marsilea 0.3.1__tar.gz → 0.3.3__tar.gz

{marsilea-0.3.1 → marsilea-0.3.3}/.github/workflows/build.yaml

@@ -37,7 +37,7 @@ jobs:
         run: |
           pip install pytest
           pip install pytest-cov
-          pytest --cov=heatgraphy/ --cov-report=xml tests/
+          pytest --cov=marsilea/ --cov-report=xml tests/
 
   Upload_to_test_pypi:
     runs-on: ubuntu-latest
@@ -57,14 +57,14 @@ jobs:
       - name: Publish to test.ipynb pypi
         env:
           FLIT_INDEX_URL: https://test.ipynb.pypi.org/legacy/
-          FLIT_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          FLIT_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+          FLIT_USERNAME: __token__
+          FLIT_PASSWORD: ${{ secrets.PYPI_TOKEN }}
         run: flit publish || exit 0
 
       - name: Publish to pypi
         if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
         env:
           FLIT_INDEX_URL: https://upload.pypi.org/legacy/
-          FLIT_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          FLIT_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+          FLIT_USERNAME: __token__
+          FLIT_PASSWORD: ${{ secrets.PYPI_TOKEN }}
         run: flit publish

marsilea-0.3.3/.github/workflows/deploy_streamlit.yaml

@@ -0,0 +1,39 @@
+name: Deploy streamlit docker to Azure
+on: []
+#  push:
+#    paths:
+#      - '.github/**'
+#      - 'app/**'
+#      - 'marsilea/**'
+#      - 'pyproject.toml'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Login to Azure
+        uses: azure/login@v1
+        with:
+          creds: ${{ secrets.AZURE_CREDENTIALS }}
+      - name: Build and push
+        uses: azure/docker-login@v1
+        with:
+          login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
+          username: ${{ secrets.REGISTRY_USERNAME }}
+          password: ${{ secrets.REGISTRY_PASSWORD }}
+      - run: |
+          docker build . -t ${{ secrets.REGISTRY_LOGIN_SERVER }}/marsilea:${{ github.sha }}
+          docker push ${{ secrets.REGISTRY_LOGIN_SERVER }}/marsilea:${{ github.sha }}
+
+      - name: Deploy to Azure Web App
+        uses: azure/webapps-deploy@v2
+        with:
+          resource-group: ${{ secrets.RESOURCE_GROUP }}
+          dns-name-label: ${{ secrets.RESOURCE_GROUP }}${{ github.run_number }}
+          image: ${{ secrets.REGISTRY_LOGIN_SERVER }}/marsilea:${{ github.sha }}
+          registry-login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
+          registry-username: ${{ secrets.REGISTRY_USERNAME }}
+          registry-password: ${{ secrets.REGISTRY_PASSWORD }}
+          name: marsilea
+          location: 'northeurope'

{marsilea-0.3.1 → marsilea-0.3.3}/.github/workflows/lint.yaml

@@ -7,4 +7,4 @@ jobs:
       - uses: actions/checkout@v3
       - uses: chartboost/ruff-action@v1
         with:
-          src: "./marsilea"
+          src: "./src"

{marsilea-0.3.1 → marsilea-0.3.3}/.gitignore

@@ -160,4 +160,5 @@ cython_debug/
 .idea/
 
 *.ipynb
-.fonts/
+.fonts/
+.DS_Store

marsilea-0.3.3/CITATION.cff

@@ -0,0 +1,37 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: Marsilea
+message: >-
+  An intuitive generalized visualization paradigm for
+  complex datasets
+type: software
+authors:
+  - given-names: Yimin
+    family-names: Zheng
+    email: yzheng@cemm.at
+    affiliation: CeMM
+    orcid: 'https://orcid.org/0000-0002-0394-9735'
+  - given-names: Zhihang
+    family-names: Zheng
+    affiliation: >-
+      Hong Kong University of Science and Technology
+      (Guangzhou)
+    orcid: 'https://orcid.org/0000-0001-7986-4925'
+  - given-names: Andre
+    family-names: Rendeiro
+    affiliation: CeMM
+    orcid: 'https://orcid.org/0000-0001-9362-5373'
+  - given-names: Edwin
+    family-names: Cheung
+    affiliation: University of Macau
+    orcid: 'https://orcid.org/0000-0001-8034-2833'
+identifiers:
+  - type: doi
+    value: 10.1101/2024.02.14.580236
+    description: Bioarxiv
+repository-code: 'https://github.com/Marsilea-viz/marsilea'
+keywords:
+  - Visualization
+license: MIT

{marsilea-0.3.1 → marsilea-0.3.3}/LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2023 Mr-Milk
+Copyright (c) 2024 Mr-Milk
 
 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-0.3.3/PKG-INFO

@@ -0,0 +1,74 @@
+Metadata-Version: 2.1
+Name: marsilea
+Version: 0.3.3
+Summary: Create x-layout visualization
+Author: Zhihang Zheng
+Author-email: Mr-Milk <yzheng@cemm.at>
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Classifier: License :: OSI Approved :: MIT License
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: matplotlib>=3.6
+Requires-Dist: seaborn
+Requires-Dist: scipy
+Requires-Dist: legendkit
+Requires-Dist: platformdirs
+Requires-Dist: ruff ; extra == "dev"
+Requires-Dist: icecream ; extra == "dev"
+Requires-Dist: python-hmr ; extra == "dev"
+Requires-Dist: pytest ; extra == "dev"
+Requires-Dist: scikit-learn ; extra == "dev"
+Requires-Dist: sphinx ; extra == "dev"
+Requires-Dist: numpydoc ; extra == "dev"
+Requires-Dist: sphinx_design ; extra == "dev"
+Requires-Dist: pydata-sphinx-theme ; extra == "dev"
+Requires-Dist: sphinx-copybutton ; extra == "dev"
+Requires-Dist: sphinx_gallery ; extra == "dev"
+Requires-Dist: mpl_fontkit ; extra == "dev"
+Project-URL: Home, https://github.com/Marsilea-viz/marsilea
+Provides-Extra: dev
+
+<p align="center">
+  <picture align="center">
+    <source media="(prefers-color-scheme: dark)" srcset="https://github.com/Marsilea-viz/marsilea/raw/main/img/banner-dark.jpg">
+    <source media="(prefers-color-scheme: light)" srcset="https://github.com/Marsilea-viz/marsilea/raw/main/img/banner-blue.jpg">
+    <img alt="Shows a bar chart with benchmark results." src="https://github.com/Marsilea-viz/marsilea/raw/main/img/banner-dark.jpg" width="400">
+  </picture>
+</p>
+
+[![Documentation Status](https://img.shields.io/readthedocs/marsilea?color=57B77E&logo=readthedocs&logoColor=white&style=flat-square)](https://marsilea.readthedocs.io/en/stable)
+![pypi version](https://img.shields.io/pypi/v/marsilea?color=0098FF&logo=python&logoColor=white&style=flat-square)
+
+❗We are in beta, API may change and bugs expected
+
+### Declarative creation of composable visualization!
+
+[Read Documentation](https://marsilea.readthedocs.io/)
+
+
+### Installation
+
+```shell
+pip install marsilea
+```
+
+[//]: # (### Examples)
+
+[//]: # ()
+[//]: # (|                                                                                                                 |                                                                                                               |)
+
+[//]: # (|-----------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------|)
+
+[//]: # (|                                                     Heatmap                                                     |                                                   Oncoprint                                                   |)
+
+[//]: # (| <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_pbmc3k_001_2_00x.png" width=400>      | <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_oncoprint_005_2_00x.png" width=400> |)
+
+[//]: # (|                                                    Upsetplot                                                    |                                            Composition Stacked Bar                                            |)
+
+[//]: # (| <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_upset_001_2_00x.png" width=400>       | <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_oil_well_001_2_00x.png" width=400>  |)
+
+[//]: # (|                                                   Arc Diagram                                                   |                                           Protein sequence alignment                                          |)
+
+[//]: # (| <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_arc_diagram_001_2_00x.png" width=400> | <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_seqalign_001_2_00x.png" width=400>  |)
+

marsilea-0.3.3/README.md

@@ -0,0 +1,42 @@
+<p align="center">
+  <picture align="center">
+    <source media="(prefers-color-scheme: dark)" srcset="https://github.com/Marsilea-viz/marsilea/raw/main/img/banner-dark.jpg">
+    <source media="(prefers-color-scheme: light)" srcset="https://github.com/Marsilea-viz/marsilea/raw/main/img/banner-blue.jpg">
+    <img alt="Shows a bar chart with benchmark results." src="https://github.com/Marsilea-viz/marsilea/raw/main/img/banner-dark.jpg" width="400">
+  </picture>
+</p>
+
+[![Documentation Status](https://img.shields.io/readthedocs/marsilea?color=57B77E&logo=readthedocs&logoColor=white&style=flat-square)](https://marsilea.readthedocs.io/en/stable)
+![pypi version](https://img.shields.io/pypi/v/marsilea?color=0098FF&logo=python&logoColor=white&style=flat-square)
+
+❗We are in beta, API may change and bugs expected
+
+### Declarative creation of composable visualization!
+
+[Read Documentation](https://marsilea.readthedocs.io/)
+
+
+### Installation
+
+```shell
+pip install marsilea
+```
+
+[//]: # (### Examples)
+
+[//]: # ()
+[//]: # (|                                                                                                                 |                                                                                                               |)
+
+[//]: # (|-----------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------|)
+
+[//]: # (|                                                     Heatmap                                                     |                                                   Oncoprint                                                   |)
+
+[//]: # (| <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_pbmc3k_001_2_00x.png" width=400>      | <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_oncoprint_005_2_00x.png" width=400> |)
+
+[//]: # (|                                                    Upsetplot                                                    |                                            Composition Stacked Bar                                            |)
+
+[//]: # (| <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_upset_001_2_00x.png" width=400>       | <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_oil_well_001_2_00x.png" width=400>  |)
+
+[//]: # (|                                                   Arc Diagram                                                   |                                           Protein sequence alignment                                          |)
+
+[//]: # (| <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_arc_diagram_001_2_00x.png" width=400> | <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_seqalign_001_2_00x.png" width=400>  |)

marsilea-0.3.3/app/Dockerfile

@@ -0,0 +1,20 @@
+# 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-0.3.1 → marsilea-0.3.3}/app/Home.py

@@ -2,7 +2,7 @@ import streamlit as st
 
 from components.initialize import init_page, inject_css
 
-init_page("Heatgraphy")
+init_page("Marsilea")
 inject_css()
 
 banner, title = st.columns([1, 1.2])
@@ -10,12 +10,12 @@ 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/Heatgraphy/'
+        '<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("Heatgraphy")
+    st.title("Marsilea")
     st.subheader("Create :blue[x-layout] visualization")
     st.text("")
     st.markdown(
@@ -25,7 +25,7 @@ with title:
 st.markdown("---")
 
 st.subheader("About")
-st.markdown("Heatgraphy is a tool for you to create x-layout visualization. "
+st.markdown("Marsilea is a tool for you to create x-layout visualization. "
             "x-layout is a way to visualize a multi-feature dataset. "
             "Instead of creating one plot for each feature, x-layout groups "
             "the plots of different features together "
@@ -50,17 +50,17 @@ def tools(name, img, page, size=150):
 
 
 with t1:
-    tools("Simple Heatmap", "https://heatgraphy.readthedocs.io/en/latest/"
-                            "_images/customized_render-1.png",
+    tools("Simple Heatmap", "https://marsilea.readthedocs.io/en/latest/"
+                            "_images/concatenation-1.png",
           page="/Simple_Heatmap", size=130)
 
 with t2:
-    tools("x-layout", "https://heatgraphy.readthedocs.io/en/latest/"
+    tools("x-layout", "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://heatgraphy.readthedocs.io/en/latest/"
+    tools("Upset Plot", "https://marsilea.readthedocs.io/en/latest/"
                         "_images/sphx_glr_plot_upset_thumb.png",
           page="/Upsetplot", size=220)
 
@@ -83,4 +83,4 @@ with s3:
 
 st.markdown("---")
 
-st.markdown("Copyright © 2023 [Heatgraphy](https://github.com/Heatgraphy)")
+st.markdown("Copyright © 2024 [Marsilea](https://github.com/Marsilea-viz)")

marsilea-0.3.3/app/README.md

@@ -0,0 +1,17 @@
+# 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-0.3.1 → marsilea-0.3.3}/app/components/initialize.py

