sipnet

Simplified Photosynthesis and Evapotranspiration Model: process-based ecosystem model for simulating carbon and water fluxes.

https://github.com/pecanproject/sipnet

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
○
Academic publication links
✓
Committers with academic emails
4 of 7 committers (57.1%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (11.6%) to scientific vocabulary

Keywords

biogeochemical-model carbon-credits carbon-cycle ecosystem-model greenhouse-gas hydrological-modelling photosynthesis simulation-model

Last synced: 6 months ago · JSON representation ·

Repository

Simplified Photosynthesis and Evapotranspiration Model: process-based ecosystem model for simulating carbon and water fluxes.

Basic Info

Host: GitHub
Owner: PecanProject
License: bsd-3-clause
Language: C
Default Branch: master
Homepage: https://pecanproject.github.io/sipnet/
Size: 46 MB

Statistics

Stars: 7
Watchers: 4
Forks: 14
Open Issues: 18
Releases: 0

Topics

biogeochemical-model carbon-credits carbon-cycle ecosystem-model greenhouse-gas hydrological-modelling photosynthesis simulation-model

Created over 6 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Code of conduct Citation

SIPNET

SIPNET (Simplified Photosynthesis and Evapotranspiration Model) is an ecosystem model designed to efficiently simulate carbon and water dynamics. Originally developed for assimilation of eddy covariance flux data in forest ecosystems, current development is focused on representing carbon balance and GHG fluxes and agricultural management practices.

Quick Start

Clone the repository: bash git clone https://github.com/PecanProject/sipnet.git cd sipnet
Build the SIPNET executable: bash make
Change directory and run a test simulation: bash cd tests/smoke/niwot ../../../sipnet -i sipnet.in
Check the output: bash cat niwot.out

Getting Started

Installing

See the quickstart above.

Executing the Program

[Link to cli docs, when they get written]

[Link to description of all the input files]

Running Tests

Smoke Tests

From the root sipnet directory, run:

bash ./tests/smoke/run_smoke.sh

The end of the output from that script should be:

```shell

SUMMARY: Skipped directories: 0 SIPNET OUTPUT: Passed: 5/5 Failed: 0 EVENT OUTPUT: Passed: 5/5 Failed: 0 CONFIG OUTPUT: Passed: 5/5

Failed: 0

```

Unit Tests

Build and run the unit tests with the script:

bash ./tools/run_unit_tests.sh

The summary block at the end should show PASSED for each test.

Documentation

Documentation for SIPNET is published at pecanproject.github.io/sipnet, which is built using mkdocs. See the Documentation section in the CONTRIBUTING page for more information about how to write and compile the documentation.

Contributing

See the main Contributing page

License

Distributed under the BSD 3-Clause license. See LICENSE for more information.

Owner

Name: PEcAn Project
Login: PecanProject
Kind: organization

Website: http://pecanproject.org
Repositories: 22
Profile: https://github.com/PecanProject

Citation (CITATION.cff)

cff-version: 1.2.0
title: "SIPNET: Simple Photosynthesis and Evapotranspiration Model"
version: 1.3.0
abstract: >
  SIPNET (Simple Photosynthesis and Evapotranspiration Model) is a process-based
  ecosystem model designed to simulate carbon and water fluxes and (optionally) agricultural management
  events in terrestrial ecosystems.
  SIPNET is used for research in ecosystem ecology, carbon and greenhouse gas accounting, 
  data assimilation, and model benchmarking.
  Model development and recent features are detailed in the CHANGELOG and relevant literature.
license: BSD-3-Clause
message: "Please cite SIPNET using the metadata from 'preferred-citation'."
type: software
authors:
  - family-names: Sacks
    given-names: William J.
    orcid: "https://orcid.org/0000-0003-2902-5263"
  - family-names: Moore
    given-names: David J.P.
    orcid: "https://orcid.org/0000-0002-6462-3288"
  - family-names: Zobitz
    given-names: John M.
    orcid: "https://orcid.org/0000-0002-1830-143X"
  - family-names: Braswell
    given-names: Bobby H.
    orcid: "https://orcid.org/0000-0002-4061-9516"
  - family-names: Schimel
    given-names: David S.
    orcid: "https://orcid.org/0000-0003-3473-8065"
  - family-names: LeBauer
    given-names: David S.
    orcid: "https://orcid.org/0000-0001-7228-053X"
  - family-names: Kooper
    given-names: Rob
    orcid: "https://orcid.org/0000-0002-5781-7287"
  - family-names: Dietze
    given-names: Michael C.
    orcid: "https://orcid.org/0000-0002-2324-2518"
  - family-names: Fer
    given-names: Istem
    orcid: "https://orcid.org/0000-0001-8236-303X"
  - family-names: (other contributors)
    given-names: See https://github.com/PecanProject/sipnet/graphs/contributors
  - family-names: Michael
    given-names: Longfritz

repository-code: https://github.com/PecanProject/sipnet
keywords:
  - ecosystem model
  - carbon cycle
  - water cycle
  - terrestrial biosphere
  - data assimilation

preferred-citation:
  type: software
  title: "SIPNET: Simple Photosynthesis and Evapotranspiration Model"
  version: 1.3.0
  url: https://github.com/PecanProject/sipnet
  authors:
    - family-names: Sacks
      given-names: William J.
    - family-names: Moore
      given-names: David J.P.
    - family-names: Zobitz
      given-names: John M.
    - family-names: Braswell
      given-names: Bobby H.
    - family-names: Schimel
      given-names: David S.
    - family-names: LeBauer
      given-names: David S.
    - family-names: Kooper
      given-names: Rob
    - family-names: Dietze
      given-names: Michael C.
    - family-names: Fer
      given-names: Istem
    - family-names: Michael
      given-names: Longfritz
    - family-names: (other contributors)
      given-names: See https://github.com/PecanProject/sipnet/graphs/contributors

