MicahGale commented 2 years ago

Merges develop -> main

Features Added

Object numbers are now generalized: e.g., cell.cell_number has changed to cell.number. The .number property is standardized across all numbered objects.
Implementation of the NumberedObjectCollections which is implemented for cells, surfaces, and materials. This changed these collections from being a list to acting like a dict. Objects are now retrievable by their number e.g., cells[1005] will retrieve cell 1005.
Implemented integration testing; test suite now has over 100 test cases, with over 90% code coverage.
Implemented "pass-through" of the original inputs. If an object is not edited or mutated, the original formatting from the input file will be copied out to the output.
Support was added for most MCNP shortcuts: (R, I, M, LOG), J still needs some better support. MCNPy will expand these shortcuts, but will not "recompress" them.
Added sphinx documentation website. This documents the API, has a starting guide for the users, and a guide for developers.

Bugs Fixed

Comments that "cut" a parent card are now supported.

Issues

2, #6, #11, #13, #17, #18, #19, #20, #28,

MRs

!9, !11, !16, !18, !13, !19, !20, !22, !23

MicahGale commented 2 years ago

marked this merge request as draft

MicahGale commented 2 years ago

Make sure to update the readme as needed.

MicahGale commented 2 years ago

added 2 commits

15e3640e - Made first official license file for now
50e39627 - Merge branch 'license' into 'develop'

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MicahGale commented 2 years ago

added 13 commits

c7fac545 - Revert "Delete .gitlab-ci.yml, because runners are annoying"
cd4548e8 - Update .gitlab-ci.yml file
1cf03088 - Update .gitlab-ci.yml file
a0cf8015 - Added requirements files
7f09a301 - Added pip install to setup
39a725f9 - Downgraded numpy requirement
30f9d5d7 - Added sphinx requirements
8efcda07 - First pass at badges!
0f414c20 - Updated yaml for coverage badges
a5904e26 - Removed bad formatting
e35b4b61 - Fixed python coverage run
e933d9ae - Added coverage regex
82db254e - Merge branch '29-add-badges' into 'develop'

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MicahGale commented 2 years ago

added 2 commits

0d0105f6 - Update .gitlab-ci.yml file
a1eac68b - Merge branch 'fix-CI-pages' into 'develop'

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MicahGale commented 2 years ago

added 25 commits

a8d5f1dd - Added fields to comment to track cutting comments
5adba15b - Moved Line by line parsing to standard init function
891038e5 - Reworked File parser to be clearer, and not flush input cards as aggressively
671107b3 - Fixed issue with test case missing input lines
905866f5 - Fixed bugs with variable names in classes
32a479f0 - Fixed issues with file parser state issues
3bb67797 - Updated tests with new Card Constructor
f0382d41 - Fixed bad comment constructor in test
9a80dc2c - Fixed error so regex is case insensitive
5ad50288 - Fixed comment generator to avoid blank comments
6e5da17e - Fixed comment flusher to ensure input order is preserved
dc80e0fd - Fixed issue with comment finder stripping off final space sometimes
f14ec955 - Changed infrastructure to hold multiple comments for every card
a35e50ab - Started writing test cases for new comments
57bca083 - Fixed tests for breaking comments
c6db4dc2 - Fixed test comment casing
13319503 - Made card_line public property
8eb41d9c - Made general function for handling cutting comments in unmutated cards
4adf3a1d - Merge branch 'develop' into 2-cards-cannot-be-cut-by-comments-in-mcnpy
2123fc60 - Removed old function definition that was left.
f821cfbd - Made coverage clearer to exclude test case coverage
7de96033 - Added test for mass density formatting
d475b328 - Added test to cover complicated cell parameters
130a6773 - Wrote comments setter tests
58cdfabd - Merge branch '2-cards-cannot-be-cut-by-comments-in-mcnpy' into 'develop'

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MicahGale commented 2 years ago

added 174 commits

d5348d0d - Wrote shell of Cells collection object
62ed1f51 - Added Cells object to problem
e0ef8215 - Removed expected failure resolved by Cells
c27dac6d - Made generic collection abstract class
c81d984c - Created surfaces collection
8c165961 - Integrated surfaces
17f7e069 - Fixed all expected failures
956eec8a - Added parameters setter
a83d6782 - Improved how data cards are sorted
902b698f - Wrote more integration tests
f594b22a - Fixed how string checking is done
5e917d0e - Changed how data cards in verified
3161d63c - Switched to using deque for performance and robustness
cbccbaaf - Made top level init imports
dc0d92fc - Made it so that the geometry logic string generation doesn't need an old surface number necessarily
5cd1af4f - Added more high level imports
dd06c26f - Made transform init able to start fresh
0a8e36e0 - Ensured no adding surfaces and materials twice to a problem.
275e992f - Exposed Comment as a top level object
9817ba7c - Fixed some minor errors
ca7d6a95 - Wrote more integral testing
03861be7 - REformatted with black
39ad8d5e - Fixed axis plane issue with matching similar planes that do and don't have transforms
d1e820dc - Added transform test for CZ
aadc32bf - Fixed Cylinder matching based on transforms
266b7a30 - Added more tests for different C/Z
54960d6c - Added C/Z transform test
c798038e - Added periodic and transform testing
2a20c3a6 - Added tests for periodic and transform links on surfaces
8f70fb4a - Fixed bugs with how surface handles Null values
97304670 - Removed errors in how redundant surfaces are removed
1889675c - Fixed stupid typo
0eeaca41 - Supported general planes specified by 3 points
ffc25765 - Removed duplicate finder for general plane; too immature to support
7b10bab9 - Made error message for missing links
e2974c9a - Added raw input storage to input parser only
324a8bef - Reformatted code changes
03fc390d - Rewrote tests to use new INPUT card init arguments
484ab83f - marked failing tests to avoid confusion
0045e04f - Made raw input accessible to high level objects.
1fff9a11 - Made test cases work with new preservation of original inputs
eb3cab5a - Found a missing __ that was still there
01f1c6bf - Set density to None by default
f3f33cfc - Reformatted with black
37569674 - Fixed test name changes
e51a598a - Added edge test case I found with complement parsing
4f4ed315 - Fixed complement cell finder
46f06934 - Wrote shell of Cells collection object
0226e3a6 - Added Cells object to problem
a41050a8 - Removed expected failure resolved by Cells
912ac0ce - Made generic collection abstract class
1f58ce26 - Created surfaces collection
04e09554 - Integrated surfaces
a5105876 - Fixed all expected failures
acd316ff - Added parameters setter
db12b6c1 - Improved how data cards are sorted
46e073c0 - Wrote test cases for the shortcuts
72528588 - Implemented the shortcuts parser
8d2cdd18 - Merge branch 'shortcuts' into objectCollections
8e4dfc5d - Actually called the shortcut parsing function
b43e8d6f - Fixed issue with leading ID for failing cases
0bdc905e - Found edge case for the interpolate in whole core model
6ef83284 - Fixed the edge cases
86746509 - Reformatted with black
a2c81cde - Made collections act more like lists
9651a51f - Hackily made sure that transforms are always sortable
7d1decd3 - Wrote test cases for wierd fill edge cases
abafe5e9 - Fixed issues with multi-part parameters lacking space
e87f7706 - Fixed issue with final parameter getting spliced up
e087823e - Ensured that the fill card is always the final parameter
0f31418a - made it so that you can delete comments
3da9e7e7 - Made it better for surfaces hashing
cb47491b - Updated the surface number collision error message
19d901ba - Started debugging issues with the surface numbers
b1aa2409 - Switched back to making numbers a property
97a73db3 - Went back to generator format
1d954566 - Made it so collections is in only if it's the exact object
04c27fd8 - Made edge case test for wierd surface parsing
36439bb2 - Made cells handle list additions
dd5fb585 - Fixed list issue with surfaces
3f8b4d83 - Changed materials to be a collection object; first pass
f42bff9c - Made it better for surfaces hashing
fef69067 - Made it so collections is in only if it's the exact object
b34d14e8 - Made cells handle list additions
f79bdc87 - Fixed list issue with surfaces
bf706790 - Fixed materials error with numbers not being property
a5415cb7 - Fixed issue with materials getting switched to list
f59dd567 - Fixed issue with materials and surfaces being compared
9c5260d9 - Implemented hash and eq for Materials to allow merging of the same mat
ebd577e6 - Made materials settable in problem
f1cd283f - Updated test cases to force new number system
3b8a8c0f - Made cell_number, etc into number
bfd60e24 - Made collections generalized for to handling general number property
f58f1bbb - Merge branch 'numbers' into 'objectCollections'
bd5da474 - Fixed bug with material_number
d898e3b6 - Explained wierd hacky code.
03810ecb - Fixed type mismatch in test case
30c6c53c - Renamed collections to avoid namespace collisions
d0065021 - Updated test cases to use the new dict-list thing
74d5aca9 - Unbroke comparison
b5ef483c - Fixed missed test access
88e3fae3 - Started writing the new getitem method for collections
f386371b - Fixed more legacy tests that used list and not dict indexes
08297f3c - Moved abstract methods to parent NumberedObjectCollection
a717d88c - Made internal list accessible with a read-only getter
1a1115c6 - Completed writing num_cache maintanence code
47a25506 - Provided default numbers for all objects to avoid breakings NumberedObjectCollections
c2867edd - Avoided issues with surface number collisions in cells with redundant surfaces
8f736484 - Allowed setitem to work
0c0d698c - Merge branch 'issue21Fill' into objectCollections
570523a5 - Cleaned up missed merge conflicts
62e4730e - Found accidental number collision
6b4514be - Fixed tests in fill card broken by new NumberedObjectCollections
8c679398 - Made surfaces.pz work with MAGIC!!
6b8e6acc - Added docstrings
d600c1da - Simplified internal pointer code with new NumberObjectCollections
1c8ab06a - Added links to problems for MCNP cards
73a2ca71 - Added system to avoid number collisions with polite number changes
f33d8eea - Added a next_number method
63f4d260 - Update .gitlab-ci.yml file
2508dd4f - Added docstrings
c0e775b3 - Do not rely on num_cache for accuracy on what numbers are used
f5dbd08f - Update num_cache as frequently as possible.
bc00e1bc - Ensured users don't introduce number conflicts at set time
3a8c59a5 - Added properties to reverse lookup pointers
dcd9600c - Added conflict checking at Collection construction
e2a8b0f8 - added tests for reverse linking of objects
a8fc5c3e - Fixed issues found with the collections
360f8cca - Merge branch 'develop' into objectCollections
f0cda39b - Added more tests, and cleaned up docs
de04ffc9 - Merge branch 'develop' into objectCollections
d3761eb0 - Started doing Sphinx docs
5031833c - Fixed docstrings formatting
12372e67 - Merge branch 'objectCollections' into 28-create-user-documentation
76858f9b - Wrote 95% of User documentation
97bcee01 - Removed API docs; it's autogenerated
aa8ba714 - Added missing docstrings
d0f85c02 - Clarified treatment of shortcuts
b6bd57e4 - Wrote up developer's guide
002283e6 - Merge branch 'develop' into objectCollections
7e49b103 - Fixed test cases using legacy API tools
5a28b3e0 - Removed add_cells method; probably never will implement
5e8f5194 - Delete .gitlab-ci.yml, because runners are annoying
4a6b8461 - Fixed python docs typos
764c6d69 - Fixed typos in user guide
a96eb296 - fixed typos and improved developer guide
ad9c4b71 - Fixed test cause to ensure materials line up nicely
f9339a3d - Reformatted test cases
7728d9d2 - Improved format strings
55341cfa - Fixed Isotope to be formattable
bc31aa5f - Removed commented out code
67a04b65 - Allowed ab initio creation of materials
26279c0c - Fixed material parameter test spaces
51ef30a2 - Implemented recomendations from #18
c963fcc5 - Merge branch 'objectCollections' into 28-create-user-documentation
c4369936 - Merge branch '28-create-user-documentation' into 'objectCollections'
33902048 - Revert "Delete .gitlab-ci.yml, because runners are annoying"
c200bf69 - Merge branch 'develop' into objectCollections
806b80bd - Revert "Update .gitlab-ci.yml file" to add pages
6514ab55 - Merge branch 'develop' into 18-improve-how-material-init-function-is-parsed
2f19e698 - Merge branch 'develop' into 17-format_for_mcnp_input
2acd135f - Wanting to get something onto pages for now
cd7d02a3 - Removed redundant badges
35b145e6 - Fixed readme to be more accurate
85d39ebb - Revert "Wanting to get something onto pages for now"
8f103286 - Added user documentation link
3c760a0d - Made data cards words settable
c9e70183 - Merge branch 'objectCollections' into 17-format_for_mcnp_input
e3eeca42 - Merge branch '17-format_for_mcnp_input' into 'objectCollections'
05732ce8 - Merge branch 'develop' into objectCollections
d5bee4c4 - Updated new tests to work with new API
ca9083c6 - Updated comment deleter name
b333c17e - Merge branch 'objectCollections' into 18-improve-how-material-init-function-is-parsed
2018dd66 - Merge branch '18-improve-how-material-init-function-is-parsed' into 'develop'

