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5112f05
Migrate from previous repo
CBroz1 Feb 20, 2023
2f67dcc
Update .github/ISSUE_TEMPLATE/config.yml
CBroz1 Feb 21, 2023
1c57a6e
Apply suggestions from code review
CBroz1 Feb 22, 2023
b8e3660
Apply suggestions from code review
CBroz1 Feb 22, 2023
a5bda82
Update tests/test_pipeline_generation.py
CBroz1 Feb 22, 2023
e996a75
Apply suggestions from code review
CBroz1 Feb 22, 2023
776e579
Remove cell metadata titles. Spelling/Pre-commit fixes
CBroz1 Feb 22, 2023
27745fc
Remove jupytext synced scripts
kabilar Apr 3, 2023
3c08e79
Remove `ingest.py`
kabilar Apr 3, 2023
4eb18a2
Remove notebooks
kabilar Apr 3, 2023
3b0a3eb
Update changelog
kabilar Apr 3, 2023
cfc4003
Update requirements
kabilar Apr 3, 2023
0a8e515
Add vscode settings
kabilar Apr 5, 2023
bd21ad9
Rename file
kabilar Apr 11, 2023
b4ec243
Update for rename
kabilar Apr 11, 2023
baf317a
Update pipeline
kabilar Apr 11, 2023
1535fda
Add Compose file
kabilar Apr 11, 2023
afc7ef5
Update pipeline
kabilar Apr 15, 2023
6a938d7
Remove csv files
kabilar Apr 15, 2023
e8ea937
Remove path function
kabilar Apr 15, 2023
14c2dd5
Update requirements
kabilar Apr 15, 2023
49b4ba3
Remove ingestion pytest
kabilar Apr 15, 2023
04abda7
Add dev container
kabilar Apr 16, 2023
e43f79a
Update requirements for testing
kabilar Apr 16, 2023
7f1e18b
Update Docker and Compose files
kabilar Apr 16, 2023
644a5bb
Increase resources
kabilar Apr 17, 2023
1948bd4
Revert base image
kabilar Apr 17, 2023
174d71d
Update Docker and Compose files
kabilar Apr 17, 2023
914b3d3
Update tests
kabilar Apr 18, 2023
870ffbb
Update pipeline
kabilar Apr 18, 2023
b4d91a3
Add Dev Container for pytest environment
kabilar Apr 18, 2023
4e74820
Update setup
kabilar Apr 18, 2023
8490173
Remove Docker files in place of Dev Container
kabilar Apr 18, 2023
26cf8c0
Move to `__init__.py`
kabilar Apr 18, 2023
8ea99e0
Update test init
kabilar Apr 18, 2023
5ea8930
Add database prefix to dj.config
kabilar Apr 18, 2023
9ba4d95
Update gitignore
kabilar Apr 18, 2023
1c75498
Update readme
kabilar Apr 20, 2023
560b092
Update gitignore
kabilar Apr 20, 2023
54a6cd0
Update readme
kabilar Apr 20, 2023
e4bb279
Update changelog
kabilar Apr 20, 2023
904569c
Update Compose file
kabilar Apr 20, 2023
4c96191
Fix typo
kabilar Apr 20, 2023
07ab078
Update comment
kabilar Apr 20, 2023
77de4ed
Update comment
kabilar Apr 20, 2023
11e6ac4
Add tutorial notebook
kabilar May 4, 2023
11f77ca
Add default python kernel
kabilar May 5, 2023
9e22a81
Update notebook with outputs
kabilar May 5, 2023
dcbed01
Update readme
kabilar May 5, 2023
147f876
Update changelog
kabilar May 5, 2023
06acd65
Update python kernel
kabilar May 5, 2023
6bd7c47
Update resources
kabilar May 5, 2023
38ebbab
Add extension
kabilar May 5, 2023
e528e42
Update requirements
kabilar May 5, 2023
961aa30
Add extension
kabilar May 5, 2023
8dbee85
Add print statements
kabilar May 5, 2023
64ff479
Minor typo fix in `tutorial.ipynb`
kushalbakshi May 5, 2023
98aad0d
Fix typo in notebook
kushalbakshi May 8, 2023
44d2f56
Merge pull request #1 from kushalbakshi/main
kabilar May 8, 2023
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37 changes: 37 additions & 0 deletions .cspell.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,37 @@
// cSpell Settings
//https://github.com/streetsidesoftware/vscode-spell-checker
{
"version": "0.2", // Version of the setting file. Always 0.2
"language": "en", // language - current active spelling language
"enabledLanguageIds": [
"markdown",
"yaml",
"python"
],
// flagWords - list of words to be always considered incorrect
// This is useful for offensive words and common spelling errors.
// For example "hte" should be "the"
"flagWords": [],
"allowCompoundWords": true,
"ignorePaths": [
"./*.egg-info/*",
"./images/*"
],
"words": [
"dorso",
"FUCNTION",
"ipykernel",
"jupytext",
"neuro",
"OPTG",
"opto",
"Opto",
"optogenetic",
"Optogenetic",
"optogenetics",
"Optogenetics",
"pytest",
"stim",
"Stim"
]
}
43 changes: 43 additions & 0 deletions .devcontainer/Dockerfile
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FROM python:3.9-slim

RUN \
adduser --system --disabled-password --shell /bin/bash vscode && \
# install docker
apt-get update && \
apt-get install ca-certificates curl gnupg lsb-release -y && \
mkdir -m 0755 -p /etc/apt/keyrings && \
curl -fsSL https://download.docker.com/linux/debian/gpg | gpg --dearmor -o /etc/apt/keyrings/docker.gpg && \
echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/debian $(lsb_release -cs) stable" | tee /etc/apt/sources.list.d/docker.list > /dev/null && \
apt-get update && \
apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin -y && \
usermod -aG docker vscode && \
apt-get clean

RUN \
# dev setup
apt update && \
apt-get install sudo git bash-completion graphviz default-mysql-client s3fs procps -y && \
usermod -aG sudo vscode && \
echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers && \
pip install --no-cache-dir --upgrade black pip && \
echo '. /etc/bash_completion' >> /home/vscode/.bashrc && \
echo 'export PS1="\[\e[32;1m\]\u\[\e[m\]@\[\e[34;1m\]\H\[\e[m\]:\[\e[33;1m\]\w\[\e[m\]$ "' >> /home/vscode/.bashrc && \
# dircolors -b >> /home/vscode/.bashrc && \ # somehow fix colors
apt-get clean
COPY ./requirements.txt /tmp/
RUN \
# workflow dependencies
apt-get install gcc ffmpeg libsm6 libxext6 -y && \
pip install --no-cache-dir -r /tmp/requirements.txt && \
# clean up
rm /tmp/requirements.txt && \
apt-get clean

ENV DJ_HOST fakeservices.datajoint.io
ENV DJ_USER root
ENV DJ_PASS simple

ENV DATABASE_PREFIX neuro_

USER vscode
CMD bash -c "sudo rm /var/run/docker.pid; sudo dockerd"
30 changes: 30 additions & 0 deletions .devcontainer/devcontainer.json
Original file line number Diff line number Diff line change
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{
"name": "Tutorial",
"dockerComposeFile": "docker-compose.yaml",
"service": "app",
"workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
"remoteEnv": {
"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
},
"onCreateCommand": "pip install -e . && MYSQL_VER=8.0 docker compose down && MYSQL_VER=8.0 docker compose up --build --wait",
"postStartCommand": "docker volume prune -f",
"hostRequirements": {
"cpus": 8,
"memory": "16gb",
"storage": "32gb"
},
"forwardPorts": [
3306
],
"customizations": {
"settings": {
"python.pythonPath": "/usr/local/bin/python"
},
"vscode": {
"extensions": [
"ms-python.python",
"ms-toolsai.jupyter"
]
}
}
}
12 changes: 12 additions & 0 deletions .devcontainer/docker-compose.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
version: "3"
services:
app:
extends:
file: ./local-test/docker-compose.yaml
service: app
devices:
- /dev/fuse
cap_add:
- SYS_ADMIN
security_opt:
- apparmor:unconfined
30 changes: 30 additions & 0 deletions .devcontainer/local-test/devcontainer.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,30 @@
{
"name": "Local Test",
"dockerComposeFile": "docker-compose.yaml",
"service": "app",
"workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
"remoteEnv": {
"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
},
"onCreateCommand": "pip install -r ./requirements_dev.txt && pip install -e . && pip install -e ../element-optogenetics && MYSQL_VER=8.0 docker compose down && MYSQL_VER=8.0 docker compose up --build --wait",
"postStartCommand": "docker volume prune -f",
"hostRequirements": {
"cpus": 8,
"memory": "16gb",
"storage": "32gb"
},
"forwardPorts": [
3306
],
"customizations": {
"settings": {
"python.pythonPath": "/usr/local/bin/python"
},
"vscode": {
"extensions": [
"ms-python.python",
"ms-toolsai.jupyter"
]
}
}
}
13 changes: 13 additions & 0 deletions .devcontainer/local-test/docker-compose.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
version: "3"
services:
app:
cpus: 4
mem_limit: 8g
build:
context: ../..
dockerfile: ./.devcontainer/Dockerfile
extra_hosts:
- fakeservices.datajoint.io:127.0.0.1
volumes:
- ../../..:/workspaces
privileged: true # only because of dind
39 changes: 39 additions & 0 deletions .github/ISSUE_TEMPLATE/bug_report.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
---
name: Bug report
about: Create a report to help us improve
title: ''
labels: 'bug'
assignees: ''

---

## Bug Report

### Description

A clear and concise description of what is the overall operation that is intended to be
performed that resulted in an error.

