JGCRI · crvernon · Feb 27, 2019 · Feb 27, 2019 · Feb 27, 2019 · Feb 27, 2019
diff --git a/.gitattributes b/.gitattributes
diff --git a/.travis.yml b/.travis.yml
@@ -1,11 +1,17 @@
 language: python
+
 matrix:
+
   include:
-    - python: 2.7
     - python: 3.6
       dist: xenial
+
 cache: pip
+
 install:
-  - pip install .
+  - pip install -r requirements.txt
+  - python setup.py -q install
+  - python travis_setup.py
+
 script:
   - travis_wait 35 python -m unittest discover
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,9 @@
+include README.md
+include requirements.txt
+include DISCLAIMER
+include LICENSE
+include docs/*.md
+include docs/*.png
+include xanthos/data/*.txt
+include xanthos/data/*.csv
+include xanthos/test/data/configs/*.ini
diff --git a/README.md b/README.md
@@ -16,8 +16,7 @@ Hejazi, Mohamad I <[email protected]>
 
 
 # Notice
-Xanthos currently supports both Python 2.7 and Python 3.3+, however future support for Python 2 is not guaranteed.  This repository also uses the Git Large File Storage (LFS) extension (see https://git-lfs.github.com/ for details).  Please run the following command before cloning if you do not already have Git LFS installed:
-`git lfs install`.
+Xanthos currently supports both Python 2.7 and Python 3.3+, however future support for Python 2 is not guaranteed.  This repository no longer uses the Git Large File Storage (LFS) extension.  Instead, we now have supplementary data to Xanthos archived on Zenodo.  This data is automatically downloaded from our current release upon running installing Xanthos locally.
 
 # Xanthos 2 - Upgrades
 With the ability to simulate historical and future global water availability on a monthly time step at a spatial resolution of 0.5 geographic degrees, Xanthos version 1.0 provided a solid foundation for continued advancements in global water dynamics science.  The goal of Xanthos version 2 was to build upon previous investments by creating an accessible computing environment where core components of the model (potential evapotranspiration (PET), runoff generation, and river routing) could be interchanged or added to without having to start from scratch.  Xanthos 2 utilizes a component-style architecture which enables researchers to quickly incorporate and test cutting-edge research in a stable modeling environment prebuilt with a diagnostics module.  Major advancements for Xanthos 2.0 were also achieved by creating a more robust default configuration for the model that is now available to the scientific community.  These advancements include the addition of:  the Penman-Monteith PET module to capture the impacts of evolving land cover, the ABCD water balance module to account for groundwater recharge and discharge in runoff projections, improved water velocity considerations for the Modified River Transport Model (MRTM) routing module, a built-in differential evolution optimization module to calibrate ABCD parameters to modeled global runoff, and hydropower production assessment and potential capacity modules.  The figure below demonstrates the optimization module’s ability to calibrate Xanthos 2 runoff to the complex Variable Infiltration Capacity (VIC) model runoff projections when forced by the same climate data. Xanthos can be calibrated against other land surface models and Earth system models.
@@ -40,4 +39,4 @@ Set up Xanthos using the following steps:
 A detailed Wiki set up to describe how to set up a Xanthos run can be viewed here:  https://github.com/JGCRI/xanthos/wiki/Tutorial-1:--Setting-up-a-Xanthos-run
 
 # Available Modules
-A detailed Wiki set up to describe available modules, as well as their associated configuration settings, can be viewed here: https://github.com/JGCRI/xanthos/wiki/Available-modules
+A detailed Wiki set up to describe available modules, as well as their associated configuration settings, can be viewed here: https://github.com/JGCRI/xanthos/wiki/Available-modules
diff --git a/docs/InstallationRequirements.pdf b/docs/InstallationRequirements.pdf
diff --git a/docs/diag_basin.png b/docs/diag_basin.png
diff --git a/docs/flowchart.png b/docs/flowchart.png
diff --git a/docs/structure.png b/docs/structure.png
diff --git a/docs/workflow.png b/docs/workflow.png
diff --git a/docs/xanthos2_to_vic_watch_basins.png b/docs/xanthos2_to_vic_watch_basins.png
diff --git a/example/example.py b/example/example.py
diff --git a/example/input/ReadMe_Input_Data.txt b/example/input/ReadMe_Input_Data.txt
diff --git a/example/input/accessible_water/bfi_per_basin.csv b/example/input/accessible_water/bfi_per_basin.csv
diff --git a/example/input/accessible_water/total_reservoir_storage_capacity_BM3.csv b/example/input/accessible_water/total_reservoir_storage_capacity_BM3.csv
diff --git a/example/input/ancillary/penman_monteith_watch_historical_1971_2001_decadal_lc.npy b/example/input/ancillary/penman_monteith_watch_historical_1971_2001_decadal_lc.npy
diff --git a/example/input/calibration/vic_watch_basin_km3_1971_2001_monthly.csv b/example/input/calibration/vic_watch_basin_km3_1971_2001_monthly.csv
diff --git a/example/input/climate/pr_gpcc_watch_monthly_mmpermth_1971_2001.npy b/example/input/climate/pr_gpcc_watch_monthly_mmpermth_1971_2001.npy
diff --git a/example/input/climate/tasmin_watch_monthly_degc_1971_2001.npy b/example/input/climate/tasmin_watch_monthly_degc_1971_2001.npy
diff --git a/example/input/diagnostics/UNH_GRDC_average_annual_1986_1995.nc b/example/input/diagnostics/UNH_GRDC_average_annual_1986_1995.nc
diff --git a/example/input/diagnostics/vic_watch_hist_nosoc_co2_qtot_global_annual_1971_2000.nc b/example/input/diagnostics/vic_watch_hist_nosoc_co2_qtot_global_annual_1971_2000.nc
diff --git a/example/input/diagnostics/wbm_qestimates.csv b/example/input/diagnostics/wbm_qestimates.csv
diff --git a/example/input/diagnostics/wbmc_qestimates.csv b/example/input/diagnostics/wbmc_qestimates.csv
diff --git a/example/input/hydropower_actual/DRT_half_SourceArea_globe_float.txt b/example/input/hydropower_actual/DRT_half_SourceArea_globe_float.txt
diff --git a/example/input/hydropower_actual/gridData.csv b/example/input/hydropower_actual/gridData.csv
diff --git a/example/input/hydropower_actual/resData_1593.csv b/example/input/hydropower_actual/resData_1593.csv
diff --git a/example/input/hydropower_actual/rule_curves_1593.npy b/example/input/hydropower_actual/rule_curves_1593.npy
diff --git a/example/input/hydropower_actual/simulated_cap_by_country.csv b/example/input/hydropower_actual/simulated_cap_by_country.csv
diff --git a/example/input/pet/penman_monteith/elev.npy b/example/input/pet/penman_monteith/elev.npy
diff --git a/example/input/pet/penman_monteith/gcam_ET_para.csv b/example/input/pet/penman_monteith/gcam_ET_para.csv
diff --git a/example/input/pet/penman_monteith/gcam_albedo.csv b/example/input/pet/penman_monteith/gcam_albedo.csv
diff --git a/example/input/pet/penman_monteith/gcam_lai.csv b/example/input/pet/penman_monteith/gcam_lai.csv
diff --git a/example/input/pet/penman_monteith/gcam_laimax.csv b/example/input/pet/penman_monteith/gcam_laimax.csv
diff --git a/example/input/pet/penman_monteith/gcam_laimin.csv b/example/input/pet/penman_monteith/gcam_laimin.csv
diff --git a/example/input/pet/penman_monteith/lucc1901_2010_lump.npy b/example/input/pet/penman_monteith/lucc1901_2010_lump.npy
diff --git a/example/input/pet/penman_monteith/rhs_watch_monthly_percent_1971_2001.npy b/example/input/pet/penman_monteith/rhs_watch_monthly_percent_1971_2001.npy
diff --git a/example/input/pet/penman_monteith/rlds_watch_monthly_wperm2_1971_2001.npy b/example/input/pet/penman_monteith/rlds_watch_monthly_wperm2_1971_2001.npy
diff --git a/example/input/pet/penman_monteith/rsds_watch_monthly_wperm2_1971_2001.npy b/example/input/pet/penman_monteith/rsds_watch_monthly_wperm2_1971_2001.npy
diff --git a/example/input/pet/penman_monteith/tas_watch_monthly_degc_1971_2001.npy b/example/input/pet/penman_monteith/tas_watch_monthly_degc_1971_2001.npy
diff --git a/example/input/pet/penman_monteith/tasmin_watch_monthly_degc_1971_2001.npy b/example/input/pet/penman_monteith/tasmin_watch_monthly_degc_1971_2001.npy
diff --git a/example/input/pet/penman_monteith/wind_watch_monthly_mpers_1971_2001.npy b/example/input/pet/penman_monteith/wind_watch_monthly_mpers_1971_2001.npy
diff --git a/example/input/reference/BasinNames235.txt b/example/input/reference/BasinNames235.txt
diff --git a/example/input/reference/Grid_Areas_ID.csv b/example/input/reference/Grid_Areas_ID.csv
diff --git a/example/input/reference/Rgn32Names.csv b/example/input/reference/Rgn32Names.csv
diff --git a/example/input/reference/basin.csv b/example/input/reference/basin.csv
diff --git a/example/input/reference/coordinates.csv b/example/input/reference/coordinates.csv
diff --git a/example/input/reference/country-names.csv b/example/input/reference/country-names.csv
diff --git a/example/input/reference/country.csv b/example/input/reference/country.csv
diff --git a/example/input/reference/region32_grids.csv b/example/input/reference/region32_grids.csv
diff --git a/example/input/routing/mrtm/DRT_half_FDISTANCE_globe.txt b/example/input/routing/mrtm/DRT_half_FDISTANCE_globe.txt
diff --git a/example/input/routing/mrtm/DRT_half_FDR_globe_bystr50.txt b/example/input/routing/mrtm/DRT_half_FDR_globe_bystr50.txt
diff --git a/example/input/routing/mrtm/velocity_half_degree.npy b/example/input/routing/mrtm/velocity_half_degree.npy
diff --git a/example/input/runoff/abcd/pars_watch_1971_1990_decadal_lc.npy b/example/input/runoff/abcd/pars_watch_1971_1990_decadal_lc.npy
diff --git a/example/input/runoff/gwam/Addit_water421.csv b/example/input/runoff/gwam/Addit_water421.csv
diff --git a/example/input/runoff/gwam/Lakes_wo_casp.csv b/example/input/runoff/gwam/Lakes_wo_casp.csv
diff --git a/example/input/runoff/gwam/soil_moisture.csv b/example/input/runoff/gwam/soil_moisture.csv
diff --git a/...put/pm_abcd_mrtm_watch_1971_2001/Basin_runoff_km3peryear_pm_abcd_mrtm_watch_1971_2001.csv b/...put/pm_abcd_mrtm_watch_1971_2001/Basin_runoff_km3peryear_pm_abcd_mrtm_watch_1971_2001.csv
diff --git a/...t/pm_abcd_mrtm_watch_1971_2001/Country_runoff_km3peryear_pm_abcd_mrtm_watch_1971_2001.csv b/...t/pm_abcd_mrtm_watch_1971_2001/Country_runoff_km3peryear_pm_abcd_mrtm_watch_1971_2001.csv
diff --git a/example/output/pm_abcd_mrtm_watch_1971_2001/Diagnostics_Runoff_Basin_Scale_km3peryr.csv b/example/output/pm_abcd_mrtm_watch_1971_2001/Diagnostics_Runoff_Basin_Scale_km3peryr.csv
diff --git a/example/output/pm_abcd_mrtm_watch_1971_2001/Diagnostics_Runoff_Country_Scale_km3peryr.csv b/example/output/pm_abcd_mrtm_watch_1971_2001/Diagnostics_Runoff_Country_Scale_km3peryr.csv
diff --git a/example/output/pm_abcd_mrtm_watch_1971_2001/Diagnostics_Runoff_Region_Scale_km3peryr.csv b/example/output/pm_abcd_mrtm_watch_1971_2001/Diagnostics_Runoff_Region_Scale_km3peryr.csv
diff --git a/...m_abcd_mrtm_watch_1971_2001/GCAMRegion_runoff_km3peryear_pm_abcd_mrtm_watch_1971_2001.csv b/...m_abcd_mrtm_watch_1971_2001/GCAMRegion_runoff_km3peryear_pm_abcd_mrtm_watch_1971_2001.csv
diff --git a/...t/pm_abcd_mrtm_watch_1971_2001/accessible_water_km3peryr_pm_abcd_mrtm_watch_1971_2001.csv b/...t/pm_abcd_mrtm_watch_1971_2001/accessible_water_km3peryr_pm_abcd_mrtm_watch_1971_2001.csv
diff --git a/...mrtm_watch_1971_2001/actual_hydro_by_gcam_region_EJperyr_pm_abcd_mrtm_watch_1971_2001.csv b/...mrtm_watch_1971_2001/actual_hydro_by_gcam_region_EJperyr_pm_abcd_mrtm_watch_1971_2001.csv
diff --git a/example/output/pm_abcd_mrtm_watch_1971_2001/aet_km3peryear_pm_abcd_mrtm_watch_1971_2001.csv b/example/output/pm_abcd_mrtm_watch_1971_2001/aet_km3peryear_pm_abcd_mrtm_watch_1971_2001.csv
diff --git a/...e/output/pm_abcd_mrtm_watch_1971_2001/avgchflow_m3persec_pm_abcd_mrtm_watch_1971_2001.csv b/...e/output/pm_abcd_mrtm_watch_1971_2001/avgchflow_m3persec_pm_abcd_mrtm_watch_1971_2001.csv
diff --git a/example/output/pm_abcd_mrtm_watch_1971_2001/logfile.log b/example/output/pm_abcd_mrtm_watch_1971_2001/logfile.log
diff --git a/example/output/pm_abcd_mrtm_watch_1971_2001/pet_km3peryear_pm_abcd_mrtm_watch_1971_2001.csv b/example/output/pm_abcd_mrtm_watch_1971_2001/pet_km3peryear_pm_abcd_mrtm_watch_1971_2001.csv
diff --git a/example/output/pm_abcd_mrtm_watch_1971_2001/q_km3peryear_pm_abcd_mrtm_watch_1971_2001.csv b/example/output/pm_abcd_mrtm_watch_1971_2001/q_km3peryear_pm_abcd_mrtm_watch_1971_2001.csv
diff --git a/...put/pm_abcd_mrtm_watch_1971_2001/soilmoisture_km3peryear_pm_abcd_mrtm_watch_1971_2001.csv b/...put/pm_abcd_mrtm_watch_1971_2001/soilmoisture_km3peryear_pm_abcd_mrtm_watch_1971_2001.csv
diff --git a/...ch_1971_2001/tech_expliot_hyd_pot_by_gcam_region_EJperyr_pm_abcd_mrtm_watch_1971_2001.csv b/...ch_1971_2001/tech_expliot_hyd_pot_by_gcam_region_EJperyr_pm_abcd_mrtm_watch_1971_2001.csv
diff --git a/...tm_watch_1971_2001/tech_hydro_pot_by_gcam_region_EJperyr_pm_abcd_mrtm_watch_1971_2001.csv b/...tm_watch_1971_2001/tech_hydro_pot_by_gcam_region_EJperyr_pm_abcd_mrtm_watch_1971_2001.csv