Merge pull request #39 from AlexandrovLab/u56_m2

U56 m2

.gitignore

@@ -34,3 +34,8 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
+
+
+# test output
+tests/input/*/output/*
+sigProfilerPlotting/examples/output/

.travis.yml

@@ -6,7 +6,10 @@ python:
 
 install:
   - pip install -q matplotlib
-  - pip install . -v
-
-script: python3 plot_example.py
+  - pip install .[tests]
 
+script: 
+  # run integration test
+  - python3 sigProfilerPlotting/examples/plot_example.py
+  # run unit tests
+  - pytest -s -rw tests

MANIFEST.in

@@ -1,2 +1,3 @@
-include fonts/*
-include reference_formats/*
+include sigProfilerPlotting/fonts/*
+include sigProfilerPlotting/reference_formats/*
+include tests/*

README.md

@@ -58,10 +58,9 @@ sigPlt.plotID(matrix_path, output_path, project, plot_type, percentage=False)
 ```python
 import sigProfilerPlotting as sigPlt
 
-matrix_path = "./input/examples/samples/breast_cancer_samples_example.CNV48.all" #Output of CNVMatrixGenerator
-output_path = "./output/examples/samples/"
+matrix_path = "./sigProfilerPlotting/examples/input/breast_cancer_samples_example.CNV48.all" #Output of CNVMatrixGenerator
+output_path = "./sigProfilerPlotting/examples/output/"
 project = "Breast"
-
 ```
 
 **AVAILABLE FUNCTIONS**
@@ -106,12 +105,12 @@ sP.samplePortrait(sample_matrices_path, output_path, project, percentage=False)
 
 **EXAMPLE**
 
-This package comes with an example test for each plot type. Run the script plot_example.py from within the downloaded repo after installation:
+This package comes with an example test for each plot type. Run the script plot_example.py from within the examples directory in the downloaded repo after installation:
 ```python
-python3 plot_example.py
+python3 sigProfilerPlotting/examples/plot_example.py
 ```
 
-This example will create plots for each context for each of the included four samples. These plots will be saved within the BRCA_plot/plots/ folder.
+This example will create plots for each context for each of the included four samples. These plots will be saved within the `sigProfilerPlotting/examples/output/` folder.
 
 **CITATION**
 

setup.py

@@ -1,6 +1,5 @@
 import os
 import shutil
-import warnings
 
 from setuptools import setup
 from setuptools.command.install import install
@@ -15,7 +14,7 @@ def readme():
         return f.read()
 
 
-VERSION = "1.3.14"
+VERSION = "1.3.15"
 
 
 def write_version_py(filename="sigProfilerPlotting/version.py"):
@@ -28,54 +27,17 @@ def write_version_py(filename="sigProfilerPlotting/version.py"):
     """
     fh = open(filename, "w")
     fh.write(
-        cnt % {"version": VERSION,}
+        cnt
+        % {
+            "version": VERSION,
+        }
     )
     fh.close()
 
 
 write_version_py()
 
 
-# Set up the machinery to install custom fonts.  Subclass the setup tools install
-# class in order to run custom commands during installation.
-class move_ttf(install):
-    def run(self):
-        """
-        Performs the usual install process and then copies the True Type fonts
-        that come with clearplot into matplotlib's True Type font directory,
-        and deletes the matplotlib fontList.cache
-        """
-        # Perform the usual install process
-        install.run(self)
-        # Try to install custom fonts
-        try:
-            import os, shutil
-            import matplotlib
-            import matplotlib.font_manager
-
-            # Find where matplotlib stores its True Type fonts
-            mpl_data_dir = os.path.dirname(matplotlib.matplotlib_fname())
-            mpl_ttf_dir = os.path.join(mpl_data_dir, "fonts", "ttf")
-            cp_ttf_dir = os.path.dirname(os.path.realpath(__file__))
-
-            file_names = [
-                "Times New Roman.ttf",
-                "Arial.ttf",
-                "Courier New.ttf",
-                "Courier New Bold.ttf",
-                "Arial Bold.ttf",
-                "Times New Roman Bold.ttf",
-            ]
-            for file in file_names:
-                old_path = os.path.join(cp_ttf_dir, "fonts/" + file)
-                new_path = os.path.join(mpl_ttf_dir, file)
-                shutil.copyfile(old_path, new_path)
-            matplotlib.font_manager._rebuild()
-
-        except:
-            warnings.warn("WARNING: An issue occured while installing the fonts.")
-
-
 with open("README.md") as f:
     readme = f.read()
 
@@ -89,15 +51,25 @@ def run(self):
     author="Erik Bergstrom",
     author_email="[email protected]",
     license="UCSD",
-    packages=["sigProfilerPlotting"],
+    packages=[
+        "sigProfilerPlotting",
+        "sigProfilerPlotting.reference_formats",
+        "sigProfilerPlotting.fonts",
+    ],
     install_requires=[
         "matplotlib>=3.4.3",
         "pandas>=1.2.4,<2.0.0",
         "scikit-learn>=1.1.3",
+        "pillow>=10.0.0",
     ],
+    extras_require={
+        "tests": [
+            "pytest",
+            "scikit-image>=0.21.0",
+            "numpy>=1.21.2",
+        ],
+    },
     package_data={"": ["fonts/*.ttf"]},
     include_package_data=True,
-    # Specify the custom install class
-    cmdclass={"install": move_ttf},
     zip_safe=False,
 )

plot_example.py → sigProfilerPlotting/examples/plot_example.py

@@ -2,11 +2,11 @@
 
 import sigProfilerPlotting as sigPlt
 
-matrix_path = "input/examples/samples/"
-output_path = "output/examples/"
+SPP_EXAMPLE_PATH = os.path.dirname(os.path.abspath(__file__))
+
+matrix_path = os.path.join(SPP_EXAMPLE_PATH, "input/")
+output_path = os.path.join(SPP_EXAMPLE_PATH, "output/")
 
-# matrix_path = ''
-# output_path = ''
 if not os.path.exists(output_path):
     os.makedirs(output_path)
 
@@ -39,6 +39,3 @@
     percentage=False,
     aggregate=False,
 )  # plotting of SV counts
-
-# sigPlt.plotDBS(matrix_path + "breast_cancer_samples_example.DBS78.all", output_path, "BRCA_example", "78")
-# sigPlt.plotID(matrix_path + "breast_cancer_samples_example.ID94.all", output_path,  "BRCA_example", "94")