refactor: support python 3.12, various updates (#124)

* add python 3.12 classifier to `pyproject.toml`
* explicitly specify packages in `pyproject.toml`
* add authors to `pyproject.toml`
* remove version fn from `Executables`
* move tests from main module to `autotest/`
* remove `BIN_PATH` testing environment variable
* remove testing dependency on mf6 & related exes
* remove `pytest-virtualenv` testing dependency
* add `.vscode/` to `.gitignore`

.github/workflows/ci.yml

@@ -16,7 +16,7 @@ jobs:
     steps:
 
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v4
@@ -80,24 +80,24 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-22.04, macos-12, windows-2022 ]
-        python: [ 3.8, 3.9, "3.10", "3.11" ]
+        python: [ 3.8, 3.9, "3.10", "3.11", "3.12" ]
     env:
       GCC_V: 11
     steps:
 
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: modflow-devtools
 
       - name: Checkout modflow6
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: MODFLOW-USGS/modflow6
           path: modflow6
 
       - name: Checkout modflow6 examples
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: MODFLOW-USGS/modflow6-examples
           path: modflow6-examples
@@ -113,7 +113,6 @@ jobs:
         with:
           repository: MODFLOW-USGS/modflow6-largetestmodels
           path: modflow6-largetestmodels
-          token: ${{ github.token }}
 
       - name: Install executables
         uses: modflowpy/install-modflow-action@v1
@@ -128,10 +127,6 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python }}
-          cache: 'pip'
-          cache-dependency-path: |
-            modflow-devtools/pyproject.toml
-            modflow6-examples/etc/requirements*.txt
 
       - name: Install Python packages
         working-directory: modflow-devtools
@@ -159,22 +154,19 @@ jobs:
         run: python ci_build_files.py
 
       - name: Run local tests
-        working-directory: modflow-devtools
+        working-directory: modflow-devtools/autotest
         env:
-          BIN_PATH: ~/.local/bin/modflow
           REPOS_PATH: ${{ github.workspace }}
-          GITHUB_TOKEN: ${{ github.token }}
         # use --dist loadfile to so tests requiring pytest-virtualenv run on the same worker
-        run: pytest -v -n auto --dist loadfile --durations 0 --ignore modflow_devtools/test/test_download.py
+        run: pytest -v -n auto --dist loadfile --durations 0 --ignore test_download.py
 
       - name: Run network-dependent tests
         # only invoke the GH API on one OS and Python version
         # to avoid rate limits (1000 rqs / hour / repository)
         # https://docs.github.com/en/actions/learn-github-actions/usage-limits-billing-and-administration#usage-limits
         if: runner.os == 'Linux' && matrix.python == '3.8'
-        working-directory: modflow-devtools
+        working-directory: modflow-devtools/autotest
         env:
-          BIN_PATH: ~/.local/bin/modflow
           REPOS_PATH: ${{ github.workspace }}
           GITHUB_TOKEN: ${{ github.token }}
-        run: pytest -v -n auto --durations 0 modflow_devtools/test/test_download.py
+        run: pytest -v -n auto --durations 0 test_download.py

.gitignore

@@ -128,8 +128,9 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
-# pycharme
+# IDEs
 .idea/
+.vscode/
 
 # downloaded exe
 modflow_devtools/bin/

DEVELOPER.md

@@ -38,37 +38,33 @@ This repository's tests use [`pytest`](https://docs.pytest.org/en/latest/) and s
 
 This repository's tests expect a few environment variables:
 
-- `BIN_PATH`: path to MODFLOW 6 and related executables
 - `REPOS_PATH`: the path to MODFLOW 6 example model repositories
 - `GITHUB_TOKEN`: a GitHub authentication token
 
 These may be set manually, but the recommended approach is to configure environment variables in a `.env` file in the project root, for instance:
 
 ```
-BIN_PATH=/path/to/modflow/executables
 REPOS_PATH=/path/to/repos
 GITHUB_TOKEN=yourtoken...
 ```
 
 The tests use [`pytest-dotenv`](https://github.com/quiqua/pytest-dotenv) to detect and load variables from this file.
 
-**Note:** at minimum, the tests require that the `mf6` (or `mf6.exe` on Windows) executable is present in `BIN_PATH`.
-
 ### Running the tests
 
-Tests should be run from the project root. To run the tests in parallel with verbose output:
+Tests should be run from the `autotest` directory. To run the tests in parallel with verbose output:
 
 ```shell
 pytest -v -n auto
 ```
 
 ### Writing new tests
 
-Tests should follow a few conventions for ease of use and maintenance.
+Tests follow a few conventions for ease of use and maintenance.
 
 #### Temporary directories
 
-Tests which must write to disk should use `pytest`'s built-in `temp_dir` fixture or one of this package's own scoped temporary directory fixtures.
+Tests which must write to disk use `pytest`'s built-in `temp_dir` fixture or one of this package's own scoped temporary directory fixtures.
 
