gyoshu 0.1.0 → 0.2.1

package/README.md

@@ -46,28 +46,30 @@ Think of it like a research lab:
 
 ## 🚀 One-Click Installation
 
-### Option 1: curl (Recommended)
+### Option 1: bunx (Recommended)
+
+```bash
+bunx gyoshu install
+```
+
+### Option 2: curl
 
 ```bash
 curl -fsSL https://raw.githubusercontent.com/Yeachan-Heo/My-Jogyo/refs/heads/main/install.sh | bash
 ```
 
-### Option 2: Clone & Install
+### Option 3: Clone & Install
 
 ```bash
 git clone https://github.com/Yeachan-Heo/My-Jogyo.git
 cd My-Jogyo && ./install.sh
 ```
 
-### Option 3: Manual Installation
+### Option 4: npm global install
 
 ```bash
-# Clone the repo
-git clone https://github.com/Yeachan-Heo/My-Jogyo.git
-
-# Copy to global config
-mkdir -p ~/.config/opencode/
-cp -r My-Jogyo/src/* ~/.config/opencode/
+npm install -g gyoshu
+gyoshu install
 ```
 
 ---

package/bin/gyoshu.js

@@ -168,11 +168,11 @@ function uninstall() {
     'command/gyoshu.md', 'command/gyoshu-auto.md',
     'tool/gyoshu-completion.ts', 'tool/gyoshu-snapshot.ts', 'tool/python-repl.ts',
     'tool/notebook-writer.ts', 'tool/notebook-search.ts', 'tool/research-manager.ts',
-    'tool/session-manager.ts', 'tool/migration-tool.ts', 'tool/literature-search.ts',
+    'tool/session-manager.ts', 'tool/migration-tool.ts',
     'tool/retrospective-store.ts', 'tool/checkpoint-manager.ts',
     'bridge',
     'skill/ml-rigor', 'skill/scientific-method', 'skill/experiment-design', 'skill/data-analysis',
-    'lib/quality-gates.ts', 'lib/marker-parser.ts', 'lib/literature-client.ts',
+    'lib/quality-gates.ts', 'lib/marker-parser.ts',
     'lib/notebook-frontmatter.ts', 'lib/report-markdown.ts', 'lib/pdf-export.ts',
     'lib/paths.ts', 'lib/atomic-write.ts', 'lib/cell-identity.ts',
     'lib/checkpoint-schema.ts', 'lib/environment-capture.ts', 'lib/session-lock.ts',

package/install.sh

@@ -140,7 +140,7 @@ uninstall() {
     echo -e "🗑️  ${CYAN}Uninstalling Gyoshu...${NC}"
     
     # Gyoshu-specific directories/files
-    local gyoshu_items="agent/gyoshu.md agent/jogyo.md agent/baksa.md agent/jogyo-paper-writer.md agent/jogyo-feedback.md agent/jogyo-insight.md command/gyoshu.md command/gyoshu-auto.md tool/gyoshu-completion.ts tool/gyoshu-snapshot.ts tool/python-repl.ts tool/notebook-writer.ts tool/notebook-search.ts tool/research-manager.ts tool/session-manager.ts tool/migration-tool.ts tool/literature-search.ts tool/retrospective-store.ts tool/checkpoint-manager.ts bridge skill/ml-rigor skill/scientific-method skill/experiment-design skill/data-analysis lib/quality-gates.ts lib/marker-parser.ts lib/literature-client.ts lib/notebook-frontmatter.ts lib/report-markdown.ts lib/pdf-export.ts lib/paths.ts lib/atomic-write.ts lib/cell-identity.ts lib/checkpoint-schema.ts lib/environment-capture.ts lib/session-lock.ts lib/readme-index.ts lib/filesystem-check.ts lib/artifact-security.ts plugin/gyoshu-hooks.ts"
+    local gyoshu_items="agent/gyoshu.md agent/jogyo.md agent/baksa.md agent/jogyo-paper-writer.md agent/jogyo-feedback.md agent/jogyo-insight.md command/gyoshu.md command/gyoshu-auto.md tool/gyoshu-completion.ts tool/gyoshu-snapshot.ts tool/python-repl.ts tool/notebook-writer.ts tool/notebook-search.ts tool/research-manager.ts tool/session-manager.ts tool/migration-tool.ts tool/retrospective-store.ts tool/checkpoint-manager.ts bridge skill/ml-rigor skill/scientific-method skill/experiment-design skill/data-analysis lib/quality-gates.ts lib/marker-parser.ts lib/notebook-frontmatter.ts lib/report-markdown.ts lib/pdf-export.ts lib/paths.ts lib/atomic-write.ts lib/cell-identity.ts lib/checkpoint-schema.ts lib/environment-capture.ts lib/session-lock.ts lib/readme-index.ts lib/filesystem-check.ts lib/artifact-security.ts plugin/gyoshu-hooks.ts"
     