### Reproducibility
Include:
- OS (WIN | MACOS | Linux)
- DataJoint Element Version
- MySQL Version
- MySQL Deployment Strategy (local-native | local-docker | remote)
- Minimum number of steps to reliably reproduce the issue
- Complete error stack as a result of evaluating the above steps

### Expected Behavior
A clear and concise description of what you expected to happen.

### Screenshots
If applicable, add screenshots to help explain your problem.

### Additional Research and Context
Add any additional research or context that was conducted in creating this report.

For example:
- Related GitHub issues and PR's either within this repository or in other relevant
repositories.
- Specific links to specific lines or a focus within source code.
- Relevant summary of Maintainers development meetings, milestones, projects, etc.
5 changes: 5 additions & 0 deletions .github/ISSUE_TEMPLATE/config.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
blank_issues_enabled: false
contact_links:
- name: DataJoint Contribution Guideline
url: https://datajoint.com/docs/community/contribute/
about: Please make sure to review the DataJoint Contribution Guidelines
57 changes: 57 additions & 0 deletions .github/ISSUE_TEMPLATE/feature_request.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,57 @@
---
name: Feature request
about: Suggest an idea for a new feature
title: ''
labels: 'enhancement'
assignees: ''

---

## Feature Request

### Problem

A clear and concise description how this idea has manifested and the context. Elaborate
on the need for this feature and/or what could be improved. Ex. I'm always frustrated
when [...]

### Requirements

A clear and concise description of the requirements to satisfy the new feature. Detail
what you expect from a successful implementation of the feature. Ex. When using this
feature, it should [...]

### Justification

Provide the key benefits in making this a supported feature. Ex. Adding support for this
feature would ensure [...]

### Alternative Considerations

Do you currently have a work-around for this? Provide any alternative solutions or
features you've considered.

### Related Errors
Add any errors as a direct result of not exposing this feature.

Please include steps to reproduce provided errors as follows:
- OS (WIN | MACOS | Linux)
- DataJoint Element Version
- MySQL Version
- MySQL Deployment Strategy (local-native | local-docker | remote)
- Minimum number of steps to reliably reproduce the issue
- Complete error stack as a result of evaluating the above steps

### Screenshots
If applicable, add screenshots to help explain your feature.

### Additional Research and Context
Add any additional research or context that was conducted in creating this feature request.

For example:
- Related GitHub issues and PR's either within this repository or in other relevant
repositories.
- Specific links to specific lines or a focus within source code.
- Relevant summary of Maintainers development meetings, milestones, projects, etc.
- Any additional supplemental web references or links that would further justify this
feature request.
18 changes: 18 additions & 0 deletions .github/workflows/u24_workflow_before_release.yaml
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@@ -0,0 +1,18 @@
name: u24_workflow_before_release_0.0.1
on:
pull_request:
push:
branches:
- '**'
tags-ignore:
- '**'
workflow_dispatch:
jobs:
call_context_check:
uses: dj-sciops/djsciops-cicd/.github/workflows/context_check.yaml@main
call_u24_workflow_build_debian:
uses: dj-sciops/djsciops-cicd/.github/workflows/u24_workflow_build.yaml@main
with:
jhub_ver: 1.4.2
py_ver: 3.9
dist: debian
20 changes: 20 additions & 0 deletions .github/workflows/u24_workflow_release_call.yaml
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@@ -0,0 +1,20 @@
name: u24_workflow_release_call_0.0.1
on:
workflow_run:
workflows: ["u24_workflow_tag_to_release_0.0.1"]
types:
- completed
jobs:
call_context_check:
uses: dj-sciops/djsciops-cicd/.github/workflows/context_check.yaml@main
call_u24_workflow_release_debian:
if: >-
github.event.workflow_run.conclusion == 'success' && github.repository_owner == 'datajoint'
uses: dj-sciops/djsciops-cicd/.github/workflows/u24_workflow_release.yaml@main
with:
jhub_ver: 1.4.2
py_ver: 3.9
dist: debian
secrets:
REGISTRY_USERNAME: ${{secrets.DOCKER_USERNAME}}
REGISTRY_PASSWORD: ${{secrets.DOCKER_PASSWORD}}
15 changes: 15 additions & 0 deletions .github/workflows/u24_workflow_tag_to_release.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
name: u24_workflow_tag_to_release_0.0.1
on:
push:
tags:
- '*.*.*'
- 'test*.*.*'
jobs:
call_context_check:
uses: dj-sciops/djsciops-cicd/.github/workflows/context_check.yaml@main
call_u24_workflow_build_debian:
uses: dj-sciops/djsciops-cicd/.github/workflows/u24_workflow_build.yaml@main
with:
jhub_ver: 1.4.2
py_ver: 3.9
dist: debian
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