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Merge pull request #185 from EcoExtreML/add_changelog
Add a changelog file
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| # Unreleased | ||
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| <a name="1.3.0"></a> | ||
| # [1.3.0](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.3.0) - 22 Jun 2023 | ||
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| This version of STEMMUS_SCOPE is only compatible with [PyStemmusScope 0.3.0.](https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing/releases/tag/v0.3.0) | ||
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| **Added:** | ||
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| - A license file, indicating that the code is under the GNU GPL-3.0 license ([#153](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/153)) | ||
| - A notebook to (more) easily compare the results of different STEMMUS_SCOPE git branches ([#177](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/177)) | ||
| - Changes in the land cover over time are now supported by the model ([#182](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/182)). | ||
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| **Changed:** | ||
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| - All code has been formatted with [MISS_HIT](https://misshit.org/), to improve readability ([#147](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/147)). All new or modified code should follow this style as well. | ||
| - The `Constants.m` file has been refactored ([#158](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/158)): | ||
| - Removed unused script `src/CnvrgnCHK.m` | ||
| - Removed unused global variables | ||
| - Replaced `Constants.m` with `io.loadModelSettings` and `init.defineInitialValues` | ||
| - The files `calcLambda.m` and `calcPhi_s.m` have been moved to the `+equations` module ([#171](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/171)) | ||
| - The scripts `SOIL1.m` and `SOIL2.m` have been refactored. The code is now in the files `UpdateSoilWaterContent.m` and `updateWettingHistory.m`([#180](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/180)) | ||
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| **Fixed:** | ||
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| - An error in the sign of NEE has been corrected ([#151](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/151)). | ||
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| [Changes][1.3.0] | ||
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| <a name="1.2.0"></a> | ||
| # [1.2.0](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.2.0) - 21 Feb 2023 | ||
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| This version of STEMMUS_SCOPE is only compatible with [PyStemmusScope 0.2.0.](https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing/releases/tag/v0.2.0) | ||
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| ### Changed: | ||
| - The StartInit file has been refactored to improve the code quality, and to remove global variables ([#113](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/113)). This also lead to various bugfixes ([#144](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/144)) | ||
| - Soil initial conditions are now read from a .mat file generated by [PyStemmusScope](https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing/), see the [release there](https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing/releases/tag/v0.2.0). | ||
| - The STEMMUS_SCOPE configuration file has been modified. PLUMBER2 sites are now defined as, e.g. `Location=AU-DaS`, and the time range for the model is defined as `StartTime=2001-01-01T00:00`, `EndTime=2001-01-02T00:00`. See [PyStemmusScope](https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing/) for more information. | ||
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| [Changes][1.2.0] | ||
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| <a name="1.1.11"></a> | ||
| # [1.1.11](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.1.11) - 15 Nov 2022 | ||
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| STEMMUS_SCOPE model that is Octave compatible. The input data and config file can be prepared using PyStemmusScope python package, see [readme](https://github.com/EcoExtreML/STEMMUS_SCOPE/tree/main#stemmus_scope). Changes are introduced in [#128](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/128) | ||
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| [Changes][1.1.11] | ||
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| <a name="1.1.10"></a> | ||
| # [1.1.10](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.1.10) - 15 Nov 2022 | ||
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| STEMMUS_SCOPE model. | ||
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| **Added:** | ||
| - `pull_request_template.md` in [#116](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/116) | ||
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| **Removed:** | ||
| - `src/filesread.m` in [#107](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/107) | ||
| - `src/set_parameter_filenames.m` in [#109](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/109) | ||
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| **Fixed:** | ||
| - the function `bin_to_csv` for storing the values of `sim_temp` and `sim_theta` in [#103](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/103). | ||
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| **Changed:** | ||
| - the function `filesread` is replaced with `prepareForcingData` in [#107](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/107) | ||
| - a more user-friendly readme in [#117](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/117) | ||
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| [Changes][1.1.10] | ||
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| <a name="1.1.9"></a> | ||
| # [1.1.9](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.1.9) - 28 Jul 2022 | ||
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| STEMMUS_SCOPE model. | ||
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| **Fixed**: | ||
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| - function `es_fun` [#81](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/81) | ||
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| **Changed**: | ||
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| - era5cli notebook checks sites against land sea mask [#79](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/79) | ||
| - Number of canopy layers in [#85](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/85) | ||
| - Convergence criteria in ebal `abs(PSI-PSI1)` and stemmus scope `max(CHK)` in [#85](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/85) | ||
| - Module parallel replaced with for loop in snellius bash script in [#91](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/91) | ||
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| **Removed**: | ||
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| - Variables for boundary condition settings from Constants.m in [#85](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/85) | ||
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| [Changes][1.1.9] | ||
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| <a name="1.1.8"></a> | ||
| # [1.1.8](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.1.8) - 08 Jul 2022 | ||
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| STEMMUS_SCOPE model. | ||
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| **Fixed:** | ||
| - maximum fractional saturated area in [#78](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/78) | ||
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| **Changed:** | ||
| - the parameter of evergreen broadleaf forests in [#78](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/78) | ||
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| [Changes][1.1.8] | ||
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| <a name="1.1.7"></a> | ||
| # [1.1.7](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.1.7) - 30 Jun 2022 | ||
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| STEMMUS_SCOPE model. | ||
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| **Fixed:** | ||
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| - Fix vegetation type and T min in [#72](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/72) | ||
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| [Changes][1.1.7] | ||
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| <a name="1.1.6"></a> | ||
| # [1.1.6](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.1.6) - 29 Jun 2022 | ||
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| STEMMUS_SCOPE model. | ||
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| **Fixed:** | ||
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| - Fix bugs in DoY and vegetation type processing [#67](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/67) | ||
| - Re-generate the exe file in [#70](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/70) | ||
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| [Changes][1.1.6] | ||
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| <a name="1.1.5"></a> | ||
| # [1.1.5](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.1.5) - 10 Jun 2022 | ||
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| STEMMUS_SCOPE model updating the scripts `StartInit.m` and `Constants.m` to use soil era5 land data in [#58](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/58) | ||
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| **Changed:** | ||
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| - `src/StartInit.m`, `src/Constants.m` and `src/filesread.m` in [#58](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/58) | ||
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| **Fixed:** | ||
| - fix warning message in [#57](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/57) | ||
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| **Added:** | ||
| - add `InitialConditionPath` to config files in [#58](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/58) and [#59](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/59) | ||
| - add the notebook `download_era5_data.ipynb` to `utils/notebooks` in [#54](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/54) | ||
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| [Changes][1.1.5] | ||
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| <a name="1.1.4b"></a> | ||
| # [1.1.4 (1.1.4b)](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.1.4b) - 11 May 2022 | ||
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| STEMMUS_SCOPE model updating the scripts `StartInit.m` and `Constants.m` to modify initial soil moisture in [#49](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/49) | ||
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| **Changed:** | ||
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| - `src/StartInit.m` and `src/Constants.m` in [#49](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/49) | ||
| - use warning off in `src/STEMMUS_SCOPE_exe.m` in [#45](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/45) | ||
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| **Fixed:** | ||
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| - Use warning instead of fprintf [#45](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/45) | ||
| - Fix `var_t_length` so it matches `DurationSize` in `utils/csv_to_nc` in [#47](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/47) | ||
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| **Removed:** | ||
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| - unused scripts in [#48](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/48) | ||
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| [Changes][1.1.4b] | ||
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| <a name="1.1.3"></a> | ||
| # [1.1.3](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.1.3) - 19 Apr 2022 | ||
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| STEMMUS_SCOPE model updating the equation `calc_rssrbs.m` and refactoring the script `soilpropertyread.m` to use a high-resolution global soil property datasets in [#39](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/39) | ||
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| **Changed:** | ||
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| - `src/+equations/calc_rssrbs.m`, `src/Constants.m`, `src/Initial_root_biomass.m`, `src/soilpropertyread.m` in [#39](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/39) | ||
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| **Fixed:** | ||
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| - fix the input/output paths in crib config file, see [#34](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/34) | ||
| - replacing the `keyboard` command with a `fprintf` statement, see [#40](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/40) | ||
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| [Changes][1.1.3] | ||
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| <a name="1.1.2"></a> | ||
| # [1.1.2](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.1.2) - 12 Apr 2022 | ||
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| STEMMUS_SCOPE model updating `ebal` script in [#24](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/24) and [#37](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/37). | ||
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| **Added** | ||
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| - output of NEE in [#37](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/37) | ||
| - documentation in [#32](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/32) and [#33](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/33) | ||
| - variable `DurationSize` to config file in [#36](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/36) | ||
| - documentation of how to convert the model output to netcdf files in `utils/csv_to_nc/README.md` [#27](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/27) | ||
| - python utility for converting the model output to netcdf files in [#27](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/27) | ||
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| **Removed** | ||
| - utils/csv_to_nc/write.py and utils/csv_to_nc/read.py in [#27](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/27) | ||
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| **Changed** | ||
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| - `src/ebal.m` in [#24](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/24) and [#37](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/37) | ||
| - `src/+io/bin_to_csv.m`, `src/+io/output_data_binary.m`, and | ||
| - `src/filesread.m` in [#24](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/24) and [#36](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/36) | ||
| - update `utils/csv_to_nc/Variables_will_be_in_NetCDF_file.csv` in [#27](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/27) | ||
| - replace `mean` with `nanmean` in [#37](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/37) | ||
| - readme in [#36](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/36) | ||
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| **Fixed** | ||
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| - the bash script of the running model on Snellius in [#25](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/25) | ||
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| [Changes][1.1.2] | ||
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| <a name="1.1.1"></a> | ||
| # [1.1.1](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.1.1) - 02 Feb 2022 | ||
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| STEMMUS_SCOPE model including the simplification of freeze/thaw in subroutines introduced in [#14](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/14). | ||
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| **Added** | ||
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| - Python scripts in Utils to convert the output in csv format to netcdf format, see [#11](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/11) | ||
| - The script `soilpropertyread.m` requires the data of `surfdata.nc`, see [#14](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/14). | ||
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| **Removed** | ||
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| - Files `src/+io/create_output_files.m` , `src/+io/output_data.m`, `src/SCOPE.exe`, in [#14](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/14). | ||
| - Files `src/PHENOLOGY_STATE.m`, `src/Root_Fraction_General.m`, `src/VEGETATION_DYNAMIC.m`, `src/calc_root_growth.m` in [#14](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/14). | ||
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| **Changed** | ||
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| - `src/+equations/Soil_Inertia1.m`, `src/soilpropertyread.m`, `src/filesread.m`, `src/ebal.m`, `src/StartInit.m` , `src/STEMMUS_SCOPE.m`, `src/Initial_root_biomass.m`, `src/Evap_Cal.m, src/Enrgy_sub.m`, `src/Constants.m`, `src/+plot/plots.m`, `src/+io/select_input.m`, `src/+io/output_data_binary.m`, `src/+io/bin_to_csv.m` , in [#14](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/14). | ||
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| **Fixed** | ||
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| - Output path and forcing path in [#10](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/10) | ||
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| [Changes][1.1.1] | ||
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| <a name="1.1.0"></a> | ||
| # [1.1.0](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.1.0) - 25 Jan 2022 | ||
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| STEMMUS_SCOPE model including changes from pull requests [#4](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/4) and [#9](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/9). The changes are summarized below: | ||
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| **Added** | ||
| - Add subfunction and module for "Root Properties" | ||
| - Add modules `HT_frez`, `Initial_root_biomass` | ||
| - Add module `filesread` to get input/output paths and prepare input data | ||
| - Add module `soilpropertyread` to prepare soil property input data | ||
| - Add module `soltir_tp7` to read MODTRAN tp7 file and applies a new MIT algorithm | ||
| - Add functions to convert the outputs format from binary to csv | ||
| - Add the function `output_verfication` from SCOPE code | ||
| - Add a function to convert timestamp to datetime array from SCOPE code | ||
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| **Changed** | ||
| - Modify equation of `rssrbs` | ||
| - Modify the equation of "soil respiration" | ||
| - Modify modules `AirPARM`, `Air_sub`, `CnvrgCHK`, `CondL_Tdisp`, `CondL_h`, `CondT_coeff`, `CondV_DE`, `CondV_DVg`, `Cond_k_g`, `Constants`, `Density_V`, `Dtrmn_Z`, `EfeCapCond`, `EnrgyPARM`, `Enrgy_BC`, `Enrgy_Solve`, `Enrgy_sub`, `Evap_Cal`, `Forcing_PARM`, `Max_Rootdepth`, `ObservationPoints`, `SOIL2`, `StartInit`, `TimestepCHK`, `biochemical`, `calc_rsoil`, `calc_sfactor`, `ebal`, `hPARM`, `h_BC`, `h_sub`, `hh_Solve` | ||
| - Modify `STEMMUS_SCOPE` | ||
| - Refactor function `PlotResults1` | ||
| - Remove some of the print statements related to outputs in module IO | ||
| - Refactor function plot in module plot to read csv format instead dat format | ||
| - Update readme | ||
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| [Changes][1.1.0] | ||
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| <a name="1.0.0"></a> | ||
| # [1.0.0](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.0.0) - 17 Dec 2021 | ||
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| Snapshots of codes used for the paper [Integrated modeling of canopy photosynthesis, fluorescence, and the transfer of energy, mass, and momentum in the soil–plant–atmosphere continuum (STEMMUS–SCOPE v1.0.0)](https://doi.org/10.5194/gmd-14-1379-2021). | ||
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| [Changes][1.0.0] | ||
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| [1.3.0]: https://github.com/EcoExtreML/STEMMUS_SCOPE/compare/1.2.0...1.3.0 | ||
| [1.2.0]: https://github.com/EcoExtreML/STEMMUS_SCOPE/compare/1.1.11...1.2.0 | ||
| [1.1.11]: https://github.com/EcoExtreML/STEMMUS_SCOPE/compare/1.1.10...1.1.11 | ||
| [1.1.10]: https://github.com/EcoExtreML/STEMMUS_SCOPE/compare/1.1.9...1.1.10 | ||
| [1.1.9]: https://github.com/EcoExtreML/STEMMUS_SCOPE/compare/1.1.8...1.1.9 | ||
| [1.1.8]: https://github.com/EcoExtreML/STEMMUS_SCOPE/compare/1.1.7...1.1.8 | ||
| [1.1.7]: https://github.com/EcoExtreML/STEMMUS_SCOPE/compare/1.1.6...1.1.7 | ||
| [1.1.6]: https://github.com/EcoExtreML/STEMMUS_SCOPE/compare/1.1.5...1.1.6 | ||
| [1.1.5]: https://github.com/EcoExtreML/STEMMUS_SCOPE/compare/1.1.4b...1.1.5 | ||
| [1.1.4b]: https://github.com/EcoExtreML/STEMMUS_SCOPE/compare/1.1.3...1.1.4b | ||
| [1.1.3]: https://github.com/EcoExtreML/STEMMUS_SCOPE/compare/1.1.2...1.1.3 | ||
| [1.1.2]: https://github.com/EcoExtreML/STEMMUS_SCOPE/compare/1.1.1...1.1.2 | ||
| [1.1.1]: https://github.com/EcoExtreML/STEMMUS_SCOPE/compare/1.1.0...1.1.1 | ||
| [1.1.0]: https://github.com/EcoExtreML/STEMMUS_SCOPE/compare/1.0.0...1.1.0 | ||
| [1.0.0]: https://github.com/EcoExtreML/STEMMUS_SCOPE/tree/1.0.0 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,14 +1,13 @@ | ||
| ### Description | ||
| Please add a description of the changes proposed in the pull request. | ||
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| ### Update executable file | ||
| Please re-generate exe file if matlab codes are changed. About how to create an exe file, see [exe readme](https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/run_model_on_snellius/exe/README.md). | ||
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| ### Checklist | ||
| - [ ] Add a reference to related issues. | ||
| - [ ] @mentions of the person or team responsible for reviewing proposed changes. | ||
| - [ ] This pull request has a descriptive title. | ||
| - [ ] Code is written according to the [guidelines](http://cnl.sogang.ac.kr/cnlab/lectures/programming/matlab/Richard_Johnson-MatlabStyle2_book.pdf). | ||
| - [ ] The checks by [MISS_HIT style checker and linter](https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/CONTRIBUTING.md#follow-matlab-style-guidelines), below the pull request, are successful (green). | ||
| - [ ] Documentation is available. | ||
| - [ ] Add changes to the [changelog file](CHANGELOG.md) under section `Unreleased`. | ||
| - [ ] Model runs successfully. | ||
| - [ ] Ask a meinatainer to re-generate exe file if matlab codes are changed. About how to create an exe file, see [exe readme](https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/run_model_on_snellius/exe/README.md). |