vivarium-testing-utils 0.1.1__tar.gz

vivarium_testing_utils-0.1.1/.gitattributes

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+* text=auto

vivarium_testing_utils-0.1.1/.github/CODEOWNERS

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+# default owners
+* @albrja @collijk @hussain-jafari @patricktnast @rmudambi @stevebachmeier

vivarium_testing_utils-0.1.1/.github/pull_request_template.md

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+## Title: Summary, imperative, start upper case, don't end with a period
+<!-- Ideally, <=50 chars. 50 chars is here..: -->
+
+### Description
+<!-- For use in commit message, wrap at 72 chars. 72 chars is here: -->
+- *Category*: <!-- one of bugfix, feature, refactor, POC, CI/infrastructure, documentation, 
+                   revert, test, release, other/misc -->
+- *JIRA issue*: https://jira.ihme.washington.edu/browse/MIC-XYZ
+
+### Changes and notes
+<!-- 
+Change description – why, what, anything unexplained by the above.
+Include guidance to reviewers if changes are complex.
+--> 
+
+### Testing
+<!--
+Details on how code was verified, any unit tests local for the
+repo, regression testing, etc. At a minimum, this should include an
+integration test for a framework change. Consider: plots, images,
+(small) csv file.
+-->
+

vivarium_testing_utils-0.1.1/.github/workflows/build.yml

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+# -----------------------------------------------------------------------------
+#   - invoked on push, pull_request, manual trigger, or schedule
+#   - test under at least 3 versions of python
+# -----------------------------------------------------------------------------
+name: build
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 8 * * *"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Print environment values
+        run: |
+          python --version
+          cat $GITHUB_ENV
+      - name: Update pip
+        run: |
+          python -m pip install --upgrade pip
+      - name: Install dependencies
+        run: |
+          pip install .[dev]
+      - name: Lint
+        run: |
+          pip install black==22.3.0 isort
+          black . --check --diff
+          isort . --check --verbose --only-modified --diff
+      - name: Test
+        run: |
+         if "${{ github.event_name == 'schedule' }}"; then
+           pytest --runslow ./tests
+         else
+           pytest ./tests
+         fi
+      # - name: Doc build
+      #   run: |
+      #     make html -C docs/ SPHINXOPTS="-W --keep-going -n"
+      # - name: Doctest
+      #   run: |
+      #     make doctest -C docs/
+      - name: Send mail
+        # Notify when cron job fails
+        if: (github.event_name == 'schedule' && failure())
+        uses: dawidd6/action-send-mail@v2
+        with:
+          # mail server settings
+          server_address: smtp.gmail.com
+          server_port: 465
+          # user credentials
+          username: ${{ secrets.NOTIFY_EMAIL }}
+          password: ${{ secrets.NOTIFY_PASSWORD }}
+          # email subject
+          subject: ${{ github.job }} job of ${{ github.repository }} has ${{ job.status }}
+          # email body as text
+          body: ${{ github.job }} job in worflow ${{ github.workflow }} of ${{ github.repository }} has ${{ job.status }}
+          # comma-separated string, send email to
+          to: uw_ihme_simulationscience@uw.edu
+          # from email name
+          from: Vivarium Notifications

vivarium_testing_utils-0.1.1/.github/workflows/deploy.yml

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+name: deploy
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+      - name: Install dependencies
+        run: |
+          python --version
+          python -m pip install --upgrade pip
+          pip install setuptools wheel build
+      # - name: Test
+      #   run: |
+      #     pip install .[test]
+      #     pytest --runslow ./tests
+      - name: Build
+        run: python -m build
+      - name: Publish
+        uses: pypa/gh-action-pypi-publish@release/v1
+      - name: Send mail
+        # Notify when cron job fails
+        if: failure()
+        uses: dawidd6/action-send-mail@v2
+        with:
+          # mail server settings
+          server_address: smtp.gmail.com
+          server_port: 465
+          # user credentials
+          username: ${{ secrets.NOTIFY_EMAIL }}
+          password: ${{ secrets.NOTIFY_PASSWORD }}
+          # email subject
+          subject: ${{ github.job }} job of ${{ github.repository }} has ${{ job.status }}
+          # email body as text
+          body: ${{ github.job }} job in worflow ${{ github.workflow }} of ${{ github.repository }} has ${{ job.status }}
+          # comma-separated string, send email to
+          to: uw_ihme_simulationscience@uw.edu
+          # from email name
+          from: Vivarium Notifications
+      

