like-sci-figures 0.0.0-stage → 1.0.0

package/LICENSE

@@ -0,0 +1,56 @@
+LIKE Sci Figures — Source-Available License (v1.2.0)
+Copyright (c) 2026 LIKE
+
+-------------------------------------------------------------------------------
+本作品（LIKE Sci Figures / like-sci-figures，下称"本软件"）
+基于 SkillHub 上 science-figures v1.0.1（MIT 兼容社区技能）二次开发而来。
+上游作者的原始版权与 MIT 许可条款随上游代码保留（见文末"上游归属"），
+本派生作品的增量贡献按本许可证发布。
+-------------------------------------------------------------------------------
+
+授予的权利（允许）
+
+1. 个人与学术使用：为个人科研、教学、学术论文 / 学位论文 / 期刊投稿 / 会议
+   海报 / 汇报材料的配图，安装、运行、复制、修改本软件。此类使用无需授权费。
+2. 平台分发：在 SkillHub 平台按其官方分发机制安装与分发本软件。
+3. 内部评估：为评估本软件是否适合某项目而进行的内部试用。
+
+限制（不得）
+
+4. 商业性再分发 / 转售：不得将本软件或其任何部分、修改版本，作为独立产品或
+   服务的核心，进行商业性转售、再分发、出租或对外授权。
+5. 竞争性产品：不得将本软件的源码（或其修改版）用于开发、发布、销售任何与本
+   软件构成竞争关系的产品 / 服务，或用于其他商业目的的产品化。
+6. 版权移除：不得移除或遮盖本软件中的版权声明、本许可证、水印标识。
+
+免责声明
+
+本软件按"AS IS"提供，不附带任何明示或暗示的担保，包括但不限于对适销性、
+特定用途适用性及非侵权的担保。在任何情况下，作者或版权持有人均不对任何
+索赔、损害或其他责任负责，无论是否因合同、侵权或其他原因引起，且无论是否
+源于本软件或本软件的使用或其他交易。
+
+-------------------------------------------------------------------------------
+上游归属（MIT License，适用于 science-figures 原始贡献部分）
+
+MIT License
+
+Copyright (c) 上游作者（science-figures v1.0.1 原始权利持有人）
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

