Update to v2 pre-release

.github/workflows/ci.yaml

@@ -40,7 +40,6 @@ jobs:
         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'
-
       - name: Base installation
         run: |
           pip --verbose install .
@@ -124,8 +123,7 @@ jobs:
       - name: Set environment variables
         run: |
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
-          echo "PYWS_FORTRAN=true" >> $GITHUB_ENV
-          echo 'SETUPTOOLS_ENABLE_FEATURES="legacy-editable"' >> $GITHUB_ENV
+          echo "PYWS_FORTRAN=false" >> $GITHUB_ENV
           cat .mf6_ci_ref_remote  >> $GITHUB_ENV
 
       - name: Enforce MF6 ref and remote merge to main
@@ -150,8 +148,9 @@ jobs:
         run: .github/scripts/symlink_gfortran_mac.sh
 
       - name: Install Dependencies via Micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v1.9.0
         with:
+          micromamba-version: '1.5.10-0'
           log-level: debug
           environment-file: environment.yml
           cache-environment: true
@@ -191,7 +190,14 @@ jobs:
 
       - name: domainless - run tests not requiring domain data
         working-directory: autotest
-        run: pytest -m domainless -n=auto -vv
+        run: pytest
+          -m domainless
+          -n=auto
+          -vv
+          --durations=0
+          --cov=pywatershed
+          --cov-report=xml
+          --junitxml=pytest_domainless.xml
 
       - name: sagehen_5yr_no_cascades - generate and manage test data domain, run PRMS and convert csv output to NetCDF
         working-directory: autotest

.github/workflows/ci_examples.yaml

@@ -43,12 +43,30 @@ jobs:
           echo "SETUPTOOLS_ENABLE_FEATURES=legacy-editable" >> $GITHUB_ENV
 
       - name: Setup micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v1.9.0
         with:
+          micromamba-version: '1.5.10-0'
           environment-file: environment.yml
           cache-environment: true
           cache-downloads: true
 
+      - name: Checkout MODFLOW 6
+        uses: actions/checkout@v4
+        with:
+          repository: MODFLOW-USGS/modflow6
+          ref: develop
+          path: modflow6
+
+      - name: Update flopy MODFLOW 6 classes
+        working-directory: modflow6/autotest
+        run: |
+          python update_flopy.py
+
+      - name: Install mf6 nightly build binaries
+        uses: modflowpy/install-modflow-action@v1
+        with:
+          repo: modflow6-nightly-build
+
       - name: Install error reporter
         run: |
           pip install pytest-github-actions-annotate-failures

README.md

@@ -13,6 +13,8 @@
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/pywatershed/badges/version.svg)](https://anaconda.org/conda-forge/pywatershed)
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/pywatershed/badges/platforms.svg)](https://anaconda.org/conda-forge/pywatershed)
 
+[![DOI:10.5066/P9AVWA7Z](https://img.shields.io/badge/DOI-10.5066/P9AVWA7Z-b4a9fe.svg)](https://doi.org/10.5066/P9AVWA7Z)
+
 [![WholeTale](https://raw.githubusercontent.com/whole-tale/wt-design-docs/master/badges/wholetale-explore.svg)](https://dashboard.wholetale.org/run/64ae29e8a887f48b9f173678?tab=metadata)
 
 
@@ -24,6 +26,7 @@
 - [Installation](#installation)
 - [Getting started / Example notebooks](#getting-started--example-notebooks)
 - [Community engagement](#community-engagement)
+- [How to Cite](#how-to-cite)
 - [Disclaimer](#disclaimer)
 
 <!-- END doctoc generated TOC please keep comment here to allow auto update -->
@@ -149,6 +152,8 @@ guidelines.
 
 Thank you for your interest.
 
+## How to Cite
+McCreight, J., Langevin, C. D., & Hughes, J. D. (2023). pywatershed (Version 1.0.0) [Computer software]. [https://doi.org/10.5066/P9AVWA7Z](https://doi.org/10.5066/P9AVWA7Z)
 
 ## Disclaimer
 

autotest/test_mmr_to_mf6_dfw.py

@@ -15,14 +15,14 @@
 # Getting the gis files causes problems in parallel in CI. See regression test.
 
