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Merge for release_proposal_v4.3.0 with numba replacing Cython. Updated docs and lisflood flags.
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‎.coveragerc

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[run]
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omit =
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src/lisflood/hydrological_modules/compile_kinematic_wave_parallel_tools.py
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tests/*

‎.gitignore

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__pycache__/
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build/
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*.so
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kinematic_wave_parallel_tools.html
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lisflood_model.egg-info
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/dist/
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.eggs
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.tox
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/src/dist/
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/src/lisflood/hydrological_modules/kinematic_wave_parallel_tools.c
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.coverage
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*.tox.ini
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.vscode/

‎Dockerfile

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COPY LICENSE /
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COPY VERSION /
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# Compile kwpt
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RUN cd /lisflood/hydrological_modules && conda run -n lisflood python compile_kinematic_wave_parallel_tools.py build_ext --inplace
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# RUN Tests
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COPY tests/. /tests/
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COPY pytest.ini /tests

‎MANIFEST.in

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include src/lisflood/hydrological_modules/kinematic_wave_parallel_tools.pyx
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include requirements.txt
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include *.xml
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include VERSION

‎README.md

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```bash
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conda create --name lisflood python=3.7 -c conda-forge
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conda activate lisflood
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conda install -c conda-forge pcraster
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conda install -c conda-forge pcraster gdal
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```
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* Install lisflood-model pypi package
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If you don't use conda but a plain virtualenv, you need to install PCRaster and GDAL by your own and include its python interface in PYTHONPATH environment variable.
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For details, please follow instruction on [official docs](http://pcraster.geo.uu.nl).
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3. Compile the cython module kinematic_wave_parallel_tool
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To compile this Cython module to enable OpenMP multithreading (parallel kinematic wave):
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* Delete the files *.so (if any) in directory hydrological-modules
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* Inside the hydrological_modules folder, execute "python compile_kinematic_wave_parallel_tools.py build_ext --inplace"
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Important: the module has to be compiled on the machine where the model is run - the resulting binary is not portable.
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Then in the settings file the option "numberParallelThreadsKinematicWave" may take the following values:
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- "0" : auto-detection of the machine/node's number of CPUs (all CPUs are used minus 1) (do not set it if other simulations are running on the same machine/node)
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- "1" : serial execution (not parallel)
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- "2", "3", ... : manual setting of the number of parallel threads.
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(if exceeding the number of CPUs, the option is set to "0") -->
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```xml
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<textvar name="numCPUs_parallelKinematicWave" value="3"/>
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```
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4. Run a cold run for the test catchment
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3. Run a cold run for the test catchment
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Now your environment should be set up to run lisflood. Try with a prepared settings file for one of the two test catchments:
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‎VERSION

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4.2.0
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4.3.0

‎docs/3_step2_installation/index.md

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For details, please follow instruction on [official docs](https://pcraster.geo.uu.nl/pcraster/4.3.1/documentation/pcraster_project/install.html).
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3. **Compile the cython module kinematic_wave_parallel_tool**
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To compile this Cython module to enable OpenMP multithreading (parallel kinematic wave):
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* Delete the files *.so (if any) in directory hydrological-modules
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* Inside the hydrological_modules folder, execute `python compile_kinematic_wave_parallel_tools.py build_ext --inplace`
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Important: the module has to be compiled on the machine where the model is run - the resulting binary is not portable.
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Then in the settings file the option "numberParallelThreadsKinematicWave" may take the following values:
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* "0" : auto-detection of the machine/node's number of CPUs (all CPUs are used minus 1) (do not set it if other simulations are running on the same machine/node)
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* "1" : serial execution (not parallel)
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* "2", "3", ... : manual setting of the number of parallel threads.
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(if exceeding the number of CPUs, the option is set to "0")
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```xml
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<textvar name="numCPUs_parallelKinematicWave" value="3"/>
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```
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4. **Run a cold run for the test catchment**
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3. **Run a cold run for the test catchment**
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Now that your environment should be set up to run lisflood, you may try with a prepared settings file for test catchment included into the tests/data folder:
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```bash
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python src/lisf1.py tests/data/<TestCatchmentFolder>/settings/cold_day_base.xml
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python src/lisf1.py tests/data/<TestCatchmentFolder>/settings/cold.xml
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```
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4. **Run LISFLOOD unit tests**
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