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Merge branch 'codespace' of https://github.com/kushalbakshi/element-f…
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…acemap into codespace_test
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sidhulyalkar committed Dec 13, 2023
2 parents bf227e2 + a2d1e6b commit 4f23212
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50 changes: 50 additions & 0 deletions .devcontainer/Dockerfile
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FROM python:3.9-slim@sha256:5f0192a4f58a6ce99f732fe05e3b3d00f12ae62e183886bca3ebe3d202686c7f

ENV PATH /usr/local/bin:$PATH
ENV PYTHON_VERSION 3.9.17

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 nbconvert && \
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 && \
apt-get clean

COPY ./ /tmp/element-facemap/

RUN \
# pipeline dependencies
apt-get install gcc g++ ffmpeg libsm6 libxext6 libgl1 libegl1 -y && \
# git clone https://github.com/kushalbakshi/facemap.git && \
# pip install ./facemap[gui] && \
pip install --no-cache-dir -e /tmp/element-facemap[elements,tests] && \
# clean up
rm -rf /tmp/element-facemap && \
apt-get clean

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

ENV FACEMAP_ROOT_DATA_DIR /workspaces/element-facemap/example_data
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
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{
"name": "Environment + Data",
"dockerComposeFile": "docker-compose.yaml",
"service": "app",
"workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
"remoteEnv": {
"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
},
"onCreateCommand": "mkdir -p ${FACEMAP_ROOT_DATA_DIR} && pip install -e .",
"postStartCommand": "docker volume prune -f && s3fs ${DJ_PUBLIC_S3_LOCATION} ${FACEMAP_ROOT_DATA_DIR} -o nonempty,multipart_size=530,endpoint=us-east-1,url=http://s3.amazonaws.com,public_bucket=1",
"hostRequirements": {
"cpus": 4,
"memory": "8gb",
"storage": "32gb"
},
"forwardPorts": [
3306
],
"customizations": {
"settings": {
"python.pythonPath": "/usr/local/bin/python"
},
"vscode": {
"extensions": [
"[email protected]",
"[email protected]"
]
}
}
}
25 changes: 25 additions & 0 deletions .devcontainer/docker-compose.yaml
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version: "3"
services:
app:
cpus: 4
mem_limit: 8g
build:
context: ..
dockerfile: ./.devcontainer/Dockerfile
# image: datajoint/element_array_ephys:latest
extra_hosts:
- fakeservices.datajoint.io:127.0.0.1
environment:
- DJ_PUBLIC_S3_LOCATION=djhub.vathes.datapub.elements:/workflow-facemap/0.0.0
devices:
- /dev/fuse
cap_add:
- SYS_ADMIN
security_opt:
- apparmor:unconfined
volumes:
- ..:/workspaces/element-facemap:cached
- docker_data:/var/lib/docker # persist docker images
privileged: true # only because of dind
volumes:
docker_data:
27 changes: 27 additions & 0 deletions .github/workflows/release.yaml
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name: Release
on:
workflow_dispatch:
jobs:
make_github_release:
uses: datajoint/.github/.github/workflows/make_github_release.yaml@main
pypi_release:
needs: make_github_release
uses: datajoint/.github/.github/workflows/pypi_release.yaml@main
secrets:
TWINE_USERNAME: ${{secrets.TWINE_USERNAME}}
TWINE_PASSWORD: ${{secrets.TWINE_PASSWORD}}
with:
UPLOAD_URL: ${{needs.make_github_release.outputs.release_upload_url}}
mkdocs_release:
uses: datajoint/.github/.github/workflows/mkdocs_release.yaml@main
permissions:
contents: write
devcontainer-build:
uses: datajoint/.github/.github/workflows/devcontainer-build.yaml@main
devcontainer-publish:
needs:
- devcontainer-build
uses: datajoint/.github/.github/workflows/devcontainer-publish.yaml@main
secrets:
DOCKERHUB_USERNAME: ${{secrets.DOCKERHUB_USERNAME}}
DOCKERHUB_TOKEN: ${{secrets.DOCKERHUB_TOKEN_FOR_ELEMENTS}}
36 changes: 36 additions & 0 deletions .github/workflows/test.yaml
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name: Test
on:
push:
pull_request:
workflow_dispatch:
schedule:
- cron: "0 8 * * 1"
jobs:
devcontainer-build:
uses: datajoint/.github/.github/workflows/devcontainer-build.yaml@main
tests:
runs-on: ubuntu-latest
strategy:
matrix:
py_ver: ["3.9", "3.10"]
mysql_ver: ["8.0", "5.7"]
include:
- py_ver: "3.8"
mysql_ver: "5.7"
- py_ver: "3.7"
mysql_ver: "5.7"
steps:
- uses: actions/checkout@v3
- name: Set up Python ${{matrix.py_ver}}
uses: actions/setup-python@v4
with:
python-version: ${{matrix.py_ver}}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install flake8 "black[jupyter]"
- name: Run style tests
run: |
python_version=${{matrix.py_ver}}
black element_facemap --check --verbose --target-version py${python_version//.}
black notebooks --check --verbose --target-version py${python_version//.}
17 changes: 0 additions & 17 deletions .github/workflows/u24_element_before_release.yaml

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28 changes: 0 additions & 28 deletions .github/workflows/u24_element_release_call.yaml

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14 changes: 0 additions & 14 deletions .github/workflows/u24_element_tag_to_release.yaml

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14 changes: 13 additions & 1 deletion .gitignore
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Expand Up @@ -116,5 +116,17 @@ temp*
**/#*#
**/.#*

# datajoint, notes, nwb export
dj_local_c*.json
temp*
temp/*
*nwb

# docs
/docs/site
/docs/site/
/docs/src/tutorials/*ipynb
/docs/mike-mkdocs*
element_miniscope/qc.py

# DevContainer/Codespaces
example_data/
3 changes: 2 additions & 1 deletion .markdownlint.yaml
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Expand Up @@ -11,6 +11,7 @@ MD030: false # Number of spaces after a list
MD033: # HTML elements allowed
allowed_elements:
- "br"
- "sup"
MD034: false # Permit bare URLs
MD031: false # Spacing w/code blocks. Conflicts with `??? Note` and code tab styling
MD046: false # Spacing w/code blocks. Conflicts with `??? Note` and code tab styling
MD046: false # Spacing w/code blocks. Conflicts with `??? Note` and code tab styling
16 changes: 16 additions & 0 deletions .vscode/launch.json
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{
// Use IntelliSense to learn about possible attributes.
// Hover to view descriptions of existing attributes.
// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
"version": "0.2.0",
"configurations": [
{
"name": "Python: Current File",
"type": "python",
"request": "launch",
"program": "${file}",
"console": "integratedTerminal",
"justMyCode": false
}
]
}
15 changes: 15 additions & 0 deletions .vscode/settings.json
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{
"editor.formatOnPaste": false,
"editor.formatOnSave": true,
"editor.rulers": [
88
],
"python.formatting.provider": "black",
"[python]": {
"editor.defaultFormatter": null
},
"[markdown]": {
"editor.defaultFormatter": "disable"
},
"files.autoSave": "off"
}
14 changes: 14 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,18 @@
Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
[Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.

## [0.2.0] - 2023-11-29

+ Add - Inference module as `facemap_inference.py`
+ Add - DevContainer for codespaces
+ Add - `tutorial_pipeline.py`
+ Add - 60 min tutorial using Jupyter Notebooks
+ Update - General improvements to increase consistency with other DataJoint Elements

## [0.1.7] - 2023-10-18

+ Fix - Index `mot_Sv` and `movSv` by `roi_no` in `FacialSignal`

## [0.1.6] - 2023-05-22

+ Add - Facemap citation
Expand Down Expand Up @@ -43,6 +55,8 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
the diagonal matrix
+ Add - Output directory inferral, if unspecified.

[0.2.0]: https://github.com/datajoint/element-facemap/releases/tag/0.2.0
[0.1.7]: https://github.com/datajoint/element-facemap/releases/tag/0.1.7
[0.1.6]: https://github.com/datajoint/element-facemap/releases/tag/0.1.6
[0.1.5]: https://github.com/datajoint/element-facemap/releases/tag/0.1.5
[0.1.4]: https://github.com/datajoint/element-facemap/releases/tag/0.1.4
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2 changes: 1 addition & 1 deletion CONTRIBUTING.md
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# Contribution Guidelines

This project follows the
[DataJoint Contribution Guidelines](https://datajoint.com/docs/community/contribute/).
[DataJoint Contribution Guidelines](https://datajoint.com/docs/about/contribute/).
Please reference the link for more full details.
15 changes: 0 additions & 15 deletions Dockerfile

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2 changes: 1 addition & 1 deletion LICENSE
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MIT License

Copyright (c) 2022 DataJoint
Copyright (c) 2023 DataJoint

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
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