Push krvzusoqpkoz

.github/workflows/docs.yml

@@ -0,0 +1,29 @@
+name: Documentation
+on:
+  push:
+    branches:
+      - master
+      - main
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+jobs:
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/configure-pages@v5
+      - uses: actions/checkout@v5
+      - run: cp CHANGELOG.md docs/changelog.md
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - run: pip install zensical
+      - run: zensical build --clean
+      - uses: actions/upload-pages-artifact@v4
+        with:
+          path: site
+      - uses: actions/deploy-pages@v4

.github/workflows/release.yml → .github/workflows/release-please.yml

@@ -1,22 +1,26 @@
-on:
-  workflow_dispatch: # makes it possible to run the workflow manually
-  push:
-    branches:
-      - main
-
-permissions:
-  contents: write
-  pull-requests: write
-
-name: release-please
-
-jobs:
-  release-please:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: googleapis/release-please-action@v4.2.0
-        id: release
-        with:
-          token: ${{ secrets.RELEASE_PLEASE_ACCESS_TOKEN }}
-          config-file: release-please-config.json
-          manifest-file: .release-please-manifest.json
+on:
+  workflow_dispatch: # makes it possible to run the workflow manually
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: write
+  pull-requests: write
+
+name: release-please
+
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: googleapis/release-please-action@v4
+        with:
+          # this assumes that you have created a personal access token
+          # (PAT) and configured it as a GitHub action secret named
+          # `MY_RELEASE_PLEASE_TOKEN` (this secret name is not important).
+          token: ${{ secrets.RELEASE_PLEASE_ACCESS_TOKEN }}
+          # optional. customize path to release-please-config.json
+          config-file: release-please-config.json
+          # optional. customize path to .release-please-manifest.json
+          manifest-file: .release-please-manifest.json

CHANGELOG.md

@@ -13,62 +13,7 @@
 
 ### Features ✨
 
-* **bar:** add one-sample t-test functionality ([00fdceb](https://github.com/RicardoRyn/plotfig/commit/00fdceb4b2b565fb33580a45f88f1ad5f5a8a258)), closes [#5](https://github.com/RicardoRyn/plotfig/issues/5)
-* **bar:** allow single-group bar plots to optionally show dots ([de2a2bb](https://github.com/RicardoRyn/plotfig/commit/de2a2bb5ab846041b380cf6225002575beb0406a))
-* **bar:** support color transparency adjustment via `color_alpha` argument ([530980d](https://github.com/RicardoRyn/plotfig/commit/530980dc346a338658d8333bb274004fcaac8d7d))
-* **bar:** support combining multiple statistical test methods ([34b6960](https://github.com/RicardoRyn/plotfig/commit/34b6960ff705468154bc5fbf75b9917ba8ac64fd))
-* **bar:** 增加函数绘制多组bar图 ([d740fbe](https://github.com/RicardoRyn/plotfig/commit/d740fbec2534fd91f660ca183323fdf014c5537a))
-* **bar:** 每个独立的样本点都能够指定颜色 ([8c0f297](https://github.com/RicardoRyn/plotfig/commit/8c0f297c7a6c847e53db3ee3f2719568ff644d72))
-* **bar:** 能够绘制间渐变色的bar图，设置bar边框颜色 ([02d163f](https://github.com/RicardoRyn/plotfig/commit/02d163ffbe0b0d51cb7c7b59ca7d75b71da4ed9d))
-* **circos:** add support for changing node label orientation via `node_label_orientation` ([abb7746](https://github.com/RicardoRyn/plotfig/commit/abb77465b33ea91d1a23592436b27d400799995f))
-* **circos:** Implement a new method for drawing circos plots ([ebf3352](https://github.com/RicardoRyn/plotfig/commit/ebf3352491566817fc6202c1a9323e9f6e8a323a))
-* **connec:** Add `line_color` parameter to customize connection line colors ([e4de41e](https://github.com/RicardoRyn/plotfig/commit/e4de41effe495767cde0980ce5e2cee458d8b3a8))
 * **connection:** add batch image cropping and GIF creation utilities ([f6554aa](https://github.com/RicardoRyn/plotfig/commit/f6554aaac27549428b10646d11a646b93ce389af))
-* **connection:** 可为脑连接html文件截图 ([5172a89](https://github.com/RicardoRyn/plotfig/commit/5172a890cea45b3405c3fb4a2048fc0d81295c4b))
-* **connection:** 增加函数绘制玻璃大脑连接图 ([43ac5e5](https://github.com/RicardoRyn/plotfig/commit/43ac5e53f92b37b03b475c95fd930cb79cbfeb45)), closes [#1](https://github.com/RicardoRyn/plotfig/issues/1)
-* **connection:** 现在默认不显示没有任何连接的节点 ([25c9e0d](https://github.com/RicardoRyn/plotfig/commit/25c9e0de1dd89ccec9755a2b365f1746778cf8ee)), closes [#2](https://github.com/RicardoRyn/plotfig/issues/2)
-* **corr:** 在绘制相关点线图时，允许用正六边形展示大量散点的分布密度 ([8e25741](https://github.com/RicardoRyn/plotfig/commit/8e25741fa2337eb8e356f4ae5467ac782b2f0311))
-* **corr:** 现在可以手动选择是否显示p值 ([d93e719](https://github.com/RicardoRyn/plotfig/commit/d93e71946cb802b949097e0d5b5fb560e561b05b))
-* **surface:** 增加函数绘制猕猴D99图集的脑区图 ([ae33f94](https://github.com/RicardoRyn/plotfig/commit/ae33f94319aa7e4fcb849c11624523da01cbb6ab))
-* **surface:** 增加函数绘制黑猩猩BNA图集脑图 ([95aaae1](https://github.com/RicardoRyn/plotfig/commit/95aaae12cf0b9b5c43a7259ecd39dbffdefab515))
-* **utils:** Add several utility functions ([b59f2a4](https://github.com/RicardoRyn/plotfig/commit/b59f2a49a6683e8ce942f47a2adc2a79a94e6f84))
-* **violin:** add function to plot single-group violin fig ([5c15b21](https://github.com/RicardoRyn/plotfig/commit/5c15b2172ab6df3eb40722f33374abcc606b9be5))
-* **violin:** add function to plot single-group violin fig ([8b2884b](https://github.com/RicardoRyn/plotfig/commit/8b2884bdb7eb2a839c46e673e3f29901ec433722))
-* **连接:** 添加 `line_color` 参数以自定义连接线颜色 ([e4de41e](https://github.com/RicardoRyn/plotfig/commit/e4de41effe495767cde0980ce5e2cee458d8b3a8))
-
-
-### Bug Fixes 🔧
-
-* **bar:** fix bug causing multi_bar plot failure ([a797006](https://github.com/RicardoRyn/plotfig/commit/a797006ed7b0598f65ff14f29d1c4c0280b1d811))
-* **bar:** fix the statistic line color not displaying as expected ([51489d4](https://github.com/RicardoRyn/plotfig/commit/51489d4231711f756e24203dd25b70e8128fc89f))
