aind-ibl-ephys-alignment-preprocessing 0.1.1__tar.gz

aind_ibl_ephys_alignment_preprocessing-0.1.1/.copier-answers.yml

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+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: 0.1.4
+_src_path: /home/galen.lynch/Documents/Code/aind-python-copier-template
+author_email: galen@galenlynch.com
+author_fullname: Galen Lynch
+current_year: '2026'
+github_org: AllenNeuralDynamics
+github_url: https://github.com/AllenNeuralDynamics/aind-ibl-ephys-alignment-preprocessing
+include_cli: true
+include_docs: true
+include_notebooks: false
+include_type_hints: true
+institute_name: Allen Institute for Neural Dynamics
+license: MIT
+project_description: Library to prepare histology and ephys for the IBL ephys alignment
+    GUI
+project_name: AIND IBL Ephys Alignment Preprocessing
+project_slug: aind-ibl-ephys-alignment-preprocessing
+publish_to_pypi: false
+python_package_import_name: aind_ibl_ephys_alignment_preprocessing
+python_version: '3.11'
+target_python_version: '3.13'
+workflow_source: AllenNeuralDynamics/galen-uv-workflows
+workflow_version: v2

aind_ibl_ephys_alignment_preprocessing-0.1.1/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

aind_ibl_ephys_alignment_preprocessing-0.1.1/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

aind_ibl_ephys_alignment_preprocessing-0.1.1/.github/ISSUE_TEMPLATE/user-story.md

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+---
+name: User story
+about: This template provides a basic structure for user story issues.
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+# User story
+As a ..., I want to ..., so I can ...
+
+*Ideally, this is in the issue title, but if not, you can put it here. If so, delete this section.*
+
+# Acceptance criteria
+- [ ] This is something that can be verified to show that this user story is satisfied.
+
+# Sprint Ready Checklist 
+- [ ] 1. Acceptance criteria defined 
+- [ ] 2. Team understands acceptance criteria 
+- [ ] 3. Team has defined solution / steps to satisfy acceptance criteria 
+- [ ] 4. Acceptance criteria is verifiable / testable 
+- [ ] 5. External / 3rd Party dependencies identified
+- [ ] 6. Ticket is prioritized and sized
+
+# Notes
+*Add any helpful notes here.*

aind_ibl_ephys_alignment_preprocessing-0.1.1/.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  # Enable version updates for GitHub Actions
+  - package-ecosystem: "github-actions"
+    # Workflow files stored in the default location of `.github/workflows`
+    # You don't need to specify `/.github/workflows` for `directory`. You can use `directory: "/"`.
+    directory: "/"
+    schedule:
+      interval: "weekly"
+  # Enable version updates for pip
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"

aind_ibl_ephys_alignment_preprocessing-0.1.1/.github/workflows/bump-call.yml

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+name: Bump Version
+
+on:
+  workflow_run:
+    workflows: ["CI"]
+    branches: [ main ]
+    types: [ completed ]
+  workflow_dispatch:
+
+permissions:
+  contents: write    # needed to push commits/tags
+  id-token: write    # needed if your reusable workflow exchanges OIDC tokens
+
+concurrency:
+  group: bump-${{ github.workflow }}-${{ github.event.workflow_run.head_branch || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  bump:
+    # Only run when:
+    #  • a CI run just succeeded (and the head commit message doesn't start with 'bump:')
+    #  • OR this is a manual dispatch
+    if: >
+      (github.event_name == 'workflow_run' &&
+       github.event.workflow_run.conclusion == 'success' &&
+       !startsWith(github.event.workflow_run.head_commit.message, 'bump:')) ||
+      (github.event_name == 'workflow_dispatch' &&
+      github.ref == 'refs/heads/main')
+    uses: AllenNeuralDynamics/galen-uv-workflows/.github/workflows/bump-version.yml@v2
+    with:
+      default-branch: main
+    secrets:
+      repo-token: ${{ secrets.SERVICE_TOKEN }}

