test(examples): replace conftest parametrization with devtools (#67)

Replace the old song and dance to get the example models with the new modflow_devtools.models module

Author: wpbonelli

.github/workflows/ci.yml

@@ -4,13 +4,11 @@ on:
   schedule:
     - cron: '0 8 * * *' # run at 8 AM UTC (12 am PST)
   push:
-    branches:
-      - main
-      - develop
-      - 'release*'
   pull_request:
     branches: [main, develop]
-
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
 
   std_setup:
@@ -24,7 +22,7 @@ jobs:
     steps:
 
     - name: Checkout repo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Setup uv
       uses: astral-sh/setup-uv@v5
@@ -158,13 +156,7 @@ jobs:
         shell: bash
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
-
-      - name: Checkout mf6-examples
         uses: actions/checkout@v4
-        with:
-          repository: MODFLOW-ORG/modflow6-examples
-          path: modflow6-examples
 
       - name: Setup uv
         uses: astral-sh/setup-uv@v5
@@ -175,25 +167,6 @@ jobs:
       - name: Install
         run: uv sync --all-extras
 
-      - name: Install Python dependencies
-        run: |
-          uv pip install git+https://git@github.com/Deltares/xmipy@develop
-          uv pip install git+https://git@github.com/MODFLOW-ORG/modflow-devtools@develop
-          uv pip install git+https://git@github.com/modflowpy/flopy@develop
-
-      - name: update flopy for mf6-examples
-        run: uv run python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
-
-      - name: Install modflow6 for modflow6-examples
-        uses: modflowpy/install-modflow-action@v1
-        with:
-          path: ${{ github.workspace }}/modflow6-examples/autotest
-
-      - name: Build mf6-examples
-        working-directory: modflow6-examples/autotest
-        run: |
-          uv run pytest -v -n=auto --init test_scripts.py -k "not synthetic-valley"
-
       - name: Install modflow6 nightly build
         uses: modflowpy/install-modflow-action@v1
         with:
@@ -203,4 +176,4 @@ jobs:
       - name: Run autotests
         working-directory: ./autotest
         shell: bash -l {0}
-        run: uv run pytest -v -n=auto test_mf6_examples.py --mf6-examples-path=../modflow6-examples/examples
+        run: uv run pytest -v -n auto test_mf6_examples.py

.github/workflows/release.yml

@@ -21,7 +21,7 @@ jobs:
     steps:
 
       - name: Checkout release branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -131,7 +131,7 @@ jobs:
     steps:
 
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: main
 
@@ -179,7 +179,7 @@ jobs:
     steps:
 
       - name: Checkout main branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: main
 

.gitignore

@@ -137,4 +137,7 @@ dmypy.json
 **.dylib
 
 # uv lockfile
-uv.lock
+uv.lock
+
+# temporary test folders
+autotest/temp/**

autotest/conftest.py

@@ -1,122 +1 @@
-from itertools import groupby
-from os import linesep
-from pathlib import Path
-from tempfile import gettempdir
-
-import pytest
-from filelock import FileLock
-from modflow_devtools.download import download_and_unzip
-
-# import modflow-devtools fixtures
 pytest_plugins = ["modflow_devtools.fixtures"]
-
-
-__mf6_examples = "mf6_examples"
-__mf6_examples_path = Path(gettempdir()) / __mf6_examples
-__mf6_examples_lock = FileLock(Path(gettempdir()) / f"{__mf6_examples}.lock")
-
-
-def get_mf6_examples_path() -> Path:
-    # use file lock so mf6 distribution is downloaded once,
-    # even when tests are run in parallel with pytest-xdist
-    __mf6_examples_lock.acquire()
-    try:
-        if not __mf6_examples_path.is_dir():
-            __mf6_examples_path.mkdir(exist_ok=True)
-            download_and_unzip(
-                url="https://github.com/MODFLOW-ORG/modflow6-examples/releases/download/current/mf6examples.zip",
-                path=__mf6_examples_path,
-                verbose=True,
-            )
-        return __mf6_examples_path
-    finally:
-        __mf6_examples_lock.release()
-
-
-def pytest_addoption(parser):
-    parser.addoption("--mf6-examples-path", action="store", default=None)
-
-
-def is_nested(namfile) -> bool:
-    p = Path(namfile)
-    if not p.is_file() or not p.name.endswith(".nam"):
-        raise ValueError(f"Expected a namfile path, got {p}")
-    return p.parent.parent.name != __mf6_examples
-
-
-def pytest_generate_tests(metafunc):
-    # examples to skip:
-    #   - ex-gwtgwt-mt3dms-p10: https://github.com/MODFLOW-ORG/modflow6/pull/1008
-    option_value = metafunc.config.option.mf6_examples_path
-    t = metafunc.fixturenames
-    if "mf6_example_namfiles" in metafunc.fixturenames and option_value is not None:
-        mf6_examples_path = Path(option_value)
-        global __mf6_examples
-        __mf6_examples = str(mf6_examples_path.name)
-    else:
-        mf6_examples_path = get_mf6_examples_path()
-
-    # grouping...
-    exclude = [
-        "ex-gwt-gwtgwt-mt3dms-p10",
-        "mp7-p02",
-        "mp7-p04",
-        "synthetic-valley",
-    ]
-    namfiles = [
-        str(p)
-        for p in mf6_examples_path.rglob("mfsim.nam")
-        if not any(e in str(p) for e in exclude)
-    ]
-
-    # parametrization by model
-    #   - single namfile per test case
-    #   - no coupling (only first model in each simulation subdir is used)
-    key = "mf6_example_namfile"
-    if key in metafunc.fixturenames:
-        metafunc.parametrize(key, sorted(namfiles))
-
-    # parametrization by simulation
-    #   - each test case gets an ordered list of 1+ namfiles
-    #   - models can be coupled (run in order provided, sharing workspace)
-    key = "mf6_example_namfiles"
-    if key in metafunc.fixturenames:
-        simulations = []
-
-        def simulation_name_from_model_path(p):
-            p = Path(p)
-            return p.parent.parent.name if is_nested(p) else p.parent.name
-
-        for model_name, model_namfiles in groupby(
-            namfiles, key=simulation_name_from_model_path
-        ):
-            models = []
-            model_namfiles = list(model_namfiles)
-            if len(model_namfiles) > 1:
-                # trap gwf models as first set of models
-                idxs = [ix for ix, _ in enumerate(model_namfiles) if "gwf" in _]
-                if len(idxs) > 0:
-                    for ix in idxs[::-1]:
-                        models.append(model_namfiles.pop(ix))
-
-            # sort remaining models in alphabetical order (gwe < gwt < prt)
-            models += list(sorted(model_namfiles))
-            simulations.append(models)
-            print(
-                f"Simulation {model_name} has {len(models)} model(s):\n"
-                f"{linesep.join(model_namfiles)}"
-            )
-
-        def simulation_name_from_model_namfiles(mnams):
-            try:
-                namfile = next(iter(mnams), None)
-            except TypeError:
-                namfile = None
-            if namfile is None:
-                pytest.skip("No namfiles (expected ordered collection)")
-            namfile = Path(namfile)
-            return (
-                namfile.parent.parent if is_nested(namfile) else namfile.parent
-            ).name
-
-        metafunc.parametrize(key, simulations, ids=simulation_name_from_model_namfiles)

autotest/test_mf6_examples.py

@@ -1,55 +1,24 @@
-from pathlib import Path
-from shutil import copytree
-
+import modflow_devtools.models as models
 import pytest
 
-from autotest.conftest import is_nested
 from modflowapi import run_simulation
 
+examples = models.get_examples()
 pytestmark = pytest.mark.mf6
 dll = "libmf6"
-
-
-def test_mf6_example_simulations(function_tmpdir, mf6_example_namfiles):
-    """
-    MF6 examples parametrized by simulation. `mf6_example_namfiles` is a list
-    of models to run in order provided. Coupled models share the same tempdir
-
-    Parameters
-    ----------
-    function_tmpdir: function-scoped temporary directory fixture
-    mf6_example_namfiles: ordered list of namfiles for 1+ coupled models
-    """
-    if len(mf6_example_namfiles) == 0:
-        pytest.skip("No namfiles (expected ordered collection)")
-    namfile = Path(mf6_example_namfiles[0])
-
-    nested = is_nested(namfile)
-    function_tmpdir = Path(function_tmpdir / "workspace")
-
-    copytree(
-        src=namfile.parent.parent if nested else namfile.parent, dst=function_tmpdir
-    )
-
-    def callback(sim, step):
-        pass
-
-    def run_models():
-        # run models in order received (should be alphabetical,
-        # so gwf precedes gwt)
-        for namfile in mf6_example_namfiles:
-            namfile_path = Path(namfile).resolve()
-            model_path = namfile_path.parent
-
-            # working directory must be named according to namefile's parent
-            # (e.g. 'mf6gwf') because coupled models refer to each other with
-            # relative paths
-            wrkdir = (
-                Path(function_tmpdir / model_path.name) if nested else function_tmpdir
-            )
-            try:
-                run_simulation(dll, wrkdir, callback, verbose=True)
-            except Exception as e:
-                raise Exception(e)
-
-    run_models()
+skip = [
+    # https://github.com/MODFLOW-ORG/modflowapi/issues/53
+    "ex-prt-mp7-p02",
+    "ex-prt-mp7-p04",
+]
+
+
+@pytest.mark.parametrize("example_name", examples.keys())
+def test_example(function_tmpdir, example_name):
+    if example_name in skip:
+        pytest.skip(f"Skipping example {example_name}")
+    for model_name in examples[example_name]:
+        model_relpath = model_name.rpartition(example_name + "/")[-1]
+        model_workspace = function_tmpdir / model_relpath
+        models.copy_to(model_workspace, model_name, verbose=True)
+        run_simulation(dll, model_workspace, lambda sim, step: None, verbose=True)