-* **bar:** handle empty significance plot without error ([a048ef2](https://github.com/RicardoRyn/plotfig/commit/a048ef272e40cdc85be99adcb4dfc11911abf964))
-* **bar:** isolate random number generator inside function ([a423c90](https://github.com/RicardoRyn/plotfig/commit/a423c90a3ba6ecdd0950ca10de6e61e9bb94fd64))
-* **bar:** remove leftover debug print in bar functions ([37f6f4c](https://github.com/RicardoRyn/plotfig/commit/37f6f4cfe55ed7ad0578040838f09f5966ce89cf))
-* **bar:** rename `y_lim_range` to `y_lim` in `plot_one_group_bar_figure` ([8d18d3a](https://github.com/RicardoRyn/plotfig/commit/8d18d3ad24708c0de621cf0fddc7e3382992895c))
-* **circos:** prevent type warning from type annotations ([b3552da](https://github.com/RicardoRyn/plotfig/commit/b3552dafd21fe72d9a294e0a52b8dc286d6a108e))
-* **connec:** Fix color bug caused by integer values ([b104c1f](https://github.com/RicardoRyn/plotfig/commit/b104c1f985c4aeaf1576c716fc1f0b7725774e26))
-* **connec:** fix issue with line_color display under color scale ([83d46d7](https://github.com/RicardoRyn/plotfig/commit/83d46d7031c49a455ab2648a92193ae5278750f4))
-* **deps:** update surfplot dependency info to use GitHub version ([de4ad0c](https://github.com/RicardoRyn/plotfig/commit/de4ad0ce889b418a788659e6f700eebc34a02a33))
-* **deps:** use the correct version of surfplot ([7467c20](https://github.com/RicardoRyn/plotfig/commit/7467c200f46af37a7ad0cac6aef464d1e24d9ef8))
-* **matrix:** 改成返回None ([b7d1b8d](https://github.com/RicardoRyn/plotfig/commit/b7d1b8d8cabbc0e57bd3245baccbcb71a5edfda8))
-* **surface:** 修复函数并非仅返回fig的bug ([e0eb9f7](https://github.com/RicardoRyn/plotfig/commit/e0eb9f7fc2fba3ab02ca880c012445f22fd6c22d))
-* **surface:** 修复当值为0的情况下，脑区不显示的bug ([ba792de](https://github.com/RicardoRyn/plotfig/commit/ba792dee52827fa5643adc48934e2155e7dcd1ad))
-
-
-### Code Refactoring ♻️
-
-* **bar:** mark string input for `test_method` as planned for deprecation ([e56d6d7](https://github.com/RicardoRyn/plotfig/commit/e56d6d7b79104b6079619b73158e21ee284a5304))
-* **bar:** Remove the legacy `plot_one_group_violin_figure_old` function ([6d1316d](https://github.com/RicardoRyn/plotfig/commit/6d1316d3050279f849d5c941ff6280c0ce419145))
-* **bar:** rename arguments in plot_one_group_bar_figure ([22a19cb](https://github.com/RicardoRyn/plotfig/commit/22a19cb35b46b334ee0498b740d085f3a0591dc8))
-* **bar:** replace print with warnings.warn ([3560d64](https://github.com/RicardoRyn/plotfig/commit/3560d64bf41237cbbc9311eb380665133b803d7b))
-* **bar:** 将 `test_method` 的字符串输入标记为即将弃用 ([e56d6d7](https://github.com/RicardoRyn/plotfig/commit/e56d6d7b79104b6079619b73158e21ee284a5304))
-* **circos:** Temporarily disable circos plot ([a96bb09](https://github.com/RicardoRyn/plotfig/commit/a96bb09cc799ce34785146f6bd855631ae1ad73a))
-* **corr/matrix:** function now returns Axes object ([e47cada](https://github.com/RicardoRyn/plotfig/commit/e47cada18a411fe28f7dc8a6ef62dea00acd3888))
-* **corr:** change default ax title font size in correlation plots to 12 ([5aab9fe](https://github.com/RicardoRyn/plotfig/commit/5aab9fe082f05894379c90b7e7a4a5a3a4739c49))
-* **src:** 重构代码，更加可读，易维护 ([d50e40d](https://github.com/RicardoRyn/plotfig/commit/d50e40d45a20b0c355553f1634eac9bdcca74d39))
-* **surface:** Deprecate old functions ([d90dc92](https://github.com/RicardoRyn/plotfig/commit/d90dc927731cd369d2ac1cc0939556b13d54158c))
-* **surface:** unify brain surface plotting with new plot_brain_surface_figure ([b566e23](https://github.com/RicardoRyn/plotfig/commit/b566e23cf435197dc4ca4da418f09cdc8641829d))
-* **tests:** remove unused tests folder ([b4a2b69](https://github.com/RicardoRyn/plotfig/commit/b4a2b697ed9d5c976bf3cf5858f67d7033cc3aa3))
 
 ## [1.8.1](https://github.com/RicardoRyn/plotfig/compare/v1.8.0...v1.8.1) (2025-10-29)
 

README.md

@@ -2,8 +2,10 @@
 
 ## 简介
 
-`plotfig` 是一个专为科学数据可视化设计的 Python 库，致力于为认知神经科研工作人员提供高效、易用且美观的图形绘制工具。
-该项目基于业界主流的可视化库—— `matplotlib`、`surfplot` 和 `plotly`等库开发，融合了三者的强大功能，能够满足神经科学以及脑连接组学中多种场景下的复杂绘图需求。
+`plotfig` 是一个专为科学数据可视化设计的 Python 库，
+致力于为认知神经科研工作人员提供高效、易用且美观的图形绘制工具。
+该项目基于业界主流的可视化库—— `matplotlib`、`surfplot` 和 `plotly`等库开发，
+融合了三者的强大功能，能够满足神经科学以及脑连接组学中多种场景下的复杂绘图需求。
 
 ![plotfig](https://github.com/RicardoRyn/plotfig/blob/main/docs/assets/plotfig.png)
 
@@ -12,10 +14,10 @@
 项目采用模块化设计，核心代码位于 `src/plotfig/` 目录下，包含如下主要功能模块：
 
 - `bar.py`：条形图绘制，适用于分组数据的对比展示。
-- `correlation.py`：相关性矩阵可视化，便于分析变量间的相关性分布。
 - `matrix.py`：通用矩阵可视化，支持多种配色和注释方式。
-- `brain_surface.py`：脑表面可视化，实现三维脑表面图集结构的绘制。
+- `correlation.py`：相关性矩阵可视化，便于分析变量间的相关性分布。
 - `circos.py`：弦图可视化，适合平面展示脑区之间的连接关系。
+- `brain_surface.py`：脑表面可视化，实现三维脑表面图集结构的绘制。
 - `brain_connection.py`：玻璃脑连接可视化，支持复杂的脑网络结构展示。
 
 ### 文档与示例
@@ -68,16 +70,14 @@ rm -rf surfplot
 
 ## 贡献
 
-**_`dev` 分支通常包含最新功能以及尚未合并到 `main` 的修复。_**
-
 如果您希望体验这些功能或参与 `plotfig` 的开发，可以选择以 开发模式（editable mode） 安装项目。
 
 这种安装方式允许您对本地源码的修改立即生效，非常适合调试、开发和贡献代码。
 
-推荐先 Fork 仓库，然后克隆您自己的 Fork 并安装 `dev` 分支：
+推荐先 Fork 仓库，然后克隆您自己的 Fork 并安装 `main` 分支：
 
 ```bash
-git clone -b dev https://github.com/<your-username>/plotfig.git
+git clone https://github.com/USERNAME/plotfig.git
 cd plotfig
 pip install -e .
 ```

docs/installation.md

@@ -46,16 +46,14 @@ pip install .
 
 ## 贡献指南
 
-**_`dev` 分支通常包含最新功能以及尚未合并到 `main` 的修复。_**
-
 如果您希望体验这些功能或参与 `plotfig` 的开发，可以选择以 开发模式（editable mode） 安装项目。
 
 这种安装方式允许您对本地源码的修改立即生效，非常适合调试、开发和贡献代码。
 
-推荐先 Fork 仓库，然后克隆您自己的 Fork 并安装 `dev` 分支：
+推荐先 Fork 仓库，然后克隆您自己的 Fork 并安装 `main` 分支：
 
 ```bash
-git clone -b dev https://github.com/<your-username>/plotfig.git
+git clone https://github.com/USERNAME/plotfig.git
 cd plotfig
 pip install -e .
 ```