marsilea 0.3.6__tar.gz → 0.4.0__tar.gz

{marsilea-0.3.6 → marsilea-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: marsilea
-Version: 0.3.6
+Version: 0.4.0
 Summary: Declarative creation of composable visualization
 Author: Zhihang Zheng
 Author-email: Mr-Milk <yzheng@cemm.at>

{marsilea-0.3.6 → marsilea-0.4.0}/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-0.4.0}/src/marsilea/__init__.py

@@ -1,6 +1,6 @@
 """Declarative creation of composable visualization"""
 
-__version__ = "0.3.6"
+__version__ = "0.4.0"
 
 import marsilea.plotter as plotter
 from ._deform import Deformation

{marsilea-0.3.6 → marsilea-0.4.0}/src/marsilea/base.py

@@ -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

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

marsilea-0.3.6/app/components/data_input.py

@@ -1,154 +0,0 @@
-from pathlib import Path
-from typing import Any
-
-import numpy as np
-import pandas as pd
-import streamlit as st
-
-from openpyxl import load_workbook
-
-
-class InputBase:
-    sep: str
-    user_input: Any
-
-    def __init__(self, key=None):
-        self.key = f"{self.__class__.__name__}-{key}"
-
-    def parse(self):
-        pass
-
-    def seperator(self):
-        sep_options = {"Tab (\\t)": "\t", "Comma (,)": ",", "Space (' ')": " "}
-        user_sep = st.selectbox("Seperator", key=self.key, options=sep_options.keys())
-        self.sep = sep_options[user_sep]
-
-
-@st.cache_data
-def parse_file(file, header=False, index=False, sheet_name=0):
-    index_col = None if not index else 0
-    suffix = file.name.split(".")[-1]
-    if suffix in ["csv", "txt", "tsv"]:
-        header = None if not header else "infer"
-        reader = pd.read_csv
-        sep = "," if suffix == "csv" else "\t"
-        kws = dict(sep=sep, header=header, index_col=index_col)
-    else:
-        header = None if not header else 0
-        reader = pd.read_excel
-        kws = dict(header=header, index_col=index_col, sheet_name=sheet_name)
-    data = reader(file, **kws)
-    return data
-
-
-class FileUpload(InputBase):
-    def __init__(
-        self, key=None, header=False, index=False, use_header=False, use_index=False
-    ):
-        super().__init__(key=key)
-        self.header = use_header
-        self.index = use_index
-        self.user_input = st.file_uploader(
-            "Choose a table file",
-            key=f"table_reader-{self.key}",
-            accept_multiple_files=False,
-            label_visibility="collapsed",
-            type=["txt", "csv", "xlsx"],
-        )
-
-        if index & header:
-            h1, h2 = st.columns(2)
-            with h1:
-                self.header = self._header_checkbox()
-            with h2:
-                self.index = self._index_checkbox()
-
-        elif header:
-            self.header = self._header_checkbox()
-
-        elif index:
-            self.index = self._index_checkbox()
-
-        self.sheet_name = 0
-        if self.user_input is not None:
-            suffix = self.user_input.name.split(".")[-1]
-            if suffix == "xlsx":
-                wb = load_workbook(self.user_input, read_only=True, keep_links=False)
-                sheetnames = wb.sheetnames
-                if len(sheetnames) > 1:
-                    self.sheet_name = st.selectbox(
-                        "Please select a sheet", options=sheetnames
-                    )
-
-    def _header_checkbox(self):
-        return st.checkbox(
-            "Use first row as header?",
-            value=self.header,
-            key=f"select-header-{self.key}",
-        )
-
-    def _index_checkbox(self):
-        return st.checkbox(
-            "Use first column as row labels?",
-            value=self.index,
-            key=f"select-index-{self.key}",
-        )
-
-    def _parse_to_df(self):
-        if self.user_input is not None:
-            return parse_file(
-                self.user_input,
-                header=self.header,
-                index=self.index,
-                sheet_name=self.sheet_name,
-            )
-
-    def parse(self) -> np.ndarray:
-        if self.user_input is not None:
-            data = self._parse_to_df()
-            if len(data.columns) == 1:
-                return data.to_numpy().flatten()
-            return data.to_numpy()
-
-    def parse_parts(self, row_label=True, col_label=True):
-        if self.user_input is not None:
-            data = parse_file(
-                self.user_input,
-                header=col_label,
-                index=row_label,
-                sheet_name=self.sheet_name,
-            )
-            row = data.index.to_numpy(dtype=str)
-            col = data.columns.to_numpy(dtype=str)
-            data = data.to_numpy()
-            return data, row, col
-
-    def parse_dataframe(self) -> pd.DataFrame:
-        return self._parse_to_df()
-
-    @property
-    def name(self):
-        if self.user_input is None:
-            return ""
-        else:
-            return Path(self.user_input.name).stem
-
-
-class PasteText(InputBase):
-    def __init__(self, cast_number=True, key=None):
-        super().__init__(key=key)
-        self.cast_number = cast_number
-        self.user_input = st.text_area("Paste data here", key=self.key)
-        self.seperator()
-
-    def parse(self):
-        if len(self.user_input) > 0:
-            rows = self.user_input.strip().split("\n")
-            raw_data = [row.split(self.sep) for row in rows]
-            try:
-                data = np.array(raw_data)
-                if self.cast_number:
-                    data = data.astype(float)
-                return pd.DataFrame(data)
-            except Exception:
-                st.error("Your seperator seems incorrect")

marsilea-0.3.6/app/components/example_download.py

@@ -1,71 +0,0 @@
-import base64
-import io
-import zipfile
-
-import numpy as np
-import pandas as pd
-import streamlit as st
-from random_word.random_word import RandomWords
-
-
-class ExampleDataGenerator:
-    def __init__(self, col, row):
-        np.random.seed(0)
-        self.col = col
-        self.row = row
-        self.words = RandomWords()
-        self.export_kws = dict(sep="\t", index=False, header=None)
-
-    def matrix(self):
-        return np.random.randint(0, 101, (self.row, self.col))
-
-    def col_labels(self):
-        labels = [self.words.get_random_word() for _ in range(self.col)]
-        return np.array(labels)
-
-    def row_labels(self):
-        labels = [self.words.get_random_word() for _ in range(self.row)]
-        return np.array(labels)
-
-    def stats_data(self):
-        return np.random.randn(10, self.row)
-
-    def numbers(self):
-        return np.random.randint(10, 100, self.row)
-
-    def get_text(self, data):
-        return pd.DataFrame(data=data).to_csv(**self.export_kws)
-
-    def to_zip(self):
-        zip_buffer = io.BytesIO()
-        with zipfile.ZipFile(zip_buffer, "a") as z:
-            z.writestr("matrix_data.txt", self.get_text(self.matrix()))
-            z.writestr("labels (row).txt", self.get_text(self.row_labels()))
-            z.writestr("labels (col).txt", self.get_text(self.col_labels()))
-            z.writestr("statistic plot.txt", self.get_text(self.stats_data()))
-            z.writestr("numbers.txt", self.get_text(self.numbers()))
-        return zip_buffer
-
-    def to_base64(self):
-        zip_bytes = self.to_zip()
-        return base64.b64encode(zip_bytes.getvalue()).decode()
-
-
-@st.cache_resource
-def get_base64():
-    g = ExampleDataGenerator(20, 20)
-    return g.to_base64()
-
-
-class ExampleDownloader:
-    def __init__(self):
-        self.b64 = get_base64()
-        href = (
-            f'<a href="data:file/zip;base64,{self.b64}" '
-            f'download="example.zip">Example Data</a>'
-        )
-        st.markdown(href, unsafe_allow_html=True)
-
-
-if __name__ == "__main__":
-    g = ExampleDataGenerator(20, 20)