marsilea 0.3.4__tar.gz → 0.3.6__tar.gz

{marsilea-0.3.4 → marsilea-0.3.6}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: marsilea
-Version: 0.3.4
-Summary: Create x-layout visualization
+Version: 0.3.6
+Summary: Declarative creation of composable visualization
 Author: Zhihang Zheng
 Author-email: Mr-Milk <yzheng@cemm.at>
 Requires-Python: >=3.8

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

@@ -0,0 +1,24 @@
+[[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-0.3.4 → marsilea-0.3.6}/app/Home.py

@@ -1,35 +1,37 @@
 import streamlit as st
-
 from components.initialize import init_page, inject_css
 
 init_page("Marsilea")
 inject_css()
 
-banner, title = st.columns([1, 1.2])
+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)
+        'type="video/mp4" /></video>',
+        unsafe_allow_html=True,
+    )
 
 with title:
     st.title("Marsilea")
-    st.subheader("Create :blue[x-layout] visualization")
+    st.subheader("Create :blue[composable] visualization")
     st.text("")
     st.markdown(
         "*By [Mr.Milk](https://github.com/Mr-Milk) and "
-        "[Squirtle692](https://github.com/Squirtle692)*")
+        "[Squirtle692](https://github.com/Squirtle692)*"
+    )
 
 st.markdown("---")
 
 st.subheader("About")
-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 "
-            "to make them annotate each other.")
+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("---")
 
@@ -45,24 +47,36 @@ def tools(name, img, page, size=150):
         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)
+        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)
+    tools(
+        "Simple Heatmap",
+        "https://marsilea.readthedocs.io/en/latest/" "_images/concatenation-1.png",
+        page="/Simple_Heatmap",
+        size=130,
+    )
 
 with t2:
-    tools("x-layout", "https://marsilea.readthedocs.io/en/latest/"
-                      "_images/sphx_glr_plot_pbmc3k_thumb.png",
-          page="X-Layout_Heatmap", size=200)
+    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)
+    tools(
+        "Upset Plot",
+        "https://marsilea.readthedocs.io/en/latest/"
+        "_images/sphx_glr_plot_upset_thumb.png",
+        page="/Upsetplot",
+        size=220,
+    )
 
 st.markdown("---")
 
@@ -72,13 +86,15 @@ 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)
+        width=50,
+    )
 
 with s2:
-    st.markdown("Familiar with Python? Try our Python package "
-                "that can be easily integrated into your data pipeline!")
+    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("---")

{marsilea-0.3.4 → marsilea-0.3.6}/app/components/cmap_selector/selector.py

@@ -3,8 +3,12 @@ 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
+from matplotlib.colors import (
+    LinearSegmentedColormap,
+    Normalize,
+    CenteredNorm,
+    TwoSlopeNorm,
+)
 
 
 @st.cache_data
@@ -21,7 +25,7 @@ def get_colormap_images(cmap):
     gradient = np.linspace(0, 1, 256)
     gradient = np.vstack((gradient, gradient))
 
-    fig = plt.figure(figsize=(6, .5), dpi=90)
+    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()
@@ -30,11 +34,10 @@ def get_colormap_images(cmap):
 
 
 def random_color():
-    return "#" + "".join(np.random.choice(list('0123456789ABCDEF'), 6))
+    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())
@@ -46,28 +49,29 @@ class ColormapSelector:
         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'
-                                  )
+            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')
+            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 = 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()
@@ -79,29 +83,36 @@ class ColormapSelector:
             select_box, cmap_box = st.columns(2)
             with select_box:
                 ncolors = st.selectbox(
-                    label="Colormap Type", key=f'{key}-select-gradient',
+                    label="Colormap Type",
+                    key=f"{key}-select-gradient",
                     label_visibility="collapsed",
-                    options=["One Gradient", "Two Gradient"])
+                    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', )
+                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', )
+                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', )
+                    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))
+            self.cmap = LinearSegmentedColormap.from_list("user_cmap", colors)
 
