drawing-yh 0.1.0__tar.gz

drawing_yh-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Genesi599
+
+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.

drawing_yh-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: drawing-yh
+Version: 0.1.0
+Summary: Publication-quality scientific figures with automated layout audits: volcano, heatmap, PCA, violin, chord, venn, and more
+Requires-Python: >=3.8
+License-File: LICENSE
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: shapely
+Requires-Dist: scikit-learn
+Requires-Dist: matplotlib-venn
+Requires-Dist: pycirclize
+Requires-Dist: Pillow
+Requires-Dist: python-pptx
+Requires-Dist: pywin32; platform_system == "Windows"
+Dynamic: license-file

drawing_yh-0.1.0/README.md

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+# python-drawing-yh (`drawing_yh`)
+
+Publication-quality scientific plotting toolkit for Python — the plotting layer behind multi-module slide-style research reports.
+
+`import drawing_yh` applies the house style automatically (Arial, 8 pt base, editable text in SVG/PDF, three-format export), and every chart family ships as a reusable template instead of ad-hoc scripts.
+
+## Highlights
+
+- **Chart families** — bar / box / heatmap / scatter / violin / volcano / PCA / venn / pie / network / chord / dotplot / dumbbell / lollipop / embedding / dose-response / Michaelis-Menten … each with a documented template module.
+- **Report suite (`drawing_yh.report`)** — Markdown → multi-module slide-style HTML websites (three-level nav: module / chapter / section) and same-source native PPTX inheriting a master theme. See the companion skill [local-report-builder](https://github.com/Genesi599/local-report-builder) for the full playbook.
+- **Text audit helpers** — `get_text_bboxes` / `find_overlaps` to programmatically verify no text overlaps or canvas overflow (the two hard rules every figure must pass).
+- **Style constants** — Okabe-Ito / DEEP-20 / age / sex / species palettes, `compute_figsize` layout helpers, `save_fig` one-call pdf+png+svg export.
+- **Example gallery** — `example_gallery/` renders one preview per template; rebuilt automatically by a pre-commit hook when templates change.
+
+## Install
+
+```bash
+pip install -e .          # from a checkout
+```
+
+Requires Python ≥ 3.11, matplotlib / numpy / pandas / scipy, plus `matplotlib-venn` and `pycirclize` for those chart families. The report suite additionally needs system `pandoc`, `python-pptx` and `Pillow`.
+
+## Usage sketch
+
+```python
+import drawing_yh                    # applies rcParams (Arial 8pt, editable fonts)
+from drawing_yh import save_fig      # pdf + png + svg in one call
+
+fig, ax = plt.subplots()
+...
+save_fig(fig, "my_figure.pdf", also=(".png", ".svg"))
+```
+
+## Conventions (STANDARDS.md)
+
+- Base font 8 pt locked; figure size adapts to content, never the other way.
+- All text in English inside figures; significance markers as plain black `*`.
+- Every figure ships with a plotted-data CSV sidecar where applicable.
+
+See `STANDARDS.md` for the full checklist.
+
+## License
+
+MIT

drawing_yh-0.1.0/drawing_yh/__init__.py

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+"""
+drawing_yh — Python 科研作图工具包
+
+**import 即应用项目科研出图标准**(可编辑字体、Arial、SVG 不转曲、统一字号),
+并导出常用工具:`save_fig`、命名色板、`compute_figsize`、文字防重叠 helper。
+
+完整标准见包根 `STANDARDS.md`,或 `LLM-yh/LLM_textbook/sci_plot_subplot_notes.md`。
+
+Quick start
+-----------
+    from drawing_yh import save_fig, OKABE_ITO, compute_figsize, DOUBLE_COL_IN
+    import matplotlib.pyplot as plt
+
+    fig, ax = plt.subplots(figsize=compute_figsize(n_items=len(df),
+                                                   width=DOUBLE_COL_IN))
+    # ... 用 OKABE_ITO 或 DEEP_20 上色 ...
+    save_fig(fig, 'out/fig1.pdf', also=('.png', '.svg'))   # 一次写三份
+"""
+from importlib.metadata import version, PackageNotFoundError
+import matplotlib as _mpl
+
+try:
+    __version__ = version("drawing-yh")
+except PackageNotFoundError:
+    __version__ = "0.0.0"
+
+
+# ============================================================
+# 项目常量
+# ============================================================
+DEFAULT_FONT_SIZE = 8        # 印刷字号(5–8pt 范围,统一 8)
+SVG_DPI = 72                 # SVG 必须 72 才能 1:1 渲染文字
+PNG_DPI = 300                # PNG 默认印刷质量
+
+SINGLE_COL_IN = 3.35         # 单栏 ~ 8.5 cm
+ONE_HALF_COL_IN = 4.49       # 1.5 栏 ~ 11.4 cm
+DOUBLE_COL_IN = 6.89         # 双栏 ~ 17.5 cm
+
+
+# ============================================================
+# rcParams —— 包级一次性设置(import 时生效)
+# ============================================================
+RC_DEFAULTS = {
+    # —— 字体可编辑性(投稿必需)——
+    'pdf.fonttype':         42,         # 嵌入 TrueType,Illustrator 可编辑
+    'ps.fonttype':          42,
+    'svg.fonttype':         'none',     # SVG 文字保持文字对象,不转曲
+    'pdf.use14corefonts':   False,      # 不替换为不可编辑的核心字体
+    # —— 字体 ——
+    'font.family':          'Arial',    # 期刊通用;装不上会回退到默认 sans-serif
+    'font.size':            DEFAULT_FONT_SIZE,
+    'axes.titlesize':       DEFAULT_FONT_SIZE,
+    'axes.labelsize':       DEFAULT_FONT_SIZE,
+    'xtick.labelsize':      DEFAULT_FONT_SIZE,
+    'ytick.labelsize':      DEFAULT_FONT_SIZE,
+    'legend.fontsize':      DEFAULT_FONT_SIZE,
+    'figure.titlesize':     DEFAULT_FONT_SIZE,
+    # —— 保存默认 ——
+    'savefig.bbox':         'tight',
+    'savefig.pad_inches':   0.02,
+    'savefig.facecolor':    'white',
+}
+
+
+def set_rc(overrides: dict = None) -> None:
+    """
+    应用项目标准 rcParams。
+
+    包 import 时已自动调用一次。如果脚本里临时改了 rc(比如调字号),
+    想恢复到标准,可以再 `drawing_yh.set_rc()` 一下。
+    """
+    rc = dict(RC_DEFAULTS)
+    if overrides:
+        rc.update(overrides)
+    _mpl.rcParams.update(rc)
+
+
+# 包加载时立即应用一次;所有 `import drawing_yh` / `from drawing_yh import …`
+# 的脚本都自动享受标准 rc,不必每个文件再写一遍。
+set_rc()
+
+
+# ============================================================
+# 顶层导出
+# ============================================================
+from .io import save_fig                                # noqa: E402
+from .palettes import (                                 # noqa: E402
+    OKABE_ITO, DEEP_20, AGE_GRADIENT, SEX, SPECIES, THREE_GROUP,
+    to_grayscale, grayscale_distinct, preview_palette, family_palette,
+)
+from .layout import (                                   # noqa: E402
+    compute_figsize, get_text_bboxes, find_overlaps, nudge_no_overlap_y,
+    autoshrink_figsize,
+    TextBBox,
+)
+from .dumbbell import render_mean_dumbbell              # noqa: E402
+from .venn import venn_diagram                          # noqa: E402
+from .dotplot import (                                  # noqa: E402
+    marker_dotplot,
+    dot_sizes, pad_axes, style_colorbar,
+    add_size_legend, add_block_separators, add_row_color_dots,
+)
+from . import dotplot                                   # noqa: E402,F401
+from .embedding import (                                # noqa: E402
+    feature_plot,
+    resolve_vlim, scatter_embedding, add_embedding_axes, auto_ncols,
+    cluster_atlas, cluster_centroids,
+)
+from . import embedding                                 # noqa: E402,F401
+from .embedding_domain import (                         # noqa: E402
+    GapfilledOutlineResult,
+    gapfilled_embedding_outline,
+    draw_gapfilled_embedding_domains,
+    embedding_knn_density_mask,
+    filter_main_embedding_components,
+    label_point_for_outline,
+    trim_points_inside_reference_domain,
+)
+from .heatmap import (heatmap_with_row_bars, clustermap_annot,  # noqa: E402
+                      plot_oydeg_heatmap_enrichment,
+                      plot_enrichment_dotplot, pick_enrich_terms,
+                      plot_rescue_arrow_heatmap,
+                      plot_staircase_rescue_heatmap, missingness_matrix)
+from . import report                                    # noqa: E402,F401
+from .network import hub_spoke                          # noqa: E402
+from .volcano_plot import volcano, volcano_with_gene_rails   # noqa: E402
+from .umap_overlay import (                             # noqa: E402
+    DA_CMAP, GRAY_NA,
+    draw_da_umap_panel, build_key_lines, umap_value_panels,
+)
+from . import umap_overlay                              # noqa: E402,F401
+from .bubble import bubble_plot, two_tone_ticklabels    # noqa: E402
+from . import bubble                                    # noqa: E402,F401
+from .box_plot import box_strip, box_stats              # noqa: E402
+from . import box_plot                                  # noqa: E402,F401
+from .bar import grouped_stack_bar, grouped_hbar, enrich_up_down        # noqa: E402
+from . import bar                                       # noqa: E402,F401
+from .histogram import hist_panel, hist_grid            # noqa: E402
+from . import histogram                                 # noqa: E402,F401
+from .scatter import threshold_scatter                  # noqa: E402
+from .scatter import da_dot_summary                       # noqa: E402
+from . import scatter                                   # noqa: E402,F401
+from .proportion_strip import (                         # noqa: E402
+    DEFAULT_AGE_COLORS,
+    fraction_by_age_panel, fraction_by_age_figure,
+)
+from . import proportion_strip                          # noqa: E402,F401
+from .pca import parallel_centroid_guides, pca_score_plot, pca_iqr_outlier_screen   # noqa: E402
+from . import pca as pca                                 # noqa: E402,F401
+from .tile_heatmap import tile_heatmap                  # noqa: E402
+from .lollipop import lollipop_plot                     # noqa: E402
+from .cell_schematic import (                           # noqa: E402
+    IconPlacement,
+    copy_flat_cell_template,
+    default_anchor_map,
+    flat_cell_attribution_path,
+    flat_cell_preview_path,
+    flat_cell_template_path,
+)
+from . import cell_schematic                            # noqa: E402,F401
+
+__all__ = [
+    # version
+    "__version__",
+    # constants
+    "DEFAULT_FONT_SIZE", "SVG_DPI", "PNG_DPI",
+    "SINGLE_COL_IN", "ONE_HALF_COL_IN", "DOUBLE_COL_IN",
+    "RC_DEFAULTS",
+    # rc
+    "set_rc",
+    # io
+    "save_fig",
+    # palettes
+    "OKABE_ITO", "DEEP_20", "AGE_GRADIENT", "SEX", "SPECIES", "THREE_GROUP",
+    "to_grayscale", "grayscale_distinct", "preview_palette", "family_palette",
+    # layout
+    "compute_figsize", "get_text_bboxes", "find_overlaps",
+    "nudge_no_overlap_y", "autoshrink_figsize", "TextBBox",
+    # charts
+    "render_mean_dumbbell",
+    "venn_diagram",
+    "marker_dotplot",
+    "feature_plot",
+    "pca_score_plot",
+    "heatmap_with_row_bars",
+    "plot_oydeg_heatmap_enrichment",
+    "plot_rescue_arrow_heatmap",
+    "plot_staircase_rescue_heatmap",
+    "plot_enrichment_dotplot",
+    "pick_enrich_terms",
+    "clustermap_annot",
+    # dot-plot style primitives (re-exported from drawing_yh.dotplot)
+    "dot_sizes", "pad_axes", "style_colorbar",
+    "add_size_legend", "add_block_separators", "add_row_color_dots",
+    # embedding feature-plot primitives (re-exported from drawing_yh.embedding)
+    "resolve_vlim", "scatter_embedding", "add_embedding_axes", "auto_ncols",
+    "cluster_atlas", "cluster_centroids",
+    "GapfilledOutlineResult", "gapfilled_embedding_outline",
+    "draw_gapfilled_embedding_domains", "embedding_knn_density_mask",
+    "filter_main_embedding_components", "label_point_for_outline",
+    "trim_points_inside_reference_domain",
+    # subpackages
+    "dotplot",
+    "embedding",
+    "report",
+    # network
+    "hub_spoke",
+    # umap value-overlay
+    "DA_CMAP", "GRAY_NA",
+    "draw_da_umap_panel", "build_key_lines", "umap_value_panels",
+    "umap_overlay",
+    # bubble plot
+    "bubble_plot", "two_tone_ticklabels",
+    "bubble",
+    # box plot (grouped boxes + optional per-sample points)
+    "box_strip", "box_stats", "box_plot",
+    # bar (grouped / stacked / grouped-horizontal)
+    "grouped_stack_bar", "grouped_hbar", "enrich_up_down", "bar",
+    # histogram (distribution of a numeric vector)
+    "hist_panel", "hist_grid", "histogram",
+    # threshold scatter (continuous x/y + highlight mask)
+    "threshold_scatter", "scatter",
+    # proportion strip (boxplot + dots)
+    "DEFAULT_AGE_COLORS",
+    "fraction_by_age_panel", "fraction_by_age_figure",
+    "proportion_strip",
+    # tile heatmap (TF-style square-cell)
+    "tile_heatmap",
+    # lollipop / stem plot
+    "lollipop_plot",
+    # flat editable cell schematic
+    "IconPlacement", "copy_flat_cell_template", "default_anchor_map",
+    "flat_cell_attribution_path", "flat_cell_preview_path",
+    "flat_cell_template_path", "cell_schematic",
+    "pca_iqr_outlier_screen",
+]
+from .layout_audit import audit_layout, LayoutAuditError     # noqa: E402
+from . import layout_audit                                   # noqa: E402,F401

