Merge pull request #99 from jmccreight/feat(intro_usage)

Feat(intro usage) #1

Author: jmccreight

.gitignore

@@ -1,6 +1,7 @@
 # python
 build/
 *.egg-info/
+*.pkl
 
 # Jupyter Notebook
 .ipynb_checkpoints
@@ -32,7 +33,6 @@ prms_src/prms5.3.0/msvs/x64/Release/
 # meson build information
 prms_src/prms5.3.0/builddir/
 
-
 # prms binaries
 prms_src/prms5.2.1/bin
 prms_src/prms5.3.0/bin
@@ -55,4 +55,16 @@ autotest/.coverage
 autotest/temp
 
 # sphinx
-generated/
+generated/
+
+# gis data
+examples/pynhm_gis
+
+# graphics
+*.pnh
+*.svg
+*.jpg
+
+# compressed/tarballs
+*.gz
+*.zip

README.md

@@ -4,6 +4,44 @@
 [![Documentation Status](https://readthedocs.org/projects/pynhm/badge/?version=latest)](https://pynhm.readthedocs.io/en/latest/?badge=latest)
 <img src="https://raw.githubusercontent.com/ec-usgs/pynhm/main/resources/images/prms_flow.png" alt="prms_flow" style="width:50;height:20">
 
+Overview
+==========
+The contents of directories at this level is described. Therein you may discover another README.md for more information.
+
+```
+.github/    Github actions for deploying continuous integration (CI)
+autotest/   pynhm package testing using pytest
+bin/        PRMS executables distributed 
+ci/         Python environments for CI
+doc/        Package/code documentation source code
+examples/   How to use the package, mostly jupyter notebooks
+prms_src/   PRMS source used for generating executables in bin/
+pynhm/      Package source
+reference/  Ancillary materials for development
+resources/  Static stuff like images
+test_data/  Data used for automated testing
+```
+
+
+Requirements and Python Environments
+==========
+Git and python 3.8 - 3.10 are required. 
+
+We suggest installing the python dependencies using conda and the following yaml files. 
+
+* Minimal: ci/requirements/environment.yml
+* Documentation: ci/requirements/doc.yml
+* Notebooks: examples/examples_env.yml
+
+```conda env create -f env_of_choice.yml```
+
+More detailed installation instructions using conda can be found in `examples/00_python_virtual_env.ipynb`.
+
+There are aksi .txt equivalents that can be used for installing from pip, like so:
+
+```pip install -r env_of_choice.txt```
+
+
 Disclaimer
 ==========
 

autotest/test_model.py

@@ -181,18 +181,18 @@ def test_model(domain, control, processes, tmp_path):
         9: {
             "PRMSChannel": {
                 "seg_outflow": {
-                    "drb_2yr": 1306.7499262980173,
-                    "hru_1": 13.690165950142445,
-                    "ucb_2yr": 1694.4729153330018,
+                    "drb_2yr": 1152.9343097732165,
+                    "hru_1": 13.37194463307104,
+                    "ucb_2yr": 1694.47282087809,
                 },
             },
         },
         99: {
             "PRMSChannel": {
                 "seg_outflow": {
-                    "drb_2yr": 1818.6285476625615,
-                    "hru_1": 14.70413315830374,
-                    "ucb_2yr": 710.2513423457016,
+                    "drb_2yr": 1785.102361378249,
+                    "hru_1": 14.614890968139237,
+                    "ucb_2yr": 710.4918051193282,
                 },
             },
         },
@@ -233,6 +233,8 @@ def test_model(domain, control, processes, tmp_path):
                 if not success:
                     fail_prms_compare = True
                     all_success = False
+                    if failfast:
+                        assert False, "PRMS comparison failfast"
 
         # Regression checking
         if istep in regression_ans:
@@ -251,6 +253,8 @@ def test_model(domain, control, processes, tmp_path):
                         if not success:
                             fail_regression = True
                             all_success = False
+                            if failfast:
+                                assert False, "Regression failffast"
 
     # check at the end and error if one or more steps didn't pass
     if not all_success:

autotest/test_soilzone.py

@@ -37,6 +37,7 @@ def test_init(self, domain, control, tmp_path):
             "soil_lower",
             # "soil_lower_ratio",
             "soil_moist",
+            "soil_moist_prev",
             "soil_moist_tot",
             "soil_rechr",
             "soil_to_gw",

doc/api/atmosphere.rst

@@ -11,4 +11,4 @@ Atmospheric forcing models.
    :toctree: generated/
 
    PRMSSolarGeometry
-   PRMSBoundaryLayer
+   PRMSAtmosphere

doc/api/base.rst

@@ -13,7 +13,7 @@ Base classes for the modeling system.
    Accessor
    Adapter
    Control
-   Meta
+   meta
    Budget
    StorageUnit
    Model