initial setup

.github/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others’ private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project’s leadership.
+
+
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

.github/workflows/add_issue_to_dashboard.yml

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+name: Add Issue to Dashboard
+
+on:
+  issues:
+    types:
+      - opened
+
+jobs:
+  add_to_dashboard:
+    uses: catalystneuro/.github/.github/workflows/add_issue_to_dashboard.yml@main
+    secrets:
+      PROJECT_TOKEN: ${{ secrets.PROJECT_TOKEN }}

.github/workflows/add_pull_request_to_dashboard.yml

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+name: Add Pull Request to Dashboard
+
+on:
+  pull_request:
+    types:
+      - opened
+
+jobs:
+  add_to_dashboard:
+    uses: catalystneuro/.github/.github/workflows/add_pull_request_to_dashboard.yml@main
+    secrets:
+      PROJECT_TOKEN: ${{ secrets.PROJECT_TOKEN }}

.github/workflows/codespell.yml

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+name: Codespell
+
+on:
+  pull_request:
+  merge_group:
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v1

.github/workflows/dailies.yml

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+name: Daily workflows
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 16 * * *"  # Daily at noon EST
+
+jobs:
+
+  run-daily-tests:
+    uses: catalystneuro/leifer-lab-to-nwb/.github/workflows/testing.yml@main
+
+  notify:
+    runs-on: ubuntu-latest
+    needs: [run-daily-tests]
+    if: ${{ always() && contains(needs.*.result, 'failure') }}
+    steps:
+    - uses: dawidd6/action-send-mail@v3
+      with:
+        server_address: smtp.gmail.com
+        server_port: 465  # TSL
+        username: ${{ secrets.MAIL_USERNAME }}
+        password: ${{ secrets.MAIL_PASSWORD }}
+        subject: TQDM Publisher Daily Test Failure
+        to: [email protected]
+        from: TQDM Publisher
+        body: "The daily workflow for TQDM Publisher failed: please check status at https://github.com/CatalystNeuro/leifer-lab-to-nwb/actions/workflows/dailies.yml"

.github/workflows/deploy-tests.yml

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+name: Deploy tests
+
+on:
+  pull_request:
+
+concurrency:  # Cancel previous workflows on the same pull request
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  run-tests:
+    uses: catalystneuro/leifer-lab-to-nwb/.github/workflows/testing.yml@main
+
+  check-final-status:
+    name: All tests passing
+    if: always()
+
+    needs:
+    - run-tests
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Decide whether the all jobs succeeded or at least one failed
+      uses: re-actors/alls-green@release/v1
+      with:
+        allowed-skips: run-tests  # Sometimes only docs are adjusted
+        jobs: ${{ toJSON(needs) }}

.github/workflows/testing.yml

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+name: Full Tests
+on:
+  workflow_call:
+    secrets:
+      CODECOV_TOKEN:
+        required: true
+
+jobs:
+  run:
+    name: ${{ matrix.os }} Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11"]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+    steps:
+      - uses: s-weigand/setup-conda@v1
+      - uses: actions/checkout@v3
+      - run: git fetch --prune --unshallow --tags
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Global Setup
+        run: |
+          python -m pip install -U pip  # Official recommended way
+          pip install pytest-xdist
+
+      - name: Install package in editable mode
+        run: pip install -e .
+
+      - name: Test import
+        run: python -c "import leifer_lab_to_nwb"

.gitignore

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+# Dataset file / log file types:
+/**/*.log
+
+# Byte-compiled / optimized / DLL files
+/**/__pycache__/
+*.py[cod]
+
+# Datasets:
+/tests/testdatasets/
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Sphinx documentation
+docs/build
+docs/make.bat
+docs/Makefile
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/artifacts
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+#Mac
+.DS_Store
+
+# Vscode
+.vscode/
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+!.vscode/*.code-snippets
+
+# Local History for Visual Studio Code
+.history/
+
+# Built Visual Studio Code Extensions
+*.vsix
+
+# Spyder
+.spyproject/

.pre-commit-config.yaml

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+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+    -   id: check-yaml
+    -   id: check-toml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 24.2.0
+    hooks:
+    -   id: black
+-   repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    hooks:
+    -   id: isort

README.md

@@ -1 +1,14 @@
-# leifer-lab-to-nwb
+# leifer-lab-to-nwb
+
+Conversion scripts for the Leifer lab.Alternatively
+
+Includes the publication Neural signal propagation atlas of Caenorhabditis elegans (Nature, 2023).
+
+
+## Installation
+
+```
+git clone https://github.com/catalystneuro/leifer-lab-to-nwb
+cd leifer-lab-to-nwb
+pip install -e .
+```