research-copilot 0.1.0

package/app/out/skills/research-pilot-default-project-skills/matplotlib/scripts/style_configurator.py

@@ -0,0 +1,409 @@
+#!/usr/bin/env python3
+"""
+Matplotlib Style Configurator
+
+Interactive utility to configure matplotlib style preferences and generate
+custom style sheets. Creates a preview of the style and optionally saves
+it as a .mplstyle file.
+
+Usage:
+    python style_configurator.py [--preset PRESET] [--output FILE] [--preview]
+
+Presets:
+    publication, presentation, web, dark, minimal
+"""
+
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib.gridspec import GridSpec
+import argparse
+import os
+
+
+# Predefined style presets
+STYLE_PRESETS = {
+    'publication': {
+        'figure.figsize': (8, 6),
+        'figure.dpi': 100,
+        'savefig.dpi': 300,
+        'savefig.bbox': 'tight',
+        'font.family': 'sans-serif',
+        'font.sans-serif': ['Arial', 'Helvetica'],
+        'font.size': 11,
+        'axes.labelsize': 12,
+        'axes.titlesize': 14,
+        'axes.linewidth': 1.5,
+        'axes.grid': False,
+        'axes.spines.top': False,
+        'axes.spines.right': False,
+        'lines.linewidth': 2,
+        'lines.markersize': 8,
+        'xtick.labelsize': 10,
+        'ytick.labelsize': 10,
+        'xtick.direction': 'in',
+        'ytick.direction': 'in',
+        'xtick.major.size': 6,
+        'ytick.major.size': 6,
+        'xtick.major.width': 1.5,
+        'ytick.major.width': 1.5,
+        'legend.fontsize': 10,
+        'legend.frameon': True,
+        'legend.framealpha': 1.0,
+        'legend.edgecolor': 'black',
+    },
+    'presentation': {
+        'figure.figsize': (12, 8),
+        'figure.dpi': 100,
+        'savefig.dpi': 150,
+        'font.size': 16,
+        'axes.labelsize': 20,
+        'axes.titlesize': 24,
+        'axes.linewidth': 2,
+        'lines.linewidth': 3,
+        'lines.markersize': 12,
+        'xtick.labelsize': 16,
+        'ytick.labelsize': 16,
+        'legend.fontsize': 16,
+        'axes.grid': True,
+        'grid.alpha': 0.3,
+    },
+    'web': {
+        'figure.figsize': (10, 6),
+        'figure.dpi': 96,
+        'savefig.dpi': 150,
+        'font.size': 11,
+        'axes.labelsize': 12,
+        'axes.titlesize': 14,
+        'lines.linewidth': 2,
+        'axes.grid': True,
+        'grid.alpha': 0.2,
+        'grid.linestyle': '--',
+    },
+    'dark': {
+        'figure.facecolor': '#1e1e1e',
+        'figure.edgecolor': '#1e1e1e',
+        'axes.facecolor': '#1e1e1e',
+        'axes.edgecolor': 'white',
+        'axes.labelcolor': 'white',
+        'text.color': 'white',
+        'xtick.color': 'white',
+        'ytick.color': 'white',
+        'grid.color': 'gray',
+        'grid.alpha': 0.3,
+        'axes.grid': True,
+        'legend.facecolor': '#1e1e1e',
+        'legend.edgecolor': 'white',
+        'savefig.facecolor': '#1e1e1e',
+    },
+    'minimal': {
+        'figure.figsize': (10, 6),
+        'axes.spines.top': False,
+        'axes.spines.right': False,
+        'axes.spines.left': False,
+        'axes.spines.bottom': False,
+        'axes.grid': False,
+        'xtick.bottom': True,
+        'ytick.left': True,
+        'axes.axisbelow': True,
+        'lines.linewidth': 2.5,
+        'font.size': 12,
+    }
+}
+
+
+def generate_preview_data():
+    """Generate sample data for style preview."""
+    np.random.seed(42)
+    x = np.linspace(0, 10, 100)
+    y1 = np.sin(x) + 0.1 * np.random.randn(100)
+    y2 = np.cos(x) + 0.1 * np.random.randn(100)
+    scatter_x = np.random.randn(100)
+    scatter_y = 2 * scatter_x + np.random.randn(100)
+    categories = ['A', 'B', 'C', 'D', 'E']
+    bar_values = [25, 40, 30, 55, 45]
+
+    return {
+        'x': x, 'y1': y1, 'y2': y2,
+        'scatter_x': scatter_x, 'scatter_y': scatter_y,
+        'categories': categories, 'bar_values': bar_values
+    }
+
+
+def create_style_preview(style_dict=None):
+    """Create a preview figure demonstrating the style."""
+    if style_dict:
+        plt.rcParams.update(style_dict)
+
+    data = generate_preview_data()
+
+    fig = plt.figure(figsize=(14, 10))
+    gs = GridSpec(2, 2, figure=fig, hspace=0.3, wspace=0.3)
+
+    # Line plot
+    ax1 = fig.add_subplot(gs[0, 0])
+    ax1.plot(data['x'], data['y1'], label='sin(x)', marker='o', markevery=10)
+    ax1.plot(data['x'], data['y2'], label='cos(x)', linestyle='--')
+    ax1.set_xlabel('X axis')
+    ax1.set_ylabel('Y axis')
+    ax1.set_title('Line Plot')
+    ax1.legend()
+    ax1.grid(True, alpha=0.3)