references:
  - type: article
    title: "Estimating Diurnal to Annual Ecosystem Parameters by Synthesis of a Carbon Flux Model with Eddy Covariance Net Ecosystem Exchange Observations"
    authors:
      - family-names: Braswell
        given-names: Bobby H.
      - family-names: Sacks
        given-names: William J.
      - family-names: Linder
        given-names: Ernst
      - family-names: Schimel
        given-names: David S.
    year: 2005
    collection-title: Global Change Biology
    volume: 11
    pages: "335-355"
    doi: 10.1111/j.1365-2486.2005.00897.x
  - type: article
    title: "Model–data Synthesis of Diurnal and Seasonal CO2 Fluxes at Niwot Ridge, Colorado"
    authors:
      - family-names: Sacks
        given-names: William J.
      - family-names: Schimel
        given-names: David S.
      - family-names: Monson
        given-names: Russell K.
      - family-names: Braswell
        given-names: Bobby H.
    year: 2005
    collection-title: Global Change Biology
    volume: 12
    pages: "240-259"
    doi: 10.1111/j.1365-2486.2005.01059.x
  - type: article
    title: "Coupling between Carbon Cycling and Climate in a High-Elevation, Subalpine Forest: A Model-Data Fusion Analysis."
    authors:
      - family-names: Sacks
        given-names: William J.
      - family-names: Schimel
        given-names: David S.
      - family-names: Monson
        given-names: Russell K.
    year: 2007
    collection-title: Oecologia
    volume: 151
    pages: "54-68"
    doi: 10.1007/s00442-006-0565-2
  - type: article
    title: "Integration of Process-Based Soil Respiration Models with Whole-Ecosystem CO2 Measurements"
    authors:
      - family-names: Zobitz
        given-names: John M.
      - family-names: Moore
        given-names: David J.P.
      - family-names: Sacks
        given-names: William J.
      - family-names: Monson
        given-names: Russell K.
      - family-names: Bowling
        given-names: David R.
      - family-names: Schimel
        given-names: David S.
    year: 2008
    collection-title: Ecosystems
    volume: 40
    pages: "2723-2731"
    doi: 10.1007/s10021-007-9120-1
  - type: article
    title: "Joint data assimilation of satellite reflectance and net ecosystem exchange data constrains ecosystem carbon fluxes at a high-elevation subalpine forest"
    authors:
      - family-names: Zobitz
        given-names: John M.
      - family-names: Moore
        given-names: David J.P.
      - family-names: Quaife
        given-names: Tristan
      - family-names: Braswell
        given-names: Bobby H.
      - family-names: Bergeson
        given-names: Andrew
      - family-names: Anthony
        given-names: Jeremy A.
      - family-names: Monson
        given-names: Russell K.
    year: 2014
    collection-title: Global Change Biology
    volume: 20
    doi: 10.1016/j.agrformet.2014.04.011

GitHub Events

Total

Create event: 60
Release event: 5
Issues event: 70
Watch event: 1
Delete event: 52
Member event: 1
Issue comment event: 153
Push event: 332
Pull request review event: 273
Pull request review comment event: 230
Pull request event: 114
Fork event: 12

Last Year

Create event: 60
Release event: 5
Issues event: 70
Watch event: 1
Delete event: 52
Member event: 1
Issue comment event: 153
Push event: 332
Pull request review event: 273
Pull request review comment event: 230
Pull request event: 114
Fork event: 12

Committers

Last synced: about 2 years ago

All Time

Total Commits: 81
Total Committers: 7
Avg Commits per committer: 11.571
Development Distribution Score (DDS): 0.654

Past Year

Commits: 2
Committers: 1
Avg Commits per committer: 2.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Bill Sacks	s**s@u**u	28
David Moore	d**e@e**u	22
John Zobitz	z**z@a**u	13
Rob Kooper	k**r@i**u	7
istfer	f**m@g**m	6
Steve Aulenbach	a**h@m**m	3
Olli Niemitalo	o**4@h**i	2

Committer Domains (Top 20 + Academic)

hamk.fi: 1 me.com: 1 illinois.edu: 1 augsburg.edu: 1 email.arizona.edu: 1 ucar.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 50
Total pull requests: 72
Average time to close issues: 8 months
Average time to close pull requests: 9 days
Total issue authors: 8
Total pull request authors: 10
Average comments per issue: 0.88
Average comments per pull request: 1.0
Merged pull requests: 49
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 45
Pull requests: 65
Average time to close issues: 19 days
Average time to close pull requests: 8 days
Issue authors: 4
Pull request authors: 7
Average comments per issue: 0.73
Average comments per pull request: 0.92
Merged pull requests: 42
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

dlebauer (24)
Alomir (18)
infotroph (4)
ashiklom (2)
istfer (1)
mdietze (1)
AritraDey-Dev (1)
billsacks (1)

Pull Request Authors

Alomir (27)
dlebauer (26)
shah0108 (4)
AritraDey-Dev (4)
infotroph (3)
istfer (3)
robkooper (3)
mdietze (1)
Qianyuxuan (1)
thedgarg31 (1)
olli4 (1)

Top Labels

Issue Labels

documentation (3) good first issue (2) bug (1)

Pull Request Labels

documentation (4)

Dependencies

.github/workflows/ci.yml actions

actions/checkout v2 composite

sipnet

Science Score: 54.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

docs/README.md

SIPNET

Quick Start

Getting Started

Installing

Executing the Program

Running Tests

Smoke Tests

```shell

Failed: 0

Unit Tests

Documentation

Contributing

License

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies