dsh-molbio-tools 0.22.2 → 0.24.0

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "dsh-molbio-tools",
-  "version": "0.22.2",
-  "description": "Zero-dependency molecular-biology plugin bundle for the DeepSeek Harness: sequence analysis, primer design (incl. cross-intron qPCR primers, TaqMan hydrolysis/MGB probes with ordering CSV and multiplex compatibility), in-silico PCR, cloning simulation, SnapGene .dna parsing and plasmid maps, Sanger verification, protein tools (incl. helical wheel and hydropathy plots), methylation-aware restriction analysis with double-digest buffer checks, qPCR analysis and plotting, multiple sequence alignment that conserves every input residue, conservation analysis, sequence logos, codon-usage analysis, phylogenetic trees with bootstrap support, Newick I/O and long-name label wrapping, CpG-island/GC-skew composition analysis, read-level FASTQ QC, batch file analysis with CSV export, silent restriction-site mutagenesis, family-aware CRISPR gRNA design (SpCas9/SaCas9/Cas12a/Cas13) with off-target search, an opt-in hand-off that shows a generated plot to the model as an attached image, plus a browser-side right-sidebar panel (plasmid maps and sequence logos drawn in the Web GUI) and a literature/protocol/experiment record system.",
+  "version": "0.24.0",
+  "description": "Zero-dependency molecular-biology plugin bundle for the DeepSeek Harness: sequence analysis, primer design (incl. cross-intron qPCR primers, TaqMan hydrolysis/MGB probes with ordering CSV and multiplex compatibility), in-silico PCR, cloning simulation, SnapGene .dna parsing and plasmid maps, Sanger verification, protein tools (incl. helical wheel, hydropathy and charge-pH plots), methylation-aware restriction analysis with double-digest buffer checks, qPCR analysis and plotting, multiple sequence alignment that conserves every input residue, conservation analysis, sequence logos, codon-usage analysis, phylogenetic trees with bootstrap support, Newick I/O and long-name label wrapping, CpG-island/GC-skew composition analysis, k-mer dotplots, read-level FASTQ QC, vector/adapter contamination screening, FASTQ trimming/filtering, batch file analysis with CSV export, silent restriction-site mutagenesis, family-aware CRISPR gRNA design (SpCas9/SaCas9/Cas12a/Cas13) with off-target search, an opt-in hand-off that shows a generated plot to the model as an attached image, plus a browser-side right-sidebar panel (plasmid maps and sequence logos drawn in the Web GUI) and a literature/protocol/experiment record system.",
   "type": "module",
   "main": "index.mjs",
   "engines": {
@@ -59,6 +59,10 @@
     "sanger.mjs",
     "protein.mjs",
     "protein-structure.mjs",
+    "protein-charge.mjs",
+    "dotplot.mjs",
+    "contamination.mjs",
+    "fastq-trim.mjs",
     "taqman.mjs",
     "multiplex.mjs",
     "methylation.mjs",
@@ -98,7 +102,8 @@
         "0.2.1-rc.2": "compatible",
         "0.2.1-rc.3": "compatible",
         "0.2.1-rc.4": "unknown",
-        "0.2.1-rc.5": "compatible"
+        "0.2.1-rc.5": "compatible",
+        "0.2.2-rc.1": "compatible"
       }
     },
     "bundle": {

package/preset/molbio-lab/agent.cordis.yml

@@ -17,7 +17,7 @@
 #
 # Edit THIS file, then run `node build/preset-patch.mjs`.
 #
-# NOTE: the mode is the ONLY place these 60 tools load. The same bundle patch's
+# NOTE: the mode is the ONLY place these 64 tools load. The same bundle patch's
 # other insert (`molbio-client` → `./host.mjs`) deliberately registers nothing —
 # registering the tool at the host level as well would put it in every session
 # and is not what this package is for.
@@ -48,18 +48,20 @@
 # list carries no comments of its own, so none appear below; provenance and the
 # upgrade rules live in this header.
 #
-# Baseline: the `standard` preset of dsh 0.2.1-rc.3 (harness root
+# Baseline: the `standard` preset of dsh 0.2.2-rc.1 (harness root
 # `%APPDATA%\npm\node_modules\@deepseek-ai\dsh`, file
 # `node_modules/@deepseek-ai/dsh-web-app/presets/standard.patch.yml`, whose
 # rows live under the `preset-standard` row's `config.plugins:`).
 #
-# 0.2.1-rc.3 ships the SAME row list as 0.2.1-rc.2 (verified by diffing the
-# file), so no row changed in this bump. The last upstream row change was
-# 0.2.1-rc.2: it added `time-context`, `tool-schedule` and `tool-plugin-market`;
-# dropped the two disabled optional subagent providers (`tool-subagent-codex`,
-# `tool-subagent-claude-code`) and `tool-ralph`; dropped the persona `suffix` and
-# both `backgroundMode: continuable` settings; and reworded the plan-mode
-# section. Absorb such a bump verbatim — see workflow.md §4.
+# 0.2.2-rc.1 is the FIRST row change since 0.2.1-rc.2 dropped the optional
+# subagent providers and `tool-ralph`. It folded `list_agents` into
+# `@deepseek-ai/dsh-tool-subagent-control` (the `./list-agents` subpath export is
+# gone, so the `tool-subagent-list-agents` row was dropped here), renamed the
+# `tool-subagent` model-selection settings to `modelSelection` +
+# `modelDiscovery`, and made `applyPatch: false` explicit on `tool-fs`. A row
+# that names a deleted package subpath still PASSES a directory-existence check:
+# `test/preset-health.mjs` now resolves the specifier the way the Loader does.
+# Absorb such a bump verbatim — see workflow.md §4.
 #
 # Keeping the text verbatim is not cosmetic: a preset mounts DSH's OWN
 # packages, so upstream drift here kills the whole preset at mount (the failure
@@ -100,6 +102,11 @@
   disabled: !!js process.platform !== 'win32'
 - id: tool-fs
   name: '@deepseek-ai/dsh-tool-fs'
+  config:
+    # Set false to drop the apply_patch tool beside edit. (0.2.2-rc.1 makes this
+    # explicit in the shipped standard preset; the package default is false, and
+    # the row is kept verbatim so the two stay comparable.)
+    applyPatch: false
 - id: tool-fs-search
   name: '@deepseek-ai/dsh-tool-fs-search'
   config:
@@ -162,14 +169,13 @@
   config:
     - id: tool-subagent-control
       name: '@deepseek-ai/dsh-tool-subagent-control'
-    - id: tool-subagent-list-agents
-      name: '@deepseek-ai/dsh-tool-subagent-control/list-agents'
     - id: tool-subagent
       name: '@deepseek-ai/dsh-tool-subagent'
       config:
         provider: spawn
         toolName: subagent
-        modelSelectionSettings: true
+        modelSelection: true
+        modelDiscovery: true
     - id: tool-subagent-fork
       name: '@deepseek-ai/dsh-tool-subagent'
       config:
@@ -201,7 +207,7 @@
   name: '@deepseek-ai/dsh-plugin-market/tools'
   disabled: true
 
-# dsh-molbio-tools: molecular-biology toolset (60 tools across sequence
+# dsh-molbio-tools: molecular-biology toolset (64 tools across sequence
 # analysis, primers (incl. TaqMan probes and multiplex compatibility),
 # in-silico PCR, cloning (incl. Golden Gate), enzyme catalog, methylation-aware
 # and double digests, plasmids, Sanger verification, proteins (incl. helical

package/preset/molbio-lab/preset.yml

@@ -1,2 +1,2 @@
 name: Molecular Biology Lab
-description: 分子生物学专属模式：标准编码能力 + 60 个 molbio_* 工具（序列分析、引物设计（含跨内含子 qPCR、盐/浓度旋钮与目标位置偏好）、TaqMan 水解探针（含 MGB 与订购 CSV）与多重 PCR 互扰/退火温度/浓度建议、克隆模拟与选酶（含 Golden Gate）、酶目录查询、甲基化敏感位点与双酶切 buffer 兼容检查、多序列比对（每个输入残基都会进比对结果）、保守性分析与比对后处理（共识/缺口修剪/同一性矩阵/逐列覆盖度，含 sequence logo 图）、CRISPR gRNA 设计（SpCas9/SaCas9/Cas12a/Cas13，家族特定 PAM/PFS/种子）与脱靶搜索、SnapGene/GenBank 解析与质粒图谱、Sanger 测序验证、蛋白性质/密码子优化/螺旋轮投影与疏水性图、qPCR 与绘图、虚拟凝胶、实验台分析（FASTQ 质控、密码子使用、系统发生树（长叶名自动折行）、in-silico PCR、CpG/GC 组成、批量文件分析/CSV）、静默酶切位点突变设计——生成的 SVG 图片自动用系统默认应用打开，文献/协议/实验记录）。
+description: 分子生物学专属模式：标准编码能力 + 64 个 molbio_* 工具（序列分析、引物设计（含跨内含子 qPCR、盐/浓度旋钮与目标位置偏好）、TaqMan 水解探针（含 MGB 与订购 CSV）与多重 PCR 互扰/退火温度/浓度建议、克隆模拟与选酶（含 Golden Gate）、酶目录查询、甲基化敏感位点与双酶切 buffer 兼容检查、多序列比对（每个输入残基都会进比对结果）、保守性分析与比对后处理（共识/缺口修剪/同一性矩阵/逐列覆盖度，含 sequence logo 图）、CRISPR gRNA 设计（SpCas9/SaCas9/Cas12a/Cas13，家族特定 PAM/PFS/种子）与脱靶搜索、SnapGene/GenBank 解析与质粒图谱、Sanger 测序验证、蛋白性质/电荷-pH 曲线/密码子优化/螺旋轮投影与疏水性图、qPCR 与绘图、虚拟凝胶、实验台分析（FASTQ 质控、密码子使用、系统发生树（长叶名自动折行）、in-silico PCR、CpG/GC 组成、序列 dotplot、载体/接头污染筛查、FASTQ 修剪/过滤、批量文件分析/CSV）、静默酶切位点突变设计——生成的 SVG 图片自动用系统默认应用打开，文献/协议/实验记录）。

