research-copilot 0.1.0

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

@@ -0,0 +1,39 @@
+---
+name: citation-management
+description: Manage references, fetch BibTeX by DOI, validate bibliography quality, and keep citation keys consistent.
+allowed-tools:
+  - skill-script-run
+id: citation-management
+shortDescription: Citation workflow for DOI->BibTeX, key normalization, and bibliography validation
+loadingStrategy: lazy
+tools:
+  - skill-script-run
+tags:
+  - community
+  - citations
+  - bibtex
+meta:
+  approvedByUser: true
+  upstream:
+    repo: https://github.com/K-Dense-AI/claude-scientific-writer
+    path: skills/citation-management
+---
+
+# Summary
+Use this skill to keep references reproducible and clean. It standardizes DOI lookup, BibTeX storage, and quality checks before manuscript delivery.
+
+## Procedures
+1. Fetch missing BibTeX entries from DOI.
+2. Normalize citation keys and deduplicate near-identical entries.
+3. Validate the `.bib` file for missing required fields.
+4. Run consistency checks before final writing/export.
+
+## Scripts
+- `setup-citation-tools`: Install optional helper dependencies.
+- `doi-to-bibtex`: Resolve DOI to BibTeX and append/save.
+- `validate-bib`: Quick structural quality checks for `.bib`.
+- `normalize-bibtex-keys`: Rewrite keys to deterministic lowercase format.
+
+## Notes
+- Prefer DOI as canonical ID when available.
+- Keep one canonical `.bib` file per project to avoid drift.

package/app/out/skills/research-pilot-default-project-skills/citation-management/scripts/doi-to-bibtex.sh

@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [ "$#" -lt 1 ]; then
+  echo "Usage: doi-to-bibtex.sh <doi> [output-bib]" >&2
+  exit 1
+fi
+
+DOI="$1"
+OUT_FILE="${2:-}"
+
+ENTRY="$(curl -fsSL -H 'Accept: application/x-bibtex; charset=utf-8' "https://doi.org/${DOI}")"
+
+if [ -z "$ENTRY" ]; then
+  echo "No BibTeX returned for DOI: $DOI" >&2
+  exit 1
+fi
+
+if [ -n "$OUT_FILE" ]; then
+  mkdir -p "$(dirname "$OUT_FILE")"
+  printf "%s\n\n" "$ENTRY" >> "$OUT_FILE"
+  echo "appended BibTeX to $OUT_FILE"
+else
+  printf "%s\n" "$ENTRY"
+fi

package/app/out/skills/research-pilot-default-project-skills/citation-management/scripts/normalize-bibtex-keys.sh

@@ -0,0 +1,51 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [ "$#" -lt 1 ]; then
+  echo "Usage: normalize-bibtex-keys.sh <file.bib>" >&2
+  exit 1
+fi
+
+BIB_FILE="$1"
+TMP_FILE="${BIB_FILE}.tmp"
+
+if [ ! -f "$BIB_FILE" ]; then
+  echo "BibTeX file not found: $BIB_FILE" >&2
+  exit 1
+fi
+
+python3 - "$BIB_FILE" "$TMP_FILE" <<'PY'
+import re
+import sys
+
+src = sys.argv[1]
+dst = sys.argv[2]
+counter = 0
+
+entry_re = re.compile(r'^@([A-Za-z]+)\{([^,]+),')
+
+with open(src, "r", encoding="utf-8") as f:
+    lines = f.readlines()
+
+normalized = []
+for line in lines:
+    m = entry_re.match(line)
+    if not m:
+        normalized.append(line)
+        continue
+
+    entry_type, raw_key = m.group(1), m.group(2)
+    key = raw_key.lower()
+    key = re.sub(r'[^a-z0-9:_-]+', '-', key).strip('-')
+    if not key:
+        counter += 1
+        key = f"entry-{counter:04d}"
+
+    normalized.append(entry_re.sub(f"@{entry_type}" + "{" + key + ",", line, count=1))
+
+with open(dst, "w", encoding="utf-8") as f:
+    f.writelines(normalized)
+PY
+
+mv "$TMP_FILE" "$BIB_FILE"
+echo "normalized keys in $BIB_FILE"

package/app/out/skills/research-pilot-default-project-skills/citation-management/scripts/setup-citation-tools.sh

@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if command -v uv >/dev/null 2>&1; then
+  uv pip install "bibtexparser>=1.4.0"
+else
+  python3 -m pip install --user "bibtexparser>=1.4.0"
+fi
+
+echo "citation tools setup complete"

package/app/out/skills/research-pilot-default-project-skills/citation-management/scripts/validate-bib.sh

@@ -0,0 +1,31 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [ "$#" -lt 1 ]; then
+  echo "Usage: validate-bib.sh <file.bib>" >&2
+  exit 1
+fi
+
+BIB_FILE="$1"
+
+if [ ! -f "$BIB_FILE" ]; then
+  echo "BibTeX file not found: $BIB_FILE" >&2
+  exit 1
+fi
+
+ENTRY_COUNT="$(grep -cE '^@[A-Za-z]+' "$BIB_FILE" || true)"
+YEAR_FIELDS="$(grep -cE '^\s*year\s*=' "$BIB_FILE" || true)"
+TITLE_FIELDS="$(grep -cE '^\s*title\s*=' "$BIB_FILE" || true)"
+AUTHOR_FIELDS="$(grep -cE '^\s*author\s*=' "$BIB_FILE" || true)"
+
+echo "entries: $ENTRY_COUNT"
+echo "title fields: $TITLE_FIELDS"
+echo "author fields: $AUTHOR_FIELDS"
+echo "year fields: $YEAR_FIELDS"
+
+if [ "$ENTRY_COUNT" -eq 0 ]; then
+  echo "warning: no BibTeX entries found" >&2
+  exit 2
+fi
+
+echo "basic validation complete"

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

@@ -0,0 +1,34 @@
+---
+name: matplotlib
+description: Reusable plotting templates and style presets for scientific figures.
+allowed-tools:
+  - skill-script-run
+id: matplotlib
+shortDescription: Plot template + style presets for consistent matplotlib figures
+loadingStrategy: on-demand
+tools:
+  - skill-script-run
+tags:
+  - data
+  - visualization
+  - matplotlib
+  - plotting
+meta:
+  approvedByUser: true
+---
+
+# Summary
+Use this skill when you need fast, consistent matplotlib scaffolding (plot examples and style presets) before or alongside `data-analyze`.
+
+## Procedures
+1. For quick plot structure examples, run `plot_template`.
+2. For style presets (`publication`, `presentation`, `web`, `dark`, `minimal`), run `style_configurator`.
+3. Use generated examples/styles as references, then produce dataset-specific outputs with `data-analyze`.
+
+## Scripts
+- `plot_template`: Demonstrates common plot types and layout patterns.
+- `style_configurator`: Generates and previews matplotlib style presets.
+
+## Notes
+- Keep project outputs in `.research-pilot/outputs/*`.
+- Prefer `data-analyze` for final dataset-driven figures; use this skill to accelerate setup and styling decisions.

package/app/out/skills/research-pilot-default-project-skills/matplotlib/references/api_reference.md

