Skip to content
This repository was archived by the owner on Dec 8, 2023. It is now read-only.
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
15 changes: 0 additions & 15 deletions .datajoint_config.json

This file was deleted.

27 changes: 16 additions & 11 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -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

+ Add - Version
6 changes: 3 additions & 3 deletions docker/Dockerfile.dev
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
3 changes: 3 additions & 0 deletions docker/Dockerfile.test
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down
1 change: 1 addition & 0 deletions docker/docker-compose-dev.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
1 change: 1 addition & 0 deletions docker/docker-compose-test.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down
2 changes: 1 addition & 1 deletion notebooks/01-configure.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@
"outputs": [],
"source": [
"import os\n",
"os.chdir('..')"
"if os.path.basename(os.getcwd())=='notebooks': os.chdir('..')"
]
},
{
Expand Down
2 changes: 1 addition & 1 deletion notebooks/02-workflow-structure-optional.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@
"outputs": [],
"source": [
"import os\n",
"os.chdir('..')"
"if os.path.basename(os.getcwd())=='notebooks': os.chdir('..')"
]
},
{
Expand Down
8 changes: 4 additions & 4 deletions requirements.txt
Original file line number Diff line number Diff line change
@@ -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
ipykernel>=6.0.1
5 changes: 3 additions & 2 deletions user_data/sessions.csv
Original file line number Diff line number Diff line change
@@ -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
3 changes: 2 additions & 1 deletion user_data/subjects.csv
Original file line number Diff line number Diff line change
@@ -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,
2 changes: 1 addition & 1 deletion workflow_array_ephys/version.py
Original file line number Diff line number Diff line change
Expand Up @@ -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'