package/protein-charge.mjs

@@ -0,0 +1,158 @@
+/**
+ * dsh-molbio-tools/protein-charge.mjs
+ *
+ * Net-charge-vs-pH titration for a protein, with the pI found on the same
+ * curve. Pure calculation plus an SVG renderer: no external data, no services.
+ *
+ * The pK tables live in `protein.mjs` (PK_SETS) so `molbio_protein_props` and
+ * this tool can never disagree about the default set. `emboss` is offered as an
+ * explicitly named alternative; every result carries the set it used, because a
+ * pI is only meaningful together with its pK values.
+ */
+import { MolbioInputError } from './lib.mjs';
+import { PK_SETS, countAminoAcids, isoelectricPoint, netCharge, normalizeProtein } from './protein.mjs';
+import { axis, linearScale, niceTicks, panel, rect, series, svgDocument, textRun } from './svgio.mjs';
+
+/** Accepted ranges; the schema checks types and the module checks values. */
+export const CHARGE_LIMITS = {
+  maxLength: 20_000,
+  minPh: 0,
+  maxPh: 14,
+  minSteps: 2,
+  maxSteps: 141,
+};
+
+const round = (value, digits = 4) => Math.round(value * 10 ** digits) / 10 ** digits;
+
+/**
+ * Compute the titration curve and the pI for one protein.
+ *
+ * @param {string} raw protein sequence (one-letter codes).
+ * @param {{pkaSet?: string, phMin?: number, phMax?: number, steps?: number}} [options]
+ * @returns {{length: number, pka_set: string, pka_label: string, ph_min: number,
+ *   ph_max: number, steps: number, pI: number, charge_at_7_4: number,
+ *   charge_min: number, charge_max: number, points: Array<{ph: number, charge: number}>}}
+ */
+export function chargeCurve(raw, options = {}) {
+  const seq = normalizeProtein(raw);
+  if (seq.length > CHARGE_LIMITS.maxLength) {
+    throw new MolbioInputError('the protein is ' + seq.length + ' aa; the titration limit is ' + CHARGE_LIMITS.maxLength);
+  }
+  const pkaSet = options.pkaSet ?? 'bjellqvist';
+  const pk = PK_SETS[pkaSet];
+  if (pk === undefined) {
+    throw new MolbioInputError('unknown pka_set ' + JSON.stringify(pkaSet) + '; expected one of ' + Object.keys(PK_SETS).join(', '));
+  }
+  const phMin = options.phMin ?? 0;
+  const phMax = options.phMax ?? 14;
+  const steps = options.steps ?? 29;
+  if (!(typeof phMin === 'number' && Number.isFinite(phMin) && phMin >= CHARGE_LIMITS.minPh && phMin <= CHARGE_LIMITS.maxPh)) {
+    throw new MolbioInputError('ph_min must be a number between ' + CHARGE_LIMITS.minPh + ' and ' + CHARGE_LIMITS.maxPh);
+  }
+  if (!(typeof phMax === 'number' && Number.isFinite(phMax) && phMax >= CHARGE_LIMITS.minPh && phMax <= CHARGE_LIMITS.maxPh)) {
+    throw new MolbioInputError('ph_max must be a number between ' + CHARGE_LIMITS.minPh + ' and ' + CHARGE_LIMITS.maxPh);
+  }
+  if (!(phMax > phMin)) throw new MolbioInputError('ph_max must be greater than ph_min');
+  if (!Number.isInteger(steps) || steps < CHARGE_LIMITS.minSteps || steps > CHARGE_LIMITS.maxSteps) {
+    throw new MolbioInputError('steps must be an integer between ' + CHARGE_LIMITS.minSteps + ' and ' + CHARGE_LIMITS.maxSteps);
+  }
+  const counts = countAminoAcids(seq);
+  const points = [];
+  for (let index = 0; index < steps; index++) {
+    const ph = phMin + ((phMax - phMin) * index) / (steps - 1);
+    points.push({ ph: round(ph, 3), charge: round(netCharge(seq, counts, ph, pkaSet), 4) });
+  }
+  const charges = points.map((point) => point.charge);
+  return {
+    length: seq.length,
+    pka_set: pkaSet,
+    pka_label: pk.label,
+    ph_min: phMin,
+    ph_max: phMax,
+    steps,
+    pI: isoelectricPoint(seq, counts, pkaSet),
