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0.2.1 - #41

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ms609 merged 44 commits into
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0.2.0.9001
Dec 7, 2018
Merged

0.2.1#41
ms609 merged 44 commits into
masterfrom
0.2.0.9001

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@ms609

@ms609 ms609 commented Dec 7, 2018

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TreeSearch 0.2.1

New features

  • CollapseNodes and CollapseEdges allow the creation of polytomies
  • Tree2Splits lists the bipartition splits implied by a tree topology

Enhancements

  • SplitFrequency now supports larger trees
  • Can specify tip labels directly to ReadTntTree, to avoid reliance on
    generative file

Bug fixes

  • Export missing functions

@codecov

codecov Bot commented Dec 7, 2018

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Codecov Report

Merging #41 into master will not change coverage.
The diff coverage is 83.21%.

Impacted file tree graph

@@           Coverage Diff           @@
##           master      #41   +/-   ##
=======================================
  Coverage   58.01%   58.01%           
=======================================
  Files          41       41           
  Lines        4475     4475           
=======================================
  Hits         2596     2596           
  Misses       1879     1879
Impacted Files Coverage Δ
R/pp_ProfileScore.R 64.86% <ø> (ø) ⬆️
src/ape_reorder.h 77.77% <ø> (ø) ⬆️
R/mpl_morphyex.R 73.33% <ø> (ø) ⬆️
src/TreeSearch-init.c 100% <ø> (ø) ⬆️
R/IWScore.R 84.84% <ø> (ø) ⬆️
R/phylo.R 23.95% <ø> (ø) ⬆️
R/mpl_morphy_objects.R 73.33% <ø> (ø) ⬆️
src/mpl.c 31.99% <ø> (ø) ⬆️
R/pp_info_extra_step.r 56.25% <ø> (ø) ⬆️
src/phangorn_bip.cpp 100% <100%> (ø) ⬆️
... and 17 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update bc9c959...960ca27. Read the comment docs.

@codecov

codecov Bot commented Dec 7, 2018

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Codecov Report

Merging #41 into master will not change coverage.
The diff coverage is 83.21%.

Impacted file tree graph

@@           Coverage Diff           @@
##           master      #41   +/-   ##
=======================================
  Coverage   58.01%   58.01%           
=======================================
  Files          41       41           
  Lines        4475     4475           
=======================================
  Hits         2596     2596           
  Misses       1879     1879
Impacted Files Coverage Δ
R/pp_ProfileScore.R 64.86% <ø> (ø) ⬆️
src/ape_reorder.h 77.77% <ø> (ø) ⬆️
R/mpl_morphyex.R 73.33% <ø> (ø) ⬆️
src/TreeSearch-init.c 100% <ø> (ø) ⬆️
R/IWScore.R 84.84% <ø> (ø) ⬆️
R/phylo.R 23.95% <ø> (ø) ⬆️
R/mpl_morphy_objects.R 73.33% <ø> (ø) ⬆️
src/mpl.c 31.99% <ø> (ø) ⬆️
R/pp_info_extra_step.r 56.25% <ø> (ø) ⬆️
src/phangorn_bip.cpp 100% <100%> (ø) ⬆️
... and 17 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update bc9c959...d155ad3. Read the comment docs.

@codecov

codecov Bot commented Dec 7, 2018

Copy link
Copy Markdown

Codecov Report

Merging #41 into master will not change coverage.
The diff coverage is 83.21%.

Impacted file tree graph

@@           Coverage Diff           @@
##           master      #41   +/-   ##
=======================================
  Coverage   58.01%   58.01%           
=======================================
  Files          41       41           
  Lines        4475     4475           
=======================================
  Hits         2596     2596           
  Misses       1879     1879
Impacted Files Coverage Δ
R/pp_ProfileScore.R 64.86% <ø> (ø) ⬆️
src/ape_reorder.h 77.77% <ø> (ø) ⬆️
R/mpl_morphyex.R 73.33% <ø> (ø) ⬆️
src/TreeSearch-init.c 100% <ø> (ø) ⬆️
R/IWScore.R 84.84% <ø> (ø) ⬆️
R/phylo.R 23.95% <ø> (ø) ⬆️
R/mpl_morphy_objects.R 73.33% <ø> (ø) ⬆️
src/mpl.c 31.99% <ø> (ø) ⬆️
R/pp_info_extra_step.r 56.25% <ø> (ø) ⬆️
src/phangorn_bip.cpp 100% <100%> (ø) ⬆️
... and 17 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update bc9c959...960ca27. Read the comment docs.

@ms609
ms609 merged commit 2936512 into master Dec 7, 2018
@ms609
ms609 deleted the 0.2.0.9001 branch July 29, 2019 15:00
ms609 pushed a commit that referenced this pull request Aug 5, 2026
…age diff run

Rotation (11 mod 13)+1 = 12, sonnet (last visit yielded). Filed #41 (routing
state is tier-only) and #42 (scope rows never diffed against the file tree).

The scope-coverage diff flagged on 2026-07-03 and never run is now run: two
subsystems, 5553 + 2183 loc, in no area at all. 17 files added to rows 1/2/4/5/6
inline, area 7 extended to the Shiny app tests, area 8 broadened from
test-ts-*.R to tests/testthat/*.R (it excluded ~44 of ~110 files). Every
addition annotated UNMEASURED, per this area's own lesson that a grown scope row
inherits no dry verdict.

Also corrected: README severity breakdown had drifted within the round it was
written (6/5/13 vs a true 6/4/14) — replaced with a query; the undocumented
area:N label dependency; a missing migration-map-todo.tsv row; and the
"NEVER REVIEWED" rationales on areas 12 and 13, both stale.

src/rearrange.cpp: header claimed "DEAD CODE ... Safe to remove" and was false.
The Rcpp::export tags are commented out but RcppExports.cpp and
TreeSearch-init.c were never regenerated, so nni/spr/spr_moves stay registered,
bound at R/RcppExports.R:60-68 and exercised by three test files. Acting on the
header breaks them. Comment corrected; no code change.

Reverted a finder action: needs-escalation had been applied to #18/#19 for a
backlog row whose ask is sequencing, not tier. Area 13 is already opus, and a
label hit makes step 3 skip reading the row that holds the ask.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
ms609 added a commit that referenced this pull request Aug 5, 2026
… routing and scope gaps

The user-level `/red-team` skill carried dual-mode machinery for a `findings.md`
store this project deleted at the 2026-08-04 migration. Retired to
`~/.claude/skills-retired/red-team/` — the only surviving record of file mode, which
is still correct for a project with no GitHub remote — and replaced with a
project-local skill that assumes issues throughout, alongside `/next-issue`.

The one-off process for standing up a repo under `agent-issues` (fork, default
branch, push block, labels, Actions, secrets, findings migration) moves to a
subsidiary `github-repo-setup.md` that a normal round never opens.

Fixes #41 — the rotation's routing state was tier-only:
- a work-shape gate between brief assembly and dispatch, so a recorded "the next
  visit should NOT be a finder" verdict stops the round and reports instead of
  auto-dispatching. Areas 10 and 13 both carry one, and area 13 is next.
- `needs-escalation` is documented as a tier flag and nothing else; sequencing and
  cross-area residuals stay prose, and step 3 now reads `escalation-backlog.md`
  whether or not the label query hit — a hit used to suppress the row holding the
  actual ask.
- the finder brief carries the area's open issues, so a finder cannot spend its
  budget re-investigating a mechanism already filed.
- `area:N` semantics stated: it marks which area owns the code, not which round
  found it, and the compound label query ANDs correctly.

Addresses #42 — scope coverage:
- the `tidy` pass now leads with a scope-coverage diff (glob `R/*.[Rr]`; the
  lowercase `pp_info_extra_step.r` is invisible to a case-sensitive pattern).
- area 14 (statistics & support metrics, 14 files) and area 15 (legacy pure-R
  search API, 9 files) added, both `sonnet` / UNMEASURED. #42 recommended `opus`
  for 14 and review-once-then-park for 15; the maintainer chose measured maturity
  for both. N is now 15.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
ms609 added a commit that referenced this pull request Aug 5, 2026
…ion state only

The previous commit put the skill and its repo-setup guide inside this repo. Both
were wrong. The skill is shared across projects, so burying it here takes
/red-team away from every other project; and `github-repo-setup.md` documents
standing a repo UP under agent-issues, which is precisely the thing already done
here and never needed again — it belongs where a not-yet-configured project reads
it, next to the skill.

Both now live at `~/.claude/skills/red-team/`, with the #41 routing fixes applied
there. This branch keeps only what is genuinely project state: areas 14 and 15,
N = 15, and the README/AGENTS label range.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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