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FIMS

A software system designed and architected to support next-generation fisheries stock assessment, ecosystem, and socioeconomic modeling.
https://github.com/noaa-fims/fims

Last synced: about 11 hours ago
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Repository metadata

The repository for development of FIMS

README

        


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# Overview
The repository for development of FIMS.

The NOAA Fisheries Integrated Modeling System is a software system designed and architected to support next-generation fisheries stock assessment, ecosystem, and socioeconomic modeling. A team of experts within NOAA Fisheries is designing and developing the system, and we are advised by the FIMS Council which includes academic, industry, and international partners. The roles of internal and external collaborators are outlined in the [governance section](https://noaa-fims.github.io/collaborative_workflow/fims-governance.html) of our developer guide. We plan to have an operational software system that is released to the public in 2023. In the meantime, users and developers are welcome to submit feedback using Github issues. Please use the issues under [collaborative workflow](https://github.com/NOAA-FIMS/collaborative_workflow/issues) to make suggestions about the [developer guide](https://noaa-fims.github.io/collaborative_workflow/) and the issues under the FIMS software [repo](https://github.com/NOAA-FIMS/FIMS/issues) for software design and development feedback. You can follow the team discussion [here](https://github.com/NOAA-FIMS/FIMS/discussions).

## Installation

The following software is required:

- R version 4.0.0 or newer (or RStudio version 1.2.5042 or newer)
- the `remotes` R package
- `TMB` version 1.8.0 or newer (install instructions are [here](https://github.com/kaskr/adcomp/wiki/Download).)

### Windows Users

- Rtools4 (available from [here](https://cran.r-project.org/bin/windows/Rtools/rtools40.html))

#### Fixing Fatal Error

Windows users can expect to see some derivative of the following error message in their R session if they have not yet set some flags using {withr}.
```
Fatal error: can't write bytes to section .text of FIMS.o: 'file too big
```
You can easily fix this by running the following line in your local R session. Note that this call will need to be repeated each time you open a new session.
```
withr::local_options(pkg.build_extra_flags = FALSE)
```
This fix does not work when `devtools::test()` is called and FIMS is re-compiled. The call to `devtools::test()` in this case overwrites the local options set by withr. Compile FIMS first using `devtools::load_all()` prior to running `devtools::test()`.

This fix removes the debugger flag `-O0 -g` from being automatically inserted for certain devtools calls (e.g. `devtools::load_all()`). Windows developers wanting to compile FIMS with the debugger turned on will need to run the above script in addition to manually modifying the call to PKG_CXXFLAGS in the [Makevars.win](https://github.com/NOAA-FIMS/FIMS/blob/doc-install/src/Makevars.win) file in the src directory to the following:

```
PKG_CXXFLAGS = -DTMB_MODEL -DTMB_EIGEN_DISABLE_WARNINGS -O1 -g
```
To turn off the debugger flag, remove the `-O1 -g` flag:
```
PKG_CXXFLAGS = -DTMB_MODEL -DTMB_EIGEN_DISABLE_WARNINGS
```

### Installing from R

```
remotes::install_github("NOAA-FIMS/FIMS")
library(FIMS)
```

## Getting Help
Please report bugs along with a minimal reproducible example on github [issues](https://github.com/NOAA-FIMS/FIMS/issues)

## Code of Conduct
All contributors participating and contributing to the FIMS project are expected to adhere to the [FIMS Code of Conduct](https://noaa-fims.github.io/collaborative_workflow/code-of-conduct.html#code-of-conduct)

****************************

## NOAA Disclaimer

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an 'as is' basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.

Software code created by U.S. Government employees is not subject to copyright in the United States (17 U.S.C. ยง105). The United States/Department of Commerce reserve all rights to seek and obtain copyright protection in countries other than the United States for Software authored in its entirety by the Department of Commerce. To this end, the Department of Commerce hereby grants to Recipient a royalty-free, nonexclusive license to use, copy, and create derivative works of the Software outside of the United States.

