Create template for element

.github/workflow/development.yaml

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+name: Development
+on:
+  pull_request:
+  push:
+    tags:
+      - '*.*.*'
+jobs:
+  test-changelog:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Get changelog entry
+        id: changelog_reader
+        uses: guzman-raphael/changelog-reader-action@v5
+        with:
+          path: ./CHANGELOG.md
+      - name: Verify changelog parsing
+        env:
+          TAG_NAME: ${{steps.changelog_reader.outputs.version}}
+          RELEASE_NAME: Release ${{steps.changelog_reader.outputs.version}}
+          BODY: ${{steps.changelog_reader.outputs.changes}}
+          PRERELEASE: ${{steps.changelog_reader.outputs.status == 'prereleased'}}
+          DRAFT: ${{steps.changelog_reader.outputs.status == 'unreleased'}}
+        run: |
+          echo "TAG_NAME=${TAG_NAME}"
+          echo "RELEASE_NAME=${RELEASE_NAME}"
+          echo "BODY=${BODY}"
+          echo "PRERELEASE=${PRERELEASE}"
+          echo "DRAFT=${DRAFT}"
+  build:
+    needs: test-changelog
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        include:
+          - py_ver: 3.8
+            distro: alpine
+            image: djbase
+    env:
+      PY_VER: ${{matrix.py_ver}}
+      DISTRO: ${{matrix.distro}}
+      IMAGE: ${{matrix.image}}
+      DOCKER_CLIENT_TIMEOUT: "120"
+      COMPOSE_HTTP_TIMEOUT: "120"
+    steps:
+      - uses: actions/checkout@v2
+      - name: Compile image
+        run: |
+          export PKG_NAME=$(python3 -c "print([p for p in __import__('setuptools').find_packages() if '.' not in p][0])")
+          export PKG_VERSION=$(cat ${PKG_NAME}/version.py | awk -F\' '/__version__ = / {print $2}')
+          export HOST_UID=$(id -u)
+          docker-compose -f docker-compose-build.yaml up --exit-code-from element --build
+          IMAGE=$(docker images --filter "reference=datajoint/${PKG_NAME}*" \
+            --format "{{.Repository}}")
+          TAG=$(docker images --filter "reference=datajoint/${PKG_NAME}*" --format "{{.Tag}}")
+          docker save "${IMAGE}:${TAG}" | \
+            gzip > "image-${PKG_NAME}-${PKG_VERSION}-py${PY_VER}-${DISTRO}.tar.gz"
+          echo "PKG_NAME=${PKG_NAME}" >> $GITHUB_ENV
+          echo "PKG_VERSION=${PKG_VERSION}" >> $GITHUB_ENV
+      - name: Add image artifact
+        uses: actions/upload-artifact@v2
+        with:
+          name: image-${{env.PKG_NAME}}-${{env.PKG_VERSION}}-py${{matrix.py_ver}}-${{matrix.distro}}
+          path: "image-${{env.PKG_NAME}}-${{env.PKG_VERSION}}-py${{matrix.py_ver}}-\
+            ${{matrix.distro}}.tar.gz"
+          retention-days: 1
+      - if: matrix.py_ver == '3.8' && matrix.distro == 'alpine'
+        name: Add pip artifacts
+        uses: actions/upload-artifact@v2
+        with:
+          name: pip-${{env.PKG_NAME}}-${{env.PKG_VERSION}}
+          path: dist
+          retention-days: 1
+  publish-release:
+    if: github.event_name == 'push'
+    needs: build
+    runs-on: ubuntu-latest
+    env:
+      TWINE_USERNAME: ${{secrets.twine_username}}
