Merge pull request #126 from MODFLOW-USGS/v1.3.0

Release 1.3.0

.github/workflows/ci.yml

@@ -1,15 +1,12 @@
 name: CI
 on:
   push:
-    branches:
-      - main
-      - develop*
     paths-ignore:
       - '**.md'
   pull_request:
     branches:
       - main
-      - develop*
+      - develop
     paths-ignore:
       - '**.md'
 jobs:
@@ -19,7 +16,7 @@ jobs:
     steps:
 
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v4
@@ -83,24 +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
@@ -116,7 +113,6 @@ jobs:
         with:
           repository: MODFLOW-USGS/modflow6-largetestmodels
           path: modflow6-largetestmodels
-          token: ${{ github.token }}
 
       - name: Install executables
         uses: modflowpy/install-modflow-action@v1
@@ -131,10 +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
@@ -162,22 +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

.github/workflows/release.yml

@@ -164,6 +164,10 @@ jobs:
     permissions:
       contents: write
       pull-requests: write
+      id-token: write  # mandatory for trusted publishing
+    environment:  # requires a 'release' environment in repo settings
+      name: release
+      url: https://pypi.org/p/modflow-devtools
     steps:
 
       - name: Checkout main branch
@@ -188,12 +192,14 @@ jobs:
       - name: Check package
         run: twine check --strict dist/*
 
-      - name: Publish package
-        if: ${{ env.TWINE_USERNAME != '' }}
-        env:
-          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-        run: twine upload dist/*
+      - name: Upload package
+        uses: actions/upload-artifact@v3
+        with:
+          name: dist
+          path: dist
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
 
   reset:
     name: Draft reset PR

.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
 

HISTORY.md

@@ -1,3 +1,15 @@
+### Version 1.3.0
+
+#### New features
+
+* [feat(fixtures)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/0ce571411b6b35bc62d4f333d1a961bd2f202784): Add --tabular pytest CLI arg and corresponding fixture (#116). Committed by wpbonelli on 2023-09-12.
+* [feat(timeit)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/506a238f6f31d827015a6c6f5ba1867ee55948a7): Add function timing decorator (#118). Committed by wpbonelli on 2023-09-12.
+* [feat(executables)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/5b61a4b393b0bcd40aafeb87d1e80b3e557e0f05): Support .get(key, default) like dict (#125). Committed by wpbonelli on 2023-11-21.
+
+#### Refactoring
+
+* [refactor](https://github.com/MODFLOW-USGS/modflow-devtools/commit/cd644fa90885cde04f36f24e44cfe922b2a38897): Support python 3.12, various updates (#124). Committed by wpbonelli on 2023-11-11.
+
 ### Version 1.2.0
 
 #### New features

pytest.ini → autotest/pytest.ini

@@ -1,8 +1,8 @@
 [pytest]
-addopts = -ra
+addopts = -ra --color=yes
 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 +1,28 @@
+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
+    # .get() works too
+    assert exes.get("not a target") is None
+    assert exes.get("not a target", exes["pytest"]) == exes["pytest"]

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
@@ -316,3 +311,34 @@ def test_pandas(pandas, arg, function_tmpdir):
         assert "True" in res
     elif pandas == "no":
         assert "False" in res
+
+
+test_tabular_fname = "tabular.txt"
+
+
+@pytest.mark.meta("test_tabular")
+def test_tabular_inner(function_tmpdir, tabular):
+    with open(function_tmpdir / test_tabular_fname, "w") as f:
+        f.write(str(tabular))
+
+
+@pytest.mark.parametrize("tabular", ["raw", "recarray", "dataframe"])
+@pytest.mark.parametrize("arg", ["--tabular", "-T"])
+def test_tabular(tabular, arg, function_tmpdir):
+    inner_fn = test_tabular_inner.__name__
+    args = [
+        __file__,
+        "-v",
+        "-s",
+        "-k",
+        inner_fn,
+        arg,
+        tabular,
+        "--keep",
+        function_tmpdir,
+        "-M",
+        "test_tabular",
+    ]
+    assert pytest.main(args) == ExitCode.OK
+    res = open(next(function_tmpdir.rglob(test_tabular_fname))).readlines()[0]
+    assert tabular == res

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)