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[release/v1] Updating from main in preparation for PR to main. (ESCOMP#127)
This PR merges the latest commits from main, reconciling with recent rules/standards changes in this branch. After this is merged we can start the process of making this major merge back to main.
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‎.github/PULL_REQUEST_TEMPLATE‎

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<!-- Please read all instructions, then fill out the following template.-->
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<!-- If this PR includes changes to standard names, you must update the Markdown and YAML files
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to be consistent with your changes to standard_names.xml.
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This can be done by running the following commands:
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tools/write_standard_name_table.py --output-format md standard_names.xml
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This script requires the pyyaml Python package; to install with pip use command:
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python -m pip install PyYaml
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For conda users, environment file tools/environment.yml is provided.
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Note that the above procedure assumes your changes were made to standard_names.xml If you instead
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made your changes to one of the human-readable files (Metadata-standard-names.md or
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Metadata-standard-names.yaml), YOU MUST UPDATE THE FILE standard_names.xml MANUALLY, otherwise your
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changes may be lost.
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-->
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<!-- Include a short, descriptive title in the field above. If this PR is for a branch other than
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`main`, include the destination branch name in brackets at the beginning, e.g.:
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[release/v1] Bugfix for release/v1 branch
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Tag this pull request with appropriate labels. If you do not have permission to add labels, list
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the labels you’d like to include in your PR description
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If this PR is not ready to be reviewed or merged, open as a draft, and include "DRAFT:" as a prefix
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to the title above.
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Developers listed in the CODEOWNERS file will automatically be assigned to review your Pull Request.
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If your contribution should be reviewed by anyone else, assign those reviewers manually from the
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menu at right, or by tagging them with @USERNAME in the Description text.
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Changes to standard names and/or descriptions should be made in the standard_names.xml file. The
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files Metadata-standard-names.md and Metadata-standard-names.yaml will need to be updated before
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a pull request is merged; this can be done manually by the PR author using the script
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tools/write_standard_name_table.py or will be done by the Code Manager prior to merging via Github
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Actions.
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Be sure to check in on the PR regularly to respond to comments/questions/reviews!
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-->
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## Description
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<!-- One or more paragraphs describing the proposed changes and the reasoning behind them. -->
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## Issues
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<!-- Link any associated GitHub issues in this or other repositories here. -->
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‎.github/workflows/pull_request_ci.yml‎

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name: Pull request checks
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on:
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pull_request:
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workflow_dispatch:
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pull_request:
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branches:
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- main
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- release/*
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jobs:
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check-unique-standard-names:
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name: Check for duplicates in standard names
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Checkout repository
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uses: actions/checkout@v4
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- uses: actions/setup-python@v4
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- name: Setup Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.x"
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- name: Install xmllint
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- name: Install dependencies
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run: |
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sudo apt-get update
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sudo apt-get -y install libxml2-utils
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sudo apt-get update
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sudo apt-get -y install libxml2-utils
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- name: Check for duplicate standard names, descriptions
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run: |
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- name: Checkout repository
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uses: actions/checkout@v4
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- uses: actions/setup-python@v4
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- name: Setup Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.x"
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# Install dependencies
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- name: Install dependencies
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run: |
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sudo apt-get update
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sudo apt-get -y install libxml2-utils
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- name: Checks standard names against character rules
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run: |
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python3 tools/check_name_rules.py -s standard_names.xml
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check-rerendered-markdown:
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test-rendering:
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name: Test rendering xml file to markdown and yaml
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Checkout repository
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uses: actions/checkout@v4
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- uses: actions/setup-python@v4
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- name: Setup Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.x"
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- name: Install xmllint
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- name: Install dependencies
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run: |
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sudo apt-get update
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sudo apt-get -y install libxml2-utils
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sudo apt-get update
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sudo apt-get -y install libxml2-utils
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python -m pip install --upgrade pip
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python -m pip install PyYaml
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- name: Check markdown has been rerendered
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- name: Test rendering xml file to markdown
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run: |
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# Checks if the saved markdown matches freshly rendered markdown.
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# If this fails you have likely forgotten to rerun the write script
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# after adding a new name, or updating its description.
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checksum=$(sha256sum Metadata-standard-names.md)
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tools/write_standard_name_table.py standard_names.xml
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test "$checksum" = "$(sha256sum Metadata-standard-names.md)"
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# Checks if the saved markdown matches freshly rendered markdown.
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# If this fails, prompt user to update
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tools/write_standard_name_table.py --output-format md standard_names.xml
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if ! git diff --exit-code --quiet; then
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echo "❌ Detected that Metadata-standard-names.md is not consistent with standard_names.xml"
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echo "✅ To fix: Run the following command locally and commit the result:"
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echo " tools/write_standard_name_table.py --output-format md standard_names.xml"
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echo "📘 This script requires the pyyaml Python package; to install with pip use command:"
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echo " python -m pip install PyYaml"
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echo "📘 For conda users, environment file tools/environment.yml is provided."
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echo
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exit 1
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fi
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- name: Test rendering xml file to yaml
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run: |
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tools/write_standard_name_table.py --output-format yaml standard_names.xml
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if ! git diff --exit-code --quiet; then
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echo "❌ Detected that Metadata-standard-names.yaml is not consistent with standard_names.xml"
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echo "✅ To fix: Run the following command locally and commit the result:"
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echo " tools/write_standard_name_table.py --output-format yaml standard_names.xml"
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echo "📘 This script requires the pyyaml Python package; to install with pip use command:"
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echo " python -m pip install PyYaml"
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echo "📘 For conda users, environment file tools/environment.yml is provided."
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echo
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exit 1
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fi
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‎CODEOWNERS‎

