Merge pull request #114 from apriha/hotfix/fix-ci-issues

Fix CI issues

Author: apriha

.github/workflows/deploy.yml

@@ -13,9 +13,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies

README.rst

@@ -247,7 +247,7 @@ Thanks to Whit Athey, Ryan Dale, Binh Bui, Jeff Gill, Gopal Vashishtha,
 `CS50 <https://cs50.harvard.edu>`_, and `openSNP <https://opensnp.org>`_.
 
 ``lineage`` incorporates code and concepts generated with the assistance of
-`OpenAI's <https://openai.com>`_ `ChatGPT <https://chat.openai.com>`_ (GPT-3.5). ✨
+`OpenAI's <https://openai.com>`_ `ChatGPT <https://chatgpt.com>`_ . ✨
 
 .. https://github.com/rtfd/readthedocs.org/blob/master/docs/badges.rst
 .. |ci| image:: https://github.com/apriha/lineage/actions/workflows/ci.yml/badge.svg?branch=master

docs/conf.py

@@ -19,6 +19,7 @@
 #
 import os
 import sys
+from unittest.mock import MagicMock
 
 # http://docs.readthedocs.io/en/latest/faq.html#i-get-import-errors-on-libraries-that-depend-on-c-modules
 autodoc_mock_imports = [
@@ -31,6 +32,17 @@
 
 sys.path.insert(0, os.path.abspath("../"))
 
+
+class Mock(MagicMock):
+    @classmethod
+    def __getattr__(cls, name):
+        return MagicMock()
+
+
+# Apply the mock for each module
+for mod_name in autodoc_mock_imports:
+    sys.modules[mod_name] = Mock()
+
 import lineage
 
 # https://samnicholls.net/2016/06/15/how-to-sphinx-readthedocs/

src/lineage/visualization.py

@@ -70,7 +70,6 @@
 
 matplotlib.use("Agg")
 from matplotlib import pyplot as plt
-from matplotlib.collections import BrokenBarHCollection
 from matplotlib import patches
 
 logger = logging.getLogger(__name__)
@@ -139,7 +138,8 @@ def plot_chromosomes(one_chrom_match, two_chrom_match, cytobands, path, title, b
 
     # Now all we have to do is call our function for the chromosome data...
     for collection in _chromosome_collections(df, chrom_ybase, chrom_height):
-        ax.add_collection(collection)
+        xranges, yrange, colors = collection
+        ax.broken_barh(xranges, yrange, facecolors=colors)
 
     # Axes tweaking
     ax.set_yticks([chrom_centers[i] for i in chromosome_list])
@@ -184,8 +184,8 @@ def plot_chromosomes(one_chrom_match, two_chrom_match, cytobands, path, title, b
 def _chromosome_collections(df, y_positions, height, **kwargs):
     """
 
-    Yields BrokenBarHCollection of features that can be added to an Axes
-    object.
+    Yields data for features that can be added to an Axes
+    object using ax.broken_barh.
 
     Parameters
     ----------
@@ -195,13 +195,12 @@ def _chromosome_collections(df, y_positions, height, **kwargs):
         column 'width', it will be calculated from start/end.
 
     y_positions : dict
-        Keys are chromosomes, values are y-value at which to anchor the
-        BrokenBarHCollection
+        Keys are chromosomes, values are y-value at which to anchor the bars
 
     height : float
-        Height of each BrokenBarHCollection
+        Height of each bar
 
-    Additional kwargs are passed to BrokenBarHCollection
+    Additional kwargs are passed to ax.broken_barh
     """
     del_width = False
     if "width" not in df.columns:
@@ -210,9 +209,8 @@ def _chromosome_collections(df, y_positions, height, **kwargs):
     for chrom, group in df.groupby("chrom"):
         yrange = (y_positions["chr" + chrom], height)
         xranges = group[["start", "width"]].values
-        yield BrokenBarHCollection(
-            xranges, yrange, facecolors=group["colors"], **kwargs
-        )
+        colors = group["colors"].values
+        yield xranges, yrange, colors
     if del_width:
         del df["width"]