Merge pull request #150 from jmccreight/feat_pywatershed

Rename to pywatershed

.github/workflows/ci.yaml

@@ -9,7 +9,7 @@ on:
 
 jobs:
 
-  pynhm_setup:
+  pyws_setup:
     name: standard installation
     runs-on: ubuntu-latest
     strategy:
@@ -23,7 +23,7 @@ jobs:
 
       - name: Set environment variables
         run: |
-          echo "PYNHM_FORTRAN=true" >> $GITHUB_ENV
+          echo "PYWS_FORTRAN=true" >> $GITHUB_ENV
           echo 'SETUPTOOLS_ENABLE_FEATURES="legacy-editable"' >> $GITHUB_ENV
 
       - name: Setup Python
@@ -42,14 +42,14 @@ jobs:
 
       - name: Print pyhmn version
         run: |
-          python -c "import pynhm; print(pynhm.__version__)"
+          python -c "import pywatershed; print(pywatershed.__version__)"
 
-      - name: Build pynhm, check dist outputs
+      - name: Build pywatershed, check dist outputs
         run: |
           python -m build
           twine check --strict dist/*
 
-  pynhm_lint:
+  pyws_lint:
     name: linting
     runs-on: ubuntu-latest
     strategy:
@@ -81,26 +81,26 @@ jobs:
           echo "if isort check fails update isort using"
           echo "  pip install isort --upgrade"
           echo "and run"
-          echo "  isort ./pynhm ./autotest"
+          echo "  isort ./pywatershed ./autotest"
           echo "and then commit the changes."
-          isort --check --diff ./pynhm
+          isort --check --diff ./pywatershed
 
       - name: Run black
         run: |
           echo "if black check fails update black using"
           echo "  pip install black --upgrade"
           echo "and run"
-          echo "  black ./pynhm ./autotest"
+          echo "  black ./pywatershed ./autotest"
           echo "and then commit the changes."
-          black --check --diff ./pynhm
+          black --check --diff ./pywatershed
 
       - name: Run flake8
         run: |
-          flake8 --count --show-source --exit-zero ./pynhm ./autotest
+          flake8 --count --show-source --exit-zero ./pywatershed ./autotest
 
       - name: Run pylint
         run: |
-          pylint --jobs=2 --errors-only --exit-zero ./pynhm ./autotest
+          pylint --jobs=2 --errors-only --exit-zero ./pywatershed ./autotest
 
   test:
     name: ${{ matrix.os}} py${{ matrix.python-version }}
@@ -120,7 +120,7 @@ jobs:
       - name: Set environment variables
         run: |
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
-          echo "PYNHM_FORTRAN=true" >> $GITHUB_ENV
+          echo "PYWS_FORTRAN=true" >> $GITHUB_ENV
           echo 'SETUPTOOLS_ENABLE_FEATURES="legacy-editable"' >> $GITHUB_ENV
           cat .mf6_ci_ref_remote  >> $GITHUB_ENV
 
@@ -166,7 +166,7 @@ jobs:
         run: |
           python update_flopy.py
 
-      - name: Install pynhm
+      - name: Install pywatershed
         run: |
           pip install .
 
@@ -193,7 +193,7 @@ jobs:
           -n=auto
           --durations=0
           --all_domains
-          --cov=pynhm
+          --cov=pywatershed
           --cov-report=xml
           --junitxml=pytest.xml
 

.github/workflows/ci_examples.yaml

@@ -35,7 +35,7 @@ jobs:
       - name: Download GIS files
         working-directory: examples
         run: |
-          curl -LO https://github.com/EC-USGS/pynhm/releases/download/v2022.0.1/pynhm_gis.zip
+          curl -LO https://github.com/EC-USGS/pywatershed/releases/download/v2022.0.1/pynhm_gis.zip
           unzip pynhm_gis.zip
 
       - name: Set environment variables
@@ -47,7 +47,7 @@ jobs:
         uses: mamba-org/provision-with-micromamba@main
         with:
           environment-file: examples/examples_env.yml
-          environment-name: pynhm_nb
+          environment-name: pyws_nb
           cache-env: true
           # cache-env-key: "${{runner.os}}-${{runner.arch}}-py${{matrix.python-version}}-${{env.TODAY}}"
 
@@ -70,9 +70,9 @@ jobs:
           echo -------
           pip list
 
-      - name: Import pynhm
+      - name: Import pywatershed
         run: |
-          python -c "import pynhm"
+          python -c "import pywatershed"
 
       - name: Run tests
         working-directory: autotest_exs

.gitignore

@@ -59,6 +59,7 @@ generated/
 
 # gis data
 examples/pynhm_gis
+examples/pywatershed_gis
 examples/model_loop_custom_output
 
 # graphics

README.md

@@ -1,9 +1,9 @@
-# pynhm
-[![ci-badge](https://github.com/ec-usgs/pynhm/workflows/CI/badge.svg?branch=main)](https://github.com/ec-usgs/pynhm/actions?query=workflow%3ACI)
-[![codecov-badge](https://codecov.io/gh/ec-usgs/pynhm/branch/main/graph/badge.svg)](https://codecov.io/gh/ec-usgs/pynhm)
-[![Documentation Status](https://readthedocs.org/projects/pynhm/badge/?version=latest)](https://pynhm.readthedocs.io/en/latest/?badge=latest)
+# pywatershed
+[![ci-badge](https://github.com/ec-usgs/pywatershed/workflows/CI/badge.svg?branch=main)](https://github.com/ec-usgs/pywatershed/actions?query=workflow%3ACI)
+[![codecov-badge](https://codecov.io/gh/ec-usgs/pywatershed/branch/main/graph/badge.svg)](https://codecov.io/gh/ec-usgs/pywatershed)
+[![Documentation Status](https://readthedocs.org/projects/pywatershed/badge/?version=latest)](https://pywatershed.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">)
+[//]: # (<img src="https://raw.githubusercontent.com/ec-usgs/pywatershed/main/resources/images/prms_flow.png" alt="prms_flow" style="width:50;height:20">)
 
 Purpose
 =========
@@ -26,7 +26,7 @@ Goals for EC Watershed Modeling:
   * Redesign PRMS to be more modern and flexible
   * Prioritize process representations in the current National Hydrological Model (NHM) based on PRMS 5.2.1
 
-Prototype an EC watershed model: "pynhm"
+Prototype an EC watershed model: "pywatershed"
   * Redesign PRMS quickly in python
   * Couple to MF6 via BMI/XMI interface (Hughes et al, 2021; Hutton et al, 2020)
   * Establish a prototyping ground for EC codes that couples to the compiled framework: low cost proof of concepts (at the price of potentially less computational performance)
@@ -45,7 +45,7 @@ instructions.
 
 To install the software you will need Python >= 3.8. We recommend installing
 the python package dependencies using anaconda or miniconda. Most users will
-likely want to create the `pynhm_nb` conda environment by running
+likely want to create the `pyws_nb` conda environment by running
 
 ```conda env create -f examples/examples_env.yml```.
 
@@ -56,15 +56,15 @@ One could also do
 but this is not guaranteed.
 
 Once the environment is established, activate the environment and install
-pynhm
+pywatershed
 
-`conda activate pynhm_nb; cd pynhm; pip install .`
+`conda activate pyws_nb; cd pywatershed; pip install .`
 
 If you would like to compile the fortran computational kernels for
 certain physical process representations (not required), you'll need a fortran
 compiler and you will run
 
-`export PYNHM_FORTRAN=true; cd pynhm;  pip install .`
+`export PYWS_FORTRAN=true; cd pywatershed;  pip install .`
 
 See Developer Requirements below for more details.
 
@@ -82,17 +82,17 @@ two applications:
 
   1. Compiling and running C/Fortran PRMS code to generate testing/verification data
   2. Compiling (installing) and running fortran backends/kernels for some hydrological
-     process representations in pynhm
+     process representations in pywatershed
 
 On Apple Silicon, the PRMS source code is only currently known to compile with intel while
-the fortran kernels in pynhm only compile with gnu.
+the fortran kernels in pywatershed only compile with gnu.
 
 Python >= 3.8 is required. Three different python environments are specified within the repository.
 These are:
 
-* Minimal (for developing/testing), 'pynhm': ci/requirements/environment.yml
-* Notebooks (~= minimal + jupyter), 'pynhm_nb': examples/examples_env.yml
-* Documentation (only if you want to build the documentation), 'pynhm-docs': ci/requirements/doc.yml
+* Minimal (for developing/testing), 'pyws': ci/requirements/environment.yml
+* Notebooks (~= minimal + jupyter), 'pyws_nb': examples/examples_env.yml
+* Documentation (only if you want to build the documentation), 'pyws-docs': ci/requirements/doc.yml
 
 We recommend (because we test it in CI) using anacoda or miniconda to establish these environments
 with the following commands
@@ -112,9 +112,9 @@ There are also .txt equivalents that can be used for installing from pip, like s
 though these are not comprehensive installs as with conda and not tested.
 
 Once the python environment and dependencies are established and activated (`conda activate env_of_choice`),
-pynhm is installed for development into that environment with the following command
+pywatershed is installed for development into that environment with the following command
 
-`cd pynhm; pip install -e .`
+`cd pywatershed; pip install -e .`
 
 The numpy extension F2PY is used to provide fortran compiled kernels of core calculations to boost
 performance. F2PY is documented [within numpy](https://numpy.org/doc/stable/f2py/index.html). This
@@ -126,8 +126,8 @@ installation is achieved by the following code:
 export SETUPTOOLS_ENABLE_FEATURES="legacy-editable"
 export CC=path/to/gcc  # for example
 export FC=path/to/gfortran  # for example
-export PYNHM_FORTRAN=true
-cd path/to/pynhm
+export PYWS_FORTRAN=true
+cd path/to/pywatershed
 pip install -e .
 ```
 
