<p align="center">
<a href="https://egiron.github.io/pywheat/">
<img src="https://raw.githubusercontent.com/egiron/pywheat/master/docs/assets/logo_iwin2.png" alt="IWIN tools library">
</a>
</p>
<p align="center"><h1 align="center">Welcome to PyWheat</h1></p>
<p align="center">
<!-- <a href="https://orderseed.cimmyt.org/iwin-results.php"><img
src="https://img.shields.io/badge/CIMMYT-IWIN-blue"
alt="CIMMYT IWIN"
/></a> -->
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alt="Build"
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src="https://img.shields.io/pypi/dm/pywheat.svg"
alt="Downloads"
/></a>
<a href="https://pypi.org/project/pywheat"><img
src="https://img.shields.io/pypi/v/pywheat.svg"
alt="Python Package Index"
/></a>
<a href="https://opensource.org/licenses/"><img
src="https://img.shields.io/badge/License-GPL%20v3-yellow.svg"
alt="GPLv3 License"
/></a>
</p>
Python library for simulation of wheat phenological development, crop growth and yield at large scales.
# Intro
The PyWheat simulates the wheat growth and development in a daily time-step at field, local, regional and global scales. Most of the algorithms are based on the original Fortran routines of the CERES-Wheat 2.0[^1].
To accurately simulate wheat growth, development, and yield, the model takes into account the following processes:
* Phenological development, especially as it is affected by genetics and weather.
* Extension growth of leaves, stems, and roots.
* Biomass accumulation and partitioning, especially reproductive organs.
* Soil water balance and water use by the crop.
## Quick start
The package for estimating wheat grain yield using pywheat can be installed with `pip`:
``` sh
pip install pywheat
```
For detailed installation instructions visit [installation]
This will add a command-line interface (CLI) that you can then use like so:
``` sh
pywheat
```
This simple command shows the following message:
``` sh
Usage: pywheat [OPTIONS] COMMAND [ARGS]...
Options:
-h, --help Show this message and exit.
Commands:
pheno
phenology
```
You can see two functions or commands you will be able to run. Use the help option (-h) to see how to proceed.
``` sh
pywheat phenology -h
```
```
Usage: pywheat phenology [OPTIONS]
Options:
-lat, --latitude FLOAT Latitude of the site [required]
-lon, --longitude FLOAT Longitude of the site
-sd, --sowing_date TEXT Sowing date of the crop. eg. 1972-03-13
[required]
-tbase, --tbase FLOAT Base temperature for estimate Thermal time.
Default 0.0
-tt_topt, --tt_topt FLOAT Thermal time optimum temperature. Default 26
-tt_tmax, --tt_tmax FLOAT Thermal time maximum temperature. Default 34
-sa, --sunangle FLOAT Sun angle with the horizon. eg. p = 6.0 : civil
twilight. Default 0.0
-sn, --snow FLOAT Snow fall. Default 0.0
-sdepth, --sdepth FLOAT Sowing depth in cm. Default 3.0 cm
-gdde, --gdde FLOAT Growing degree days per cm seed depth required
for emergence, Default 6.2 GDD/cm.
-dsgft, --dsgft FLOAT GDD from End Ear Growth to Start Grain Filling
period. Default 200 degree-days
-vreq, --vreq FLOAT Vernalization required for max.development rate
(VDays). Default 505 degree-days
-phint, --phint FLOAT Phyllochron. A good estimate for PHINT is 95
degree days. This value for PHINT is
appropriate except for spring sown wheat in
latitudes greater than 30 degrees north and 30
degrees south, in which cases a value for PHINT
of 75 degree days is suggested. Default 95.0
degree-days
-p1v, --p1v FLOAT Development genetic coefficients,
vernalization. 1 for spring type, 5 for winter
type. Default 4.85
-p1d, --p1d FLOAT Development genetic coefficients, Photoperiod
(1 - 6, low- high sensitive to day length).
Default 3.675
-p5, --p5 FLOAT Grain filling degree days. Old value was
divided by 10. Default 500 degree-days.
-p6, --p6 FLOAT Approximate the thermal time from physiological
maturity to harvest. Default 250.
-glim, --glim FLOAT Threshold for days to germination. Default 40
-elim, --elim FLOAT Threshold for thermal time to emergence.
Default 300
-tdu, --tdu FLOAT Threshold for thermal development units (TDU).
Default 400
-fmt, --inputformat TEXT File format of the input weather file. Options
CSV, DSSAT .WTH or Parquet
-ofmt, --outputformat TEXT File format of the output phenology file.
Options txt or csv
-best, --bestmodel BOOLEAN Use the calibration parameters to estimate
phenology
-w, --weather FILE Path to input weather file in CSV or Parquet
format [required]
-o, --output FILE Path to output phenology file.
-verbose, --verbose BOOLEAN Display comments
-h, --help Show this message and exit.
