fix test bugs

GangCaoLab · Jul 14, 2024 · 73896b0 · 73896b0
1 parent 9f0c24f
commit 73896b0
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Showing 8 changed files with 152 additions and 104 deletions.
diff --git a/coolbox/cli.py b/coolbox/cli.py
@@ -250,7 +250,6 @@ def source(self) -> str:
     def print_source(self):
         """Print the browser composing code."""
         print(self.source())
-        return self
 
     def gen_notebook(self, notebook_path, notes=True, figsave=True):
         """Generate The notebook contain codes for run coolbox browser.
@@ -288,7 +287,6 @@ def gen_notebook(self, notebook_path, notes=True, figsave=True):
             )
         nb['cells'] = cells
         nbf.write(nb, notebook_path)
-        return self
 
     def run_jupyter(self, jupyter_args="--ip=0.0.0.0"):
         """Create a notebook according to command line, then start a jupyter process.

diff --git a/coolbox/core/coverage/highlights.py b/coolbox/core/coverage/highlights.py
@@ -87,9 +87,9 @@ def __init__(self, file_, **kwargs):
             "file": file_,
             "color": "bed_rgb",
             "alpha": 0.1,
-            "border_line": True,
+            "border_line": False,
             "border_line_style": "dashed",
-            "border_line_width": 0,
+            "border_line_width": 2,
             "border_line_color": "#000000",
             "border_line_alpha": 0.8,
         }
@@ -168,9 +168,9 @@ def __init__(self, highlight_regions, **kwargs):
             "highlight_regions": highlight_regions,
             "color": HighLights.DEFAULT_COLOR,
             "alpha": 0.25,
-            "border_line": True,
+            "border_line": False,
             "border_line_style": "dashed",
-            "border_line_width": 0,
+            "border_line_width": 2,
             "border_line_color": "#000000",
             "border_line_alpha": 0.8,
         }

diff --git a/coolbox/core/frame/frame.py b/coolbox/core/frame/frame.py
@@ -146,7 +146,7 @@ def get_tracks_height(self, default_height=3):
                 heights.append(default_height)
         return heights
 
-    def plot(self, *args):
+    def plot(self, *args, close_fig=True):
         """
         Plot all tracks.
 
@@ -231,7 +231,8 @@ def plot(self, *args):
                             bottom=margins['bottom'],
                             top=margins['top'])
 
-        plt.close()
+        if close_fig:
+            plt.close()
 
         return fig
 

diff --git a/coolbox/core/track/ideogram.py b/coolbox/core/track/ideogram.py
@@ -1,5 +1,5 @@
 import pandas as pd
-from matplotlib.collections import BrokenBarHCollection
+import matplotlib.pyplot as plt
 
 from coolbox.utilities import (
     get_logger, GenomeRange, file_to_intervaltree, hex2rgb,
@@ -102,9 +102,10 @@ def plot(self, ax, gr: GenomeRange, **kwargs):
                 and gr.length < 80_000_000
             ):
                 self.plot_text(band_name, start, end, gr, band_color)
-        coll = BrokenBarHCollection(xranges, (0, band_height), facecolors=colors,
-                                    linewidths=self.properties['border_width'],
-                                    edgecolors=self.properties['border_color'])
+        coll = plt.broken_barh(
+            xranges, (0, band_height), facecolors=colors,
+            linewidth=self.properties['border_width'],
+            edgecolor=self.properties['border_color'])
         ax.add_collection(coll)
         ax.set_ylim(-0.1, band_height + 0.1)
         ax.set_xlim(gr.start, gr.end)

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -1,5 +1,7 @@
 import os
 import os.path as osp
+import pytest
+from coolbox.utilities import GenomeRange
 
 
 HERE = osp.dirname(osp.abspath(__file__))
@@ -24,3 +26,47 @@ def pytest_sessionstart(session):
 def pytest_sessionfinish(session):
     clear_bgz_and_indexes()
 
+
+@pytest.fixture
+def data_dir():
+    return DATA_DIR
+
+
+@pytest.fixture
+def test_interval():
+    test_interval = GenomeRange("chr9:4000000-6000000")
+    return test_interval
+
+
+@pytest.fixture
+def test_itv(test_interval):
+    return str(test_interval).replace(':', '_').replace('-', '_')
+
+
+@pytest.fixture
+def empty_interval():
+    empty_interval = GenomeRange("chr10:4000000-6000000")
+    return empty_interval
+
+
+@pytest.fixture
+def sub_interval1():
+    sub_interval1 = GenomeRange("chr9:4500000-5000000")
+    return sub_interval1
+
+
+@pytest.fixture
+def sub_interval2():
+    sub_interval2 = GenomeRange("chr9:5200000-5850000")
+    return sub_interval2
+
+
+@pytest.fixture
+def tmp_dir():
+    # yield a temporary directory
+    # delete it after the test
+    from tempfile import mkdtemp
+    import shutil
+    tmpdir = mkdtemp()
+    yield tmpdir
+    shutil.rmtree(tmpdir)
diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -1,21 +1,19 @@
 import os.path as osp
 import subprocess as subp
 
-
 HERE = osp.dirname(osp.abspath(__file__))
-DATA_DIR = f"{HERE}/test_data"
 test_interval = "chr9:4000000-6000000"
 empty_interval = "chr10:4000000-6000000"
 test_itv = test_interval.replace(':', '_').replace('-', '_')
 
 
-def test_cli_plot():
+def test_cli_plot(data_dir, tmp_dir):
     cmd = [
         "python", "-m", "coolbox.cli",
         "add", "XAxis", "-",
-        "add", "BigWig", f"{DATA_DIR}/bigwig_{test_itv}.bw", "-",
-        "add", "BedGraph", f"{DATA_DIR}/bedgraph_{test_itv}.bg", "-",
-        "add", "GTF", f"{DATA_DIR}/gtf_{test_itv}.gtf", "-",
+        "add", "BigWig", f"{data_dir}/bigwig_{test_itv}.bw", "-",
+        "add", "BedGraph", f"{data_dir}/bedgraph_{test_itv}.bg", "-",
+        "add", "GTF", f"{data_dir}/gtf_{test_itv}.gtf", "-",
         "goto", test_interval, "-",
         "plot", "/tmp/test_coolbox.pdf",
     ]
@@ -25,43 +23,48 @@ def test_cli_plot():
         python -m coolbox.cli
           joint_view top - 
             add XAxis - 
-            add GTF {DATA_DIR}/gtf_{test_itv}.gtf - 
+            add GTF {data_dir}/gtf_{test_itv}.gtf - 
             add Title GTF - 
           joint_view right - 
             add XAxis - 
-            add BigWig {DATA_DIR}/bigwig_{test_itv}.bw - 
+            add BigWig {data_dir}/bigwig_{test_itv}.bw - 
             add TrackHeight 2 - 
             add MinValue 0 - 
           joint_view center - 
-            add Cool {DATA_DIR}/cool_{test_itv}.mcool  - 
+            add Cool {data_dir}/cool_{test_itv}.mcool  - 
           goto 'chr9:4500000-5000000' 'chr9:5200000-5850000' - 
-          plot /tmp/test_coolbox_joint_view.svg
+          plot {tmp_dir}/test_coolbox_joint_view.svg
         """
-
-    subp.check_call(cmd.replace("\n", ""), shell=True)
+    cmd = cmd.replace("\n", "")
+    print(cmd)
+    subp.check_call(cmd, shell=True)
 
 
-def test_cli_gen_notebook():
+def test_cli_gen_notebook(data_dir, tmp_dir):
     cmd = [
         "python", "-m", "coolbox.cli",
         "add", "XAxis", "-",
-        "add", "BigWig", f"{DATA_DIR}/bigwig_{test_itv}.bw", "-",
-        "add", "BedGraph", f"{DATA_DIR}/bedgraph_{test_itv}.bg", "-",
-        "add", "GTF", f"{DATA_DIR}/gtf_{test_itv}.gtf", "-",
+        "add", "BigWig", f"{data_dir}/bigwig_{test_itv}.bw", "-",
+        "add", "BedGraph", f"{data_dir}/bedgraph_{test_itv}.bg", "-",
+        "add", "GTF", f"{data_dir}/gtf_{test_itv}.gtf", "-",
         "goto", test_interval, "-",
-        "gen_notebook", "/tmp/test_coolbox.ipynb",
+        "gen_notebook", f"{tmp_dir}/test_coolbox.ipynb",
     ]
-    subp.check_call(cmd)
+    cmd = " ".join(cmd)
+    print(cmd)
+    subp.check_call(cmd, shell=True)
 
 
-def test_cli_import_custom():
+def test_cli_import_custom(tmp_dir):
     custom_path = osp.join(HERE, "custom_track.py")
     cmd = [
         "python", "-m", "coolbox.cli",
         "load_module", custom_path, "-",
         "add", "XAxis", "-",
         "add", "CustomTrack", "-",
         "goto", test_interval, "-",
-        "plot", "/tmp/test_coolbox_custom.pdf"
+        "plot", f"{tmp_dir}/test_coolbox_custom.pdf"
     ]
-    subp.check_call(cmd)
+    cmd = " ".join(cmd)
+    print(cmd)
+    subp.check_call(cmd, shell=True)
diff --git a/tests/test_coverage.py b/tests/test_coverage.py
@@ -1,54 +1,52 @@
-import os.path as osp
 from coolbox.api import *
 
-HERE = osp.dirname(osp.abspath(__file__))
-DATA_DIR = f"{HERE}/test_data"
-test_interval = "chr9:4000000-6000000"
-empty_interval = "chr10:4000000-6000000"
-test_itv = test_interval.replace(':', '_').replace('-', '_')
 
-
-def test_vlines():
+def test_vlines(test_interval, tmp_dir):
     vlines = Vlines([("chr9", 4000000),
                      "chr9:5000000-6000000",
                      ("chr1", 4000000)])
     with vlines:
         frame = XAxis() + XAxis()
     fig = frame.plot(test_interval)
-    fig.savefig("/tmp/test_coolbox_vline.pdf")
+    fig.savefig(f"{tmp_dir}/test_coolbox_vline.pdf")
 
 
-def test_highlights():
+def test_highlights(test_interval, tmp_dir):
     highlights = HighLights([
         ("chr9", 4000000, 5000000),
         "chr9:5000000-6000000",
     ])
     with highlights:
         frame = XAxis() + XAxis()
-    fig = frame.plot(test_interval)
-    fig.savefig("/tmp/test_coolbox_highlights.pdf")
+    fig = frame.plot(test_interval, close_fig=False)
+    fig.savefig(f"{tmp_dir}/test_coolbox_highlights.pdf")
 
 
-def test_bigwig_coverage():
+def test_bigwig_coverage(data_dir, test_itv, test_interval, tmp_dir):
     frame = XAxis() +\
-        BigWig(f"{DATA_DIR}/bigwig_{test_itv}.bw", style="line:1") + \
-        BigWigCoverage(f"{DATA_DIR}/bigwig_{test_itv}.bw", style="fill", color="red", alpha=0.3) +\
-        BigWigCoverage(f"{DATA_DIR}/bigwig_{test_itv}.bw", style="fill", color="blue", alpha=0.3)
+        BigWig(f"{data_dir}/bigwig_{test_itv}.bw", style="line:1") + \
+        BigWigCoverage(f"{data_dir}/bigwig_{test_itv}.bw", style="fill", color="red", alpha=0.3) +\
+        BigWigCoverage(f"{data_dir}/bigwig_{test_itv}.bw", style="fill", color="blue", alpha=0.3)
     fig = frame.plot(test_interval)
-    fig.savefig("/tmp/test_coolbox_bwcov.pdf")
+    fig.savefig(f"{tmp_dir}/test_coolbox_bwcov.pdf")
 
 
-def test_arcs_coverage():
+def test_arcs_coverage(data_dir, test_itv, test_interval, tmp_dir):
     frame = XAxis() + \
-        BigWig(f"{DATA_DIR}/bigwig_{test_itv}.bw", style="fill", alpha=0.5) + \
-        ArcsCoverage(f"{DATA_DIR}/bedpe_{test_itv}.bedpe")
+        BigWig(f"{data_dir}/bigwig_{test_itv}.bw", style="fill", alpha=0.5) + \
+        ArcsCoverage(f"{data_dir}/bedpe_{test_itv}.bedpe")
     fig = frame.plot(test_interval)
-    fig.savefig("/tmp/test_coolbox_arcscov.pdf")
+    fig.savefig(f"{tmp_dir}/test_coolbox_arcscov.pdf")
 
 
-def test_tad_coverage():
+def test_tad_coverage(data_dir, test_itv, test_interval, tmp_dir):
     frame = XAxis() + \
-        Cool(f"{DATA_DIR}/cool_{test_itv}.mcool") + \
-        TADCoverage(f"{DATA_DIR}/tad_{test_itv}.bed")
+        Cool(f"{data_dir}/cool_{test_itv}.mcool") + \
+        TADCoverage(f"{data_dir}/tad_{test_itv}.bed")
     fig = frame.plot(test_interval)
-    fig.savefig("/tmp/test_coobox_tadcov.pdf")
+    fig.savefig(f"{tmp_dir}/test_coobox_tadcov.pdf")
+
+
+if __name__ == '__main__':
+    test_highlights(GenomeRange("chr9:3000000-7000000"), "/tmp")
+    #test_vlines(GenomeRange("chr9:4000000-6000000"), "/tmp")