aind-metadata-validator 0.3.1__tar.gz

aind_metadata_validator-0.3.1/.flake8

@@ -0,0 +1,7 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    build
+max-complexity = 10
+max-line-length = 120

aind_metadata_validator-0.3.1/.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.

aind_metadata_validator-0.3.1/.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_metadata_validator-0.3.1/.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.*

aind_metadata_validator-0.3.1/.github/workflows/init.yml

@@ -0,0 +1,52 @@
+# 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: ${{secrets.GITHUB_TOKEN}}
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+    - name: Rename package
+      run: |
+        pkg_name=$(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 }}"

aind_metadata_validator-0.3.1/.github/workflows/tag_and_publish.yml

@@ -0,0 +1,88 @@
+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@v3
+      with:
+        ref: ${{ env.DEFAULT_BRANCH }}
+        fetch-depth: 0
+        token: ${{ secrets.SERVICE_TOKEN }}
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: | 
+        python -m pip install -e .[dev] --no-cache-dir
+    - name: Get Python version and Update README.md
+      run: |
+        python_version=$(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@v3
+      - name: Pull latest changes
+        run: git pull origin main
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v2
+        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 }}

aind_metadata_validator-0.3.1/.github/workflows/test_and_lint.yml

@@ -0,0 +1,26 @@
+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', '3.13' ]
+    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 linter checks
+      run: flake8 . && interrogate --verbose .
+    - name: Run tests and coverage
+      run: coverage run -m unittest discover && coverage report

aind_metadata_validator-0.3.1/.gitignore

@@ -0,0 +1,140 @@
+# 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
+validation_results.csv

aind_metadata_validator-0.3.1/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.

aind_metadata_validator-0.3.1/PKG-INFO

@@ -0,0 +1,30 @@
+Metadata-Version: 2.1
+Name: aind-metadata-validator
+Version: 0.3.1
+Summary: Generated from aind-library-template
+Author: Allen Institute for Neural Dynamics
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pydantic
+Requires-Dist: aind-data-schema
+Requires-Dist: aind-data-access-api[docdb]
+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"
+
+# aind-metadata-validator
+
+`pip install aind-metadata-validator`
+
+```
+from aind_metadata_validator import [todo]
+```

aind_metadata_validator-0.3.1/README.md

@@ -0,0 +1,7 @@
+# aind-metadata-validator
+
+`pip install aind-metadata-validator`
+
+```
+from aind_metadata_validator import [todo]
+```

aind_metadata_validator-0.3.1/docs/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_metadata_validator-0.3.1/docs/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

aind_metadata_validator-0.3.1/docs/source/_static/dark-logo.svg

@@ -0,0 +1,129 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Generator: Adobe Illustrator 26.2.1, SVG Export Plug-In . SVG Version: 6.00 Build 0)  -->
+<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+	 viewBox="0 0 397.34 91.96" style="enable-background:new 0 0 397.34 91.96;" xml:space="preserve">
+<style type="text/css">
+	.st0{fill:#CFCFCE;}
+	.st1{fill:#7DC2EB;}
+	.st2{fill:#358CCB;}
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