Reorganize code into src folder to avoid import issues

Author: thalassemia

.github/workflows/release.yml

@@ -108,22 +108,7 @@ jobs:
           CIBW_FREE_THREADED_SUPPORT: ${{ matrix.free_threaded_support }}
           CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
           CIBW_TEST_REQUIRES: pytest psutil
-          CIBW_TEST_COMMAND: |
-            mkdir tmp_test_dir
-            cp -r {project}/stochastic_arrow/test tmp_test_dir/test
-            cp -r {project}/data tmp_test_dir/data
-            cd tmp_test_dir
-            pytest
-          CIBW_TEST_COMMAND_WINDOWS: |
-            echo "Starting tests on Windows";
-            mkdir tmp_test_dir;
-            echo "Copying test directory";
-            xcopy /E /I /Y stochastic_arrow\test tmp_test_dir\test;
-            echo "Copying data directory";
-            xcopy /E /I /Y stochastic_arrow\data tmp_test_dir\data;
-            cd tmp_test_dir;
-            echo "Running pytest on Windows";
-            pytest -v
+          CIBW_TEST_COMMAND: pytest -v {project}/test
           CIBW_ENVIRONMENT: USE_CYTHON=1
         uses: pypa/cibuildwheel@v2.22.0
 

.gitignore

@@ -10,9 +10,9 @@ profile
 /.idea/
 /tmp/
 
-stochastic_arrow/arrowhead.c
-stochastic_arrow/arrowhead.*.pyd
-stochastic_arrow/*.html
+src/stochastic_arrow/arrowhead.c
+src/stochastic_arrow/arrowhead.*.pyd
+src/stochastic_arrow/*.html
 
 arrow.egg-info/
 stochastic_arrow.egg-info/

MANIFEST.in

@@ -1,2 +1,2 @@
-include stochastic_arrow/obsidian.h
-include stochastic_arrow/mersenne.h
+include src/stochastic_arrow/obsidian.h
+include src/stochastic_arrow/mersenne.h

Makefile

@@ -2,9 +2,11 @@
 .DEFAULT_GOAL := compile
 
 clean:
-	### Files for older versions of stochastic_arrow are in arrow folder
+	### Files for older versions of stochastic_arrow are in arrow or stochastic_arrow folder
 	rm -rf arrow/arrowhead*.so arrow/arrowhead.c arrow/arrowhead.html
 	rm -rf stochastic_arrow/arrowhead*.so stochastic_arrow/arrowhead.c stochastic_arrow/arrowhead.html build/ dist/ MANIFEST .pytest_cache/ stochastic_arrow.egg-info/
+	### Newer versions of stochastic_arrow are in src/stochastic_arrow folder
+	rm -rf src/stochastic_arrow/arrowhead*.so src/stochastic_arrow/arrowhead.c src/stochastic_arrow/arrowhead.html src/stochastic_arrow.egg-info/
 	find . -name "*.pyc" -delete
 	find . -name "__pycache__" -delete
 

stochastic_arrow/analysis/__init__.py analysis/__init__.pystochastic_arrow/analysis/__init__.py renamed to analysis/__init__.py

@@ -1,5 +1,5 @@
 import os
-from setuptools import Extension, setup
+from setuptools import Extension, find_packages, setup
 import sys
 import numpy as np
 
@@ -20,28 +20,31 @@
 
 ext = '.pyx' if USE_CYTHON else '.c'
 
+arrow_dir = os.path.join('src', 'stochastic_arrow')
+
 cython_extensions = [
     Extension('stochastic_arrow.arrowhead',
               sources=[
-                  'stochastic_arrow/mersenne.c',
-                  'stochastic_arrow/obsidian.c',
-                  'stochastic_arrow/arrowhead'+ext,],
-              include_dirs=['stochastic_arrow', np.get_include()],
+                  os.path.join(arrow_dir, 'mersenne.c'),
+                  os.path.join(arrow_dir, 'obsidian.c'),
+                  os.path.join(arrow_dir, 'arrowhead'+ext),],
+              include_dirs=[arrow_dir, np.get_include()],
               define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
               )]
 
 if USE_CYTHON:
     from Cython.Build import cythonize
     cython_extensions = cythonize(
         cython_extensions,
-        include_path=['stochastic_arrow'],
+        include_path=[arrow_dir],
         annotate=True,  # to get an HTML code listing
     )
 
 setup(
     name='stochastic-arrow',
     version='1.0.0',
-    packages=['stochastic_arrow'],
+    packages=find_packages('src'),
+    package_dir={'': 'src'},
     author='Ryan Spangler, John Mason, Jerry Morrison, Chris Skalnik, Travis Ahn-Horst, Sean Cheah',
     author_email='ryan.spangler@gmail.com',
     url='https://github.com/CovertLab/arrow',