npm - @rho-workspace/rho - Versions diffs - 0.5.3 → 0.5.5 - Mend

@rho-workspace/rho 0.5.3 → 0.5.5

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package/example/pa14-qs/.rho/rho/conversations/c-91aa2e46b1ac1a6c.json CHANGED Viewed

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1	- {"format":2,"backend":"claude-acp","id":"c-91aa2e46b1ac1a6c","changeId":"q-swarming","requestDigest":"8768aafc6cd76952c7446b526364137ecc37cbd14395556f83d8dcfb1dbaff74","createdAt":"2026-11-01T15:47:51.144Z","createdBy":"browser:local","updatedAt":"2026-11-01T16:13:02.661Z","version":1979,"client":"claude-code","nativeSessionId":null,"confirmed":true,"principal":"agent:ad4b351ff45965f9f469ec1dd25cd2e4","title":"Let's start with the swarming assay of the single mutants. I want to know wheth…","turns":[{"id":"t1","changeId":"q-swarming","requestDigest":"8768aafc6cd76952c7446b526364137ecc37cbd14395556f83d8dcfb1dbaff74","by":"browser:local","text":"Let's start with the swarming assay of the single mutants. I want to know whether losing either quorum-sensing system makes PA14 swarm worse than wild type: compare the mutants against wild type on colony area, say how big the difference is, and whether the colonies also change shape. Do the analysis in R and leave a figure and a table of the numbers in results/ so I can look at them.","sentAt":"2026-11-01T15:47:51.144Z","state":"completed","startedAt":"2026-11-01T15:47:51.296Z","endedAt":"2026-11-01T16:05:14.004Z","pid":98686,"model":"westlakehpc/deepseek-v4.1-flash[1m]","stop":null,"exit":null,"steps":[{"kind":"tool","at":"2026-11-01T15:48:02.720Z","id":"chatcmpl-tool-8d8caa58938f174f","tool":"Bash","title":"rtk ls PA14 quorum sensing","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T15:47:59.251Z","detail":"rtk ls PA14 quorum sensing","purpose":"List project directory contents","output":{"text":"data/\nREADME.md 1.9K","lines":2,"bytes":21,"cut":false},"exitCode":0},{"kind":"tool","at":"2026-11-01T15:48:02.813Z","id":"chatcmpl-tool-b9d99b05723e1d84","tool":"Bash","title":"rtk git -C PA14 quorum sensing status","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T15:48:00.658Z","detail":"rtk git -C PA14 quorum sensing status","purpose":"Show git status of project","output":{"text":"* main...origin/main\n?? final4.mjs\n?? findover.mjs\n?? narrow.mjs\n?? overlap.mjs\n?? shot-artifact.mjs\n?? shot2.mjs\n?? shot3.mjs\n?? shot3all.mjs","lines":9,"bytes":142,"cut":false},"exitCode":0},{"kind":"tool","at":"2026-11-01T15:48:05.412Z","id":"chatcmpl-tool-805a0a31713672e8","tool":"Bash","title":"rtk ls PA14 quorum sensing/data","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T15:48:03.742Z","detail":"rtk ls PA14 quorum sensing/data","purpose":"List data directory","output":{"text":"rnaseq/\nswarming/","lines":2,"bytes":17,"cut":false},"exitCode":0},{"kind":"tool","at":"2026-11-01T15:48:05.431Z","id":"chatcmpl-tool-849afeb55cf26fcb","tool":"Read","title":"Read README.md","toolKind":"read","outcome":"returned","startedAt":"2026-11-01T15:48:03.968Z","detail":"PA14 quorum sensing/README.md"},{"kind":"tool","at":"2026-11-01T15:48:11.461Z","id":"chatcmpl-tool-8a616c9b30582347","tool":"Bash","title":"ls -la PA14 quorum sensing/; ls -la PA14 quorum sensing/data/swarming/","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T15:48:10.082Z","detail":"ls -la PA14 quorum sensing/; ls -la PA14 quorum sensing/data/swarming/","purpose":"Check