LCNE-patchseq-analysis 0.0.1__tar.gz

lcne_patchseq_analysis-0.0.1/.flake8

@@ -0,0 +1,9 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    build,
+    .venv,
+    venv
+max-complexity = 10
+max-line-length = 100

lcne_patchseq_analysis-0.0.1/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+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.

lcne_patchseq_analysis-0.0.1/.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.

lcne_patchseq_analysis-0.0.1/.github/ISSUE_TEMPLATE/user-story.md

@@ -0,0 +1,27 @@
+---
+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.*

lcne_patchseq_analysis-0.0.1/.github/workflows/init.yml

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+# Workflow runs only once when the template is first used.
+# File can be safely deleted after repo is initialized.
+name: Initialize repository
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  initialize-package:
+    name: Initialize the package
+    if: ${{github.event.repository.name != 'aind-library-template'}}
+    runs-on: ubuntu-latest
+    env:
+      REPO_NAME: ${{ github.event.repository.name }}
+      GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+    - name: Rename package
+      run: |
+        pkg_name=$(echo "${REPO_NAME}" | tr - _)
+        current_description='description = "Prints messages to stdout. Simple boilerplate for libraries."'
+        new_description='description = "Generated from aind-library-template"'
+        readme_description='Template for a minimal, basic repository for an AIND library.'
+        new_readme_description='Generated from aind-library-template'
+        echo "Package Name ${pkg_name}"
+        mkdir src/${pkg_name}
+        touch src/${pkg_name}/__init__.py
+        echo '"""Init package"""' >> src/${pkg_name}/__init__.py
+        echo '__version__ = "0.0.0"' >> src/${pkg_name}/__init__.py
+        sed -i "s/aind_library_template/${pkg_name}/" pyproject.toml
+        sed -i "s/aind-library-template/${REPO_NAME}/" pyproject.toml
+        sed -i "s/aind_library_template/${pkg_name}/" docs/source/conf.py
+        sed -i "s/${current_description}/${new_description}/" pyproject.toml
+        sed -i "/pandas/d" pyproject.toml
+        sed -i "s/aind-library-template/${REPO_NAME}/" README.md
+        sed -i "s/${readme_description}/${new_readme_description}/" README.md
+    - name: Commit changes
+      uses: EndBug/add-and-commit@v9
+      with:
+        default_author: github_actions
+        message: "ci: version bump [skip actions]"
+        add: '["pyproject.toml", "README.md", "src/*", "docs/source/conf.py"]'
+        remove: '["-r src/aind_library_template", "tests/test_message_handler.py"]'
+    - name: Add first tag
+      run: |
+        git tag v0.0.0
+        git push origin v0.0.0
+    - name: Disable workflow
+      run: |
+        gh workflow disable -R $GITHUB_REPOSITORY "${{ github.workflow }}"

