Merge pull request #93 from CoBrALab/updates

Changed to version 0.2.0
CoBrALab · Sep 30, 2020 · 905939b · 905939b
2 parents 0d63835 + 9ad428c
commit 905939b
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diff --git a/Dockerfile b/Dockerfile
@@ -158,24 +158,24 @@ RUN export PATH="$HOME/miniconda-latest/bin:$PATH" \
 
 
 #### install RABIES
-ENV export RABIES_VERSION=0.1.3-dev \
+ENV export RABIES_VERSION=0.2.0 \
     export RABIES=$HOME/RABIES-${RABIES_VERSION} \
     export PYTHONPATH="${PYTHONPATH}:$RABIES"
 
-RUN export RABIES_VERSION=0.1.3-dev && \
+RUN export RABIES_VERSION=0.2.0 && \
   export RABIES=$HOME/RABIES-${RABIES_VERSION} && \
-  #mkdir -p temp && \
-  #curl -L --retry 5 -o temp/RABIES.tar.gz https://github.com/CoBrALab/RABIES/archive/${RABIES_VERSION}.tar.gz && \
-  #cd temp && \
-  #tar zxf RABIES.tar.gz && \
-  #cd .. && \
-  #conda env create -f temp/RABIES-${RABIES_VERSION}/rabies_environment.yml && \
-  #bash temp/RABIES-${RABIES_VERSION}/install.sh && \
-  #rm -r temp && \
-  git clone https://github.com/CoBrALab/RABIES && \
-  mv RABIES $RABIES && \
-  conda env create -f $RABIES/rabies_environment.yml && \
-  bash $RABIES/install.sh && \
+  mkdir -p temp && \
+  curl -L --retry 5 -o temp/RABIES.tar.gz https://github.com/CoBrALab/RABIES/archive/${RABIES_VERSION}.tar.gz && \
+  cd temp && \
+  tar zxf RABIES.tar.gz && \
+  cd .. && \
+  conda env create -f temp/RABIES-${RABIES_VERSION}/rabies_environment.yml && \
+  bash temp/RABIES-${RABIES_VERSION}/install.sh && \
+  rm -r temp && \
+  #git clone https://github.com/CoBrALab/RABIES && \
+  #mv RABIES $RABIES && \
+  #conda env create -f $RABIES/rabies_environment.yml && \
+  #bash $RABIES/install.sh && \
   DSURQE_100micron_labels=${RABIES}/template_files/DSURQE_100micron_labels.nii.gz && \
   csv_labels=${RABIES}/template_files/DSURQE_40micron_R_mapping.csv && \
   /home/rabies/miniconda-latest/envs/rabies/bin/python ${RABIES}/gen_masks.py $DSURQE_100micron_labels $csv_labels ${RABIES}/template_files/DSURQE_100micron && \
@@ -194,7 +194,7 @@ RUN export FSLDIR="/usr/share/fsl/5.0/" && \
   . ${FSLDIR}/etc/fslconf/fsl.sh && \
   export PATH="/usr/share/fsl/5.0/bin:$PATH" && \
   export LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH && \
-  export RABIES_VERSION=0.1.3-dev && \
+  export RABIES_VERSION=0.2.0 && \
   export RABIES=$HOME/RABIES-${RABIES_VERSION} && \
   export PATH=$PATH:$RABIES/rabies/shell_scripts && \
   echo "#! /home/rabies/miniconda-latest/envs/rabies/bin/python" > ${RABIES}/exec.py && \
@@ -218,4 +218,4 @@ WORKDIR /tmp/
 ENV PATH /home/rabies/miniconda-latest/envs/rabies/bin:$PATH
 RUN /bin/bash -c "source activate rabies"
 
