Disable clang format cli take2 #2818
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When clang-format, introduced in #2652, applied its changes to MRtrix3 code relating to the command-line interface (particularly the way that options and their arguments are concatenated through the addition operator), the resulting code was often quite ugly. This commit replaces code relating to CLI configuration (both the usage() function in cmd/*.cpp, and in definitions of options and option groups utilised by multiple commands) with manually formatted code, and includes comment fields to disable further manipulation of that code by clang-format. This commit is a refactor of 0cec87a generated as part of #2815, with the changes being to omit other modifications to the command documentation that are not directly related to clang-format (those changes are in the parent commit to this commit: 15e253c), and to change authorship of the commit.
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| " from the tracks passing through each voxel;" | ||
| " options are: " + join(voxel_statistics, ", ") + | ||
| " (default: mean)") | ||
| + Argument ("type").type_choice(voxel_statistics) |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
+ Argument ("type").type_choice(voxel_statistics)
^| " Valid choices are: " | ||
| "FACT, iFOD1, iFOD2, Nulldist1, Nulldist2, SD_Stream, Seedtest, Tensor_Det, Tensor_Prob" | ||
| " (default: iFOD2).") | ||
| + Argument ("name").type_choice(algorithms) |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
+ Argument ("name").type_choice(algorithms)
^| const OptionGroup OutputHeaderOption = | ||
| OptionGroup("Options for the header of the output image") | ||
| // clang-format off | ||
| const OptionGroup OutputHeaderOption = OptionGroup ("Options for the header of the output image") |
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warning: initializing non-local variable with non-const expression depending on uninitialized non-local variable 'identifiers' [cppcoreguidelines-interfaces-global-init]
const OptionGroup OutputHeaderOption = OptionGroup ("Options for the header of the output image")
^| " or comma-separated list of 3 voxel dimensions.") | ||
| + Argument ("size").type_sequence_float() | ||
| + Option ("datatype", "specify output image data type.") | ||
| + Argument ("spec").type_choice(DataType::identifiers); |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
+ Argument ("spec").type_choice(DataType::identifiers);
^| " when generating Apodised Point Spread Functions") | ||
| + Argument ("lmax").type_integer (2, 20); | ||
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| const OptionGroup TWIOption = OptionGroup ("Options for the TWI image contrast properties") |
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warning: initializing non-local variable with non-const expression depending on uninitialized non-local variable 'contrasts' [cppcoreguidelines-interfaces-global-init]
const OptionGroup TWIOption = OptionGroup ("Options for the TWI image contrast properties")
^| Argument("out", "the output warp image.").type_image_out(); | ||
| + Argument ("in", "the input warp image.").type_image_in() | ||
| + Argument ("type", "the conversion type required;" | ||
| " valid choices are: " + join(conversion_types, ", ")).type_choice(conversion_types) |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
" valid choices are: " + join(conversion_types, ", ")).type_choice(conversion_types)
^| Argument("out", "the output warp image.").type_image_out(); | ||
| + Argument ("in", "the input warp image.").type_image_in() | ||
| + Argument ("type", "the conversion type required;" | ||
| " valid choices are: " + join(conversion_types, ", ")).type_choice(conversion_types) |
There was a problem hiding this comment.
warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
" valid choices are: " + join(conversion_types, ", ")).type_choice(conversion_types)
^| return OptionGroup("Data type options") | ||
| + Option("datatype", "specify output image data type." | ||
| " Valid choices are: " | ||
| + join(identifiers, ", ") + ".") |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
+ join(identifiers, ", ") + ".")
^| + Option("datatype", "specify output image data type." | ||
| " Valid choices are: " | ||
| + join(identifiers, ", ") + ".") | ||
| + Argument("spec").type_choice(identifiers); |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
+ Argument("spec").type_choice(identifiers);
^| Argument("spec").type_choice(error_types) | ||
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| "specify nature of errors for shuffling;" | ||
| " options are: " + join(error_types, ",") + |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
" options are: " + join(error_types, ",") +
^
| "specify nature of errors for shuffling;" | ||
| " options are: " + join(error_types, ",") + | ||
| " (default: ee)") | ||
| + Argument("spec").type_choice(error_types) |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
+ Argument("spec").type_choice(error_types)
^| + Option("output", | ||
| "output only the field specified." | ||
| " Multiple such options can be supplied if required." | ||
| " Choices are: " + join(field_choices, ", ") + "." |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
" Choices are: " + join(field_choices, ", ") + "."
^| " For complex data, min, max and std are calculated separately for real and imaginary parts," | ||
| " std_rv is based on the real valued variance" | ||
| " (equals sqrt of sum of variances of imaginary and real parts).").allow_multiple() | ||
| + Argument("field").type_choice(field_choices) |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
+ Argument("field").type_choice(field_choices)
^| .allow_multiple() + | ||
| Argument("value").type_choice(tractogram_geometry_types) | ||
| "The geometry type to use when rendering tractograms" | ||
| " (options are: " + join(tractogram_geometry_types, ", ") + ")").allow_multiple() |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
" (options are: " + join(tractogram_geometry_types, ", ") + ")").allow_multiple()
^| Argument("value").type_choice(tractogram_geometry_types) | ||
| "The geometry type to use when rendering tractograms" | ||
| " (options are: " + join(tractogram_geometry_types, ", ") + ")").allow_multiple() | ||
| + Argument("value").type_choice(tractogram_geometry_types) |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
+ Argument("value").type_choice(tractogram_geometry_types)
^| " l2 (ordinary least squares);" | ||
| " lp (least powers: |x|^1.2);" | ||
| " Default: l2") | ||
| + Argument("type").type_choice(linear_robust_estimator_choices) |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
+ Argument("type").type_choice(linear_robust_estimator_choices)
^| " geometric (aligns geometric image centres);" | ||
| " none." | ||
| " (Default: mass)") | ||
| + Argument("type").type_choice(initialisation_translation_choices) |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
+ Argument("type").type_choice(initialisation_translation_choices)
^| " moments (rotation based on directions of intensity variance with respect to centre of mass);" | ||
| " none" | ||
| " (Default: none).") // TODO This can be combined with affine_init_translation. | ||
| + Argument("type").type_choice(initialisation_rotation_choices) |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
+ Argument("type").type_choice(initialisation_rotation_choices)
^| "Default: diff") + | ||
| Argument("type").type_choice(linear_metric_choices) | ||
| " Default: diff") | ||
| + Argument("type").type_choice(linear_metric_choices) |
There was a problem hiding this comment.
warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
+ Argument("type").type_choice(linear_metric_choices)
^| " l2 (ordinary least squares);" | ||
| " lp (least powers: |x|^1.2);" | ||
| " Default: l2") | ||
| + Argument("type").type_choice(linear_robust_estimator_choices) |
There was a problem hiding this comment.
warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
+ Argument("type").type_choice(linear_robust_estimator_choices)
^
Replaces #2815.
Closes #2701.
While the content here did take a lot of effort to create, the resulting attribution of ~ 5,000 line additions & deletions was not commensurate with the volume of that effort. This replacement PR attributes the majority of the changes to MRtrixBot. It also explicitly separates myriad changes that I made to command interfaces that I discovered during the course of undoing
clang-format's changes (& tweaking some of the code structure as I went), from the gross reversion ofclang-format's changes.