Merge branch 'develop' into MLE-working-branch

README.md

@@ -17,7 +17,7 @@ DESKTOP_PARALLEL_JOBS = 2
 PYTHON_SCRIPT_DIR = /some/directory
 ```
 
-As last step, run `pip install .` in the directory with setup.py. 
+**IMPORTANT**: As last step, run `python setup.py clean --all; pip install . ; python setup.py clean --all` in the directory with setup.py. This combined command is the safest way for installation in all situations. For further explanation: in theory `pip install .` is sufficient for a first installation after initially cloning the repo. **But** newer versions of pip create a `build` directory inside the repository and do not clean it up automatically after the installation. During development or when pulling new versions this directory can cause issues if it is not cleaned up after the installation. Therefore it is advised to adapt this installation routine in order to make sure no old build artifacts can mess with the installation process.
 
 Note: If you are using the system wide python environment (not recommended) instead of a virtual environment (e.g. with Anaconda) the package data will go to `/usr/local`, which causes access permission issues with Docker. As a workaround use `pip install -e .` which creates symlinks to the repo instead of copying files.
 

setup.py

@@ -5,13 +5,14 @@
 
 """
 
-from distutils.cmd import Command
+
 from setuptools import setup
 import setuptools
 from setuptools.command.build_py import build_py
 import versioneer
 import subprocess
-import glob
+from pathlib import Path
+import shutil
 
 from hercules import _versionhelper
 
@@ -23,9 +24,17 @@ def run(self) -> None:
         #pickle CRESana models
         try:
             import cresana
-            path = 'hercules/hexbug/Phase4/CRESana_models'
-            for file in glob.glob(path+'/*.py'):
-                subprocess.run(['python', file])
+            path = Path('hercules/hexbug/Phase4/CRESana_models')
+            paths_to_delete = [p for p in path.glob('*') if not p.suffix=='.py']
+
+            for p in paths_to_delete:
+                if p.is_file():
+                    p.unlink()
+                else:
+                    shutil.rmtree(p)
+
+            for file in path.glob('*.py'):
+                subprocess.run(['python', str(file)])
 
         except:
             print('Not installing CRESana models')