 # See below to check if these answers are still up-to-date with
-# mf6/autotest/test_swf_dfw.py
+# mf6/autotest/test_chf_dfw.py
 # Note the answers are from the binary FLW files in
-# mf6/autotest/test_swf_dfw.py, if you switch to text files, the line should be
+# mf6/autotest/test_chf_dfw.py, if you switch to text files, the line should be
 # flw_list = [
 #     (int(binary), 100),
 # ]  # one-based cell numbers here if binary, zero-based if text
 
-answers_swf_dfw = {
+answers_chf_dfw = {
     "ia": np.array([0, 2, 5, 7]),
     "ja": np.array([0, 1, 1, 0, 2, 2, 1], dtype=np.int32),
     "stage": np.array([[[[1.00196123, 1.00003366, 1.0]]]]),
@@ -52,9 +52,9 @@
 @pytest.mark.skipif(mf6_bin_unavailable, reason="mf6 binary not available")
 @pytest.mark.domainless
 @pytest.mark.parametrize("binary_flw", [True, False])
-def test_mmr_to_mf6_swf_dfw(tmp_path, binary_flw):
+def test_mmr_to_mf6_chf_dfw(tmp_path, binary_flw):
     # The point of this test is to reproduce the
-    # modflow6/autotest/test_swf_dfw.py
+    # modflow6/autotest/test_chf_dfw.py
 
     # Here we supply "seg_mid_elevation" in the parameter data and
     # "stress_period_data" in chd options. This bypasses the calculation of
@@ -68,8 +68,8 @@ def test_mmr_to_mf6_swf_dfw(tmp_path, binary_flw):
     # stream segments, the other is about the units of volume/flow being in
     # cubicfeet.
 
-    name = "swf-dfw01"
-    output_dir = tmp_path / "test_swf_dfw01"
+    name = "chf-dfw01"
+    output_dir = tmp_path / "test_chf_dfw01"
     save_flows = True
     print_flows = True
 
@@ -123,16 +123,16 @@ def test_mmr_to_mf6_swf_dfw(tmp_path, binary_flw):
     # vertices could also be supplied by shapefiles
     vertices = []
     vertices = [[j, j * dx, 0.0] for j in range(nreach + 1)]
-    cell2d = []
+    cell1d = []
     for j in range(nreach):
-        cell2d.append([j, 0.5, 2, j, j + 1])
-    nodes = len(cell2d)
+        cell1d.append([j, 0.5, 2, j, j + 1])
+    nodes = len(cell1d)
     nvert = len(vertices)
     disv1d_options = {
         "nodes": nodes,
         "nvert": nvert,
         "vertices": vertices,
-        "cell2d": cell2d,
+        "cell1d": cell1d,
     }
 
     # dfw
@@ -191,9 +191,14 @@ def test_mmr_to_mf6_swf_dfw(tmp_path, binary_flw):
         else:
             flw_vol = 0.0
 
+        # <
+        time_coord_data = np.array([control.start_time]).astype(
+            "datetime64[ns]"
+        )
+
         _ = xr.Dataset(
             coords=dict(
-                time=np.array([control.start_time]),
+                time=time_coord_data,
                 nsegment=params.parameters["seg_id"],
             ),
             data_vars={
@@ -246,26 +251,30 @@ def test_mmr_to_mf6_swf_dfw(tmp_path, binary_flw):
     # Checks
     assert success
 
-    # one can verify the answers match the current mf6 results for test_swf_dfw
-    # by placing the path to its output here
+    # one can verify the answers match the current mf6 results for test_chf_dfw
+    # by placing the path to its output here. Run the following lines to
+    # generate the mf6 results:
+    #   cd modflow6_for_pws_ci/autotest  # or your mf6 repo location
+    #   pytest -s -vv test_chf_dfw.py --keep=keepers
     # output_dir = pl.Path(
-    #     "../../modflow6/autotest/keepers/test_mf6model[0-swf-dfw01]0"
+    #     "../../modflow6_for_pws_ci/autotest/keepers/"
+    #     "test_mf6model[0-chf-dfw01]0"
     # )
 
     # check binary grid file
     grb = flopy.mf6.utils.MfGrdFile(output_dir / f"{name}.disv1d.grb")
     ia = grb.ia
     ja = grb.ja
-    assert (answers_swf_dfw["ia"] == ia).all()
-    assert (answers_swf_dfw["ja"] == ja).all()
+    assert (answers_chf_dfw["ia"] == ia).all()
+    assert (answers_chf_dfw["ja"] == ja).all()
     assert ia.shape[0] == grb.nodes + 1, "ia in grb file is not correct size"
 