     for item in $gyoshu_items; do
         if [ -e "$OPENCODE_CONFIG/$item" ] || [ -L "$OPENCODE_CONFIG/$item" ]; then

package/package.json

@@ -1,10 +1,10 @@
 {
   "name": "gyoshu",
-  "version": "0.1.0",
+  "version": "0.2.1",
   "description": "Scientific research agent extension for OpenCode - turns research goals into reproducible Jupyter notebooks",
   "type": "module",
   "bin": {
-    "gyoshu": "./bin/gyoshu.js"
+    "gyoshu": "bin/gyoshu.js"
   },
   "files": [
     "bin/",

package/src/lib/report-markdown.ts

@@ -24,12 +24,19 @@ import { parseMarkers, ParsedMarker, getMarkersByType } from "./marker-parser";
 import { Notebook, NotebookCell } from "./cell-identity";
 import { extractFrontmatter, GyoshuFrontmatter } from "./notebook-frontmatter";
 import { getNotebookPath, getReportDir, getReportReadmePath, getReportsRootDir } from "./paths";
-import { 
-  Citation, 
-  getCitationByDOI, 
-  getArxivPaper, 
-  formatCitationAPA 
-} from "./literature-client";
+// Literature client deprecated - citations now use fallback identifiers only
+// TODO: Re-enable when a reliable citation API is available
+
+/**
+ * Minimal citation interface for fallback mode.
+ */
+interface Citation {
+  doi?: string;
+  arxivId?: string;
+  title?: string;
+  authors?: string[];
+  year?: number;
+}
 
 // =============================================================================
 // FINDING VERIFICATION - Separate verified vs unverified findings
@@ -218,64 +225,15 @@ export function collectCitationIdentifiers(markers: ParsedMarker[]): string[] {
   return identifiers;
 }
 
-/**
- * Resolve citation identifiers to full citation metadata.
- *
- * Uses getCitationByDOI for DOIs and getArxivPaper for arXiv IDs.
- * Failed resolutions return null citation with a fallback formatted string.
- *
- * @param identifiers - Array of citation identifiers (DOIs or arXiv IDs)
- * @returns Array of resolved citations with formatted strings
- */
 export async function resolveCitations(identifiers: string[]): Promise<ResolvedCitation[]> {
-  const results: ResolvedCitation[] = [];
-
-  for (let i = 0; i < identifiers.length; i++) {
-    const identifier = identifiers[i];
-    const number = i + 1;
-
-    try {
-      let citation: Citation | null = null;
-
-      if (isArxivId(identifier)) {
-        citation = await getArxivPaper(identifier);
-      } else {
-        // Assume it's a DOI
-        citation = await getCitationByDOI(identifier);
-      }
-
-      if (citation) {
-        results.push({
-          identifier,
-          number,
-          citation,
-          formatted: formatCitationAPA(citation),
-        });
-      } else {
-        // Resolution failed - provide fallback
-        results.push({
-          identifier,
-          number,
-          citation: null,
-          formatted: isArxivId(identifier)
-            ? `arXiv:${identifier}`
-            : `https://doi.org/${identifier}`,
-        });
-      }
-    } catch (error) {
-      // API error - provide fallback
-      results.push({
-        identifier,
-        number,
-        citation: null,
-        formatted: isArxivId(identifier)
-          ? `arXiv:${identifier}`
-          : `https://doi.org/${identifier}`,
-      });
-    }
-  }
-
-  return results;
+  return identifiers.map((identifier, i) => ({
+    identifier,
+    number: i + 1,
+    citation: null,
+    formatted: isArxivId(identifier)
+      ? `arXiv:${identifier}`
+      : `https://doi.org/${identifier}`,
+  }));
 }
 
 export interface ArtifactEntry {