Merge pull request #13 from kushalbakshi/main

Add Codespaces tutorial + general updates to the Element

.devcontainer/Dockerfile

@@ -0,0 +1,47 @@
+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-optogenetics/
+
+RUN \
+    # pipeline dependencies
+    apt-get install gcc g++ ffmpeg libsm6 libxext6 -y && \
+    pip install --no-cache-dir -e /tmp/element-optogenetics[elements,tests] && \
+    # clean up
+    rm -rf /tmp/element-optogenetics && \
+    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"

.devcontainer/devcontainer.json

@@ -0,0 +1,30 @@
+{
+	"name": "Environment + Data",
+	"dockerComposeFile": "docker-compose.yaml",
+	"service": "app",
+	"workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
+	"remoteEnv": {
+		"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
+	},
+	"onCreateCommand": "pip install -e .",
+	"postStartCommand": "docker volume prune -f",
+	"hostRequirements": {
+		"cpus": 4,
+		"memory": "8gb",
+		"storage": "32gb"
+	},
+	"forwardPorts": [
+		3306
+	],
+	"customizations": {
+		"settings": {
+			"python.pythonPath": "/usr/local/bin/python"
+		},
+		"vscode": {
+			"extensions": [
+				"[email protected]",
+				"[email protected]"
+			]
+		}
+	}
+}

.devcontainer/docker-compose.yaml

@@ -0,0 +1,23 @@
+version: "3"
+services:
+  app:
+    cpus: 4
+    mem_limit: 8g
+    build:
+      context: ..
+      dockerfile: ./.devcontainer/Dockerfile
+    # image: datajoint/element_optogenetics:latest
+    extra_hosts:
+      - fakeservices.datajoint.io:127.0.0.1
+    devices:
+      - /dev/fuse
+    cap_add:
+      - SYS_ADMIN
+    security_opt:
+      - apparmor:unconfined
+    volumes:
+      - ..:/workspaces/element-optogenetics:cached
+      - docker_data:/var/lib/docker # persist docker images
+    privileged: true # only because of dind
+volumes:
+  docker_data:

.github/workflows/release.yaml

@@ -0,0 +1,19 @@
+name: Release
+on:
+  workflow_dispatch:
+jobs:
+  make_github_release:
+    uses: datajoint/.github/.github/workflows/make_github_release.yaml@main
+  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}}

.github/workflows/test.yaml

@@ -0,0 +1,34 @@
+name: Test
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+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_optogenetics --check --verbose --target-version py${python_version//.}
+

.gitignore

@@ -1,9 +1,15 @@
+# User data
+.DS_Store
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
 *$py.class
 
-# Distribution, packaging, PyInstaller
+# C extensions
+*.so
+
+# Distribution / packaging
 .Python
 env/
 build/
@@ -21,11 +27,17 @@ wheels/
 *.egg-info/
 .installed.cfg
 *.egg
+.idea/
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
 *.manifest
 *.spec
+
+# Installer logs
 pip-log.txt
-pip-delete*.txt
-.idea/
+pip-delete-this-directory.txt
 
 # Unit test / coverage reports
 htmlcov/
@@ -37,52 +49,82 @@ nosetests.xml
 coverage.xml
 *.cover
 .hypothesis/
-.pytest_cache/
 
-# C extension, Translations
-*.so
+# Translations
 *.mo
 *.pot
 
-# editors: vscode, emacs, Mac
-.vscode
-**/*~
-**/#*#
-**/.#*
-.DS_Store
-
-# Django, Flask, Scrapy, Sphinx, mkdocs:
-# PyBuilder, Jupyter, SageMath, celery beat
+# Django stuff:
 *.log
 local_settings.py
+
+# Flask stuff:
 instance/
 .webassets-cache
+
+# Scrapy stuff:
 .scrapy
 scratchpaper.*
+
+# Sphinx documentation
 docs/_build/
-/site
+
+# PyBuilder
 target/
+
+# Jupyter Notebook
 .ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
 celerybeat-schedule
+
+# SageMath parsed files
 *.sage.py
 
-# dotenv, virtualenv, pyenv, mypy
+# dotenv
 ./.env
+.env
+
+# virtualenv
 .venv
 venv/
 ENV/
-.python-version
-.mypy_cache/
 
-# Spyder/Rope project settings
+# Spyder project settings
 .spyderproject
 .spyproject
+
+# Rope project settings
 .ropeproject
 
-# datajoint, notes, nwb export
-dj_local_c*.json
+# mkdocs documentation
+docs/site
+docs/src/tutorials/*ipynb
+
+# mypy
+.mypy_cache/
+
+# datajoint
+dj_local_conf.json
+dj_local_conf_old.json
+
+# emacs
+**/*~
+**/#*#
+**/.#*
+
+
+# include
+!docs/docker-compose.yaml
+
+# vscode settings
+*.code-workspace
+
+# exports/notes
 temp*
-temp/*
-*nwb
-/docs/site
-/docs/src/tutorials/*ipynb
+
+# Codespaces
+example_data/

.markdownlint.yaml

@@ -0,0 +1,18 @@
+# Markdown Linter configuration for docs
+# https://github.com/DavidAnson/markdownlint
+# https://github.com/DavidAnson/markdownlint/blob/main/doc/Rules.md
+MD009: false # permit trailing spaces
+MD007: false # List indenting - permit 4 spaces
+MD013:
+    line_length: "88" # Line length limits
+    tables: false # disable for tables
+    headings: false # disable for headings
+MD030: false # Number of spaces after a list
+MD033: # HTML elements allowed
+    allowed_elements:
+        - "br"
+        - "figure"
+        - "figcaption"
+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