     # check stage file
     qobj = flopy.utils.HeadFile(
         output_dir / f"{name}.stage", precision="double", text="STAGE"
     )
     stage = qobj.get_alldata()
-    assert ((answers_swf_dfw["stage"] - stage) < 1.0e-7).all()
+    assert ((answers_chf_dfw["stage"] - stage) < 1.0e-7).all()
 
     # read the budget file
     budobj = flopy.utils.binaryfile.CellBudgetFile(output_dir / f"{name}.bud")
@@ -275,17 +284,17 @@ def test_mmr_to_mf6_swf_dfw(tmp_path, binary_flw):
     qchd = np.array(budobj.get_data(text="CHD")[0].tolist()[0])
     qresidual = np.zeros(grb.nodes)[0]
 
-    assert (answers_swf_dfw["flowja"] - flowja < 1.0e-7).all()
-    assert (answers_swf_dfw["qstorage"] - qstorage < 1.0e-7).all()
-    assert (answers_swf_dfw["qflw"] - qflw < 1.0e-7).all()
-    assert (answers_swf_dfw["qchd"] - qchd < 1.0e-7).all()
-    assert (answers_swf_dfw["qresidual"] - qresidual < 1.0e-7).all()
+    assert (answers_chf_dfw["flowja"] - flowja < 1.0e-7).all()
+    assert (answers_chf_dfw["qstorage"] - qstorage < 1.0e-7).all()
+    assert (answers_chf_dfw["qflw"] - qflw < 1.0e-7).all()
+    assert (answers_chf_dfw["qchd"] - qchd < 1.0e-7).all()
+    assert (answers_chf_dfw["qresidual"] - qresidual < 1.0e-7).all()
 
 
 # <
 answers_regression_means = {
-    "stage_all": 1.03667372881148,
-    "flow_all": 44.685014111989425,
+    "stage_all": 1.0372047024253908,
+    "flow_all": 44.70210250910929,
 }
 
 
@@ -406,6 +415,7 @@ def test_mmr_to_mf6_dfw_regression(simulation, tmp_path):
         inflow_dir=inflow_dir,
     )
 
+    dfw.write()
     success, buff = dfw.run(silent=False, report=True)
     assert success
 
@@ -468,4 +478,5 @@ def get_outflow(itime):
 
     for kk, vv in answers_regression_means.items():
         abs_diff = abs(locals()[kk].mean() - vv)
+
         assert abs_diff < 1e-5, f"results for {kk} are not close"

autotest/test_obsin_flow_node.py

@@ -1,14 +1,14 @@
 import numpy as np
 import pytest
-from pyPRMS import Streamflow as PRMSStreamflowData
+from pyPRMS import DataFile as PRMSStreamflowData
 
 from pywatershed import PRMSChannel
 from pywatershed.base.adapter import Adapter, AdapterNetcdf, adapter_factory
 from pywatershed.base.control import Control
 from pywatershed.base.flow_graph import FlowGraph
 from pywatershed.base.parameters import Parameters
 from pywatershed.constants import nan, zero
-from pywatershed.hydrology.obsin_node import ObsInNodeMaker
+from pywatershed.hydrology.obsin_flow_node import ObsInFlowNodeMaker
 from pywatershed.hydrology.prms_channel_flow_graph import (
     HruSegmentFlowAdapter,
     PRMSChannelFlowNodeMaker,
@@ -68,7 +68,13 @@ def test_prms_channel_obsin_compare_prms(
     )
     control_parameters = PrmsParameters.load(control_param_file)
     obsout_seg = control_parameters.parameters["obsout_segment"] - 1
-    sf_data = PRMSStreamflowData(simulation["dir"] / "sf_data").data
+    sf_data = PRMSStreamflowData(
+        simulation["dir"] / "sf_data"
+    ).data_by_variable("runoff")
+    old_names = sf_data.columns.tolist()
+    new_names = [cc.split("_")[1] for cc in sf_data.columns.tolist()]
+    sf_data.rename(columns=dict(zip(old_names, new_names)), inplace=True)
+
     poi_inds = obsout_seg[np.where(obsout_seg >= 0)].tolist()
     npoi = len(poi_inds)
     poi_ids = discretization_prms.parameters["poi_gage_id"][(poi_inds),]
@@ -119,13 +125,14 @@ def advance(self) -> None:
         "prms_channel": PRMSChannelFlowNodeMaker(
             discretization_prms, parameters_prms
         ),
-        "obsin": ObsInNodeMaker(obsin_params, obsin_data),
+        "obsin": ObsInFlowNodeMaker(obsin_params, obsin_data),
     }
     nnodes = parameters_prms.dims["nsegment"] + npoi
     node_maker_name = ["prms_channel"] * nnodes
     node_maker_name[-npoi:] = ["obsin"] * npoi
     node_maker_index = np.arange(nnodes)
     node_maker_index[-npoi:] = np.arange(npoi)
+    node_maker_id = np.arange(nnodes)
     to_graph_index = np.zeros(nnodes, dtype=np.int64)
     dis_params = discretization_prms.parameters
     to_graph_index[0:-npoi] = dis_params["tosegment"] - 1
@@ -171,12 +178,14 @@ def advance(self) -> None:
         data_vars={
             "node_maker_name": node_maker_name,
             "node_maker_index": node_maker_index,
+            "node_maker_id": node_maker_id,
             "to_graph_index": to_graph_index,
         },
         metadata={
             "nnodes": {"dims": ["nnodes"]},
             "node_maker_name": {"dims": ["nnodes"]},
             "node_maker_index": {"dims": ["nnodes"]},
+            "node_maker_id": {"dims": ["nnodes"]},
             "to_graph_index": {"dims": ["nnodes"]},
         },
         validate=True,

autotest/test_pass_through_flow_graph.py

@@ -10,7 +10,9 @@
 from pywatershed.base.model import Model
 from pywatershed.base.parameters import Parameters
 from pywatershed.constants import nan, zero
-from pywatershed.hydrology.pass_through_node import PassThroughNodeMaker
+from pywatershed.hydrology.pass_through_flow_node import (
+    PassThroughFlowNodeMaker,
+)
 from pywatershed.hydrology.prms_channel_flow_graph import (
     HruSegmentFlowAdapter,
     PRMSChannelFlowNodeMaker,
@@ -63,8 +65,10 @@ def parameters_flow_graph(parameters_prms, discretization_prms):
     nnodes = parameters_prms.dims["nsegment"] + 1
     node_maker_name = ["prms_channel"] * nnodes
     node_maker_name[-1] = "pass_throughs"
+    node_maker_name = np.array(node_maker_name, dtype="U")
     node_maker_index = np.arange(nnodes)
     node_maker_index[-1] = 0
+    node_maker_id = np.arange(nnodes)
     to_graph_index = np.zeros(nnodes, dtype=np.int64)
     dis_params = discretization_prms.parameters
     to_graph_index[0:-1] = dis_params["tosegment"] - 1
@@ -77,11 +81,11 @@ def parameters_flow_graph(parameters_prms, discretization_prms):
     )
     # have to map to the graph from an index found in prms_channel
     wh_intervene_above_graph = np.where(
-        (np.array(node_maker_name) == "prms_channel")
+        (node_maker_name == "prms_channel")
         & (node_maker_index == wh_intervene_above_nhm[0][0])
     )
     wh_intervene_below_graph = np.where(
-        (np.array(node_maker_name) == "prms_channel")
+        (node_maker_name == "prms_channel")
         & np.isin(node_maker_index, wh_intervene_below_nhm)
     )
 
@@ -98,12 +102,14 @@ def parameters_flow_graph(parameters_prms, discretization_prms):
         data_vars={
             "node_maker_name": node_maker_name,
             "node_maker_index": node_maker_index,
+            "node_maker_id": node_maker_id,
             "to_graph_index": to_graph_index,
         },
         metadata={
             "node_coord": {"dims": ["nnodes"]},
             "node_maker_name": {"dims": ["nnodes"]},
             "node_maker_index": {"dims": ["nnodes"]},
+            "node_maker_id": {"dims": ["nnodes"]},
             "to_graph_index": {"dims": ["nnodes"]},
         },
         validate=True,
@@ -117,7 +123,7 @@ def node_maker_dict(parameters_prms, discretization_prms):
         "prms_channel": PRMSChannelFlowNodeMaker(
             discretization_prms, parameters_prms
         ),
-        "pass_throughs": PassThroughNodeMaker(),
+        "pass_throughs": PassThroughFlowNodeMaker(),
     }