             if self.reverse:
                 self.cmap = self.cmap.reversed()
@@ -113,44 +124,50 @@ class ColormapSelector:
         if data_mapping:
             norm_strategy = st.selectbox(
                 "Mapping Strategy",
-                key=f'{key}-norm-selector',
-                options=["Linear", "Min-Max", "Centered On", "Two Range"])
+                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')
+                    vmin = st.number_input("Min", key=f"{key}-norm-vmin")
                 with v2:
-                    vmax = st.number_input("Max", key=f'{key}-norm-vmax')
+                    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')
+                    vcenter = st.number_input(
+                        "Center", key=f"{key}-center_norm-vcenter"
+                    )
                 with v2:
-                    vhalf = st.number_input("Extend", min_value=0., value=1.,
-                                            key=f'{key}-center_norm-vhalf')
+                    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., key=f'{key}-tsnorm-vmin')
+                    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')
+                        "Center", value=vmin + 1, key=f"{key}-tsnorm-vcenter"
+                    )
                 with v3:
                     vmax = st.number_input(
-                        "Max", value=vcenter+1, key=f'{key}-tsnorm-vmax')
+                        "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)
+                    self.norm = TwoSlopeNorm(vcenter=vcenter, vmin=vmin, vmax=vmax)
 
     def get_cmap(self):
         return self.cmap

{marsilea-0.3.4 → marsilea-0.3.6}/app/components/data_input.py

@@ -19,20 +19,13 @@ class InputBase:
         pass
 
     def seperator(self):
-        sep_options = {
-            "Tab (\\t)": "\t",
-            "Comma (,)": ",",
-            "Space (' ')": " "
-        }
-        user_sep = st.selectbox("Seperator", key=self.key,
-                                options=sep_options.keys())
+        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):
-
+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"]:
@@ -49,17 +42,19 @@ def parse_file(file, header=False, index=False,
 
 
 class FileUpload(InputBase):
-
-    def __init__(self, key=None, header=False, index=False,
-                 use_header=False, use_index=False):
+    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"])
+        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)
@@ -78,28 +73,35 @@ class FileUpload(InputBase):
         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)
+                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)
+                    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}")
+        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}")
+        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)
+            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:
@@ -110,8 +112,12 @@ class FileUpload(InputBase):
 
     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)
+            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()
@@ -129,7 +135,6 @@ class FileUpload(InputBase):
 
 
 class PasteText(InputBase):
-
     def __init__(self, cast_number=True, key=None):
         super().__init__(key=key)
         self.cast_number = cast_number

{marsilea-0.3.4 → marsilea-0.3.6}/app/components/example_download.py

@@ -9,7 +9,6 @@ from random_word.random_word import RandomWords
 
 
 class ExampleDataGenerator:
-
     def __init__(self, col, row):
         np.random.seed(0)
         self.col = col
@@ -59,11 +58,12 @@ def get_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>'
+        href = (
+            f'<a href="data:file/zip;base64,{self.b64}" '
+            f'download="example.zip">Example Data</a>'
+        )
         st.markdown(href, unsafe_allow_html=True)
 
 

{marsilea-0.3.4 → marsilea-0.3.6}/app/components/initialize.py

@@ -10,8 +10,8 @@ from streamlit.runtime import caching
 
 
 def _nestable_block(
-        self,
-        block_proto: Block_pb2.Block = Block_pb2.Block(),
+    self,
+    block_proto: Block_pb2.Block = Block_pb2.Block(),
 ) -> "DeltaGenerator":
     # Operate on the active DeltaGenerator, in case we're in a `with` block.
     dg = self._active_dg
@@ -74,7 +74,8 @@ def enable_nested_columns():
 
 def inject_css():
     # Hack the style of elements in streamlit
-    st.markdown("""
+    st.markdown(
+        """
     <style>
 
         # .main .block-container {
@@ -105,12 +106,13 @@ def inject_css():
         }
 
     </style>
-    """, unsafe_allow_html=True)
+    """,
+        unsafe_allow_html=True,
+    )
 
 
 def init_page(title):
-    IMG_ROOT = "https://raw.githubusercontent.com/" \
-               "Marsilea-viz/marsilea/main/app/img"
+    IMG_ROOT = "https://raw.githubusercontent.com/" "Marsilea-viz/marsilea/main/app/img"
 
     st.set_page_config(
         page_title=title,
@@ -118,7 +120,7 @@ def init_page(title):
         page_icon=f"{IMG_ROOT}/favicon.png",
         # initial_sidebar_state="collapsed",
         menu_items={
-            'Report a bug': 'https://github.com/Marsilea-viz/marsilea/issues/new/choose',
-            'About': 'A web interface for Marsilea'
-        }
+            "Report a bug": "https://github.com/Marsilea-viz/marsilea/issues/new/choose",
+            "About": "A web interface for Marsilea",
+        },
     )