Merge pull request #156 from EcoExtreML/fix_linter_issues

Fix linter issues

CONTRIBUTING.md

@@ -12,6 +12,7 @@ you need to configure a few things following steps 1 through 5 below.
 
 <details>
   <summary>Steps 1 to 5 </summary>
+
 ### 1. Enable two-factor authentication
 
 It is strongly recommended using two-factor authentication. Here is the link of
@@ -154,4 +155,54 @@ See the [exe readme](./exe/README.md).
 
 ## Follow MATLAB style guidelines
 
-Please follow the style introduced in [MATLAB Guidelines 2.0, Richard Johnson](http://cnl.sogang.ac.kr/cnlab/lectures/programming/matlab/Richard_Johnson-MatlabStyle2_book.pdf).
+When you are introducing new changes to the codes, please follow the style introduced in [MATLAB Guidelines 2.0, Richard Johnson](http://cnl.sogang.ac.kr/cnlab/lectures/programming/matlab/Richard_Johnson-MatlabStyle2_book.pdf).
+
+When you submit a pull request, the code is also [checked](https://github.com/EcoExtreML/STEMMUS_SCOPE/actions/workflows/lint.yml) by the [MISS_HIT](misshit.org/) linter and style checker. 
+The status of `MISS_HIT` checks is shown below the pull request. The checks should be successful (green) before merging the pull request. 
+MISS_HIT is configured in [`miss_hit.cfg`](./miss_hit.cfg).
+
+### Installing MISS_HIT
+It is best practice to install packages in environments. See the dropdown menu for instructions.
+However, you can also continue below to install MISS_HIT without these steps.
+
+<details><summary>Python environment / conda instructions</summary>
+
+You need to have a valid python installation on your system.
+
+Create an enviroment with `venv` or conda:
+
+### **Venv**
+```bash
+python3 -m venv misshit # python on windows.
+```
+Activate this environment
+```bash
+source misshit/bin/activate
+```
+
+Or on Windows:
+```pwsh
+./misshit/Scripts/Activate.ps1
+```
+
+### **conda**
+```bash
+conda env create --name misshit
+conda activate misshit
+```
+
+</details>
+
+Install miss hit (optionally in the conda or venv environment) with:
+```bash
+pip install miss-hit
+```
+
+To run the style checker or linter, navigate to the STEMMUS_SCOPE repository, and run the following commands:
+
+```
+mh_style
+mh_lint
+```
+
+For more information on installing and using MISS_HIT, look at [MISS_HIT's readme](https://github.com/florianschanda/miss_hit#installation-via-pip).

pull_request_template.md

@@ -9,5 +9,6 @@ Please re-generate exe file if matlab codes are changed. About how to create an
 - [ ] @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.
 - [ ] Model runs successfully.

src/+init/calcSoilMatricHead.m

@@ -4,7 +4,7 @@
         section 5.4.3 in Yijian Zeng & Zhongbo Su (2013): STEMMUS (Simultaneous
         Transfer of Energy, Mass and Momentum in Unsaturated Soil): Department
         of Water Resources, ITC Faculty of Geo-Information Science and Earth
-        Observation, University of Twente ISBN: 978–90–6164–351–7
+        Observation, University of Twente ISBN: 978-90-6164-351-7
     %}
     matricHead = H02 + domainZ * (H01 - H02) / delta;
 

src/+init/calcSoilTemp.m

@@ -4,7 +4,7 @@
         section 5.4.3 in Yijian Zeng & Zhongbo Su (2013): STEMMUS (Simultaneous
         Transfer of Energy, Mass and Momentum in Unsaturated Soil): Department
         of Water Resources, ITC Faculty of Geo-Information Science and Earth
-        Observation, University of Twente ISBN: 978–90–6164–351–7
+        Observation, University of Twente ISBN: 978-90-6164-351-7
     %}
     soilTemperature = T02 + domainZ * (T01 - T02) / delta;
 

src/+io/prepareInputData.m

@@ -6,7 +6,7 @@
         InputPath: path of input data.
 