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# These owners will be the default owners for everything in the repo.
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* @cacraigucar @climbfuji @dustinswales @gold2718 @grantfirl @mattldawson @mkavulich @mwaxmonsky @nusbaume @peverwhee @svahl991 @MayeulDestouches @ss421
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* @cacraigucar @climbfuji @dustinswales @gold2718 @grantfirl @mattldawson @mkavulich @mwaxmonsky @nusbaume @peverwhee @MarekWlasak @svahl991 @ss421
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# Order is important. The last matching pattern has the most precedence.
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# So if a pull request only touches javascript files, only these owners

‎Metadata-standard-names.md‎

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* [diagnostics](#diagnostics)
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* [atmospheric_composition](#atmospheric_composition)
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* [atmospheric_composition: GOCART aerosols](#atmospheric_composition-gocart-aerosols)
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* [atmospheric_composition: GLOMAP/UKCA aerosols](#atmospheric_composition-glomapukca-aerosols)
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* [emissions](#emissions)
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* [Application-specific variables](#application-specific-variables)
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* [system variables](#system-variables)
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* `integer`: units = index
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* `vertical_index_at_top_interface`: Vertical index at top interface
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* `integer`: units = index
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* `number_of_openmp_threads`: Total number of OpenMP (shared-memory) parallel threads.
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* `number_of_openmp_threads`: Total number of thread blocks OpenMP (shared-memory) parallel threads.
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* `integer`: units = count
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## constants
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Constant parameters that should be identical across a full modeling system
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* `real`: units = m-1
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* `volume_extinction_in_air_due_to_aerosol_particles_lambda3`: Aerosol extinction at wavelength3
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* `real`: units = m-1
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## atmospheric_composition: GLOMAP/UKCA aerosols
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* `mass_fraction_of_dust_coarse_aerosol_particles_in_air`: Mass fraction of dust coarse aerosol particles in air
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* `real(kind=kind_phys)`: units = kg kg-1
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* `mass_fraction_of_dust_accumulation_aerosol_particles_in_air`: Mass fraction of dust accumulation aerosol particles in air
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* `real(kind=kind_phys)`: units = kg kg-1
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* `number_fraction_of_coarse_aerosol_particles_in_air`: Number fraction of coarse aerosol particles in air
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* `real(kind=kind_phys)`: units = 1
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* `number_fraction_of_accumulation_aerosol_particles_in_air`: Number fraction of accumulation aerosol particles in air
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* `real(kind=kind_phys)`: units = 1
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## emissions
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Emissions variables, contributed for the Community Emissions Data System (CEDS)
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* `emissions_of_co_due_to_anthropogenic_sources`: Carbon monoxide emissions from anthropogenic sources, total

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