diff --git a/.datajoint_config.json b/.datajoint_config.json deleted file mode 100644 index 0c20cf3d..00000000 --- a/.datajoint_config.json +++ /dev/null @@ -1,15 +0,0 @@ -{ - "database.host": "tutorial-db.datajoint.io", - "database.port": 3306, - "database.reconnect": true, - "connection.init_function": null, - "connection.charset": "", - "loglevel": "INFO", - "safemode": true, - "fetch_format": "array", - "display.limit": 12, - "display.width": 14, - "display.show_tuple_count": true, - "database.use_tls": null, - "enable_python_native_blobs": true -} diff --git a/CHANGELOG.md b/CHANGELOG.md index 2529e30c..4584e21a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,23 +3,28 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention. +## 0.1.0 - 2022-06-02 + ++ Update - Docker and Compose files ++ Add - NWB export pytests + ## 0.1.0a4 - 2022-01-21 -### Added -+ Created Docker and Compose files for active development. + ++ Add - Create Docker and Compose files for active development. ## 0.1.0a3 - 2022-01-18 -### Updated -+ Updated notebooks -+ Moved instructions to [datajoint-elements/install.md]( + ++ Update - Notebooks ++ Update - Move instructions to [datajoint-elements/install.md]( https://github.com/datajoint/datajoint-elements/blob/main/install.md). -+ Updated Docker and Compose files for new base image and added options to install ++ Update - Docker and Compose files for new base image and added options to install specific forks for tests. ## 0.1.0a2 - 2021-04-12 -### Updated -+ Updated tests -+ Changed version to reflect release phase. + ++ Update - Pytests ++ Update - Change version to reflect release phase. ## 0.1.1 - 2021-03-26 -### Added -+ Added version \ No newline at end of file + ++ Add - Version diff --git a/docker/Dockerfile.dev b/docker/Dockerfile.dev index a36f080e..babb5543 100644 --- a/docker/Dockerfile.dev +++ b/docker/Dockerfile.dev @@ -8,25 +8,25 @@ RUN /entrypoint.sh echo "Installed dependencies." RUN mkdir /main/element-lab \ /main/element-animal \ /main/element-session \ - /main/element-array-ephys \ /main/element-interface \ + /main/element-array-ephys \ /main/workflow-array-ephys # Copy user's local fork of elements and workflow COPY --chown=anaconda:anaconda ./element-lab /main/element-lab COPY --chown=anaconda:anaconda ./element-animal /main/element-animal COPY --chown=anaconda:anaconda ./element-session /main/element-session -COPY --chown=anaconda:anaconda ./element-array-ephys /main/element-array-ephys COPY --chown=anaconda:anaconda ./element-interface /main/element-interface +COPY --chown=anaconda:anaconda ./element-array-ephys /main/element-array-ephys COPY --chown=anaconda:anaconda ./workflow-array-ephys /main/workflow-array-ephys # Install packages 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-interface RUN pip install -e /main/element-array-ephys RUN pip install -e /main/workflow-array-ephys -RUN pip install -e /main/element-interface RUN pip install -r /main/workflow-array-ephys/requirements_test.txt WORKDIR /main/workflow-array-ephys diff --git a/docker/Dockerfile.test b/docker/Dockerfile.test index dfdd7542..9f894569 100644 --- a/docker/Dockerfile.test +++ b/docker/Dockerfile.test @@ -22,18 +22,21 @@ WORKDIR /main/workflow-array-ephys RUN mkdir /main/element-lab \ /main/element-animal \ /main/element-session \ + /main/element-interface \ /main/element-array-ephys \ /main/workflow-array-ephys COPY --chown=anaconda:anaconda ./element-lab /main/element-lab COPY --chown=anaconda:anaconda ./element-animal /main/element-animal COPY --chown=anaconda:anaconda ./element-session /main/element-session +COPY --chown=anaconda:anaconda ./element-interface /main/element-interface