@@ -0,0 +1,412 @@
+# Matplotlib API Reference
+
+This document provides a quick reference for the most commonly used matplotlib classes and methods.
+
+## Core Classes
+
+### Figure
+
+The top-level container for all plot elements.
+
+**Creation:**
+```python
+fig = plt.figure(figsize=(10, 6), dpi=100, facecolor='white')
+fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(10, 6))
+fig, axes = plt.subplots(2, 2, figsize=(12, 10))
+```
+
+**Key Methods:**
+- `fig.add_subplot(nrows, ncols, index)` - Add a subplot
+- `fig.add_axes([left, bottom, width, height])` - Add axes at specific position
+- `fig.savefig(filename, dpi=300, bbox_inches='tight')` - Save figure
+- `fig.tight_layout()` - Adjust spacing to prevent overlaps
+- `fig.suptitle(title)` - Set figure title
+- `fig.legend()` - Create figure-level legend
+- `fig.colorbar(mappable)` - Add colorbar to figure
+- `plt.close(fig)` - Close figure to free memory
+
+**Key Attributes:**
+- `fig.axes` - List of all axes in the figure
+- `fig.dpi` - Resolution in dots per inch
+- `fig.figsize` - Figure dimensions in inches (width, height)
+
+### Axes
+
+The actual plotting area where data is visualized.
+
+**Creation:**
+```python
+fig, ax = plt.subplots()  # Single axes
+ax = fig.add_subplot(111)  # Alternative method
+```
+
+**Plotting Methods:**
+
+**Line plots:**
+- `ax.plot(x, y, **kwargs)` - Line plot
+- `ax.step(x, y, where='pre'/'mid'/'post')` - Step plot
+- `ax.errorbar(x, y, yerr, xerr)` - Error bars
+
+**Scatter plots:**
+- `ax.scatter(x, y, s=size, c=color, marker='o', alpha=0.5)` - Scatter plot
+
+**Bar charts:**
+- `ax.bar(x, height, width=0.8, align='center')` - Vertical bar chart
+- `ax.barh(y, width)` - Horizontal bar chart
+
+**Statistical plots:**
+- `ax.hist(data, bins=10, density=False)` - Histogram
+- `ax.boxplot(data, labels=None)` - Box plot
+- `ax.violinplot(data)` - Violin plot
+
+**2D plots:**
+- `ax.imshow(array, cmap='viridis', aspect='auto')` - Display image/matrix
+- `ax.contour(X, Y, Z, levels=10)` - Contour lines
+- `ax.contourf(X, Y, Z, levels=10)` - Filled contours
+- `ax.pcolormesh(X, Y, Z)` - Pseudocolor plot
+
+**Filling:**
+- `ax.fill_between(x, y1, y2, alpha=0.3)` - Fill between curves
+- `ax.fill_betweenx(y, x1, x2)` - Fill between vertical curves
+
+**Text and annotations:**
+- `ax.text(x, y, text, fontsize=12)` - Add text
+- `ax.annotate(text, xy=(x, y), xytext=(x2, y2), arrowprops={})` - Annotate with arrow
+
+**Customization Methods:**
+
+**Labels and titles:**
+- `ax.set_xlabel(label, fontsize=12)` - Set x-axis label
+- `ax.set_ylabel(label, fontsize=12)` - Set y-axis label
+- `ax.set_title(title, fontsize=14)` - Set axes title
+
+**Limits and scales:**
+- `ax.set_xlim(left, right)` - Set x-axis limits
+- `ax.set_ylim(bottom, top)` - Set y-axis limits
+- `ax.set_xscale('linear'/'log'/'symlog')` - Set x-axis scale
+- `ax.set_yscale('linear'/'log'/'symlog')` - Set y-axis scale
+
+**Ticks:**
+- `ax.set_xticks(positions)` - Set x-tick positions
+- `ax.set_xticklabels(labels)` - Set x-tick labels
+- `ax.tick_params(axis='both', labelsize=10)` - Customize tick appearance
+
+**Grid and spines:**
+- `ax.grid(True, alpha=0.3, linestyle='--')` - Add grid
+- `ax.spines['top'].set_visible(False)` - Hide top spine
+- `ax.spines['right'].set_visible(False)` - Hide right spine
+
+**Legend:**
+- `ax.legend(loc='best', fontsize=10, frameon=True)` - Add legend
+- `ax.legend(handles, labels)` - Custom legend
+
+**Aspect and layout:**
+- `ax.set_aspect('equal'/'auto'/ratio)` - Set aspect ratio
+- `ax.invert_xaxis()` - Invert x-axis
+- `ax.invert_yaxis()` - Invert y-axis
+
+### pyplot Module
+
+High-level interface for quick plotting.
+
+**Figure creation:**
+- `plt.figure()` - Create new figure
+- `plt.subplots()` - Create figure and axes
+- `plt.subplot()` - Add subplot to current figure
+
+**Plotting (uses current axes):**
+- `plt.plot()` - Line plot