 ## Releasing
 

pytest.ini → autotest/pytest.ini

@@ -4,5 +4,5 @@ python_files =
     test_*.py
     *_test*.py
 markers =
-    slow: tests that don't complete in a few seconds
+    slow: tests not completing in a few seconds
     meta: run by other tests (e.g. testing fixtures)

modflow_devtools/test/test_build.py → autotest/test_build.py

@@ -3,6 +3,7 @@
 from pathlib import Path
 
 import pytest
+
 from modflow_devtools.build import meson_build
 from modflow_devtools.markers import requires_pkg
 

modflow_devtools/test/test_download.py → autotest/test_download.py

@@ -1,5 +1,6 @@
 import pytest
 from flaky import flaky
+
 from modflow_devtools.download import (
     download_and_unzip,
     download_artifact,

autotest/test_executables.py

@@ -0,0 +1,26 @@
+import subprocess
+import sys
+from pathlib import Path
+from shutil import which
+
+import pytest
+
+from modflow_devtools.executables import Executables
+from modflow_devtools.misc import add_sys_path, get_suffixes
+
+ext, _ = get_suffixes(sys.platform)
+exe_stem = "pytest"
+exe_path = Path(which(exe_stem))
+bin_path = exe_path.parent
+exe = f"{exe_stem}{ext}"
+
+
+@pytest.fixture
+def exes():
+    with add_sys_path(bin_path):
+        yield Executables(**{exe_stem: bin_path / exe})
+
+
+def test_access(exes):
+    # support both attribute and dictionary style access
+    assert exes.pytest == exes["pytest"] == exe_path

modflow_devtools/test/test_fixtures.py → autotest/test_fixtures.py

@@ -139,7 +139,7 @@ def test_keep_class_scoped_tmpdir(tmp_path, arg):
         TestKeepClassScopedTmpdirInner.test_keep_class_scoped_tmpdir_inner.__name__,
         "-M",
         "test_keep",
-        "-K",
+        arg,
         tmp_path,
     ]
     assert pytest.main(args) == ExitCode.OK
@@ -160,19 +160,14 @@ def test_keep_module_scoped_tmpdir(tmp_path, arg):
         test_keep_module_scoped_tmpdir_inner.__name__,
         "-M",
         "test_keep",
-        "-K",
+        arg,
         tmp_path,
     ]
     assert pytest.main(args) == ExitCode.OK
     this_path = Path(__file__)
     keep_path = (
-        tmp_path
-        / f"{str(this_path.parent.parent.name)}.{str(this_path.parent.name)}.{str(this_path.stem)}0"
+        tmp_path / f"{str(this_path.parent.name)}.{str(this_path.stem)}0"
     )
-    from pprint import pprint
-
-    print(keep_path)
-    pprint(list(keep_path.glob("*")))
     assert test_keep_fname in [f.name for f in keep_path.glob("*")]
 
 
@@ -186,7 +181,7 @@ def test_keep_session_scoped_tmpdir(tmp_path, arg, request):
         test_keep_session_scoped_tmpdir_inner.__name__,
         "-M",
         "test_keep",
-        "-K",
+        arg,
         tmp_path,
     ]
     assert pytest.main(args) == ExitCode.OK

autotest/test_markers.py

@@ -0,0 +1,59 @@
+from os import environ
+from platform import python_version, system
+from shutil import which
+
+from packaging.version import Version
+
+from modflow_devtools.markers import *
+
+exe = "pytest"
+
+
+@requires_exe(exe)
+def test_require_exe():
+    assert which(exe)
+    require_exe(exe)
+    require_program(exe)
+
+
+exes = [exe, "python"]
+
+
+@require_exe(*exes)
+def test_require_exe_multiple():
+    assert all(which(exe) for exe in exes)
+
+
+@requires_pkg("pytest")
+def test_requires_pkg():
+    import numpy
+
+    assert numpy is not None
+
+
+@requires_pkg("pytest", "pluggy")
+def test_requires_pkg_multiple():
+    import pluggy
+    import pytest
+
+    assert pluggy is not None and pytest is not None
+
+
+@requires_platform("Windows")
+def test_requires_platform():
+    assert system() == "Windows"
+
+
+@excludes_platform("Darwin", ci_only=True)
+def test_requires_platform_ci_only():
+    if "CI" in environ:
+        assert system() != "Darwin"
+
+
+py_ver = python_version()
+
+
+@pytest.mark.parametrize("version", ["3.12", "3.11"])
+def test_requires_python(version):
+    if Version(py_ver) >= Version(version):
+        assert requires_python(version)

modflow_devtools/test/test_misc.py → autotest/test_misc.py

@@ -7,12 +7,13 @@
 from typing import List
 
 import pytest
-from conftest import project_root_path
+
 from modflow_devtools.misc import (
     get_model_paths,
     get_namefile_paths,
     get_packages,
     has_package,
+    has_pkg,
     set_dir,
     set_env,
     timed,
@@ -255,35 +256,9 @@ def test_get_namefile_paths_select_packages():
     assert len(paths) >= 43
 
 
-@pytest.mark.slow
-def test_has_pkg(virtualenv):
-    python = virtualenv.python
-    venv = Path(python).parent
-    pkg = "pytest"
-    dep = "pluggy"
-    print(
-        f"Using temp venv at {venv} with python {python} to test has_pkg('{pkg}') with and without '{dep}'"
-    )
-
-    # install a package and remove one of its dependencies
-    virtualenv.run(f"pip install {project_root_path}")
-    virtualenv.run(f"pip install {pkg}")
-    virtualenv.run(f"pip uninstall -y {dep}")
-
-    # check with/without strict mode
-    for strict in [False, True]:
-        cmd = (
-            f"from modflow_devtools.misc import has_pkg; print(has_pkg('{pkg}'"
-            + (", strict=True))" if strict else "))")
-        )
-        exp = "False" if strict else "True"
-        assert (
-            virtualenv.run(
-                f'{python} -c "{cmd}"',
-                capture=True,
-            ).strip()
-            == exp
-        )
+def test_has_pkg():
+    assert has_pkg("pytest")
+    assert not has_pkg("notapkg")
 
 
 def test_timed1(capfd):

modflow_devtools/test/test_ostags.py → autotest/test_ostags.py

@@ -1,6 +1,7 @@
 from platform import system
 
 import pytest
+
 from modflow_devtools.ostags import (
     OSTag,
     get_binary_suffixes,