COPY --chown=anaconda:anaconda ./element-array-ephys /main/element-array-ephys COPY --chown=anaconda:anaconda ./workflow-array-ephys /main/workflow-array-ephys 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-interface RUN pip install -e /main/element-array-ephys RUN rm -f /main/workflow-array-ephys/dj_local_conf.json diff --git a/docker/docker-compose-dev.yaml b/docker/docker-compose-dev.yaml index 4bfb0108..3921b0ad 100644 --- a/docker/docker-compose-dev.yaml +++ b/docker/docker-compose-dev.yaml @@ -28,6 +28,7 @@ services: - ../../element-lab:/main/element-lab - ../../element-animal:/main/element-animal - ../../element-session:/main/element-session + - ../../element-interface:/main/element-interface - ../../element-array-ephys:/main/element-array-ephys - ../../element-interface:/main/element-interface - ..:/main/workflow-array-ephys diff --git a/docker/docker-compose-test.yaml b/docker/docker-compose-test.yaml index e27cb3c2..da819d9a 100644 --- a/docker/docker-compose-test.yaml +++ b/docker/docker-compose-test.yaml @@ -42,6 +42,7 @@ services: - ../../element-lab:/main/element-lab - ../../element-animal:/main/element-animal - ../../element-session:/main/element-session + - ../../element-interface:/main/element-interface - ../../element-array-ephys:/main/element-array-ephys - ..:/main/workflow-array-ephys depends_on: diff --git a/notebooks/01-configure.ipynb b/notebooks/01-configure.ipynb index 5fc00572..91745f77 100644 --- a/notebooks/01-configure.ipynb +++ b/notebooks/01-configure.ipynb @@ -26,7 +26,7 @@ "outputs": [], "source": [ "import os\n", - "os.chdir('..')" + "if os.path.basename(os.getcwd())=='notebooks': os.chdir('..')" ] }, { diff --git a/notebooks/02-workflow-structure-optional.ipynb b/notebooks/02-workflow-structure-optional.ipynb index 34fa7f1a..ba548aa2 100644 --- a/notebooks/02-workflow-structure-optional.ipynb +++ b/notebooks/02-workflow-structure-optional.ipynb @@ -31,7 +31,7 @@ "outputs": [], "source": [ "import os\n", - "os.chdir('..')" + "if os.path.basename(os.getcwd())=='notebooks': os.chdir('..')" ] }, { diff --git a/requirements.txt b/requirements.txt index 341d4326..74172987 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,7 +1,7 @@ datajoint>=0.13.0 -element-array-ephys==0.1.0b0 +element-array-ephys>=0.1.1 element-lab>=0.1.0b0 -element-animal==0.1.0b0 -element-session==0.1.0b0 +element-animal>=0.1.0b0 +element-session>=0.1.0b0 element-interface @ git+https://github.com/datajoint/element-interface.git -ipykernel==6.0.1 \ No newline at end of file +ipykernel>=6.0.1 \ No newline at end of file diff --git a/user_data/sessions.csv b/user_data/sessions.csv index 1983068b..5cd95cd1 100644 --- a/user_data/sessions.csv +++ b/user_data/sessions.csv @@ -1,2 +1,3 @@ -subject,session_dir -subject6,/tmp/test_data/workflow-array-ephys-test-set/subject6/session1/ +subject,session_dir,session_note,user +subject5,subject5/session1/,Successful data collection,User1 +subject6,subject6/session1/,Ambient temp abnormally low,User2 diff --git a/user_data/subjects.csv b/user_data/subjects.csv index f5d2dc25..0db4cfd9 100644 --- a/user_data/subjects.csv +++ b/user_data/subjects.csv @@ -1,2 +1,3 @@ subject,sex,subject_birth_date,subject_description -subject6,M,2020-01-03,hneih_E105 +subject5,F,2020-01-01 00:00:01, +subject6,F,2020-01-01 00:00:01, \ No newline at end of file diff --git a/workflow_array_ephys/version.py b/workflow_array_ephys/version.py index 126776b1..3105c048 100644 --- a/workflow_array_ephys/version.py +++ b/workflow_array_ephys/version.py @@ -2,4 +2,4 @@ Package metadata Update the Docker image tag in `docker-compose.yaml` to match """ -__version__ = '0.1.0a4' +__version__ = '0.1.0'