merge master

.github/workflows/cmd_provider.yml

@@ -39,6 +39,11 @@ jobs:
     with:
       pytest-suite: tests/test_cmd.py --config config_files/quicktest_stream_rill.ini
 
+  # smoderp2d-quicktest-implicit-stream-rill:
+  #   uses: ./.github/workflows/cmd_template.yml
+  #   with:
+  #     pytest-suite: tests/test_cmd.py --config config_files/quicktest_stream_rill.ini --hidden_config config_files/.config_implicit.ini --reference_dir data/reference/quicktest_implicit_stream_rill/
+
   smoderp2d-longtest-sheet:
     uses: ./.github/workflows/cmd_template.yml
     with:
@@ -59,6 +64,11 @@ jobs:
     with:
       pytest-suite: tests/test_cmd.py --config config_files/test_stream_rill_mfda.ini
 
+  # smoderp2d-longtest-implicit-stream-rill-mfda:
+  #   uses: ./.github/workflows/cmd_template.yml
+  #   with:
+  #     pytest-suite: tests/test_cmd.py --config config_files/test_stream_rill_mfda.ini --hidden_config config_files/.config_implicit.ini --reference_dir data/reference/test_implicit_stream_rill_mfda/
+
   smoderp2d-longtest-stream-rill-mfda-diffusion:
     uses: ./.github/workflows/cmd_template.yml
     with:

.github/workflows/requirements3.11.txt

@@ -0,0 +1,4 @@
+pytest
+numpy==1.23.5
+matplotlib==3.6.3
+scipy==1.11.3

.github/workflows/requirements3.12.txt

@@ -1,2 +1,4 @@
 pytest==8.2.0
 numpy==1.26.4
+matplotlib==3.6.3
+scipy==1.11.3

.github/workflows/requirements3.9.txt

@@ -1,2 +1,4 @@
 pytest==7.2.2
 numpy==1.26.4
+matplotlib==3.5.3
+scipy==1.7.3

.gitignore

@@ -1,5 +1,6 @@
 *.pyc
 *~
+*.swp
 
 tests/data/log
 tests/data/output*
@@ -16,6 +17,8 @@ tests/data/reference/gistest_*/*/control/*.prj
 tests/data/reference/gistest_*/*/temp/*.prj
 tests/log
 
+tests/grassdata/
+
 bin/qgis/smoderp2d-plugin/smoderp2d/
 bin/qgis/smoderp2d-plugin/zip_build/
 
@@ -30,3 +33,7 @@ smoderp2d.egg-info
 # direnv
 .envrc
 .direnv
+
+#rfiles
+.Rhistory
+.RData

README.md

@@ -22,6 +22,8 @@ Distributed event-based model for surface and subsurface runoff and erosion.
                                 \___________________ @ @ @ @  @ @ @
 ```
 
+User documentation: <https://storm-fsv-cvut.github.io/smoderp2d-manual/>
+
 ## How to test
 
 Download SMODERP2D source code to your computer.
@@ -39,7 +41,7 @@ docker build \
  --tag smoderp2d:latest --file docker/Dockerfile .
 ```
 
-Run SMODERP command line tool from Docker container:
+Run SMODERP2D command line tool from Docker container:
 
 ```sh
 docker run \
@@ -48,82 +50,43 @@ docker run \
  --config tests/config_files/quicktest_stream_rill.ini
 ```
 
-### Run locally
+#### GRASS GIS
 
-Build and install SMODERP2D Python package:
+Build an image with GRASS GIS support:
 
 ```sh
-pip install .
+docker build \
+ --tag smoderp2d-grass:latest --file docker/grass/Dockerfile .
 ```
 
-#### Command line
+Run SMODERP2D with GRASS GIS provider from Docker container:
 
 ```sh
-./bin/start-smoderp2d.py --config tests/config_files/quicktest_stream_rill.ini
+docker run \
+ -v `pwd`:/opt/smoderp2d -w /opt/smoderp2d/ --rm --entrypoint \
+ ./tests/run_grass_gistest.sh smoderp2d-grass \
+ nucice
 ```
 
-#### GRASS GIS
-
-Note: GRASS GIS 8.3+ required
-
-Create testing mapset:
-
-```sh
-grass --text -c tests/grassdata/smoderp2d-location/test/
-```
+### Run locally
 
-Run `r.smoderp2d` module:
+#### Command line
 
 ```sh
-PYTHONPATH=$PYTHONPATH:`pwd` ./bin/grass/r.smoderp2d/r.smoderp2d.py \
-    elevation=dem@PERMANENT \
-    soil=soils@PERMANENT \
-    soil_type_fieldname=Soil \
-    vegetation=landuse@PERMANENT \
-    vegetation_type_fieldname=LandUse \
-    rainfall_file=tests/data/rainfall_nucice.txt \
-    maxdt=5 end_time=5 \
-    points=points@PERMANENT points_fieldname='point_id' \
-    table_soil_vegetation=soil_veg_tab@PERMANENT \
-    table_soil_vegetation_fieldname=soilveg \
-    streams=streams@PERMANENT \
-    channel_properties_table=streams_shape@PERMANENT \
-    streams_channel_type_fieldname=channel_id \
-    output=tests/data/output
+PYTHONPATH=$PYTHONPATH:`pwd` ./bin/start-smoderp2d.py --config tests/config_files/quicktest_stream_rill.ini
 ```
 
-#### ArcGIS Pro
-
-Launch SMODERP2D ArcToolbox from `bin\arcgis` directory.
-
-![SMODERP2D ArcToolbox in action](img/arctoolbox.png?raw=true "SMODERP2D ArcToolbox in action")
-
 #### QGIS
 
 Requirements: QGIS 3.28.10 and higher
 
 Define `QGIS_PLUGINPATH` and `PYTHONPATH` environmental variables in
-`Settings -> Options -> System` and restart QGIS:
-
-![SMODERP2D QGIS settings](img/qgis_settings.png?raw=true "QGIS settings")
+`Settings -> Options -> System` and restart QGIS.
 
 Than enable SMODERP2D plugin in `Plugins -> Manage and Install Plugins...`.
 
 Alternatively set up environment variables in command line before starting QGIS:
 
 ```sh
-PYTHONPATH=`pwd` QGIS_PLUGINPATH=`pwd`/bin/qgis qgis tests/data/nucice/qgis_project.qgz
+PYTHONPATH=$PYTHONPATH:`pwd` QGIS_PLUGINPATH=`pwd`/bin/qgis qgis tests/data/nucice/qgis_project.qgz
 ```
-
-#### Known issue
-
-On MS Windows QGIS plugin suffers by poping-up windows when starting computation.
-This can be solved by copying ``core.py`` file located in ``smoderp2d\bin\qgis\grass_patch``
-to a GRASS target directory.
-
-GRASS target directory is typically located in:
-
-- ``C:\Program Files\QGIS 3.**.*\apps\grass\grass83\etc\python\grass\script`` in the case that QGIS has been installed by standalone installer, or
-- ``C:\OSGeo4W\apps\grass\grass83\etc\python\grass\script`` in the case that QGIS has been installed by OSGeo4W network installer.
-
-Update: This bug has been fixed in GRASS GIS 8.4.

bin/arcgis/SMODERP2D.pyt

@@ -250,17 +250,19 @@ class SMODERP2D(object):
 
     def execute(self, parameters, messages):
         """The source code of the tool."""
+        runner = None
         try:
             runner = ArcGisRunner()
-
             runner.set_options(
                 self._get_input_params(parameters)
             )
-
             runner.run()
         except ProviderError as e:
             arcpy.AddError(e)
 
+        if runner is not None:
+            runner.finish()
+
         return
 
     @staticmethod

bin/arcgis/SMODERP2D.pyt.xml

@@ -1,2 +1,2 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<metadata xml:lang="cs"><Esri><CreaDate>20230116</CreaDate><CreaTime>10441900</CreaTime><ArcGISFormat>1.0</ArcGISFormat><SyncOnce>TRUE</SyncOnce><ModDate>20240410</ModDate><ModTime>132913</ModTime></Esri><toolbox name="SMODERP2D" alias=""><arcToolboxHelpPath>e:\arcgis pro\Resources\Help\gp</arcToolboxHelpPath><toolsets/></toolbox><dataIdInfo><idCitation><resTitle>SMODERP2D</resTitle></idCitation></dataIdInfo><distInfo><distributor><distorFormat><formatName>ArcToolbox Toolbox</formatName></distorFormat></distributor></distInfo></metadata>
+<metadata xml:lang="cs"><Esri><CreaDate>20230116</CreaDate><CreaTime>10441900</CreaTime><ArcGISFormat>1.0</ArcGISFormat><SyncOnce>TRUE</SyncOnce><ModDate>20240605</ModDate><ModTime>111141</ModTime></Esri><toolbox name="SMODERP2D" alias=""><arcToolboxHelpPath>c:\program files\arcgis\pro\Resources\Help\gp</arcToolboxHelpPath><toolsets/></toolbox><dataIdInfo><idCitation><resTitle>SMODERP2D</resTitle></idCitation></dataIdInfo><distInfo><distributor><distorFormat><formatName>ArcToolbox Toolbox</formatName></distorFormat></distributor></distInfo></metadata>

bin/grass/batch_process.py

@@ -0,0 +1,80 @@
+#!/usr/bin/env python3
+
+import os
+import sys
+import argparse
+
+from smoderp2d.runners.grass import GrassGisRunner
+from smoderp2d.exceptions import ProviderError, MaxIterationExceeded
+
+def run_process(params, epsg):
+    retcode = 0
+    runner = None
+    try:
+        runner = GrassGisRunner()
+        runner.create_location(f'EPSG:{epsg}')
+        runner.set_options(params)
+        runner.import_data()
+        runner.run()
+    except (ProviderError, MaxIterationExceeded) as e:
+        print(f'ERORR: {e}', file=sys.stderr)
+        retcode = 1
+
+    if runner is not None:
+        runner.finish()
+
+    return retcode
+
+def main(params, epsg):
+    sys.exit(run_process(params, epsg))
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        prog='batch_process',
+        description='Run SMODERP2D as batch process'
+    )
+    parser.add_argument('--elevation', required=True)
+    parser.add_argument('--soil', required=True)
+    parser.add_argument('--soil_type_fieldname', required=True)
+    parser.add_argument('--vegetation', required=True)
+    parser.add_argument('--vegetation_type_fieldname', required=True)
+    parser.add_argument('--rainfall_file', required=True)
+    parser.add_argument('--end_time', required=True)
+    parser.add_argument('--maxdt', required=True)
+    parser.add_argument('--table_soil_vegetation', required=True)
+    parser.add_argument('--table_soil_vegetation_fieldname', required=True)
+    parser.add_argument('--output', required=True)    
+    parser.add_argument('--points')
+    parser.add_argument('--points_fieldname')
+    parser.add_argument('--streams')
+    parser.add_argument('--channel_properties_table')
+    parser.add_argument('--streams_channel_type_fieldname')
+    parser.add_argument('--flow_direction', default='single')
+    parser.add_argument('--wave', default='kinematic')
+    parser.add_argument('--generate_temporary', action='store_true')
+    parser.add_argument('--epsg', default=5514)
+
+    args = parser.parse_args()
+
+    main({
+        'elevation': args.elevation,
+        'soil': args.soil,
+        'soil_type_fieldname': args.soil_type_fieldname,
+        'vegetation': args.vegetation,
+        'vegetation_type_fieldname': args.vegetation_type_fieldname,
+        'rainfall_file': args.rainfall_file,
+        'end_time': args.end_time,
+        'maxdt': args.maxdt,
+        'output': args.output,
+        'points': args.points,
+        'points_fieldname': args.points_fieldname,
+        'streams': args.streams,
+        'table_soil_vegetation': args.table_soil_vegetation,
+        'table_soil_vegetation_fieldname': args.table_soil_vegetation_fieldname,
+        'channel_properties_table': args.channel_properties_table,
+        'streams_channel_type_fieldname': args.streams_channel_type_fieldname,
+        'flow_direction': args.flow_direction,
+        'wave': args.wave,
+        'generate_temporary': bool(args.generate_temporary)
+    }, epsg=args.epsg
+         )

bin/grass/batch_process_csv.py

@@ -0,0 +1,66 @@
+#!/usr/bin/env python3
+
+import sys
+import argparse
+import csv
+
+from smoderp2d.exceptions import ProviderError, MaxIterationExceeded
+
+from batch_process import run_process
+
+def get_params_epsg(params):
+    epsg = params.pop('epsg')
+
+    return params, int(epsg)
+
+def run_process_single(params, epsg):
+    # run single process
+    print('-' * 80)
+    print(f'Run process with {params}...')
+    print('-' * 80)
+
+    return run_process(params, epsg)
+
+def main(csv_file, workers):
+    # collect params
+    params = []
+    with open(csv_file, newline='') as fd:
+        reader = csv.DictReader(fd, delimiter=';')
+        for row in reader:
+            if row['epsg'].startswith('#'):
+                # skip commented rows
+                continue
+            for k, v in row.items():
+                if v in ('true', 'false'):
+                    row[k] = True if v.lower() == 'true' else False
+            params.append(row)
+
+    # check for duplicated output paths
+    output_paths = set(p['output'] for p in params)
+    if len(params) != len(output_paths):
+        sys.exit("ERROR: Duplicated output paths detected")
+
+    # run processes
+    if workers > 1:
+        from joblib import Parallel, delayed
+
+        Parallel(n_jobs=workers, backend="multiprocessing", verbose=10)(
+            delayed(run_process_single)(*get_params_epsg(p)) for p in params
+        )
+    else:
+        for p in params:
+            run_process_single(*get_params_epsg(p))
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        prog='batch_process_csv',
+        description='Run SMODERP2D as batch processes from CSV',
+        epilog=r'Usage: PYTHONPATH=`pwd` python3 bin/grass/batch_process_csv.py --csv \ bin/grass/batch_process.csv'
+    )
+
+    parser.add_argument('--csv', required=True)
+    parser.add_argument('--workers', default=1)
+
+    args = parser.parse_args()
+
+    main(args.csv, int(args.workers))

bin/grass/r.smoderp2d/r.smoderp2d.py

@@ -137,19 +137,16 @@
 
 from smoderp2d.runners.grass import GrassGisRunner
 from smoderp2d.providers.base import WorkflowMode
-from smoderp2d.exceptions import ProviderError
+from smoderp2d.exceptions import ProviderError, MaxIterationExceeded
 
 if __name__ == "__main__":
     options, flags = gs.parser()
     options['generate_temporary'] = flags['t']
 
     try:
         runner = GrassGisRunner()
-
         runner.set_options(options)
-
-        sys.exit(
-            runner.run()
-        )
-    except ProviderError as e:
+        runner.run()
+        runner.finish()
+    except (ProviderError, MaxIterationExceeded) as e:
         gs.fatal(e)

bin/qgis/grass_patch/core.py

@@ -1,5 +1,5 @@
 """
-Core functions to be used in Python scripts.
+Core functions to be used in Python scripts (SMODERP2D patch applied).
 
 Usage: