Fix multiple docs warnings #258
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Additional details and impacted files@@ Coverage Diff @@
## master #258 +/- ##
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Coverage 90.26% 90.26%
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Files 33 33
Lines 2291 2291
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Misses 223 223
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Does this actually remove the warnings? (screenshot) |
The warnings, such as 'Warning: undefined binding...,' 'Warning: no doc found for reference...,' and 'Warning: invalid local link...,' have been resolved. However, This is the output when generating the documentation now:
```
julia> include("make.jl")
[ Info: Precompiling KomaMRI [6a340f8b-2cdf-4c04-99be-4953d9b66d0a]
[ Info: generating markdown page from `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\examples\literate\examples\01-FID.jl`
[ Info: writing result to `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\docs\src\generated\examples\01-FID.md`
[ Info: generating plain script file from `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\examples\literate\examples\01-FID.jl`
[ Info: writing result to `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\docs\src\generated\examples\01-FID.jl`
[ Info: generating notebook from `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\examples\literate\examples\01-FID.jl`
[ Info: writing result to `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\docs\src\generated\examples\01-FID.ipynb`
[ Info: generating markdown page from `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\examples\literate\examples\02-SmallTipApproximation.jl`
[ Info: writing result to `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\docs\src\generated\examples\02-SmallTipApproximation.md`
[ Info: generating plain script file from `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\examples\literate\examples\02-SmallTipApproximation.jl`
[ Info: writing result to `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\docs\src\generated\examples\02-SmallTipApproximation.jl`
[ Info: generating notebook from `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\examples\literate\examples\02-SmallTipApproximation.jl`
[ Info: writing result to `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\docs\src\generated\examples\02-SmallTipApproximation.ipynb`
[ Info: generating markdown page from `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\examples\literate\examples\03-ChemicalShiftEPI.jl`
[ Info: writing result to `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\docs\src\generated\examples\03-ChemicalShiftEPI.md`
[ Info: generating plain script file from `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\examples\literate\examples\03-ChemicalShiftEPI.jl`
[ Info: writing result to `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\docs\src\generated\examples\03-ChemicalShiftEPI.jl`
[ Info: generating notebook from `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\examples\literate\examples\03-ChemicalShiftEPI.jl`
[ Info: writing result to `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\docs\src\generated\examples\03-ChemicalShiftEPI.ipynb`
[ Info: generating markdown page from `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\examples\literate\examples\04-3DSliceSelective.jl`
[ Info: writing result to `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\docs\src\generated\examples\04-3DSliceSelective.md`
[ Info: generating plain script file from `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\examples\literate\examples\04-3DSliceSelective.jl`
[ Info: writing result to `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\docs\src\generated\examples\04-3DSliceSelective.jl`
[ Info: generating notebook from `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\examples\literate\examples\04-3DSliceSelective.jl`
[ Info: writing result to `C:\Users\beorostica\Nextcloud2\ihealth\koma-shared-readonly\KomaMRI.jl\docs\src\generated\examples\04-3DSliceSelective.ipynb`
┌ Warning: Unable to determine HTML(edit_link = ...) from remote HEAD branch, defaulting to "master".
│ Calling `git remote` failed with an exception. Set JULIA_DEBUG=Documenter to see the error.
│ Unless this is due to a configuration error, the relevant variable should be set explicitly.
└ @ Documenter.Utilities C:\Users\beorostica\.julia\packages\Documenter\bYYzK\src\Utilities\Utilities.jl:822
WARNING: both Distributions and SparsityOperators export "Dirac"; uses of it in module MRIOperators must be qualified
[ Info: SetupBuildDirectory: setting up build directory.
[ Info: Doctest: running doctests.
[ Info: ExpandTemplates: expanding markdown templates.
[ Info: CrossReferences: building cross-references.
[ Info: CheckDocument: running document checks.