     Output:
-        SiteProperties： A structure containing site properties variables.
+        SiteProperties: A structure containing site properties variables.
         SoilProperties: A structure containing soil variables.
         TimeProperties: A structure containing time variables like time interval in seconds, normal is 1800 s in STEMMUS-SCOPE
             and the total number of time steps.

src/+io/select_input.m

@@ -8,7 +8,7 @@
     SoilProperties.CSSOIL        = ScopeParameters.CSSOIL(digitsVector(43));
     SoilProperties.lambdas       = ScopeParameters.lambdas(digitsVector(21));
     SoilProperties.rbs           = ScopeParameters.rbs(digitsVector(44));
-    SoilProperties.SMC           = Theta_LL(54, 1); %%%%%%% SoilProperties.SMC = flip£¨Theta_LL£©£¨:,1£©
+    SoilProperties.SMC           = Theta_LL(54, 1);
     SoilProperties.BSMBrightness = ScopeParameters.BSMBrightness(digitsVector(61));
     SoilProperties.BSMlat          = ScopeParameters.BSMlat(digitsVector(62));
     SoilProperties.BSMlon          = ScopeParameters.BSMlon(digitsVector(63));

src/Condg_k_g.m

@@ -17,5 +17,5 @@
         end
     end
 
-    %%%%%% Unit of k_g is m^2 , with UnitC^2, unit has been converted as cm^2 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-    %%%%%% 10^(-12)is used to convert the micrometer(¦Ìm) to meter(m)%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    %%% Unit of k_g is m^2 , with UnitC^2, unit has been converted as cm^2 %
+    %%% 10^(-12)is used to convert the micrometer to meter %

src/Constants.m

@@ -73,7 +73,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % Meteorological Forcing Information Variables
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-global MO Ta U Ts Zeta_MO        % U_wind is the mean wind speed at height z_ref (m��s^-1), U is the wind speed at each time step.
+global MO Ta U Ts Zeta_MO        % U_wind is the mean wind speed at height z_ref (m/s^-1), U is the wind speed at each time step.
 global Precip SH HR_a UseTs_msrmn      % Notice that Evap and Precip have only one value for each time step. Precip needs to be measured in advance as the input.
 global Gsc Sigma_E
 global Rns Rnl
@@ -166,11 +166,11 @@
 SAVEDTheta_LLh = zeros(mL, nD);
 SAVEDTheta_LLT = zeros(mL, nD);
 Ratio_ice = zeros(mL, nD);
-KL_h = zeros(mL, nD);       % The hydraulic conductivity(m��s^-1);
-KfL_h = zeros(mL, nD);       % The hydraulic conductivity considering ice blockking effect(m��s^-1);
-KfL_T = zeros(mL, nD);       % The depression temperature controlled by ice(m^2��Cels^-1��s^-1);
-KL_T = zeros(mL, nD);       % The conductivity controlled by thermal gradient(m^2��Cels^-1��s^-1);
-D_Ta = zeros(mL, nD);      % The thermal dispersivity for soil water (m^2��Cels^-1��s^-1);
+KL_h = zeros(mL, nD);       % The hydraulic conductivity(m/s^-1);
+KfL_h = zeros(mL, nD);       % The hydraulic conductivity considering ice blockking effect(m/s^-1);
+KfL_T = zeros(mL, nD);       % The depression temperature controlled by ice(m^2/Cels^-1/s^-1);
+KL_T = zeros(mL, nD);       % The conductivity controlled by thermal gradient(m^2/Cels^-1/s^-1);
+D_Ta = zeros(mL, nD);      % The thermal dispersivity for soil water (m^2/Cels^-1/s^-1);
 Theta_L = zeros(mL, nD);   % The soil moisture at the start of current time step;
 Theta_LL = zeros(mL, nD);  % The soil moisture at the end of current time step;
 Theta_U = zeros(mL, nD);   % The total soil moisture(water+ice) at the start of current time step;
@@ -189,12 +189,12 @@
 TT_CRIT = zeros(mN, 1);              % The soil ice critical temperature at the start of current time step;
 EPCT = zeros(mN, 1);
 Theta_V = zeros(mL, nD);    % Volumetric gas content;
-W = zeros(mL, nD);             % Differential heat of wetting at the start of current time step(J��kg^-1);
-WW = zeros(mL, nD);          % Differential heat of wetting at the end of current time step(J��kg^-1);
-% Integral heat of wetting in individual time step(J��m^-2); %%%%%%%%%%%%%%% Notice: the formulation of this in 'CondL_Tdisp' is not a sure. %%%%%%%%%%%%%%
-MU_W = zeros(mL, nD);        % Visocity of water(kg��m^?6?1��s^?6?1);
+W = zeros(mL, nD);             % Differential heat of wetting at the start of current time step(J/kg^-1);
+WW = zeros(mL, nD);          % Differential heat of wetting at the end of current time step(J/kg^-1);
+% Integral heat of wetting in individual time step(J/m^-2); %%%%%%%%%%%%%%% Notice: the formulation of this in 'CondL_Tdisp' is not a sure. %%%%%%%%%%%%%%
+MU_W = zeros(mL, nD);        % Visocity of water(kg/m^?6?1/s^?6?1);
 f0 = zeros(mL, nD);              % Tortusity factor [Millington and Quirk (1961)];                   kg.m^2.s^-2.m^-2.kg.m^-3
-L_WT = zeros(mL, nD);         % Liquid dispersion factor in Thermal dispersivity(kg��m^-1��s^-1)=-------------------------- m^2 (1.5548e-013 m^2);
+L_WT = zeros(mL, nD);         % Liquid dispersion factor in Thermal dispersivity(kg/m^-1/s^-1)=-------------------------- m^2 (1.5548e-013 m^2);
 DhT = zeros(mN, 1);             % Difference of matric head with respect to temperature;              m. kg.m^-1.s^-1
 RHS = zeros(mN, 1);             % The right hand side part of equations in '*_EQ' subroutine;
 EHCAP = zeros(mL, nD);        % Effective heat capacity;
@@ -214,29 +214,29 @@
 C6 = zeros(mL, nD);            % Conductivity term coefficients related to soil air pressure;
 C7 = zeros(mN, 1);             % Gravity term coefficients;
 C9 = zeros(mN, 1);             % root water uptake coefficients;
-QL = zeros(mL, nD);            % Soil moisture mass flux (kg��m^-2��s^-1);
-QL_D = zeros(mL, nD);         % Convective moisturemass flux (kg��m^-2��s^-1);
-QL_disp = zeros(mL, nD);     % Dispersive moisture mass flux (kg��m^-2��s^-1);
-QL_h = zeros(mL, nD);     % potential driven moisture mass flux (kg��m^-2��s^-1);
-QL_T = zeros(mL, nD);     % temperature driven moisture mass flux (kg��m^-2��s^-1);
+QL = zeros(mL, nD);            % Soil moisture mass flux (kg/m^-2/s^-1);
+QL_D = zeros(mL, nD);         % Convective moisturemass flux (kg/m^-2/s^-1);
+QL_disp = zeros(mL, nD);     % Dispersive moisture mass flux (kg/m^-2/s^-1);
+QL_h = zeros(mL, nD);     % potential driven moisture mass flux (kg/m^-2/s^-1);
+QL_T = zeros(mL, nD);     % temperature driven moisture mass flux (kg/m^-2/s^-1);
 HR = zeros(mN, 1);             % The relative humidity in soil pores, used for calculatin the vapor density;
-RHOV_s = zeros(mN, 1);      % Saturated vapor density in soil pores (kg��m^-3);
-RHOV = zeros(mN, 1);         % Vapor density in soil pores (kg��m^-3);
+RHOV_s = zeros(mN, 1);      % Saturated vapor density in soil pores (kg/m^-3);
+RHOV = zeros(mN, 1);         % Vapor density in soil pores (kg/m^-3);
 DRHOV_sT = zeros(mN, 1);   % Derivative of saturated vapor density with respect to temperature;
 DRHOVh = zeros(mN, 1);      % Derivative of vapor density with respect to matric head;
 DRHOVT = zeros(mN, 1);      % Derivative of vapor density with respect to temperature;
-RHODA = zeros(mN, 1);        % Dry air density in soil pores(kg��m^-3);
+RHODA = zeros(mN, 1);        % Dry air density in soil pores(kg/m^-3);
 DRHODAt = zeros(mN, 1);     % Derivative of dry air density with respect to time;
 DRHODAz = zeros(mN, 1);     % Derivative of dry air density with respect to distance;
 Xaa = zeros(mN, 1);            % Coefficients of derivative of dry air density with respect to temperature and matric head;
 XaT = zeros(mN, 1);            % Coefficients of derivative of dry air density with respect to temperature and matric head;
 Xah = zeros(mN, 1);            % Coefficients of derivative of dry air density with respect to temperature and matric head;
-D_Vg = zeros(mL, 1);           % Gas phase longitudinal dispersion coefficient (m^2��s^-1);
-D_V = zeros(mL, nD);           % Molecular diffusivity of water vapor in soil(m^2��s^-1);
-D_A = zeros(mN, 1);            % Diffusivity of water vapor in air (m^2��s^-1);
+D_Vg = zeros(mL, 1);           % Gas phase longitudinal dispersion coefficient (m^2/s^-1);
+D_V = zeros(mL, nD);           % Molecular diffusivity of water vapor in soil(m^2/s^-1);
+D_A = zeros(mN, 1);            % Diffusivity of water vapor in air (m^2/s^-1);
 k_g = zeros(mL, nD);           % Intrinsic air permeability (m^2);
 Sa = zeros(mL, nD);            % Saturation degree of gas in soil pores;
-V_A = zeros(mL, nD);           % Soil air velocity (m��s^-1);
+V_A = zeros(mL, nD);           % Soil air velocity (m/s^-1);
 Alpha_Lg = zeros(mL, nD);    % Longitudinal dispersivity in gas phase (m);
 POR_C = zeros(mL, nD);        % The threshold air-filled porosity;
 Eta = zeros(mL, nD);            % Enhancement factor for thermal vapor transport in soil.
@@ -290,11 +290,11 @@
 Ts = zeros(Nmsrmn, 1);         % Surface temperature;
 U = zeros(Nmsrmn, 1);          % Wind speed (m.s^-1);
 HR_a = zeros(Nmsrmn, 1);      % Air relative humidity;
-Rns = zeros(Nmsrmn, 1);        % Net shortwave radiation(W��m^-2);
-Rnl = zeros(Nmsrmn, 1);        % Net longwave radiation(W��m^-2);
+Rns = zeros(Nmsrmn, 1);        % Net shortwave radiation(W/m^-2);
+Rnl = zeros(Nmsrmn, 1);        % Net longwave radiation(W/m^-2);
 Rn = zeros(Nmsrmn, 1);
 h_SUR = zeros(Nmsrmn, 1);    % Observed matric potential at surface;
-SH = zeros(Nmsrmn, 1);         % Sensible heat (W��m^-2);
+SH = zeros(Nmsrmn, 1);         % Sensible heat (W/m^-2);
 MO = zeros(Nmsrmn, 1);         % Monin-Obukhov's stability parameter (MO Length);
 Zeta_MO = zeros(Nmsrmn, 1); % Atmospheric stability parameter;
 TopPg = zeros(Nmsrmn, 1);     % Atmospheric pressure above the surface as the boundary condition (Pa);
@@ -385,7 +385,7 @@
 h_TE = 0;                               % Value of 1 means that the temperature dependence                                      %
 % of matric head would be considered.Otherwise,0;                                       %
 W_Chg = 1;                            % Value of 0 means that the heat of wetting would                                       %
-% be calculated by Milly's method��Otherwise,1. The                                     %
+% be calculated by Milly's method/Otherwise,1. The                                     %
 % method of Lyle Prunty would be used;                                                  %
 ThmrlCondCap = 1; % 1;            % The indicator for choosing Milly's effective thermal capacity and conductivity         %
 % formulation to verify the vapor and heat transport in extremly dry soil.              %
@@ -424,13 +424,13 @@
 W0 = 1.001 * 10^3;                % Coefficient for calculating differential heat of wetting by Milly's method
 L0 = 597.3 * 4.182;
 Tr = 20;                              % Reference temperature
-c_L = 4.186;                        % Specific heat capacity of liquid water (J��g^-1��Cels^-1) %%%%%%%%% Notice the original unit is 4186kg^-1
-c_V = 1.870;                        % Specific heat capacity of vapor (J��g^-1��Cels^-1)
+c_L = 4.186;                        % Specific heat capacity of liquid water (J/g^-1/Cels^-1) %%%%%%%%% Notice the original unit is 4186kg^-1
+c_V = 1.870;                        % Specific heat capacity of vapor (J/g^-1/Cels^-1)
 c_a = 1.005;
-% c_a=1.005;                        % 0.0003*4.186; %Specific heat capacity of dry air (J��g^-1��Cels^-1)
-c_i = 2.0455;                        % Specific heat capacity of ice (J��g^-1��Cels^-1)
-Gsc = 1360;                         % The solar constant (1360 W��m^-2)
-Sigma_E = 4.90 * 10^(-9);       % The stefan-Boltzman constant.(=4.90*10^(-9) MJ��m^-2��Cels^-4��d^-1)
+% c_a=1.005;                        % 0.0003*4.186; %Specific heat capacity of dry air (J/g^-1/Cels^-1)
+c_i = 2.0455;                        % Specific heat capacity of ice (J/g^-1/Cels^-1)
+Gsc = 1360;                         % The solar constant (1360 W/m^-2)
+Sigma_E = 4.90 * 10^(-9);       % The stefan-Boltzman constant.(=4.90*10^(-9) MJ/m^-2/Cels^-4/d^-1)
 P_g0 = 95197.850; % 951978.50;               % The mean atmospheric pressure (Should be given in new simulation period subroutine.)
 rroot = 1.5 * 1e-3;
 RTB = 1000;                    % initial root total biomass (g m-2)

src/STEMMUS_SCOPE.m

@@ -1,7 +1,7 @@
 %% STEMMUS-SCOPE.m (script)
 
 %     STEMMUS-SCOPE is a model for Integrated modeling of canopy photosynthesis, fluorescence,
-%     and the transfer of energy, mass, and momentum in the soil–plant–atmosphere continuum
+%     and the transfer of energy, mass, and momentum in the soil-plant-atmosphere continuum
 %
 %     Version: 1.0.1
 %
@@ -115,9 +115,9 @@
 end
 
 F = struct('FileID', {'Simulation_Name', 'soil_file', 'leaf_file', 'atmos_file'...
-                     'Dataset_dir', 't_file', 'year_file', 'Rin_file', 'Rli_file' ...
-                     , 'p_file', 'Ta_file', 'ea_file', 'u_file', 'CO2_file', 'z_file', 'tts_file' ...
-                     , 'LAI_file', 'hc_file', 'SMC_file', 'Vcmax_file', 'Cab_file', 'LIDF_file'});
+                      'Dataset_dir', 't_file', 'year_file', 'Rin_file', 'Rli_file' ...
+                      , 'p_file', 'Ta_file', 'ea_file', 'u_file', 'CO2_file', 'z_file', 'tts_file' ...
+                      , 'LAI_file', 'hc_file', 'SMC_file', 'Vcmax_file', 'Cab_file', 'LIDF_file'});
 for i = 1:length(F)
     k = find(strcmp(F(i).FileID, strtok(X(:, 1))));
     if ~isempty(k)

src/ebal.m

@@ -380,7 +380,8 @@
         Tch(abs(Tch) > 100) = Ta;
         Tcu(abs(Tcu) > 100) = Ta;
         Ts(abs(Ts) > 100) = Ta;
-        if any(isnan(Tch)) || any(isnan(Tcu(:))) warning('Canopy temperature gives NaNs');
+        if any(isnan(Tch)) || any(isnan(Tcu(:)))
+            warning('Canopy temperature gives NaNs');
         end
         if any(isnan(Ts))
             warning('Soil temperature gives NaNs');

src/hPARM.m

@@ -1,6 +1,6 @@
 function [Chh, ChT, Khh, KhT, Kha, Vvh, VvT, Chg, DTheta_LLh, DTheta_LLT, DTheta_UUh, SAVEDTheta_UUh, SAVEDTheta_LLh] = hPARM(NL, hh, ...
-                                                                                                                h, TT, T, Theta_LL, Theta_L, DTheta_LLh, DTheta_LLT, RHOV, RHOL, Theta_V, V_A, Eta, DRHOVh, ...
-                                                                                                                DRHOVT, KfL_h, D_Ta, KL_T, D_V, D_Vg, COR, Beta_g, Gamma0, Gamma_w, KLa_Switch, DVa_Switch, hThmrl, Thmrlefc, nD, TT_CRIT, T0, h_frez, hh_frez, Theta_UU, Theta_U, CORh, DTheta_UUh, Chh, ChT, Khh, KhT)
+                                                                                                                              h, TT, T, Theta_LL, Theta_L, DTheta_LLh, DTheta_LLT, RHOV, RHOL, Theta_V, V_A, Eta, DRHOVh, ...
+                                                                                                                              DRHOVT, KfL_h, D_Ta, KL_T, D_V, D_Vg, COR, Beta_g, Gamma0, Gamma_w, KLa_Switch, DVa_Switch, hThmrl, Thmrlefc, nD, TT_CRIT, T0, h_frez, hh_frez, Theta_UU, Theta_U, CORh, DTheta_UUh, Chh, ChT, Khh, KhT)
 
     % piecewise linear reduction function parameters of h;(Wesseling
     % 1991,Veenhof and McBride 1994)