-ENTRYPOINT ["/home/rabies/RABIES-0.1.3-dev/exec.py"]
+ENTRYPOINT ["/home/rabies/RABIES-0.2.0/exec.py"]
diff --git a/README.md b/README.md
@@ -298,28 +298,28 @@ Specify Slice Timing Correction info that is fed to AFNI 3dTshift
 Provided commonspace atlas files.:
   --anat_template ANAT_TEMPLATE
                         Anatomical file for the commonspace template.
-                        (default: /home/gabriel/RABIES-0.1.3-dev/rabies/../tem
+                        (default: /home/gabriel/RABIES-0.2.0/rabies/../tem
                         plate_files/DSURQE_40micron_average.nii.gz)
   --brain_mask BRAIN_MASK
                         Brain mask for the template. (default: /home/gabriel/R
-                        ABIES-0.1.3-dev/rabies/../template_files/DSURQE_100mic
+                        ABIES-0.2.0/rabies/../template_files/DSURQE_100mic
                         ron_mask.nii.gz)
   --WM_mask WM_MASK     White matter mask for the template. (default: /home/ga
-                        briel/RABIES-0.1.3-dev/rabies/../template_files/DSURQE
+                        briel/RABIES-0.2.0/rabies/../template_files/DSURQE
                         _100micron_eroded_WM_mask.nii.gz)
   --CSF_mask CSF_MASK   CSF mask for the template. (default: /home/gabriel/RAB
-                        IES-0.1.3-dev/rabies/../template_files/DSURQE_100micro
+                        IES-0.2.0/rabies/../template_files/DSURQE_100micro
                         n_eroded_CSF_mask.nii.gz)
   --vascular_mask VASCULAR_MASK
                         Can provide a mask of major blood vessels for
                         computing confound timeseries. The default mask was
                         generated by applying MELODIC ICA and selecting the
                         resulting component mapping onto major veins.
                         (Grandjean et al. 2020, NeuroImage; Beckmann et al.
-                        2005) (default: /home/gabriel/RABIES-0.1.3-dev/rabies/
+                        2005) (default: /home/gabriel/RABIES-0.2.0/rabies/
                         ../template_files/vascular_mask.nii.gz)
   --labels LABELS       Atlas file with anatomical labels. (default: /home/gab
-                        riel/RABIES-0.1.3-dev/rabies/../template_files/DSURQE_
+                        riel/RABIES-0.2.0/rabies/../template_files/DSURQE_
                         40micron_labels.nii.gz)
 ```
 

diff --git a/install.sh b/install.sh
@@ -1,23 +1,23 @@
 ### setup RABIES execution and DSURQE atlas
 
 #will install RABIES in HOME directory
-export RABIES_VERSION=0.1.3-dev
+export RABIES_VERSION=0.2.0
 export RABIES=$HOME/RABIES-${RABIES_VERSION}
 export PYTHONPATH="${PYTHONPATH}:$RABIES"
 
 cd $HOME
-#curl -L --retry 5 -o $HOME/RABIES.tar.gz https://github.com/CoBrALab/RABIES/archive/${RABIES_VERSION}.tar.gz
-#tar zxf $HOME/RABIES.tar.gz
-#rm $HOME/RABIES.tar.gz
-git clone https://github.com/CoBrALab/RABIES
-mv RABIES $RABIES
+curl -L --retry 5 -o $HOME/RABIES.tar.gz https://github.com/CoBrALab/RABIES/archive/${RABIES_VERSION}.tar.gz
+tar zxf $HOME/RABIES.tar.gz
+rm $HOME/RABIES.tar.gz
+#git clone https://github.com/CoBrALab/RABIES
+#mv RABIES $RABIES
 
 #creates an executable script to execute rabies
 mkdir -p $RABIES/bin
 echo -e '#! /usr/bin/env python \nfrom rabies.run_main import execute_workflow \nexecute_workflow()' > $RABIES/bin/rabies
 chmod +x $RABIES/bin/rabies
 echo "# added by RABIES" >> $HOME/.bashrc
-echo "export RABIES_VERSION=0.1.3-dev" >> $HOME/.bashrc
+echo "export RABIES_VERSION=0.2.0" >> $HOME/.bashrc
 echo "export RABIES=$RABIES" >> $HOME/.bashrc
 echo 'export PYTHONPATH="${PYTHONPATH}:$RABIES"' >> $HOME/.bashrc
 echo 'export PATH=$PATH:$RABIES/bin' >> $HOME/.bashrc

diff --git a/rabies/_info.py b/rabies/_info.py
@@ -1,4 +1,4 @@
-__version__ = "0.1.3-dev"
+__version__ = "0.2.0"
 __packagename__ = 'RABIES'
 __url__ = 'https://github.com/CoBrALab/'