From e59556dd605b3e0671b65b86ba01666ed2fc9c75 Mon Sep 17 00:00:00 2001
From: SCM <samuel.musson@durham.ac.uk>
Date: Fri, 20 May 2022 16:27:05 +0100
Subject: [PATCH] Fixed setuptools so that cython works nicely in the modern
 era. python setup.py install actually installs now, while python setup.py
 build_ext --inplace builds the cython scripts

---
 README.md                                |   2 +-
 setup.py                                 |  51 +++++++----------------
 {src/biobox/test => test}/EMD-1080.mrc   | Bin
 {src/biobox/test => test}/HSP.pdb        |   0
 {src/biobox/test => test}/test_biobox.py |  21 +++++++---
 5 files changed, 30 insertions(+), 44 deletions(-)
 rename {src/biobox/test => test}/EMD-1080.mrc (100%)
 rename {src/biobox/test => test}/HSP.pdb (100%)
 rename {src/biobox/test => test}/test_biobox.py (89%)

diff --git a/README.md b/README.md
index b4addee..0e8c6ae 100644
--- a/README.md
+++ b/README.md
@@ -24,7 +24,7 @@ Biobox requires Python3.x and the following packages:
 * scikit-learn
 * cython
 
-Biobox can be installed with: `pip install biobox`. Biobox can otherwise be installed manually typing the followin command in the Biobox folder: `python setup.py install`. Please make sure the folder where Biobox is located is in your PYTHONPATH.
+Biobox can be installed with: `pip install biobox`. Biobox can otherwise be installed manually typing the followin command in the Biobox folder: `python setup.py build_ext --inplace` followed by `python setup.py install`. Please make sure the folder where Biobox is located is in your PYTHONPATH.
 
 Optional external software:
 * CCS calculation relies on a call to [IMPACT](
diff --git a/setup.py b/setup.py
index 696e665..3c488fd 100644
--- a/setup.py
+++ b/setup.py
@@ -18,46 +18,23 @@
 from Cython.Build import cythonize
 
 
-class InstallCommand(build_ext):
-
-    def run(self):
-
-        build_ext.run(self)
-
-        try:
-            for root, dirnames, filenames in os.walk("build"):
-                for filename in filenames:
-                    extension = filename.split(".")[-1]
-                    if extension in ["pyd", "so"]:
-                        os.rename(os.path.join(root, filename), filename)
-
-        except Exception:
-            print("files already exist, skipping...")
-
-        shutil.rmtree("build")
-
-os.chdir(f"src{os.sep}biobox{os.sep}lib")
-
-# small hack to get around a problem in older cython versions, i.e.
-# an infinite dependencies loop when __init__.py file is in the same folder as pyx
-#if os.path.exists("__init__.py"):
-#    os.rename("__init__.py", "tmp")
-
-
+packages=find_packages(where='src')
+print('packages being: ', packages)
+pyx_files = []
+for package in packages:
+    package_path = f'src{os.sep}{os.sep.join(package.split("."))}'
+    for file in os.listdir(package_path):
+        if file.split('.')[-1]=='pyx':
+            pyx_files.append(f'{package_path}{os.sep}{file}')
 setup(
     name = 'biobox',
-    version='1.0.0',
-    #authors='Many Handsome People',
-    #license = '',
+    version='1.1.0',
     include_dirs=[np.get_include()],
     ext_modules=cythonize(
-        "*.pyx",
+        pyx_files,#"*.pyx",
         include_path=[np.get_include()],
-            compiler_directives={'boundscheck': False, 'wraparound': False}),
-    cmdclass={'install': InstallCommand},
-    #packages=['biobox'],
-    packages=find_packages(where='src'),
+        compiler_directives={'boundscheck': False, 'wraparound': False}),
+    package_data={"":["*.dat"]},
+    packages=packages,
+    package_dir={"":"src"},
 )
-
-# continuation of the small hack
-#os.rename("tmp", "__init__.py")
diff --git a/src/biobox/test/EMD-1080.mrc b/test/EMD-1080.mrc
similarity index 100%
rename from src/biobox/test/EMD-1080.mrc
rename to test/EMD-1080.mrc
diff --git a/src/biobox/test/HSP.pdb b/test/HSP.pdb
similarity index 100%
rename from src/biobox/test/HSP.pdb
rename to test/HSP.pdb
diff --git a/src/biobox/test/test_biobox.py b/test/test_biobox.py
similarity index 89%
rename from src/biobox/test/test_biobox.py
rename to test/test_biobox.py
index 0fac03f..7255756 100644
--- a/src/biobox/test/test_biobox.py
+++ b/test/test_biobox.py
@@ -1,9 +1,11 @@
 import unittest
 import sys, os
-
-sys.path.append(os.sep.join(os.getcwd().split(os.sep)[:-2]))
+if 'CONDA_BUILD_STATE' in os.environ and os.environ['CONDA_BUILD_STATE']=='TEST':
+    pass
+else:
+    sys.path.append(os.sep.join(os.getcwd().split(os.sep)[:-1])+os.sep+'src')
 import biobox as bb
-     
+
 class test_density(unittest.TestCase):
 
     def setUp(self):
@@ -74,8 +76,11 @@ def test_SASA(self):
 
 
     def test_monomer_CCS(self):
-
-        print("\n> testing CCS")
+        if 'IMPACTPATH' in os.environ:
+            print("\n> testing CCS")
+        else:
+            print("\n\n> IMPACTPATH not set therefore can't test CCS. \n WARNING: If you want CCS calculations you need to set IMPACTPATH")
+            return
 
         try:
             ccs1 = bb.ccs(self.M)
@@ -91,8 +96,12 @@ def test_monomer_CCS(self):
 
 
     def test_multimer_CCS(self):
+        if 'IMPACTPATH' in os.environ:
+            print("\n> testing multimer CCS")
+        else:
+            print("\n\n> IMPACTPATH not set therefore can't test CCS. \n WARNING: If you want CCS calculations you need to set IMPACTPATH")
+            return
 
-        print("\n> testing multimer CCS")
 
         try:
             A = bb.Multimer()