Standard integration tests, PEP8, docker adjustments #23
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| # Changelog | ||
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| Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and | ||
| [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention. | ||
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| ## [0.1.0] - 2021-05-04 | ||
| ### Added | ||
| + Added version | ||
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| FROM datajoint/djbase:py3.9-debian-8eb1715 | ||
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| ARG GITHUB_USERNAME=cbroz1 | ||
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| USER anaconda:anaconda | ||
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| COPY ./docker/apt_requirements.txt /tmp/ | ||
| RUN /entrypoint.sh echo "Installed dependencies." | ||
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| # Install CaImAn | ||
| WORKDIR /main | ||
| 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 | ||
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| WORKDIR /main/workflow-miniscope | ||
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| # 1. Install Elements from github user | ||
| RUN pip install --no-deps "element-interface@git+https://github.com/${GITHUB_USERNAME}/element-interface" | ||
| RUN pip install --no-deps "djarchive-client@git+https://github.com/${GITHUB_USERNAME}/djarchive-client" | ||
| RUN pip install git+https://github.com/${GITHUB_USERNAME}/element-lab.git | ||
| RUN pip install git+https://github.com/${GITHUB_USERNAME}/element-animal.git | ||
| RUN pip install git+https://github.com/${GITHUB_USERNAME}/element-session.git | ||
| RUN pip install git+https://github.com/${GITHUB_USERNAME}/element-event.git | ||
| RUN pip install git+https://github.com/${GITHUB_USERNAME}/element-miniscope.git | ||
| # RUN pip install git+https://github.com/${GITHUB_USERNAME}/workflow-miniscope.git | ||
| # end 1 | ||
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| # 2. Install local fork of element and workflow | ||
| # COPY --chown=anaconda:anaconda ../element-lab /main/ | ||
| # COPY --chown=anaconda:anaconda ../element-animal /main/ | ||
| # COPY --chown=anaconda:anaconda ../element-session /main/ | ||
| # COPY --chown=anaconda:anaconda ../element-event /main/ | ||
| # COPY --chown=anaconda:anaconda ../element-interface /main/ | ||
| # COPY --chown=anaconda:anaconda ../element-miniscope /main/ | ||
| COPY --chown=anaconda:anaconda . ./ | ||
| # RUN pip install -e /main/element-lab | ||
| # RUN pip install -e /main/element-animal | ||
| # RUN pip install -e /main/element-session | ||
| # RUN pip install -e /main/element-event | ||
| # RUN pip install -e /main/element-interface | ||
| # RUN pip install -e /main/element-miniscope | ||
| RUN pip install -e . | ||
| # end 2 | ||
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| RUN rm -f ./dj_local_conf.json | ||
| RUN pip install -r ./requirements_test.txt | ||
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@@ -5,4 +5,4 @@ ffmpeg | |
| libsm6 | ||
| libxext6 | ||
| libhdf5-dev | ||
| pkg-config | ||
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| @@ -1,30 +1,39 @@ | ||
| # docker-compose -f ./docker/docker-compose-test.yaml up --build --force-recreate --detach | ||
| # docker-compose -f ./docker/docker-compose-test.yaml down --volumes | ||
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| version: "2.4" | ||
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| services: | ||
| db: | ||
| networks: | ||
| miniscope: | ||
| image: mysql:5-debian | ||
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| platform: linux/amd64 | ||
| command: --default-authentication-plugin=mysql_native_password | ||
| restart: always | ||
| environment: | ||
| MYSQL_ROOT_PASSWORD: simple | ||
| MYSQL_USER: datajoint | ||
| MYSQL_PASSWORD: datajoint | ||
| volumes: | ||
| - mysql-miniscope:/var/lib/mysql | ||
| container_name: workflow-miniscope-test-db | ||
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| workflow: | ||
| networks: | ||
| miniscope: | ||
| build: | ||
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| context: ../. | ||
| dockerfile: ./docker/Dockerfile.test | ||
| args: | ||
| - GITHUB_USERNAME=cbroz1 | ||
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| image: workflow-miniscope-test:0.1.0 | ||
| container_name: workflow-miniscope-test | ||
| environment: | ||
| - DJ_HOST=db | ||
| - DJ_USER=root | ||
| - DJ_PASS=simple | ||
| - MINISCOPE_ROOT_DATA_DIR=/main/test_data/ | ||
| - DATABASE_PREFIX=test_ | ||
| command: | ||
| - bash | ||
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@@ -35,15 +44,29 @@ services: | |
| tail -f /dev/null | ||
| volumes: | ||
| - ${TEST_DATA_DIR}:/main/test_data | ||
| # - ./apt_requirements.txt:/tmp/apt_requirements.txt | ||
| # - ../element-lab:/main/element-lab | ||
| # - ../element-animal:/main/element-animal | ||
| # - ../element-session:/main/element-session | ||
| # - ../element-event:/main/element-event | ||
| # - ../element-interface:/main/element-interface | ||
| # - ../element-miniscope:/main/element-miniscope | ||
| - ..:/main/workflow-miniscope | ||
| depends_on: | ||
| db: | ||
| condition: service_started | ||
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| adminer: | ||
| networks: | ||
| miniscope: | ||
| image: adminer | ||
| restart: always | ||
| ports: | ||
| - 8082:8080 | ||
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| networks: | ||
| miniscope: | ||
| name: workflow-miniscope-network | ||
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| volumes: | ||
| mysql-miniscope: | ||
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There was a problem hiding this comment. Is this required since the above code is commented out? There was a problem hiding this comment. Hi @iamamutt - Could you remind me why There was a problem hiding this comment. @CBroz1 That was there to map the data from the mysql database to a docker volume instead of bind mounting to the local filesystem. If you don't need access to the database data at all, you can delete the volumes section at the bottom, +72 to +73, and also it's mention at lines +19 to +20. If you want a bind mounted volume, change There was a problem hiding this comment. That makes sense. Thanks @iamamutt! |
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| @@ -1,8 +1,8 @@ | ||
| datajoint>=0.13.0 | ||
| element-lab>=0.1.0b0 | ||
| element-animal>=0.1.0b0 | ||
| element-session>=0.1.0b0 | ||
| element-miniscope>=0.1.0 | ||
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| element-interface @ git+https://github.com/datajoint/element-interface.git | ||
| djarchive-client @ git+https://github.com/datajoint/djarchive-client.git | ||
| jupytext>=1.13.7 | ||
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