Merge pull request #46 from wpbonelli/ruff

chore: switch to ruff, use devtools fixtures for tests

.github/workflows/ci.yml

@@ -21,10 +21,8 @@ jobs:
     defaults:
       run:
         shell: bash
-
     steps:
 
-    # check out repo
     - name: Checkout repo
       uses: actions/checkout@v3
 
@@ -45,19 +43,16 @@ jobs:
       run: |
         python -c "import modflowapi; print(modflowapi.__version__)"
 
-
   lint:
     name: lint
     runs-on: ubuntu-latest
+    if: github.event_name != 'schedule'
     strategy:
       fail-fast: false
     defaults:
       run:
         shell: bash
-
-    if: github.event_name != 'schedule'
     steps:
-    # check out repo
     - name: Checkout repo
       uses: actions/checkout@v3
 
@@ -78,20 +73,11 @@ jobs:
         python -m pip install --upgrade pip
         pip install -e .[lint]
 
-    - name: Run black
-      run: |
-        echo "if black check fails run"
-        echo "  black ./modflowapi"
-        echo "and then commit the changes."
-        black --check ./modflowapi
-
-    - name: Run flake8
-      run: |
-        flake8 --count --show-source --exit-zero ./modflowapi
+    - name: Lint
+      run: ruff check .
 
-    - name: Run pylint
-      run: |
-        pylint --jobs=2 --errors-only --exit-zero ./modflowapi
+    - name: Check format
+      run: ruff format . --check
 
   autotest_extensions:
     name: modflowapi extensions autotests
@@ -105,9 +91,7 @@ jobs:
     defaults:
       run:
         shell: bash
-
     steps:
-      # check out repo
       - name: Checkout repo
         uses: actions/checkout@v3
 
@@ -148,9 +132,7 @@ jobs:
     defaults:
       run:
         shell: bash
-
     steps:
-      # check out repo
       - name: Checkout repo
         uses: actions/checkout@v3
 
@@ -192,9 +174,7 @@ jobs:
     defaults:
       run:
         shell: bash
-
     steps:
-      # check out repo
       - name: Checkout repo
         uses: actions/checkout@v3
 
@@ -212,12 +192,12 @@ jobs:
           pip install git+https://[email protected]/MODFLOW-USGS/modflow-devtools@develop
           pip install .[test]
 
-      - name: Install modflow executables
+      - name: Install modflow6 nightly build
         uses: modflowpy/install-modflow-action@v1
         with:
           path: ${{ github.workspace }}/autotest
           repo: modflow6-nightly-build
-
+      
       - name: Run autotests
         working-directory: ./autotest
         shell: bash -l {0}

.gitignore

@@ -130,3 +130,8 @@ dmypy.json
 
 # pycharm
 .idea/
+
+# library files
+**.dll
+**.so
+**.dylib

autotest/conftest.py

@@ -6,16 +6,18 @@
 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:
-    pytest.importorskip("modflow_devtools")
-    from modflow_devtools.download import download_and_unzip
-
     # use file lock so mf6 distribution is downloaded once,
     # even when tests are run in parallel with pytest-xdist
     __mf6_examples_lock.acquire()
@@ -95,45 +97,3 @@ def simulation_name_from_model_namfiles(mnams):
         metafunc.parametrize(
             key, simulations, ids=simulation_name_from_model_namfiles
         )
-
-
-@pytest.fixture(scope="function")
-def tmpdir(tmpdir_factory, request) -> Path:
-    node = (
-        request.node.name.replace("/", "_")
-        .replace("\\", "_")
-        .replace(":", "_")
-    )
-    temp = Path(tmpdir_factory.mktemp(node))
-    yield Path(temp)
-
-    keep = request.config.getoption("--keep")
-    if keep:
-        copytree(temp, Path(keep) / temp.name)
-
-    keep_failed = request.config.getoption("--keep-failed")
-    if keep_failed and request.node.rep_call.failed:
-        copytree(temp, Path(keep_failed) / temp.name)
-
-
-def pytest_addoption(parser):
-    parser.addoption(
-        "-K",
-        "--keep",
-        action="store",
-        default=None,
-        help="Move the contents of temporary test directories to correspondingly named subdirectories at the given "
-        "location after tests complete. This option can be used to exclude test results from automatic cleanup, "
-        "e.g. for manual inspection. The provided path is created if it does not already exist. An error is "
-        "thrown if any matching files already exist.",
-    )
-
-    parser.addoption(
-        "--keep-failed",
-        action="store",
-        default=None,
-        help="Move the contents of temporary test directories to correspondingly named subdirectories at the given "
-        "location if the test case fails. This option automatically saves the outputs of failed tests in the "
-        "given location. The path is created if it doesn't already exist. An error is thrown if files with the "
-        "same names already exist in the given location.",
-    )

autotest/test_interface.py

@@ -11,7 +11,6 @@
     AdvancedPackage,
     ArrayPackage,
     ListPackage,
-    pkgvars,
 )
 
 data_pth = Path("../examples/data")
@@ -20,35 +19,39 @@
 so = "libmf6" + (
     ".so"
     if os == "Linux"
-    else ".dylib" if os == "Darwin" else ".dll" if os == "Windows" else None
+    else ".dylib"
+    if os == "Darwin"
+    else ".dll"
+    if os == "Windows"
+    else None
 )
 if so is None:
     pytest.skip("Unsupported operating system", allow_module_level=True)
 
 
 @pytest.mark.parametrize("use_str", [True, False])
 def test_ctor_finds_libmf6_by_name(use_str):
-    api = ModflowApi(so if use_str else Path(so))
+    ModflowApi(so if use_str else Path(so))
 
 
 @pytest.mark.parametrize("use_str", [True, False])
-def test_ctor_finds_libmf6_by_relpath(tmpdir, use_str):
-    shutil.copy(so, tmpdir)
-    inner = tmpdir / "inner"
+def test_ctor_finds_libmf6_by_relpath(function_tmpdir, use_str):
+    shutil.copy(so, function_tmpdir)
+    inner = function_tmpdir / "inner"
     inner.mkdir()
     with set_dir(inner):
         so_path = f"../{so}"
-        api = ModflowApi(so_path if use_str else Path(so_path))
+        ModflowApi(so_path if use_str else Path(so_path))
 
 
 @pytest.mark.parametrize("use_str", [True, False])
-def test_ctor_finds_libmf6_by_abspath(tmpdir, use_str):
-    shutil.copy(so, tmpdir)
-    so_path = tmpdir / so
-    api = ModflowApi(str(so_path) if use_str else so_path)
+def test_ctor_finds_libmf6_by_abspath(function_tmpdir, use_str):
+    shutil.copy(so, function_tmpdir)
+    so_path = function_tmpdir / so
+    ModflowApi(str(so_path) if use_str else so_path)
 
 
-def test_dis_model(tmpdir):
+def test_dis_model(function_tmpdir):
     def callback(sim, step):
         """
         Callback function
@@ -134,7 +137,7 @@ def callback(sim, step):
 
     name = "dis_model"
     sim_pth = data_pth / name
-    test_pth = tmpdir / name
+    test_pth = function_tmpdir / name
     shutil.copytree(sim_pth, test_pth, dirs_exist_ok=True)
 
     try:
@@ -143,7 +146,7 @@ def callback(sim, step):
         raise Exception(e)
 
 
-def test_disv_model(tmpdir):
+def test_disv_model(function_tmpdir):
     def callback(sim, step):
         """
         Callback function
@@ -220,7 +223,7 @@ def callback(sim, step):
 
     name = "disv_model"
     sim_pth = data_pth / name
-    test_pth = tmpdir / name
+    test_pth = function_tmpdir / name
     shutil.copytree(sim_pth, test_pth, dirs_exist_ok=True)
 
     try:
@@ -229,7 +232,7 @@ def callback(sim, step):
         raise Exception(e)
 
 
-def test_disu_model(tmpdir):
+def test_disu_model(function_tmpdir):
     def callback(sim, step):
         """
         Callback function
@@ -300,7 +303,7 @@ def callback(sim, step):
 
     name = "disu_model"
     sim_pth = data_pth / name
-    test_pth = tmpdir / name
+    test_pth = function_tmpdir / name
     shutil.copytree(sim_pth, test_pth, dirs_exist_ok=True)
 
     try:
@@ -309,7 +312,7 @@ def callback(sim, step):
         raise Exception(e)
 
 
-def test_two_models(tmpdir):
+def test_two_models(function_tmpdir):
     def callback(sim, step):
         """
         Callback function
@@ -326,7 +329,7 @@ def callback(sim, step):
 
     name = "two_models"
     sim_pth = data_pth / name
-    test_pth = tmpdir / name
+    test_pth = function_tmpdir / name
     shutil.copytree(sim_pth, test_pth, dirs_exist_ok=True)
 
     try:
@@ -335,7 +338,7 @@ def callback(sim, step):
         raise Exception(e)
 
 
-def test_ats_model(tmpdir):
+def test_ats_model(function_tmpdir):
     def callback(sim, step):
         if step == Callbacks.stress_period_start:
             if sim.kper == 0 and sim.kstp == 0:
@@ -350,7 +353,7 @@ def callback(sim, step):
 
         name = "ats0"
         sim_pth = data_pth / name
-        test_pth = tmpdir / name
+        test_pth = function_tmpdir / name
         shutil.copytree(sim_pth, test_pth, dirs_exist_ok=True)
 
         try:
@@ -359,7 +362,7 @@ def callback(sim, step):
             raise Exception(e)
 
 
-def test_rhs_hcof_advanced(tmpdir):
+def test_rhs_hcof_advanced(function_tmpdir):
     def callback(sim, step):
         model = sim.test_model
         if step == Callbacks.timestep_start:
@@ -410,7 +413,7 @@ def callback(sim, step):
 
     name = "dis_model"
     sim_pth = data_pth / name
-    test_pth = tmpdir / name
+    test_pth = function_tmpdir / name
     shutil.copytree(sim_pth, test_pth, dirs_exist_ok=True)
 
     try:

autotest/test_mf6_examples.py

@@ -9,25 +9,26 @@
 dll = "libmf6"
 
 
-def test_mf6_example_simulations(tmpdir, mf6_example_namfiles):
+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
     ----------
-    tmpdir: function-scoped temporary directory fixture
+    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)
-    tmpdir = Path(tmpdir / "workspace")
+    function_tmpdir = Path(function_tmpdir / "workspace")
 
     copytree(
-        src=namfile.parent.parent if nested else namfile.parent, dst=tmpdir
+        src=namfile.parent.parent if nested else namfile.parent,
+        dst=function_tmpdir,
     )
 
     def callback(sim, step):
@@ -37,12 +38,15 @@ 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()
-            namfile_name = namfile_path.name
             model_path = namfile_path.parent
 
             # working directory must be named according to the name file's parent (e.g.
             # 'mf6gwf') because coupled models refer to each other with relative paths
-            wrkdir = Path(tmpdir / model_path.name) if nested else tmpdir
+            wrkdir = (
+                Path(function_tmpdir / model_path.name)
+                if nested
+                else function_tmpdir
+            )
             try:
                 run_simulation(dll, wrkdir, callback, verbose=True)
             except Exception as e: