Merge pull request #53 from JGCRI/no-lfs

remove git lfs and travis
JGCRI · Apr 29, 2021 · bb956d6 · bb956d6
2 parents f743131 + 116e839
commit bb956d6
Show file tree

Hide file tree

Showing 77 changed files with 130 additions and 607 deletions.
diff --git a/.gitattributes b/.gitattributes
diff --git a/.travis.yml b/.travis.yml
diff --git a/README.md b/README.md
@@ -1,43 +1,52 @@
-[![DOI](https://zenodo.org/badge/88797535.svg)](https://zenodo.org/badge/latestdoi/88797535) [![Build Status](https://travis-ci.org/JGCRI/xanthos.svg?branch=master)](https://travis-ci.org/JGCRI/xanthos)
+[![DOI](https://zenodo.org/badge/88797535.svg)](https://zenodo.org/badge/latestdoi/88797535)
 
 # Xanthos
 Xanthos is an open-source hydrologic model, written in Python, designed to quantify and analyze global water availability. Xanthos simulates historical and future global water availability on a monthly time step at a spatial resolution of 0.5 geographic degrees. Xanthos was designed to be extensible and used by scientists that study global water supply and work with the Global Change Analysis Model (GCAM). Xanthos uses a user-defined configuration file to specify model inputs, outputs and parameters. Xanthos has been tested using actual global data sets and the model is able to provide historical observations and future estimates of renewable freshwater resources in the form of total runoff, average streamflow, potential evapotranspiration, actual evapotranspiration, accessible water, hydropower potential, and more.
 
-# Contact Us
-For questions, technical supporting and user contribution, please contact:
-
-Vernon, Chris R <Chris.Vernon@pnnl.gov>
-
-Li, Xinya <Xinya.Li@pnnl.gov>
-
-Link, Robert P <Robert.Link@pnnl.gov>
-
-Hejazi, Mohamad I <Mohamad.Hejazi@pnnl.gov>
+# Get Started with Xanthos
+Set up Xanthos using the following steps:
+1.  Install Xanthos from GitHub using:
+    ```bash
+    python -m pip install git+https://github.com/JGCRI/xanthos.git
+    ```
+2.  Download the example data using the following in a Python prompt:
+    ```python
+    import xanthos
+    
+    # the directory that you want to download and extract the example data to
+    data_dir = "<my data download location>"
+    
+    # download and unzip the package data to your local machine
+    xanthos.get_package_data(data_dir)
+    ```
+3.  Setup your configuration file (.ini).  Examples are located in the "example" directory that you just downloaded.  Be sure to change the following variables to represent the local path to your example data:  `RootDir`, `TempMinFile`, `PrecipitationFile`.
+4.  To run Xanthos:
+
+    ```python
+    import xanthos
+    
+    # the path and file name that my example configuration (.ini) file was downloaded to
+    config_file = '<path to my example config file>/pm_abcd_mrtm.ini'
+    
+    # run Xanthos 
+    xanthos.run_model(config_file)
+    ```
 
+# Setting up a Xanthos run
+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
 
-# 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`.
+# 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
 
 # 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.
 
 ![Xanthos to VIC](https://github.com/JGCRI/xanthos/blob/master/docs/xanthos2_to_vic_watch_basins.png)
 Figure:  Xanthos 2.0 performance when calibrated to the VIC model forced by WATCH observational climate data.  Each point represents the mean annual runoff for each of the 235 river basins in GCAM.
 
-# Get Started (Xanthos 2)
-Set up Xanthos using the following steps:
-1.  This repository uses the Git Large File Storage (LFS) extension (see https://git-lfs.github.com/ for details).  Please install GitLFS and run the following command before cloning if you do not already have Git LFS initialized:
-`git lfs install`.
-2.  Clone Xanthos into your desired location `git clone https://github.com/JGCRI/xanthos.git`.  Some Windows users have had better luck with `git lfs clone https://github.com/JGCRI/xanthos.git`
-3.  Make sure that `setuptools` is installed for your Python version.  This is what will be used to support the installation of the Xanthos package.
-4.  From the directory you cloned Xanthos into run `python setup.py install` .  This will install Xanthos as a Python package on your machine and install of the needed dependencies.  If installing in an HPC environment, a community user advised that it is best to install the anaconda environment before running the installation command.  HPC environments may also require the use of the `--user` flag in the install command to avoid permissions errors.
-5.  Setup your configuration file (.ini).  Examples are located in the "example" directory.  Be sure to change the root directory to the directory that holds your data (use the `xanthos/example` directory as an example).
-6. If running Xanthos from an IDE:  Be sure to include the path to your config file.  See the "xanthos/example/example.py" script as a reference.
-7. If running Xanthos from terminal:  Run model.py found in xanthos/xanthos/model.py passing the full path to the config file as the only argument. (e.g., `python model.py <dirpath>/config.ini`).
+# Contact Us
+For questions, technical supporting and user contribution, please contact:
 
-# Setting up a Xanthos run
-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
+Chris Vernon <chris.vernon@pnnl.gov>
 
-# 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
+Zarrar Khan <zarrar.khan@pnnl.gov>
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