Merge pull request #154 from MODFLOW-USGS/v1.5.0

Release 1.5.0

Author: wpbonelli

.github/workflows/ci.yml

@@ -30,21 +30,10 @@ jobs:
           cache-dependency-path: pyproject.toml
 
       - name: Install Python packages
-        run: |
-          pip install .
-          pip install ".[lint]"
-
-      - name: Run isort
-        run: isort --verbose --check --diff modflow_devtools
-
-      - name: Run black
-        run: black --check --diff modflow_devtools
-
-      - name: Run flake8
-        run: flake8 --count --show-source --exit-zero modflow_devtools
+        run: pip install ".[lint]"
 
-      - name: Run pylint
-        run: pylint --jobs=0 --errors-only --exit-zero modflow_devtools
+      - name: Run ruff
+        run: ruff check .
 
   build:
     name: Build
@@ -120,6 +109,11 @@ jobs:
 
       - name: Install executables
         uses: modflowpy/install-modflow-action@v1
+      
+      - name: Install nightly build
+        uses: modflowpy/install-modflow-action@v1
+        with:
+          repo: modflow6-nightly-build
 
       - name: Setup GNU Fortran ${{ env.GCC_V }}
         uses: awvwgk/setup-fortran@main
@@ -134,26 +128,29 @@ jobs:
 
       - name: Install Python packages
         working-directory: modflow-devtools
-        run: |
-          pip install .
-          pip install ".[test]"
-      
+        run: pip install ".[test]"
+
       - name: Cache modflow6 examples
+        if: matrix.python != 3.8
         id: cache-examples
         uses: actions/cache@v3
         with:
           path: modflow6-examples/examples
           key: modflow6-examples-${{ hashFiles('modflow6-examples/data/**') }}
 
       - name: Install extra Python packages
-        if: steps.cache-examples.outputs.cache-hit != 'true'
+        if: matrix.python != 3.8
         working-directory: modflow6-examples/etc
         run: |
           pip install -r requirements.pip.txt
           pip install -r requirements.usgs.txt
 
+      - name: Update FloPy packages
+        if: matrix.python != 3.8
+        run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
+
       - name: Build modflow6 example models
-        if: steps.cache-examples.outputs.cache-hit != 'true'
+        if: matrix.python != 3.8 && steps.cache-examples.outputs.cache-hit != 'true'
         working-directory: modflow6-examples/autotest
         run: pytest -v -n auto test_scripts.py --init
 
@@ -173,4 +170,17 @@ jobs:
         env:
           REPOS_PATH: ${{ github.workspace }}
           GITHUB_TOKEN: ${{ github.token }}
-        run: pytest -v -n auto --durations 0 test_download.py
+        run: pytest -v -n auto --durations 0 test_download.py
+  
+  rtd:
+    name: Docs
+    needs: test
+    runs-on: ubuntu-22.04
+    if: github.repository_owner == 'MODFLOW-USGS' && github.event_name == 'push'
+    steps:
+      - name: Trigger RTD
+        uses: dfm/rtds-action@v1
+        with:
+          webhook_url: ${{ secrets.RTDS_WEBHOOK_URL }}
+          webhook_token: ${{ secrets.RTDS_WEBHOOK_TOKEN }}
+          commit_ref: ${{ github.ref }}

.github/workflows/release.yml

@@ -45,7 +45,6 @@ jobs:
           ref="${{ github.ref_name }}"
           version="${ref#"v"}"
           python scripts/update_version.py -v "$version"
-          python scripts/lint.py
           python -c "import modflow_devtools; print('Version: ', modflow_devtools.__version__)"
           echo "version=$version" >> $GITHUB_OUTPUT
 

HISTORY.md

@@ -1,19 +1,26 @@
-### Version 1.4.0
+### Version 1.5.0
 
 #### New features
 
-* [feat(Executables)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/3129417dae2de3aece80c8056a2ac50eede56b91): Support collection-style membership test (#131). Committed by wpbonelli on 2023-12-18.
-* [feat](https://github.com/MODFLOW-USGS/modflow-devtools/commit/6728859a984a3080f8fd4f1135de36bc17454098): Add latex and plot style utilities (#132). Committed by wpbonelli on 2024-01-09.
-* [feat(misc)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/a9b801932866a26a996ed3a45f16048b15246472): Parse literals from environment variables (#135). Committed by wpbonelli on 2024-01-21.
-* [feat(ostags)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/0ad10751ea6ce752e59d83e8cd6275906d73fa70): Apple silicon (#139). Committed by wpbonelli on 2024-02-18.
+* [feat(markers)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/1f358de2bc721c1000c3d0823b9440776432e3b0): Add no_parallel marker, support differing pkg/module names (#148). Committed by wpbonelli on 2024-04-12.
+* [feat(snapshots)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/c9e445dd1544413f3729c7a78c2a77038db80050): Add snapshot fixtures, remove pandas fixture (#151). Committed by wpbonelli on 2024-05-13.
 