lcne_patchseq_analysis-0.0.1/.github/workflows/tag_and_publish.yml

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+name: Tag and publish
+on:
+  push:
+    branches:
+      - main
+# Remove line 65 to enable automated semantic version bumps.
+# Change line 71 from "if: false" to "if: true" to enable PyPI publishing. 
+# Requires that svc-aindscicomp be added as an admin to repo.
+jobs:
+  update_badges:
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        ref: ${{ env.DEFAULT_BRANCH }}
+        fetch-depth: 0
+        token: ${{ secrets.SERVICE_TOKEN }}
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: | 
+        python -m pip install -e .[dev] --no-cache-dir
+    - name: Get Python version and Update README.md
+      run: |
+        python_version=$(grep "requires-python" pyproject.toml | grep -o ">=[^\"]*")
+        python_badge=$(grep -o 'python-[^)]*' README.md)
+        new_python_badge="python-$python_version-blue?logo=python"
+        sed -i "s/$python_badge/$new_python_badge/g" README.md
+    - name: Get interrogate values and Update README.md
+      run: |
+        interrogate_val=$(interrogate . | grep -o 'actual: [0-9]*\.[0-9]*' | awk '{print $2}')
+        interrogate_badge=$(grep -o 'interrogate-[^)]*' README.md)
+        if (( $(echo "$interrogate_val >= 90.00" | bc -l) )); then
+            new_interrogate_badge="interrogate-$interrogate_val%25-brightgreen"
+        elif (( $(echo "$interrogate_val < 80.00" | bc -l) )); then
+            new_interrogate_badge="interrogate-$interrogate_val%25-red"
+        else
+            new_interrogate_badge="interrogate-$interrogate_val%25-yellow"
+        fi
+        sed -i "s/$interrogate_badge/$new_interrogate_badge/g" README.md
+    - name: Get Coverage values and Update README.md
+      run: |
+        coverage run -m unittest discover
+        coverage_val=$(coverage report | grep "^TOTAL" | grep -o '[0-9]\+%' | grep -o '[0-9]\+')
+        coverage_badge=$(grep -o "coverage-[^?]*" README.md)
+        if (( $(echo "$coverage_val >= 90.00" | bc -l) )); then 
+            new_coverage_badge="coverage-$coverage_val%25-brightgreen"
+        elif (( $(echo "$coverage_val < 80.00" | bc -l) )); then
+            new_coverage_badge="coverage-$coverage_val%25-red"
+        else
+            new_coverage_badge="coverage-$coverage_val%25-yellow"
+        fi
+        sed -i "s/$coverage_badge/$new_coverage_badge/g" README.md
+    - name: Commit changes
+      uses: EndBug/add-and-commit@v9
+      with:
+        default_author: github_actions
+        message: "ci: update badges [skip actions]"
+        add: '["README.md"]'
+  tag:
+    needs: update_badges
+    uses: AllenNeuralDynamics/aind-github-actions/.github/workflows/tag.yml@main
+    secrets:
+      SERVICE_TOKEN: ${{ secrets.SERVICE_TOKEN }}
+  publish:
+    needs: tag
+    if: true
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Pull latest changes
+        run: git pull origin main
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - name: Install dependencies
+        run: |
+          pip install --upgrade setuptools wheel twine build
+          python -m build
+          twine check dist/*
+      - name: Publish on PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.AIND_PYPI_TOKEN }}

lcne_patchseq_analysis-0.0.1/.github/workflows/test_and_lint.yml

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+name: Lint and run tests
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  ci:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.10', '3.11', '3.12' ]
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: | 
+        python -m pip install -e .[dev]
+    - name: Run linter checks
+      run: flake8 . && interrogate --verbose .
+    - name: Run tests and coverage
+      run: coverage run -m unittest discover && coverage report

lcne_patchseq_analysis-0.0.1/.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

lcne_patchseq_analysis-0.0.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 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.

