Tag and release historical SIPNET versions

[dlebauer]

Key objective here is to figure out what version we are on, and in the process we can tagging and release historical versions. I'd plan to find the appropriate commit and paste the following:

Feedback appreciated: mostly to make sure it is correct, but any additional detail, features missed, alternate version names, welcome.

It seems each paper added one or more features that warrant a minor version bump but please correct if I am wrong. Note that release descriptions can be edited in the future. (from all, but esp. @jmzobitz, @billsacks; also other prev. developers @aulenbac @davidjpmoore).

SIPNET 1.0.0 - "SIPNET First Release"

The first release of SIPNET reflected a series of improvements over the original SIPNET model (Braswell et al., 2005).
The model was developed by Bill Sacks and Dave Moore, with contributions from John Zobitz. The model was parameterized using data from the Harvard Forest flux tower using MCMC (Sacks et al., 2006).
The model was designed to simulate the carbon and water cycles of a forest ecosystem at half-daily time steps.

47d6546

Braswell et al. (2005)

• Initial version of SIPNET.
• Half-daily time step with two vegetation carbon pools and one soil pool.
• MCMC parameter fitting with observations from Harvard forest flux tower.

Sacks et al. (2006)

• More complex water routine incorporating evaporation and snow pack.
• Evergreen leaf phenology.

Sacks et al. (2007): "Better Respiration"

• Shut down photosynthesis and foliar respiration when soil temperature < threshold.
• Partition autotrophic and heterotrophic respiration.

SIPNET 1.1.0 - "Roots and Microbes"

Moore et al. (2008)

• Support joint CO2 and H2O assimilation.
• Commit: [Reference commit hash not specified]

Zobitz et al. (2008)

• Add process-based soil respiration with microbes "soil quality model".
• Add fine and coarse root pools.
• Compare different model structures (base, soil quality, and roots).
• Calculate Transpiration using Ball Berry, initial implementation of and Penman-Monteith

SIPNET 1.2.0 - "fAPAR assimilation"

• Modify fAPAR calculation to enable assimilation of MODIS satellite-derived fAPAR.
• Commit: 97a2259
• Zobitz et al. (2014)

SIPNET 1.2.1 - "Add LICENSE and minor fixes"

0c77ce8

• Add BSD 3-Clause LICENSE file.
• Minor fixes prior to agricultural management implementation.
• Bug fix for output formatting (identified by @Qianyuxuan).
• Migrate documentation from Word to Markdown.

SIPNET 1.3.0 - "Event Handler"

v1.3.0 represents the initial development of support for agricultural management events.

• Introduced Event Handler infrastructure ran doxygen -u to remove deprecated settings #23
• Add testing infrastructure.

Minor changes:

• Code cleanup (including comment standardization and spelling corrections).
• Update Doxyfile
• Add make help.

Potential Future Releases

• 1.3.1 - Add canopy and soil irrigation.
• 1.3.2 - Planting and harvest events.
• 1.3.3 - Organic matter addition
• 1.4.0 - Initial N cycle integration.
• 1.4.1 - Soil and Plant N Pool expansion.
• 1.4.1 - Enhancements in N mineralization and volatilization.
• 1.4.2 - Nitrogen Fertilization
• 1.5.0 - CH4 fluxes and extended event handling.

[billsacks]

Thanks for working on this @dlebauer ! At a glance, this seems reasonable, but I don't think you'll be able to find commits for the first few versions you mentioned, because the initial development was done without the benefit of version control.

See 47d6546 for some comments relating to what I think was the first "real" commit. That might have been related to this 2008 paper that I don't think you mentioned above:

Moore DJP, Hu J, Sacks WJ, Schimel DS, Monson RK (2008). Estimating transpiration and the sensitivity of carbon uptake to water availability in a subalpine forest using a simple ecosystem process model informed by measured CO2 and H2O fluxes. Agricultural and Forest Meteorology, 148: 1467-1477.

[jmzobitz]

The paper that @billsacks mentions by @davidjpmoore occurred around the same time I added the roots / quality piece. I think we may have been working in parallel on it at the time - which led to a two hour session at NCAR where we tried to figure out why out codes crashed when we merged them(😭). I wish @aulenbac 's wisdom about git/subversion had sunk in with me some more at the time.

Is the fAPAR assimilation still useful?

[dlebauer]

Thanks @billsacks and @jmzobitz for the feedback and context.

@jmzobitz - I've heard @mdietze mention using fAPAR but I am not sure of the status. Our project is primarily focused on the SOC and GHG, but I'll keep it in mind if the opportunity arises.
And Thanks for reminding me of Dave's paper - I was mostly focusing on model structure rather than analysis when reviewing the evolution of the model, but it makes sense to add a release since all of his code is in the repository.

[dlebauer]

Releases released, including binaries and source code!
https://github.com/PecanProject/sipnet/releases

Code used to tag and generate binaries

git tag v1.3.0 8ff893e61d69d0374bdf0fa14d156fd621c40eb4
git tag v1.2.1 0c77ce863ac61113740c759dbe502a74e2d64edf
git tag v1.2.0 97a225956775035506f573a29c7022de8d7d269d
git tag v1.1.0 f776a12e422b0934ea3c2325874460000eebc4b7
git tag v1.0.0 47d6546e245384dbda7e981a3bc8b729d4f756fc


# Define the tags
tags=("v1.3.0" "v1.2.1" "v1.2.0" "v1.1.0" "v1.0.0")

# Loop through each tag
for tag in "${tags[@]}"; do
  # Checkout the tag
  git checkout $tag

  # Build the project
  make sipnet

  # Rename the output
  mv sipnet "sipnet-linux-$tag"
done

# Checkout back to the master branch
git checkout master