Include notebook into package

MANIFEST.in

@@ -1,2 +1,4 @@
 global-include *.pyx
 global-include *.pxd
+graft notebooks
+include annotate/ldlr_exons.fa

bean/cli/profile.py

@@ -22,7 +22,7 @@ def main(args):
         "python -m ipykernel install --user --name bean_python3 --display-name bean_python3"
     )
     pm.execute_notebook(
-        f"{os.path.dirname(be.__file__)}/../notebooks/profile_editing_preference.ipynb",
+        f"{os.path.dirname(be.__file__)}/notebooks/profile_editing_preference.ipynb",
         f"{args.output_prefix}.ipynb",
         parameters=dict(
             bdata_path=args.bdata_path,

bean/cli/qc.py

@@ -26,7 +26,7 @@ def main(args):
         "python -m ipykernel install --user --name bean_python3 --display-name bean_python3"
     )
     pm.execute_notebook(
-        f"{os.path.dirname(be.__file__)}/../notebooks/sample_quality_report.ipynb",
+        f"{os.path.dirname(be.__file__)}/notebooks/sample_quality_report.ipynb",
         f"{args.out_report_prefix}.ipynb",
         parameters=dict(
             bdata_path=args.bdata_path,

bean/plotting/utils.py

@@ -1,4 +1,5 @@
 import argparse
+import os
 
 
 def parse_args(parser=None):
@@ -23,7 +24,7 @@ def parse_args(parser=None):
         "--condition-col",
         help="Column name in `bdata.samples` that describes experimental condition. (sorting bin, time, etc.)",
         type=str,
-        default="bin",
+        default="condition",
     )
     parser.add_argument(
         "--pam-col",
@@ -49,6 +50,8 @@ def parse_args(parser=None):
 
 
 def check_args(args):
+    if args.output_prefix is None:
+        args.output_prefix = os.path.splitext(args.bdata_path)[0]
     if args.window_length < 1:
         raise ValueError(f"window_length {args.window_length} is too small.")
     if args.window_length > 20:

setup.py

@@ -1,5 +1,5 @@
 import numpy as np
-from setuptools import setup, find_packages
+from setuptools import setup, find_namespace_packages
 from Cython.Build import cythonize
 
 with open("README.md", "r") as fh:
@@ -16,7 +16,7 @@
     long_description=long_description,
     long_description_content_type="text/markdown",
     url="https://github.com/pinellolab/crispr-bean",
-    packages=find_packages(),
+    packages=find_namespace_packages(),
     ext_modules=cythonize(["bean/mapping/CRISPResso2Align.pyx"]),
     include_dirs=np.get_include(),
     setup_requires=[
@@ -45,14 +45,14 @@
         "nbconvert",
         "logomaker",
     ],
-    extras_require={"model": ["pyBigWig", "pyro-ppl<=1.8.1", "statsmodels", "torch"]},
+    extras_require={"model": ["pyBigWig", "pyro-ppl", "statsmodels", "torch"]},
     include_package_data=True,
     package_data={
-        "": [
-            "bean/annotate/ldlr_exons.fa",
-            "notebooks/sample_quality_report.ipynb",
-            "notebooks/profile_editing_preference.ipynb",
-        ]
+        "bean.annotate": ["ldlr_exons.fa"],
+        "bean.notebooks": [
+            "sample_quality_report.ipynb",
+            "profile_editing_preference.ipynb",
+        ],
     },
     classifiers=[
         "Programming Language :: Python :: 3",