+
+    # Scatter plot
+    ax2 = fig.add_subplot(gs[0, 1])
+    colors = np.sqrt(data['scatter_x']**2 + data['scatter_y']**2)
+    scatter = ax2.scatter(data['scatter_x'], data['scatter_y'],
+                         c=colors, cmap='viridis', alpha=0.6, s=50)
+    ax2.set_xlabel('X axis')
+    ax2.set_ylabel('Y axis')
+    ax2.set_title('Scatter Plot')
+    cbar = plt.colorbar(scatter, ax=ax2)
+    cbar.set_label('Distance')
+    ax2.grid(True, alpha=0.3)
+
+    # Bar chart
+    ax3 = fig.add_subplot(gs[1, 0])
+    bars = ax3.bar(data['categories'], data['bar_values'],
+                   edgecolor='black', linewidth=1)
+    # Color bars with gradient
+    colors = plt.cm.viridis(np.linspace(0.2, 0.8, len(bars)))
+    for bar, color in zip(bars, colors):
+        bar.set_facecolor(color)
+    ax3.set_xlabel('Categories')
+    ax3.set_ylabel('Values')
+    ax3.set_title('Bar Chart')
+    ax3.grid(True, axis='y', alpha=0.3)
+
+    # Multiple line plot with fills
+    ax4 = fig.add_subplot(gs[1, 1])
+    ax4.plot(data['x'], data['y1'], label='Signal 1', linewidth=2)
+    ax4.fill_between(data['x'], data['y1'] - 0.2, data['y1'] + 0.2,
+                     alpha=0.3, label='±1 std')
+    ax4.plot(data['x'], data['y2'], label='Signal 2', linewidth=2)
+    ax4.fill_between(data['x'], data['y2'] - 0.2, data['y2'] + 0.2,
+                     alpha=0.3)
+    ax4.set_xlabel('X axis')
+    ax4.set_ylabel('Y axis')
+    ax4.set_title('Time Series with Uncertainty')
+    ax4.legend()
+    ax4.grid(True, alpha=0.3)
+
+    fig.suptitle('Style Preview', fontsize=16, fontweight='bold')
+
+    return fig
+
+
+def save_style_file(style_dict, filename):
+    """Save style dictionary as .mplstyle file."""
+    with open(filename, 'w') as f:
+        f.write("# Custom matplotlib style\n")
+        f.write("# Generated by style_configurator.py\n\n")
+
+        # Group settings by category
+        categories = {
+            'Figure': ['figure.'],
+            'Font': ['font.'],
+            'Axes': ['axes.'],
+            'Lines': ['lines.'],
+            'Markers': ['markers.'],
+            'Ticks': ['tick.', 'xtick.', 'ytick.'],
+            'Grid': ['grid.'],
+            'Legend': ['legend.'],
+            'Savefig': ['savefig.'],
+            'Text': ['text.'],
+        }
+
+        for category, prefixes in categories.items():
+            category_items = {k: v for k, v in style_dict.items()
+                            if any(k.startswith(p) for p in prefixes)}
+            if category_items:
+                f.write(f"# {category}\n")
+                for key, value in sorted(category_items.items()):
+                    # Format value appropriately
+                    if isinstance(value, (list, tuple)):
+                        value_str = ', '.join(str(v) for v in value)
+                    elif isinstance(value, bool):
+                        value_str = str(value)
+                    else:
+                        value_str = str(value)
+                    f.write(f"{key}: {value_str}\n")
+                f.write("\n")
+
+    print(f"Style saved to {filename}")
+
+
+def print_style_info(style_dict):
+    """Print information about the style."""
+    print("\n" + "="*60)
+    print("STYLE CONFIGURATION")
+    print("="*60)
+
+    categories = {
+        'Figure Settings': ['figure.'],
+        'Font Settings': ['font.'],
+        'Axes Settings': ['axes.'],
+        'Line Settings': ['lines.'],
+        'Grid Settings': ['grid.'],
+        'Legend Settings': ['legend.'],
+    }
+
+    for category, prefixes in categories.items():
+        category_items = {k: v for k, v in style_dict.items()
+                        if any(k.startswith(p) for p in prefixes)}
+        if category_items:
+            print(f"\n{category}:")
+            for key, value in sorted(category_items.items()):
+                print(f"  {key}: {value}")
+
+    print("\n" + "="*60 + "\n")
+
+
+def list_available_presets():
+    """Print available style presets."""
+    print("\nAvailable style presets:")
+    print("-" * 40)
+    descriptions = {
+        'publication': 'Optimized for academic publications',
+        'presentation': 'Large fonts for presentations',
+        'web': 'Optimized for web display',
+        'dark': 'Dark background theme',
+        'minimal': 'Minimal, clean style',
+    }
+    for preset, desc in descriptions.items():
+        print(f"  {preset:15s} - {desc}")
+    print("-" * 40 + "\n")
+
+
+def interactive_mode():
+    """Run interactive mode to customize style settings."""
+    print("\n" + "="*60)
+    print("MATPLOTLIB STYLE CONFIGURATOR - Interactive Mode")
+    print("="*60)
+
+    list_available_presets()
+
+    preset = input("Choose a preset to start from (or 'custom' for default): ").strip().lower()
+
+    if preset in STYLE_PRESETS:
+        style_dict = STYLE_PRESETS[preset].copy()
+        print(f"\nStarting from '{preset}' preset")
+    else:
+        style_dict = {}
+        print("\nStarting from default matplotlib style")
+
+    print("\nCommon settings you might want to customize:")
+    print("  1. Figure size")
+    print("  2. Font sizes")
+    print("  3. Line widths")
+    print("  4. Grid settings")
+    print("  5. Color scheme")
+    print("  6. Done, show preview")
+
+    while True:
+        choice = input("\nSelect option (1-6): ").strip()
+
+        if choice == '1':
+            width = input("  Figure width (inches, default 10): ").strip() or '10'
+            height = input("  Figure height (inches, default 6): ").strip() or '6'
+            style_dict['figure.figsize'] = (float(width), float(height))
+
+        elif choice == '2':
+            base = input("  Base font size (default 12): ").strip() or '12'
+            style_dict['font.size'] = float(base)
+            style_dict['axes.labelsize'] = float(base) + 2
+            style_dict['axes.titlesize'] = float(base) + 4
+
+        elif choice == '3':
+            lw = input("  Line width (default 2): ").strip() or '2'
+            style_dict['lines.linewidth'] = float(lw)
+
+        elif choice == '4':
+            grid = input("  Enable grid? (y/n): ").strip().lower()
+            style_dict['axes.grid'] = grid == 'y'
+            if style_dict['axes.grid']:
+                alpha = input("  Grid transparency (0-1, default 0.3): ").strip() or '0.3'
+                style_dict['grid.alpha'] = float(alpha)
+
+        elif choice == '5':
+            print("  Theme options: 1=Light, 2=Dark")
+            theme = input("  Select theme (1-2): ").strip()
+            if theme == '2':
+                style_dict.update(STYLE_PRESETS['dark'])
+
+        elif choice == '6':
+            break
+
+    return style_dict
+
+
+def main():
+    """Main function."""
+    parser = argparse.ArgumentParser(
+        description='Matplotlib style configurator',
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Examples:
+  # Show available presets
+  python style_configurator.py --list
+
+  # Preview a preset
+  python style_configurator.py --preset publication --preview
+
+  # Save a preset as .mplstyle file
+  python style_configurator.py --preset publication --output my_style.mplstyle
+
+  # Interactive mode
+  python style_configurator.py --interactive
+        """
+    )
+    parser.add_argument('--preset', type=str, choices=list(STYLE_PRESETS.keys()),
+                       help='Use a predefined style preset')
+    parser.add_argument('--output', type=str,
+                       help='Save style to .mplstyle file')
+    parser.add_argument('--preview', action='store_true',
+                       help='Show style preview')
+    parser.add_argument('--list', action='store_true',
+                       help='List available presets')
+    parser.add_argument('--interactive', action='store_true',
+                       help='Run in interactive mode')
+
+    args = parser.parse_args()
+
+    if args.list:
+        list_available_presets()
+        # Also show currently available matplotlib styles
+        print("\nBuilt-in matplotlib styles:")
+        print("-" * 40)
+        for style in sorted(plt.style.available):
+            print(f"  {style}")
+        return
+
+    if args.interactive:
+        style_dict = interactive_mode()
+    elif args.preset:
+        style_dict = STYLE_PRESETS[args.preset].copy()
+        print(f"Using '{args.preset}' preset")
+    else:
+        print("No preset or interactive mode specified. Showing default preview.")
+        style_dict = {}
+
+    if style_dict:
+        print_style_info(style_dict)
+
+    if args.output:
+        save_style_file(style_dict, args.output)
+
+    if args.preview or args.interactive:
+        print("Creating style preview...")
+        fig = create_style_preview(style_dict if style_dict else None)
+
+        if args.output:
+            preview_filename = args.output.replace('.mplstyle', '_preview.png')
+            plt.savefig(preview_filename, dpi=150, bbox_inches='tight')
+            print(f"Preview saved to {preview_filename}")
+
+        plt.show()
+
+
+if __name__ == "__main__":
+    main()

