * Load files and unit tests. this refs #57 * Added dependency. Rebin code and started unit tests. this refs #57 * all unit tests for rebin. this refs #57 * crop code and unit test. this refs #57 * fixed unit tests and code. this refs #57 * combine, code and tests. this refs #57 * Added code to test normalization. this refs #57 * added needed packages. this refs #57 * fixed a few bugs. Added logger. this refs #57 * added dependency. working on retrieving proton charge and time spectra infos. this refs #57 * get proton charge unit tests. this refs #57 * refactoring code to make it work with timepix. this refs #57 * refactoring the way the data and metadata for each sample and ob are stored. this refs #57 * shutter counts retrieved. this refs #57 * adding shutter values for each image. this refs #57 * refactorization and improved log messages. this refs #57 * Added dependency (tomopy). Implemented remove outliers. this refs #57 * Refactoring and regrouping at the top the common methods, rebin, loading. this refs #57 * combine obs working. this refs #57 * combine data. this refs #57 * normalization. this refs #57 * More refactoring and applying proton charge and shutter counts ahead of normalization loop. this refs #57 * normalization with code in main file. this refs #57 * added code and unit test to switch units from lambda to ev. this refs #57 * Fixed unit tests. this refs #57 * unit conversion. this refs #57 * code to convert time spectra into energy. this refs #57 * Fixed conversion to energy units. this refs #57 * producing time spectra for LANL data set. this refs #57 * Roi takes x2 or width and y2 or height. Added unit tests. this refs #57 * full process works for ORNL data. this refs #57 * Added default uncertainties for now. this refs #57 * forgot save. this refs #57 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Updated pixi.lock file. this refs #57 * fix import error * adjust importing order * Update src/pleiades/utils/units.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update src/pleiades/utils/units.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tests/unit/pleiades/utils/test_load.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update src/pleiades/processing/normalization.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Improved doc of normalization. Make unit tests I wrote conform to the rest. this refs #57 * started moving from os to Pathlib. this refs #57 * fixed doc. this refs #57 * fixed doc with missing ev. this refs #57 * fixed format of files.py. this refs #57 * added doc. this refs #57 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated doc. this refs #57 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add missing import * update test to match code behavior --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Chen Zhang <zhangc@ornl.gov> Co-authored-by: Chen Zhang <chenzhang8722@gmail.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Complete end to end integration for VENUS (#135) * Fix division by zero errors and improve transmission calculation in normalization workflow * Enhance normalization export functionality to handle multiple sample runs and calculate combined transmission results * fix incorrect data clipping * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add twenty formater * add new json manager for multi-fit route * update json manager and expand test coverage * fix endf and json pairing logic * update runner to support multi mode * add multi-isotope configuration support in FitOptions and InpManager * add multi-isotope INP generation and number density calculation functions * add plot file options and enhance physical constants generation in InpManager * add isotope section generation and update tests for multi-isotope handling * add integration notebook * add end to end notebook * fix lpt parser bugs sneaked in previous PR * enhance isotope section generation to use Card Set 2 format and update tests accordingly * fix missig new line issue * adjust default alphanumerics * refactor FitOptions to use Optional types for several attributes to improve flexibility --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Enhance CSV conversion functionality in data_manager (#138) * Enhance CSV conversion function to support both tab- and comma-separated formats, and improve handling of 2-column input by adding uncertainty column. Update documentation for clarity. * Modified docstring for convert_csv_to_sammy_twenty to clarify input CSV format * Update src/pleiades/sammy/io/data_manager.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update src/pleiades/sammy/io/data_manager.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * WIP: local changes before pulling * Update src/pleiades/sammy/io/data_manager.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update src/pleiades/sammy/io/data_manager.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Refactor data reading in convert_csv_to_sammy_twenty to use a list comprehension for better clarity --------- Co-authored-by: Alexander M. Long <alexlong@lanl.gov> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Proper VENUS End-to-end integration (#140) * adjust default inp options * add ROI to exclude sample holder * add new ornl spefici normalization modules * add ornl normalization pipeline * deprecate original normalization module * add normalization router * update example usage * Add pleiades_data submodule for large test datasets * Quality of life improvement (#142) * robust handling of white space delimenator * improved demo notebook for using PLEIADES at VENUS * update demo notebook to use proper visualization func * enable figure customization * Implement placeholders and TODOs for SAMMY and PLEIADES modules * Refactor: Remove unused example code and async context manager from SammyRunner; add TODOs for background, detector efficiency, last card, and resolution parameter parsing and formatting * Enhance type hints for function signatures in lpt_manager, models, config, and helper modules * Refactor: Improve exception handling in file deletion and parsing functions * fix potential security risk (shell injection) * Update src/pleiades/utils/helper.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * INP manager refactor (#143) * Implement Card Set 2 (Element Information) for SAMMY INP files with parsing and generation functionality * Add Card Set 3 (Physical Constants) implementation and tests for SAMMY INP files * Add Card03Density class and unit tests for sample density in SAMMY INP files * Refactor InpManager to remove unused normalization parameters and update element information formatting * Update InpManager to use default values for title and reaction type in generated sections * update pixi lock file * Improve test coverage (#147) * Add UserResolutionParameters and IsotopeCard for backward compatibility * Add comprehensive unit tests for LptManager and related functions * Add comprehensive tests for load functions and improve error handling * Add comprehensive unit tests for LstManager and related functionalities * further improve test coverage * exclude depreated module in test cov calc * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * do not pre-comiit check legacy code --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alexander Long <along4@users.noreply.github.com> Co-authored-by: Alexander M. Long <alexlong@lanl.gov> Co-authored-by: Alexander Long <alexanderlong5@gmail.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Jean Bilheux <bilheuxjm@ornl.gov>
This file contains hidden or 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
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.
Working on parameter file manager to read in or write SAMMY parameter files based FitConfig objects.
This functionality with be based on creating a ParManager that will be passed a parameter file path and a FitConfig object.
Read functionality - Taking a parameter file and populating a given FitConfig object.
Write functionality - Taking a given FitConfig object and writing a parameter file.
Write unit tests for par_manager and card_formats.