drawing_yh-0.1.0/drawing_yh/assembly/__init__.py

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+"""drawing_yh.assembly — 统一排图工具(2026-09-02 合并:
+原 figure_assembly/build_layout.py 的 flow 排版 + MRI-yh/assemble_age_compare.py 的固定网格算法)。
+
+模式(每页 page 级 `mode` 键):
+  flow(默认) — 子图保持原始物理尺寸(不缩放, 2026-09-02 用户确认规则)逐行流式排版,
+               画布按内容自适应; 超宽面板单独成行。
+  grid       — 固定网格(原 assemble_age_compare 算法): cell 尺寸 + 行分组标签 +
+               顶部标题, 每格内 thumbnail 式等比 fit 居中(默认只缩不放, enlarge=true 才放大)。
+  abs        — 面板显式 x_mm/y_mm 绝对定位(旧布局表兼容)。
+  有意缩放: 任何模式下面板显式 width_mm/height_mm 即覆盖自然尺寸(须在 YAML 注释原因)。
+
+用法:
+    python -m drawing_yh.assembly.build_layout <layout.yaml> [--ink <inkscape.exe>]
+
+layout YAML:
+    name / out
+    pages:
+      - page: {width_mm, height_mm, background}
+        mode: flow | grid | abs
+        grid: {cell_w_mm, cell_h_mm, cols?, label_w_mm, title, title_h_mm, enlarge}
+        gutters: {label_gap_mm, caption_gap_mm, col_gap_mm, row_gap_mm, margin_mm}
+        panels:
+          - {id, src, label?, caption?, row?(grid 行分组), x_mm/y_mm(abs), width_mm/height_mm(有意缩放)}
+
+实现要点(踩坑修正):
+    - 嵌入不用嵌套 <svg>(Inkscape 1.4 导 PDF 时每个嵌套 svg 变独立页),
+      改深度合并: 子 SVG children 搬进 <g translate+scale>, id/url(#id)/href 加 "<pid>__" 前缀。
+    - 子 SVG 的 inkscape:page / sodipodi:namedview 多页标记必须丢弃。
+    - 根元素勿手写 xmlns(ET.register_namespace 已注册, 手写重复属性)。
+"""