package/app/out/skills/research-pilot-default-project-skills/research-grants/SKILL.md

@@ -0,0 +1,38 @@
+---
+name: research-grants
+description: Plan and draft grant proposals with agency-aware structure, compliance checks, and reviewer-oriented framing.
+allowed-tools:
+  - skill-script-run
+id: research-grants
+shortDescription: Grant proposal workflow for scope design, compliance checks, and draft assembly
+loadingStrategy: lazy
+tools:
+  - skill-script-run
+tags:
+  - community
+  - grants
+  - proposal
+meta:
+  approvedByUser: true
+  upstream:
+    repo: https://github.com/K-Dense-AI/claude-scientific-writer
+    path: skills/research-grants
+---
+
+# Summary
+Use this skill to build fundable grant drafts that are specific, compliant, and reviewer-readable.
+
+## Procedures
+1. Initialize a proposal folder with standard sections for the target agency.
+2. Draft problem statement, aims, methods, milestones, risk mitigation, and evaluation.
+3. Run compliance checks (word/page budgets, required sections, format constraints).
+4. Produce a reviewer-oriented summary that maps each requirement to evidence in the draft.
+
+## Scripts
+- `init-grant-structure`: Scaffold proposal markdown files by agency.
+- `check-grant-compliance`: Quick section/length checks.
+- `grant-summary-card`: Build a one-page review summary from draft files.
+
+## Notes
+- Keep claims measurable and verifiable.
+- Tie deliverables to timeline and budget assumptions.

package/app/out/skills/research-pilot-default-project-skills/research-grants/scripts/check-grant-compliance.sh

@@ -0,0 +1,40 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [ "$#" -lt 1 ]; then
+  echo "Usage: check-grant-compliance.sh <proposal-dir>" >&2
+  exit 1
+fi
+
+PROPOSAL_DIR="$1"
+REQUIRED_FILES=(
+  "00-overview.md"
+  "01-specific-aims.md"
+  "02-methods.md"
+  "03-risks-mitigation.md"
+  "04-timeline-budget.md"
+)
+
+missing=0
+for file in "${REQUIRED_FILES[@]}"; do
+  if [ ! -f "$PROPOSAL_DIR/$file" ]; then
+    echo "missing: $file"
+    missing=$((missing + 1))
+  fi
+done
+
+total_words=0
+for file in "$PROPOSAL_DIR"/*.md; do
+  [ -f "$file" ] || continue
+  words="$(wc -w < "$file" | awk '{print $1}')"
+  total_words=$((total_words + words))
+  echo "$(basename "$file"): ${words} words"
+done
+
+echo "total_words: $total_words"
+if [ "$missing" -gt 0 ]; then
+  echo "compliance check failed: missing ${missing} required files" >&2
+  exit 2
+fi
+
+echo "compliance check passed"

package/app/out/skills/research-pilot-default-project-skills/research-grants/scripts/grant-summary-card.sh

@@ -0,0 +1,32 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [ "$#" -lt 2 ]; then
+  echo "Usage: grant-summary-card.sh <proposal-dir> <output-file>" >&2
+  exit 1
+fi
+
+PROPOSAL_DIR="$1"
+OUTPUT_FILE="$2"
+
+{
+  echo "# Grant Summary Card"
+  echo
+  echo "Generated: $(date -u '+%Y-%m-%dT%H:%M:%SZ')"
+  echo
+  for file in \
+    "00-overview.md" \
+    "01-specific-aims.md" \
+    "02-methods.md" \
+    "03-risks-mitigation.md" \
+    "04-timeline-budget.md"; do
+    target="$PROPOSAL_DIR/$file"
+    if [ -f "$target" ]; then
+      echo "## ${file}"
+      sed -n '1,40p' "$target"
+      echo
+    fi
+  done
+} > "$OUTPUT_FILE"
+
+echo "summary card written to $OUTPUT_FILE"

package/app/out/skills/research-pilot-default-project-skills/research-grants/scripts/init-grant-structure.sh