+      TWINE_PASSWORD: ${{secrets.twine_password}}
+    outputs:
+      release_upload_url: ${{steps.create_gh_release.outputs.upload_url}}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Determine package version
+        run: |
+          PKG_NAME=$(python3 -c "print([p for p in __import__('setuptools').find_packages() if '.' not in p][0])")
+          SDIST_PKG_NAME=$(echo ${PKG_NAME} | sed 's|_|-|g')
+          PKG_VERSION=$(cat ${PKG_NAME}/version.py | awk -F\' '/__version__ = / {print $2}')
+          echo "PKG_NAME=${PKG_NAME}" >> $GITHUB_ENV
+          echo "PKG_VERSION=${PKG_VERSION}" >> $GITHUB_ENV
+          echo "SDIST_PKG_NAME=${SDIST_PKG_NAME}" >> $GITHUB_ENV
+      - name: Get changelog entry
+        id: changelog_reader
+        uses: guzman-raphael/changelog-reader-action@v5
+        with:
+          path: ./CHANGELOG.md
+          version: ${{env.PKG_VERSION}}
+      - name: Create GH release
+        id: create_gh_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        with:
+          tag_name: ${{steps.changelog_reader.outputs.version}}
+          release_name: Release ${{steps.changelog_reader.outputs.version}}
+          body: ${{steps.changelog_reader.outputs.changes}}
+          prerelease: ${{steps.changelog_reader.outputs.status == 'prereleased'}}
+          draft: ${{steps.changelog_reader.outputs.status == 'unreleased'}}
+      - name: Fetch image artifact
+        uses: actions/download-artifact@v2
+        with:
+          name: image-${{env.PKG_NAME}}-${{env.PKG_VERSION}}-py3.8-alpine
+      - name: Fetch pip artifacts
+        uses: actions/download-artifact@v2
+        with:
+          name: pip-${{env.PKG_NAME}}-${{env.PKG_VERSION}}
+          path: dist
+      - name: Publish pip release
+        run: |
+          export HOST_UID=$(id -u)
+          docker load < "image-${{env.PKG_NAME}}-${PKG_VERSION}-py3.8-alpine.tar.gz"
+          docker-compose -f docker-compose-build.yaml run \
+            -e TWINE_USERNAME=${TWINE_USERNAME} -e TWINE_PASSWORD=${TWINE_PASSWORD} element \
+            sh -lc "pip install twine && python -m twine upload dist/*"
+      - name: Determine pip artifact paths
+        run: |
+          echo "PKG_WHEEL_PATH=$(ls dist/${PKG_NAME}-*.whl)" >> $GITHUB_ENV
+          echo "PKG_SDIST_PATH=$(ls dist/${SDIST_PKG_NAME}-*.tar.gz)" >> $GITHUB_ENV
+      - name: Upload pip wheel asset to release
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        with:
+          upload_url: ${{steps.create_gh_release.outputs.upload_url}}
+          asset_path: ${{env.PKG_WHEEL_PATH}}
+          asset_name: pip-${{env.PKG_NAME}}-${{env.PKG_VERSION}}.whl
+          asset_content_type: application/zip
+      - name: Upload pip sdist asset to release
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        with:
+          upload_url: ${{steps.create_gh_release.outputs.upload_url}}
+          asset_path: ${{env.PKG_SDIST_PATH}}
+          asset_name: pip-${{env.SDIST_PKG_NAME}}-${{env.PKG_VERSION}}.tar.gz
+          asset_content_type: application/gzip