```
### Usage in CLI
``` sh
pywheat phenology -lat 37.18 -lon -99.75 -sd '1981-10-16' \
-w ./pywheat/data/example/KSAS.WTH -fmt wth -o ./outputs.txt -verbose False
```
The above instruction use 3 variables (_latitude, longitude and sowing date of the site_) to run the phenology model. It also requires the path of the weather data file in this case in DSSAT format. This will take a minute or so at the first time to compile the main functions and save them to the cache. Next time will be much faster.
```
RSTG GROWTH STAGE DAP DOY CROP AGE SUMDTT DATE
7 Sowing 0 289 0 0 1981-10-16
8 Germinate 1 290 1 28 1981-10-17
9 Emergence 5 294 5 66 1981-10-21
1 Term Spklt 36 325 31 1683 1981-11-21
2 End Veg 147 71 111 290 1982-03-12
3 End Ear Gr 169 93 22 202 1982-04-03
4 Beg Gr Fil 184 108 15 158 1982-04-18
5 End Gr Fil 214 138 30 459 1982-05-18
6 Harvest 228 152 14 267 1982-06-01
```
For detailed instructions of how-to get started, configuration options, and a demo, visit [Getting Started]
[installation]: installation.md
[Getting Started]: getting_started.md
## Feedback
If you have any feedback, please reach out to us at [Feedback](mailto://e.giron.e@gmail.com)
## FAQ
Please read out [frequently asked questions](faq.md) before you send an email.
## Authors
- [@egiron](https://www.github.com/egiron)
## License
**MIT License**
Copyright (c) 2023
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to
deal in the Software without restriction, including without limitation the
rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
sell copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
IN THE SOFTWARE.
**Additional License** please check out [License](license.md)
<p align="center"><strong>Sponsors</strong></p>
<p align="center">
<a href="https://www.cimmyt.org/" target=_blank><img
src="./docs/assets/logoCIMMYT_letters.png" height="auto" width="200"
/></a>
</p>
<p> </p>
[^1]: CERES-Wheat version 2.0 by Dr. Joe T. Ritchie and Dr. Doug Godwin. https://nowlin.css.msu.edu/wheat_book/
[^2]: DSSAT. https://dssat.net/
[^3]: The Agricultural Production Systems sIMulator (APSIM). https://www.apsim.info/
[^4]: Ritchie, J.T.1991. Wheat phasic development. p. 31-54. In Hanks and Ritchie (ed.) Modeling plant and soil systems. Agron. Monogr. 31, ASA, CSSSA, SSSA, Madison, WI.
[^5]: Ritchie, J.T. and D.S. NeSmith. 1991. Temperature and Crop Development. p. 5-29. In Hanks and Ritchie (ed.) Modeling plant and soil systems. Agron. Monogr. 31, ASA, CSSSA, SSSA, Madison, WI.
Raw data
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"description": "<p align=\"center\">\n <a href=\"https://egiron.github.io/pywheat/\">\n <img src=\"https://raw.githubusercontent.com/egiron/pywheat/master/docs/assets/logo_iwin2.png\" alt=\"IWIN tools library\">\n </a>\n</p>\n\n<p align=\"center\"><h1 align=\"center\">Welcome to PyWheat</h1></p>\n\n<p align=\"center\">\n <!-- <a href=\"https://orderseed.cimmyt.org/iwin-results.php\"><img\n src=\"https://img.shields.io/badge/CIMMYT-IWIN-blue\"\n alt=\"CIMMYT IWIN\"\n /></a> -->\n <a href=\"https://github.com/egiron/pywheat/actions\"><img\n src=\"https://github.com/egiron/pywheat/actions/workflows/ci.yaml/badge.svg\"\n alt=\"Build\"\n /></a>\n <a href=\"https://pypistats.org/packages/pywheat\"><img\n src=\"https://img.shields.io/pypi/dm/pywheat.svg\" \n alt=\"Downloads\"\n /></a>\n <a href=\"https://pypi.org/project/pywheat\"><img \n src=\"https://img.shields.io/pypi/v/pywheat.svg\" \n alt=\"Python Package Index\"\n /></a>\n <a href=\"https://opensource.org/licenses/\"><img \n src=\"https://img.shields.io/badge/License-GPL%20v3-yellow.svg\" \n alt=\"GPLv3 License\"\n /></a>\n \n</p>\n\nPython library for simulation of wheat phenological development, crop growth and yield at large scales.\n\n# Intro\n\nThe PyWheat simulates the wheat growth and development in a daily time-step at field, local, regional and global scales. Most of the algorithms are based on the original Fortran routines of the CERES-Wheat 2.0[^1]. \n\nTo accurately simulate wheat growth, development, and yield, the model takes into account the following processes:\n\n* Phenological development, especially as it is affected by genetics and weather.\n* Extension growth of leaves, stems, and roots.\n* Biomass accumulation and partitioning, especially reproductive organs.\n* Soil water balance and water use by the crop.\n\n\n## Quick start\n\nThe package for estimating wheat grain yield using pywheat can be installed with `pip`:\n\n``` sh\npip install pywheat\n```\n\nFor detailed installation instructions visit [installation]\n\nThis will add a command-line interface (CLI) that you can then use like so:\n``` sh\npywheat\n```\nThis simple command shows the following message:\n``` sh\nUsage: pywheat [OPTIONS] COMMAND [ARGS]...\n\nOptions:\n -h, --help Show this message and exit.\n\nCommands:\n pheno\n phenology\n\n```\n\nYou can see two functions or commands you will be able to run. Use the help option (-h) to see how to proceed.\n\n``` sh\npywheat phenology -h\n```\n\n```\nUsage: pywheat phenology [OPTIONS]\n\nOptions:\n -lat, --latitude FLOAT Latitude of the site [required]\n -lon, --longitude FLOAT Longitude of the site\n -sd, --sowing_date TEXT Sowing date of the crop. eg. 1972-03-13\n [required]\n -tbase, --tbase FLOAT Base temperature for estimate Thermal time.\n Default 0.0\n -tt_topt, --tt_topt FLOAT Thermal time optimum temperature. Default 26\n -tt_tmax, --tt_tmax FLOAT Thermal time maximum temperature. Default 34\n -sa, --sunangle FLOAT Sun angle with the horizon. eg. p = 6.0 : civil\n twilight. Default 0.0\n -sn, --snow FLOAT Snow fall. Default 0.0\n -sdepth, --sdepth FLOAT Sowing depth in cm. Default 3.0 cm\n -gdde, --gdde FLOAT Growing degree days per cm seed depth required\n for emergence, Default 6.2 GDD/cm.\n -dsgft, --dsgft FLOAT GDD from End Ear Growth to Start Grain Filling\n period. Default 200 degree-days\n -vreq, --vreq FLOAT Vernalization required for max.development rate\n (VDays). Default 505 degree-days\n -phint, --phint FLOAT Phyllochron. A good estimate for PHINT is 95\n degree days. This value for PHINT is\n appropriate except for spring sown wheat in\n latitudes greater than 30 degrees north and 30\n degrees south, in which cases a value for PHINT\n of 75 degree days is suggested. Default 95.0\n degree-days\n -p1v, --p1v FLOAT Development genetic coefficients,\n vernalization. 1 for spring type, 5 for winter\n type. Default 4.85\n -p1d, --p1d FLOAT Development genetic coefficients, Photoperiod\n (1 - 6, low- high sensitive to day length).\n Default 3.675\n -p5, --p5 FLOAT Grain filling degree days. Old value was\n divided by 10. Default 500 degree-days.\n -p6, --p6 FLOAT Approximate the thermal time from physiological\n maturity to harvest. Default 250.\n -glim, --glim FLOAT Threshold for days to germination. 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It also requires the path of the weather data file in this case in DSSAT format. This will take a minute or so at the first time to compile the main functions and save them to the cache. Next time will be much faster.\n\n```\nRSTG GROWTH STAGE DAP DOY CROP AGE SUMDTT DATE \n7 Sowing 0 289 0 0 1981-10-16\n8 Germinate 1 290 1 28 1981-10-17\n9 Emergence 5 294 5 66 1981-10-21\n1 Term Spklt 36 325 31 1683 1981-11-21\n2 End Veg 147 71 111 290 1982-03-12\n3 End Ear Gr 169 93 22 202 1982-04-03\n4 Beg Gr Fil 184 108 15 158 1982-04-18\n5 End Gr Fil 214 138 30 459 1982-05-18\n6 Harvest 228 152 14 267 1982-06-01\n```\n\nFor detailed instructions of how-to get started, configuration options, and a demo, visit [Getting Started]\n\n [installation]: installation.md\n [Getting Started]: getting_started.md\n\n\n\n## Feedback\n\nIf you have any feedback, please reach out to us at [Feedback](mailto://e.giron.e@gmail.com)\n\n\n##\u00a0FAQ\n\nPlease read out [frequently asked questions](faq.md) before you send an email.\n\n## Authors\n\n- [@egiron](https://www.github.com/egiron)\n\n\n## License\n\n**MIT License**\n\nCopyright (c) 2023 \n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to\ndeal in the Software without restriction, including without limitation the\nrights to use, copy, modify, merge, publish, distribute, sublicense, and/or\nsell copies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in\nall copies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\nFROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\nIN THE SOFTWARE.\n\n\n**Additional License** please check out [License](license.md)\n\n<p align=\"center\"><strong>Sponsors</strong></p>\n<p align=\"center\">\n <a href=\"https://www.cimmyt.org/\" target=_blank><img\n src=\"./docs/assets/logoCIMMYT_letters.png\" height=\"auto\" width=\"200\"\n /></a>\n</p>\n<p> </p>\n\n\n [^1]: CERES-Wheat version 2.0 by Dr. Joe T. Ritchie and Dr. Doug Godwin. https://nowlin.css.msu.edu/wheat_book/\n\n [^2]: DSSAT. https://dssat.net/\n\n [^3]: The Agricultural Production Systems sIMulator (APSIM). https://www.apsim.info/\n\n [^4]: Ritchie, J.T.1991. Wheat phasic development. p. 31-54. In Hanks and Ritchie (ed.) Modeling plant and soil systems. Agron. 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