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Commit ab0c034

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CBroz1CBroz1
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Merge pull request #45 from kabilar/main
Update Docker and Compose files. Add pytest fixture.
2 parents 564c32f + 6c7c638 commit ab0c034

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‎docker-compose-dev.yaml

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This file was deleted.

‎Dockerfile.dev renamed to ‎docker/Dockerfile.dev

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@@ -2,7 +2,7 @@ FROM datajoint/djbase:py3.9-debian-fcd8909
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USER anaconda:anaconda
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COPY ./workflow-array-ephys/apt_requirements.txt /tmp/
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COPY ./workflow-array-ephys/docker/apt_requirements.txt /tmp/
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RUN /entrypoint.sh echo "Installed dependencies."
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RUN mkdir /main/element-lab \

‎Dockerfile.test renamed to ‎docker/Dockerfile.test

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@@ -2,7 +2,7 @@ FROM datajoint/djbase:py3.9-debian-fcd8909
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USER anaconda:anaconda
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COPY ./workflow-array-ephys/apt_requirements.txt /tmp/
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COPY ./workflow-array-ephys/docker/apt_requirements.txt /tmp/
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RUN /entrypoint.sh echo "Installed dependencies."
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WORKDIR /main/workflow-array-ephys
@@ -19,20 +19,23 @@ WORKDIR /main/workflow-array-ephys
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# RUN git clone https://github.com/<user>/workflow-array-ephys.git /main/workflow-array-ephys
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# Option 3 - Install user's local fork of element and workflow
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RUN mkdir /main/element-lab
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RUN mkdir /main/element-lab \
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/main/element-animal \
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/main/element-session \
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/main/element-array-ephys \
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/main/workflow-array-ephys
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COPY --chown=anaconda:anaconda ./element-lab /main/element-lab
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RUN pip install -e /main/element-lab
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RUN mkdir /main/element-animal
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COPY --chown=anaconda:anaconda ./element-animal /main/element-animal
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RUN pip install -e /main/element-animal
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RUN mkdir /main/element-session
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COPY --chown=anaconda:anaconda ./element-session /main/element-session
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RUN pip install -e /main/element-session
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RUN mkdir /main/element-array-ephys
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COPY --chown=anaconda:anaconda ./element-array-ephys /main/element-array-ephys
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RUN pip install -e /main/element-array-ephys
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COPY --chown=anaconda:anaconda ./workflow-array-ephys /main/workflow-array-ephys
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# RUN rm -f /main/workflow-array-ephys/dj_local_conf.json
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RUN pip install -e /main/element-lab
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RUN pip install -e /main/element-animal
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RUN pip install -e /main/element-session
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RUN pip install -e /main/element-array-ephys
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RUN rm -f /main/workflow-array-ephys/dj_local_conf.json
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# Install the workflow
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RUN pip install /main/workflow-array-ephys

‎apt_requirements.txt renamed to ‎docker/apt_requirements.txt

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‎docker/docker-compose-dev.yaml

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@@ -0,0 +1,35 @@
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# docker-compose -f ./docker/docker-compose-dev.yaml up -d --build
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# docker-compose -f ./docker/docker-compose-dev.yaml down
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version: "2.4"
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x-net: &net
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networks:
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- main
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services:
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array-ephys-dev-db:
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<<: *net
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image: datajoint/mysql:5.7
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environment:
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- MYSQL_ROOT_PASSWORD=simple
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array-ephys-dev-workflow:
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<<: *net
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build:
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context: ../../
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dockerfile: ./workflow-array-ephys/docker/Dockerfile.dev
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env_file: .env
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image: workflow_array_ephys_dev:0.1.0a4
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environment:
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- EPHYS_ROOT_DATA_DIR=/main/test_data/workflow_ephys_data1/,/main/test_data/workflow_ephys_data2/
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volumes:
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- ${TEST_DATA_DIR}:/main/test_data
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- ./apt_requirements.txt:/tmp/apt_requirements.txt
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- ../../element-lab:/main/element-lab
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- ../../element-animal:/main/element-animal
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- ../../element-session:/main/element-session
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- ../../element-array-ephys:/main/element-array-ephys
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- ..:/main/workflow-array-ephys
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depends_on:
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array-ephys-dev-db:
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condition: service_healthy
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networks:
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main:

