From 59888f969badf08f5b2aeb6c20d57281315e0e41 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Sun, 8 May 2022 23:45:12 +0000 Subject: [PATCH 1/7] Remove temporary json --- .datajoint_config.json | 15 --------------- 1 file changed, 15 deletions(-) delete mode 100644 .datajoint_config.json diff --git a/.datajoint_config.json b/.datajoint_config.json deleted file mode 100644 index 0c20cf3..0000000 --- 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 -} From 4f8cfd02f54ce1dc48bacd7610428b66b4ebfed8 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Sun, 8 May 2022 23:45:38 +0000 Subject: [PATCH 2/7] Add subject and session example data --- user_data/sessions.csv | 5 +++-- user_data/subjects.csv | 3 ++- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/user_data/sessions.csv b/user_data/sessions.csv index 1983068..5cd95cd 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 f5d2dc2..0db4cfd 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 From 0c5929a37b9895b1505f47bb75ef459c9537d6ff Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Sun, 8 May 2022 23:50:03 +0000 Subject: [PATCH 3/7] Add Elements to Docker and Compose files --- docker/Dockerfile.dev | 9 ++++++--- docker/Dockerfile.test | 6 ++++++ docker/docker-compose-dev.yaml | 2 ++ docker/docker-compose-test.yaml | 2 ++ 4 files changed, 16 insertions(+), 3 deletions(-) diff --git a/docker/Dockerfile.dev b/docker/Dockerfile.dev index a36f080..e75e806 100644 --- a/docker/Dockerfile.dev +++ b/docker/Dockerfile.dev @@ -8,25 +8,28 @@ RUN /entrypoint.sh echo "Installed dependencies." RUN mkdir /main/element-lab \ /main/element-animal \ /main/element-session \ - /main/element-array-ephys \ + /main/element-event \ /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-event /main/element-event 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-event +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 dfdd754..6b82c95 100644 --- a/docker/Dockerfile.test +++ b/docker/Dockerfile.test @@ -22,18 +22,24 @@ WORKDIR /main/workflow-array-ephys RUN mkdir /main/element-lab \ /main/element-animal \ /main/element-session \ + /main/element-event \ + /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-event /main/element-event +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-event +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 4bfb010..1613959 100644 --- a/docker/docker-compose-dev.yaml +++ b/docker/docker-compose-dev.yaml @@ -28,6 +28,8 @@ services: - ../../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-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 e27cb3c..873bf38 100644 --- a/docker/docker-compose-test.yaml +++ b/docker/docker-compose-test.yaml @@ -42,6 +42,8 @@ services: - ../../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-array-ephys:/main/element-array-ephys - ..:/main/workflow-array-ephys depends_on: From cf57c806af4ff35b4b5d6ed7025f4906f35e4750 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Sun, 8 May 2022 23:51:14 +0000 Subject: [PATCH 4/7] Check current working directory --- notebooks/01-configure.ipynb | 2 +- notebooks/02-workflow-structure-optional.ipynb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/notebooks/01-configure.ipynb b/notebooks/01-configure.ipynb index 5fc0057..91745f7 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 34fa7f1..ba548aa 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('..')" ] }, { From f17e988b4825cb00cb1fdeca2a958f9eb0d1ed28 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Thu, 2 Jun 2022 16:33:20 -0500 Subject: [PATCH 5/7] Update requirements --- requirements.txt | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/requirements.txt b/requirements.txt index 341d432..7417298 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 From 4d9a57aea602361c52e2441281c69595b35fad47 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Thu, 2 Jun 2022 16:39:25 -0500 Subject: [PATCH 6/7] Update version and changelog --- CHANGELOG.md | 27 ++++++++++++++++----------- workflow_array_ephys/version.py | 2 +- 2 files changed, 17 insertions(+), 12 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2529e30..4584e21 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/workflow_array_ephys/version.py b/workflow_array_ephys/version.py index 126776b..3105c04 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' From cab0c35cf7ecf04057bf6d9770df5465f2728300 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Thu, 2 Jun 2022 16:42:37 -0500 Subject: [PATCH 7/7] Revert update --- docker/Dockerfile.dev | 3 --- docker/Dockerfile.test | 3 --- docker/docker-compose-dev.yaml | 1 - docker/docker-compose-test.yaml | 1 - 4 files changed, 8 deletions(-) diff --git a/docker/Dockerfile.dev b/docker/Dockerfile.dev index e75e806..babb554 100644 --- a/docker/Dockerfile.dev +++ b/docker/Dockerfile.dev @@ -8,7 +8,6 @@ RUN /entrypoint.sh echo "Installed dependencies." RUN mkdir /main/element-lab \ /main/element-animal \ /main/element-session \ - /main/element-event \ /main/element-interface \ /main/element-array-ephys \ /main/workflow-array-ephys @@ -17,7 +16,6 @@ RUN mkdir /main/element-lab \ 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-event /main/element-event 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 @@ -26,7 +24,6 @@ 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-event RUN pip install -e /main/element-interface RUN pip install -e /main/element-array-ephys RUN pip install -e /main/workflow-array-ephys diff --git a/docker/Dockerfile.test b/docker/Dockerfile.test index 6b82c95..9f89456 100644 --- a/docker/Dockerfile.test +++ b/docker/Dockerfile.test @@ -22,7 +22,6 @@ WORKDIR /main/workflow-array-ephys RUN mkdir /main/element-lab \ /main/element-animal \ /main/element-session \ - /main/element-event \ /main/element-interface \ /main/element-array-ephys \ /main/workflow-array-ephys @@ -30,7 +29,6 @@ RUN mkdir /main/element-lab \ 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-event /main/element-event 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 @@ -38,7 +36,6 @@ 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-event 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 1613959..3921b0a 100644 --- a/docker/docker-compose-dev.yaml +++ b/docker/docker-compose-dev.yaml @@ -28,7 +28,6 @@ services: - ../../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-array-ephys:/main/element-array-ephys - ../../element-interface:/main/element-interface diff --git a/docker/docker-compose-test.yaml b/docker/docker-compose-test.yaml index 873bf38..da819d9 100644 --- a/docker/docker-compose-test.yaml +++ b/docker/docker-compose-test.yaml @@ -42,7 +42,6 @@ services: - ../../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-array-ephys:/main/element-array-ephys - ..:/main/workflow-array-ephys