+    charge_at_7_4: round(netCharge(seq, counts, 7.4, pkaSet), 4),
+    charge_min: Math.min(...charges),
+    charge_max: Math.max(...charges),
+    points,
+  };
+}
+
+/**
+ * Render the titration curve as an SVG document: net charge against pH, with
+ * the zero line, the pI marker and the charged ends labelled.
+ *
+ * @param {ReturnType<typeof chargeCurve>} curve
+ * @param {{title?: string}} [options]
+ * @returns {string} SVG text.
+ */
+export function renderChargeCurve(curve, options = {}) {
+  const width = 720;
+  const height = 420;
+  const frame = panel({
+    x: 16,
+    y: 16,
+    width: width - 32,
+    height: height - 32,
+    title: options.title ?? 'Net charge vs pH',
+    subtitle: curve.length + ' aa · ' + curve.pka_label + ' pK set · pI ' + curve.pI,
+  });
+  const plot = frame.plot;
+  const yMin = Math.min(0, curve.charge_min);
+  const yMax = Math.max(0, curve.charge_max);
+  const pad = Math.max(0.5, (yMax - yMin) * 0.08);
+  const domain = [yMin - pad, yMax + pad];
+  const x = linearScale([curve.ph_min, curve.ph_max], [plot.x, plot.x + plot.width]);
+  const y = linearScale(domain, [plot.y + plot.height, plot.y]);
+  const parts = [frame.markup];
+  // Zero-charge line: the sign of the charge is the point of the plot.
+  if (domain[0] < 0 && domain[1] > 0) {
+    const zero = y.of(0);
+    parts.push('<line x1="' + plot.x + '" y1="' + zero + '" x2="' + (plot.x + plot.width) + '" y2="' + zero + '" stroke="#8c959f" stroke-width="1" stroke-dasharray="4 3"/>');
+  }
+  parts.push(axis({
+    from: plot.x,
+    to: plot.x + plot.width,
+    at: plot.y + plot.height,
+    ticks: niceTicks([curve.ph_min, curve.ph_max], 7).map((tick) => x.of(tick)),
+    orientation: 'x',
+    label: 'pH',
+    tickLabel: (pixel) => String(Math.round(x.invert(pixel) * 10) / 10),
+    title: 'pH',
+  }));
+  parts.push(axis({
+    from: plot.y,
+    to: plot.y + plot.height,
+    at: plot.x,
+    ticks: niceTicks(domain, 6).map((tick) => y.of(tick)),
+    orientation: 'y',
+    label: 'net charge',
+    tickLabel: (pixel) => String(Math.round(y.invert(pixel) * 10) / 10),
+    title: 'net charge (e)',
+  }));
+  parts.push(series({
+    values: curve.points.map((point) => point.charge),
+    xOf: (index) => x.of(curve.points[index].ph),
+    yOf: (charge) => y.of(charge),
+    stroke: '#0969da',
+    width: 2,
+  }));
+  if (curve.pI >= curve.ph_min && curve.pI <= curve.ph_max) {
+    const marker = x.of(curve.pI);
+    parts.push('<line x1="' + marker + '" y1="' + plot.y + '" x2="' + marker + '" y2="' + (plot.y + plot.height) + '" stroke="#bf3989" stroke-width="1" stroke-dasharray="2 3"/>');
+    parts.push(textRun({ x: marker + 4, y: plot.y + 12, text: 'pI ' + curve.pI, size: 9, fill: '#bf3989' }));
+  }
+  // Label the two ends of the curve with the charges they represent.
+  const first = curve.points[0];
+  const last = curve.points[curve.points.length - 1];
+  parts.push(textRun({ x: x.of(first.ph) + 4, y: y.of(first.charge) - 6, text: 'pH ' + first.ph + ': ' + first.charge, size: 9, fill: '#57606a' }));
+  parts.push(textRun({ x: x.of(last.ph) - 4, y: y.of(last.charge) + 14, text: 'pH ' + last.ph + ': ' + last.charge, size: 9, fill: '#57606a', anchor: 'end' }));
+  parts.push(rect({ x: plot.x, y: plot.y, width: plot.width, height: plot.height, fill: 'none', stroke: '#d0d7de' }));
+  return svgDocument({
+    width,
+    height,
+    title: options.title ?? 'Net charge vs pH',
+    description: 'Titration curve for a ' + curve.length + ' aa protein using the ' + curve.pka_label + ' pK set; pI ' + curve.pI + '.',
+    body: parts.join('\n'),
+  });
+}

package/protein.mjs

@@ -32,48 +32,70 @@ const RESIDUE_MASS = {
 };
 const WATER = 18.015;
 
-// Bjellqvist 1993 pK values (EMBOSS-style)
-const PK = {
-  Nterm: 8.6, Cterm: 3.6, C: 9.0, D: 4.05, E: 4.45, H: 6.04,
-  K: 10.8, R: 12.0, Y: 10.3,
+/**
+ * Selectable pK sets for the Henderson-Hasselbalch charge model. `bjellqvist`
+ * is the set `proteinProperties` has always used for its pI; `emboss` is the
+ * Epk.dat table EMBOSS ships with `iep`. They are NOT interchangeable — the
+ * reported set name travels with every charge/pI value.
+ */
+export const PK_SETS = {
+  bjellqvist: {
+    label: 'Bjellqvist 1993',
+    Nterm: 8.6, Cterm: 3.6, C: 9.0, D: 4.05, E: 4.45, H: 6.04,
+    K: 10.8, R: 12.0, Y: 10.3,
+  },
+  emboss: {
+    label: 'EMBOSS Epk.dat',
+    Nterm: 8.6, Cterm: 3.6, C: 8.5, D: 3.9, E: 4.1, H: 6.5,
+    K: 10.8, R: 12.5, Y: 10.1,
+  },
 };
 
+const PK = PK_SETS.bjellqvist;
+
 const HYDROPATHY = {
   A: 1.8, R: -4.5, N: -3.5, D: -3.5, C: 2.5, Q: -3.5, E: -3.5,
   G: -0.4, H: -3.2, I: 4.5, L: 3.8, K: -3.9, M: 1.9, F: 2.8,
   P: -1.6, S: -0.8, T: -0.7, W: -0.9, Y: -1.3, V: 4.2,
 };
 
-function countAminoAcids(seq) {
+export function countAminoAcids(seq) {
   const counts = {};
   for (const aa of seq) counts[aa] = (counts[aa] ?? 0) + 1;
   return counts;
 }
 
-function chargeAt(seq, counts, pH) {
+/**
+ * Net charge at a given pH by Henderson-Hasselbalch summation. The terminal
+ * groups count once each; K/R/H are positive, D/E/C/Y negative. `pkaSet` is a
+ * key of PK_SETS (or a set object), so callers can name the table they used.
+ */
+export function netCharge(seq, counts, pH, pkaSet = 'bjellqvist') {
+  const pk = typeof pkaSet === 'string' ? PK_SETS[pkaSet] : pkaSet;
+  if (pk === undefined) throw new MolbioInputError('unknown pK set ' + JSON.stringify(pkaSet) + '; expected one of ' + Object.keys(PK_SETS).join(', '));
   let charge = 0;
   const pos = (pKa) => 1 / (1 + Math.pow(10, pH - pKa));
   const neg = (pKa) => 1 / (1 + Math.pow(10, pKa - pH));
-  charge += pos(PK.Nterm);
-  for (const [aa, pKa] of [['K', PK.K], ['R', PK.R], ['H', PK.H]]) {
+  charge += pos(pk.Nterm);
+  for (const [aa, pKa] of [['K', pk.K], ['R', pk.R], ['H', pk.H]]) {
     if (counts[aa] !== undefined) charge += counts[aa] * pos(pKa);
   }
-  charge -= neg(PK.Cterm);
-  for (const [aa, pKa] of [['D', PK.D], ['E', PK.E], ['C', PK.C], ['Y', PK.Y]]) {
+  charge -= neg(pk.Cterm);
+  for (const [aa, pKa] of [['D', pk.D], ['E', pk.E], ['C', pk.C], ['Y', pk.Y]]) {
     if (counts[aa] !== undefined) charge -= counts[aa] * neg(pKa);
   }
   return charge;
 }
 
 /** Isoelectric point by bisection over the net-charge function. */
-export function isoelectricPoint(seq, counts) {
+export function isoelectricPoint(seq, counts, pkaSet = 'bjellqvist') {
   let lo = 0;
   let hi = 14;
-  let chargeLo = chargeAt(seq, counts, lo);
-  let chargeHi = chargeAt(seq, counts, hi);
+  let chargeLo = netCharge(seq, counts, lo, pkaSet);
+  let chargeHi = netCharge(seq, counts, hi, pkaSet);
   for (let i = 0; i < 60; i++) {
     const mid = (lo + hi) / 2;
-    const chargeMid = chargeAt(seq, counts, mid);
+    const chargeMid = netCharge(seq, counts, mid, pkaSet);
     if (Math.abs(chargeMid) < 1e-4) return Math.round(mid * 100) / 100;
     if (Math.sign(chargeMid) === Math.sign(chargeLo)) {
       lo = mid;

package/seqio.mjs

@@ -84,6 +84,16 @@ export function toFasta(entries) {
   return entries.map((entry) => `>${entry.id}${entry.description !== '' ? ' ' + entry.description : ''}\n${entry.sequence}`).join('\n') + '\n';
 }
 
+/** Render entries as four-line FASTQ text (quality is preserved verbatim). */
+export function toFastq(entries) {
+  return entries.map((entry) => {
+    if (typeof entry.quality !== 'string' || entry.quality.length !== entry.sequence.length) {
+      throw new MolbioInputError(`entry ${entry.id}: sequence and quality lengths differ`);
+    }
+    return `@${entry.id}${entry.description !== undefined && entry.description !== '' ? ' ' + entry.description : ''}\n${entry.sequence}\n+\n${entry.quality}`;
+  }).join('\n') + '\n';
+}
+
 /** Summary statistics over parsed entries. */
 export function entryStats(entries, qualityMode = false) {
   const lengths = entries.map((entry) => entry.sequence.length);

package/test/client.mjs

@@ -144,6 +144,8 @@ assert.deepEqual(effects, [
   'molbio panel: papers tab title',
   'molbio panel: molbio_plasmid_map card',
   'molbio panel: molbio_plasmid_map_file card',
+  'molbio panel: molbio_sequence_logo card',
+  'molbio panel: molbio_grna_design card',
   'molbio panel: NCBI key section gate',
   'molbio panel: NCBI key section',
 ]);
@@ -186,9 +188,9 @@ assert.deepEqual(
 assert.equal(slots.registrations.length, 4, 'both tab bodies and titles land as soon as their seat exists');
 slots.declare('tool.call.toolview');
 
-// Body + title register in the keyed seats under each type's id, and the two
-// map tools claim their own `tool.call.toolview` key (an unclaimed key falls
-// back to the generic tool row, so claiming ours is additive).
+// Body + title register in the keyed seats under each type's id; two map tools
+// and two figure tools claim their own `tool.call.toolview` keys (an unclaimed
+// key falls back to the generic tool row, so claiming ours is additive).
 assert.deepEqual(
   slots.registrations.map((entry) => [entry.registration.name, entry.registration.key]),
   [
@@ -198,6 +200,8 @@ assert.deepEqual(
     ['sidebar.right.pane.tab.title', 'dsh-molbio-tools/papers'],
     ['tool.call.toolview', 'molbio_plasmid_map'],
     ['tool.call.toolview', 'molbio_plasmid_map_file'],
+    ['tool.call.toolview', 'molbio_sequence_logo'],
+    ['tool.call.toolview', 'molbio_grna_design'],
   ],
 );
 const claim = (name, key) => slots.registrations.find(
@@ -206,6 +210,9 @@ const claim = (name, key) => slots.registrations.find(
 assert.equal(typeof claim('sidebar.right.pane.tab', 'dsh-molbio-tools').component, 'function', 'the plasmid body is a component');
 assert.equal(typeof claim('sidebar.right.pane.tab', 'dsh-molbio-tools/papers').component, 'function', 'the papers body is a component');
 assert.equal(typeof claim('tool.call.toolview', 'molbio_plasmid_map').component, 'function', 'the map card is a component');
+assert.equal(typeof claim('tool.call.toolview', 'molbio_sequence_logo').component, 'function', 'the logo card is a component');
+assert.equal(claim('tool.call.toolview', 'molbio_sequence_logo').component, claim('tool.call.toolview', 'molbio_grna_design').component, 'the two figure tools share one card component');
+assert.equal(claim('tool.call.toolview', 'molbio_grna_design').registration.inject, undefined, 'the figure card declares no injection');
 for (const key of ['dsh-molbio-tools', 'dsh-molbio-tools/papers']) {
   const face = claim('sidebar.right.pane.tab', key).registration.inject('session-1', {});
   assert.equal(typeof face.remote.workspaceFiles.list, 'function', 'the inject factory hands the body the workspace Remote');
@@ -220,13 +227,13 @@ assert.equal(claim('tool.call.toolview', 'molbio_plasmid_map').registration.inje
 // A re-declaration of the seat (the shell's declaration-epoch rule) re-runs the
 // wait: the previous entries are disposed first, so claims never accumulate.
 slots.declare('tool.call.toolview');
-assert.equal(slots.registrations.length, 6, 're-declaring the seat re-installs both cards instead of duplicating them');
+assert.equal(slots.registrations.length, 8, 're-declaring the seat re-installs all four cards instead of duplicating them');
 
 // The Plugins page's detail seat belongs to the plugin manager. The section
 // lands when that seat is declared, and the component itself decides whether
 // the open subject is this package.
 slots.declare('plugins.detail.section');
-assert.equal(slots.registrations.length, 7, 'the key section lands when the plugin manager declares its seat');
+assert.equal(slots.registrations.length, 9, 'the key section lands when the plugin manager declares its seat');
 const keyClaim = slots.registrations.find((entry) => entry.registration.name === 'plugins.detail.section');
 assert.ok(keyClaim, 'the key section is claimed in plugins.detail.section');
 assert.equal(keyClaim.registration.id, 'molbio-ncbi-key', 'the list seat is addressed by an id of our own');

