Update pipeline declaration, ingestion script, and notebooks

README.md

@@ -32,6 +32,8 @@ DataJoint Elements ([element-lab](https://github.com/datajoint/element-lab),
  [element-miniscope](https://github.com/datajoint/element-miniscope)) assembled 
  together to form a fully functional workflow.
 
+![element miniscope diagram](images/attached_miniscope_element.svg)
+
 ## Installation instructions
 
 + The installation instructions can be found at the 

docker/Dockerfile.dev

@@ -1,18 +1,17 @@
-FROM datajoint/djbase:py3.8-debian-fcd8909
+FROM datajoint/djbase:py3.9-debian-8eb1715
 
 USER anaconda:anaconda
 
 COPY ./workflow-miniscope/docker/apt_requirements.txt /tmp/
 RUN /entrypoint.sh echo "Installed dependencies."
 
-# Install Caiman
-RUN git clone --branch master https://github.com/datajoint-company/CaImAn 
+# Install CaImAn
+RUN git clone --branch master https://github.com/kabilar/CaImAn 
 WORKDIR /main/CaImAn
 RUN conda install -n base -c conda-forge -y mamba
-RUN /bin/bash -c 'mamba env update --n base --file environment.yml' 
-# Suite2p requires np.__version__ == 1.21
-RUN pip install numpy==1.21
+RUN /bin/bash -c 'mamba env update --n base --file environment.yml'
 RUN pip install .
+RUN python caimanmanager.py install --inplace
 
 WORKDIR /main
 

docker/Dockerfile.test

@@ -1,10 +1,18 @@
-FROM datajoint/djbase:py3.9-debian-fcd8909
+FROM datajoint/djbase:py3.9-debian-8eb1715
 
 USER anaconda:anaconda
 
 COPY ./workflow-miniscope/docker/apt_requirements.txt /tmp/
 RUN /entrypoint.sh echo "Installed dependencies."
 
+# Install CaImAn
+RUN git clone --branch master https://github.com/kabilar/CaImAn 
+WORKDIR /main/CaImAn
+RUN conda install -n base -c conda-forge -y mamba
+RUN /bin/bash -c 'mamba env update --n base --file environment.yml' 
+RUN pip install .
+RUN python caimanmanager.py install --inplace
+
 WORKDIR /main
 
 # Option 1 - Install DataJoint's remote fork of the workflow and elements
@@ -45,4 +53,6 @@ RUN rm -f /main/workflow-miniscope/dj_local_conf.json
 RUN pip install /main/workflow-miniscope
 RUN pip install -r /main/workflow-miniscope/requirements_test.txt
 
+RUN pip uninstall datajoint
+RUN pip install git+
 WORKDIR /main/workflow-miniscope

docker/docker-compose-dev.yaml

@@ -18,7 +18,7 @@ services:
       context: ../../
       dockerfile: ./workflow-miniscope/docker/Dockerfile.dev
     env_file: .env
-    image: workflow-miniscope-dev:0.1.0a2
+    image: workflow-miniscope-dev:0.1.0
     container_name: workflow-miniscope-dev
     environment:
       - MINISCOPE_ROOT_DATA_DIR=/main/test_data/workflow_miniscope/

docker/docker-compose-test.yaml

@@ -17,7 +17,8 @@ services:
     build:
       context: ../../
       dockerfile: ./workflow-miniscope/docker/Dockerfile.test
-    image: workflow-miniscope-test:0.1.0a2
+    env_file: .env
+    image: workflow-miniscope-test:0.1.0
     container_name: workflow-miniscope-test
     environment:
       - DJ_HOST=db
@@ -30,7 +31,7 @@ services:
       - -c
       - |
         echo "------ INTEGRATION TESTS ------"
-        pytest -sv --cov-report term-missing --cov=workflow_miniscope -p no:warnings
+        pytest -sv --cov-report term-missing --cov=workflow_miniscope -p no:warnings tests/
         tail -f /dev/null
     volumes:
       - ${TEST_DATA_DIR}:/main/test_data