release 1.5.0

.circleci/config.yml

@@ -2,7 +2,7 @@ version: 2
 jobs:
   build:
     docker:
-      - image: circleci/python:3.6
+      - image: circleci/python:3.9
     steps:
       - checkout
       - run:
@@ -11,36 +11,37 @@ jobs:
             python3 -m venv venv
             . venv/bin/activate
             pip3 install twine
-
       - run:
           name: verify git tag vs. version
           command: |
             python3 -m venv venv
             . venv/bin/activate
             python3 setup.py verify
-
       - run:
           name: init .pypirc
           command: |
             echo -e "[pypi]" >> ~/.pypirc
             echo -e "username = amogh" >> ~/.pypirc
             echo -e "password = $PYPI_PASSWORD" >> ~/.pypirc
-
       - run:
           name: create packages
           command: |
             python3 setup.py sdist
             python3 setup.py bdist_wheel
-
+      - run:
+          name: run unit tests
+          command: | 
+            python3 -m venv venv
+            . venv/bin/activate
+            pip3 install pytest 
+            pytest rsHRF/unit_tests/ -p no:warnings
       - run:
           name: upload to pypi
           command: |
             . venv/bin/activate
             twine upload dist/*
-
       - setup_remote_docker:
           docker_layer_caching: false
-
       - run:
           name: Install Docker client
           command: |
@@ -49,7 +50,6 @@ jobs:
             curl -L -o /tmp/docker-$VER.tgz https://get.docker.com/builds/Linux/x86_64/docker-$VER.tgz
             tar -xz -C /tmp -f /tmp/docker-$VER.tgz
             sudo mv /tmp/docker/* /usr/bin
-
       - run:
           name: Build and push Docker image
           command: |

Dockerfile

@@ -1,4 +1,4 @@
-FROM alpine:3.8
+FROM alpine:3.11
 
 RUN apk add --no-cache python3 && \
     python3 -m ensurepip && \
@@ -28,7 +28,7 @@ RUN apk add --no-cache zlib libjpeg-turbo-dev libpng-dev freetype-dev lcms2-dev
 	&& pip3 install numpy \
 	&& pip3 install scipy==1.3.3 \
 	&& pip3 install pandas \
-	&& pip3 install pyyawt \
+	&& pip3 install pyyawt \ 
 	&& pip3 install rsHRF \
 	&& rm -r /root/.cache \
 	&& find /usr/lib/python3.*/ -name 'tests' -exec rm -r '{}' + \

index.md

@@ -41,7 +41,8 @@ In essence, the whole usage of the application can be broken down to 7 major ste
  ``--atlas`` optional argument followed by the name of the file.
 
  * The ``--brainmask`` argument which tells the application that the mask files
- are present within the BIDS formatted data-set directory itself (which was supplied with ``--bids_dir``).
+ are present within the BIDS formatted data-set directory itself (which was supplied
+ supplied with ``--bids_dir``).
 
  * Out of the above 2 options, both cannot be supplied at once. In the case where neither of the 2 options are supplied, the app proceeds to generate a mask by computing the variance, however, providing a mask-file is strongly recommended.
 
@@ -186,7 +187,7 @@ bids/rshrf --bids_dir input_dir --output_dir results --analysis_level participan
 
 In the above example, the ``output_dir`` is ``results`` directory. The 
 corresponding mask file supplied is ``mask.nii``. The BIDS formatted data-set
-lies in the ``input_dir`` directory. The analysis level is ``participant``. The analysis will be performed for all subjects since no specific subjects are mentioned using ``--participant_label``.
+lies in the ``input_dir`` directory. The analysis level is ``participant``. The analysis will be performed for all subjects since no specific subjects are mentioned using ``--analysis_level participant``.
 
 #### Running the analysis with a BIDS formatted data-set that also includes a unique mask file for each of the input file present. 
 
@@ -209,12 +210,12 @@ b) Through the BIDS-App
 docker run -ti --rm \
 -v /path/to/bids_dir:/input_dir:ro \
 -v /path/to/output/directory/results:/results \
-bids/rshrf --bids_dir input_dir --output_dir results --analysis_level participant --brainmask --estimation canon2dd --participant_label 001 002
+bids/rshrf input_dir results participant --brainmask --estimation canon2dd --participant_label 001 002
 ```
 
 In the above example, the output directory is ``results`` directory. The BIDS formatted data-set
 lies in the ``input_dir`` directory. The associated mask files also lie within the BIDS dataset.
 The analysis level is ``participant``. The analysis is performed only for ``sub-001`` & ``sub-002``
 out of all the available subjects in the BIDS dataset.
 
-### Fin.
+### Fin.