lcne_patchseq_analysis-0.0.1/PKG-INFO

@@ -0,0 +1,163 @@
+Metadata-Version: 2.2
+Name: LCNE-patchseq-analysis
+Version: 0.0.1
+Summary: Generated from aind-library-template
+Author: Allen Institute for Neural Dynamics
+Author-email: Han Hou <han.hou@alleninstitute.org>
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pandas
+Provides-Extra: dev
+Requires-Dist: black; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: interrogate; extra == "dev"
+Requires-Dist: isort; extra == "dev"
+Requires-Dist: Sphinx; extra == "dev"
+Requires-Dist: furo; extra == "dev"
+
+# LCNE-patchseq-analysis
+
+[![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
+![Code Style](https://img.shields.io/badge/code%20style-black-black)
+[![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
+![Interrogate](https://img.shields.io/badge/interrogate-100.0%25-brightgreen)
+![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen?logo=codecov)
+![Python](https://img.shields.io/badge/python->=3.9-blue?logo=python)
+
+
+
+## Usage
+ - To use this template, click the green `Use this template` button and `Create new repository`.
+ - After github initially creates the new repository, please wait an extra minute for the initialization scripts to finish organizing the repo.
+ - To enable the automatic semantic version increments: in the repository go to `Settings` and `Collaborators and teams`. Click the green `Add people` button. Add `svc-aindscicomp` as an admin. Modify the file in `.github/workflows/tag_and_publish.yml` and remove the if statement in line 65. The semantic version will now be incremented every time a code is committed into the main branch.
+ - To publish to PyPI, enable semantic versioning and uncomment the publish block in `.github/workflows/tag_and_publish.yml`. The code will now be published to PyPI every time the code is committed into the main branch.
+ - The `.github/workflows/test_and_lint.yml` file will run automated tests and style checks every time a Pull Request is opened. If the checks are undesired, the `test_and_lint.yml` can be deleted. The strictness of the code coverage level, etc., can be modified by altering the configurations in the `pyproject.toml` file and the `.flake8` file.
+
+## Installation
+To use the software, in the root directory, run
+```bash
+pip install -e .
+```
+
+To develop the code, run
+```bash
+pip install -e .[dev]
+```
+
+## Contributing
+
+### Linters and testing
+
+There are several libraries used to run linters, check documentation, and run tests.
+
+- Please test your changes using the **coverage** library, which will run the tests and log a coverage report:
+
+```bash
+coverage run -m unittest discover && coverage report
+```
+
+- Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:
+
+```bash
+interrogate .
+```
+
+- Use **flake8** to check that code is up to standards (no unused imports, etc.):
+```bash
+flake8 .
+```
+
+- Use **black** to automatically format the code into PEP standards:
+```bash
+black .
+```
+
+- Use **isort** to automatically sort import statements:
+```bash
+isort .
+```
+
+### Pull requests
+
+For internal members, please create a branch. For external members, please fork the repository and open a pull request from the fork. We'll primarily use [Angular](https://github.com/angular/angular/blob/main/CONTRIBUTING.md#commit) style for commit messages. Roughly, they should follow the pattern:
+```text
+<type>(<scope>): <short summary>
+```
+
+where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:
+
+- **build**: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)
+- **ci**: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)
+- **docs**: Documentation only changes
+- **feat**: A new feature
+- **fix**: A bugfix
+- **perf**: A code change that improves performance
+- **refactor**: A code change that neither fixes a bug nor adds a feature
+- **test**: Adding missing tests or correcting existing tests
+
+### Semantic Release
+
+The table below, from [semantic release](https://github.com/semantic-release/semantic-release), shows which commit message gets you which release type when `semantic-release` runs (using the default configuration):
+
+| Commit message                                                                                                                                                                                   | Release type                                                                                                    |
+| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------- |
+| `fix(pencil): stop graphite breaking when too much pressure applied`                                                                                                                             | ~~Patch~~ Fix Release, Default release                                                                          |
+| `feat(pencil): add 'graphiteWidth' option`                                                                                                                                                       | ~~Minor~~ Feature Release                                                                                       |
+| `perf(pencil): remove graphiteWidth option`<br><br>`BREAKING CHANGE: The graphiteWidth option has been removed.`<br>`The default graphite width of 10mm is always used for performance reasons.` | ~~Major~~ Breaking Release <br /> (Note that the `BREAKING CHANGE: ` token must be in the footer of the commit) |
+
+### Documentation
+To generate the rst files source files for documentation, run
+```bash
+sphinx-apidoc -o docs/source/ src
+```
+Then to create the documentation HTML files, run
+```bash
+sphinx-build -b html docs/source/ docs/build/html
+```
+More info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html).
+
+### Read the Docs Deployment
+Note: Private repositories require **Read the Docs for Business** account. The following instructions are for a public repo.
+
+The following are required to import and build documentations on *Read the Docs*:
+- A *Read the Docs* user account connected to Github. See [here](https://docs.readthedocs.com/platform/stable/guides/connecting-git-account.html) for more details.
+- *Read the Docs* needs elevated permissions to perform certain operations that ensure that the workflow is as smooth as possible, like installing webhooks. If you are not the owner of the repo, you may have to request elevated permissions from the owner/admin. 
+- A **.readthedocs.yaml** file in the root directory of the repo. Here is a basic template:
+```yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.13"
+
+# Path to a Sphinx configuration file.
+sphinx:
+  configuration: docs/source/conf.py
+
+# Declare the Python requirements required to build your documentation
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - dev
+```
+
+Here are the steps for building docs in *Read the Docs*. See [here](https://docs.readthedocs.com/platform/stable/intro/add-project.html) for detailed instructions:
+- From *Read the Docs* dashboard, click on **Add project**.
+- For automatic configuration, select **Configure automatically** and type the name of the repo. A repo with public visibility should appear as you type. 
+- Follow the subsequent steps.
+- For manual configuration, select **Configure manually** and follow the subsequent steps
+
+Once a project is created successfully, you will be able to configure/modify the project's settings; such as **Default version**, **Default branch** etc.