+- `plt.scatter()` - Scatter plot
+- `plt.bar()` - Bar chart
+- `plt.hist()` - Histogram
+- (All axes methods available)
+
+**Display and save:**
+- `plt.show()` - Display figure
+- `plt.savefig()` - Save figure
+- `plt.close()` - Close figure
+
+**Style:**
+- `plt.style.use(style_name)` - Apply style sheet
+- `plt.style.available` - List available styles
+
+**State management:**
+- `plt.gca()` - Get current axes
+- `plt.gcf()` - Get current figure
+- `plt.sca(ax)` - Set current axes
+- `plt.clf()` - Clear current figure
+- `plt.cla()` - Clear current axes
+
+## Line and Marker Styles
+
+### Line Styles
+- `'-'` or `'solid'` - Solid line
+- `'--'` or `'dashed'` - Dashed line
+- `'-.'` or `'dashdot'` - Dash-dot line
+- `':'` or `'dotted'` - Dotted line
+- `''` or `' '` or `'None'` - No line
+
+### Marker Styles
+- `'.'` - Point marker
+- `'o'` - Circle marker
+- `'v'`, `'^'`, `'<'`, `'>'` - Triangle markers
+- `'s'` - Square marker
+- `'p'` - Pentagon marker
+- `'*'` - Star marker
+- `'h'`, `'H'` - Hexagon markers
+- `'+'` - Plus marker
+- `'x'` - X marker
+- `'D'`, `'d'` - Diamond markers
+
+### Color Specifications
+
+**Single character shortcuts:**
+- `'b'` - Blue
+- `'g'` - Green
+- `'r'` - Red
+- `'c'` - Cyan
+- `'m'` - Magenta
+- `'y'` - Yellow
+- `'k'` - Black
+- `'w'` - White
+
+**Named colors:**
+- `'steelblue'`, `'coral'`, `'teal'`, etc.
+- See full list: https://matplotlib.org/stable/gallery/color/named_colors.html
+
+**Other formats:**
+- Hex: `'#FF5733'`
+- RGB tuple: `(0.1, 0.2, 0.3)`
+- RGBA tuple: `(0.1, 0.2, 0.3, 0.5)`
+
+## Common Parameters
+
+### Plot Function Parameters
+
+```python
+ax.plot(x, y,
+    color='blue',           # Line color
+    linewidth=2,            # Line width
+    linestyle='--',         # Line style
+    marker='o',             # Marker style
+    markersize=8,           # Marker size
+    markerfacecolor='red',  # Marker fill color
+    markeredgecolor='black',# Marker edge color
+    markeredgewidth=1,      # Marker edge width
+    alpha=0.7,              # Transparency (0-1)
+    label='data',           # Legend label
+    zorder=2,               # Drawing order
+    rasterized=True         # Rasterize for smaller file size
+)
+```
+
+### Scatter Function Parameters
+
+```python
+ax.scatter(x, y,
+    s=50,                   # Size (scalar or array)
+    c='blue',               # Color (scalar, array, or sequence)
+    marker='o',             # Marker style
+    cmap='viridis',         # Colormap (if c is numeric)
+    alpha=0.5,              # Transparency
+    edgecolors='black',     # Edge color
+    linewidths=1,           # Edge width
+    vmin=0, vmax=1,         # Color scale limits
+    label='data'            # Legend label
+)
+```
+
+### Text Parameters
+
+```python
+ax.text(x, y, text,
+    fontsize=12,            # Font size
+    fontweight='normal',    # 'normal', 'bold', 'heavy', 'light'
+    fontstyle='normal',     # 'normal', 'italic', 'oblique'
+    fontfamily='sans-serif',# Font family
+    color='black',          # Text color
+    alpha=1.0,              # Transparency
+    ha='center',            # Horizontal alignment: 'left', 'center', 'right'
+    va='center',            # Vertical alignment: 'top', 'center', 'bottom', 'baseline'
+    rotation=0,             # Rotation angle in degrees
+    bbox=dict(              # Background box
+        facecolor='white',
+        edgecolor='black',
+        boxstyle='round'
+    )
+)
+```
+
+## rcParams Configuration
+
+Common rcParams settings for global customization:
+
+```python
+# Font settings
+plt.rcParams['font.family'] = 'sans-serif'
+plt.rcParams['font.sans-serif'] = ['Arial', 'Helvetica']
+plt.rcParams['font.size'] = 12
+
+# Figure settings
+plt.rcParams['figure.figsize'] = (10, 6)
+plt.rcParams['figure.dpi'] = 100
+plt.rcParams['figure.facecolor'] = 'white'
+plt.rcParams['savefig.dpi'] = 300
