Merge pull request #331 from EC-USGS/v2.0.2

Release 2.0.2

Author: jmccreight

.github/workflows/ci.yaml

@@ -13,13 +13,12 @@ on:
     inputs:
       debug_enabled:
         type: boolean
-        description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
+        description: "Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)"
         required: false
         default: false
 
 jobs:
-
-  pyws_setup:
+  pws_install:
     name: standard installation
     runs-on: ubuntu-latest
     strategy:
@@ -39,13 +38,48 @@ jobs:
       - name: Upgrade pip and install build and twine
         run: |
           python -m pip install --upgrade pip
-          pip install wheel build 'twine<5.0.0' 'importlib_metadata<=7.0.1' 'setuptools<=72.2.0' 'numpy<2.0'
+          pip install wheel build twine importlib_metadata setuptools numpy
 
-      - name: Base installation
+      - name: Standard installation
         run: |
           pip --verbose install .
 
-      - name: Print pyhmn version
+      - name: Print pws version
+        run: |
+          python -c "import pywatershed; print(pywatershed.__version__)"
+
+      - name: Build pywatershed, check dist outputs
+        run: |
+          python -m build
+          twine check --strict dist/*
+
+  pws_editable_install:
+    name: editable installation
+    runs-on: macos-latest
+    strategy:
+      fail-fast: false
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Upgrade pip and install build and twine
+        run: |
+          python -m pip install --upgrade pip
+          pip install wheel build twine importlib_metadata setuptools numpy
+
+      - name: Editable installation
+        run: |
+          pip --verbose install -e .
+
+      - name: Print pws version
         run: |
           python -c "import pywatershed; print(pywatershed.__version__)"
 
@@ -97,11 +131,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ "ubuntu-latest", "macos-latest", "windows-latest" ]
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         python-version: ["3.10", "3.11"]
 
     steps:
-
       - name: Free Disk Space (Ubuntu)
         if: runner.os == 'Linux'
         uses: jlumbroso/free-disk-space@main
@@ -151,7 +184,7 @@ jobs:
       - name: Install Dependencies via Micromamba
         uses: mamba-org/[email protected]
         with:
-          micromamba-version: '1.5.10-0'
+          micromamba-version: "1.5.10-0"
           log-level: debug
           environment-file: environment.yml
           cache-environment: true
@@ -318,7 +351,6 @@ jobs:
           --cov-report=xml
           --junitxml=pytest_drb_2yr_no_dprst.xml
 
-
       - name: ucb_2yr_nhm - generate and manage test data
         working-directory: autotest
         run: |
@@ -358,7 +390,7 @@ jobs:
       - name: Upload code coverage to Codecov
         uses: codecov/codecov-action@v3
         with:
-          file: ./autotest/coverage.xml  # should be just the ucb result
+          file: ./autotest/coverage.xml # should be just the ucb result
           # flags: unittests
           env_vars: RUNNER_OS,PYTHON_VERSION
           # name: codecov-umbrella

.github/workflows/ci_examples.yaml

@@ -11,7 +11,6 @@ on:
       - "!v[0-9]+.[0-9]+.[0-9]+*"
 
 jobs:
-
   test:
     name: ${{ matrix.os}} py${{ matrix.python-version }}
 
@@ -24,8 +23,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ "ubuntu-latest" ]
-        python-version: [ "3.10"]
+        os: ["ubuntu-latest"]
+        python-version: ["3.10"]
 
     steps:
       - name: Checkout repo
@@ -37,15 +36,10 @@ jobs:
           compiler: gcc
           version: 11
 
-      - name: Set environment variables
-        run: |
-          echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
-          echo "SETUPTOOLS_ENABLE_FEATURES=legacy-editable" >> $GITHUB_ENV
-
       - name: Setup micromamba
         uses: mamba-org/[email protected]
         with:
-          micromamba-version: '1.5.10-0'
+          micromamba-version: "1.5.10-0"
           environment-file: environment_w_jupyter.yml
           cache-environment: true
           cache-downloads: true

README.md

@@ -15,12 +15,8 @@
 
 [![DOI:10.5066/P13EWPEV](https://img.shields.io/badge/DOI-10.5066/P13EWPEV-b4a9fe.svg)](https://doi.org/10.5066/P13EWPEV)
 
-[![WholeTale](https://raw.githubusercontent.com/whole-tale/wt-design-docs/master/badges/wholetale-explore.svg)](https://dashboard.wholetale.org/run/64ae29e8a887f48b9f173678?tab=metadata)
-
-
 <!-- START doctoc generated TOC please keep comment here to allow auto update -->
 <!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
-**Table of Contents**
 
 - [About](#about)
 - [Installation](#installation)
@@ -51,34 +47,34 @@ of well-established hydrologic process modeling.
 