@@ -1,3 +1,94 @@
-# Temporary Holding Version
+# like-sci-figures
 
-This version is a temporary placeholder for this package. An operational version to replace this has been submitted for review and is awaiting a staged release.
+> **Publication-quality academic figure generator** — 40 chart types, 11 journal styles, 34 curated color palettes, CJK auto-detection, 300DPI output. Pure local.
+
+Generate publication-ready figures for academic papers, theses, posters, and research reports from JSON/CSV data files. Powered by [scienceplots](https://github.com/garrettj403/SciencePlots) + [matplotlib](https://matplotlib.org/). No GUI, no cloud, **no data leaving your machine**.
+
+```bash
+# 安装
+npm install -g like-sci-figures
+
+# 生成图表
+like-sci-figures --type bar --data data.json --out figure.png --style nature
+```
+
+---
+
+## Requirements
+
+- **Python 3.9+** (must be on PATH, or set `LIKE_SCI_PYTHON`)
+- Python dependencies: `matplotlib`, `numpy`, `scipy`, `pillow`
+
+```bash
+python -m pip install -r requirements.txt
+# 可选：启用 LaTeX 级期刊风格（内置等效样式会自动后备）
+pip install scienceplots
+```
+
+## Features
+
+- **40 chart types**: bar, grouped bar, stacked bar, heatmap, scatter, line, box, violin, forest, histogram, density, pie, donut, radar, 3D surface, contour, 3D scatter, bubble, area/stacked-area, error-bar, Venn, PCA biplot, wind rose, Taylor diagram, Sankey, multi-panel subplots, volcano, Manhattan, Kaplan-Meier, ROC, ridge, ternary, dot plot, dendrogram, slope, waterfall, Bode, periodogram, correlation matrix, hexbin density, ECDF, Bland-Altman
+- **11 journal styles**: Nature, Science, IEEE, Springer, Lancet, ACS, APS, AAAS, Cell, NEJM, MDPI
+- **34 curated color palettes**: qualitative / sequential / diverging sets via `--palette`, or pass your own hex list
+- **CJK auto-detection**: automatically loads Chinese/Japanese/Korean fonts when needed
+- **Output**: PNG / SVG / PDF at 300 DPI (adjustable via `--dpi`)
+
+## CLI Usage
+
+```bash
+like-sci-figures --type <chart> --data <file.json|csv> --out <output.png|svg|pdf> [options]
+```
+
+| Option | Description |
+| --- | --- |
+| `--type, -t` | Chart type (required). See full list below. |
+| `--data, -d` | Input data file (JSON or CSV) |
+| `--out, -o` | Output path (`.png` / `.svg` / `.pdf`) |
+| `--title` | Figure title (use `\n` for newline) |
+| `--xlabel` / `--ylabel` | Axis labels |
+| `--style, -s` | Journal style (default `nature`) |
+| `--palette, -p` | Color palette slug or custom hex list |
+| `--dpi` | Output resolution (default 300) |
+| `--list-styles` | List available journal styles and exit |
+| `--list-palettes` | List available palettes and exit |
+| `--verify-all` | Run full engine self-check |
+
+### Chart types
+
+`bar` `grouped bar` `stacked bar` `heatmap` `scatter` `line` `box` `violin` `forest` `histogram` `density` `pie` `donut` `radar` `surface` `contour` `scatter3d` `bubble` `area` `errorbar` `venn` `pca` `windrose` `taylor` `sankey` `subplots` `volcano` `manhattan` `kaplan_meier` `roc` `ridge` `ternary` `dotplot` `dendrogram` `slope` `waterfall` `bode` `periodogram` `corr_matrix` `hexbin` `ecdf` `bland_altman`
+
+### Examples
+
+```bash
+# Nature-style bar chart with value labels
+like-sci-figures --type bar --data data.json --out figure.png --style nature --show-values
+
+# Correlation matrix heatmap (diverging palette)
+like-sci-figures --type corr_matrix --data corr.json --out corr.png --palette wx06_amber_navy
+
+# Hexbin density plot with 1:1 line
+like-sci-figures --type hexbin --data obs.json --out hex.png --style cell --palette viridis
+
+# Multi-panel subplots
+like-sci-figures --type subplots --data panel.json --out grid.png --layout 2x3 --style ieee
+```
+
+## Data Format
+
+JSON/CSV with a flexible schema that adapts to each chart type. Example for a bar chart:
+
+```json
+{
+  "categories": ["PM2.5", "PM10", "SO2", "NO2"],
+  "values": [38.2, 61.4, 9.1, 24.6],
+  "errors": [3.1, 4.2, 0.8, 2.0]
+}
+```
+
+## Environment
+
+- `LIKE_SCI_PYTHON` — path to a specific Python interpreter (default: `python` / `python3` on PATH)
+
+## License
+
+Source-Available License (see `LICENSE`). Personal and academic use permitted; commercial redistribution and competing productization prohibited. Upstream MIT attribution preserved.

