Maintenance work

[tpoisot]

This is Work in Progress to update some of the build system, documentation, etc.

Closes #37
Closes #36
Closes #35

[tpoisot]

Giving up for now.

[mkborregaard]

What's the issue @tpoisot ?

[tpoisot]

What's the issue @tpoisot ?

The tests don't run because they can't load JuliaDB, even though it's in the test/Project.toml

[mschauer]

Is this the issue?

205 WARNING: using OnlineStats.transform in module JuliaDB conflicts with an existing identifier.
206 * Testing LinkTree.jl: Error During Test at /home/runner/work/Phylo.jl/Phylo.jl/test/runtests.jl:19
207 Got exception outside of a @test
208 LoadError: ArgumentError: Package IterableTables not found in current path:
209  - Run `import Pkg; Pkg.add("IterableTables")` to install the IterableTables package.

[mschauer]

Sorry,

The princess is in another castle

  LoadError: ArgumentError: Package Random not found in current path:
250
  - Run `import Pkg; Pkg.add("Random")` to install the Random package.
251

Doesn't running Pkg.test("Phylo") locally help to check this without waiting for CI?

[mkborregaard]

Is this the current state of affairs? Essentially Phylo is in an unstable state atm? Can we just get rid of JuliaDB?

[richardreeve]

Let's see what @claireh93's reworking of the tests achieves. We were using JuliaDB, which is why it's tested with that. When I run the tests locally on 1.6-beta1, there are no problems.

[mkborregaard]

yeah here neither I also ran the tests locally

[mkborregaard]

@richardreeve @tpoisot can this be merged now? Did @claireh93 rework the tests? I'd love to use this at a workshop on Monday (in fact I'd planned to) but I'm running into issues because Phylo isn't compatible with current DataFrames

[richardreeve]

Working through it now. We have a bit too much going on in the github actions now, but I'll trim it down...

[coveralls]

Pull Request Test Coverage Report for Build 606553770

• 0 of 0 changed or added relevant lines in 0 files are covered.
• 48 unchanged lines in 5 files lost coverage.
• Overall coverage decreased (-2.5%) to 54.434%

---

Files with Coverage Reduction	New Missed Lines	%
src/Interface.jl	1	45.97%
src/LinkTree.jl	1	59.5%
src/TreeSet.jl	1	38.71%
src/trim.jl	3	90.63%
src/rcall.jl	42	0%

Totals
Change from base Build 520661805:	-2.5%
Covered Lines:	1111
Relevant Lines:	2041

---

💛 - Coveralls

[richardreeve]

@mkborregaard What is actually problematic about DataFrames? There's no changes to the code in this PR, but it works on my laptop without any constraints on DataFrames...

[mkborregaard]

Just the bounds I think. Because compathelper isn't activated before this PR it lags behind the current version

[richardreeve]

Okay, @mkborregaard - all of the tests pass now, and I've added Windows here too and removed appveyor. Do you want to see whether it works for your purposes or if I've missed something and we need to add in another test? DataFrames is not used in anger in the code - it's just the default storage type for leaves for some tree types so there's no reason for it to matter. It was all just fixing things for the registrator (which may happen again I guess?).