Dev (#744)

* read the string back

* Add chromosome()

* fix ci

* Add get_shades()

* fix ci

* draw chromosomes

* minor

* add cross symbol

* simulate sequentially

* minor fix

* update savefig

* use multiprocessing

* sort by descending weight

* update

* superfluous sorted()

* update

.github/workflows/build.yml

@@ -21,7 +21,9 @@ jobs:
           cache: 'pip'
 
       - name: Install BEDTools (Linux)
-        run: sudo apt-get install bedtools libmagickwand-dev
+        run: |
+            sudo apt-get update
+            sudo apt-get install --fix-missing bedtools libmagickwand-dev
         if: matrix.os == 'ubuntu-latest'
 
       - name: Install BEDTools (macOS)

src/jcvi/apps/base.py

@@ -26,12 +26,9 @@
 from socket import gethostname
 from subprocess import CalledProcessError, PIPE, call, check_output
 from time import ctime
-from typing import Any, Collection, List, Optional, Tuple, Union
+from typing import Collection, List, Optional, Tuple, Union
 from urllib.parse import urlencode
 
-# from optparse import OptionParser as OptionP, OptionGroup, SUPPRESS_HELP
-
-
 from natsort import natsorted
 from rich.console import Console
 from rich.logging import RichHandler

src/jcvi/graphics/base.py

@@ -17,6 +17,7 @@
 
 mpl.use("Agg")
 
+import matplotlib.colors as mcolors
 import matplotlib.pyplot as plt
 import matplotlib.ticker as ticker
 
@@ -322,39 +323,20 @@ def update_figname(figname: str, format: str) -> str:
     return figname + "." + format
 
 
-def update_figname(figname: str, format: str) -> str:
-    """Update the name of a figure to include the format.
-
-    Args:
-        figname (str): Path to the figure
-        format (str): Figure format, must be one of GRAPHIC_FORMATS
-
-    Returns:
-        str: New file path
-    """
-    _, ext = op.splitext(figname)
-    if ext.strip(".") in GRAPHIC_FORMATS:  # User suffix has precedence
-        return figname
-    # When the user has not supplied a format in the filename, use the requested format
-    assert format in GRAPHIC_FORMATS, "Invalid format"
-    return figname + "." + format
-
-
 def savefig(figname, dpi=150, iopts=None, cleanup=True, transparent=False):
     try:
         format = figname.rsplit(".", 1)[-1].lower()
     except:
         format = "pdf"
+    logger.debug("Matplotlib backend is: %s", mpl.get_backend())
     try:
-        logger.debug(f"Matplotlib backend is: {mpl.get_backend()}")
-        logger.debug(f"Attempting save as: {figname}")
+        logger.debug("Attempting save as: `%s`", figname)
         plt.savefig(figname, dpi=dpi, format=format, transparent=transparent)
     except Exception as e:
         message = "savefig failed with message:"
         message += "\n{0}".format(str(e))
         logger.error(message)
-        logger.debug(f"Matplotlib backend is: {mpl.get_backend()}")
-        logger.debug(f"Attempted save as: {format}")
+        logger.debug("Attempted save as: %s", format)
         logger.info("Try running again with --notex option to disable latex.")
         if op.exists(figname):
             if op.getsize(figname) < 1000:
@@ -677,6 +659,31 @@ def get_intensity(octal):
     return intensity
 
 
+def get_shades(base_color: str, n: int) -> np.array:
+    """
+    Generate N shades of a base color by blending with white and black. The base
+    color is in hex format, e.g., '#FF0000' for red.
+    """
+    base_rgb = np.array(mcolors.to_rgb(base_color))  # Convert hex to RGB (normalized)
+    lighter = n // 2
+    darker = n - lighter - 1
+
+    # Generate lighter shades by blending with white
+    white = np.array([1, 1, 1])  # White color as a NumPy array
+    lighter_shades = [
+        (white * (1 - i) + base_rgb * i) for i in np.linspace(0.2, 1, lighter + 1)
+    ][:-1]
+
+    # Generate darker shades by blending with black
+    black = np.array([0, 0, 0])  # Black color as a NumPy array
+    darker_shades = [
+        (base_rgb * i + black * (1 - i)) for i in np.linspace(1, 0.2, darker + 1)
+    ][1:]
+
+    # Combine all shades with the base color in the middle
+    return lighter_shades + [base_rgb] + darker_shades
+
+
 def adjust_spines(ax, spines, outward=False, color="lightslategray"):
     # Modified from <http://matplotlib.org/examples/pylab_examples/spine_placement_demo.html>
     for loc, spine in ax.spines.items():

src/jcvi/graphics/chromosome.py

@@ -9,7 +9,7 @@
 
 from itertools import groupby
 from math import ceil
-from typing import Optional, Tuple
+from typing import List, Optional, Tuple
 
 import numpy as np
 
@@ -43,15 +43,15 @@ class Chromosome(BaseGlyph):
     def __init__(
         self,
         ax,
-        x,
-        y1,
-        y2,
-        width=0.015,
-        ec="k",
-        patch=None,
-        patchcolor="lightgrey",
-        lw=1,
-        zorder=2,
+        x: float,
+        y1: float,
+        y2: float,
+        width: float = 0.015,
+        ec: str = "k",
+        patch: Optional[List[float]] = None,
+        patchcolor: str = "lightgrey",
+        lw: int = 1,
+        zorder: int = 2,
     ):
         """
         Chromosome with positions given in (x, y1) => (x, y2)