package/cli.js

@@ -0,0 +1,79 @@
+#!/usr/bin/env node
+'use strict';
+
+/**
+ * like-sci-figures — npm CLI 入口
+ *
+ * 本包是 Python 图表引擎（skill/scripts/）的轻量 Node 包装器：
+ * 定位 Python 解释器 → 检查依赖 → 透传全部参数给 scripts/gen_figure.py。
+ * 引擎本身是纯 Python（matplotlib + scienceplots），本文件只负责调度与报错。
+ *
+ * 环境变量：
+ *   LIKE_SCI_PYTHON  指定 Python 解释器路径（默认依次尝试 python / python3）
+ */
+
+const { spawn, spawnSync } = require('child_process');
+const path = require('path');
+const fs = require('fs');
+
+const PKG_DIR = __dirname;
+const ENGINE = path.join(PKG_DIR, 'scripts', 'gen_figure.py');
+const REQ_FILE = path.join(PKG_DIR, 'requirements.txt');
+
+function findPython() {
+  const candidates = [];
+  if (process.env.LIKE_SCI_PYTHON) candidates.push(process.env.LIKE_SCI_PYTHON);
+  candidates.push('python', 'python3');
+  for (const c of candidates) {
+    try {
+      const r = spawnSync(c, ['--version'], { encoding: 'utf8' });
+      if (r.status === 0) return { cmd: c, viaEnv: c === process.env.LIKE_SCI_PYTHON };
+    } catch (e) { /* keep trying */ }
+  }
+  return null;
+}
+
+function checkDeps(py) {
+  const r = spawnSync(
+    py,
+    ['-c', 'import matplotlib, numpy, scipy, PIL, sys'],
+    { encoding: 'utf8' }
+  );
+  if (r.status === 0) return null;
+  return (r.stderr || r.stdout || '').trim();
+}
+
+const py = findPython();
+if (!py) {
+  console.error(
+    '[like-sci-figures] 未找到 Python 解释器。\n' +
+    '  请安装 Python 3.9+ 并加入 PATH，或通过环境变量指定：\n' +
+    '    set LIKE_SCI_PYTHON=C:\\path\\to\\python.exe   (Windows)\n' +
+    '    export LIKE_SCI_PYTHON=/usr/bin/python3        (macOS/Linux)'
+  );
+  process.exit(1);
+}
+
+const depErr = checkDeps(py.cmd);
+if (depErr) {
+  console.error(
+    '[like-sci-figures] Python 依赖缺失（matplotlib / numpy / scipy / pillow）。\n' +
+    '  请安装依赖：\n' +
+    '    ' + py.cmd + ' -m pip install -r ' + REQ_FILE + '\n' +
+    '  缺失详情：\n' + depErr
+  );
+  process.exit(1);
+}
+
+if (!fs.existsSync(ENGINE)) {
+  console.error('[like-sci-figures] 引擎缺失：' + ENGINE);
+  process.exit(1);
+}
+
+// 透传所有 CLI 参数给 Python 引擎；stdin/out/err 继承
+const child = spawn(py.cmd, [ENGINE, ...process.argv.slice(2)], { stdio: 'inherit' });
+child.on('error', (err) => {
+  console.error('[like-sci-figures] 无法启动引擎：' + err.message);
+  process.exit(1);
+});
+child.on('exit', (code) => process.exit(code === null ? 0 : code));

package/examples/area.json

@@ -0,0 +1,9 @@
+{
+  "labels": ["Jan", "Feb", "Mar", "Apr", "May"],
+  "series": {
+    "Coal": [20, 25, 30, 28, 22],
+    "Vehicle": [15, 18, 22, 25, 30],
+    "Dust": [10, 12, 11, 13, 14]
+  },
+  "stacked": true
+}

package/examples/bar.json

@@ -0,0 +1,15 @@
+{
+  "labels": ["Control", "Treat A", "Treat B", "Treat C"],
+  "series": {
+    "Metric 1": [12.5, 18.3, 15.2, 21.0],
+    "Metric 2": [10.0, 14.5, 16.8, 19.2]
+  },
+  "errors": {
+    "Metric 1": [1.2, 0.8, 1.5, 1.1],
+    "Metric 2": [0.9, 1.1, 0.7, 1.3]
+  },
+  "significance": {
+    "0,1": "**",
+    "2,3": "NS"
+  }
+}

package/examples/bland_altman.json

@@ -0,0 +1,128 @@
+{
+  "x": [
+    92.25,
+    52.07,
+    87.9,
+    60.94,
+    106.17,
+    93.52,
+    26.69,
+    97.63,
+    52.85,
+    37.96,
+    76.95,
+    61.01,
+    56.33,
+    21.77,
+    102.22,
+    37.14,
+    24.13,
+    67.97,
+    30.3,
+    87.78,
+    60.87,
+    43.87,
+    31.65,
+    112.2,
+    96.59,
+    27.32,
+    112.21,
+    100.12,
+    40.1,
+    107.61,
+    84.21,
+    51.36,
+    61.6,
+    85.33,
+    25.26,
+    41.33,
+    72.81,
+    38.59,
+    102.61,
+    41.36,
+    28.11,
+    109.03,
+    37.69,
+    98.02,
+    78.55,
+    68.99,
+    64.31,
+    100.46,
+    107.38,
+    75.49,
+    100.84,
+    117.13,
+    101.2,
+    79.24,
+    33.96,
+    44.54,
+    54.81,
+    26.09,
+    65.68,
+    41.88
+  ],
+  "y": [
+    94.61,
+    48.7,
+    93.2,
+    61.48,
+    111.44,
+    89.42,
+    28.78,
+    98.9,
+    54.84,
+    42.74,
+    78.88,
+    69.11,
+    61.2,
+    14.92,
+    102.57,
+    35.09,
+    28.34,
+    69.28,
+    27.53,
+    88.61,
+    57.2,
+    50.58,
+    34.6,
+    108.47,
+    105.92,
+    34.64,
+    114.24,
+    104.52,
+    34.34,
+    104.27,
+    87.35,
+    51.39,
+    65.13,
+    92.97,
+    27.89,
+    42.84,
+    68.38,
+    25.51,
+    102.02,
+    33.35,
+    22.69,
+    106.13,
+    32.06,
+    102.26,
+    80.65,
+    70.51,
+    67.75,
+    98.65,
+    106.84,
+    75.5,
+    101.98,
+    112.54,
+    108.48,
+    80.27,
+    34.51,
+    45.55,
+    53.67,
+    23.19,
+    70.97,
+    45.5
+  ],
+  "xlabel": "Mean of two analyzers (ug/m3)",
+  "ylabel": "Difference (Analyzer1 - Analyzer2)"
+}

package/examples/bode.json

@@ -0,0 +1,8 @@
+{
+  "freq": [0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1.0, 2.0, 5.0, 10.0, 20.0, 50.0, 100.0],
+  "mag": [60, 55, 48, 40, 30, 20, 10, 0, -10, -20, -30, -40, -50],
+  "phase": [0, 0, -10, -30, -45, -60, -75, -85, -95, -105, -115, -125, -135],
+  "gain_db": true,
+  "phase_deg": true,
+  "freq_hz": true
+}

package/examples/box.json

@@ -0,0 +1,8 @@
+{
+  "labels": ["对照组", "处理A", "处理B"],
+  "series": {
+    "对照组": [10, 12, 11, 13, 10, 14, 9, 11],
+    "处理A": [8, 9, 10, 7, 11, 9, 8, 10],
+    "处理B": [13, 15, 14, 16, 13, 15, 14, 17]
+  }
+}

package/examples/bubble.json

@@ -0,0 +1,7 @@
+{
+  "x": [1, 2, 3, 4, 5, 6],
+  "y": [2, 3, 1, 4, 2, 5],
+  "sizes": [10, 40, 25, 80, 15, 60],
+  "groups": ["A", "B", "A", "B", "A", "B"],
+  "labels": ["s1", "s2", "s3", "s4", "s5", "s6"]
+}

package/examples/contour.json

@@ -0,0 +1,10 @@
+{
+  "matrix": [
+    [10, 5, 3, 1],
+    [8, 12, 2, 0],
+    [1, 7, 15, 2],
+    [0, 3, 5, 8]
+  ],
+  "x": [0, 1, 2, 3],
+  "y": [0, 1, 2, 3]
+}