****************************

NOAA Fisheries

[U.S. Department of Commerce](https://www.commerce.gov/) | [National Oceanographic and Atmospheric Administration](https://www.noaa.gov) | [NOAA Fisheries](https://www.fisheries.noaa.gov/)


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GitHub Events

Total
Last Year

Committers metadata

Last synced: 27 days ago

Total Commits: 1,205
Total Committers: 21
Avg Commits per committer: 57.381
Development Distribution Score (DDS): 0.68

Commits in past year: 529
Committers in past year: 17
Avg Commits per committer in past year: 31.118
Development Distribution Score (DDS) in past year: 0.652

Name Email Commits
Christine Stawitz - NOAA 4****A 386
Matthew-Supernaw-NOAA m****w@n****v 152
Andrea-Havron-NOAA a****n@n****v 151
Bai Li b****i@n****v 115
Kathryn Doering k****g@n****v 95
github-actions[bot] 4****] 68
Bai Li - NOAA 5****A 67
Andrea-Havron-NOAA 8****A 52
Nathan Vaughan n****n@n****v 37
Christine.Stawitz c****z 22
kellijohnson-NOAA k****n@n****v 22
Jane Sullivan j****n@n****v 11
Jon Kenton Tarsus Brodziak j****k@n****v 6
MOshima-PIFSC m****a@n****v 5
Ian Taylor i****r@n****v 4
peterkuriyama-NOAA 1****A 3
KyleShertzer-NOAA 8****A 2
JaneSullivan-NOAA J****A 2
msupernaw m****w 2
timjmiller t****r@n****v 2
Bai.Li B****i@n****l 1

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Issue and Pull Request metadata

Last synced: 1 day ago

Total issues: 173
Total pull requests: 76
Average time to close issues: 6 months
Average time to close pull requests: 6 days
Total issue authors: 15
Total pull request authors: 7
Average comments per issue: 3.74
Average comments per pull request: 4.2
Merged pull request: 64
Bot issues: 0
Bot pull requests: 0

Past year issues: 123
Past year pull requests: 76
Past year average time to close issues: 4 months
Past year average time to close pull requests: 6 days
Past year issue authors: 12
Past year pull request authors: 7
Past year average comments per issue: 3.62
Past year average comments per pull request: 4.2
Past year merged pull request: 64
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/noaa-fims/fims

Top Issue Authors

  • Andrea-Havron-NOAA (52)
  • ChristineStawitz-NOAA (40)
  • Bai-Li-NOAA (24)
  • k-doering-NOAA (17)
  • Cole-Monnahan-NOAA (6)
  • kellijohnson-NOAA (6)
  • nathanvaughan-NOAA (6)
  • JaneSullivan-NOAA (5)
  • iantaylor-NOAA (3)
  • JonBrodziak (3)
  • KyleShertzer-NOAA (3)
  • Andrea-Havron (2)
  • cmlegault (2)
  • msupernaw (2)
  • Ovec8hkin (2)

Top Pull Request Authors

  • ChristineStawitz-NOAA (32)
  • Bai-Li-NOAA (15)
  • Andrea-Havron-NOAA (11)
  • k-doering-NOAA (9)
  • nathanvaughan-NOAA (4)
  • peterkuriyama-NOAA (3)
  • kellijohnson-NOAA (2)

Top Issue Labels

  • kind: refactor (51)
  • attribute: needs discussion (46)
  • kind: feature (43)
  • theme: NLL refactor (39)
  • status: wishlist (34)
  • theme: more features (28)
  • theme: code cleanup (24)
  • P2 (23)
  • low hanging ๐ŸŽ (19)
  • P1 (19)
  • P3 (18)
  • theme: r interface (17)
  • kind: question (14)
  • theme: documentation (11)
  • kind: documentation (9)
  • kind: bug (9)
  • status: triage_needed (6)
  • vignette (6)
  • attribute: needs more info (5)
  • theme: pilot studies (5)
  • status: help wanted (5)
  • kind: test case (3)
  • FIMS Seaside chat (1)

Top Pull Request Labels


Dependencies

DESCRIPTION cran
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  • Rcpp * imports
  • TMB >= 1.8.0 imports
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Score: 7.401231264413015