Merge pull request #111 from changliao1025/development

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changliao1025 · Jan 24, 2023 · 2c6591d · 2c6591d
2 parents 6b8a3c9 + db656ba
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diff --git a/README.md b/README.md
@@ -68,6 +68,7 @@ There are several publications that describe the algorithms used in `PyFlowline`
 
 * Liao. C. Cooper, M (2022) Pyflowline: a mesh independent river network generator for hydrologic models. Zenodo.
 https://doi.org/10.5281/zenodo.6407299
+* Liao, C., Zhou, T., Xu, D., Cooper, M. G., Engwirda, D., Li, H.-Y., & Leung, L. R. (2023). Topological relationship-based flow direction modeling: Mesh-independent river networks representation. Journal of Advances in Modeling Earth Systems, 15, e2022MS003089. https://doi.org/10.1029/2022MS003089
 
 
 

diff --git a/docs/source/faq.rst b/docs/source/faq.rst
@@ -0,0 +1,32 @@
+###########################
+Frequently Asked Questions
+###########################
+
+1. Why my `conda` cannot create environment?
+
+   Turn off the VPN or bypass it.
+
+2. Why import `GDAL` failed?
+
+   Consider using the `conda-forge` channel.
+
+3. `proj` related issue https://github.com/OSGeo/gdal/issues/1546, 
+
+   Make sure you correctly set up the `PROJ_LIB`
+
+   Because the `GDAL` library is used by this project and the `proj` library is often not configured correctly automatically. 
+   On Linux or Mac, you can set it up using the `.bash_profile` such as:
+
+   Anaconda:
+
+   `export PROJ_LIB=/people/user/.conda/envs/hexwatershed/share/proj`
+
+   Miniconda:
+
+   `export PROJ_LIB=/opt/miniconda3/envs/hexwatershed/share/proj`
+
+4. What if my model doesn't produce the correct or expected answer?
+
+   Answer: There are several hidden assumptions within the workflow. For example, if you provide the DEM and river network for two different regions, the program won't be able to tell you that. A visual inspection of your data is important.
+
+   Optionally, you can turn on the `iFlag_debug` option in the configuration file to output the `intermediate files`.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -21,6 +21,7 @@ Welcome to pyflowline's documentation!
    support
    contribution
    api/api
+   faq
    authors
 
 Addendum

diff --git a/examples/susquehanna/run_simulation_mpas.py b/examples/susquehanna/run_simulation_mpas.py
@@ -1,12 +1,14 @@
 import os, sys
 from pathlib import Path
 from os.path import realpath
-from pyflowline.pyflowline_read_model_configuration_file import pyflowline_read_model_configuration_file
-
 #===================================
 #set up workspace path
 #===================================
 sPath_parent = str(Path(__file__).parents[2]) # data is located two dir's up
+import sys
+sys.path.append(sPath_parent)
+from pyflowline.pyflowline_read_model_configuration_file import pyflowline_read_model_configuration_file
+
 sPath_data = realpath( sPath_parent +  '/data/susquehanna' )
 sWorkspace_input =  str(Path(sPath_data)  /  'input')
 sWorkspace_output=  str(Path(sPath_data)  /  'output')

diff --git a/paper.md b/paper.md
@@ -83,7 +83,7 @@ PNNL is operated for DOE by Battelle Memorial Institute under contract DE-AC05-7
 
 # References
 
-* Liao. C. Cooper, M (2022) Pyflowline: a mesh independent river network generator for hydrologic models. Zenodo.
+* Liao. C. Cooper, M (2022) Pyflowline: a mesh-independent river network generator for hydrologic models. Zenodo.
 https://doi.org/10.5281/zenodo.6407299
 
 * Liao, C., Zhou, T., Xu, D., Cooper, M. G., Engwirda, D., Li, H.-Y., & Leung, L. R. (2023). Topological relationship-based flow direction modeling: Mesh-independent river networks representation. Journal of Advances in Modeling Earth Systems, 15, e2022MS003089. https://doi.org/10.1029/2022MS003089