marsilea 0.3.6__tar.gz → 0.4.1__tar.gz

{marsilea-0.3.6 → marsilea-0.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: marsilea
-Version: 0.3.6
+Version: 0.4.1
 Summary: Declarative creation of composable visualization
 Author: Zhihang Zheng
 Author-email: Mr-Milk <yzheng@cemm.at>

{marsilea-0.3.6 → marsilea-0.4.1}/pyproject.toml

@@ -44,5 +44,16 @@ dev = [
     "mpl_fontkit"
 ]
 
+[tool.flit.sdist]
+exclude = [
+    "docs",
+    "app",
+    "data",
+    "img",
+    "tests",
+    "scripts",
+    "readthedocs.yaml",
+]
+
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401"]

{marsilea-0.3.6 → marsilea-0.4.1}/src/marsilea/__init__.py

@@ -1,6 +1,6 @@
 """Declarative creation of composable visualization"""
 
-__version__ = "0.3.6"
+__version__ = "0.4.1"
 
 import marsilea.plotter as plotter
 from ._deform import Deformation

{marsilea-0.3.6 → marsilea-0.4.1}/src/marsilea/base.py

@@ -15,7 +15,7 @@ from matplotlib.figure import Figure
 
 from ._deform import Deformation
 from .dendrogram import Dendrogram
-from .exceptions import SplitTwice
+from .exceptions import SplitTwice, DuplicatePlotter
 from .layout import CrossLayout, CompositeCrossLayout
 from .plotter import RenderPlan, Title, SizedMesh
 from .utils import pairwise, batched, get_plot_name, _check_side
@@ -67,21 +67,22 @@ class LegendMaker:
         """
         raise NotImplementedError("Should be implemented in derived class")
 
-    def custom_legend(self, legend, name=None):
+    def custom_legend(self, legend_func, name=None):
         """Add a custom legend
 
         Parameters
         ----------
 
-        legend : `Artist <matplotlib.artist.Artists>`
-            A legend object
+        legend_func : Callable
+            A function that return the legend object,
+            the legend must be an `Artist <matplotlib.artist.Artists>`
         name : str, optional
             The name of the legend
 
         """
         if name is None:
             name = str(uuid4())
-        self._user_legends[name] = [legend]
+        self._user_legends[name] = legend_func
 
     def add_legends(
         self,
@@ -159,7 +160,8 @@ class LegendMaker:
         self.layout.remove_legend_ax()
 
     def _legends_drawer(self, ax):
-        legends = {**self.get_legends(), **self._user_legends}
+        user_legends = {k: [v()] for k, v in self._user_legends.items()}
+        legends = {**self.get_legends(), **user_legends}
 
         # force to remove all legends before drawing
         # In case some legends are added implicitly
@@ -330,6 +332,8 @@ class WhiteBoard(LegendMaker):
             If True, the legend will be included when calling :meth:`~marsilea.base.LegendMaker.add_legends`
 
         """
+        if plot.name is not None:
+            raise DuplicatePlotter(plot)
         plot_name = get_plot_name(name, side, plot.__class__.__name__)
         self._legend_switch[plot_name] = legend
 
@@ -819,6 +823,9 @@ class ClusterBoard(WhiteBoard):
         )
         self._row_den = []
         self._col_den = []
+        cluster_data = np.asarray(cluster_data)
+        if cluster_data.ndim != 2:
+            raise ValueError("Cluster data must be 2D array")
         self._cluster_data = cluster_data
         self._deform = Deformation(cluster_data)
 
@@ -1041,7 +1048,8 @@ class ClusterBoard(WhiteBoard):
         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")
@@ -1108,7 +1116,8 @@ class ClusterBoard(WhiteBoard):
         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")
@@ -1293,20 +1302,20 @@ class ClusterBoard(WhiteBoard):
         if deform.is_col_split:
             for plan in self._col_plan:
                 if plan.allow_split:
-                    if deform.is_col_cluster:
-                        group_ratios = None
-                    else:
-                        group_ratios = plan.get_split_regroup()
+                    # if deform.is_col_cluster:
+                    #     group_ratios = None
+                    # else:
+                    group_ratios = plan.get_split_regroup()
                     self.layout.vsplit(plan.name, w_ratios, wspace, group_ratios)
 
         # split row axes
         if deform.is_row_split:
             for plan in self._row_plan:
                 if plan.allow_split:
-                    if deform.is_row_cluster:
-                        group_ratios = None
-                    else:
-                        group_ratios = plan.get_split_regroup()
+                    # if deform.is_row_cluster:
+                    #     group_ratios = None
+                    # else:
+                    group_ratios = plan.get_split_regroup()
                     self.layout.hsplit(plan.name, h_ratios, hspace, group_ratios)
 
     def _render_dendrogram(self):

{marsilea-0.3.6 → marsilea-0.4.1}/src/marsilea/exceptions.py

@@ -6,6 +6,18 @@ class DuplicateName(Exception):
         return f"Axes with name `{self.name}` already exists."
 
 
+class DuplicatePlotter(Exception):
+
+    def __init__(self, plotter):
+        self.plotter = plotter
+
+    def __str__(self):
+        name = self.plotter.__class__.__name__
+        return (f"You have added `{name}` "
+                f"to the `{self.plotter.side}`, "
+                f"please create a new `{name}` if you want to add it again.")
+
+
 class SplitTwice(Exception):
     def __init__(self, axis="col"):
         self.axis = axis

{marsilea-0.3.6 → marsilea-0.4.1}/src/marsilea/plotter/base.py

@@ -538,6 +538,10 @@ class RenderPlan:
         self._split_regroup = ratio
 
     def get_split_regroup(self):
+        if self._split_regroup is None:
+            return None
+        if self.is_flank:
+            return self._split_regroup[::-1]
         return self._split_regroup
 
 

{marsilea-0.3.6 → marsilea-0.4.1}/src/marsilea/utils.py

@@ -74,7 +74,10 @@ def get_colormap(cmap):
     try:
         return mpl.colormap.get(cmap)
     except AttributeError:
-        return mpl.cm.get_cmap(cmap)
+        try:
+            return mpl.cm.get_cmap(cmap)
+        except AttributeError:
+            return mpl.cm.ColormapRegistry.get_cmap(cmap)
 
 
 def get_canvas_size_by_data(

marsilea-0.3.6/app/.gitignore

@@ -1,2 +0,0 @@
-.fonts
-*.xlsx

marsilea-0.3.6/app/.streamlit/pages.toml

@@ -1,24 +0,0 @@
-[[pages]]
-path = "index.py"
-name = "Home"
-icon = "🏠"
-
-#[[pages]]
-#path = "other_pages/page2.py"
-#name = "Page 2"
-#icon = ":books:"
-#
-#[[pages]]
-#name = "My second"
-#icon = "🎈️"
-#is_section = true
-#
-## Pages after an `is_section = true` will be indented
-#[[pages]]
-#name = "Another page"
-#icon = "💪"
-#
-## Unless you explicitly say in_section = false`
-#[[pages]]
-#name = "Not in a section"
-#in_section = false

marsilea-0.3.6/app/Dockerfile

@@ -1,20 +0,0 @@
-# Use the official Python image as the base image
-FROM python:3.10
-
-# Set the working directory in the container
-WORKDIR /app
-
-# Copy the requirements.txt file into the container
-COPY requirements.txt .
-
-# Install any dependencies
-RUN pip install --no-cache-dir -r requirements.txt
-
-# Copy the content of the local src directory to the working directory
-COPY . .
-
-# Expose the port that Streamlit will run on
-EXPOSE 8501
-
-# Command to run the application when the container starts
-CMD ["streamlit", "run", "Home.py", "--server.port=8501", "--server.address=0.0.0.0"]

marsilea-0.3.6/app/Home.py

@@ -1,102 +0,0 @@
-import streamlit as st
-from components.initialize import init_page, inject_css
-
-init_page("Marsilea")
-inject_css()
-
-banner, title = st.columns([1, 1.5])
-with banner:
-    st.markdown(
-        '<video controls width="250" autoplay="true" muted="true" '
-        'loop="true" playsinline style="pointer-events: none;">'
-        '<source src="https://raw.githubusercontent.com/Marsilea-viz/'
-        'marsilea/main/app/img/V1.mp4" '
-        'type="video/mp4" /></video>',
-        unsafe_allow_html=True,
-    )
-
-with title:
-    st.title("Marsilea")
-    st.subheader("Create :blue[composable] visualization")
-    st.text("")
-    st.markdown(
-        "*By [Mr.Milk](https://github.com/Mr-Milk) and "
-        "[Squirtle692](https://github.com/Squirtle692)*"
-    )
-
-st.markdown("---")
-
-st.subheader("About")
-st.markdown(
-    "Marsilea is a tool for you to create composable visualization. "
-    "A single-plot visualization can be combined with other plots to capture"
-    "the full picture of your data."
-)
-
-st.markdown("---")
-
-st.subheader("Online Toolbox")
-st.text("")
-t1, t2, t3 = st.columns(3)
-
-
-def tools(name, img, page, size=150):
-    st.markdown(
-        f'<div style="display: flex; justify-content: center; '
-        f'align-items: center; flex-direction: column;">'
-        f'<p style="font-weight: 600;">{name}</p>'
-        f'<a target="_self" href="{page}">'
-        f'<img style="width: {size}px;" src="{img}"></a>'
-        f"</div>",
-        unsafe_allow_html=True,
-    )
-
-
-with t1:
-    tools(
-        "Simple Heatmap",
-        "https://marsilea.readthedocs.io/en/latest/" "_images/concatenation-1.png",
-        page="/Simple_Heatmap",
-        size=130,
-    )
-
-with t2:
-    tools(
-        "Complex Heatmap",
-        "https://marsilea.readthedocs.io/en/latest/"
-        "_images/sphx_glr_plot_pbmc3k_thumb.png",
-        page="X-Layout_Heatmap",
-        size=200,
-    )
-
-with t3:
-    tools(
-        "Upset Plot",
-        "https://marsilea.readthedocs.io/en/latest/"
-        "_images/sphx_glr_plot_upset_thumb.png",
-        page="/Upsetplot",
-        size=220,
-    )
-
-st.markdown("---")
-
-
-st.subheader("Python Package")
-s1, s2, s3 = st.columns([1, 4, 5])
-with s1:
-    st.image(
-        "https://cdn3.iconfinder.com/data/icons/logos-and-brands-adobe/512/267_Python-512.png",
-        width=50,
-    )
-
-with s2:
-    st.markdown(
-        "Familiar with Python? Try our Python package "
-        "that can be easily integrated into your data pipeline!"
-    )
-with s3:
-    st.code("pip install marsilea", language="bash")
-
-st.markdown("---")
-
-st.markdown("Copyright © 2024 [Marsilea](https://github.com/Marsilea-viz)")

marsilea-0.3.6/app/README.md

@@ -1,17 +0,0 @@
-# How to run the app version of Marsilea
-
-## Using Docker
-
-### Step 1: Build the image
-
-```bash
-docker build -t marsilea-app .
-```
-
-### Step 2: Run the container
-
-```bash
-docker run -p 8501:8501 marsilea-app
-```
-
-Go to http://localhost:8501 to see the app.

marsilea-0.3.6/app/components/cmap_selector/__init__.py

@@ -1 +0,0 @@
-from .selector import ColormapSelector

marsilea-0.3.6/app/components/cmap_selector/selector.py

@@ -1,176 +0,0 @@
-import matplotlib as mpl
-import matplotlib.pyplot as plt
-import numpy as np
-import streamlit as st
-from matplotlib.cm import get_cmap
-from matplotlib.colors import (
-    LinearSegmentedColormap,
-    Normalize,
-    CenteredNorm,
-    TwoSlopeNorm,
-)
-
-
-@st.cache_data
-def get_colormap_names():
-    cmap_mapper = {}
-    for i in mpl.colormaps:
-        if not i.endswith("_r"):
-            cmap_name = i
-            cmap_mapper[i] = cmap_name.capitalize()
-    return cmap_mapper
-
-
-def get_colormap_images(cmap):
-    gradient = np.linspace(0, 1, 256)
-    gradient = np.vstack((gradient, gradient))
-
-    fig = plt.figure(figsize=(6, 0.5), dpi=90)
-    ax = fig.add_axes([0, 0, 1, 1])
-    ax.imshow(gradient, aspect="auto", cmap=cmap)
-    ax.set_axis_off()
-    plt.close(fig)
-    return fig
-
-
-def random_color():
-    return "#" + "".join(np.random.choice(list("0123456789ABCDEF"), 6))
-
-
-class ColormapSelector:
-    def __init__(self, key, default="coolwarm", data_mapping=True):
-        cmap_data = get_colormap_names()
-        cmap_options = sorted(cmap_data.keys())
-        default_index = cmap_options.index(default)
-        self.reverse = False
-
-        st.markdown("**Colormap**")
-
-        radio_box, rev_box = st.columns(2)
-
-        with radio_box:
-            input_cmap = st.radio(
-                label="cmap_input",
-                label_visibility="collapsed",
-                options=["Preset", "Create New"],
-                horizontal=True,
-                key=f"{key}-input-cmap",
-            )
-        with rev_box:
-            self.reverse = st.checkbox("Reverse colormap", key=f"{key}-rev-cmap")
-
-        if input_cmap == "Preset":
-            color_box, cmap_box = st.columns(2)
-            with color_box:
-                cmap = st.selectbox(
-                    "Select Preset Colormap",
-                    label_visibility="collapsed",
-                    key=f"{key}-preset-cmap",
-                    options=cmap_options,
-                    index=default_index,
-                    format_func=lambda v: cmap_data[v],
-                    help="The preset colormap are illuminated "
-                    "compensated for best visual effect",
-                )
-                cmap = get_cmap(cmap)
-                if self.reverse:
-                    cmap = cmap.reversed()
-                self.cmap = cmap
-            with cmap_box:
-                cmap_fig = get_colormap_images(self.cmap)
-                st.pyplot(cmap_fig)
-        else:
-            select_box, cmap_box = st.columns(2)
-            with select_box:
-                ncolors = st.selectbox(
-                    label="Colormap Type",
-                    key=f"{key}-select-gradient",
-                    label_visibility="collapsed",
-                    options=["One Gradient", "Two Gradient"],
-                )
-            _, c_lower, c_center, c_upper = st.columns([4, 1, 1, 1])
-            with c_lower:
-                lower = st.color_picker(
-                    label="Lower",
-                    value="#CB1B45",
-                    key=f"{key}-lower-cmap-2",
-                )
-            with c_upper:
-                upper = st.color_picker(
-                    label="Upper",
-                    value="#7B90D2",
-                    key=f"{key}-upper-cmap-2",
-                )
-
-            if ncolors == "One Gradient":
-                colors = [lower, upper]
-            else:
-                with c_center:
-                    center = st.color_picker(
-                        label="Center",
-                        value="#BDC0BA",
-                        key=f"{key}-center-cmap-3",
-                    )
-                colors = [lower, center, upper]
-            self.cmap = LinearSegmentedColormap.from_list("user_cmap", colors)
-
-            if self.reverse:
-                self.cmap = self.cmap.reversed()
-
-            with cmap_box:
-                cmap_fig = get_colormap_images(self.cmap)
-                st.pyplot(cmap_fig)
-
-        if data_mapping:
-            norm_strategy = st.selectbox(
-                "Mapping Strategy",
-                key=f"{key}-norm-selector",
-                options=["Linear", "Min-Max", "Centered On", "Two Range"],
-            )
-            self.norm = None
-            if norm_strategy == "Min-Max":
-                st.caption("Value outside the min/max will be mapped to min/max")
-                v1, v2 = st.columns(2)
-                with v1:
-                    vmin = st.number_input("Min", key=f"{key}-norm-vmin")
-                with v2:
-                    vmax = st.number_input("Max", key=f"{key}-norm-vmax")
-                self.norm = Normalize(vmin=vmin, vmax=vmax)
-            elif norm_strategy == "Centered On":
-                st.caption("Center on a specific value and extend symmetrically")
-                v1, v2 = st.columns(2)
-                with v1:
-                    vcenter = st.number_input(
-                        "Center", key=f"{key}-center_norm-vcenter"
-                    )
-                with v2:
-                    vhalf = st.number_input(
-                        "Extend",
-                        min_value=0.0,
-                        value=1.0,
-                        key=f"{key}-center_norm-vhalf",
-                    )
-                self.norm = CenteredNorm(vcenter=vcenter, halfrange=vhalf)
-            elif norm_strategy == "Two Range":
-                st.caption("Map to two range")
-                v1, v2, v3 = st.columns(3)
-                with v1:
-                    vmin = st.number_input("Min", value=0.0, key=f"{key}-tsnorm-vmin")
-                with v2:
-                    vcenter = st.number_input(
-                        "Center", value=vmin + 1, key=f"{key}-tsnorm-vcenter"
-                    )
-                with v3:
-                    vmax = st.number_input(
-                        "Max", value=vcenter + 1, key=f"{key}-tsnorm-vmax"
-                    )
-                if not ((vmin < vcenter) and (vcenter < vmax)):
-                    st.error("Min, Center, Max must be ascending.", icon="📉")
-                else:
-                    self.norm = TwoSlopeNorm(vcenter=vcenter, vmin=vmin, vmax=vmax)
-
-    def get_cmap(self):
-        return self.cmap
-
-    def get_norm(self):
-        return self.norm