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bmaglio
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Merge branch 'master' into combined_ch4_hydro
Attempting to fix some inconsistencies observed when using projected climatewq
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‎.github/workflows/draft-joss-pdf.yml‎

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# Adapted from:
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# https://github.com/marketplace/actions/open-journals-pdf-generator
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#
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name: Draft PDF
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on:
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push:
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paths:
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- joss-paper/**
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- .github/workflows/draft-joss-pdf.yml
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jobs:
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paper:
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runs-on: ubuntu-latest
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name: Paper Draft
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Build draft PDF
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uses: openjournals/openjournals-draft-action@master
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with:
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journal: joss
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# This should be the path to the paper within your repo.
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paper-path: joss-paper/paper.md
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- name: Upload
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uses: actions/upload-artifact@v4
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with:
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name: paper
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# This is the output path where Pandoc will write the compiled
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# PDF. Note, this should be the same directory as the input
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# paper.md
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path: joss-paper/paper.pdf
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‎.gitignore‎

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# assorted temporary stuff
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bundle*
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.dvc/*

‎CITATION.cff‎

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cff-version: 1.2.0
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title: "DVMDOSTEM"
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message: "If you use this software, please cite using the metadata in this file."
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type: software
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identifiers:
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- description: "The Zenodo concept DOI of DVMDOSTEM. Use the Concept DOI representing all versions in citations when it is desirable to cite an evolving research artifact, without being specific about the version."
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type: doi
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value: 10.5281/zenodo.4281497
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- description: "The GitHub release URL."
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type: url
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value: "https://github.com/uaf-arctic-eco-modeling/dvm-dos-tem/releases/tag/v0.8.3"
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repository-code: "https://uaf-arctic-eco-modeling/dvm-dos-tem"
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url: >-
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https://uaf-arctic-eco-modeling.github.io/dvm-dos-tem/index.html#
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abstract: >-
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DVMDOSTEM is an advanced process-based terrestrial
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ecosystem model (TEM) designed to study ecosystem responses to climate changes
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and disturbances. It has a particular focus on permafrost regions (i.e. regions
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characterized by soils that stay partially frozen all year round for at
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least two consecutive years), encompassing boreal, arctic, and alpine landscapes.
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keywords:
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- C++
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- Python
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- Ecology
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- Terrestrial Ecology
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- Arctic
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- Boreal
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- Permafrost
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- Cryosphere
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- Tundra
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license: MIT
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authors:
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- family-names: "Genet" # Wildfire, calibration, scientific direction,
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given-names: "Hélène"
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orcid: "https://orcid.org/0000-0003-4537-9563"
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affiliation: "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks 99775, Alaska, USA"
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- family-names: "Euskirchen" # DVM, scientific direction
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given-names: "Eugénie"
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orcid: "https://orcid.org/0000-0002-0848-4295"
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affiliation: "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks 99775, Alaska, USA"
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- family-names: "McGuire" # TEM, scientific direction
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given-names: "A. D."
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orcid: "https://orcid.org/0000-0003-4646-0750"
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affiliation: "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks 99775, Alaska, USA"
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- family-names: "Carman" # Software development and maintenance
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given-names: "Tobey B."
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orcid: "https://orcid.org/0000-0003-4617-4674"
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affiliation: "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks 99775, Alaska, USA"
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- family-names: "Rutter" # Software development and maintenance
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given-names: "Ruth A."
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orcid: "https://orcid.org/0009-0009-7043-6081"
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affiliation: "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks 99775, Alaska, USA"
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- family-names: "Clein" # Calibration
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given-names: "Joy"
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orcid: "https://orcid.org/0000-0002-2816-5312"
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affiliation: "Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks 99775, Alaska, USA"
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- family-names: "Yuan" # Merging DVM, DOS, and TEM
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given-names: "Fengming"
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orcid: "https://orcid.org/0000-0003-0910-5231"
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affiliation: "Environmental Science Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831"
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- family-names: "Jafarov" # Calibration
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given-names: "Elchin"
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affiliation: "Woodwell Climate Research Center, Falmouth 02540, Massachusetts, USA"
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orcid: "https://orcid.org/0000-0002-8310-3261"
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- family-names: "Yi" # DOS
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given-names: "Shuhua"
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orcid: "https://orcid.org/0000-0003-4932-8237"
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affiliation: "Laboratory of Herbage Improvement And Agro-ecosystem, Lanzhou University, Lanzhou 730000, Gansu Province, P.R. China"
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- family-names: "Zhuang" # TEM
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given-names: "Qianlai"
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orcid: "https://orcid.org/0000-0002-4536-9851"
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affiliation: "Department of Earth, Atmospheric, and Planetary Science, Purdue University, West Lafayette IN 47907 USA"
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‎Dockerfile‎

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# === IMAGE FOR GENERAL C++ DEVELOPMENT =======================================
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# General development tools, compilers, text editors, etc
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FROM ubuntu:focal AS cpp-dev
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FROM ubuntu:jammy AS cpp-dev
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ENV DEBIAN_FRONTEND=noninteractive
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RUN apt-get update -y --fix-missing && apt-get install -y \
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build-essential \
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libreadline-dev \
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libsqlite3-dev \
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llvm \
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python-openssl \
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python3-openssl \
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tk-dev \
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wget \
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xz-utils \
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# A container run from this images will need to have data supplied (i.e. one or
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# more mounted volumes) in order to run dvmdostem.
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#
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FROM ubuntu:focal AS dvmdostem-run
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FROM ubuntu:jammy AS dvmdostem-run
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ARG UNAME
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ARG UID
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ARG GID

‎Dockerfile-mapping-support‎

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ARG UID=1000
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ARG GID=1000
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# Should try this updated image at some point...
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#FROM ghcr.io/osgeo/gdal:ubuntu-full-3.11.0
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# need this for netCDF
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FROM osgeo/gdal:ubuntu-full-3.2.2
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‎HOWTO_RELEASE.md‎

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go back to step 1. You will need to delete the tag created in step 3 so that
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you can re-create it.
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5. Bump the version number in `docs_src/sphinx/sources/conf.py, commit the
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change and then build the docs:
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5. Bump version numbers:
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- in `docs_src/sphinx/sources/conf.py `, and
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- in the `CITATION.cff` file, specifically under the
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`identifiers.description` for the Github release URL.
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Then commit the changes and build the docs:
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```
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$ docker compose exec --workdir /work/docs_src/sphinx \

‎README.md‎

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[![Slack](https://img.shields.io/badge/slack-login-green.svg)](https://arctic-eco-modeling.slack.com)
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The dvm-dos-tem (`dvmdostem`) model is a process based bio-geo-chemical
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ecosystem model that focuses on C and N dynamics as well as soil thermal
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dynamics in high latitude ecosystems.
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ecosystem model that focuses on C and N cycles, vegetation dynamics and soil
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thermal dynamics in high latitude ecosystems.
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For more information see the [User Guide](https://uaf-arctic-eco-modeling.github.io/dvm-dos-tem/index.html).
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‎config/config.js‎

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},
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"model_settings": {
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"cell_timelimit": 120, //Run time limit per cell in seconds. 0 for no limit.
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"dynamic_lai": 1, // from model (1) or from input (0)
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"baseline_start": 1901, //start year for baseline EQ climate
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"baseline_end": 1931, //end year for baseline EQ climate

‎config/output_spec.csv‎

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LFVN,Litterfall N from vascular PFTs,g/m2/time,,,invalid,,,invalid,double,
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LWCLAYER,LWC by layer,m3/m3,,,invalid,invalid,invalid,forced,double,
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MINEC,Mineral SOM C,g/m2,,,invalid,invalid,invalid,invalid,double,
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MOSSDEATHC,Dead moss C,g/m2,,,,invalid,invalid,invalid,double,
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MOSSDZ,Moss thickness,m,,invalid,invalid,invalid,invalid,invalid,double,
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NDRAIN,N losses from drainage (AVLN),g/m2/time,invalid,invalid,invalid,invalid,invalid,invalid,double,
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NETNMIN,Soil net N mineralization,g/m2/time,,,invalid,invalid,invalid,,double,

‎docs_src/sphinx/source/conf.py‎

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author = 'Tobey Carman, Ruth Rutter, Helene Genet, Eugenie Euskirchen'
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# The full version, including alpha/beta/rc tags
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release = 'v0.8.1'
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version = 'v0.8.1'
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release = 'v0.8.3'
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version = 'v0.8.3'
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# -- General configuration ---------------------------------------------------

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