-#### Bug fixes
+#### Refactoring
+
+* [refactor(latex)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/827b5ec63ebe0b9ea833957637d6b60fdc2f3198): Support path-like, add docstrings (#142). Committed by wpbonelli on 2024-02-25.
+* [refactor(snapshots)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/d96089e512fbb79408e4fb58c89ee63da60dc727): Move to separate module (#152). Committed by wpbonelli on 2024-05-13.
 
-* [fix](https://github.com/MODFLOW-USGS/modflow-devtools/commit/fd215000c6215b0891e78ee621e40abb2a20b28a): Drop plot styles (already in flopy) (#133). Committed by wpbonelli on 2024-01-09.
+### Version 1.4.0
+
+#### New features
+
+* [feat(latex)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/6728859a984a3080f8fd4f1135de36bc17454098): Add latex utilities (#132). Committed by wpbonelli on 2024-01-09.
+* [feat(misc)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/a9b801932866a26a996ed3a45f16048b15246472): Parse literals from environment variables (#135). Committed by wpbonelli on 2024-01-21.
+* [feat(ostags)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/0ad10751ea6ce752e59d83e8cd6275906d73fa70): add OS tags for Apple silicon (#139). Committed by wpbonelli on 2024-02-18.
 
 #### Refactoring
 
-* [refactor](https://github.com/MODFLOW-USGS/modflow-devtools/commit/9356e067ea813aeeeda2582cf7ec174c11d80159): Remove executables module/class (#136). Committed by wpbonelli on 2024-01-25.
+* [refactor](https://github.com/MODFLOW-USGS/modflow-devtools/commit/9356e067ea813aeeeda2582cf7ec174c11d80159): Remove executables module/class (#136). Committed by wpbonelli on 2024-01-25. Should be in a major release per semver, but nothing is using it, so this should be safe.
 * [refactor(fixtures)](https://github.com/MODFLOW-USGS/modflow-devtools/commit/613ad010ff6fc782f231b7fa21d1cc660732e7be): Support pytest>=8, drop pytest-cases dependency (#137). Committed by wpbonelli on 2024-01-31.
 
 ### Version 1.3.1

README.md

@@ -56,6 +56,7 @@ Python3.8+, dependency-free, but pairs well with `pytest` and select plugins, e.
 
 - [`pytest-dotenv`](https://github.com/quiqua/pytest-dotenv)
 - [`pytest-xdist`](https://github.com/pytest-dev/pytest-xdist)
+- [`syrupy`](https://github.com/tophat/syrupy)
 
 ## Installation
 
@@ -65,15 +66,15 @@ Python3.8+, dependency-free, but pairs well with `pytest` and select plugins, e.
 pip install modflow-devtools
 ```
 
-Pytest, pytest plugins, and other optional dependencies can be installed with:
+Pytest, pytest plugins, and other testing-related dependencies can be installed with:
 
 ```shell
 pip install "modflow-devtools[test]"
 ```
 
 To install from source and set up a development environment please see the [developer documentation](DEVELOPER.md).
 
-To import `pytest` fixtures in a project consuming `modflow-devtools`, add the following to a `conftest.py` file:
+To import `pytest` fixtures in a project consuming `modflow-devtools`, add the following to a test file or `conftest.py` file:
 
 ```python
 pytest_plugins = [ "modflow_devtools.fixtures" ]

autotest/__snapshots__/test_snapshots/test_binary_array_snapshot.npy

@@ -0,0 +1 @@
+[1.1 2.2 3.3]

autotest/__snapshots__/test_snapshots/test_readable_text_array_snapshot.txt

@@ -0,0 +1,3 @@
+1.100000000000000089e+00
+2.200000000000000178e+00
+3.299999999999999822e+00

autotest/__snapshots__/test_snapshots/test_text_array_snapshot.txt

@@ -16,9 +16,7 @@
 _system = platform.system()
 _exe_ext = ".exe" if _system == "Windows" else ""
 _lib_ext = (
-    ".so"
-    if _system == "Linux"
-    else (".dylib" if _system == "Darwin" else ".dll")
+    ".so" if _system == "Linux" else (".dylib" if _system == "Darwin" else ".dll")
 )
 
 

autotest/test_build.py

@@ -21,9 +21,7 @@
 @pytest.mark.parametrize("retries", [-1, 0, 1.5])
 def test_get_releases_bad_params(per_page, retries):
     with pytest.raises(ValueError):
-        get_releases(
-            "executables", per_page=per_page, retries=retries, verbose=True
-        )
+        get_releases("executables", per_page=per_page, retries=retries, verbose=True)
 
 
 @flaky
@@ -53,7 +51,8 @@ def test_get_release(repo):
     actual_names = [asset["name"] for asset in assets]
 
     if repo == "MODFLOW-USGS/modflow6":
-        # can remove if modflow6 releases follow asset name conventions followed in executables and nightly build repos
+        # can remove if modflow6 releases follow asset name
+        # conventions followed in executables and nightly build repos
         assert set([a.rpartition("_")[2] for a in actual_names]) >= set(
             [a for a in expected_names if not a.startswith("win")]
         )
@@ -109,9 +108,7 @@ def test_download_and_unzip(function_tmpdir, delete_zip):
     zip_name = "mf6.3.0_linux.zip"
     dir_name = zip_name.replace(".zip", "")
     url = f"https://github.com/MODFLOW-USGS/modflow6/releases/download/6.3.0/{zip_name}"
-    download_and_unzip(
-        url, function_tmpdir, delete_zip=delete_zip, verbose=True
-    )
+    download_and_unzip(url, function_tmpdir, delete_zip=delete_zip, verbose=True)
 
     assert (function_tmpdir / zip_name).is_file() != delete_zip
 

autotest/test_download.py

@@ -6,7 +6,8 @@
 from _pytest.config import ExitCode
 
 system = platform.system()
-proj_root = Path(__file__).parent.parent.parent.parent
+proj_root = Path(__file__).parents[1]
+module_path = Path(inspect.getmodulename(__file__))
 
 
 # test temporary directory fixtures
@@ -39,8 +40,7 @@ def test_function_scoped_tmpdir_slash_in_name(function_tmpdir, name):
     replaced1 = name.replace("/", "_").replace("\\", "_").replace(":", "_")
     replaced2 = name.replace("/", "_").replace("\\", "__").replace(":", "_")
     assert (
-        f"{inspect.currentframe().f_code.co_name}[{replaced1}]"
-        in function_tmpdir.stem
+        f"{inspect.currentframe().f_code.co_name}[{replaced1}]" in function_tmpdir.stem
         or f"{inspect.currentframe().f_code.co_name}[{replaced2}]"
         in function_tmpdir.stem
     )
@@ -64,7 +64,7 @@ def test_class_scoped_tmpdir(self, class_tmpdir):
 def test_module_scoped_tmpdir(module_tmpdir):
     assert isinstance(module_tmpdir, Path)
     assert module_tmpdir.is_dir()
-    assert Path(inspect.getmodulename(__file__)).stem in module_tmpdir.name
+    assert module_path.stem in module_tmpdir.name
 
 
 def test_session_scoped_tmpdir(session_tmpdir):
@@ -144,9 +144,7 @@ def test_keep_class_scoped_tmpdir(tmp_path, arg):
     ]
     assert pytest.main(args) == ExitCode.OK
     assert Path(
-        tmp_path
-        / f"{TestKeepClassScopedTmpdirInner.__name__}0"
-        / test_keep_fname
+        tmp_path / f"{TestKeepClassScopedTmpdirInner.__name__}0" / test_keep_fname
     ).is_file()
 
 
@@ -165,9 +163,7 @@ def test_keep_module_scoped_tmpdir(tmp_path, arg):
     ]
     assert pytest.main(args) == ExitCode.OK
     this_path = Path(__file__)
-    keep_path = (
-        tmp_path / f"{str(this_path.parent.name)}.{str(this_path.stem)}0"
-    )
+    keep_path = tmp_path / f"{str(this_path.parent.name)}.{str(this_path.stem)}0"
     assert test_keep_fname in [f.name for f in keep_path.glob("*")]
 
 
@@ -206,9 +202,7 @@ def test_keep_failed_function_scoped_tmpdir(function_tmpdir, keep):
         args += ["--keep-failed", function_tmpdir]
     assert pytest.main(args) == ExitCode.TESTS_FAILED
 
-    kept_file = Path(
-        function_tmpdir / f"{inner_fn}0" / test_keep_fname
-    ).is_file()
+    kept_file = Path(function_tmpdir / f"{inner_fn}0" / test_keep_fname).is_file()
     assert kept_file if keep else not kept_file
 
 
@@ -276,41 +270,7 @@ def test_large_test_model(large_test_model):
     assert large_test_model.name == "mfsim.nam"
 
 
-# test pandas fixture
-
-test_pandas_fname = "pandas.txt"
-
-
-@pytest.mark.meta("test_pandas")
-def test_pandas_inner(function_tmpdir, use_pandas):
-    with open(function_tmpdir / test_pandas_fname, "w") as f:
-        f.write(str(use_pandas))
-
-
-@pytest.mark.parametrize("pandas", ["yes", "no", "random"])
-@pytest.mark.parametrize("arg", ["--pandas", "-P"])
-def test_pandas(pandas, arg, function_tmpdir):
-    inner_fn = test_pandas_inner.__name__
-    args = [
-        __file__,
-        "-v",
-        "-s",
-        "-k",
-        inner_fn,
-        arg,
-        pandas,
-        "--keep",
-        function_tmpdir,
-        "-M",
-        "test_pandas",
-    ]
-    assert pytest.main(args) == ExitCode.OK
-    res = open(next(function_tmpdir.rglob(test_pandas_fname))).readlines()[0]
-    assert res
-    if pandas == "yes":
-        assert "True" in res
-    elif pandas == "no":
-        assert "False" in res
+# test tabular data format fixture
 
 
 test_tabular_fname = "tabular.txt"