Enumerate tutorials and rebuild

[goggle]

This PR is the continuation of #61.
In a first step, I have enumerated all the tutorial files in tutorials/, html/, notebook/, pdf/, script/ as suggested in #60.
The second commit rebuilds all the tutorials that could be built without unintended Weave.jl warnings/errors.

The following tutorials could not be built without errors, so I will add them in seperate commits to this PR, and we can figure out what to do:

• introduction/05-formatting_plots
• models/03-diffeqbio_I_introduction
• models/04-diffeqbio_II_networkproperties
• models/06-pendulum_bayesian_interface
• models/07-outer_solar_system
• ode_extras/ModelingToolkit
• type_handling/01-number_types
• type_handling/03-unitful

[goggle]

There is an error in the build of introduction/05-formatting_plots:

The line

plot(sol,vars=(:x,:y,:z))

fails with this error:

ERROR: MethodError: no method matching pointer(::Symbol)
Closest candidates are:
  pointer(!Matched::String) at strings/string.jl:81
  pointer(!Matched::String, !Matched::Integer) at strings/string.jl:82
  pointer(!Matched::SubString{String}) at strings/substring.jl:104
  ...

[goggle]

There are errors in the build of ode_extras/01-ModelingToolkit:

The line

using PuMaS

fails:

ERROR: ArgumentError: Package PuMaS not found in current path:
- Run `import Pkg; Pkg.add("PuMaS")` to install the PuMaS package.

Trying to install PuMaS leads to errors as well:

import Pkg; Pkg.add("PuMaS")

  Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
ERROR: The following package names could not be resolved:
 * PuMaS (not found in project, manifest or registry)
Please specify by known `name=uuid`.
Stacktrace:
 [1] #ensure_resolved at ./none:0 [inlined]
 [2] #add_or_develop#17(::Symbol, ::Bool, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{,Tuple{}}}, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /build/julia/src/julia-1.1.1/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:54
 [3] #add_or_develop at ./none:0 [inlined]
 [4] #add_or_develop#16 at /build/julia/src/julia-1.1.1/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:36 [inlined]
 [5] #add_or_develop at ./none:0 [inlined]
 [6] #add_or_develop#13 at /build/julia/src/julia-1.1.1/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:34 [inlined]
 [7] #add_or_develop at ./none:0 [inlined]
 [8] #add_or_develop#12(::Base.Iterators.Pairs{Symbol,Symbol,Tuple{Symbol},NamedTuple{(:mode,),Tuple{Symbol}}}, ::Function, ::String) at /build/julia/src/julia-1.1.1/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:33
 [9] #add_or_develop at ./none:0 [inlined]
 [10] #add#22 at /build/julia/src/julia-1.1.1/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:64 [inlined]
 [11] add(::String) at /build/julia/src/julia-1.1.1/usr/share/julia/stdlib/v1.1/Pkg/src/API.jl:64
 [12] top-level scope at none:0

[goggle]

There are errors in the build of type_handling/01-number_types:

The code

using DecFP
prob_ode_decfplinear = ODEProblem(f,Dec128(1)/Dec128(2),(Dec128(0.0),Dec128(1.0)),Dec128(1.01))
sol =solve(prob_ode_decfplinear,Tsit5())

fails:

ERROR: StackOverflowError:

The code

using Decimals
prob_ode_decimallinear = ODEProblem(f,[decimal("1.0")]./[decimal("2.0")],(0//1,1//1),decimal(1.01))
sol =solve(prob_ode_decimallinear,RK4(),dt=1/2^(6)) #Fails

fails as well, although it seems to be known (comment #Fails):

ERROR: MethodError: Decimals.Decimal(::Rational{Int64}) is ambiguous. Candidates:
  (::Type{T})(x::Rational{S}) where {S, T<:AbstractFloat} in Base at rational.jl:92
  Decimals.Decimal(num::Real) in Decimals at /home/alex/.julia/packages/Decimals/Qfcas/src/decimal.jl:13
Possible fix, define
  Decimals.Decimal(::Rational{S})

[goggle]

There are errors in type_handling/03-unitful:

The code

t + sqrt(t)

fails:

ERROR: DimensionError: 1.0 s and 1.0 s^1/2 are not dimensionally compatible.

The code

using DifferentialEquations
f = (y,p,t) -> 0.5*y
u0 = 1.5u"N"
prob = ODEProblem(f,u0,(0.0u"s",1.0u"s"))
sol = solve(prob,Tsit5())

fails:

ERROR: DimensionError: N s^-1 and 0.75 N are not dimensionally compatible.

[goggle]

Only the PDF fails to build for models/03-diffeqbio_I_introduction:

I get this LaTeX error:

! Undefined control sequence.
<argument>  \require 
                     {mhchem} \ce { \varnothing &->[\frac {\alpha \cdot K^{n...
l.188 \end{align*}

[goggle]

The PDF fails to build for models/04-diffeqbio_II_networkproperties:

I get this LaTeX error:

! Undefined control sequence.
<argument>  \require 
                     {mhchem} \ce { \varnothing &->[\frac {\alpha \cdot K^{n...
l.175 \end{align*}

Furthermore, the line

addjumps!(rn, build_regular_jumps=false, minimal_jumps=true)

fails:

ERROR: MethodError: Cannot `convert` an object of type Tuple{} to an object of type Tuple{Union{Float64, Int64, Expr, Symbol},Vararg{Union{Float64, Int64, Expr, Symbol},N} where N}
Closest candidates are:
  convert(::Type{T<:Tuple{Any,Vararg{Any,N} where N}}, !Matched::T<:Tuple{Any,Vararg{Any,N} where N}) where T<:Tuple{Any,Vararg{Any,N} where N} at essentials.jl:274
  convert(::Type{T<:Tuple{Any,Vararg{Any,N} where N}}, !Matched::Tuple{Any,Vararg{Any,N} where N}) where T<:Tuple{Any,Vararg{Any,N} where N} at essentials.jl:275
  convert(::Type{T<:Tuple}, !Matched::CartesianIndex) where T<:Tuple at multidimensional.jl:130
  ...

[goggle]

The PDF fails to build for models/06-pendulum_bayesian_inference:

LaTeX Warning: File `https://user-images.githubusercontent.com/1814174/59942945
-059c1680-942f-11e9-991c-2025e6e4ccd3.jpg' not found on input line 139.


! Package pdftex.def Error: File `https://user-images.githubusercontent.com/181
4174/59942945-059c1680-942f-11e9-991c-2025e6e4ccd3.jpg' not found: using draft 
setting.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.139 ...059c1680-942f-11e9-991c-2025e6e4ccd3.jpg}

Furthermore, I needed to add the line using StatsPlots before building, otherwise it would give me errors.

[goggle]

Only the PDF fails to build for models/07-outer_solar_system.

I get this LaTeX error:

! Undefined control sequence.
<argument> \minus 
                  
l.129 ...95912208286 \cdot 10^{\ensuremath{\minus}
                                                  4}$.

[goggle]

All the issues with the rebuild have been put in separate commits/comments.

How can we further proceed? I will be back on Monday.

[ChrisRackauckas]

The TeX issues should get upstreamed. I was just concerned about finish before so I forgot to. I ran into the same ones.

Furthermore, I needed to add the line using StatsPlots before building, otherwise it would give me errors.

Oh no! Thanks for catching that.

There is an error in the build of introduction/05-formatting_plots:

that sounds like a genuine bug :(. Should get an issue.

There are errors in the build of type_handling/01-number_types:

I think that section is marked as "will fail" IIRC.

There are errors in type_handling/03-unitful:

Those are supposed to fail IIRC

The PDF fails to build for models/04-diffeqbio_II_networkproperties:

This should get an issue.

[ChrisRackauckas]

Better than before, so IMO let's merge and keep improving :)

[ChrisRackauckas]

The README links might need an update

[goggle]

The TeX issues should get upstreamed. I was just concerned about finish before so I forgot to. I ran into the same ones.

@ChrisRackauckas By getting upstreamed you mean these issues should get reported to the Weave.jl project?

[ChrisRackauckas]

Yes

[goggle]

One of the PDF issues has been fixed in #63.
Another one has been reported upstream here: JunoLab/Weave.jl#226

The hopefully last one arises from the option mathjax=true when calling the latexify method. This option adds something like \require{mhchem} to the resulting LaTeX code, which fails when compiled to a PDF, but is probably needed for the conversion to HTML. I'm not sure what to do here...

[ChrisRackauckas]

I think that block can be set to be selectively added only when html or something like that

[goggle]

I did not have any success fixing the LaTeX issues in models/03-diffeqbio_I_introduction.jmd and models/04-diffeqbio_II_networkproperties.jmd. They are caused by code like

x = latexify(repressilator; env=:chemical, starred=true, mathjax=true); 
display("text/latex", "$x"); 

where mathjax=true leads to a \require{mhchem} in the resulting .tex file. This then fails to compile with latex.

I tried to change that skip parameter, but without success. I couldn't find any documentation about it neither...

And I'm not sure, if this is not something that should be fixed by Weave.jl.

I have opened an issue ticket JunoLab/Weave.jl#228 about expected failures. This would allow us to indicate the code which is expected to fail, without generating a warning by Weave.jl.

What about the issue with ode_extras/01-ModelingToolkit where I am not able to install PuMaS? Does this package not exist anymore?

[ChrisRackauckas]

You don't need PuMaS for that tutorial. That was an accident. It's a private repo.

[goggle]

So should I simply remove this last section Use Case: PuMaS.jl from the tutorial and rebuild?

[ChrisRackauckas]

Yup, that was just from a presentation

[goggle]

The remaining LaTeX issue has been reported to Weave.jl here: JunoLab/Weave.jl#229