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution, packaging, PyInstaller
+.Python
+env/
+build/
+*egg*/
+*dist/
+downloads/
+lib*/
+parts/
+var/
+wheels/
+.installed.cfg
+*.egg
+*.manifest
+*.spec
+pip-*.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+*.cov*
+.cache
+nosetests.xml
+coverage.xml
+.hypothesis/
+.pytest_cache/
+docker-compose.y*ml
+
+# C extension, Translations
+# editors: vscode, emacs, Mac
+*.so
+*.mo
+*.pot
+.vscode
+**/*~
+**/#*#
+**/.#*
+.DS_Store
+
+# Django, Flask, Scrapy, Sphinx, mkdocs
+# PyBuilder, Jupyter, SageMath, celery beat
+*.log
+local_settings.py
+instance/
+.webassets-cache
+.scrapy
+scratchpaper.*
+docs/_build/
+/site
+target/
+.*checkpoints
+celerybeat-schedule
+*.sage.py
+
+# dotenv, virtualenv, pyenv, mypy
+.*env
+venv/
+ENV/
+.python-version
+.mypy_cache/
+
+# Spyder/Rope project settings
+.spy*project
+.ropeproject
+
+# datajoint, notes, nwb export
+dj_local_c*.json
+temp*
+*nwb

Background.md

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+# Electrode Localization Element
+## Description of modality, user population
+
+## Acquisition tools
+
+## Preprocessing tools
+
+## Precursor projects and interviews
+
+## Pipeline Development

CHANGELOG.md

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+# Changelog
+
+Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
+
+## 0.0.0a1 - unreleased
+### Added
++ 

CONTRIBUTING.md

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+# Contribution Guidelines
+
+This project follows the [DataJoint Contribution Guidelines](https://docs.datajoint.org/python/community/02-Contribute.html). Please reference the link for more full details.

Dockerfile

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+ARG PY_VER
+ARG DISTRO
+ARG IMAGE
+ARG PKG_NAME
+ARG PKG_VERSION
+
+FROM datajoint/${IMAGE}:py${PY_VER}-${DISTRO}
+COPY --chown=anaconda:anaconda ./requirements.txt ./setup.py \
+    /main/
+COPY --chown=anaconda:anaconda ./${PKG_NAME} /main/${PKG_NAME}
+RUN \
+    cd /main && \
+    pip install . && \
+    rm -R /main/*
+WORKDIR /main

LICENSE

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+MIT License
+
+Copyright (c) 2022 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
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1 +1,51 @@
-# element-electrode-localization
+# DataJoint Element - Electrode Localization
+
+This repository is currently a work in progress.
+
+See [Background](Background.md) for the background information and development timeline.
+
+## Element architecture
+<!-- ![element-electrode-localization](https://github.com/datajoint/element-electrode-localization/blob/main/images/diagram_electrode-localization.svg) -->
+## Installation
+
++ Install `element-electrode-localization`
+    ```
+    pip install element-electrode-localization
+    ```
+
++ Upgrade `element-electrode-localization` previously installed with `pip`
+    ```
+    pip install --upgrade element-electrode-localization
+    ```
+
++ Install `element-interface`
+
+    + `element-interface` is a dependency of `element-electrode-localization`, however it is not contained within `requirements.txt`.
+
+    ```
+    pip install "element-interface @ git+https://github.com/datajoint/element-interface"
+    ```
+
+## Usage
+
+### Element activation
+
+To activate the `element-electrode-localization`, ones need to provide:
+
+1. Schema names
+    + schema name for the `electrode` module
+
+2. Upstream tables
+     + 
+
+3. Utility functions. See [example definitions](https://github.com/datajoint/workflow-array-ephys/blob/main/workflow_array_ephys/paths.py).
+    + get_ephys_root_data_dir(): Returns your root data directory.
+    + get_session_directory(): Returns the path of the session data relative to the root.
+
+For more details, check the docstring of the `element-electrode-localization`:
+
+    help(electrode.activate)
+
+### Example usage
+
+See the [workflow-array-ephys project](https://github.com/datajoint/workflow-array-ephys) for an example usage of this Element.

docker-compose-build.yaml

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+# PY_VER=3.8 IMAGE=djbase DISTRO=alpine PKG_NAME=$(python -c "print([p for p in __import__('setuptools').find_packages() if '.' not in p][0])") PKG_VERSION=$(cat ${PKG_NAME}/version.py | awk -F\' '/__version__/ {print $2}') HOST_UID=$(id -u) docker-compose -f docker-compose-build.yaml up --exit-code-from element --build
+#
+# Intended for updating dependencies and docker image.
+# Used to build release artifacts.
+version: "2.4"
+services:
+  element:
+    build:
+      context: .
+      args:
+        - PY_VER
+        - DISTRO
+        - IMAGE
+        - PKG_NAME
+        - PKG_VERSION
+    image: datajoint/${PKG_NAME}:${PKG_VERSION}
+    user: ${HOST_UID}:anaconda
+    volumes:
+      - .:/main
+    command:
+      - sh
+      - -lc
+      - |
+        set -e
+        rm -R build dist *.egg-info || echo "No prev build"
+        python setup.py bdist_wheel sdist

element_electrode_localization/version.py

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+"""Package metadata."""
+__version__ = '0.0.0a1'

requirements.txt

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+datajoint>=0.13