@@ -110,7 +110,7 @@ def inject_css():
 
 def init_page(title):
     IMG_ROOT = "https://raw.githubusercontent.com/" \
-               "Heatgraphy/marsilea/main/app/img"
+               "Marsilea-viz/marsilea/main/app/img"
 
     st.set_page_config(
         page_title=title,
@@ -118,7 +118,7 @@ def init_page(title):
         page_icon=f"{IMG_ROOT}/favicon.png",
         # initial_sidebar_state="collapsed",
         menu_items={
-            'Report a bug': 'https://github.com/heatgraphy/heatgraphy/issues/new/choose',
-            'About': 'A web interface for Heatgraphy'
+            'Report a bug': 'https://github.com/Marsilea-viz/marsilea/issues/new/choose',
+            'About': 'A web interface for Marsilea'
         }
     )

{marsilea-0.3.1 → marsilea-0.3.3}/app/components/main_plots.py

@@ -8,7 +8,7 @@ from marsilea.plotter import ColorMesh, SizedMesh, MarkerMesh
 from .cmap_selector import ColormapSelector
 
 IMG_ROOT = "https://raw.githubusercontent.com/" \
-           "Heatgraphy/marsilea/main/app/img/"
+           "Marsilea-viz/marsilea/main/app/img/"
 
 
 class MainPlotter:

{marsilea-0.3.1 → marsilea-0.3.3}/app/components/resource.py

@@ -15,7 +15,7 @@ np.random.seed(0)
 
 @st.cache_resource
 def get_font_list():
-    fonts = ["Source Sans Pro", "Roboto", "Open Sans", "Noto Sans", "Raleway",
+    fonts = ["Source Sans 3", "Roboto", "Open Sans", "Noto Sans", "Raleway",
              "Lato", "Montserrat", "Inter", "Oswald"]
     for f in fonts:
         fk.install(f, as_global=False)

{marsilea-0.3.1 → marsilea-0.3.3}/app/components/side_plots.py

@@ -6,7 +6,7 @@ import numpy as np
 import streamlit as st
 
 from marsilea.base import ClusterBoard
-from marsilea.plotter import (Bar, Box, Boxen, Colors, Count, Chunk, Strip,
+from marsilea.plotter import (Bar, Box, Boxen, Colors, Chunk, Strip,
                               Violin,
                               Point, Swarm, AnnoLabels, Labels,
                               Title)
@@ -134,7 +134,7 @@ class LabelAdder(PlotAdder):
                                        key=f"{self.plot_key}_label_pad")
 
     def get_options(self):
-        return dict(align=self.align, text_pad=self.pad,
+        return dict(align=self.align, padding=self.pad,
                     color=self.color)
 
 
@@ -524,19 +524,19 @@ class SwarmAdder(StripAdder):
     example_image = "swarm.png"
 
 
-class CountAdder(PlotAdder):
-    name = "Count"
-    plotter = Count
-    color: str
-
-    plot_explain = "Show the counts of observations in each categorical."
-    example_image = "count.svg"
-
-    def extra_options(self):
-        self.color = st.color_picker("Color", value="#00b796")
-
-    def get_options(self):
-        return dict(color=self.color)
+# class CountAdder(PlotAdder):
+#     name = "Count"
+#     plotter = Count
+#     color: str
+#
+#     plot_explain = "Show the counts of observations in each categorical."
+#     example_image = "count.svg"
+#
+#     def extra_options(self):
+#         self.color = st.color_picker("Color", value="#00b796")
+#
+#     def get_options(self):
+#         return dict(color=self.color)
 
 
 class AnnoLabelsAdder(PlotAdder):
@@ -605,7 +605,7 @@ class ChunkAdder(PlotAdder):
 
     def apply(self, h):
         p = Chunk(texts=self.labels, fill_colors=self.colors,
-                  text_pad=self.text_pad)
+                  padding=self.text_pad)
         h.add_plot(self.side, p, size=self.size, pad=self.pad)
 
 

marsilea-0.3.1/app/pages/01 /360/237/237/250 Simple_Heatmap.py" → marsilea-0.3.3/app/pages/01 Simple_Heatmap.py

@@ -1,4 +1,5 @@
 import matplotlib as mpl
+import matplotlib.pyplot as plt
 import streamlit as st
 from components.cmap_selector import ColormapSelector
 from components.data_input import FileUpload
@@ -184,7 +185,7 @@ if s['data'] is not None:
                         row_labels, mark=row_marks, fontsize=font_size
                     )
                 else:
-                    row_label_plot = Labels(row_labels, text_pad=.1,
+                    row_label_plot = Labels(row_labels, padding=1,
                                             rotation=row_rotation,
                                             fontsize=font_size)
                 h.add_right(row_label_plot)
@@ -195,7 +196,7 @@ if s['data'] is not None:
                         col_labels, mark=col_marks, fontsize=font_size
                     )
                 else:
-                    col_label_plot = Labels(col_labels, text_pad=.1,
+                    col_label_plot = Labels(col_labels, padding=1,
                                             rotation=col_rotation,
                                             fontsize=font_size)
                 h.add_bottom(col_label_plot)
@@ -205,6 +206,8 @@ if s['data'] is not None:
                                  fontsize=title_fontsize), pad=.1)
 
             h.add_legends()
+            if s['figure'] is not None:
+                plt.close(s['figure'])
             h.render()
             s['figure'] = h.figure
 

marsilea-0.3.1/app/pages/02 /360/237/215/261 X-Layout_Heatmap.py" → marsilea-0.3.3/app/pages/02 X-Layout_Heatmap.py

@@ -26,7 +26,7 @@ st.warning("We are still in beta stage, you may report to us "
 st.markdown(
     '<video controls width="250" autoplay="true" muted="true" loop="true" '
     'playsinline style="pointer-events: none;">'
-    '<source src="https://raw.githubusercontent.com/Heatgraphy'
+    '<source src="https://raw.githubusercontent.com/Marsilea-viz'
     '/marsilea/main/app/img/V2.mp4" '
     'type="video/mp4" /></video>', unsafe_allow_html=True)
 

marsilea-0.3.1/app/pages/03 /360/237/225/270/357/270/217 Upsetplot.py" → marsilea-0.3.3/app/pages/03 Upsetplot.py

@@ -1,12 +1,11 @@
 import matplotlib as mpl
 import matplotlib.pyplot as plt
-import numpy as np
 import pandas as pd
 import streamlit as st
 from components.data_input import FileUpload
 from components.initialize import init_page
 from components.initialize import inject_css
-from components.resource import get_font_list, upset_showcase_data,\
+from components.resource import get_font_list, upset_showcase_data, \
     upset_example_data
 from components.saver import ChartSaver
 from components.state import State
@@ -63,7 +62,7 @@ load = st.button("Load Example")
 if load:
     example = upset_example_data()
     s['upset_data'] = UpsetData(example.to_numpy(), items=example.index,
-                                names=example.columns,)
+                                sets_names=example.columns, )
     s["parse_success"] = True
     s['format'] = "Binary Table"
     st.experimental_rerun()
@@ -98,14 +97,13 @@ if data is not None:
 
 if s["parse_success"]:
     upset_data = s['upset_data']
-    filter, highlight, styles = st.tabs(["Filter", "Highlight", "Styles"])
+    filter, styles, highlight = st.tabs(["Filter", "Styles", "Highlight"])
 
     with filter:
-        sets_table = pd.DataFrame(upset_data.cardinality(),
-                                  columns=["size"])
+        sets_table = pd.DataFrame(upset_data.cardinality())
         sets_table["degree"] = sets_table.index.to_frame().sum(axis=1)
 
-        size_upper = int(sets_table['size'].max())
+        size_upper = int(sets_table['cardinality'].max())
         degree_upper = int(sets_table['degree'].max())
 
         c1, c2 = st.columns(2, gap="large")
@@ -118,8 +116,33 @@ if s["parse_success"]:
                                      value=(0, degree_upper),
                                      max_value=degree_upper)
 
+        sort_sets = st.selectbox("Sort sets", options=["ascending", "descending"])
+        sort_subsets = st.selectbox("Sort degree", options=["cardinality", "degree"])
+
     with styles:
         st.markdown("**General**")
+        orient_dict = {"h": "Horizontal", "v": "Vertical"}
+        orient = st.selectbox("Orientation",
+                              options=["h", "v"],
+                              format_func=lambda x: orient_dict[x]
+                              )
+
+        c1, c2, c3 = st.columns(3)
+        with c1:
+            if orient == "v":
+                options = ["left", "right"]
+            else:
+                options = ["top", "bottom"]
+            intersection_plot_pos = st.selectbox("Intersection Plot Position", options=options)
+        with c2:
+            if orient == "v":
+                options = ["top", "bottom"]
+            else:
+                options = ["left", "right"]
+            sets_size_pos = st.selectbox("Sets size Plot Position", options=options)
+        with c3:
+            label_pos = st.selectbox("Label Position", options=options)
+
         g1, g2 = st.columns(2)
         with g1:
             linewidth = st.number_input("Line Width", min_value=.5,
@@ -146,7 +169,7 @@ if s["parse_success"]:
                 "Font size", min_value=1, step=1, value=10)
         with f2:
             font_list = get_font_list()
-            DEFAULT_FONT = font_list.index("Source Sans Pro")
+            DEFAULT_FONT = font_list.index("Lato")
             fontfamily = st.selectbox("Font Family", options=font_list,
                                       index=DEFAULT_FONT)
         with f3:
@@ -166,9 +189,10 @@ if s["parse_success"]:
                              'font.size': fontsize,
                              'font.family': fontfamily}):
             fig = plt.figure()
+            upset_data.reset()
             up = Upset(upset_data,
-                       min_size=size_range[0],
-                       max_size=size_range[1],
+                       min_cardinality=size_range[0],
+                       max_cardinality=size_range[1],
                        min_degree=degree_range[0],
                        max_degree=degree_range[1],
                        color=color,
@@ -176,6 +200,11 @@ if s["parse_success"]:
                        shading=shading,
                        grid_background=grid_background,
                        radius=dot_size,
+                       sort_sets=sort_sets,
+                       sort_subsets=sort_subsets,
+                       orient=orient,
+                       add_intersections=intersection_plot_pos,
+                       add_sets_size=sets_size_pos,
                        )
             up.render(fig)
             s['figure'] = fig

marsilea-0.3.1/app/pages/04 /360/237/223/232 Manual.py" → marsilea-0.3.3/app/pages/04 Manual.py

@@ -5,7 +5,7 @@ from components.initialize import init_page
 init_page("Manual")
 
 IMG_ROOT = "https://raw.githubusercontent.com/" \
-           "Heatgraphy/marsilea/main/app/img"
+           "Marsilea-viz/marsilea/main/app/img"
 
 st.header("Manual")
 
@@ -45,8 +45,8 @@ st.markdown("## How to report a bug?")
 
 st.markdown("Click the botton on the Top Right ➡️ **Report a bug**")
 
-st.markdown("## Can I host my own version of Heatgraphy?")
+st.markdown("## Can I host my own version of Marsilea?")
 
 st.markdown("Sure! Check our "
-            "[GitHub repository](https://github.com/heatgraphy/heatgraphy) "
+            "[GitHub repository](https://github.com/Marsilea-viz/marsilea) "
             "for detail instruction.")

{marsilea-0.3.1 → marsilea-0.3.3}/app/requirements.txt

@@ -1,4 +1,4 @@
-.
+marsilea
 pandas
 openpyxl
 xlrd

{marsilea-0.3.1 → marsilea-0.3.3}/docs/Makefile

@@ -14,7 +14,17 @@ help:
 
 .PHONY: help Makefile
 
+deepclean:
+	@$(SPHINXBUILD) -M clean "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	rm -rf $(SOURCEDIR)/api/APIs/*
+	rm -rf $(SOURCEDIR)/examples
+	rm -rf $(SOURCEDIR)/how_to
+
+
+
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+

marsilea-0.3.3/docs/examples/.gitignore

@@ -0,0 +1,2 @@
+*.png
+imgs

marsilea-0.3.3/docs/examples/Basics/README.rst

@@ -0,0 +1,2 @@
+Basics
+======