┌ Warning: 121 docstrings not included in the manual:
│
│ KomaMRICore.run_spin_excitation_parallel! :: Union{Tuple{T}, Tuple{Phantom{T}, KomaMRICore.DiscreteSequence{T}, AbstractArray{Complex{T}}, KomaMRICore.SpinStateRepresentation{T}, KomaMRICore.SimulationMethod}} where T<:Real
│ KomaMRICore.get_variable_times :: Tuple{Any}
│ KomaMRICore.kfoldperm :: Tuple{Any, Any}
│ Base.isapprox :: Tuple{Phantom, Phantom}
│ KomaMRICore.get_breaks_in_RF_key_points :: Tuple{Sequence, Any}
│ KomaMRICore.get_kspace :: Tuple{Sequence}
│ KomaMRICore.get_uniform_times :: Tuple{Any, Any}
│ KomaMRICore.dur :: Tuple{Sequence}
│ KomaMRICore.dur :: Tuple{Grad}
│ KomaMRICore.dur :: Tuple{RF}
│ KomaMRICore.Rφ :: Tuple{Any, Any}
│ KomaMRIPlots.theme_chooser :: Tuple{Any}
│ KomaMRICore.initialize_spins_state :: Union{Tuple{T}, Tuple{Phantom{T}, BlochDict}} where T<:Real
│ KomaMRICore.initialize_spins_state :: Union{Tuple{T}, Tuple{Phantom{T}, Bloch}} where T<:Real
│ KomaMRIFiles.decompress_shape :: Tuple{Any, Any}
│ KomaMRICore.get_adc_phase_compensation :: Tuple{Any}
│ KomaMRICore.get_flip_angles :: Tuple{Sequence}
│ Base.size :: Tuple{Phantom}
│ KomaMRICore.pelvis_phantom2D :: Tuple{}
│ KomaMRICore.is_RF_on :: Tuple{Sequence}
│ KomaMRICore.Rx :: Tuple{Any}
│ KomaMRICore.is_ADC_on :: Tuple{Sequence}
│ KomaMRICore.get_grads :: Tuple{Any, Vector}
│ KomaMRIFiles.read_Extension :: Tuple{Any, Any}
│ KomaMRI.save_ui! :: Tuple{Blink.AtomShell.Window, Sequence, Phantom, Scanner, Vararg{Any, 4}}
│ KomaMRICore.print_gpus :: Tuple{}
│ KomaMRI.setup_scanner :: Tuple{}
│ KomaMRI.setup_sequence :: Tuple{Scanner}
│ KomaMRIPlots.plot_dict :: Tuple{Dict}
│ Base.:* :: Tuple{Spinor, Spinor}
│ Base.:* :: Tuple{Real, Phantom}
│ KomaMRI.view_ui! :: Tuple{Dict{String, Any}, Blink.AtomShell.Window}
│ KomaMRI.view_ui! :: Tuple{RawAcquisitionData, Blink.AtomShell.Window}
│ KomaMRI.view_ui! :: Tuple{Scanner, Blink.AtomShell.Window}
│ KomaMRI.view_ui! :: Tuple{Dict{Symbol, Any}, Blink.AtomShell.Window}
│ KomaMRI.view_ui! :: Tuple{Array, Blink.AtomShell.Window}
│ KomaMRI.view_ui! :: Tuple{Sequence, Blink.AtomShell.Window}
│ KomaMRICore.cross :: Tuple{Any}
│ Base.abs :: Tuple{Spinor}
│ KomaMRICore.run_spin_precession! :: Union{Tuple{T}, Tuple{Phantom{T}, KomaMRICore.DiscreteSequence{T}, AbstractArray{Complex{T}}, Mag{T}, BlochDict}} where T<:Real
│ KomaMRICore.run_spin_precession! :: Union{Tuple{T}, Tuple{Phantom{T}, KomaMRICore.DiscreteSequence{T}, AbstractArray{Complex{T}}, Mag{T}, Bloch}} where T<:Real
│ KomaMRICore.run_spin_excitation! :: Union{Tuple{T}, Tuple{Phantom{T}, KomaMRICore.DiscreteSequence{T}, AbstractArray{Complex{T}}, Mag{T}, BlochDict}} where T<:Real
│ KomaMRICore.run_spin_excitation! :: Union{Tuple{T}, Tuple{Phantom{T}, KomaMRICore.DiscreteSequence{T}, AbstractArray{Complex{T}}, Mag{T}, Bloch}} where T<:Real
│ KomaMRICore.Un :: Tuple{Any, Any}
│ KomaMRICore.is_Gx_on :: Tuple{Sequence}
│ KomaMRICore.update_blink_window_progress! :: Tuple{Nothing, Any, Any}
│ KomaMRICore.get_RF_types :: Tuple{Any, Any}