for project-notes.md and swarming files","output":{"text":"700 .rho/\n755 data/\n600 README.md 1.9K\n644 cocultures.csv 1.8K\n644 single_cultures.csv 612B","lines":5,"bytes":99,"cut":false},"exitCode":0},{"kind":"tool","at":"2026-11-01T15:48:12.622Z","id":"chatcmpl-tool-b434a91dcc7d4aff","tool":"Read","title":"Read data/swarming/single_cultures.csv","toolKind":"read","outcome":"returned","startedAt":"2026-11-01T15:48:12.599Z","detail":"PA14 quorum sensing/data/swarming/single_cultures.csv"},{"kind":"tool","at":"2026-11-01T15:48:24.496Z","id":"chatcmpl-tool-9b1a1944a209ce05","tool":"ToolSearch","title":"ToolSearch","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T15:48:24.476Z","detail":"select:mcp__rho__rho_index,mcp__rho__rho_resolve,mcp__rho__rho_call,mcp__rho__rho_read"},{"kind":"tool","at":"2026-11-01T15:48:31.461Z","id":"chatcmpl-tool-9afbc0f2ed7abaae","tool":"Write","title":"Write project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T15:48:30.091Z","detail":"PA14 quorum sensing/project-notes.md"},{"kind":"tool","at":"2026-11-01T15:48:32.894Z","id":"chatcmpl-tool-807f702211f76d08","tool":"mcp__rho__rho_index","title":"mcp__rho__rho_index","toolKind":"other","outcome":"rejected","startedAt":"2026-11-01T15:48:32.881Z","detail":"kernel run R session"},{"kind":"tool","at":"2026-11-01T15:48:34.749Z","id":"chatcmpl-tool-befff93b666abc7d","tool":"mcp__rho__rho_index","title":"mcp__rho__rho_index","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T15:48:34.542Z"},{"kind":"tool","at":"2026-11-01T15:48:36.483Z","id":"chatcmpl-tool-b848da67d6cf532c","tool":"mcp__rho__rho_resolve","title":"mcp__rho__rho_resolve","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T15:48:35.671Z"},{"kind":"tool","at":"2026-11-01T15:48:40.562Z","id":"chatcmpl-tool-b0f6ff4cd561deae","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T15:48:38.216Z","operation":"kernel.run"},{"kind":"tool","at":"2026-11-01T15:49:17.923Z","id":"chatcmpl-tool-a179113d374b7334","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T15:49:16.006Z","operation":"kernel.run"},{"kind":"tool","at":"2026-11-01T15:49:18.992Z","id":"chatcmpl-tool-9eec235736542227","tool":"Skill","title":"Load skill: dataviz","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T15:49:17.532Z"},{"kind":"tool","at":"2026-11-01T15:49:22.705Z","id":"chatcmpl-tool-9fc35e45bf8ccb93","tool":"Read","title":"Read /private/tmp/claude-501/bundled-skills/2.1.316/093806141239ac864818b8f57985587c/dataviz/references/palette.md","toolKind":"read","outcome":"returned","startedAt":"2026-11-01T15:49:22.682Z","detail":"/private/tmp/claude-501/bundled-skills/2.1.316/093806141239ac864818b8f57985587c/dataviz/references/palette.md"},{"kind":"tool","at":"2026-11-01T15:49:35.698Z","id":"chatcmpl-tool-acce4b95209e29f1","tool":"Bash","title":"cd /private/tmp/claude-501/bundled-skills/2.1.316/093806141239ac864818b8f57985587c/dataviz && node scripts/validate_palette.js \"#2a78d6,#eb6834\" --mode light","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T15:49:33.876Z","detail":"cd /private/tmp/claude-501/bundled-skills/2.1.316/093806141239ac864818b8f57985587c/dataviz && node scripts/validate_palette.js \"#2a78d6,#eb6834\" --mode light","purpose":"Validate two-hue categorical palette on light surface","output":{"text":"(node:99725) [UNDICI-EHPA] Warning: EnvHttpProxyAgent is experimental, expect them to change at any time.\n(Use `node --trace-warnings ...` to show where the warning was created)\n\nPalette (light, surface #fcfcfb, categorical): 2 slots\n [PASS] Lightness band all 2 inside L 0.43–0.77\n [PASS] Chroma floor all 2 >= 0.1\n [PASS] CVD separation worst adjacent #eb6834↔#2a78d6 ΔE 24.7 (protan) · tritan 32.7\n [PASS] Normal-vision floor worst adjacent #eb6834↔#2a78d6 ΔE 33.6 (normal)\n [PASS] Contrast vs surface all 2 >= 3:1\n\n → ALL CHECKS PASS (CVD in the 6–8 floor band is legal ONLY with secondary encoding: direct labels, gaps, or texture)\n scope: categorical palettes only. For a lone status/text color check text contrast with this script's apca() or contrast(); for a sequential ramp, lightness monotonicity.\n\nShell cwd was reset to PA14 quorum 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sensing/analysis/swarming_single_mutants.R"},{"kind":"tool","at":"2026-11-01T16:01:11.850Z","id":"chatcmpl-tool-81820e631f6695cd","tool":"mcp__rho__rho_call","title":"mcp__rho__rho_call","toolKind":"other","outcome":"returned","startedAt":"2026-11-01T16:01:09.338Z","operation":"kernel.run"},{"kind":"tool","at":"2026-11-01T16:01:24.067Z","id":"chatcmpl-tool-88e7d913d6051ba4","tool":"Read","title":"Read results/swarming_single_mutants.png","toolKind":"read","outcome":"returned","startedAt":"2026-11-01T16:01:23.940Z","detail":"PA14 quorum sensing/results/swarming_single_mutants.png"},{"kind":"tool","at":"2026-11-01T16:02:27.743Z","id":"chatcmpl-tool-811173c3c4653235","tool":"Write","title":"Write project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T16:02:27.448Z","detail":"PA14 quorum sensing/project-notes.md"},{"kind":"tool","at":"2026-11-01T16:02:43.094Z","id":"chatcmpl-tool-bbb84d3cfcca1f94","tool":"Bash","title":"Rscript analysis/swarming_single_mutants.R > /tmp/swarming_run.log 2>&1; echo \"exit=$?\"; tail -5 /tmp/swarming_run.log; ls -la results/","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T16:02:41.497Z","detail":"Rscript analysis/swarming_single_mutants.R > /tmp/swarming_run.log 2>&1; echo \"exit=$?\"; tail -5 /tmp/swarming_run.log; ls -la results/","purpose":"Run the analysis script standalone and list results","output":{"text":"exit=0\n 0.410268042 0.410268042 0.959544027 0.959544027 \n\nWrote results/swarming_single_mutants_summary.csv\nWrote results/swarming_system_contrast.csv\nWrote results/swarming_single_mutants.png\ntotal 400\ndrwxr-xr-x@ 5 project staff 160 Nov 1 10:55 .\ndrwxr-xr-x@ 8 project staff 256 Nov 1 11:02 ..\n-rw-r--r--@ 1 project staff 1273 Nov 1 11:02 swarming_single_mutants_summary.csv\n-rw-r--r--@ 1 project staff 167991 Nov 1 11:02 swarming_single_mutants.png\n-rw-r--r--@ 1 project staff 302 Nov 1 11:02 swarming_system_contrast.csv","lines":12,"bytes":563,"cut":false},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:03:17.886Z","id":"chatcmpl-tool-8aaa2f5c20ea8e62","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T16:03:17.351Z","detail":"PA14 quorum sensing/project-notes.md"},{"kind":"tool","at":"2026-11-01T16:03:51.971Z","id":"chatcmpl-tool-9fa35d7ab4cbd6d5","tool":"Bash","title":"for f in data/swarming/single_cultures.csv analysis/swarming_single_mutants.R results/swarming_single_mutants_summary.csv results/swarming_system_contrast.csv results/swarming_single_mutants.png; do test -f \"$f\" && echo \"ok $f\" \|\| echo \"MISSING $f\"; done; echo '---'; rtk git