package/test/contract.mjs

@@ -228,7 +228,14 @@ check('the shell derives hook props as use<Capitalised(Source)>', () => {
 check('a session-scope tab body receives sessionId + useSessions (official precedent)', () => {
   const files = clientBundle('@deepseek-ai/dsh-client-ui-sidebar-files');
   assert.ok(files !== undefined, 'ui-sidebar-files is installed');
-  assert.ok(files.text.includes('function FilesBody({ useTabInfo, sessionId'), 'the official tab body destructures sessionId from its props');
+  // 0.2.2-rc.1 renamed the tab body (`FilesBody` -> `FileNavigator`) without
+  // changing what the runtime injects into it. The CONTRACT is the props, not
+  // the function's name, so match the destructuring rather than one identifier.
+  assert.match(
+    files.text,
+    /function [A-Za-z_$][\w$]*\(\{(?=[^}]*\buseTabInfo\b)(?=[^}]*\bsessionId\b)(?=[^}]*\buseSessions\b)/,
+    'the official tab body receives useTabInfo + sessionId + useSessions from its props',
+  );
   assert.ok(files.text.includes('useSessions((sessions) => sessions.byId[sessionId]?.cwd)'), 'and reads the workspace root exactly as the panel does');
   assert.ok(files.text.includes('"slots"') && files.text.includes('"sidebarRightTabs"'), 'and injects the same registries');
 });
@@ -432,7 +439,7 @@ check('the published tarball carries the client half and exactly one plugin mani
   // SUBMISSION_PACKAGE_AMBIGUOUS, plus a duplicate 427 KB client bundle in every
   // download. The panel does not disappear for npm users: the root package's own
   // `lib/client.js` already carries it (the panel-only package exists for people
-  // who want the tab without the 60 tools).
+  // who want the tab without the 64 tools).
   assert.ok(
     !files.includes('packages'),
     'the root tarball must not embed packages/molbio-panel: a second `dsh` manifest inside one package is an ambiguous submission, and the panel is published separately',
@@ -468,8 +475,16 @@ check('the toolview card contract still holds (meta path + keyed seat)', () => {
   // path that still carries the value — consulted, snapshotted, attached as
   // `meta` — rather than a literal upstream is free to drop (the panel does not
   // depend on nested calls being excluded, only on the root call carrying it).
-  const tools = hostHalf('@deepseek-ai/dsh-tools');
-  assert.ok(tools !== undefined, 'dsh-tools is installed');
+  // The projection lives in the assembly pipeline. 0.2.2-rc.1 moved that code
+  // out of `lib/index.js` into `lib/pipeline.js` (same call, same snapshot, same
+  // attachment), so read whichever files the installed package ships instead of
+  // pinning the one upstream happened to use before.
+  const toolsDir = packageDir('@deepseek-ai/dsh-tools');
+  const toolsFiles = ['lib/index.js', 'lib/pipeline.js']
+    .map((rel) => join(toolsDir, rel))
+    .filter((path) => existsSync(path));
+  assert.ok(toolsFiles.length > 0, 'dsh-tools is installed');
+  const tools = { text: toolsFiles.map((path) => readFileSync(path, 'utf8')).join('\n') };
   assert.ok(/output\.presentationMeta\s*!==\s*void 0/.test(tools.text), 'the tool layer still consults output.presentationMeta');
   assert.ok(tools.text.includes('snapshotProjection(tool.name, "presentationMeta"'), 'and records the projection on the result');
   assert.ok(
@@ -493,16 +508,25 @@ check('the toolview card contract still holds (meta path + keyed seat)', () => {
   // key whose tool forgot `presentationMeta`.
   const source = readFileSync(join(packageRoot, 'index.mjs'), 'utf8');
   const bundle = readFileSync(join(packageRoot, 'lib', 'client.js'), 'utf8');
-  const keys = /const MAP_TOOL_KEYS = \[([^\]]*)\]/.exec(bundle);
-  assert.ok(keys !== null, 'the bundle declares the tool keys whose cards it draws');
-  const claimed = keys[1].split(',').map((entry) => entry.trim().replace(/^['"]|['"]$/g, '')).filter((entry) => entry !== '');
+  const keyList = (name) => {
+    const match = new RegExp('const ' + name + ' = \\[([^\\]]*)\\]').exec(bundle);
+    assert.ok(match !== null, 'the bundle declares ' + name + ', the tool keys whose cards it draws');
+    return match[1].split(',').map((entry) => entry.trim().replace(/^['"]|['"]$/g, '')).filter((entry) => entry !== '');
+  };
+  // Two card shapes share the seat: the plasmid-map card (MAP_TOOL_KEYS) and the
+  // figure card (FIGURE_TOOL_KEYS). Both lists are read from the bundle, so a
+  // third key whose tool forgets its projection fails here either way.
+  const claimed = [...keyList('MAP_TOOL_KEYS'), ...keyList('FIGURE_TOOL_KEYS')];
   assert.ok(claimed.length > 0, 'the bundle claims at least one card key');
   assert.equal(
-    (source.match(/presentationMeta\(_args, value\)/g) ?? []).length,
+    // Anchored: the file-header comment also mentions the signature, and a
+    // substring count would treat that prose as a fourth implementation.
+    (source.match(/^  presentationMeta\((?:args|_args), value\)/gm) ?? []).length,
     claimed.length,
     'every claimed card key belongs to a tool that declares the projection',
   );
-  assert.ok(source.includes('mapCardMeta'), 'and build it through the shared projection');
+  assert.ok(source.includes('mapCardMeta'), 'and build it through the shared map projection');
+  assert.ok(source.includes('figureCardMeta'), 'and the shared figure projection');
   for (const key of claimed) {
     // The host half registers a tool under that exact name.
     assert.ok(source.includes(`name: '${key}'`), `the host registers the tool ${key} whose card the bundle claims`);
@@ -710,8 +734,8 @@ check('a tool may show the model a picture the way read_image does', () => {
   // The count is deliberate: it is what catches a NEW picture tool that forgets
   // the hand-off (or a report tool that quietly grows it).
   const index = readFileSync(join(packageRoot, 'index.mjs'), 'utf8');
-  assert.equal((index.match(/image: ATTACHED_IMAGE_SCHEMA/g) ?? []).length, 15, 'all 15 picture tools declare the image output field');
-  assert.equal((index.match(/\.\.\.ATTACH_IMAGE_PARAM/g) ?? []).length, 15, 'and offer the opt-in attach_image parameter');
+  assert.equal((index.match(/image: ATTACHED_IMAGE_SCHEMA/g) ?? []).length, 17, 'all 17 picture tools declare the image output field');
+  assert.equal((index.match(/\.\.\.ATTACH_IMAGE_PARAM/g) ?? []).length, 17, 'and offer the opt-in attach_image parameter');
   assert.ok(/output\.render/.test(index) || index.includes('imageBlockFor(value)'), 'the block builder is wired into define()');
 });
 
@@ -724,7 +748,15 @@ check('the workspace still cannot hold a binary file (the reason the picture rid
   // the local backend (the base is consulted last, only as a presence fallback).
   const fsTypes = declarationEvidence('@deepseek-ai/dsh-fs', ['lib/types/types.d.ts', '../dsh-fs-local/lib/index.js', 'lib/index.js']).text;
   const fsReadme = readFileSync(join(packageDir('@deepseek-ai/dsh-fs'), 'README.md'), 'utf8');
-  assert.match(fsReadme, /binary-safe mutations remain deferred/i, 'and still documents binary mutations as deferred');
+  // 0.2.2-rc.1 reworded this: the old "binary-safe mutations remain deferred"
+  // note became the precise rule under "Known Limitations and Deferred Work"
+  // ("Literal edits, patches, and moves require UTF-8 text"). Accept either
+  // spelling of the SAME policy — the seam assertions below are the real gate.
+  assert.match(
+    fsReadme,
+    /binary-safe mutations remain deferred|Literal edits, patches, and moves require UTF-8 text/i,
+    'and still documents the text-only mutation rule the picture hand-off depends on',
+  );
   const fsIndex = readFileSync(join(packageDir('@deepseek-ai/dsh-fs'), 'lib', 'index.js'), 'utf8');
   assertFsSeamDeclared(fsTypes, fsIndex);
 });

package/test/drift-probe.mjs

@@ -29,7 +29,7 @@ import { existsSync } from 'node:fs';
 import { dirname, join, resolve } from 'node:path';
 import { fileURLToPath } from 'node:url';
 
-import { compositionDrift, toolCountDrift, presetPlugins, asPresetPatch, relativeSpecifiers, presetOrderDeclared, orderCollisions } from './preset-health.mjs';
+import { compositionDrift, toolCountDrift, presetPlugins, asPresetPatch, relativeSpecifiers, presetOrderDeclared, orderCollisions, specifierProblem } from './preset-health.mjs';
 // The three helpers this probe used to carry its own copies of. Duplicating
 // `findHarnessRoot` was the worst of them: the probe could resolve a DIFFERENT
 // harness than `preset-health` validated against, so a mutation experiment could
@@ -215,6 +215,20 @@ check('the specifier guard is quiet on a package name and catches a relative pat
   );
 });
 
+check('a row naming a removed package subpath is caught (the 0.2.2-rc.1 list-agents trap)', () => {
+  // 0.2.2-rc.1 folded `list_agents` into `@deepseek-ai/dsh-tool-subagent-control`
+  // and dropped its `./list-agents` export. `packageInstalled` still finds the
+  // package ROOT, so only a real specifier resolution notices — and this probe
+  // must not depend on one version's removals to prove the guard works. A
+  // subpath no release can export is the version-independent mutation.
+  const base = '@deepseek-ai/dsh-tool-subagent-control';
+  assert.equal(specifierProblem(base, harnessRoot), undefined, 'the package root resolves');
+  assert.equal(specifierProblem(`${base}/package.json`, harnessRoot), undefined, 'an exported subpath resolves');
+  const problem = specifierProblem(`${base}/no-such-subpath`, harnessRoot);
+  assert.ok(problem !== undefined, 'an unexported subpath is rejected');
+  assert.match(problem, /does not resolve/, problem);
+});
+
 check('the order guard reads the order under config, not the declaration row id', () => {
   const layer = [
     '  - id: preset-mine',