aind_ibl_ephys_alignment_preprocessing-0.1.1/.github/workflows/ci-call.yml

@@ -0,0 +1,38 @@
+name: CI
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+    types: [opened, synchronize, reopened, ready_for_review]
+
+permissions:
+  contents: read
+  pull-requests: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  run-ci:
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.11", "3.13"]
+
+    if: >
+      (github.event_name != 'pull_request' || github.event.pull_request.draft == false) &&
+      github.actor != 'github-actions[bot]' &&
+      !(github.event_name == 'push' && startsWith(github.event.head_commit.message, 'bump:'))
+
+    uses: AllenNeuralDynamics/galen-uv-workflows/.github/workflows/ci.yml@v2
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python-version }}
+      package-name: aind_ibl_ephys_alignment_preprocessing
+      run-mypy: true
+    secrets:
+      repo-token: ${{ secrets.GITHUB_TOKEN }}

aind_ibl_ephys_alignment_preprocessing-0.1.1/.github/workflows/docs-ci.yml

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+name: docs (CI)
+
+on:
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+jobs:
+  docs:
+    uses: AllenNeuralDynamics/galen-uv-workflows/.github/workflows/_docs-ci-reusable.yml@v2
+    with:
+      python-version: '3.13'
+      install-extras: '--group docs'
+      docs-path: 'docs/source'
+      output-dir: 'docs/build/html'
+      fail-on-warnings: true
+      linkcheck: false              # flip to true if you want it on PRs
+      run-apidoc: false             # set true if you generate pages each build

aind_ibl_ephys_alignment_preprocessing-0.1.1/.github/workflows/publish-call.yml

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+name: "Release"
+
+on:
+  push:
+    tags:
+      - 'v[0-9]*'          # semver tags
+  workflow_dispatch:
+
+permissions:
+  contents: write    # create release + upload assets
+
+concurrency:
+  group: release
+  cancel-in-progress: false   # let releases finish
+
+jobs:
+  run-release:
+    uses: AllenNeuralDynamics/galen-uv-workflows/.github/workflows/publish.yml@v2
+    with:
+      tag-name: ${{ github.ref_name }}
+      python-version: "3.13"
+      publish-to-pypi: true
+    secrets:
+      repo-token: ${{ secrets.GITHUB_TOKEN }}
+      pypi-token: ${{ secrets.AIND_PYPI_TOKEN }}

aind_ibl_ephys_alignment_preprocessing-0.1.1/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+# MacOs
+**/.DS_Store
+
+# VSCode
+.vscode/
+
+# Claude
+.claude/

aind_ibl_ephys_alignment_preprocessing-0.1.1/.python-version

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+3.13

aind_ibl_ephys_alignment_preprocessing-0.1.1/.readthedocs.yaml

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+# .readthedocs.yaml
+version: 2
+
+# RTD will run `sphinx-build` for you using this conf.py
+sphinx:
+  configuration: docs/source/conf.py
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.13"
+
+  jobs:
+    # Install uv once at the OS level, before creating the venv
+    pre_create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+
+    # Create the RTD virtualenv using uv so RTD will use it for the build
+    create_environment:
+      - uv venv "$READTHEDOCS_VIRTUALENV_PATH"
+
+    # Install your docs deps from pyproject (respects uv.lock if present)
+    install:
+      - UV_PROJECT_ENVIRONMENT="$READTHEDOCS_VIRTUALENV_PATH" uv sync --frozen --group docs

aind_ibl_ephys_alignment_preprocessing-0.1.1/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## v0.1.1 (2026-03-24)
+
+### Fix
+
+- publish to pypi, use published aind-ephys-ibl-gui-conversion
+
+## v0.1.0 (2026-03-23)
+
+### Fix
+
+- Add Manifest (#1)

aind_ibl_ephys_alignment_preprocessing-0.1.1/LICENSE

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+MIT License
+
+Copyright (c) 2026 Allen Institute for Neural Dynamics
+
+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.
+

aind_ibl_ephys_alignment_preprocessing-0.1.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: aind-ibl-ephys-alignment-preprocessing
+Version: 0.1.1
+Summary: Library to prepare histology and ephys for the IBL ephys alignment GUI
+Project-URL: Repository, https://github.com/AllenNeuralDynamics/aind-ibl-ephys-alignment-preprocessing/
+Project-URL: Issues, https://github.com/AllenNeuralDynamics/aind-ibl-ephys-alignment-preprocessing/issues
+Project-URL: Changelog, https://github.com/AllenNeuralDynamics/aind-ibl-ephys-alignment-preprocessing/blob/main/CHANGELOG.md
+Author: Allen Institute for Neural Dynamics
+Author-email: Galen Lynch <galen@galenlynch.com>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.11
+Requires-Dist: aind-anatomical-utils>=0.4
+Requires-Dist: aind-ephys-ibl-gui-conversion>=0.2
+Requires-Dist: aind-registration-utils>=0.4
+Requires-Dist: aind-s3-cache>=0.1
+Requires-Dist: aind-zarr-utils>=0.11.2
+Requires-Dist: antspyx>=0.3.0
+Requires-Dist: filelock
+Requires-Dist: iblatlas>=0.4.0
+Requires-Dist: numpy>=1.21.0
+Requires-Dist: pandas>=1.3.0
+Requires-Dist: pydantic>=2
+Requires-Dist: simpleitk
+Description-Content-Type: text/markdown
+
+# AIND IBL Ephys Alignment Preprocessing
+
+![CI](https://github.com/AllenNeuralDynamics/aind-ibl-ephys-alignment-preprocessing/actions/workflows/ci-call.yml/badge.svg)
+[![PyPI - Version](https://img.shields.io/pypi/v/aind-ibl-ephys-alignment-preprocessing)](https://pypi.org/project/aind-ibl-ephys-alignment-preprocessing/)
+[![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
+[![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
+[![ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
+[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border.json)](https://github.com/copier-org/copier)
+Library to prepare histology and ephys for the IBL ephys alignment GUI
+
+## Installation
+
+If you choose to clone the repository, you can install the package by running the following command from the root directory of the repository:
+
+```bash
+pip install .
+```
+
+Otherwise, you can use pip:
+
+```bash
+pip install aind-ibl-ephys-alignment-preprocessing
+```
+
+
+
+To develop the code, run:
+```bash
+uv sync
+```
+
+## Development
+
+Please test your changes using the full linting and testing suite:
+
+```bash
+./scripts/run_linters_and_checks.sh -c
+```
+
+Or run individual commands:
+```bash
+uv run --frozen ruff format          # Code formatting
+uv run --frozen ruff check           # Linting
+uv run --frozen mypy                 # Type checking
+uv run --frozen interrogate -v       # Documentation coverage
+uv run --frozen codespell --check-filenames  # Spell checking
+uv run --frozen pytest --cov aind_ibl_ephys_alignment_preprocessing # Tests with coverage
+```
+
+
+### Documentation
+```bash
+sphinx-build -b html docs/source/ docs/build/html
+```
+
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.

aind_ibl_ephys_alignment_preprocessing-0.1.1/README.md

@@ -0,0 +1,60 @@
+# AIND IBL Ephys Alignment Preprocessing
+
+![CI](https://github.com/AllenNeuralDynamics/aind-ibl-ephys-alignment-preprocessing/actions/workflows/ci-call.yml/badge.svg)
+[![PyPI - Version](https://img.shields.io/pypi/v/aind-ibl-ephys-alignment-preprocessing)](https://pypi.org/project/aind-ibl-ephys-alignment-preprocessing/)
+[![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
+[![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
+[![ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
+[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border.json)](https://github.com/copier-org/copier)
+Library to prepare histology and ephys for the IBL ephys alignment GUI
+
+## Installation
+
+If you choose to clone the repository, you can install the package by running the following command from the root directory of the repository:
+
+```bash
+pip install .
+```
+
+Otherwise, you can use pip:
+
+```bash
+pip install aind-ibl-ephys-alignment-preprocessing
+```
+
+
+
+To develop the code, run:
+```bash
+uv sync
+```
+
+## Development
+
+Please test your changes using the full linting and testing suite:
+
+```bash
+./scripts/run_linters_and_checks.sh -c
+```
+
+Or run individual commands:
+```bash
+uv run --frozen ruff format          # Code formatting
+uv run --frozen ruff check           # Linting
+uv run --frozen mypy                 # Type checking
+uv run --frozen interrogate -v       # Documentation coverage
+uv run --frozen codespell --check-filenames  # Spell checking
+uv run --frozen pytest --cov aind_ibl_ephys_alignment_preprocessing # Tests with coverage
+```
+
+
+### Documentation
+```bash
+sphinx-build -b html docs/source/ docs/build/html
+```
+
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.