marsilea 0.4.7__tar.gz → 0.5.0__tar.gz

{marsilea-0.4.7 → marsilea-0.5.0}/LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2024 Mr-Milk
+Copyright (c) 2025 Yimin Zheng
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{marsilea-0.4.7 → marsilea-0.5.0}/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: marsilea
-Version: 0.4.7
-Dynamic: Summary
+Version: 0.5.0
+Summary: Declarative creation of composable visualizations
 Project-URL: Home, https://github.com/Marsilea-viz/marsilea
-Author: Zhihang Zheng
-Author-email: Mr-Milk <yzheng@cemm.at>
+Project-URL: Documentation, https://marsilea.readthedocs.io
+Author-email: Yimin Zheng <yzheng@cemm.at>, Zhihang Zheng <zhihang.zheng@connect.polyu.hk>
 License: The MIT License (MIT)
         
-        Copyright (c) 2024 Mr-Milk
+        Copyright (c) 2025 Yimin Zheng
         
         Permission is hereby granted, free of charge, to any person obtaining a copy
         of this software and associated documentation files (the "Software"), to deal
@@ -30,6 +30,8 @@ License-File: LICENSE
 Classifier: Framework :: Matplotlib
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Visualization
 Requires-Python: >=3.8
 Requires-Dist: legendkit
 Requires-Dist: matplotlib>=3.6
@@ -38,20 +40,6 @@ Requires-Dist: pandas[parquet]
 Requires-Dist: platformdirs
 Requires-Dist: scipy
 Requires-Dist: seaborn
-Provides-Extra: dev
-Requires-Dist: icecream; extra == 'dev'
-Requires-Dist: mpl-fontkit; extra == 'dev'
-Requires-Dist: numpydoc; extra == 'dev'
-Requires-Dist: pre-commit; extra == 'dev'
-Requires-Dist: pydata-sphinx-theme; extra == 'dev'
-Requires-Dist: pytest; extra == 'dev'
-Requires-Dist: python-hmr; extra == 'dev'
-Requires-Dist: ruff; extra == 'dev'
-Requires-Dist: scikit-learn; extra == 'dev'
-Requires-Dist: sphinx; extra == 'dev'
-Requires-Dist: sphinx-copybutton; extra == 'dev'
-Requires-Dist: sphinx-design; extra == 'dev'
-Requires-Dist: sphinx-gallery; extra == 'dev'
 Description-Content-Type: text/markdown
 
 <p align="center">
@@ -66,6 +54,7 @@ Description-Content-Type: text/markdown
 ![pypi version](https://img.shields.io/pypi/v/marsilea?color=0098FF&logo=python&logoColor=white&style=flat-square)
 ![Conda Version](https://img.shields.io/conda/vn/conda-forge/marsilea?style=flat-square&logo=anaconda&logoColor=white&color=%2344A833)
 ![PyPI - License](https://img.shields.io/pypi/l/marsilea?color=FFD43B&style=flat-square)
+[![DOI](https://img.shields.io/badge/DOI-10.1186%2Fs13059--024--03469--3-blue?color=0098FF&style=flat-square)](https://doi.org/10.1186/s13059-024-03469-3)
 
 # Marsilea: Declarative creation of composable visualization!
 
@@ -104,6 +93,16 @@ and then create a bar chart to show the expression of genes in different cell ty
 A visualization contains multiple plots is called a composable visualization.
 In Marsilea, we employ a declarative approach for user to create composable visualization incrementally.
 
+## Citation
+
+If you use Marsilea in your research, please cite the following:
+
+> Marsilea: an intuitive generalized paradigm for composable visualizations
+> 
+> Yimin Zheng, Zhihang Zheng, André F. Rendeiro & Edwin Cheung
+> 
+> _Genome Biology_ 2025 Jan 06. DOI: [10.1186/s13059-017-1382-0](https://doi.org/10.1186/s13059-024-03469-3)
+
 ## Examples
 
 <table>

{marsilea-0.4.7 → marsilea-0.5.0}/README.md

@@ -10,6 +10,7 @@
 ![pypi version](https://img.shields.io/pypi/v/marsilea?color=0098FF&logo=python&logoColor=white&style=flat-square)
 ![Conda Version](https://img.shields.io/conda/vn/conda-forge/marsilea?style=flat-square&logo=anaconda&logoColor=white&color=%2344A833)
 ![PyPI - License](https://img.shields.io/pypi/l/marsilea?color=FFD43B&style=flat-square)
+[![DOI](https://img.shields.io/badge/DOI-10.1186%2Fs13059--024--03469--3-blue?color=0098FF&style=flat-square)](https://doi.org/10.1186/s13059-024-03469-3)
 
 # Marsilea: Declarative creation of composable visualization!
 
@@ -48,6 +49,16 @@ and then create a bar chart to show the expression of genes in different cell ty
 A visualization contains multiple plots is called a composable visualization.
 In Marsilea, we employ a declarative approach for user to create composable visualization incrementally.
 
+## Citation
+
+If you use Marsilea in your research, please cite the following:
+
+> Marsilea: an intuitive generalized paradigm for composable visualizations
+> 
+> Yimin Zheng, Zhihang Zheng, André F. Rendeiro & Edwin Cheung
+> 
+> _Genome Biology_ 2025 Jan 06. DOI: [10.1186/s13059-017-1382-0](https://doi.org/10.1186/s13059-024-03469-3)
+
 ## Examples
 
 <table>

{marsilea-0.4.7 → marsilea-0.5.0}/pyproject.toml

@@ -4,9 +4,10 @@ build-backend = "hatchling.build"
 
 [project]
 name = "marsilea"
+description = "Declarative creation of composable visualizations"
 authors = [
-    {name = "Mr-Milk", email = "yzheng@cemm.at"},
-    {name = "Zhihang Zheng"}
+    {name = "Yimin Zheng", email = "yzheng@cemm.at"},
+    {name = "Zhihang Zheng", email = "zhihang.zheng@connect.polyu.hk"},
 ]
 license = {file = "LICENSE"}
 readme = "README.md"
@@ -14,10 +15,12 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",
     "Framework :: Matplotlib",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Visualization",
 ]
-dynamic = ["version", "description"]
+dynamic = ["version"]
 requires-python = ">=3.8"
-urls = {Home="https://github.com/Marsilea-viz/marsilea"}
+urls = { Home="https://github.com/Marsilea-viz/marsilea", Documentation="https://marsilea.readthedocs.io"}
 dependencies = [
     "numpy",
     "pandas[parquet]",
@@ -28,23 +31,6 @@ dependencies = [
     "platformdirs"
 ]
 
-[project.optional-dependencies]
-dev = [
-    "ruff",
-    "icecream",
-    "python-hmr",
-    "pytest",
-    "scikit-learn",
-    "sphinx",
-    "numpydoc",
-    "sphinx_design",
-    "pydata-sphinx-theme",
-    "sphinx-copybutton",
-    "sphinx_gallery",
-    "mpl_fontkit",
-    "pre-commit",
-]
-
 [tool.hatch.version]
 path = "src/marsilea/__init__.py"
 
@@ -76,4 +62,30 @@ docstring-code-format = true
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401"]
 "docs/*" = ["E402", "E731"]
-"scripts/*" = ["E402", "E731"]
+"scripts/*" = ["E402", "E731"]
+
+[tool.taskipy.tasks]
+hello = "echo Hello, World!"
+test = "pytest tests"
+doc-build = "sphinx-build -b html docs/source docs/build"
+doc-clean-build = "python docs/clean_up.py && sphinx-build -b html docs/source docs/build"
+doc-serve = "python -m http.server -d docs/build"
+fmt = "ruff format docs/source wsidata tests"
+
+[dependency-groups]
+dev = [
+    "sphinx>=7.1.2",
+    "ruff",
+    "pytest",
+    "scikit-learn",
+    "sphinx",
+    "numpydoc",
+    "sphinx_design",
+    "pydata-sphinx-theme",
+    "sphinx-copybutton",
+    "sphinx_gallery",
+    "mpl_fontkit",
+    "pre-commit",
+    "taskipy",
+    "emoji>=2.14.1",
+]

{marsilea-0.4.7 → marsilea-0.5.0}/src/marsilea/__init__.py

@@ -1,6 +1,6 @@
 """Declarative creation of composable visualization"""
 
-__version__ = "0.4.7"
+__version__ = "0.5.0"
 
 import marsilea.plotter as plotter
 from ._deform import Deformation

{marsilea-0.4.7 → marsilea-0.5.0}/src/marsilea/base.py

@@ -169,7 +169,14 @@ class LegendMaker:
         for _, legs in legends.items():
             for leg in legs:
                 try:
+                    # Try to detach legend from figure
                     leg.remove()
+                    # For matplotlib >= 3.10.0
+                    if hasattr(leg, "_parent_figure"):
+                        setattr(leg, "_parent_figure", None)
+                    # For matplotlib < 3.10.0
+                    if hasattr(leg, "figure"):
+                        setattr(leg, "figure", None)
                 except Exception:
                     pass
 
@@ -1135,142 +1142,6 @@ class ClusterBoard(WhiteBoard):
                 rasterized=rasterized,
             )
 
