LoadError: UndefVarError: NetCDFError not defined

[ryofurue]

Describe the bug
I get the error message in the subject line of this thread. Because my program doesn't use NetCDFError directly, the error must be from within the NCDatasets package:

ERROR: LoadError: UndefVarError: `NetCDFError` not defined

[Full stack trace at the bottom of this message.]

To Reproduce
[I hope that the above description is enough to direct you to the right place in your code, but if you developers don't find the error obvious, I'll try to create a minimal example code to reproduce the error.]

Expected behavior
N/A

Environment

• operating system: macOS 13.4
• Julia version: 1.9.1 from juliaup
• Output of the julia command versioninfo()
  Julia Version 1.9.1
  Commit 147bdf428cd (2023-06-07 08:27 UTC)
  Platform Info:
  OS: macOS (arm64-apple-darwin22.4.0)
  CPU: 10 × Apple M2 Pro
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, apple-m1)
  Threads: 1 on 6 virtual cores
• NCDatasets version: v0.12.16
• Output of using Pkg; Pkg.status(mode=PKGMODE_MANIFEST)
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Full output

In case of an error, please paste the full error message and stack trace.

ERROR: LoadError: UndefVarError: `NetCDFError` not defined
Stacktrace:
 [1] setindex!(v::CommonDataModel.CFVariable{Float64, 1, NCDatasets.Variable{Float64, 1, NCDataset{Nothing}}, NCDatasets.Attributes{NCDataset{Nothing}}, NamedTuple{(:fillvalue, :missing_values, :scale_factor, :add_offset, :calendar, :time_origin, :time_factor), Tuple{Nothing, Tuple{}, Vararg{Nothing, 5}}}}, data::Vector{DateTime}, indexes::Colon)
   @ CommonDataModel ~/.julia/packages/CommonDataModel/7hLGg/src/cfvariable.jl:412
 [2] (::var"#18#19"{Vector{Union{Missing, Float64}}, String, Vector{DateTime}, Vector{Float64}})(ds::NCDataset{Nothing})
   @ Main ~/Dropbox/work/trenches/bottom_pressure-03.jl:305
 [3] NCDataset(::var"#18#19"{Vector{Union{Missing, Float64}}, String, Vector{DateTime}, Vector{Float64}}, ::String, ::Vararg{String}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
   @ NCDatasets ~/.julia/packages/NCDatasets/wsGwu/src/dataset.jl:255
 [4] NCDataset
   @ ~/.julia/packages/NCDatasets/wsGwu/src/dataset.jl:252 [inlined]
 [5] calc_save_pres_1d(; sta::ObsStation, slp::Vector{Union{Missing, Float64}}, em::Vector{Union{Missing, Float64}}, sm::Matrix{Union{Missing, Float64}}, tm::Matrix{Union{Missing, Float64}}, delz::Vector{Float64}, lon::Float64, lat::Float64, tax::Tuple{Vector{DateTime}, String})
   @ Main ~/Dropbox/work/trenches/bottom_pressure-03.jl:297
 [6] process_sta(sta::ObsStation)
   @ Main ~/Dropbox/work/trenches/bottom_pressure-03.jl:353
 [7] top-level scope
   @ ~/Dropbox/work/trenches/bottom_pressure-03.jl:400
 [8] include(fname::String)
   @ Base.MainInclude ./client.jl:478
 [9] top-level scope
   @ REPL[1]:1
in expression starting at /Users/furue/Dropbox/work/trenches/bottom_pressure-03.jl:400

[Alexander-Barth]

I believe that this is an issue with CommonDataModel.jl 0.2.2 which should be fixed by the new released 0.2.3:

JuliaRegistries/General#85186

Note however, that after updating you will see this error message:
https://github.com/JuliaGeo/CommonDataModel.jl/blob/v0.2.2/src/cfvariable.jl#L412

It seems that you are changing the time units or calendar attribute. Is this fixed if you use this instead?
https://alexander-barth.github.io/NCDatasets.jl/dev/issues/#Defining-the-attributes-_FillValue,-add_offset,-scale_factor,-units-and-calendar

[ryofurue]

It seems that you are changing the time units or calendar attribute

Close. After I submitted this report, I found the cause of the error: I was trying to assign an array of DateTimes to the time axis, which is defined to be an array of Float64s:

taxis = defVar(ds,"time",Float64,("time",))
taxis[:] = tvals[:] # array of DateTime

Incidentally, how do you use the array of DateTimes for the time axis? This time axis is actually read from another netCDF file. I just want to use the same axis for the new netCDF file I'm creating.

[Alexander-Barth]

something like this?

other_ds = NCDataset("other_file.nc");
taxis = defVar(ds,"time",Float64,("time",),attrib = other_ds["time"].attrib)
taxis[:] = other_ds["time"][:]

maybe we can have something like this in future to make this simpler:

other_ds = NCDataset("other_file.nc");
taxis = defVar(ds,other_ds["time"]) # copies all data and attributes under the same name (to be implemented)

[ryofurue]

taxis = defVar(ds,"time",Float64, . . .)
taxis[:] = other_ds["time"][:]

It's quite surprising! (I'm not against it. I'm just surprised.) that you can assignDateTime objects to taxis[:]. Do you mean that currently works?

Because taxis[:] behaves like a vector of Float64, I thought that assignment wouldn't work.

maybe we can have something like this in future to make this simpler:

other_ds = NCDataset("other_file.nc");
taxis = defVar(ds,other_ds["time"]) # copies all data and attributes under the same name (to be implemented)

That would be definitely nicer!

Here is a concrete scenario I sometimes have to deal with. Suppose you have a timeseries defined at the beginning of each hour. Now you want to shift the time axis by 30 minutes (because the time axis of the original dataset is wrong):

newtaxis = defVar(ds,other_ds["time"])
newtaxis[:] = newtaxis[:] + Dates.Minute(30)

and you don't have to worry about the attributes of the axis.

Also, it would be nice if the time origin attribute accepts a DateTime object.

[Alexander-Barth]

This code should work now with the master version (of NCDatasets and CommonDataModel).

newtaxis = defVar(ds,other_ds["time"])
newtaxis[:] = newtaxis[:] .+ Dates.Minute(30)

There is a test case here:
https://github.com/Alexander-Barth/NCDatasets.jl/blob/master/test/test_variable.jl#L263

(for your information: defVar should also work between NetCDF and GRIB files; so you can copy a variable in a GRIB file and write it with metadata to a NetCDF file, @tcarion )

Thank you for your feedback. Can this issue be closed?

[ryofurue]

Can this issue be closed?

I thought the original issue has long been closed. Specifically, the issue my original report pointed out was closed by your comment "I believe that this is an issue with CommonDataModel.jl 0.2.2 which should be fixed by the new released 0.2.3" more than a week ago.

After that, we have been discussing a potential enhancement to the NCDatasets package. That is, we have been "abusing" this thread :-)

Okay, I'll press the "Close with comment" button now, if I have the right to do so.

[tcarion]

(for your information: defVar should also work between NetCDF and GRIB files; so you can copy a variable in a GRIB file and write it with metadata to a NetCDF file, @tcarion )

Another reason why CommonDataModel was definitely worth it :-)