Testing BW and more

[nantonel]

Re-written many functions using in-place versions, changed names of parameters, added new tests including to Baum Welch. Should take into account most of the issues of #1. Benchmarks not updated yet.

[codecov]

Codecov Report

Merging #6 into master will decrease coverage by 0.06%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master       #6      +/-   ##
==========================================
- Coverage   97.53%   97.46%   -0.07%     
==========================================
  Files           6        5       -1     
  Lines         162      237      +75     
==========================================
+ Hits          158      231      +73     
- Misses          4        6       +2

Impacted Files	Coverage Δ
src/HMMBase.jl	100% <ø> (ø)	⬆️
src/messages.jl	100% <100%> (ø)	⬆️
src/hmm.jl	100% <100%> (+10.52%)	⬆️
src/baum_welch.jl	100% <100%> (ø)
src/utilities.jl	0% <0%> (-100%)	⬇️

---

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[codecov]

Codecov Report

Merging #6 into master will increase coverage by 0.82%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master       #6      +/-   ##
==========================================
+ Coverage   96.63%   97.46%   +0.82%     
==========================================
  Files           6        5       -1     
  Lines         119      237     +118     
==========================================
+ Hits          115      231     +116     
- Misses          4        6       +2

Impacted Files	Coverage Δ
src/HMMBase.jl	100% <ø> (ø)	⬆️
src/messages.jl	100% <100%> (ø)	⬆️
src/hmm.jl	100% <100%> (+11.11%)	⬆️
src/baum_welch.jl	100% <100%> (ø)
src/utilities.jl	0% <0%> (-100%)	⬇️

---

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[maxmouchet]

Thanks for the PR! Give me a few days to review the changes :-)
Changing the fields and functions names is a big changes but yours are indeed more consistent. Since we're still at an early stage this may be doable :-)

[nantonel]

yes, that's what I had in my mind when I've made these mods! 😃

[maxmouchet]

The tests fails on my installation with Distributions v0.16.4:

suffstats is not implemented for (DiscreteNonParametric{Int64,Float64,Base.OneTo{Int64},Array{Float64,1}}, Array{Int64,1}, Array{Float64,1})
suffstats is not implemented for (Gamma{Float64}, Array{Float64,1}, Array{Float64,1})

However they pass with the latest version v0.20.0. Can you add the following in Project.toml:

[compat]
Distributions = ">= 0.20.0"

Thanks!

[nantonel]

should be fixed now! 😉

[codecov-io]

Codecov Report

Merging #6 into master will increase coverage by 0.82%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master       #6      +/-   ##
==========================================
+ Coverage   96.63%   97.46%   +0.82%     
==========================================
  Files           6        5       -1     
  Lines         119      237     +118     
==========================================
+ Hits          115      231     +116     
- Misses          4        6       +2

Impacted Files	Coverage Δ
src/HMMBase.jl	100% <ø> (ø)	⬆️
src/messages.jl	100% <100%> (ø)	⬆️
src/hmm.jl	100% <100%> (+11.11%)	⬆️
src/baum_welch.jl	100% <100%> (ø)
src/utilities.jl	0% <0%> (-100%)	⬇️

---

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Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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[maxmouchet]

Hi, I'm a bit busy for the moment but I haven't forgotten you :-)

[maxmouchet]

I've rebased your changes in the refactor_v1 branch where I'll prepare the release of the v1.0.
I want to make a few cosmetic changes to the code before merging to master.

[maxmouchet]

Hi, I finally released the new version of the library, including the renaming of the HMM fields.

I did not merged all of your changes as-is, as I wanted to preserve some of the original design decisions (AbstractHMM types parameters, for example), and the PR was quite big with intertwined commits.

I mentioned you where I thought it was appropriate (release notes, messages.jl and viterbi.jl files).

Thanks for your improvements, your implementations were much cleaner and faster :-)

[nantonel]

That's great! Thank you! 😄