status","toolKind":"execute","outcome":"rejected","startedAt":"2026-11-01T16:03:50.660Z","detail":"for f in data/swarming/single_cultures.csv analysis/swarming_single_mutants.R results/swarming_single_mutants_summary.csv results/swarming_system_contrast.csv results/swarming_single_mutants.png; do test -f \"$f\" && echo \"ok $f\" \|\| echo \"MISSING $f\"; done; echo '---'; rtk git status","purpose":"Verify output files and show git status","output":{"text":"User refused permission to run tool","lines":1,"bytes":35,"cut":false}},{"kind":"tool","at":"2026-11-01T16:04:30.102Z","id":"chatcmpl-tool-abc43fa4c646e1d2","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T16:04:29.300Z","detail":"PA14 quorum sensing/project-notes.md"},{"kind":"text","at":"2026-11-01T16:05:13.659Z","id":"msg_resp_aab6f8b770c8d8d6","text":"Both quorum-sensing systems matter: every single mutant swarmed far less than wild type, and losing the rhl system hurt about twice as much as losing las.\n\nColony area (wild-type geometric mean 81,732 imaging units; arithmetic mean 82,442 ± 13,203):\n\n\| Genotype \| System \| Area ratio vs WT (95% CI) \| Change \| Holm p \|\n\|---\|---\|---\|---\|---\|\n\| ΔlasI \| las \| 0.27 (0.13–0.57) \| −73% \| 0.016 \|\n\| ΔlasR \| las \| 0.29 (0.16–0.50) \| −72% \| 0.016 \|\n\| ΔrhlI \| rhl \| 0.15 (0.063–0.34) \| −85% \| 0.016 \|\n\| rhlR- \| rhl \| 0.13 (0.091–0.19) \| −87% \| 0.0035 \|\n\nPooling the two mutants of each system, rhl mutant colonies were half the area of las mutant colonies (ratio 0.50, 95% CI 0.35–0.71, p = 0.0015).\n\nShape. Circularity rose 5.2–8.2× above wild type (0.076 → 0.40–0.62; all Holm p ≤ 0.002), so mutant colonies are much less irregular/dendritic, though still not circular (highest single dish 0.71). Roundness did not change consistently (wild type 0.886; mutants 0.788–0.975; all Holm p ≥ 0.41), so the change is in perimeter irregularity rather than elongation.\n\nCaveat. There are only three dishes per genotype. The exact rank test cannot go below p = 0.1 for 3 vs 3, so the inference rests on Welch tests on log area/circularity with Holm adjustment within each metric. Under the strictest correction across all 12 comparisons, ΔlasI area becomes borderline (Holm p = 0.063); every circularity result stays significant. Group variances were homogeneous on the analysed scales (Levene p ≥ 0.32), and pooled-variance t-tests give the same conclusions.\n\nFiles:\n- [analysis/swarming_single_mutants.R](analysis/swarming_single_mutants.R) — the R analysis; runs standalone with `Rscript analysis/swarming_single_mutants.R` from the project root.\n- [results/swarming_single_mutants_summary.csv](results/swarming_single_mutants_summary.csv) — the table of numbers (means, SDs, ratios/differences, 95% CIs, adjusted p).\n- [results/swarming_system_contrast.csv](results/swarming_system_contrast.csv) — rhl vs las mutants.\n- [results/swarming_single_mutants.png](results/swarming_single_mutants.png) — three-panel figure (area, circularity, roundness), also embedded in the project 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1	+ {"format":2,"backend":"claude-acp","id":"c-91aa2e46b1ac1a6c","changeId":"q-swarming","requestDigest":"8768aafc6cd76952c7446b526364137ecc37cbd14395556f83d8dcfb1dbaff74","createdAt":"2026-11-01T15:47:51.144Z","createdBy":"browser:local","updatedAt":"2026-11-01T16:13:02.661Z","version":1979,"client":"claude-code","nativeSessionId":null,"confirmed":true,"principal":"agent:ad4b351ff45965f9f469ec1dd25cd2e4","title":"Let's