 For more information on the goals and status of pywatershed, please see the [pywatershed docs](https://pywatershed.readthedocs.io/).
 
-
 ## Installation
 
 `pywatershed` uses Python 3.10 or 3.11.
 
 The `pywatershed` package is [available on
 PyPI](https://pypi.org/project/pywatershed/) but installation of all
 dependencies sets (lint, test, optional, doc, and all) may not be reliable on
-all platforms. 
+all platforms.
 
 The `pywatershed` package is [available on
 conda-forge](https://anaconda.org/conda-forge/pywatershed). The installation
 is the quickest way to get up and running by provides only the minimal set of
 dependencies (not including Jupyter nor all packages needed for running the
-example notebooks, also not suitable for development purposes). 
+example notebooks, also not suitable for development purposes).
 
 We recommend the following installation procedures to get fully-functional
 environments for running `pywatershed` and its example notebooks. We strongly
 recommend using [Mamba](https://mamba.readthedocs.io/en/latest/)to first
 instal dependencies from the `environment_y_jupyter.yml` file in the
 repository before installing `pywatershed` itself. Mamba will be much faster
-than Ananconda (but the conda command could also be used). 
+than Ananconda (but the conda command could also be used).
 
-If you wish to use the stable release, you will use `main` in place of 
+If you wish to use the stable release, you will use `main` in place of
 `<branch>` in the following commands. If you want to follow development, you'll
 use `develop` instead.
 
 Without using `git` (directly), you may:
+
 ```
 curl -L -O https://raw.githubusercontent.com/EC-USGS/pywatershed/<branch>/environment_w_jupyter.yml
 mamba env create -f environment_w_jupyter.yml
@@ -97,53 +93,35 @@ pip install -e .
 ```
 
 (If you want to name the environment other than the default `pws`, use the
-command 
+command
 `mamba env update --name your_env_name --file environment_w_jupyter.yml --prune`
 you will also need to activate this environment by name.)
 
-
-We install the `environment_w_jupyter.yml` to provide all known dependencies 
-including those for running the example notebooks. (The `environment.yml` 
-does not contain Jupyter or JupyterLab because this interferes with installation
-on WholeTale, see Getting Started section below.)
-
+We install the `environment_w_jupyter.yml` to provide all known dependencies
+including those for running the example notebooks.
 
 ## Getting started / Example notebooks
 
 Please note that you can browse the API reference, developer info, and index
-in the [pywatershed docs]((https://pywatershed.readthedocs.io/)). But
-*the best way to get started with pywatershed is to dive into the example
-notebooks*.
+in the [pywatershed docs](<(https://pywatershed.readthedocs.io/)>). But
+_the best way to get started with pywatershed is to dive into the example
+notebooks_.
 
 For introductory example notebooks, look in the
 [`examples/`](https://github.com/EC-USGS/pywatershed/tree/main/examples>)
 directory in the repository. Numbered starting at 00, these are meant to be
 completed in order. Numbered starting at 00, these are meant to be completed
-in order. Notebook outputs are not saved in Github. But you can run these
-notebooks locally or using WholeTale (an NSF funded project supporting logins
-from many institutions, free but sign-up or log-in required)
-where the pywatershed environment is all ready to go:
-
-[![WholeTale](https://raw.githubusercontent.com/whole-tale/wt-design-docs/master/badges/wholetale-explore.svg)](https://dashboard.wholetale.org)
-
-  * [Run latest release in WholeTale](https://dashboard.wholetale.org/run/64ae29e8a887f48b9f173678?tab=metadata)
-  * [Run the develop branch in WholeTale](https://dashboard.wholetale.org/run/64ae25c3a887f48b9f1735c8?tab=metadata)
-
-WholeTale will give you a JupyterLab running in the root of this
-repository. You can navigate to `examples/` and then open and run the notebooks
-of your choice.  The develop container may require the user to update the
-repository (`git pull origin`) to stay current with development.
+in order. Notebook outputs are not saved in Github.
 
 Non-numbered notebooks in `examples/` cover additional topics. These
 notebooks are not yet covered by testing and you may encounter some
 issues. In `examples/developer/` there are notebooks of interest to
 developers who may want to learn about running the software tests.
 
-
 ## Community engagement
 
 We value your feedback! Please use [discussions](https://github.com/EC-USGS/pywatershed/discussions)
-or [issues](https://github.com/EC-USGS/pywatershed/issues) on Github. 
+or [issues](https://github.com/EC-USGS/pywatershed/issues) on Github.
 For more in-depth contributions, please start by reading over
 the pywatershed
 [DEVELOPER.md](https://github.com/EC-USGS/pywatershed/blob/develop/DEVELOPER.md) and
@@ -164,4 +142,4 @@ software as needed pursuant to further analysis and review. No warranty, express
 is made by the USGS or the U.S. Government as to the functionality of the software and related
 material nor shall the fact of release constitute any such warranty. Furthermore, the software
 is released on condition that neither the USGS nor the U.S. Government shall be held liable
-for any damages resulting from its authorized or unauthorized use.
+for any damages resulting from its authorized or unauthorized use.

autotest/ci_local.sh

@@ -89,7 +89,7 @@ if [ ! -z "${h}" ]; then
 
     exit 0
 fi
-    
+
 echo ""
 echo ""
 
@@ -119,8 +119,7 @@ if [ -z "${i}" ]; then
 
     ## name: Upgrade pip and install build and twine
     python -m pip install --upgrade pip || exit 1
-    pip install wheel build 'twine<5.0.0' 'importlib_metadata<=7.0.1' || exit 1
-
+    pip install wheel build twine importlib_metadata || exit 1
     ## name: Base installation
     pip --verbose install . || exit 1
 
@@ -194,8 +193,8 @@ if [ -z "${m}" ]; then
     # mamba create -y --name $env_name || exit 1
     # mamba env update --name $env_name --file $env_file --prune  || exit 1
 
-    # conda activate $env_name
-    source /Users/jmccreight/mambaforge/bin/activate $env_name
+    conda_dir=`dirname $CONDA_EXE`
+    source $conda_dir/activate $env_name  || exit 1
     # only necessary the first time
     # meson setup --prefix=$(pwd) --libdir=bin builddir
     meson install -C builddir
@@ -437,17 +436,18 @@ if [ -z "${t}" ]; then
            --control_pattern=nhm.control \
            --durations=0 || exit 1
    fi
-       
+
 fi
 
 if [ -z "${i}" ]; then
+    cd $start_dir || exit 3
     # If install was done, put the install back to its original, editable state.
     # Do it here so the tests use the test install if it is done.
     pip uninstall -y pywatershed || exit 1
     cd .. || exit 1
-    pip install -e . || exit 1
+    pip install -e . || exit 2
 
-    cd $start_dir || exit 1
+    cd $start_dir || exit 3
 fi
 
 exit 0

autotest/generate_test_data.py

@@ -205,6 +205,13 @@ def main():
             "convert_prms_output_to_nc.py",
         ]
 
+    # do NOT run in parallel
+    conv_final_arg_list = arg_list + [
+        "-vv",
+        "-n=0",
+        "convert_final_prms_output_to_nc.py",
+    ]
+
     retcode_run = pytest.main(run_arg_list)
     if retcode_run != pytest.ExitCode.OK:
         print("Running PRMS domains failed.")
@@ -216,6 +223,12 @@ def main():
         print("\nConverting PRMS output to NetCDF failed.")
         sys.exit(retcode_run.value)
 
+    print("\nConverting final PRMS output to NetCDF ...")
+    retcode_conv = pytest.main(conv_final_arg_list)
+    if retcode_conv != pytest.ExitCode.OK:
+        print("\nConverting final PRMS output to NetCDF failed.")
+        sys.exit(retcode_run.value)
+
     for ss in simulations:
         ss_pl = pl.Path(ss)
         domain_tag = ss_pl.parent.name

autotest/test_netcdf_read.py

@@ -12,9 +12,9 @@ def test_netcdf(simulation):
 
     for idx in range(ntimes):
         arr = nc_data.advance(variable)
-        assert (
-            arr.shape == shape
-        ), f"shape is {arr.shape} but should be {shape}"
+        assert arr.shape == shape, (
+            f"shape is {arr.shape} but should be {shape}"
+        )
 
     shape = (ntimes, nhru)
     arr = nc_data.get_data(variable)

autotest/test_preprocess_csv.py

@@ -26,9 +26,9 @@ def compare_netcdf(csv, nc_name):
         for idx, hru in enumerate(hrus):
             key = f"{variable}_{hru}"
             csv_data[:, idx] = np_data[key][:]
-        assert np.allclose(
-            nc_data, csv_data
-        ), f"comparision for {variable} is not close"
+        assert np.allclose(nc_data, csv_data), (
+            f"comparision for {variable} is not close"
+        )
 
     # close the netcdf file and return
     ds.close()