@@ -137,15 +137,15 @@ To run the tests, we first need to generate the test data. This consists of runn
 and then converting the output to netcdf:
 
 ```
-cd path/to/pynhm/test_data/scripts
+cd path/to/pywatershed/test_data/scripts
 pytest -v -n=4 test_run_domains.py
 pytest -v -n=8 test_nc_domains.py
 ```
 
 Finally, run the tests themselves,
 
 ```
-cd path/to/pynhm/autotest
+cd path/to/pywatershed/autotest
 pytest -v -n=8
 ```
 
@@ -164,9 +164,9 @@ be verified moving ahead in time.
 Example Notebooks
 ==================
 Jupyter notebooks containing examples are found in the
-[examples/](https://github.com/EC-USGS/pynhm/tree/main/examples) directory. Numbered notebooks are tested.
+[examples/](https://github.com/EC-USGS/pywatershed/tree/main/examples) directory. Numbered notebooks are tested.
 Notebooks 00 and 01 walk the user through the setting the python environment and running the software tests.
-Notebook 02 demonstrates modeling with pynhm. Non-numbered notebooks cover additional topics. These notebooks
+Notebook 02 demonstrates modeling with pywatershed. Non-numbered notebooks cover additional topics. These notebooks
 are note yet covered by testing and so may be expected to have some issues until they are added to testing.
 
 
@@ -176,13 +176,13 @@ The contents of directories at this level is described. Therein you may discover
 
 ```
 .github/    Github actions for deploying continuous integration (CI)
-autotest/   pynhm package testing using pytest
+autotest/   pywatershed 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
+pywatershed/      Package source
 reference/  Ancillary materials for development
 resources/  Static stuff like images
 test_data/  Data used for automated testing

autotest/README.md

@@ -11,7 +11,7 @@ Pytest options can be explored via `pytest --help`.
 
 ## Developer
 
-This is how the pynhm package tests itself.
+This is how the pywatershed package tests itself.
 
 The test suite consists both
 	* stand alone tests, and
@@ -40,9 +40,9 @@ inputs (e.g. CBH forcing files, parameter files), static or reference model
 output (from PRMS/NHM), and the answers to domain tests.
 
 Examples of `domain_yaml` files can be found in, for example, in
-`pynhm/test_data/drb_2yr/drb_2yr.yaml`
+`pywatershed/test_data/drb_2yr/drb_2yr.yaml`
 and
-`pynhm/test_data/conus_2yr/conus_2yr.yaml`.
+`pywatershed/test_data/conus_2yr/conus_2yr.yaml`.
 
 
 ### Domain inputs

autotest/test_atmosphere.py

@@ -3,10 +3,10 @@
 import numpy as np
 import pytest
 
-from pynhm.atmosphere.PRMSAtmosphere import PRMSAtmosphere
-from pynhm.base.adapter import adapter_factory
-from pynhm.base.control import Control
-from pynhm.parameters import PrmsParameters
+from pywatershed.atmosphere.PRMSAtmosphere import PRMSAtmosphere
+from pywatershed.base.adapter import adapter_factory
+from pywatershed.base.control import Control
+from pywatershed.parameters import PrmsParameters
 
 
 @pytest.fixture(scope="function")
@@ -104,7 +104,7 @@ def test_init(self, domain, control, tmp_path):
                     print(f"time step {istep}")
                     print(f"output variable {key}")
                     print(f"prms   {a1.min()}    {a1.max()}")
-                    print(f"pynhm  {a2.min()}    {a2.max()}")
+                    print(f"pywatershed  {a2.min()}    {a2.max()}")
                     print(f"diff   {diffmin}  {diffmax}")
                     print(f"absdiffmax  {absdiffmax}")
                     print(f"wh_absdiffmax  {wh_absdiffmax}")
@@ -113,4 +113,4 @@ def test_init(self, domain, control, tmp_path):
         atm.finalize()
 
         if not all_success:
-            raise Exception("pynhm results do not match prms results")
+            raise Exception("pywatershed results do not match prms results")

autotest/test_base.py

@@ -1,6 +1,6 @@
 import pytest
 
-from pynhm.base.accessor import Accessor
+from pywatershed.base.accessor import Accessor
 
 
 class TestAccessor:

autotest/test_budget.py

@@ -1,8 +1,8 @@
 import numpy as np
 import pytest
 
-from pynhm.base.budget import Budget
-from pynhm.base.control import Control
+from pywatershed.base.budget import Budget
+from pywatershed.base.control import Control
 
 # TODO
 # * Test restart more robustly