start with the swarming assay of the single mutants. I want to know wheth…","turns":[{"id":"t1","changeId":"q-swarming","requestDigest":"8768aafc6cd76952c7446b526364137ecc37cbd14395556f83d8dcfb1dbaff74","by":"browser:local","text":"Let's start with the swarming assay of the single mutants. I want to know whether losing either quorum-sensing system makes PA14 swarm worse than wild type: compare the mutants against wild type on colony area, say how big the difference is, and whether the colonies also change shape. Do the analysis in R and leave a figure and a table of the numbers in results/ so I can look at them.","sentAt":"2026-11-01T15:47:51.144Z","state":"completed","startedAt":"2026-11-01T15:47:51.296Z","endedAt":"2026-11-01T16:05:14.004Z","pid":98686,"model":"westlakehpc/deepseek-v4.1-flash[1m]","stop":null,"exit":null,"steps":[{"kind":"tool","at":"2026-11-01T15:48:02.720Z","id":"chatcmpl-tool-8d8caa58938f174f","tool":"Bash","title":"rtk ls PA14 quorum sensing","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T15:47:59.251Z","detail":"rtk ls PA14 quorum sensing","purpose":"List project directory contents","output":{"text":"data/\nREADME.md 1.9K","lines":2,"bytes":21,"cut":false},"exitCode":0},{"kind":"tool","at":"2026-11-01T15:48:02.813Z","id":"chatcmpl-tool-b9d99b05723e1d84","tool":"Bash","title":"rtk git -C PA14 quorum sensing status","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T15:48:00.658Z","detail":"rtk git -C PA14 quorum sensing status","purpose":"Show git status of project","output":{"text":"* main...origin/main\n?? final4.mjs\n?? findover.mjs\n?? narrow.mjs\n?? overlap.mjs\n?? shot-artifact.mjs\n?? shot2.mjs\n?? shot3.mjs\n?? shot3all.mjs","lines":9,"bytes":142,"cut":false},"exitCode":0},{"kind":"tool","at":"2026-11-01T15:48:05.412Z","id":"chatcmpl-tool-805a0a31713672e8","tool":"Bash","title":"rtk ls PA14 quorum sensing/data","toolKind":"execute","outcome":"returned","startedAt":"2026-11-01T15:48:03.742Z","detail":"rtk ls PA14 quorum sensing/data","purpose":"List data directory","output":{"text":"rnaseq/\nswarming/","lines":2,"bytes":17,"cut":false},"exitCode":0},{"kind":"tool","at":"2026-11-01T15:48:05.431Z","id":"chatcmpl-tool-849afeb55cf26fcb","tool":"Read","title":"Read README.md","toolKind":"read","outcome":"returned","startedAt":"2026-11-01T15:48:03.968Z","detail":"README.md"},{"kind":"tool","at":"2026-11-01T15:48:11.461Z","id":"chatcmpl-tool-8a616c9b30582347","tool":"Bash","title":"ls -la PA14 quorum sensing/; 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For a lone status/text color check text contrast with this script's apca() or contrast(); for a sequential ramp, lightness monotonicity.\n\nShell cwd was reset to PA14 quorum 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1 project staff 1273 Nov 1 11:02 swarming_single_mutants_summary.csv\n-rw-r--r--@ 1 project staff 167991 Nov 1 11:02 swarming_single_mutants.png\n-rw-r--r--@ 1 project staff 302 Nov 1 11:02 swarming_system_contrast.csv","lines":12,"bytes":563,"cut":false},"exitCode":0},{"kind":"tool","at":"2026-11-01T16:03:17.886Z","id":"chatcmpl-tool-8aaa2f5c20ea8e62","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T16:03:17.351Z","detail":"project-notes.md"},{"kind":"tool","at":"2026-11-01T16:03:51.971Z","id":"chatcmpl-tool-9fa35d7ab4cbd6d5","tool":"Bash","title":"for