@@ -0,0 +1,70 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [ "$#" -lt 1 ]; then
+  echo "Usage: init-grant-structure.sh <target-dir> [agency]" >&2
+  exit 1
+fi
+
+TARGET_DIR="$1"
+AGENCY="${2:-generic}"
+
+mkdir -p "$TARGET_DIR"
+
+cat > "$TARGET_DIR/00-overview.md" <<EOF
+# Proposal Overview
+
+Agency: ${AGENCY}
+
+## Problem
+
+## Why now
+
+## Expected impact
+EOF
+
+cat > "$TARGET_DIR/01-specific-aims.md" <<'EOF'
+# Specific Aims
+
+## Aim 1
+- Hypothesis:
+- Method:
+- Milestone:
+
+## Aim 2
+- Hypothesis:
+- Method:
+- Milestone:
+EOF
+
+cat > "$TARGET_DIR/02-methods.md" <<'EOF'
+# Methods and Technical Plan
+
+## Study design
+
+## Data and infrastructure
+
+## Validation and evaluation
+EOF
+
+cat > "$TARGET_DIR/03-risks-mitigation.md" <<'EOF'
+# Risks and Mitigation
+
+## Technical risks
+
+## Programmatic risks
+
+## Fallback plans
+EOF
+
+cat > "$TARGET_DIR/04-timeline-budget.md" <<'EOF'
+# Timeline and Budget Rationale
+
+## Timeline (quarterly milestones)
+
+## Budget categories
+
+## Budget justification
+EOF
+
+echo "grant structure initialized in $TARGET_DIR"

package/app/package.json

@@ -0,0 +1,77 @@
+{
+  "name": "@research-copilot/app",
+  "version": "0.1.0",
+  "private": true,
+  "description": "AI-powered research assistant desktop application",
+  "main": "./out/main/index.mjs",
+  "scripts": {
+    "dev": "electron-vite dev",
+    "build": "electron-vite build",
+    "preview": "electron-vite preview",
+    "icon:generate": "python3 scripts/generate-app-icon.py",
+    "pack": "electron-vite build && electron-builder --mac"
+  },
+  "author": "Research Copilot",
+  "build": {
+    "appId": "com.research-copilot.app",
+    "productName": "Research Copilot",
+    "electronVersion": "33.4.11",
+    "mac": {
+      "target": "dmg",
+      "category": "public.app-category.productivity",
+      "identity": null
+    },
+    "directories": {
+      "output": "release"
+    },
+    "files": [
+      "out/**/*",
+      "node_modules/**/*"
+    ],
+    "extraResources": [
+      {
+        "from": "../lib/skills/builtin",
+        "to": "skills/builtin",
+        "filter": ["**/*"]
+      },
+      {
+        "from": "../lib/skills/data-analysis",
+        "to": "skills/data-analysis",
+        "filter": ["**/*"]
+      }
+    ]
+  },
+  "dependencies": {
+    "@mariozechner/pi-agent-core": "^0.61.1",
+    "@mariozechner/pi-ai": "^0.61.1",
+    "@mariozechner/pi-coding-agent": "^0.61.1",
+    "@milkdown/plugin-diagram": "^7.7.0",
+    "@milkdown/react": "^7.18.0",
+    "@sinclair/typebox": "^0.34.48",
+    "@xterm/addon-fit": "^0.11.0",
+    "@xterm/addon-web-links": "^0.12.0",
+    "@xterm/xterm": "^6.0.0",
+    "adm-zip": "^0.5.16",
+    "katex": "^0.16.28",
+    "lucide-react": "^0.469.0",
+    "mermaid": "^11.12.2",
+    "node-pty": "^1.1.0",
+    "react": "^19.0.0",
+    "react-dom": "^19.0.0",
+    "react-markdown": "^9.0.3",
+    "remark-gfm": "^4.0.0",
+    "zustand": "^5.0.3"
+  },
+  "devDependencies": {
+    "@electron-toolkit/utils": "^4.0.0",
+    "@tailwindcss/vite": "^4.0.0",
+    "@types/adm-zip": "^0.5.8",
+    "@types/react": "^19.0.0",
+    "@types/react-dom": "^19.0.0",
+    "electron": "^33.3.1",
+    "electron-builder": "^26.8.1",
+    "electron-vite": "^5.0.0",
+    "tailwindcss": "^4.0.0",
+    "typescript": "^5.7.0"
+  }
+}