Bug fixes

[richardreeve]

Minor fixes:

• unrooted trees weren't always creating branches as expected
• ensure types returned are the same as received
• node order requests are not obeyed for getnodes() - was for traversal()
• remove JuliaDB dependency
• fix R workflow
• fix Migrate from LightGraphs to Graphs #77

[github-actions]

Pull Request Test Coverage Report for Build 4778535667

• 18 of 24 (75.0%) changed or added relevant lines in 4 files are covered.
• 149 unchanged lines in 15 files lost coverage.
• Overall coverage increased (+1.3%) to 58.093%

---

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
src/rand.jl	0	3	0.0%
src/rcall.jl	0	3	0.0%

Files with Coverage Reduction	New Missed Lines	%
src/Branch.jl	1	70.0%
src/trim.jl	1	97.22%
src/Iterators.jl	2	95.05%
src/metrics.jl	3	48.65%
src/TreeSet.jl	4	40.63%
src/routes.jl	5	63.64%
src/Tree.jl	5	81.71%
src/rand.jl	6	61.34%
src/API.jl	8	59.15%
src/Node.jl	8	39.29%

Totals
Change from base Build 1356629049:	1.3%
Covered Lines:	1267
Relevant Lines:	2181

---

💛 - Coveralls

[richardreeve]

Hi @mkborregaard - no problem if you're busy, I don't think there's anything controversial here - but I just thought I'd ask if you had time to check these fixes that we need before we merge in the inference work.

[coveralls]

Pull Request Test Coverage Report for Build 4778535667

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

• For more information on this, see Tracking coverage changes with pull request builds.
• To avoid this issue with future PRs, see these Recommended CI Configurations.
• For a quick fix, rebase this PR at GitHub. Your next report should be accurate.

Details

• 21 of 24 (87.5%) changed or added relevant lines in 4 files are covered.
• 141 unchanged lines in 15 files lost coverage.
• Overall coverage increased (+5.1%) to 61.896%

---

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
src/rand.jl	0	3	0.0%

Files with Coverage Reduction	New Missed Lines	%
src/Branch.jl	1	72.73%
src/trim.jl	1	97.56%
src/Iterators.jl	2	95.37%
src/TreeSet.jl	3	45.45%
src/metrics.jl	4	50.0%
src/newick.jl	5	76.43%
src/routes.jl	7	65.12%
src/Node.jl	8	43.33%
src/Tree.jl	8	81.56%
src/API.jl	9	59.76%

Totals
Change from base Build 1356629049:	5.1%
Covered Lines:	1410
Relevant Lines:	2278

---

💛 - Coveralls

[coveralls]

Pull Request Test Coverage Report for Build 4778535667

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

• For more information on this, see Tracking coverage changes with pull request builds.
• To avoid this issue with future PRs, see these Recommended CI Configurations.
• For a quick fix, rebase this PR at GitHub. Your next report should be accurate.

Details

• 21 of 24 (87.5%) changed or added relevant lines in 4 files are covered.
• 141 unchanged lines in 15 files lost coverage.
• Overall coverage increased (+5.1%) to 61.896%

---

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
src/rand.jl	0	3	0.0%

Files with Coverage Reduction	New Missed Lines	%
src/Branch.jl	1	72.73%
src/trim.jl	1	97.56%
src/Iterators.jl	2	95.37%
src/TreeSet.jl	3	45.45%
src/metrics.jl	4	50.0%
src/newick.jl	5	76.43%
src/routes.jl	7	65.12%
src/Node.jl	8	43.33%
src/Tree.jl	8	81.56%
src/API.jl	9	59.76%

Totals
Change from base Build 1356629049:	5.1%
Covered Lines:	1410
Relevant Lines:	2278

---

💛 - Coveralls