f in data/swarming/single_cultures.csv analysis/swarming_single_mutants.R results/swarming_single_mutants_summary.csv results/swarming_system_contrast.csv results/swarming_single_mutants.png; do test -f \"$f\" && echo \"ok $f\" \|\| echo \"MISSING $f\"; done; echo '---'; rtk git status","toolKind":"execute","outcome":"rejected","startedAt":"2026-11-01T16:03:50.660Z","detail":"for f in data/swarming/single_cultures.csv analysis/swarming_single_mutants.R results/swarming_single_mutants_summary.csv results/swarming_system_contrast.csv results/swarming_single_mutants.png; do test -f \"$f\" && echo \"ok $f\" \|\| echo \"MISSING $f\"; done; echo '---'; rtk git status","purpose":"Verify output files and show git status","output":{"text":"User refused permission to run tool","lines":1,"bytes":35,"cut":false}},{"kind":"tool","at":"2026-11-01T16:04:30.102Z","id":"chatcmpl-tool-abc43fa4c646e1d2","tool":"Edit","title":"Edit project-notes.md","toolKind":"edit","outcome":"returned","startedAt":"2026-11-01T16:04:29.300Z","detail":"project-notes.md"},{"kind":"text","at":"2026-11-01T16:05:13.659Z","id":"msg_resp_aab6f8b770c8d8d6","text":"Both quorum-sensing systems matter: every single mutant swarmed far less than wild type, and losing the rhl system hurt about twice as much as losing las.\n\nColony area (wild-type geometric mean 81,732 imaging units; arithmetic mean 82,442 ± 13,203):\n\n\| Genotype \| System \| Area ratio vs WT (95% CI) \| Change \| Holm p \|\n\|---\|---\|---\|---\|---\|\n\| ΔlasI \| las \| 0.27 (0.13–0.57) \| −73% \| 0.016 \|\n\| ΔlasR \| las \| 0.29 (0.16–0.50) \| −72% \| 0.016 \|\n\| ΔrhlI \| rhl \| 0.15 (0.063–0.34) \| −85% \| 0.016 \|\n\| rhlR- \| rhl \| 0.13 (0.091–0.19) \| −87% \| 0.0035 \|\n\nPooling the two mutants of each system, rhl mutant colonies were half the area of las mutant colonies (ratio 0.50, 95% CI 0.35–0.71, p = 0.0015).\n\nShape. Circularity rose 5.2–8.2× above wild type (0.076 → 0.40–0.62; all Holm p ≤ 0.002), so mutant colonies are much less irregular/dendritic, though still not circular (highest single dish 0.71). Roundness did not change consistently (wild type 0.886; mutants 0.788–0.975; all Holm p ≥ 0.41), so the change is in perimeter irregularity rather than elongation.\n\nCaveat. There are only three dishes per genotype. The exact rank test cannot go below p = 0.1 for 3 vs 3, so the inference rests on Welch tests on log area/circularity with Holm adjustment within each metric. Under the strictest correction across all 12 comparisons, ΔlasI area becomes borderline (Holm p = 0.063); every circularity result stays significant. Group variances were homogeneous on the analysed scales (Levene p ≥ 0.32), and pooled-variance t-tests give the same conclusions.\n\nFiles:\n- [analysis/swarming_single_mutants.R](analysis/swarming_single_mutants.R) — the R analysis; runs standalone with `Rscript analysis/swarming_single_mutants.R` from the project root.\n- [results/swarming_single_mutants_summary.csv](results/swarming_single_mutants_summary.csv) — the table of numbers (means, SDs, ratios/differences, 95% CIs, adjusted p).\n- [results/swarming_system_contrast.csv](results/swarming_system_contrast.csv) — rhl vs las mutants.\n- [results/swarming_single_mutants.png](results/swarming_single_mutants.png) — three-panel figure (area, circularity, roundness), also embedded in the project 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