aind-mri-utils 0.0.24__tar.gz

aind_mri_utils-0.0.24/.flake8

@@ -0,0 +1,6 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    build
+max-complexity = 10

aind_mri_utils-0.0.24/.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.

aind_mri_utils-0.0.24/.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_mri_utils-0.0.24/.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.*

aind_mri_utils-0.0.24/.github/workflows/tag_and_publish.yml

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+name: Tag and publish
+on:
+  push:
+    branches:
+      - main
+jobs:
+  tag:
+    uses: AllenNeuralDynamics/aind-github-actions/.github/workflows/tag.yml@main
+    secrets:
+      SERVICE_TOKEN: ${{ secrets.SERVICE_TOKEN }}
+  publish:
+    needs: tag
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Pull latest changes
+        run: git pull origin main
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - 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 }}

aind_mri_utils-0.0.24/.github/workflows/test_and_lint.yml

@@ -0,0 +1,26 @@
+name: CI
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  ci:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.8', '3.9', '3.10' ]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: | 
+        python -m pip install -e .[dev]
+    - name: Run linters
+      run: flake8 . && interrogate .
+    - name: Run tests and coverage
+      run: coverage run -m unittest discover && coverage report

aind_mri_utils-0.0.24/.gitignore

@@ -0,0 +1,142 @@
+# 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
+
+# VS Code
+.vscode/

aind_mri_utils-0.0.24/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 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_mri_utils-0.0.24/PKG-INFO

@@ -0,0 +1,106 @@
+Metadata-Version: 2.1
+Name: aind_mri_utils
+Version: 0.0.24
+Summary: MRI utilities library for aind teams.
+Author: Allen Institute for Neural Dynamics
+Author-email: Galen Lynch <galen@galenlynch.com>, Yoni Browning <yoni.browning@alleninstitute.org>
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: matplotlib<4,>=3
+Requires-Dist: numpy<3,>=1.7
+Requires-Dist: pywavefront<2,>=1.3
+Requires-Dist: scipy<2,>=1
+Requires-Dist: SimpleITK<3,>=2
+Requires-Dist: vtk<10,>=9
+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"
+
+# aind-mri-utils
+
+[![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)
+
+Library for aind mri utilities.
+
+## 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
+
+### Documentation
+To generate the rst files source files for documentation, run
+```bash
+sphinx-apidoc -o doc_template/source/ src
+```
+Then to create the documentation HTML files, run
+```bash
+sphinx-build -b html doc_template/source/ doc_template/build/html
+```
+More info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html).

aind_mri_utils-0.0.24/README.md

@@ -0,0 +1,80 @@
+# aind-mri-utils
+
+[![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)
+
+Library for aind mri utilities.
+
+## 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
+
+### Documentation
+To generate the rst files source files for documentation, run
+```bash
+sphinx-apidoc -o doc_template/source/ src
+```
+Then to create the documentation HTML files, run
+```bash
+sphinx-build -b html doc_template/source/ doc_template/build/html
+```
+More info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html).

aind_mri_utils-0.0.24/doc_template/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

aind_mri_utils-0.0.24/doc_template/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd