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Kevin Paul
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Merge pull request #108 from NCAR/devel
Merge for release v0.3.0
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‎.github/workflows/linting.yml

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name: Linting
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on:
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push:
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branches:
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- '*'
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pull_request:
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branches:
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- '*'
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jobs:
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linting:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: actions/setup-python@v2
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- uses: pre-commit/[email protected]

‎.github/workflows/pypipublish.yml

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name: Upload Python Package to PyPI
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on:
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release:
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types: [created]
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jobs:
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deploy:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v2
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install setuptools setuptools-scm wheel twine
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- name: Build and publish
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env:
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TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
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TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
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run: |
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python setup.py sdist bdist_wheel
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twine upload dist/*

‎.github/workflows/tests.yml

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name: Tests
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on:
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push:
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branches:
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- '*'
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pull_request:
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branches:
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- '*'
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workflow_dispatch: # allows you to trigger manually
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jobs:
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build:
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name: python-${{ matrix.python }}
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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strategy:
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fail-fast: false
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matrix:
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python: ['3.6', '3.7', '3.8']
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env:
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PYTHON: ${{ matrix.python }}
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OMPI_MCA_rmaps_base_oversubscribe: '1'
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OMPI_ALLOW_RUN_AS_ROOT: '1'
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OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: '1'
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steps:
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- uses: actions/checkout@v2
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- name: Cache conda
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uses: actions/cache@v2
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env:
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# Increase this value to reset cache if ci/environment.yml has not changed
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CACHE_NUMBER: 0
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with:
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path: ~/conda_pkgs_dir
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key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('ci/environment.yml') }}
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- name: Setup miniconda
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uses: goanpeca/setup-miniconda@v1
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with:
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activate-environment: pyconform # Defined in ci/environment.yml
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auto-update-conda: false
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python-version: ${{ matrix.python }}
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environment-file: ci/environment.yml
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use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
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- name: Install package
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run: python -m pip install --no-deps .
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- name: Check Installation
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run: |
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conda list
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pip list
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- name: Run Tests
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run: ci/runtests.sh
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- name: Upload code coverage to Codecov
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uses: codecov/codecov-action@v1
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with:
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file: ./coverage.xml
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flags: unittests
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env_vars: PYTHON,MPI
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name: codecov-umbrella
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fail_ci_if_error: false

‎.gitignore

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*.spec
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*.pyc
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*.nc
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.cache
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.pytest_cache
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.DS_Store
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temp
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build
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dist
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PyConform.egg-info
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.idea/
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.vscode/
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__pycache__
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.coverage*
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coverage.xml

‎.pre-commit-config.yaml

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exclude: '(docs\/|examples\/)'
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v3.2.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-docstring-first
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- id: check-json
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- id: check-yaml
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- repo: https://github.com/ambv/black
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rev: 20.8b1
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hooks:
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- id: black
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- repo: https://github.com/keewis/blackdoc
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rev: v0.1.2
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hooks:
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- id: blackdoc
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- repo: https://gitlab.com/pycqa/flake8
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rev: 3.8.3
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hooks:
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- id: flake8
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- repo: https://github.com/asottile/seed-isort-config
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rev: v2.2.0
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hooks:
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- id: seed-isort-config
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args: [--exclude=docs/*|examples/*]
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- repo: https://github.com/pre-commit/mirrors-isort
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rev: v5.5.3
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hooks:
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- id: isort

‎CHANGES.rst renamed to ‎CHANGELOG.rst

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PyConform ChangeLog
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===================
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Copyright 2017-2018, University Corporation for Atmospheric Research
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Copyright 2017-2020, University Corporation for Atmospheric Research
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See the LICENSE.rst file for details
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VERSION 0.0.1
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VERSION 0.2.2
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-------------
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- New user-defined function API
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VERSION 0.3.0
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-------------
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- Code ported to Python 3.6+ (No longer supports Python 2.7)
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- Update to testing suite (using PyTest) and adding GitHub Actions
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- General modernization of the package repository

‎CODE_OF_CONDUCT.md

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@@ -14,7 +14,7 @@ Examples of behaviors that contribute to a positive environment include:
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* Communicate openly with respect for others, critiquing ideas rather than individuals and gracefully accepting criticism
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* Acknowledging the contributions of others
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* Avoid personal attacks directed toward other participants
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* Be mindful of your surroundings and of your fellow participants
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* Be mindful of your surroundings and of your fellow participants
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* Alert UCAR staff and suppliers/vendors if you notice a dangerous situation or someone in distress
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* Respect the rules and policies of the project and venue
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* Personal attacks directed at other guests, members, participants, etc.
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* Publishing others' private information, such as a physical or electronic address, without explicit permission
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* Alarming, intimidating, threatening, or hostile comments or conduct
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* Inappropriate use of nudity and/or sexual images
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* Inappropriate use of nudity and/or sexual images
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* Threatening or stalking anyone, including a participant
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* Other conduct which could reasonably be considered inappropriate in a professional setting
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## Reporting
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Instances of unacceptable behavior can be brought to the attention of the project administrator(s) who may take any action as outlined in the [Consequences](#consequences) section below.
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However, making a report to a project administrator is not considered an 'official report' to UCAR.
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However, making a report to a project administrator is not considered an 'official report' to UCAR.
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Instances of unacceptable behavior may also be reported directly to UCAR pursuant to [UCAR's Harassment Reporting and Complaint Procedure](https://www2.fin.ucar.edu/procedures/hr/harassment-reporting-and-complaint-procedure), or anonymously through [UCAR's EthicsPoint Hotline](https://www2.fin.ucar.edu/ethics/anonymous-reporting).
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‎LICENSE.rst

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Contributor License Agreement
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-----------------------------
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This Contributor License Agreement ("Agreement") is a legal agreement between you (in your capacity as an individual and
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as an agent for your company, institution or other entity) (collectively, "you" or "your" or "Licensee") and the University
8+
This Contributor License Agreement ("Agreement") is a legal agreement between you (in your capacity as an individual and
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as an agent for your company, institution or other entity) (collectively, "you" or "your" or "Licensee") and the University
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Corporation for Atmospheric Research ("UCAR").
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1. **License Grant to Technology.** UCAR grants to Licensee a restricted, royalty-free, perpetual, nonexclusive,
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nontransferable, noncommercial license to copy, modify, enhance, improve and use the NCAR PyConform code set for
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transformation and standardization of NetCDF datasets into the approved formats for publication (**Technology**)
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for research purposes and for collaborating with UCAR only; provided, however, that Licensee does not commercialize,
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sell, license, distribute, or transfer the Technology, or any work that contains the Technology. Licensee may freely
17-
use the data and results from the Technology. Licensee shall note in all publications of data or results that this
18-
Technology is provided by UCAR and the NCAR Computational and Information Systems Laboratory. Licensee must reproduce
19-
all copyright notices and other proprietary notices on any copies of the Technology, and Licensee shall not remove any
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1. **License Grant to Technology.** UCAR grants to Licensee a restricted, royalty-free, perpetual, nonexclusive,
13+
nontransferable, noncommercial license to copy, modify, enhance, improve and use the NCAR PyConform code set for
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transformation and standardization of NetCDF datasets into the approved formats for publication (**Technology**)
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for research purposes and for collaborating with UCAR only; provided, however, that Licensee does not commercialize,
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sell, license, distribute, or transfer the Technology, or any work that contains the Technology. Licensee may freely
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use the data and results from the Technology. Licensee shall note in all publications of data or results that this
18+
Technology is provided by UCAR and the NCAR Computational and Information Systems Laboratory. Licensee must reproduce
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all copyright notices and other proprietary notices on any copies of the Technology, and Licensee shall not remove any
2020
copyright information appearing in or on the Technology files.
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2. **Ownership of Technology.** UCAR owns and retains all title, copyright, and other proprietary interests in the
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2. **Ownership of Technology.** UCAR owns and retains all title, copyright, and other proprietary interests in the
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Technology, including any copies thereof. No ownership rights of any kind are transferred to you.
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3. **Licensee Contributions.** Licensee shall submit contributions to the Technology to UCAR through the collaboration
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tools provided by UCAR. "Contribution" shall mean any independent original work of authorship, including any enhancements,
25-
improvements, modifications, additions, bug fixes, patches, or upgrades to the Technology that is intentionally submitted
26-
by you to UCAR for inclusion in the Technology. You are the owner of your Contributions, but you acknowledge that UCAR
23+
3. **Licensee Contributions.** Licensee shall submit contributions to the Technology to UCAR through the collaboration
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tools provided by UCAR. "Contribution" shall mean any independent original work of authorship, including any enhancements,
25+
improvements, modifications, additions, bug fixes, patches, or upgrades to the Technology that is intentionally submitted
26+
by you to UCAR for inclusion in the Technology. You are the owner of your Contributions, but you acknowledge that UCAR
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retains ownership of the Technology.
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4. **License Grant to Licensee Contributions.** You hereby grant to UCAR, and to any recipients of the Technology distributed
29-
by UCAR, a perpetual, worldwide, non-exclusive, royalty-free, irrevocable license to reproduce, incorporate freely into the
30-
Technology, sublicense, display, and distribute your Contributions. You represent that you are legally entitled to grant the
28+
4. **License Grant to Licensee Contributions.** You hereby grant to UCAR, and to any recipients of the Technology distributed
29+
by UCAR, a perpetual, worldwide, non-exclusive, royalty-free, irrevocable license to reproduce, incorporate freely into the
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Technology, sublicense, display, and distribute your Contributions. You represent that you are legally entitled to grant the
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above license. If your employer(s) has rights to intellectual property that you create that includes your Contributions, you
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acknowledge that you are allowed to make Contributions on behalf of that employer.
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5. **Disclaimer of Warranty/Noninfringement.** THE TECHNOLOGY IS SUPPLIED **AS IS** WITHOUT WARRANTY OF ANY KIND. UCAR DISCLAIMS
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ALL WARRANTIES, EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION, ANY IMPLIED WARRANTIES OF NONINFRINGEMENT, ORIGINALITY,
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MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE WITH REGARD TO THE TECHNOLOGY PROVIDED HEREUNDER. UCAR MAKES NO
36-
REPRESENTATIONS THAT THE USE, OPERATION, SALE, PERFORMANCE, MODIFICATION, REPRODUCTION, DISPLAY OF THE TECHNOLOGY WILL
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ALL WARRANTIES, EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION, ANY IMPLIED WARRANTIES OF NONINFRINGEMENT, ORIGINALITY,
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MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE WITH REGARD TO THE TECHNOLOGY PROVIDED HEREUNDER. UCAR MAKES NO
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REPRESENTATIONS THAT THE USE, OPERATION, SALE, PERFORMANCE, MODIFICATION, REPRODUCTION, DISPLAY OF THE TECHNOLOGY WILL
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NOT INFRINGE UPON ANY PROPRIETARY RIGHTS OF ANY THIRD PARTY.
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6. **Limitation of Liability.** IN NO EVENT SHALL UCAR BE LIABLE TO LICENSEE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL
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OR CONSEQUENTIAL DAMAGES, INCLUDING LOST OR ANTICIPATED PROFITS OR REVENUE INCURRED BY LICENSEE OR ANY THIRD PARTY, WHETHER
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IN AN ACTION IN CONTRACT OR TORT, EVEN IF UCAR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES IN THE PERFORMANCE OF
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THIS LICENSE, OR RELATED TO THE TECHNOLOGY. LICENSEE ALSO ACKNOWLEDGES THAT ANY BREACH OF ITS OBLIGATIONS WITH RESPECT TO
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PROPRIETARY RIGHTS WILL CAUSE UCAR IRREPARABLE INJURY FOR WHICH THERE ARE INADEQUATE REMEDIES AT LAW. AS SUCH, UCAR SHALL
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6. **Limitation of Liability.** IN NO EVENT SHALL UCAR BE LIABLE TO LICENSEE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL
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OR CONSEQUENTIAL DAMAGES, INCLUDING LOST OR ANTICIPATED PROFITS OR REVENUE INCURRED BY LICENSEE OR ANY THIRD PARTY, WHETHER
40+
IN AN ACTION IN CONTRACT OR TORT, EVEN IF UCAR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES IN THE PERFORMANCE OF
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THIS LICENSE, OR RELATED TO THE TECHNOLOGY. LICENSEE ALSO ACKNOWLEDGES THAT ANY BREACH OF ITS OBLIGATIONS WITH RESPECT TO
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PROPRIETARY RIGHTS WILL CAUSE UCAR IRREPARABLE INJURY FOR WHICH THERE ARE INADEQUATE REMEDIES AT LAW. AS SUCH, UCAR SHALL
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BE ENTITLED TO EQUITABLE RELIEF IN ADDITION TO ALL OTHER REMEDIES AVAILABLE TO IT.
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7. **High Risk Activities.** The Technology is research-based, not fault-tolerant, and is not designed, manufactured or
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intended for use in any operational activities including activities or hazardous environments requiring fail-safe
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performance, such as in aircraft navigation or communication systems, air traffic control, weapons systems, nuclear
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power plants or critical 24/7 operations, in which the failure of the Technology could lead directly to death, personal
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injury, or severe physical or environmental damage (**High Risk Activities**). Accordingly, UCAR specifically disclaims
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any express or implied warranties of fitness for High Risk Activities. You agree that UCAR shall not be liable for any
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7. **High Risk Activities.** The Technology is research-based, not fault-tolerant, and is not designed, manufactured or
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intended for use in any operational activities including activities or hazardous environments requiring fail-safe
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performance, such as in aircraft navigation or communication systems, air traffic control, weapons systems, nuclear
47+
power plants or critical 24/7 operations, in which the failure of the Technology could lead directly to death, personal
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injury, or severe physical or environmental damage (**High Risk Activities**). Accordingly, UCAR specifically disclaims
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any express or implied warranties of fitness for High Risk Activities. You agree that UCAR shall not be liable for any
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claims or damages arising from High Risk Activities.
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8. **Controlling Law.** This Agreement shall be governed by the laws of the State of Colorado and of the United States.

‎MANIFEST.in

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include CHANGELOG.rst
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include CODE_OF_CONDUCT.md
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include LICENSE.rst
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include README.rst
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include requirements.txt
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recursive-include pyconform *.py
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recursive-exclude * __pycache__
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recursive-exclude * *.py[co]
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prune ci*

‎README.rst

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.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3895009.svg
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:target: https://doi.org/10.5281/zenodo.3895009
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.. image:: https://codecov.io/gh/NCAR/PyConform/branch/master/graph/badge.svg
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:target: https://codecov.io/gh/NCAR/PyConform
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.. image:: https://github.com/NCAR/PyConform/workflows/Tests/badge.svg
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:target: https://github.com/NCAR/PyConform/actions?query=workflow%3ATests
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.. image:: https://github.com/NCAR/PyConform/workflows/Linting/badge.svg
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:target: https://github.com/NCAR/PyConform/actions?query=workflow%3ALinting
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PyConform
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=========
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A package for transforming a NetCDF dataset into a defined format
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suitable for publication according to a defined publication standard.
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:AUTHORS: Sheri Mickelson, Kevin Paul
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:COPYRIGHT: 2017, University Corporation for Atmospheric Research
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:COPYRIGHT: 2020, University Corporation for Atmospheric Research
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:LICENSE: See the LICENSE.rst file for details
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Send questions and comments to Kevin Paul ([email protected]) or
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The PyConform package directly depends upon 4 main external packages:
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* ASAPTools (>=0.6)
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* netCDF4-python
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* cf-units
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* dreqpy
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* netCDF4-python
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* ply
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* python-dateutil
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These dependencies imply the dependencies:
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The documentation_ for PyConform is hosted on GitHub Pages.
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.. _documentation: https://ncar.github.io/pyconform
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Before Using the PyConform Package
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----------------------------------
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Before the PyConform package can be used, you must make sure that the
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site-packages directory containing the 'pyconform' source directory is in
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your PYTHONPATH. Depending on the PREFIX used during installation, this
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path should look like be::
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$PREFIX/lib/python2.7/site-packages
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depending on the version of Python that you
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are using to install the package.
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To use the PyConform scripts (e.g., ...), you must add the
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script binary directory to your PATH. Depending on the PREFIX used during
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installation, this path will be::
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$PREFIX/bin/
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Once the script binary directory has been added to your PATH and the
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site-packages directory has been added to your PYTHONPATH, you may use the
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PyConform package without issue.

‎ci/environment.yml

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name: pyconform
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channels:
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- conda-forge
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- defaults
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dependencies:
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- bumpversion
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- coverage
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- mpi4py
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- netcdf4
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- numpy
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- pip
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- ply
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- pynio
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- pyngl
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- pytest
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- pytest-cov
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- python-dateutil
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- pip:
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- asaptools
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- cf_units
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- dreqPy

‎ci/runtests.sh

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#!/bin/bash
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set -e
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set -eo pipefail
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coverage run -m pytest tests/
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coverage xml

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