│ KomaMRIFiles.read_ADC :: Tuple{Any, Any}
│ KomaMRIFiles.read_events :: Tuple{Any, Any}
│ KomaMRI.setup_raw :: Tuple{}
│ KomaMRICore.rotz :: Tuple{Real}
│ KomaMRICore.discretize :: Tuple{Sequence}
│ KomaMRICore.get_flip_angle :: Tuple{RF}
│ KomaMRICore.Limit
│ KomaMRICore.check_use_cuda :: Tuple{}
│ KomaMRICore.trapz :: Union{Tuple{T}, Tuple{AbstractArray{T}, AbstractArray{T}}} where T<:Real
│ KomaMRICore.is_Gy_on :: Tuple{Sequence}
│ MRIFiles.insertNode :: Tuple{Any, String, KomaMRICore.Limit}
│ KomaMRICore.get_M1 :: Tuple{Sequence}
│ KomaMRIFiles.get_block :: Tuple{Any, Any}
│ KomaMRICore.f32 :: Tuple{Any}
│ KomaMRICore.mul! :: Tuple{Spinor, Mag}
│ KomaMRIPlots.interp_map :: Tuple{Any, Any}
│ KomaMRICore.Rz :: Tuple{Any}
│ KomaMRICore.Ry :: Tuple{Any}
│ KomaMRIPlots.plot_seqd :: Tuple{Sequence}
│ Base.show :: Tuple{IO, Sequence}
│ Base.show :: Tuple{IO, Grad}
│ Base.show :: Tuple{IO, RF}
│ Base.show :: Tuple{IO, Delay}
│ Base.show :: Tuple{IO, Spinor}
│ Base.getindex :: Tuple{Phantom, AbstractRange}
│ KomaMRI.setup_phantom :: Tuple{}
│ KomaMRICore.is_Gz_on :: Tuple{Sequence}
│ KomaMRICore.run_sim_time_iter! :: Union{Tuple{T}, Tuple{Phantom, KomaMRICore.DiscreteSequence, AbstractArray{Complex{T}}, KomaMRICore.SpinStateRepresentation{T}, KomaMRICore.SimulationMethod}} where T<:Real
│ KomaMRIFiles.read_RF :: NTuple{4, Any}
│ KomaMRICore.get_theo_A :: Tuple{Grad}
│ KomaMRIFiles.read_version :: Tuple{Any}
│ KomaMRICore.get_M2 :: Tuple{Sequence}
│ KomaMRICore.get_theo_t :: Tuple{Grad}
│ Base.getproperty :: Tuple{Vector{ADC}, Symbol}
│ Base.getproperty :: Tuple{Vector{Grad}, Symbol}
│ Base.getproperty :: Tuple{Vector{RF}, Symbol}
│ KomaMRICore.cpu :: Tuple{Any}
│ KomaMRI.setup_blink_window :: Tuple{}
│ KomaMRICore.durs :: Tuple{Sequence}
│ KomaMRICore.get_adc_sampling_times :: Tuple{Any}
│ KomaMRI.view_ui_phantom! :: Tuple{Phantom, Blink.AtomShell.Window, Sequence, Vector{Widgets.Widget{:button, Int64}}}
│ KomaMRICore.run_spin_precession_parallel! :: Union{Tuple{T}, Tuple{Phantom{T}, KomaMRICore.DiscreteSequence{T}, AbstractArray{Complex{T}}, KomaMRICore.SpinStateRepresentation{T}, KomaMRICore.SimulationMethod}} where T<:Real
│ KomaMRICore.gpu :: Tuple{Any}
│ KomaMRICore.get_slew_rate :: Tuple{Sequence}
│ KomaMRICore.get_RF_center :: Tuple{RF}
│ KomaMRIFiles.read_blocks :: Tuple{Any, Any, Any}
│ KomaMRICore.⏢ :: NTuple{6, Any}
│ KomaMRICore.is_GR_on :: Tuple{Sequence}
│ KomaMRIFiles.read_definitions :: Tuple{Any}
│ KomaMRICore.rotx :: Tuple{Real}
│ KomaMRI.display_loading! :: Tuple{Blink.AtomShell.Window, String}
│ KomaMRICore.get_theo_RF :: Tuple{Any, Any}
│ KomaMRICore.get_theo_Gi :: Tuple{Any, Any}
│ KomaMRICore.Rg :: Tuple{Any, Any, Any}
│ KomaMRICore.cumtrapz :: Union{Tuple{T}, Tuple{AbstractArray{T}, AbstractArray{T}}} where T<:Real
│ Base.view :: Tuple{Phantom, AbstractRange}
│ KomaMRICore.Q :: Tuple{Any, Any, Any}
│ KomaMRICore.Spinor
│ KomaMRICore.is_Delay :: Tuple{Sequence}
│ KomaMRICore.f64 :: Tuple{Any}
│ KomaMRIFiles.read_shapes :: Tuple{Any, Any}
