General CSV reader

[hugary1995]

This PR adds a header-only CSV reader from https://github.com/vincentlaucsb/csv-parser. I didn't include the library as a cmake subdirectory because it's folder hierarchy makes install very difficult. Since it is MIT license, I just copied the single header file into our contrib folder.

The primary entry point for CSV reader is Sequence. It is designed as a sequence reader to retrieve a single column from a CSV file. Design details are included in the class docstring. It's zero-effort for developers to opt-in to use a CSV to fill a vector by changing

options.set<std::vector<Real>>("foo");

to

options.set<Sequence<Real>>("foo");

With the above code, users are able to specify the sequence in one of three ways:

1. foo = '1 2 3 4 5 6' <-- equivalent to parsing std::vector<Real>
2. foo = 'my.csv:key' <-- we try to read my.csv and fill the vector with the CSV column with name key.
3. foo = 'my.csv:[2]' <-- we try to read my.csv and fill the vector with the CSV column with index 2.

Other changes are just for expanding parser support and test coverage.

This is the (big) first step towards @sapitts 's request of defining irradiation eigenstrain using a CSV file.

close #154

[github-actions[bot]]

PR Preview Action v1.4.7 :---: :rocket: Deployed preview to https://reverendbedford.github.io/neml2/pr-preview/pr-152/ on branch gh-pages at 2024-06-23 02:25 UTC

[reverendbedford]

Syntax check

No syntax error, good job! :purple_heart:

[github-actions[bot]]

Python Binding Test Results (macos-12)

63 tests  ±0   39 :white_check_mark: ±0   2s :stopwatch: -1s  1 suites ±0   24 :zzz: ±0   1 files   ±0    0 :x: ±0 

Results for commit 84a866ab. ± Comparison against base commit 067f935a.

:recycle: This comment has been updated with latest results.

[github-actions[bot]]

Test Results (macos-12-Release-ON)

    3 files  ± 0      3 suites  ±0   1m 4s :stopwatch: -3s   495 tests + 5    495 :white_check_mark: + 5  0 :zzz: ±0  0 :x: ±0  3 079 runs  +14  3 079 :white_check_mark: +14  0 :zzz: ±0  0 :x: ±0 

Results for commit 84a866ab. ± Comparison against base commit 067f935a.

[github-actions[bot]]

Test Results (macos-12-Debug-ON)

    3 files  ± 0      3 suites  ±0   2m 34s :stopwatch: +18s   495 tests + 5    495 :white_check_mark: + 5  0 :zzz: ±0  0 :x: ±0  3 081 runs  +14  3 081 :white_check_mark: +14  0 :zzz: ±0  0 :x: ±0 

Results for commit 84a866ab. ± Comparison against base commit 067f935a.

[github-actions[bot]]

Test Results (ubuntu-latest-Release-ON)

    3 files  ± 0      3 suites  ±0   52s :stopwatch: -1s   495 tests + 5    495 :white_check_mark: + 5  0 :zzz: ±0  0 :x: ±0  3 079 runs  +14  3 079 :white_check_mark: +14  0 :zzz: ±0  0 :x: ±0 

Results for commit 84a866ab. ± Comparison against base commit 067f935a.

[github-actions[bot]]

Test Results (ubuntu-latest-Debug-ON)

    3 files  ± 0      3 suites  ±0   2m 1s :stopwatch: -6s   495 tests + 5    495 :white_check_mark: + 5  0 :zzz: ±0  0 :x: ±0  3 081 runs  +14  3 081 :white_check_mark: +14  0 :zzz: ±0  0 :x: ±0 

Results for commit 84a866ab. ± Comparison against base commit 067f935a.

[github-actions[bot]]

Python Binding Test Results (ubuntu-latest)

63 tests  ±0   39 :white_check_mark: ±0   2s :stopwatch: ±0s  1 suites ±0   24 :zzz: ±0   1 files   ±0    0 :x: ±0 

Results for commit 84a866ab. ± Comparison against base commit 067f935a.

[github-actions[bot]]

Test Results (macos-12-Release-OFF)

    3 files  ± 0      3 suites  ±0   1m 10s :stopwatch: -17s   495 tests + 5    495 :white_check_mark: + 5  0 :zzz: ±0  0 :x: ±0  3 079 runs  +14  3 079 :white_check_mark: +14  0 :zzz: ±0  0 :x: ±0 

Results for commit 84a866ab. ± Comparison against base commit 067f935a.

[github-actions[bot]]

Test Results (macos-12-Debug-OFF)

    3 files  ± 0      3 suites  ±0   2m 20s :stopwatch: +3s   495 tests + 5    495 :white_check_mark: + 5  0 :zzz: ±0  0 :x: ±0  3 081 runs  +14  3 081 :white_check_mark: +14  0 :zzz: ±0  0 :x: ±0 

Results for commit 84a866ab. ± Comparison against base commit 067f935a.

[github-actions[bot]]

Test Results (ubuntu-latest-Release-OFF)

    3 files  ± 0      3 suites  ±0   51s :stopwatch: ±0s   495 tests + 5    495 :white_check_mark: + 5  0 :zzz: ±0  0 :x: ±0  3 079 runs  +14  3 079 :white_check_mark: +14  0 :zzz: ±0  0 :x: ±0 

Results for commit 84a866ab. ± Comparison against base commit 067f935a.

[github-actions[bot]]

Test Results (ubuntu-latest-Debug-OFF)

    3 files  ± 0      3 suites  ±0   2m 4s :stopwatch: ±0s   495 tests + 5    495 :white_check_mark: + 5  0 :zzz: ±0  0 :x: ±0  3 081 runs  +14  3 081 :white_check_mark: +14  0 :zzz: ±0  0 :x: ±0 

Results for commit 84a866ab. ± Comparison against base commit 067f935a.

[reverendbedford]

Coverage after merging csv_reader into main will be

86.91%

Coverage Report

File	Stmts	Branches	Funcs	Lines	Uncovered Lines
include/neml2/base
CrossRef.h	34.21%	100%	31.37%	58.33%	105, 107–108, 72, 79
DependencyResolver.h	86.13%	100%	88.24%	85.83%	219, 221–222, 226, 229–231, 264, 291, 303, 313–314, 344, 346–347, 349–350
Factory.h	39.42%	100%	24.69%	91.30%	148, 156
NEML2Object.h	45.45%	100%	20%	66.67%	50, 52, 63, 66
OptionCollection.h	0%	100%	0%	0%	40, 49
OptionSet.h	32.93%	100%	30.02%	57.69%	128, 134, 137, 143, 149, 214, 216–217, 379, 381–383, 385, 61, 66, 79, 81, 85, 89, 91, 93, 95
Registry.h	80.04%	100%	79.81%	100%
Sequence.h	6.06%	100%	3.33%	10.26%	115, 118–119, 123–124, 126–130, 136–137, 141, 144–146, 148, 152, 156–157, 159, 162–165, 167–168, 171–172, 176, 178–179, 64, 80, 83
Storage.h	56.10%	100%	39.13%	77.78%	147–148, 150, 177
include/neml2/drivers
Driver.h	0%	100%	0%	0%	56
TransientDriver.h	85.71%	100%	100%	75%	149
include/neml2/misc
error.h	30.81%	100%	28.88%	63.64%	37–38, 40, 94, 96–99
math.h	100%	100%	100%	100%
parser_utils.h	42.96%	100%	32.73%	88%	37–38, 40
utils.h	56.40%	100%	47.30%	77.78%	173, 239, 241–246, 267, 302, 304–307
include/neml2/models
BufferStore.h	34.43%	100%	18.92%	58.33%	113, 115, 117–121, 133, 147, 151
ComposedModel.h	100%	100%	100%	100%
Data.h	100%	100%	100%	100%
Interpolation.h	69.81%	100%	55.56%	100%
LinearInterpolation.h	20%	100%	8.57%	100%
Model.h	85.19%	100%	75%	89.47%	116, 75
NonlinearParameter.h	10.53%	100%	5.56%	100%
ParameterStore.h	21.43%	100%	5.41%	52.63%	132, 134, 136–140, 148, 152
VariableStore.h	62.45%	100%	54.59%	89.47%	236, 238–239, 260, 91, 97
include/neml2/models/crystallography
CrystalGeometry.h	0%	100%	0%	0%	90, 92
MillerIndex.h	100%	100%	100%	100%
crystallography.h	100%	100%	100%	100%
include/neml2/solvers
Newton.h	100%	100%	100%	100%
NonlinearSystem.h	66.67%	100%	66.67%	66.67%	66
include/neml2/tensors
BatchTensorBase.h	59.80%	100%	44.68%	93.65%	212, 214, 256, 258
FixedDimTensor.h	26.44%	100%	19.32%	65.63%	152, 156, 168, 171, 176, 178, 183, 188, 66, 89, 91
LabeledAxis.h	0%	100%	0%	0%	142, 67, 72, 74–75, 77
LabeledAxisAccessor.h	72.50%	100%	65.38%	85.71%	46, 77
LabeledTensor.h	56.04%	100%	46.88%	77.78%	108, 112, 127, 176, 178–179
Scalar.h	44%	100%	34.55%	70%	82, 84–88
TensorValue.h	14%	100%	10.87%	50%	39, 63, 65, 75
Transformable.h	0%	100%	0%	0%	44
Variable.h	40%	100%	31.06%	82%	101, 107, 43–47, 49, 51
VecBase.h	80.95%	100%	50%	100%
src/neml2/base
CrossRef.cxx	83.87%	100%	75%	100%
Factory.cxx	100%	100%	100%	100%
HITParser.cxx	100%	100%	100%	100%
NEML2Object.cxx	91.67%	100%	100%	90%	35
OptionCollection.cxx	100%	100%	100%	100%
OptionSet.cxx	97.67%	100%	100%	96.88%	35
Parser.cxx	66.67%	100%	100%	64.29%	39–42, 54
Registry.cxx	75%	100%	66.67%	76.92%	38, 40–41, 56, 58–59
src/neml2/drivers
Driver.cxx	91.67%	100%	100%	90%	39
TransientDriver.cxx	86.60%	100%	100%	85.39%	142, 239–240, 245–247, 250–251, 255–259, 261–266, 269, 274–278, 99