vivarium_testing_utils-0.1.1/.github/workflows/pr_metrics.yml

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+name: Post-Sprint PR metrics
+on:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: issue metrics
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: read
+
+    steps:
+      - name: Set REPO_LIST environment variable
+        run: |
+          echo "REPO_LIST=repo:ihmeuw/vivarium repo:ihmeuw/vivarium_public_health repo:ihmeuw/vivarium_inputs repo:ihmeuw/vivarium_cluster_tools repo:ihmeuw/risk_distributions" >> $GITHUB_ENV
+      - name: Get dates for previous sprint
+        shell: bash
+        run: |
+          # Calculate the date two weeks ago
+          fourteen_days_ago=$(date -d "14 days ago" +%Y-%m-%d)
+          
+          # Calculate yesterday's date
+          yesterday=$(date -d "today" +%Y-%m-%d)
+          
+          # Set an environment variable with the date range
+          echo "$fourteen_days_ago..$yesterday"
+          echo "last_two_weeks=$fourteen_days_ago..$yesterday" >> "$GITHUB_ENV"
+
+      - name: Get issue metrics for PRs closed in last sprint
+        uses: github/issue-metrics@v3
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SEARCH_QUERY: $${{ env.REPO_LIST }} is:pr closed:${{ env.last_two_weeks }}
+
+      - name: Create issue for PRs closed in last sprint
+        uses: peter-evans/create-issue-from-file@v4
+        with:
+          title: Post-Sprint Closed Pull Request Metrics Report (dev)
+          token: ${{ secrets.GITHUB_TOKEN }}
+          content-filepath: ./issue_metrics.md
+          assignees: patricktnast
+          
+      - name: Get issue metrics for currently open PRs
+        uses: github/issue-metrics@v3
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SEARCH_QUERY: '$${{ env.REPO_LIST }} is:pr is:open'
+
+      - name: Create issue for currently open PRs
+        uses: peter-evans/create-issue-from-file@v4
+        with:
+          title: Post-Sprint Open Pull Request Metrics Report (dev)
+          token: ${{ secrets.GITHUB_TOKEN }}
+          content-filepath: ./issue_metrics.md
+          assignees: patricktnast

vivarium_testing_utils-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/
+*.egg-info/
+.installed.cfg
+*.egg
+*.pyc
+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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# 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/
+
+# Pycharm project settings
+.idea/
+
+# Visual Studio Code project settings
+.vscode/
+
+# Local user jupyter notebooks directory
+notebooks/
+
+# Version file
+src/vivarium_testing_utils/_version.py

vivarium_testing_utils-0.1.1/.readthedocs.yml

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+# This is the version for the readthedocs configuration. Version 2 ignores
+# web-based configuration and uses everything from this file.
+version: 2
+
+# Configure the python version and environment construction run before
+# docs are built.
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+python:
+  install:
+      # This runs pip install .[docs] from the project root.
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+
+# Doc builds will fail if there are any warnings
+sphinx:
+  fail_on_warning: true

vivarium_testing_utils-0.1.1/CHANGELOG.rst

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+**0.1.1 - 10/14/24**
+
+ - Make name an optional parameter to fuzzy_assert_proportion
+
+**0.1.0 - 03/01/24**
+
+ - Repository creation

vivarium_testing_utils-0.1.1/CODE_OF_CONDUCT.rst

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+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 current maintainer (found in this repositories AUTHORS.md). 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`_, version 1.4,
+available at `version`_.
+
+.. _Contributor Covenant: http://contributor-covenant.org
+.. _version: http://contributor-covenant.org/version/1/4/

vivarium_testing_utils-0.1.1/CONTRIBUTING.rst

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+Contributing
+============
+
+When contributing to this repository, please first discuss the change you wish to make via issue,
+email, or any other method with the owners of this repository before making a change.
+
+Please note we have a code of conduct, please follow it in all your interactions with the project.
+
+Submitting Changes
+------------------
+
+- Always make a new branch for your work.
+- Patches should be small to facilitate easier review. Sometimes this will result in many small
+  PRs to land a single large feature.
+- Larger changes should be discussed in the project's GitHub issues page.
+- New features and significant bug fixes should be documented in the changelog.
+- You must have legal permission to distribute any code you contribute to ``vivarium_testing_utils``, and it
+  must be available under both the GNU GPLv3 license.
+

vivarium_testing_utils-0.1.1/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2024, Institute for Health Metrics and Evaluation
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