│ Base.:+ :: Tuple{Phantom, Phantom}
│ Base.:+ :: Tuple{Sequence, Delay}
│ KomaMRICore.roty :: Tuple{Real}
│ KomaMRICore.get_eddy_currents :: Tuple{Sequence}
│ KomaMRICore.DiscreteSequence
│ KomaMRI.callback_filepicker :: Tuple{String, Blink.AtomShell.Window, Phantom}
│ KomaMRI.callback_filepicker :: Tuple{String, Blink.AtomShell.Window, RawAcquisitionData}
│ KomaMRI.callback_filepicker :: Tuple{String, Blink.AtomShell.Window, Sequence}
│ KomaMRICore.Mag
│ KomaMRICore.points_from_key_times :: Tuple{Any}
│ KomaMRIFiles.read_Grad :: NTuple{4, Any}
│ KomaMRIFiles.compress_shape :: Tuple{Any}
│ KomaMRICore.get_rfs :: Tuple{Sequence, Any}
│
│ These are docstrings in the checked modules (configured with the modules keyword)
│ that are not included in @docs or @autodocs blocks.
└ @ Documenter.DocChecks C:\Users\beorostica\.julia\packages\Documenter\bYYzK\src\Utilities\Utilities.jl:34
[ Info: Populate: populating indices.
[ Info: RenderDocument: rendering document.
[ Info: HTMLWriter: rendering HTML pages.
┌ Warning: Unable to determine deploydocs(devbranch = ...) from remote HEAD branch, defaulting to "master".
│ Calling `git remote` failed with an exception. Set JULIA_DEBUG=Documenter to see the error.
│ Unless this is due to a configuration error, the relevant variable should be set explicitly.
└ @ Documenter.Utilities C:\Users\beorostica\.julia\packages\Documenter\bYYzK\src\Utilities\Utilities.jl:822
┌ Warning: Documenter could not auto-detect the building environment Skipping deployment.
└ @ Documenter C:\Users\beorostica\.julia\packages\Documenter\bYYzK\src\deployconfig.jl:75
```
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Then it is not fixing the warnings yet. |
My mistake. I had to review the logs from the CI output, which doesn't encounter issues with branches or the environment. The persistent warnings are related to docstrings that are not part of the API. This is the output when generating the documentation in the CI now:
```julia
Run julia --project=docs docs/make.jl
[ Info: generating markdown page from `~/work/KomaMRI.jl/KomaMRI.jl/examples/literate/examples/01-FID.jl`
[ Info: writing result to `~/work/KomaMRI.jl/KomaMRI.jl/docs/src/generated/examples/01-FID.md`
[ Info: generating plain script file from `~/work/KomaMRI.jl/KomaMRI.jl/examples/literate/examples/01-FID.jl`
[ Info: writing result to `~/work/KomaMRI.jl/KomaMRI.jl/docs/src/generated/examples/01-FID.jl`
[ Info: generating notebook from `~/work/KomaMRI.jl/KomaMRI.jl/examples/literate/examples/01-FID.jl`
[ Info: writing result to `~/work/KomaMRI.jl/KomaMRI.jl/docs/src/generated/examples/01-FID.ipynb`
[ Info: generating markdown page from `~/work/KomaMRI.jl/KomaMRI.jl/examples/literate/examples/02-SmallTipApproximation.jl`
[ Info: writing result to `~/work/KomaMRI.jl/KomaMRI.jl/docs/src/generated/examples/02-SmallTipApproximation.md`
[ Info: generating plain script file from `~/work/KomaMRI.jl/KomaMRI.jl/examples/literate/examples/02-SmallTipApproximation.jl`
