Merge pull request #86 from AICONSlab/jo-STA_workflow_fix

Re-release v2.2.2

.circleci/config.yml

@@ -62,7 +62,7 @@ jobs:
             # Change permissions for code directory for any Singularity user
             sed -i '/#STOPUNCOMMENT#/a # Change permissions for code dir\nchmod -R 777 /code' miracl.def && \
             # Log in to cloud.sylabs.io
-            echo $SYLABS_TOKEN_JAN_25_2023 > tokenfile && \
+            echo $SYLABS_TOKEN_JAN_30_2023 > tokenfile && \
             singularity remote login -u aiconslab --tokenfile tokenfile && \
             # Setting trap in case image cannot be deleted
             set -e

Dockerfile

@@ -5,6 +5,10 @@ ADD . /code
 # delete ruamel pkg
 RUN rm -rf $(python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")/ruamel* && \
     pip install markupsafe==2.0.1 && \
+    # Install setuptools v65.6.0 as latest version (v67.0.0)
+    # breaks parsing. Temporary fix only. In the long run,
+    # scripts should be refactored to work with current version!
+    pip install setuptools==65.6.0 && \
     pip install -e /code/ "botocore >= 1.20.110"
 ENV MIRACL_HOME=/code/miracl
 

setup.py

@@ -37,9 +37,25 @@
         'Topic :: Scientific/Engineering :: Image Recognition',
     ],
     install_requires=[
-        'numpy', 'pandas', 'scipy', 'opencv-python', 'tifffile', 'nibabel', 'argparse', 'tables', 'statsmodels',
-        'allensdk', 'lightning-python', 'joblib', 'matplotlib', 'argcomplete', 'dipy', 'seaborn', 'pyqt5', 'nipype'
-    ],
+        'numpy==1.21.6',
+        'pandas==1.3.5',
+        'scipy==1.6.2',
+        'opencv-python==4.2.0.32',
+        'tifffile==2021.11.2',
+        'nibabel==4.0.2',
+        'argparse==1.4.0',
+        'tables==3.7.0',
+        'statsmodels==0.13.0',
+        'allensdk==2.15.1',
+        'lightning-python==1.2.1',
+        'joblib==1.2.0',
+        'matplotlib==3.4.2',
+        'argcomplete==2.0.0',
+        'dipy==1.6.0',
+        'seaborn==0.12.2',
+        'pyqt5==5.15.8',
+        'nipype==1.8.5'
+        ],
     entry_points={'console_scripts': ['miracl=miracl.cli:main'],
                   'gui_scripts': ['miraclGUI=miracl.miraclGUI:main']},
     keywords=[