+plt.rcParams['savefig.bbox'] = 'tight'
+
+# Axes settings
+plt.rcParams['axes.labelsize'] = 14
+plt.rcParams['axes.titlesize'] = 16
+plt.rcParams['axes.grid'] = True
+plt.rcParams['axes.grid.alpha'] = 0.3
+
+# Line settings
+plt.rcParams['lines.linewidth'] = 2
+plt.rcParams['lines.markersize'] = 8
+
+# Tick settings
+plt.rcParams['xtick.labelsize'] = 10
+plt.rcParams['ytick.labelsize'] = 10
+plt.rcParams['xtick.direction'] = 'in'  # 'in', 'out', 'inout'
+plt.rcParams['ytick.direction'] = 'in'
+
+# Legend settings
+plt.rcParams['legend.fontsize'] = 12
+plt.rcParams['legend.frameon'] = True
+plt.rcParams['legend.framealpha'] = 0.8
+
+# Grid settings
+plt.rcParams['grid.alpha'] = 0.3
+plt.rcParams['grid.linestyle'] = '--'
+```
+
+## GridSpec for Complex Layouts
+
+```python
+from matplotlib.gridspec import GridSpec
+
+fig = plt.figure(figsize=(12, 8))
+gs = GridSpec(3, 3, figure=fig, hspace=0.3, wspace=0.3)
+
+# Span multiple cells
+ax1 = fig.add_subplot(gs[0, :])      # Top row, all columns
+ax2 = fig.add_subplot(gs[1:, 0])     # Bottom two rows, first column
+ax3 = fig.add_subplot(gs[1, 1:])     # Middle row, last two columns
+ax4 = fig.add_subplot(gs[2, 1])      # Bottom row, middle column
+ax5 = fig.add_subplot(gs[2, 2])      # Bottom row, right column
+```
+
+## 3D Plotting
+
+```python
+from mpl_toolkits.mplot3d import Axes3D
+
+fig = plt.figure()
+ax = fig.add_subplot(111, projection='3d')
+
+# Plot types
+ax.plot(x, y, z)                    # 3D line
+ax.scatter(x, y, z)                 # 3D scatter
+ax.plot_surface(X, Y, Z)            # 3D surface
+ax.plot_wireframe(X, Y, Z)          # 3D wireframe
+ax.contour(X, Y, Z)                 # 3D contour
+ax.bar3d(x, y, z, dx, dy, dz)       # 3D bar
+
+# Customization
+ax.set_xlabel('X')
+ax.set_ylabel('Y')
+ax.set_zlabel('Z')
+ax.view_init(elev=30, azim=45)      # Set viewing angle
+```
+
+## Animation
+
+```python
+from matplotlib.animation import FuncAnimation
+
+fig, ax = plt.subplots()
+line, = ax.plot([], [])
+
+def init():
+    ax.set_xlim(0, 2*np.pi)
+    ax.set_ylim(-1, 1)
+    return line,
+
+def update(frame):
+    x = np.linspace(0, 2*np.pi, 100)
+    y = np.sin(x + frame/10)
+    line.set_data(x, y)
+    return line,
+
+anim = FuncAnimation(fig, update, init_func=init,
+                     frames=100, interval=50, blit=True)
+
+# Save animation
+anim.save('animation.gif', writer='pillow', fps=20)
+anim.save('animation.mp4', writer='ffmpeg', fps=20)
+```
+
+## Image Operations
+
+```python
+# Read and display image
+img = plt.imread('image.png')
+ax.imshow(img)
+
+# Display matrix as image
+ax.imshow(matrix, cmap='viridis', aspect='auto',
+          interpolation='nearest', origin='lower')
+
+# Colorbar
+cbar = plt.colorbar(im, ax=ax)
+cbar.set_label('Values')
+
+# Image extent (set coordinates)
+ax.imshow(img, extent=[x_min, x_max, y_min, y_max])
+```
+
+## Event Handling
+
+```python
+# Mouse click event
+def on_click(event):
+    if event.inaxes:
+        print(f'Clicked at x={event.xdata:.2f}, y={event.ydata:.2f}')
+
+fig.canvas.mpl_connect('button_press_event', on_click)
+
+# Key press event
+def on_key(event):
+    print(f'Key pressed: {event.key}')
+
+fig.canvas.mpl_connect('key_press_event', on_key)
+```
+
+## Useful Utilities
+
+```python
+# Get current axis limits
+xlims = ax.get_xlim()
+ylims = ax.get_ylim()
+
+# Set equal aspect ratio
+ax.set_aspect('equal', adjustable='box')
+
+# Share axes between subplots
+fig, (ax1, ax2) = plt.subplots(2, 1, sharex=True)
+
+# Twin axes (two y-axes)
+ax2 = ax1.twinx()
+
+# Remove tick labels
+ax.set_xticklabels([])
+ax.set_yticklabels([])
+
+# Scientific notation
+ax.ticklabel_format(style='scientific', axis='y', scilimits=(0,0))
+
+# Date formatting
+import matplotlib.dates as mdates
+ax.xaxis.set_major_formatter(mdates.DateFormatter('%Y-%m-%d'))
+ax.xaxis.set_major_locator(mdates.DayLocator(interval=7))
+```