[ Info: writing result to `~/work/KomaMRI.jl/KomaMRI.jl/docs/src/generated/examples/02-SmallTipApproximation.jl`
[ Info: generating notebook from `~/work/KomaMRI.jl/KomaMRI.jl/examples/literate/examples/02-SmallTipApproximation.jl`
[ Info: writing result to `~/work/KomaMRI.jl/KomaMRI.jl/docs/src/generated/examples/02-SmallTipApproximation.ipynb`
[ Info: generating markdown page from `~/work/KomaMRI.jl/KomaMRI.jl/examples/literate/examples/03-ChemicalShiftEPI.jl`
[ Info: writing result to `~/work/KomaMRI.jl/KomaMRI.jl/docs/src/generated/examples/03-ChemicalShiftEPI.md`
[ Info: generating plain script file from `~/work/KomaMRI.jl/KomaMRI.jl/examples/literate/examples/03-ChemicalShiftEPI.jl`
[ Info: writing result to `~/work/KomaMRI.jl/KomaMRI.jl/docs/src/generated/examples/03-ChemicalShiftEPI.jl`
[ Info: generating notebook from `~/work/KomaMRI.jl/KomaMRI.jl/examples/literate/examples/03-ChemicalShiftEPI.jl`
[ Info: writing result to `~/work/KomaMRI.jl/KomaMRI.jl/docs/src/generated/examples/03-ChemicalShiftEPI.ipynb`
[ Info: generating markdown page from `~/work/KomaMRI.jl/KomaMRI.jl/examples/literate/examples/04-3DSliceSelective.jl`
[ Info: writing result to `~/work/KomaMRI.jl/KomaMRI.jl/docs/src/generated/examples/04-3DSliceSelective.md`
[ Info: generating plain script file from `~/work/KomaMRI.jl/KomaMRI.jl/examples/literate/examples/04-3DSliceSelective.jl`
[ Info: writing result to `~/work/KomaMRI.jl/KomaMRI.jl/docs/src/generated/examples/04-3DSliceSelective.jl`
[ Info: generating notebook from `~/work/KomaMRI.jl/KomaMRI.jl/examples/literate/examples/04-3DSliceSelective.jl`
[ Info: writing result to `~/work/KomaMRI.jl/KomaMRI.jl/docs/src/generated/examples/04-3DSliceSelective.ipynb`
WARNING: both Distributions and SparsityOperators export "Dirac"; uses of it in module MRIOperators must be qualified
[ Info: SetupBuildDirectory: setting up build directory.
[ Info: Doctest: running doctests.
[ Info: ExpandTemplates: expanding markdown templates.
[ Info: CrossReferences: building cross-references.
[ Info: CheckDocument: running document checks.
┌ Warning: [12](https://github.com/cncastillo/KomaMRI.jl/actions/runs/7263405838/job/19788629748?pr=258#step:6:13)1 docstrings not included in the manual:
│
│ KomaMRIFiles.read_ADC :: Tuple{Any, Any}
│ KomaMRICore.cross :: Tuple{Any}
│ KomaMRICore.get_flip_angles :: Tuple{Sequence}
│ KomaMRIPlots.plot_seqd :: Tuple{Sequence}
│ KomaMRIPlots.interp_map :: Tuple{Any, Any}
│ KomaMRICore.Rφ :: Tuple{Any, Any}
│ KomaMRICore.cpu :: Tuple{Any}
│ KomaMRICore.rotz :: Tuple{Real}
│ Base.getindex :: Tuple{Phantom, AbstractRange}
│ KomaMRICore.f64 :: Tuple{Any}
│ KomaMRICore.run_spin_excitation! :: Union{Tuple{T}, Tuple{Phantom{T}, KomaMRICore.DiscreteSequence{T}, AbstractArray{Complex{T}}, Mag{T}, BlochDict}} where T<:Real
│ KomaMRICore.run_spin_excitation! :: Union{Tuple{T}, Tuple{Phantom{T}, KomaMRICore.DiscreteSequence{T}, AbstractArray{Complex{T}}, Mag{T}, Bloch}} where T<:Real
│ KomaMRICore.get_theo_t :: Tuple{Grad}
│ KomaMRICore.is_GR_on :: Tuple{Sequence}
│ KomaMRICore.Mag
│ KomaMRICore.is_ADC_on :: Tuple{Sequence}
│ KomaMRICore.get_adc_phase_compensation :: Tuple{Any}
│ KomaMRIFiles.read_blocks :: Tuple{Any, Any, Any}
│ Base.:* :: Tuple{Real, Phantom}
│ Base.:* :: Tuple{Spinor, Spinor}
│ KomaMRICore.is_Gy_on :: Tuple{Sequence}
│ KomaMRICore.get_theo_A :: Tuple{Grad}
│ KomaMRICore.Limit
│ KomaMRICore.get_eddy_currents :: Tuple{Sequence}
│ KomaMRIFiles.read_Grad :: NTuple{4, Any}
│ KomaMRICore.Rg :: Tuple{Any, Any, Any}
│ KomaMRIFiles.read_RF :: NTuple{4, Any}
│ KomaMRIFiles.read_shapes :: Tuple{Any, Any}
│ KomaMRIFiles.read_Extension :: Tuple{Any, Any}
│ KomaMRICore.get_slew_rate :: Tuple{Sequence}
│ KomaMRICore.get_grads :: Tuple{Any, Vector}
│ KomaMRICore.is_Gz_on :: Tuple{Sequence}
│ KomaMRI.save_ui! :: Tuple{Blink.AtomShell.Window, Sequence, Phantom, Scanner, Vararg{Any, 4}}
│ KomaMRIFiles.get_block :: Tuple{Any, Any}
│ KomaMRICore.discretize :: Tuple{Sequence}
│ KomaMRICore.get_breaks_in_RF_key_points :: Tuple{Sequence, Any}
│ KomaMRICore.durs :: Tuple{Sequence}
│ KomaMRI.setup_phantom :: Tuple{}
│ KomaMRI.setup_scanner :: Tuple{}
│ KomaMRICore.is_Gx_on :: Tuple{Sequence}
│ KomaMRIFiles.read_events :: Tuple{Any, Any}
│ KomaMRICore.run_spin_excitation_parallel! :: Union{Tuple{T}, Tuple{Phantom{T}, KomaMRICore.DiscreteSequence{T}, AbstractArray{Complex{T}}, KomaMRICore.SpinStateRepresentation{T}, KomaMRICore.SimulationMethod}} where T<:Real
│ KomaMRICore.initialize_spins_state :: Union{Tuple{T}, Tuple{Phantom{T}, Bloch}} where T<:Real
│ KomaMRICore.initialize_spins_state :: Union{Tuple{T}, Tuple{Phantom{T}, BlochDict}} where T<:Real
│ KomaMRICore.is_RF_on :: Tuple{Sequence}
│ KomaMRICore.Ry :: Tuple{Any}
│ KomaMRI.setup_raw :: Tuple{}
│ KomaMRICore.get_theo_Gi :: Tuple{Any, Any}
│ KomaMRIFiles.read_definitions :: Tuple{Any}
│ KomaMRICore.is_Delay :: Tuple{Sequence}
│ KomaMRICore.get_RF_center :: Tuple{RF}
│ KomaMRICore.get_adc_sampling_times :: Tuple{Any}
│ KomaMRICore.roty :: Tuple{Real}
│ KomaMRICore.get_variable_times :: Tuple{Any}
│ KomaMRICore.cumtrapz :: Union{Tuple{T}, Tuple{AbstractArray{T}, AbstractArray{T}}} where T<:Real
│ KomaMRI.view_ui! :: Tuple{Array, Blink.AtomShell.Window}
│ KomaMRI.view_ui! :: Tuple{Scanner, Blink.AtomShell.Window}
│ KomaMRI.view_ui! :: Tuple{Dict{Symbol, Any}, Blink.AtomShell.Window}
│ KomaMRI.view_ui! :: Tuple{RawAcquisitionData, Blink.AtomShell.Window}
│ KomaMRI.view_ui! :: Tuple{Sequence, Blink.AtomShell.Window}
│ KomaMRI.view_ui! :: Tuple{Dict{String, Any}, Blink.AtomShell.Window}
│ KomaMRICore.Q :: Tuple{Any, Any, Any}
│ KomaMRICore.run_sim_time_iter! :: Union{Tuple{T}, Tuple{Phantom, KomaMRICore.DiscreteSequence, AbstractArray{Complex{T}}, KomaMRICore.SpinStateRepresentation{T}, KomaMRICore.SimulationMethod}} where T<:Real
│ KomaMRICore.get_rfs :: Tuple{Sequence, Any}
│ KomaMRICore.Un :: Tuple{Any, Any}
│ KomaMRICore.get_flip_angle :: Tuple{RF}
│ KomaMRIFiles.decompress_shape :: Tuple{Any, Any}
│ KomaMRICore.get_M1 :: Tuple{Sequence}
│ Base.isapprox :: Tuple{Phantom, Phantom}
│ Base.view :: Tuple{Phantom, AbstractRange}
│ KomaMRICore.points_from_key_times :: Tuple{Any}
│ KomaMRICore.rotx :: Tuple{Real}
│ KomaMRICore.Rz :: Tuple{Any}
│ KomaMRICore.get_RF_types :: Tuple{Any, Any}
│ KomaMRIFiles.read_version :: Tuple{Any}
│ Base.:+ :: Tuple{Sequence, Delay}
│ Base.:+ :: Tuple{Phantom, Phantom}
│ KomaMRICore.update_blink_window_progress! :: Tuple{Blink.AtomShell.Window, Any, Any}
│ KomaMRI.callback_filepicker :: Tuple{String, Blink.AtomShell.Window, Sequence}
│ KomaMRI.callback_filepicker :: Tuple{String, Blink.AtomShell.Window, RawAcquisitionData}
│ KomaMRI.callback_filepicker :: Tuple{String, Blink.AtomShell.Window, Phantom}
│ KomaMRICore.print_gpus :: Tuple{}
│ KomaMRICore.run_spin_precession_parallel! :: Union{Tuple{T}, Tuple{Phantom{T}, KomaMRICore.DiscreteSequence{T}, AbstractArray{Complex{T}}, KomaMRICore.SpinStateRepresentation{T}, KomaMRICore.SimulationMethod}} where T<:Real
│ KomaMRIPlots.theme_chooser :: Tuple{Any}
│ KomaMRICore.Spinor
│ Base.abs :: Tuple{Spinor}
│ Base.getproperty :: Tuple{Vector{RF}, Symbol}
│ Base.getproperty :: Tuple{Vector{Grad}, Symbol}
│ Base.getproperty :: Tuple{Vector{ADC}, Symbol}
│ KomaMRI.display_loading! :: Tuple{Blink.AtomShell.Window, String}
│ MRIFiles.insertNode :: Tuple{Any, String, KomaMRICore.Limit}
│ KomaMRICore.run_spin_precession! :: Union{Tuple{T}, Tuple{Phantom{T}, KomaMRICore.DiscreteSequence{T}, AbstractArray{Complex{T}}, Mag{T}, BlochDict}} where T<:Real
│ KomaMRICore.run_spin_precession! :: Union{Tuple{T}, Tuple{Phantom{T}, KomaMRICore.DiscreteSequence{T}, AbstractArray{Complex{T}}, Mag{T}, Bloch}} where T<:Real
│ KomaMRI.setup_blink_window :: Tuple{}
│ KomaMRICore.trapz :: Union{Tuple{T}, Tuple{AbstractArray{T}, AbstractArray{T}}} where T<:Real
│ KomaMRIPlots.plot_dict :: Tuple{Dict}
│ KomaMRICore.kfoldperm :: Tuple{Any, Any}
│ KomaMRICore.check_use_cuda :: Tuple{}
│ KomaMRICore.Rx :: Tuple{Any}
│ KomaMRICore.mul! :: Tuple{Spinor, Mag}
│ KomaMRI.view_ui_phantom! :: Tuple{Phantom, Blink.AtomShell.Window, Sequence, Vector{Widgets.Widget{:button, Int64}}}
│ KomaMRICore.get_theo_RF :: Tuple{Any, Any}
│ KomaMRI.setup_sequence :: Tuple{Scanner}
│ KomaMRICore.⏢ :: NTuple{6, Any}
│ Base.show :: Tuple{IO, Spinor}
│ Base.show :: Tuple{IO, Grad}
│ Base.show :: Tuple{IO, RF}
│ Base.show :: Tuple{IO, Sequence}
│ Base.show :: Tuple{IO, Delay}
│ KomaMRICore.f[32](https://github.com/cncastillo/KomaMRI.jl/actions/runs/7263405838/job/19788629748?pr=258#step:6:33) :: Tuple{Any}
│ KomaMRICore.get_M2 :: Tuple{Sequence}
│ Base.size :: Tuple{Phantom}
│ KomaMRIFiles.compress_shape :: Tuple{Any}
│ KomaMRICore.get_kspace :: Tuple{Sequence}
│ KomaMRICore.pelvis_phantom2D :: Tuple{}
│ KomaMRICore.gpu :: Tuple{Any}
│ KomaMRICore.DiscreteSequence
│ KomaMRICore.dur :: Tuple{Grad}
│ KomaMRICore.dur :: Tuple{Sequence}
│ KomaMRICore.dur :: Tuple{RF}
│ KomaMRICore.get_uniform_times :: Tuple{Any, Any}
│
│ These are docstrings in the checked modules (configured with the modules keyword)
│ that are not included in @docs or @autodocs blocks.
└ @ Documenter.DocChecks ~/.julia/packages/Documenter/bYYzK/src/Utilities/Utilities.jl:[34](https://github.com/cncastillo/KomaMRI.jl/actions/runs/7263405838/job/19788629748?pr=258#step:6:35)
[ Info: Populate: populating indices.
[ Info: RenderDocument: rendering document.
[ Info: HTMLWriter: rendering HTML pages.
```
|
|
Is the problem that a lot of these functions shouldn't be exported ? |
Initially, Documenter was checking all docstrings. I have now modified it to display warnings only for exported functions. However, there are still some warnings present:
```julia
┌ Warning: 26 docstrings not included in the manual:
│
│ KomaMRICore.get_kspace :: Tuple{Sequence}
│ KomaMRICore.dur :: Tuple{Sequence}
│ KomaMRICore.dur :: Tuple{Grad}
│ KomaMRICore.dur :: Tuple{RF}
│ KomaMRICore.get_flip_angles :: Tuple{Sequence}
│ KomaMRICore.is_RF_on :: Tuple{Sequence}
│ KomaMRICore.Rx :: Tuple{Any}
│ KomaMRICore.is_ADC_on :: Tuple{Sequence}
│ KomaMRIPlots.plot_dict :: Tuple{Dict}
│ KomaMRICore.Un :: Tuple{Any, Any}
│ KomaMRICore.rotz :: Tuple{Real}
│ KomaMRICore.get_M1 :: Tuple{Sequence}
│ KomaMRICore.f32 :: Tuple{Any}
│ KomaMRICore.Rz :: Tuple{Any}
│ KomaMRICore.Ry :: Tuple{Any}
│ KomaMRIPlots.plot_seqd :: Tuple{Sequence}
│ KomaMRICore.get_M2 :: Tuple{Sequence}
│ KomaMRICore.cpu :: Tuple{Any}
│ KomaMRICore.gpu :: Tuple{Any}
│ KomaMRICore.is_GR_on :: Tuple{Sequence}
│ KomaMRICore.rotx :: Tuple{Real}
│ KomaMRICore.Q :: Tuple{Any, Any, Any}
│ KomaMRICore.Spinor
│ KomaMRICore.f64 :: Tuple{Any}
│ KomaMRICore.roty :: Tuple{Real}
│ KomaMRICore.Mag
│
│ These are docstrings in the checked modules (configured with the modules keyword)
│ that are not included in @docs or @autodocs blocks.
└ @ Documenter.DocChecks C:\Users\beorostica\.julia\packages\Documenter\bYYzK\src\Utilities\Utilities.jl:34
```
Should none of them be exported? |
|
They should be exported, and they are missing a docstring. |
|
You could also fix the documentation docstrings that are wrong, like |
Addressed in a900ca1 |
I opened issue #260 |
cncastillo
reviewed
Dec 19, 2023
cncastillo
reviewed
Dec 19, 2023
cncastillo
reviewed
Dec 19, 2023
cncastillo
reviewed
Dec 19, 2023
docs/src/api.md
Outdated
| @@ -100,6 +100,64 @@ ADC | |||
| Delay | |||
| ``` | |||
|
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|||
| ## Functions for structs | |||
There was a problem hiding this comment.
This is only for Sequence Events.
There was a problem hiding this comment.
Addressed in 109eb65. Renamed to "Sequence-related Functions".
cncastillo
reviewed
Dec 19, 2023
docs/src/api.md
Outdated
| is_ADC_on | ||
| ``` | ||
|
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||
|
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||
| ## Read Data |
There was a problem hiding this comment.
Not sure what this section mean, IO?
There was a problem hiding this comment.
Addressed in 109eb65. Renamed to "Input/Output".
cncastillo
reviewed
Dec 19, 2023
cncastillo
reviewed
Dec 19, 2023
cncastillo
reviewed
Dec 19, 2023
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This pull request is intended to resolve issue #255