package/examples/corr_matrix.json

@@ -0,0 +1,99 @@
+{
+  "series": {
+    "PM2.5": [
+      -0.94,
+      0.44,
+      -1.97,
+      1.35,
+      0.83,
+      0.26,
+      -0.53,
+      0.71,
+      -0.64,
+      -0.17,
+      0.37,
+      0.92,
+      0.19,
+      0.26,
+      -0.1,
+      -0.41,
+      -0.56,
+      0.41,
+      0.02,
+      -1.11
+    ],
+    "PM10": [
+      -0.45,
+      -0.15,
+      -1.74,
+      1.7,
+      0.74,
+      0.16,
+      0.87,
+      -0.2,
+      1.09,
+      1.42,
+      1.31,
+      0.77,
+      -0.38,
+      0.44,
+      -0.11,
+      -0.44,
+      -0.43,
+      0.53,
+      0.55,
+      -1.24
+    ],
+    "SO2": [
+      -0.02,
+      -0.65,
+      0.65,
+      -1.55,
+      -0.84,
+      0.82,
+      -0.11,
+      -0.05,
+      -0.45,
+      0.22,
+      -1.3,
+      -0.66,
+      1.17,
+      -0.24,
+      0.46,
+      0.6,
+      0.17,
+      -0.66,
+      0.72,
+      0.74
+    ],
+    "NO2": [
+      1.53,
+      -0.72,
+      0.06,
+      0.47,
+      0.37,
+      -1.23,
+      -0.66,
+      -0.2,
+      -0.85,
+      0.68,
+      0.59,
+      -1.96,
+      -1.81,
+      -1.28,
+      0.12,
+      2.03,
+      -0.38,
+      0.25,
+      -1.06,
+      -1.05
+    ]
+  },
+  "labels": [
+    "PM2.5",
+    "PM10",
+    "SO2",
+    "NO2"
+  ],
+  "method": "pearson"
+}

package/examples/dendrogram.json

@@ -0,0 +1,5 @@
+{
+  "leaves": ["Gene A", "Gene B", "Gene C", "Gene D", "Gene E", "Gene F"],
+  "merges": [[0, 1, 1.2], [2, 3, 1.8], [4, 5, 2.5], [0, 2, 3.0], [0, 4, 3.5]],
+  "threshold": 3.0
+}

package/examples/density.json

@@ -0,0 +1,8 @@
+{
+  "series": {
+    "对照组": [1.2, 2.3, 2.1, 3.4, 2.8, 3.1, 2.9, 2.2, 2.6, 3.0, 2.4, 2.7],
+    "处理组": [3.1, 3.9, 4.2, 3.5, 4.4, 3.7, 4.0, 3.3, 4.1, 3.8, 3.6, 4.3],
+    "对照": [1.2, 2.3, 2.1, 3.4, 2.8, 3.1, 2.9, 2.2, 2.6, 3.0, 2.4, 2.7],
+    "处理": [3.1, 3.9, 4.2, 3.5, 4.4, 3.7, 4.0, 3.3, 4.1, 3.8, 3.6, 4.3]
+  }
+}

package/examples/dot_plot.json

@@ -0,0 +1,8 @@
+{
+  "x": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10],
+  "y": [2.1, 2.5, 2.3, 2.8, 3.0, 2.7, 3.2, 3.5, 3.1, 3.8, 1.5, 1.8, 1.6, 2.0, 2.2, 1.9, 2.4, 2.7, 2.3, 3.0],
+  "labels": ["P1", "P2", "P3", "P4", "P5", "P6", "P7", "P8", "P9", "P10", "P11", "P12", "P13", "P14", "P15", "P16", "P17", "P18", "P19", "P20"],
+  "group": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
+  "size": [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50],
+  "color_by": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
+}