‎docker-compose-test.yaml renamed to ‎docker/docker-compose-test.yaml

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@@ -1,24 +1,24 @@
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# export COMPOSE_DOCKER_CLI_BUILD=0 # some machines need for smooth --build
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# .env file: TEST_DATA_DIR=<local parent directory of workflow_ephys_data{1,2}>
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# docker-compose -f docker-compose-test.yaml up --build
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# docker-compose -f ./docker/docker-compose-test.yaml up --build
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# docker exec -it workflow-array-ephys_workflow_1 /bin/bash
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# docker-compose -f docker-compose-test.yaml down
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# docker-compose -f ./docker/docker-compose-test.yaml down
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version: "2.4"
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x-net: &net
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networks:
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- main
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services:
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db:
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array-ephys-test-db:
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<<: *net
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image: datajoint/mysql:5.7
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environment:
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- MYSQL_ROOT_PASSWORD=simple
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workflow:
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array-ephys-test-workflow:
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<<: *net
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build:
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context: ../
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dockerfile: ./workflow-array-ephys/Dockerfile.test
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context: ../../
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dockerfile: ./workflow-array-ephys/docker/Dockerfile.test
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env_file: .env
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image: workflow_array_ephys_test:0.1.0a4
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environment:
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volumes:
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- ${TEST_DATA_DIR}:/main/test_data
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- ./apt_requirements.txt:/tmp/apt_requirements.txt
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- ../element-lab:/main/element-lab
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- ../element-animal:/main/element-animal
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- ../element-session:/main/element-session
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- ../element-array-ephys:/main/element-array-ephys
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- .:/main/workflow-array-ephys
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- ../../element-lab:/main/element-lab
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- ../../element-animal:/main/element-animal
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- ../../element-session:/main/element-session
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- ../../element-array-ephys:/main/element-array-ephys
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- ..:/main/workflow-array-ephys
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depends_on:
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db:
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array-ephys-test-db:
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condition: service_healthy
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networks:
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main:

‎tests/__init__.py

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# run all tests: pytest -sv --cov-report term-missing \
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# --cov=workflow_array_ephys -p no:warnings tests/
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# run one test, debug: pytest [above options] --pdb tests/tests_name.py -k \
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# function_name
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# run all tests:
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# pytest -sv --cov-report term-missing --cov=workflow_array_ephys -p no:warnings tests/
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# run one test, debug:
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# pytest [above options] --pdb tests/tests_name.py -k function_name
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import os
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import sys
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dj.config['custom'] = {
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'database.prefix': (os.environ.get('DATABASE_PREFIX')
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or dj.config['custom']['database.prefix']),
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'ephys_root_data_dir': (os.environ.get('EPHYS_ROOT_DATA_DIR').split(',')
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or dj.config['custom']['ephys_root_data_dir'])
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'ephys_root_data_dir': (os.environ.get('EPHYS_ROOT_DATA_DIR').split(',') if os.environ.get('EPHYS_ROOT_DATA_DIR') else dj.config['custom']['ephys_root_data_dir'])
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}
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return
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@@ -198,6 +197,28 @@ def testdata_paths():
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'npx3B-p1-ks': 'subject6/session1/towersTask_g0_imec0'
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}
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@pytest.fixture
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def ephys_insertionlocation(pipeline, ingest_sessions):
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"""Insert probe location into ephys.InsertionLocation"""
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ephys = pipeline['ephys']
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for probe_insertion_key in ephys.ProbeInsertion.fetch('KEY'):
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ephys.InsertionLocation.insert1(dict(**probe_insertion_key,
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skull_reference='Bregma',
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ap_location=0,
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ml_location=0,
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depth=0,
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theta=0,
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phi=0,
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beta=0))
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yield
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if _tear_down:
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if verbose:
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ephys.InsertionLocation.delete()
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else:
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with QuietStdOut():
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ephys.InsertionLocation.delete()
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@pytest.fixture
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def kilosort_paramset(pipeline):

‎workflow_array_ephys/pipeline.py

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from element_animal.subject import Subject
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from element_lab.lab import Source, Lab, Protocol, User, Project
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from element_session.session import Session
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from element_session.session_with_datetime import Session
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from .paths import get_ephys_root_data_dir, get_session_directory
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