-    def hsplit(self, cut=None, labels=None, order=None, spacing=0.01):
-        """Split the main canvas horizontally
-
-        .. deprecated:: 0.5.0
-            Use :meth:`~marsilea.base.ClusterBoard.cut_rows` \
-            or :meth:`~marsilea.base.ClusterBoard.group_rows` instead
-
-        Parameters
-        ----------
-        cut : array-like, optional
-            The index of your data to specify where to split the canvas
-        labels : array-like, optional
-            The labels of your data, must be the same length as the data
-        order : array-like, optional
-            The order of the unique labels
-        spacing : float, optional
-            The spacing between each split chunks, default is 0.01
-
-        Examples
-        --------
-        Split the canvas by the unique labels
-
-        .. plot::
-            :context: close-figs
-
-            >>> data = np.random.rand(10, 11)
-            >>> import marsilea as ma
-            >>> h = ma.Heatmap(data)
-            >>> labels = ["A", "B", "C", "A", "B", "C", "A", "B", "C", "A"]
-            >>> h.hsplit(labels=labels, order=["A", "B", "C"])
-            >>> h.add_left(ma.plotter.Labels(labels), pad=.1)
-            >>> h.render()
-
-
-        Split the canvas by the index
-
-        .. plot::
-            :context: close-figs
-
-            >>> h = ma.Heatmap(data)
-            >>> h.hsplit(cut=[4, 8])
-            >>> h.render()
-
-
-        """
-        warnings.warn(
-            DeprecationWarning(
-                "`hsplit` will be deprecated in v0.5.0, use `cut_rows` or `group_rows` instead"
-            ),
-            stacklevel=2,
-        )
-        if self._split_row:
-            raise SplitTwice(axis="horizontally")
-        self._split_row = True
-
-        deform = self.get_deform()
-        deform.hspace = spacing
-        if cut is not None:
-            deform.set_split_row(breakpoints=cut)
-        else:
-            labels = np.asarray(labels)
-
-            reindex, order = reorder_index(labels, order=order)
-            deform.set_data_row_reindex(reindex)
-
-            breakpoints = get_breakpoints(labels[reindex])
-            deform.set_split_row(breakpoints=breakpoints, order=order)
-
-    def vsplit(self, cut=None, labels=None, order=None, spacing=0.01):
-        """Split the main canvas vertically
-
-        .. deprecated:: 0.5.0
-            Use :meth:`~marsilea.base.ClusterBoard.cut_cols` \
-            or :meth:`~marsilea.base.ClusterBoard.group_cols` instead
-
-        Parameters
-        ----------
-        cut : array-like, optional
-            The index of your data to specify where to split the canvas
-        labels : array-like, optional
-            The labels of your data, must be the same length as the data
-        order : array-like, optional
-            The order of the unique labels
-        spacing : float, optional
-            The spacing between each split chunks, default is 0.01
-
-        Examples
-        --------
-        Split the canvas by the unique labels
-
-        .. plot::
-            :context: close-figs
-
-            >>> data = np.random.rand(10, 11)
-            >>> import marsilea as ma
-            >>> h = ma.Heatmap(data)
-            >>> labels = ["A", "B", "C", "A", "B", "C", "A", "B", "C", "A", "B"]
-            >>> h.vsplit(labels=labels, order=["A", "B", "C"])
-            >>> h.add_top(ma.plotter.Labels(labels), pad=.1)
-            >>> h.render()
-
-
-        Split the canvas by the index
-
-        .. plot::
-            :context: close-figs
-
-            >>> h = ma.Heatmap(data)
-            >>> h.vsplit(cut=[4, 8])
-            >>> h.render()
-
-
-        """
-        warnings.warn(
-            DeprecationWarning(
-                "`vsplit` will be deprecated in v0.5.0, use `cut_cols` or `group_cols` instead"
-            ),
-            stacklevel=2,
-        )
-        if self._split_col:
-            raise SplitTwice(axis="vertically")
-        self._split_col = True
-
-        deform = self.get_deform()
-        deform.wspace = spacing
-        if cut is not None:
-            deform.set_split_col(breakpoints=cut)
-        else:
-            labels = np.asarray(labels)
-
-            reindex, order = reorder_index(labels, order=order)
-            deform.set_data_col_reindex(reindex)
-
-            breakpoints = get_breakpoints(labels[reindex])
-            deform.set_split_col(breakpoints=breakpoints, order=order)
-
     def group_rows(self, group, order=None, spacing=0.01):
         """Group rows into chunks
 

{marsilea-0.4.7 → marsilea-0.5.0}/src/marsilea/heatmap.py

@@ -50,6 +50,7 @@ class Heatmap(ClusterBoard):
         height=None,
         cluster_data=None,
         init_main=True,
+        legend=True,
         **kwargs,
     ):
         if cluster_data is None:
@@ -80,7 +81,7 @@ class Heatmap(ClusterBoard):
         )
         name = get_plot_name(name, "main", mesh.__class__.__name__)
         mesh.set(name=name)
-        self.add_layer(mesh)
+        self.add_layer(mesh, legend=legend)
 
 
 class CatHeatmap(ClusterBoard):
@@ -109,6 +110,7 @@ class CatHeatmap(ClusterBoard):
         name=None,
         width=None,
         height=None,
+        legend=True,
         cluster_data=None,
         linewidth=0,
         linecolor="white",
@@ -128,7 +130,7 @@ class CatHeatmap(ClusterBoard):
         super().__init__(cluster_data, width=width, height=height, name=name)
         name = get_plot_name(name, "main", mesh.__class__.__name__)
         mesh.set(name=name)
-        self.add_layer(mesh)
+        self.add_layer(mesh, legend=legend)
 
 
 class SizedHeatmap(ClusterBoard):
@@ -156,6 +158,7 @@ class SizedHeatmap(ClusterBoard):
         name=None,
         width=None,
         height=None,
+        legend=True,
         **kwargs,
     ):
         if cluster_data is None:
@@ -166,4 +169,4 @@ class SizedHeatmap(ClusterBoard):
         super().__init__(cluster_data, width=width, height=height, name=name)
 
         mesh = SizedMesh(size=size, color=color, **kwargs)
-        self.add_layer(mesh)
+        self.add_layer(mesh, legend=legend)

{marsilea-0.4.7 → marsilea-0.5.0}/src/marsilea/plotter/arc.py

@@ -231,11 +231,9 @@ class Arc(StatsBase):
             ax.set_ylim(lim * 1.1, 0)
             ax.set_xlim(0, 1)
         if self.side == "top":
-            if not ax.yaxis_inverted():
-                ax.invert_yaxis()
+            ax.invert_yaxis()
         if self.side == "left":
-            if not ax.xaxis_inverted():
-                ax.invert_xaxis()
+            ax.invert_xaxis()
         ax.set_axis_off()
 
     def get_legends(self):

{marsilea-0.4.7 → marsilea-0.5.0}/src/marsilea/plotter/area.py

@@ -90,8 +90,7 @@ class Area(StatsBase):
                 ax.plot(data, x, **line_options)
             ax.set_ylim(-0.5, len(data) - 0.5)
             if self.side == "left":
-                if not ax.xaxis_inverted():
-                    ax.invert_xaxis()
+                ax.invert_xaxis()
         else:
             ax.fill_between(x, data, **fill_options)
             if self.add_outline:

{marsilea-0.4.7 → marsilea-0.5.0}/src/marsilea/plotter/bar.py

@@ -270,8 +270,7 @@ class CenterBar(_BarBase):
             ax.xaxis.set_major_formatter(FuncFormatter(lambda x, p: f"{np.abs(x):g}"))
 
         if self.is_flank:
-            if not ax.yaxis_inverted():
-                ax.invert_yaxis()
+            ax.invert_yaxis()
 
         if self.show_value:
             left_label = _format_labels(left_bar, self.fmt)

{marsilea-0.4.7 → marsilea-0.5.0}/src/marsilea/plotter/bio.py

@@ -171,12 +171,9 @@ class SeqLogo(StatsBase):
             ax.set_xlim(0, lim)
             ax.set_ylim(0, data.shape[1])
         if self.is_flank:
-            if not ax.yaxis_inverted():
-                ax.invert_yaxis()
+            ax.invert_yaxis()
         if self.side == "left":
-            if not ax.xaxis_inverted():
-                ax.invert_xaxis()
+            ax.invert_xaxis()
         if self.side == "bottom":
-            if not ax.yaxis_inverted():
-                ax.invert_yaxis()
+            ax.invert_yaxis()
         ax.set_axis_off()

{marsilea-0.4.7 → marsilea-0.5.0}/src/marsilea/plotter/range.py

@@ -125,8 +125,7 @@ class Range(StatsBase):
         else:
             ax.set_xlim(0, len(data))
         if self.side == "left":
-            if not ax.xaxis_inverted():
-                ax.invert_xaxis()
+            ax.invert_xaxis()
 
     def get_legends(self):
         return [

{marsilea-0.4.7 → marsilea-0.5.0}/src/marsilea/upset.py

@@ -947,7 +947,7 @@ class Upset(WhiteBoard):
     def _extra_legends(self):
         handles = [Patch(**entry) for entry in self._legend_entries]
         highlight_legend = ListLegend(handles=handles, handlelength=2)
-        highlight_legend.figure = None
+        # highlight_legend.set_figure(None)
         return {"highlight_subsets": [highlight_legend]}
 
     def render(self, figure=None, scale=1):