vivarium_testing_utils-0.1.1/MANIFEST.in

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+include AUTHORS.rst
+include CHANGELOG.rst
+include CODE_OF_CONDUCT.rst
+include CONTRIBUTING.rst
+include LICENSE.txt
+include README.rst
+
+recursive-include docs *
+prune docs/_build
+
+recursive-include src/vivarium_testing_utils *.py *.yaml
+recursive-include tests *.py *txt *.yaml

vivarium_testing_utils-0.1.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: vivarium_testing_utils
+Version: 0.1.1
+Summary: Project to store testing utilities for Vivarium software.
+Home-page: https://github.com/ihmeuw/vivarium_testing_utils
+Author: The vivarium developers
+Author-email: vivarium.dev@gmail.com
+License: BSD-3-Clause
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+Classifier: Natural Language :: English
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: POSIX :: BSD
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Topic :: Education
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Artificial Life
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Software Development :: Libraries
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: pyyaml>=5.1
+Requires-Dist: scipy
+Requires-Dist: click
+Requires-Dist: tables
+Requires-Dist: networkx
+Requires-Dist: loguru
+Provides-Extra: docs
+Requires-Dist: sphinx>=4.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: sphinx-click; extra == "docs"
+Requires-Dist: IPython; extra == "docs"
+Requires-Dist: matplotlib; extra == "docs"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-mock; extra == "test"
+Provides-Extra: interactive
+Requires-Dist: IPython; extra == "interactive"
+Requires-Dist: ipywidgets; extra == "interactive"
+Requires-Dist: jupyter; extra == "interactive"
+Provides-Extra: dev
+Requires-Dist: sphinx>=4.0; extra == "dev"
+Requires-Dist: sphinx-rtd-theme; extra == "dev"
+Requires-Dist: sphinx-click; extra == "dev"
+Requires-Dist: IPython; extra == "dev"
+Requires-Dist: matplotlib; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-mock; extra == "dev"
+Requires-Dist: IPython; extra == "dev"
+Requires-Dist: ipywidgets; extra == "dev"
+Requires-Dist: jupyter; extra == "dev"
+
+======================
+Vivarium Testing Utils
+======================
+
+This is a repository that will store utility features to help test
+Vivarium software.
+
+**Vivarium Testing Utils requires Python 3.8-3.11 to run**
+
+You can install ``vivarium_testing_utils`` from PyPI with pip:
+
+  ``> pip install vivarium_testing_utils``
+
+or build it from source with
+
+  ``> git clone https://github.com/ihmeuw/vivarium_testing_utils.git``
+
+  ``> cd vivarium_testing_utils``
+
+  ``> conda create -n ENVIRONMENT_NAME python=3.11``
+
+  ``> pip install -e .[dev]``

vivarium_testing_utils-0.1.1/README.rst

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+======================
+Vivarium Testing Utils
+======================
+
+This is a repository that will store utility features to help test
+Vivarium software.
+
+**Vivarium Testing Utils requires Python 3.8-3.11 to run**
+
+You can install ``vivarium_testing_utils`` from PyPI with pip:
+
+  ``> pip install vivarium_testing_utils``
+
+or build it from source with
+
+  ``> git clone https://github.com/ihmeuw/vivarium_testing_utils.git``
+
+  ``> cd vivarium_testing_utils``
+
+  ``> conda create -n ENVIRONMENT_NAME python=3.11``
+
+  ``> pip install -e .[dev]``

vivarium_testing_utils-0.1.1/docs/Makefile

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+# Minimal makefile for Sphinx documentation
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = vivarium_testing_utils
+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)
+
+clean:
+	rm -rf build/*

vivarium_testing_utils-0.1.1/docs/nitpick-exceptions

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+# pandas
+py:class pandas.core.indexes.base.Index
+py:class pandas.core.indexes.multi.MultiIndex
+py:class pandas._libs.tslibs.timestamps.Timestamp
+py:class pandas._libs.tslibs.timedeltas.Timedelta
+py:class pandas.core.frame.DataFrame
+py:class pandas.core.series.Series
+py:class pandas.core.generic.PandasObject
+
+#scipy
+py:class scipy.stats._distn_infrastructure.rv_continuous
+
+# loguru
+py:class loguru._logger.Logger
+
+# vivarium
+# Type aliases don't play nicely with sphinx when you import them
+# elsewhere.  Works fine for static type checker though.  I think this
+# is cause sphinx does runtime checks.
+py:class Time
+py:class vivarium.framework.time.Time
+py:class Timedelta
+py:class vivarium.framework.time.Timedelta
+
+# TODO: Need to revisit this. Nitpicking here to avoid failing builds on 3.8 and 3.9 in state_machine and testing_utils
+py:class Logger