src/neml2/drivers/solid_mechanics
LargeDeformationIncrementalSolidMechanicsDriver.cxx	32.39%	100%	25%	32.84%	100–102, 104–105, 109, 111, 113, 117, 119, 121, 125, 127–128, 130–131, 133–134, 137, 139–143, 63, 65–66, 68–74, 76, 78–79, 81, 83–84, 91–92, 94–95, 98
SolidMechanicsDriver.cxx	73.58%	100%	100%	72.55%	104, 106–107, 117, 148, 150–151, 154, 156, 158, 161, 163, 168–169, 171–173, 175, 177–178, 180, 194–196, 200–202, 77
src/neml2/misc
error.cxx	100%	100%	100%	100%
math.cxx	99.44%	100%	100%	99.33%	252
parser_utils.cxx	98.46%	100%	100%	98.18%	73
types.cxx	100%	100%	100%	100%
utils.cxx	89.47%	100%	100%	86.67%	44, 52
src/neml2/models
ArrheniusParameter.cxx	97.14%	100%	100%	96.88%	53
BackwardEulerTimeIntegration.cxx	94.12%	100%	77.78%	97.62%	56
BufferStore.cxx	33.33%	100%	33.33%	33.33%	36, 38, 40, 44, 46, 48–50
ComposedModel.cxx	95.31%	100%	100%	94.96%	149, 151, 195, 56, 86, 92
ConstantParameter.cxx	52.11%	100%	40.74%	88.24%	41, 59
CopyVariable.cxx	35.62%	100%	33.33%	42.11%	46, 49, 51–52, 54, 58, 60–61, 63–64, 70
Data.cxx	90%	100%	100%	87.50%	35
ForceRate.cxx	98%	100%	100%	97.73%	49
ForwardEulerTimeIntegration.cxx	97.67%	100%	100%	97.30%	51
ImplicitUpdate.cxx	98.39%	100%	100%	98.28%	47
LinearInterpolation.cxx	61.18%	100%	40.74%	96.77%	42
Model.cxx	91.25%	100%	94.44%	90.80%	141–144, 177–179, 286, 288–291, 297, 422, 424–426, 428–429, 51, 79–80, 88, 96
NonlinearParameter.cxx	61.90%	100%	55.56%	100%
ParameterStore.cxx	48.08%	100%	22.73%	66.67%	101, 47, 49, 51–53, 66, 93, 95–96
RotationMatrix.cxx	95.83%	100%	100%	95.24%	45
SR2Invariant.cxx	97.14%	100%	100%	97.01%	131, 48
StateRate.cxx	94%	100%	66.67%	97.73%	49
SumModel.cxx	86.96%	100%	100%	85%	75–76, 79, 81–83
VariableStore.cxx	94.25%	100%	91.67%	94.67%	165–166, 63, 65
WR2ExplicitExponentialTimeIntegration.cxx	97.37%	100%	100%	97.14%	47
WR2ImplicitExponentialTimeIntegration.cxx	97.56%	100%	100%	97.37%	54
src/neml2/models/crystallography
CrystalGeometry.cxx	98.46%	100%	100%	98.25%	198, 61
CubicCrystal.cxx	93.75%	100%	100%	92.86%	51
MillerIndex.cxx	100%	100%	100%	100%
crystallography.cxx	98.28%	100%	100%	98.08%	142
src/neml2/models/crystallography/user_tensors
FillMillerIndex.cxx	94.44%	100%	100%	93.33%	44
SymmetryFromOrbifold.cxx	93.33%	100%	100%	92.31%	47
src/neml2/models/solid_mechanics
AssociativeIsotropicPlasticHardening.cxx	96.97%	100%	100%	96.67%	51
AssociativeKinematicPlasticHardening.cxx	97.06%	100%	100%	96.77%	53
hugary1995 commented 3 months ago I just merged #151 so I'll have to rebase this one. Can we use this to parse the vtest files as well? Mechanistically yes. Though right now I rely on the glob pattern *.csv:* to distinguish between std::vector<std::string> and a CSV file column. This requires the file extension to be .csv. We need to think of some other qualification for vtest. For example, it'll be kinda neat if I can detect both .csv AND .vtest and automatically choose a parsing format -- I'll give it a shot after rebasing. © Githubissues. Githubissues is a development platform for aggregating issues.

[hugary1995]

I just merged #151 so I'll have to rebase this one.

Can we use this to parse the vtest files as well?

Mechanistically yes. Though right now I rely on the glob pattern *.csv:* to distinguish between std::vector<std::string> and a CSV file column. This requires the file extension to be .csv. We need to think of some other qualification for vtest. For example, it'll be kinda neat if I can detect both .csv AND .vtest and automatically choose a parsing format -- I'll give it a shot after rebasing.