Compare with previous version

MicahGale commented 2 years ago

added 35 commits

68ea8967 - Added parameters setter test.
762e56da - Wrote tests for broken object links
03d821b7 - Wrote data card tests for coverage
5a7cb0c9 - Fixed blank constructor for data card
d52027ab - Tested cells setter with list
0e44bcda - test adding thermal scattering to material
93d5d483 - Removed dead code
211ba6b2 - Fixed bugs with material and thermal scattering
d36650a3 - Got rid of checking for redundant numbers as it should not be possible
39f4419e - Removed function that could be handled by the parent
ad43a14b - Removed replace function that was not tested and poorly implemented
1906bad8 - Added test for blank comments
1f0ff600 - updated tests for added blank comment
b020ba3d - Fixed empty comment bug
2ae190cd - Added comment new line edge case
202d995d - Added test case for windows based CRLF files
5e71ff21 - Added test case for dos based files
0852b6d5 - Fixed typo with blank comment test case
d3feed17 - Fixed blank comment bug
dc064306 - Added other blank comment edge case
9dac0d6d - Made comment finder more robust for blank comments
111c7079 - Made test cases to detect issues with thermal scattering
7f0931e5 - Made material detect multiple s(a,b) cards
fc79de6c - Add detection of orphaned MT cards
c44f0dd6 - Increased coverage precision
dfa6c4d8 - Updated coverage regex
5e63d2c6 - Tried to add coverage visualization support
3c11ff25 - Made test names snake case to comply with pytest
4b2505b5 - Added test report storing into CI pipeline
19600242 - Fixed copypasta from MCCAFE
561c701b - Updated rtype to actually refer to numberedObjectCollections
ed385519 - Made density setter documentation clearer
01187788 - Improved NumberedObjectCollections documentation
ef911c4e - Merge branch 'develop' into objectCollections
06952dca - Merge branch 'objectCollections' into 'develop'

Compare with previous version

MicahGale commented 2 years ago

added 11 commits

06952dca...60c9c24d - 3 commits from branch main
98484675 - Added metadata; and updated version number
997bcf72 - Added lots of details to setup tools
9c30f8ee - Removed coverage badge
ab3e5a1d - Added testing for extras installation
8ac845d2 - Fixed easyinstall?
8d3b2776 - Merge branch 'main' into version
f520f6ef - Merge branch 'develop' into version
87769c24 - Merge branch 'version' into 'develop'

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MicahGale commented 2 years ago

marked this merge request as ready

MicahGale commented 2 years ago

approved this merge request

MicahGale commented 2 years ago

added 2 commits

13cdd3b5 - Updated readme for version 0.0.5
17f4a3ad - Merge branch 'version0.0.5readme' into 'develop'

Compare with previous version

MicahGale commented 2 years ago

mentioned in commit e5c77cee0419c32e833c8740a781ef2f895336dc

idaholab / MontePy

Release of version 0.0.5 - [merged] #228

Features Added

Bugs Fixed

Issues

2, #6, #11, #13, #17, #18, #19, #20, #28,

MRs