Merge pull request #76 from PennLINC/fix/pip_install

[FIX] cannot find yaml file error when installed by `pip install .`

.circleci/config.yml

@@ -25,10 +25,8 @@ jobs:
           name: pytest of BABS
           no_output_timeout: 1h
           command: |
-            pip install -e .[tests]
+            pip install .[tests]
             pytest -n 6 -sv
-      
-#           TODO: change back to `pip install .` after fixing the bug!
 
 
 workflows:

MANIFEST.in

@@ -0,0 +1,11 @@
+#Misc
+# include CHANGES.rst
+include LICENSE
+
+# necessary files in babs/:
+#   by default it only includes *.py
+recursive-include babs *.yaml
+
+# versioneer
+include versioneer.py
+include babs/_version.py

babs/babs.py

@@ -2192,7 +2192,9 @@ def __init__(self, system_type):
 
     def get_dict(self):
         # location of current python script:
-        __location__ = op.realpath(op.dirname(__file__))
+        #   `op.abspath()` is to make sure always returns abs path, regardless of python version
+        #   ref: https://note.nkmk.me/en/python-script-file-path/
+        __location__ = op.realpath(op.dirname(op.abspath(__file__)))
 
         fn_dict_cluster_systems_yaml = op.join(__location__, "dict_cluster_systems.yaml")
         with open(fn_dict_cluster_systems_yaml) as f:
@@ -2791,7 +2793,9 @@ def generate_bash_test_job(self, folder_check_setup,
 
         # Copy the existing python script to this BABS project:
         # location of current python script:
-        __location__ = op.realpath(op.dirname(__file__))
+        #   `op.abspath()` is to make sure always returns abs path, regardless of python version
+        #   ref: https://note.nkmk.me/en/python-script-file-path/
+        __location__ = op.realpath(op.dirname(op.abspath(__file__)))
         fn_from = op.join(__location__, "template_test_job.py")
         # copy:
         shutil.copy(fn_from, fn_test_job)

setup.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 import sys
-from setuptools import setup
+from setuptools import setup, find_packages
 import versioneer
 
 
@@ -15,6 +15,7 @@
 
 
 setup(name='babs',
+      packages=find_packages(),
       version=versioneer.get_version(),
       cmdclass=versioneer.get_cmdclass(),
       setup_requires=SETUP_REQUIRES

tests/get_data.py

@@ -11,7 +11,9 @@
 from babs.utils import (read_yaml)   # noqa
 
 # =============== Define several constant variables: ==================
-__location__ = op.dirname(__file__)   # the path to the directory of current python script
+__location__ = op.dirname(op.abspath(__file__))   # the path to the directory of current python script
+#   ^^ `op.abspath()` is to make sure always returns abs path, regardless of python version
+#       ref: https://note.nkmk.me/en/python-script-file-path/
 
 # containers:
 LIST_WHICH_BIDSAPP = ["toybidsapp", "fmriprep", "qsiprep"]