modflow-devtools 1.4.0__tar.gz → 1.6.0__tar.gz

{modflow-devtools-1.4.0/modflow_devtools.egg-info → modflow_devtools-1.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: modflow-devtools
-Version: 1.4.0
+Version: 1.6.0
 Summary: Python tools for MODFLOW development
 Author-email: "Joseph D. Hughes" <modflow@usgs.gov>, Michael Reno <mreno@ucar.edu>, Mike Taves <mwtoews@gmail.com>, Wes Bonelli <wbonelli@ucar.edu>
 Maintainer-email: "Joseph D. Hughes" <modflow@usgs.gov>
@@ -24,11 +24,7 @@ Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
 Provides-Extra: lint
-Requires-Dist: black; extra == "lint"
-Requires-Dist: cffconvert; extra == "lint"
-Requires-Dist: flake8; extra == "lint"
-Requires-Dist: isort; extra == "lint"
-Requires-Dist: pylint; extra == "lint"
+Requires-Dist: ruff; extra == "lint"
 Provides-Extra: test
 Requires-Dist: modflow-devtools[lint]; extra == "test"
 Requires-Dist: coverage; extra == "test"
@@ -37,11 +33,13 @@ Requires-Dist: filelock; extra == "test"
 Requires-Dist: meson!=0.63.0; extra == "test"
 Requires-Dist: ninja; extra == "test"
 Requires-Dist: numpy; extra == "test"
-Requires-Dist: pytest; extra == "test"
+Requires-Dist: pandas; extra == "test"
+Requires-Dist: pytest!=8.1.0; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
 Requires-Dist: pytest-dotenv; extra == "test"
 Requires-Dist: pytest-xdist; extra == "test"
 Requires-Dist: PyYaml; extra == "test"
+Requires-Dist: syrupy; extra == "test"
 Provides-Extra: docs
 Requires-Dist: sphinx; extra == "docs"
 Requires-Dist: sphinx-rtd-theme; extra == "docs"
@@ -105,6 +103,7 @@ 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
 
@@ -114,7 +113,7 @@ 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]"
@@ -122,7 +121,7 @@ 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" ]

{modflow-devtools-1.4.0 → modflow_devtools-1.6.0}/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
 
@@ -65,7 +66,7 @@ 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]"
@@ -73,7 +74,7 @@ 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" ]

{modflow-devtools-1.4.0 → modflow_devtools-1.6.0}/modflow_devtools/__init__.py

@@ -1,6 +1,6 @@
 __author__ = "Joseph D. Hughes"
-__date__ = "Feb 19, 2024"
-__version__ = "1.4.0"
+__date__ = "May 30, 2024"
+__version__ = "1.6.0"
 __maintainer__ = "Joseph D. Hughes"
 __email__ = "jdhughes@usgs.gov"
 __status__ = "Production"

{modflow-devtools-1.4.0 → modflow_devtools-1.6.0}/modflow_devtools/download.py

@@ -58,10 +58,10 @@ def get_releases(
     """
 
     if "/" not in repo:
-        raise ValueError(f"repo format must be owner/name")
+        raise ValueError("repo format must be owner/name")
 
     if not isinstance(retries, int) or retries < 1:
-        raise ValueError(f"retries must be a positive int")
+        raise ValueError("retries must be a positive int")
 
     params = {}
     if per_page is not None:
@@ -81,7 +81,10 @@ def get_releases(
             try:
                 if verbose:
                     print(
-                        f"Fetching releases for repo {repo} (page {page}, {per_page} per page)"
+                        f"Fetching releases for "
+                        f"repo {repo} "
+                        f"(page {page}, "
+                        f"{per_page} per page)"
                     )
                 with urllib.request.urlopen(request, timeout=10) as resp:
                     return json.loads(resp.read().decode())
@@ -96,9 +99,7 @@ def get_releases(
                     # GitHub sometimes returns this error for valid URLs, so retry
                     warn(f"URL request try {tries} failed ({err})")
                     continue
-                raise RuntimeError(
-                    f"cannot retrieve data from {req_url}"
-                ) from err
+                raise RuntimeError(f"cannot retrieve data from {req_url}") from err
 
     releases = []
     max_pages = max_pages if max_pages else sys.maxsize
@@ -132,13 +133,13 @@ def get_release(repo, tag="latest", retries=3, verbose=False) -> dict:
     """
 
     if "/" not in repo:
-        raise ValueError(f"repo format must be owner/name")
+        raise ValueError("repo format must be owner/name")
 
     if not isinstance(tag, str) or not any(tag):
-        raise ValueError(f"tag must be a non-empty string")
+        raise ValueError("tag must be a non-empty string")
 
     if not isinstance(retries, int) or retries < 1:
-        raise ValueError(f"retries must be a positive int")
+        raise ValueError("retries must be a positive int")
 
     req_url = f"https://api.github.com/repos/{repo}"
     req_url = (
@@ -209,10 +210,10 @@ def get_latest_version(repo, retries=3, verbose=False) -> str:
     """
 
     if "/" not in repo:
-        raise ValueError(f"repo format must be owner/name")
+        raise ValueError("repo format must be owner/name")
 
     if not isinstance(retries, int) or retries < 1:
-        raise ValueError(f"retries must be a positive int")
+        raise ValueError("retries must be a positive int")
 
     release = get_release(repo, retries=retries, verbose=verbose)
     return release["tag_name"]
@@ -245,13 +246,13 @@ def get_release_assets(
     """
 
     if "/" not in repo:
-        raise ValueError(f"repo format must be owner/name")
+        raise ValueError("repo format must be owner/name")
 
     if not isinstance(tag, str) or not any(tag):
-        raise ValueError(f"tag must be a non-empty string")
+        raise ValueError("tag must be a non-empty string")
 
     if not isinstance(retries, int) or retries < 1:
-        raise ValueError(f"retries must be a positive int")
+        raise ValueError("retries must be a positive int")
 
     release = get_release(repo, tag=tag, retries=retries, verbose=verbose)
     return (
@@ -287,26 +288,24 @@ def list_artifacts(
 
     Returns
     -------
-        A list of dictionaries, each containing information about an artifact as returned
-        by the GitHub API.
+        A list of dictionaries, each containing information
+        about an artifact as returned by the GitHub API.
     """
 
     if "/" not in repo:
-        raise ValueError(f"repo format must be owner/name")
+        raise ValueError("repo format must be owner/name")
 
     if not isinstance(retries, int) or retries < 1:
-        raise ValueError(f"retries must be a positive int")
+        raise ValueError("retries must be a positive int")
 
-    msg = f"artifact(s) for {repo}" + (
-        f" matching name {name}" if name else ""
-    )
+    msg = f"artifact(s) for {repo}" + (f" matching name {name}" if name else "")
     req_url = f"https://api.github.com/repos/{repo}/actions/artifacts"
     page = 1
     params = {}
 
     if name is not None:
         if not isinstance(name, str) or len(name) == 0:
-            raise ValueError(f"name must be a non-empty string")
+            raise ValueError("name must be a non-empty string")
         params["name"] = name
 
     if per_page is not None:
@@ -336,9 +335,7 @@ def list_artifacts(
                     # GitHub sometimes returns this error for valid URLs, so retry
                     warn(f"URL request try {tries} failed ({err})")
                     continue
-                raise RuntimeError(
-                    f"cannot retrieve data from {req_url}"
-                ) from err
+                raise RuntimeError(f"cannot retrieve data from {req_url}") from err
 
     artifacts = []
     diff = 1
@@ -387,10 +384,10 @@ def download_artifact(
     """
 
     if "/" not in repo:
-        raise ValueError(f"repo format must be owner/name")
+        raise ValueError("repo format must be owner/name")
 
     if not isinstance(retries, int) or retries < 1:
-        raise ValueError(f"retries must be a positive int")
+        raise ValueError("retries must be a positive int")
 
     req_url = f"https://api.github.com/repos/{repo}/actions/artifacts/{id}/zip"
     request = urllib.request.Request(req_url)
@@ -415,9 +412,7 @@ def download_artifact(
                 warn(f"URL request try {tries} failed ({err})")
                 continue
             else:
-                raise RuntimeError(
-                    f"cannot retrieve data from {req_url}"
-                ) from err
+                raise RuntimeError(f"cannot retrieve data from {req_url}") from err
 
     if verbose:
         print(f"Uncompressing: {zip_path}")
@@ -496,14 +491,8 @@ def download_and_unzip(
                     file_size = int(file_size)
 
                     bfmt = "{:" + f"{len_file_size}" + ",d}"
-                    sbfmt = (
-                        "{:>"
-                        + f"{len(bfmt.format(int(file_size)))}"
-                        + "s} bytes"
-                    )
-                    print(
-                        f"   file size: {sbfmt.format(bfmt.format(int(file_size)))}"
-                    )
+                    sbfmt = "{:>" + f"{len(bfmt.format(int(file_size)))}" + "s} bytes"
+                    print(f"   file size: {sbfmt.format(bfmt.format(int(file_size)))}")
 
                 break
         except urllib.error.HTTPError as err:
@@ -526,7 +515,7 @@ def download_and_unzip(
 
             # extract the files
             z.extractall(str(path))
-        except:
+        except:  # noqa: E722
             p = "Could not unzip the file. Stopping."
             raise Exception(p)
         z.close()

{modflow-devtools-1.4.0 → modflow_devtools-1.6.0}/modflow_devtools/fixtures.py

@@ -1,10 +1,9 @@
-import random
 from collections import OrderedDict
 from itertools import groupby
 from os import PathLike, environ
 from pathlib import Path
 from shutil import copytree, rmtree
-from typing import Dict, List, Optional
+from typing import Dict, Generator, List, Optional
 
 from modflow_devtools.imports import import_optional_dependency
 from modflow_devtools.misc import get_namefile_paths, get_packages
@@ -16,12 +15,8 @@ pytest = import_optional_dependency("pytest")
 
 
 @pytest.fixture(scope="function")
-def function_tmpdir(tmpdir_factory, request) -> Path:
-    node = (
-        request.node.name.replace("/", "_")
-        .replace("\\", "_")
-        .replace(":", "_")
-    )
+def function_tmpdir(tmpdir_factory, request) -> Generator[Path, None, None]:
+    node = request.node.name.replace("/", "_").replace("\\", "_").replace(":", "_")
     temp = Path(tmpdir_factory.mktemp(node))
     yield Path(temp)
 
@@ -41,7 +36,7 @@ def function_tmpdir(tmpdir_factory, request) -> Path:
 
 
 @pytest.fixture(scope="class")
-def class_tmpdir(tmpdir_factory, request) -> Path:
+def class_tmpdir(tmpdir_factory, request) -> Generator[Path, None, None]:
     assert (
         request.cls is not None
     ), "Class-scoped temp dir fixture must be used on class"
@@ -57,7 +52,7 @@ def class_tmpdir(tmpdir_factory, request) -> Path:
 
 
 @pytest.fixture(scope="module")
-def module_tmpdir(tmpdir_factory, request) -> Path:
+def module_tmpdir(tmpdir_factory, request) -> Generator[Path, None, None]:
     temp = Path(tmpdir_factory.mktemp(request.module.__name__))
     yield temp
 
@@ -70,7 +65,7 @@ def module_tmpdir(tmpdir_factory, request) -> Path:
 
 
 @pytest.fixture(scope="session")
-def session_tmpdir(tmpdir_factory, request) -> Path:
+def session_tmpdir(tmpdir_factory, request) -> Generator[Path, None, None]:
     temp = Path(tmpdir_factory.mktemp(request.config.rootpath.name))
     yield temp
 
@@ -89,20 +84,7 @@ def repos_path() -> Optional[Path]:
 
 
 @pytest.fixture
-def use_pandas(request):
-    pandas = request.config.option.PANDAS
-    if pandas == "yes":
-        return True
-    elif pandas == "no":
-        return False
-    elif pandas == "random":
-        return random.randint(0, 1) == 0
-    else:
-        raise ValueError(f"Unsupported value for --pandas: {pandas}")
-
-
-@pytest.fixture
-def tabular(request):
+def tabular(request) -> str:
     tab = request.config.option.TABULAR
     if tab not in ["raw", "recarray", "dataframe"]:
         raise ValueError(f"Unsupported value for --tabular: {tab}")
@@ -119,9 +101,12 @@ def pytest_addoption(parser):
         action="store",
         default=None,
         dest="KEEP",
-        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 "
+        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.",
     )
 
@@ -129,9 +114,12 @@ def pytest_addoption(parser):
         "--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 "
+        help="Move the contents of temporary test directories to "
+        "correspondingly named subdirectories at the given "
+        "location if the test case fails. This option 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.",
     )
 
@@ -148,7 +136,8 @@ def pytest_addoption(parser):
         "--meta",
         action="store",
         metavar="NAME",
-        help="Indicates a test should only be run by other tests (e.g., to test framework or fixtures).",
+        help="Indicates a test should only be run by other tests (e.g., "
+        "to test framework or fixtures).",
     )
 
     parser.addoption(
@@ -165,22 +154,14 @@ def pytest_addoption(parser):
         help="Select a subset of packages to run.",
     )
 
-    parser.addoption(
-        "-P",
-        "--pandas",
-        action="store",
-        default="yes",
-        dest="PANDAS",
-        help="Indicates whether to use pandas, where multiple approaches are available. Select 'yes', 'no', or 'random'.",
-    )
-
     parser.addoption(
         "-T",
         "--tabular",
         action="store",
         default="raw",
         dest="TABULAR",
-        help="Configure tabular data representation for model input. Select 'raw', 'recarray', or 'dataframe'.",
+        help="Configure tabular data representation for model input. "
+        "Select 'raw', 'recarray', or 'dataframe'.",
     )
 
 
@@ -269,9 +250,7 @@ def pytest_generate_tests(metafunc):
             if repo_path
             else []
         )
-        metafunc.parametrize(
-            key, namefile_paths, ids=[str(m) for m in namefile_paths]
-        )
+        metafunc.parametrize(key, namefile_paths, ids=[str(m) for m in namefile_paths])
 
     key = "test_model_mf5to6"
     if key in metafunc.fixturenames:
@@ -288,9 +267,7 @@ def pytest_generate_tests(metafunc):
             if repo_path
             else []
         )
-        metafunc.parametrize(
-            key, namefile_paths, ids=[str(m) for m in namefile_paths]
-        )
+        metafunc.parametrize(key, namefile_paths, ids=[str(m) for m in namefile_paths])
 
     key = "large_test_model"
     if key in metafunc.fixturenames:
@@ -307,9 +284,7 @@ def pytest_generate_tests(metafunc):
             if repo_path
             else []
         )
-        metafunc.parametrize(
-            key, namefile_paths, ids=[str(m) for m in namefile_paths]
-        )
+        metafunc.parametrize(key, namefile_paths, ids=[str(m) for m in namefile_paths])
 
     key = "example_scenario"
     if key in metafunc.fixturenames:
@@ -384,9 +359,7 @@ def pytest_generate_tests(metafunc):
                                 filtered.append(name)
                                 break
                 examples = {
-                    name: nfps
-                    for name, nfps in examples.items()
-                    if name in filtered
+                    name: nfps for name, nfps in examples.items() if name in filtered
                 }
 
             # exclude mf6gwf and mf6gwt subdirs
@@ -402,5 +375,5 @@ def pytest_generate_tests(metafunc):
         metafunc.parametrize(
             key,
             [(name, nfps) for name, nfps in example_scenarios.items()],
-            ids=[name for name, ex in example_scenarios.items()],
+            ids=list(example_scenarios.keys()),
         )

{modflow-devtools-1.4.0 → modflow_devtools-1.6.0}/modflow_devtools/imports.py

@@ -3,7 +3,7 @@
 # This file is dual licensed under the terms of the BSD 3-Clause License.
 # BSD 3-Clause License
 #
-# Copyright (c) 2008-2011, AQR Capital Management, LLC, Lambda Foundry, Inc. and PyData Development Team
+# Copyright (c) 2008-2011, AQR Capital Management, LLC, Lambda Foundry, Inc. and PyData Development Team  # noqa: E501
 # All rights reserved.
 #
 # Copyright (c) 2011-2021, Open source contributors.
@@ -130,9 +130,7 @@ def import_optional_dependency(
         module_to_get = sys.modules[install_name]
     else:
         module_to_get = module
-    minimum_version = (
-        min_version if min_version is not None else VERSIONS.get(parent)
-    )
+    minimum_version = min_version if min_version is not None else VERSIONS.get(parent)
     if minimum_version:
         version = get_version(module_to_get)
         if Version(version) < Version(minimum_version):

{modflow-devtools-1.4.0 → modflow_devtools-1.6.0}/modflow_devtools/latex.py

@@ -1,13 +1,38 @@
-import os
+from os import PathLike
+from pathlib import Path
+from typing import Iterable, Union
 
 
-def build_table(caption, fpth, arr, headings=None, col_widths=None):
+def build_table(
+    caption: str,
+    fpth: Union[str, PathLike],
+    arr,
+    headings: Iterable[str] = None,
+    col_widths: Iterable[float] = None,
+):
+    """
+    Build a LaTeX table from the given NumPy array.
+
+    Parameters
+    ----------
+    caption : str
+        The table's caption
+    fpth : str or path-like
+        The LaTeX file to create
+    arr : numpy recarray
+        The array
+    headings : iterable of str
+        The table headings
+    col_widths : iterable of float
+        The table's column widths
+    """
+
+    fpth = Path(fpth).expanduser().absolute().with_suffix(".tex")
+
     if headings is None:
         headings = arr.dtype.names
     ncols = len(arr.dtype.names)
-    if not fpth.endswith(".tex"):
-        fpth += ".tex"
-    label = "tab:{}".format(os.path.basename(fpth).replace(".tex", ""))
+    label = "tab:{}".format(fpth.stem)
 
     line = get_header(caption, label, headings, col_widths=col_widths)
 
@@ -29,8 +54,32 @@ def build_table(caption, fpth, arr, headings=None, col_widths=None):
 
 
 def get_header(
-    caption, label, headings, col_widths=None, center=True, firsthead=False
+    caption: str,
+    label: str,
+    headings: Iterable[str],
+    col_widths: Iterable[float] = None,
+    center: bool = True,
+    firsthead: bool = False,
 ):
+    """
+    Build a LaTeX table header.
+
+    Parameters
+    ----------
+    caption : str
+        The table's caption
+    label : str
+        The table's label
+    headings : iterable of str
+        The table's heading
+    col_widths : iterable of float
+        The table's column widths
+    center : bool
+        Whether to center-align the table text
+    firsthead : bool
+        Whether to add first header
+    """
+
     ncol = len(headings)
     if col_widths is None:
         dx = 0.8 / float(ncol)
@@ -43,11 +92,7 @@ def get_header(
     header = "\\small\n"
     header += "\\begin{longtable}[!htbp]{\n"
     for col_width in col_widths:
-        header += (
-            38 * " "
-            + f"{align}"
-            + f"{{{col_width}\\linewidth-2\\arraycolsep}}\n"
-        )
+        header += 38 * " " + f"{align}" + f"{{{col_width}\\linewidth-2\\arraycolsep}}\n"
     header += 38 * " " + "}\n"
     header += f"\t\\caption{{{caption}}} \\label{{{label}}} \\\\\n\n"
 
@@ -85,7 +130,6 @@ def exp_format(v):
     s = f"{v:.2e}"
     s = s.replace("e-0", "e-")
     s = s.replace("e+0", "e+")
-    # s = s.replace("e", " \\times 10^{") + "}$"
     return s
 
 

{modflow-devtools-1.4.0 → modflow_devtools-1.6.0}/modflow_devtools/markers.py

@@ -3,7 +3,9 @@ Pytest markers to toggle tests based on environment conditions.
 Occasionally useful to directly assert environment expectations.
 """
 
+from os import environ
 from platform import python_version, system
+from typing import Dict, Optional
 
 from packaging.version import Version
 
@@ -31,7 +33,7 @@ def requires_exe(*exes):
 
 def requires_python(version, bound="lower"):
     if not isinstance(version, str):
-        raise ValueError(f"Version must a string")
+        raise ValueError("Version must a string")
 
     py_tgt = Version(version)
     if bound == "lower":
@@ -46,8 +48,8 @@ def requires_python(version, bound="lower"):
         )
 
 
-def requires_pkg(*pkgs):
-    missing = {pkg for pkg in pkgs if not has_pkg(pkg, strict=True)}
+def requires_pkg(*pkgs, name_map: Optional[Dict[str, str]] = None):
+    missing = {pkg for pkg in pkgs if not has_pkg(pkg, strict=True, name_map=name_map)}
     return pytest.mark.skipif(
         missing,
         reason=f"missing package{'s' if len(missing) != 1 else ''}: "
@@ -57,25 +59,21 @@ def requires_pkg(*pkgs):
 
 def requires_platform(platform, ci_only=False):
     return pytest.mark.skipif(
-        system().lower() != platform.lower()
-        and (is_in_ci() if ci_only else True),
+        system().lower() != platform.lower() and (is_in_ci() if ci_only else True),
         reason=f"only compatible with platform: {platform.lower()}",
     )
 
 
 def excludes_platform(platform, ci_only=False):
     return pytest.mark.skipif(
-        system().lower() == platform.lower()
-        and (is_in_ci() if ci_only else True),
+        system().lower() == platform.lower() and (is_in_ci() if ci_only else True),
         reason=f"not compatible with platform: {platform.lower()}",
     )
 
 
 def requires_branch(branch):
     current = get_current_branch()
-    return pytest.mark.skipif(
-        current != branch, reason=f"must run on branch: {branch}"
-    )
+    return pytest.mark.skipif(current != branch, reason=f"must run on branch: {branch}")
 
 
 def excludes_branch(branch):
@@ -85,6 +83,11 @@ def excludes_branch(branch):
     )
 
 
+no_parallel = pytest.mark.skipif(
+    environ.get("PYTEST_XDIST_WORKER_COUNT"), reason="can't run in parallel"
+)
+
+
 requires_github = pytest.mark.skipif(
     not is_connected("github.com"), reason="github.com is required."
 )

{modflow-devtools-1.4.0 → modflow_devtools-1.6.0}/modflow_devtools/misc.py

@@ -12,8 +12,9 @@ from pathlib import Path
 from shutil import which
 from subprocess import PIPE, Popen
 from timeit import timeit
-from typing import List, Optional, Tuple
+from typing import Dict, List, Optional, Tuple
 from urllib import request
+from urllib.error import URLError
 
 from _warnings import warn
 
@@ -70,7 +71,8 @@ def get_ostag() -> str:
 
 def get_suffixes(ostag) -> Tuple[str, str]:
     """
-    Returns executable and library suffixes for the given OS (as returned by sys.platform)
+    Returns executable and library suffixes for the
+    given OS (as returned by sys.platform)
 
     .. deprecated:: 1.1.0
         Use ``ostags.get_binary_suffixes()`` instead.
@@ -150,9 +152,11 @@ def get_current_branch() -> str:
 
 def get_packages(namefile_path: PathLike) -> List[str]:
     """
-    Return a list of packages used by the simulation or model defined in the given namefile.
-    The namefile may be for an entire simulation or for a GWF or GWT model. If a simulation
-    namefile is given, packages used in its component model namefiles will be included.
+    Return a list of packages used by the simulation
+    or model defined in the given namefile. The namefile
+    may be for an entire simulation or  for a GWF or GWT
+    model. If a simulation namefile is given, packages
+    used in its component  model namefiles will be included.
 
     Parameters
     ----------
@@ -167,38 +171,35 @@ def get_packages(namefile_path: PathLike) -> List[str]:
     packages = []
     path = Path(namefile_path).expanduser().absolute()
     lines = open(path, "r").readlines()
-    gwf_lines = [l for l in lines if l.strip().lower().startswith("gwf6 ")]
-    gwt_lines = [l for l in lines if l.strip().lower().startswith("gwt6 ")]
+    gwf_lines = [ln for ln in lines if ln.strip().lower().startswith("gwf6 ")]
+    gwt_lines = [ln for ln in lines if ln.strip().lower().startswith("gwt6 ")]
 
     def parse_model_namefile(line):
         nf_path = [path.parent / s for s in line.split(" ") if s != ""][1]
         if nf_path.suffix != ".nam":
             raise ValueError(
-                f"Failed to parse GWF or GWT model namefile from simulation namefile line: {line}"
+                "Failed to parse GWF or GWT model namefile "
+                f"from simulation namefile line: {line}"
             )
         return nf_path
 
     # load model namefiles
     try:
         for line in gwf_lines:
-            packages = (
-                packages + get_packages(parse_model_namefile(line)) + ["gwf"]
-            )
+            packages = packages + get_packages(parse_model_namefile(line)) + ["gwf"]
         for line in gwt_lines:
-            packages = (
-                packages + get_packages(parse_model_namefile(line)) + ["gwt"]
-            )
-    except:
+            packages = packages + get_packages(parse_model_namefile(line)) + ["gwt"]
+    except:  # noqa: E722
         warn(f"Invalid namefile format: {traceback.format_exc()}")
 
     for line in lines:
         # Skip over blank and commented lines
-        ll = line.strip().split()
-        if len(ll) < 2:
+        line = line.strip().split()
+        if len(line) < 2:
             continue
 
-        l = ll[0].lower()
-        if any(l.startswith(c) for c in ["#", "!", "data", "list"]) or l in [
+        line = line[0].lower()
+        if any(line.startswith(c) for c in ["#", "!", "data", "list"]) or line in [
             "begin",
             "end",
             "memory_print_option",
@@ -206,9 +207,9 @@ def get_packages(namefile_path: PathLike) -> List[str]:
             continue
 
         # strip "6" from package name
-        l = l.replace("6", "")
+        line = line.replace("6", "")
 
-        packages.append(l.lower())
+        packages.append(line.lower())
 
     return list(set(packages))
 
@@ -242,17 +243,12 @@ def get_namefile_paths(
 
     # find simulation namefiles
     paths = [
-        p
-        for p in Path(path).rglob(
-            f"{prefix}*/**/{namefile}" if prefix else namefile
-        )
+        p for p in Path(path).rglob(f"{prefix}*/**/{namefile}" if prefix else namefile)
     ]
 
     # remove excluded
     paths = [
-        p
-        for p in paths
-        if (not excluded or not any(e in str(p) for e in excluded))
+        p for p in paths if (not excluded or not any(e in str(p) for e in excluded))
     ]
 
     # filter by package
@@ -260,9 +256,7 @@ def get_namefile_paths(
         filtered = []
         for nfp in paths:
             nf_pkgs = get_packages(nfp)
-            shared = set(nf_pkgs).intersection(
-                set([p.lower() for p in packages])
-            )
+            shared = set(nf_pkgs).intersection(set([p.lower() for p in packages]))
             if any(shared):
                 filtered.append(nfp)
         paths = filtered
@@ -271,9 +265,7 @@ def get_namefile_paths(
     if selected:
         paths = [
             namfile_path
-            for (namfile_path, model_path) in zip(
-                paths, [p.parent for p in paths]
-            )
+            for (namfile_path, model_path) in zip(paths, [p.parent for p in paths])
             if any(s in model_path.name for s in selected)
         ]
 
@@ -292,15 +284,41 @@ def get_model_paths(
     Find model directories recursively in the given location.
     A model directory is any directory containing one or more
     namefiles. Model directories can be filtered or excluded,
-    by prefix, pattern, namefile name, or packages used.
-    """
-
-    namefile_paths = get_namefile_paths(
-        path, prefix, namefile, excluded, selected, packages
-    )
-    model_paths = sorted(
-        list(set([p.parent for p in namefile_paths if p.parent.name]))
-    )
+    by prefix, pattern, namefile name, or packages used. The
+    directories are returned in order within scenario folders
+    such that groundwater flow model workspaces precede other
+    model types. This allows models which depend on the flow
+    model's outputs to consume its head or budget, and models
+    should successfully run in the sequence returned provided
+    input files (e.g. FMI) refer to output via relative paths.
+    """
+
+    def keyfunc(v):
+        v = str(v)
+        if "gwf" in v:
+            return 0
+        else:
+            return 1
+
+    model_paths = []
+    globbed = path.rglob(f"{prefix if prefix else ''}*")
+    example_paths = [p for p in globbed if p.is_dir()]
+    for p in example_paths:
+        for mp in sorted(
+            list(
+                set(
+                    [
+                        p.parent
+                        for p in get_namefile_paths(
+                            p, prefix, namefile, excluded, selected, packages
+                        )
+                    ]
+                )
+            ),
+            key=keyfunc,
+        ):
+            if mp not in model_paths:
+                model_paths.append(mp)
     return model_paths
 
 
@@ -338,19 +356,19 @@ def is_github_rate_limited() -> Optional[bool]:
 
     Returns
     -------
-        True if rate-limiting is applied, otherwise False (or None if the connection fails).
+        True if rate-limiting is applied, otherwise False
+        (or None if the connection fails).
     """
     try:
-        with request.urlopen(
-            "https://api.github.com/users/octocat"
-        ) as response:
+        with request.urlopen("https://api.github.com/users/octocat") as response:
             remaining = int(response.headers["x-ratelimit-remaining"])
             if remaining < 10:
                 warn(
-                    f"Only {remaining} GitHub API requests remaining before rate-limiting"
+                    f"Only {remaining} GitHub API requests "
+                    "remaining before rate-limiting"
                 )
             return remaining > 0
-    except:
+    except (ValueError, URLError):
         return None
 
 
@@ -369,7 +387,9 @@ def has_exe(exe):
     return _has_exe_cache[exe]
 
 
-def has_pkg(pkg: str, strict: bool = False) -> bool:
+def has_pkg(
+    pkg: str, strict: bool = False, name_map: Optional[Dict[str, str]] = None
+) -> bool:
     """
     Determines if the given Python package is installed.
 
@@ -378,8 +398,13 @@ def has_pkg(pkg: str, strict: bool = False) -> bool:
     pkg : str
         Name of the package to check.
     strict : bool
-        If False, only check if package metadata is available.
+        If False, only check if the package is cached or metadata is available.
         If True, try to import the package (all dependencies must be present).
+    name_map : dict, optional
+        Custom mapping between package names (as provided to `metadata.distribution`)
+        and module names (as used in import statements or `importlib.import_module`).
+        Useful for packages whose package names do not match the module name, e.g.
+        `pytest-xdist` and `xdist`, respectively, or `mfpymake` and `pymake`.
 
     Returns
     -------
@@ -388,12 +413,19 @@ def has_pkg(pkg: str, strict: bool = False) -> bool:
 
     Notes
     -----
+    If `strict=True` and a package name differs from its top-level module name, a
+    `name_map` must be provided, otherwise this function will return False even if
+    the package is installed.
+
     Originally written by Mike Toews (mwtoews@gmail.com) for FloPy.
     """
 
-    def try_import():
+    def get_module_name() -> str:
+        return pkg if name_map is None else name_map.get(pkg, pkg)
+
+    def try_import() -> bool:
         try:  # import name, e.g. "import shapefile"
-            importlib.import_module(pkg)
+            importlib.import_module(get_module_name())
             return True
         except ModuleNotFoundError:
             return False
@@ -405,14 +437,15 @@ def has_pkg(pkg: str, strict: bool = False) -> bool:
         except metadata.PackageNotFoundError:
             return False
 
-    found = False
-    if not strict:
-        found = pkg in _has_pkg_cache or try_metadata()
-    if not found:
-        found = try_import()
+    is_cached = pkg in _has_pkg_cache
+    has_metadata = try_metadata()
+    can_import = try_import()
+    if strict:
+        found = has_metadata and can_import
+    else:
+        found = has_metadata or is_cached
     _has_pkg_cache[pkg] = found
-
-    return _has_pkg_cache[pkg]
+    return found
 
 
 def timed(f):
@@ -481,7 +514,14 @@ def get_env(name: str, default: object = None) -> Optional[object]:
         if isinstance(default, bool):
             v = v.lower().title()
         v = literal_eval(v)
-    except:
+    except (
+        AttributeError,
+        ValueError,
+        TypeError,
+        SyntaxError,
+        MemoryError,
+        RecursionError,
+    ):
         return default
     if default is None:
         return v

{modflow-devtools-1.4.0 → modflow_devtools-1.6.0}/modflow_devtools/ostags.py

@@ -73,10 +73,10 @@ def get_binary_suffixes(ostag: str = None) -> Tuple[str, str]:
 
     try:
         return _suffixes(ostag.lower())
-    except:
+    except KeyError:
         try:
             return _suffixes(python_to_modflow_ostag(ostag))
-        except:
+        except KeyError:
             return _suffixes(github_to_modflow_ostag(ostag))
 
 

modflow_devtools-1.6.0/modflow_devtools/snapshots.py

@@ -0,0 +1,159 @@
+from io import BytesIO, StringIO
+from typing import Optional
+
+from modflow_devtools.imports import import_optional_dependency
+
+np = import_optional_dependency("numpy")
+pytest = import_optional_dependency("pytest")
+syrupy = import_optional_dependency("syrupy")
+
+# ruff: noqa: E402
+from syrupy import __import_extension
+from syrupy.assertion import SnapshotAssertion
+from syrupy.extensions.single_file import (
+    SingleFileSnapshotExtension,
+    WriteMode,
+)
+from syrupy.location import PyTestLocation
+from syrupy.types import (
+    PropertyFilter,
+    PropertyMatcher,
+    SerializableData,
+    SerializedData,
+)
+
+# extension classes
+
+
+class BinaryArrayExtension(SingleFileSnapshotExtension):
+    """
+    Binary snapshot of a NumPy array. Can be read back into NumPy with
+    .load(), preserving dtype and shape. This is the recommended array
+    snapshot approach if human-readability is not a necessity, as disk
+    space is minimized.
+    """
+
+    _write_mode = WriteMode.BINARY
+    _file_extension = "npy"
+
+    def serialize(
+        self,
+        data,
+        *,
+        exclude=None,
+        include=None,
+        matcher=None,
+    ):
+        buffer = BytesIO()
+        np.save(buffer, data)
+        return buffer.getvalue()
+
+
+class TextArrayExtension(SingleFileSnapshotExtension):
+    """
+    Text snapshot of a NumPy array. Flattens the array before writing.
+    Can be read back into NumPy with .loadtxt() assuming you know the
+    shape of the expected data and subsequently reshape it if needed.
+    """
+
+    _write_mode = WriteMode.TEXT
+    _file_extension = "txt"
+
+    def serialize(
+        self,
+        data: "SerializableData",
+        *,
+        exclude: Optional["PropertyFilter"] = None,
+        include: Optional["PropertyFilter"] = None,
+        matcher: Optional["PropertyMatcher"] = None,
+    ) -> "SerializedData":
+        buffer = StringIO()
+        np.savetxt(buffer, data.ravel())
+        return buffer.getvalue()
+
+
+class ReadableArrayExtension(SingleFileSnapshotExtension):
+    """
+    Human-readable snapshot of a NumPy array. Preserves array shape
+    at the expense of possible loss of precision (default 8 places)
+    and more difficulty loading into NumPy than TextArrayExtension.
+    """
+
+    _write_mode = WriteMode.TEXT
+    _file_extension = "txt"
+
+    def serialize(
+        self,
+        data: "SerializableData",
+        *,
+        exclude: Optional["PropertyFilter"] = None,
+        include: Optional["PropertyFilter"] = None,
+        matcher: Optional["PropertyMatcher"] = None,
+    ) -> "SerializedData":
+        return np.array2string(data, threshold=np.inf)
+
+
+class MatchAnything:
+    def __eq__(self, _):
+        return True
+
+
+# fixtures
+
+
+@pytest.fixture(scope="session")
+def snapshot_disable(pytestconfig) -> bool:
+    return pytestconfig.getoption("--snapshot-disable")
+
+
+@pytest.fixture
+def snapshot(request, snapshot_disable) -> "SnapshotAssertion":
+    return (
+        MatchAnything()
+        if snapshot_disable
+        else SnapshotAssertion(
+            update_snapshots=request.config.option.update_snapshots,
+            extension_class=__import_extension(request.config.option.default_extension),
+            test_location=PyTestLocation(request.node),
+            session=request.session.config._syrupy,
+        )
+    )
+
+
+@pytest.fixture
+def array_snapshot(snapshot, snapshot_disable):
+    return (
+        MatchAnything()
+        if snapshot_disable
+        else snapshot.use_extension(BinaryArrayExtension)
+    )
+
+
+@pytest.fixture
+def text_array_snapshot(snapshot, snapshot_disable):
+    return (
+        MatchAnything()
+        if snapshot_disable
+        else snapshot.use_extension(TextArrayExtension)
+    )
+
+
+@pytest.fixture
+def readable_array_snapshot(snapshot, snapshot_disable):
+    return (
+        MatchAnything()
+        if snapshot_disable
+        else snapshot.use_extension(ReadableArrayExtension)
+    )
+
+
+# pytest config hooks
+
+
+def pytest_addoption(parser):
+    parser.addoption(
+        "--snapshot-disable",
+        action="store_true",
+        default=False,
+        help="Disable snapshot comparisons.",
+    )

{modflow-devtools-1.4.0 → modflow_devtools-1.6.0/modflow_devtools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: modflow-devtools
-Version: 1.4.0
+Version: 1.6.0
 Summary: Python tools for MODFLOW development
 Author-email: "Joseph D. Hughes" <modflow@usgs.gov>, Michael Reno <mreno@ucar.edu>, Mike Taves <mwtoews@gmail.com>, Wes Bonelli <wbonelli@ucar.edu>
 Maintainer-email: "Joseph D. Hughes" <modflow@usgs.gov>
@@ -24,11 +24,7 @@ Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
 Provides-Extra: lint
-Requires-Dist: black; extra == "lint"
-Requires-Dist: cffconvert; extra == "lint"
-Requires-Dist: flake8; extra == "lint"
-Requires-Dist: isort; extra == "lint"
-Requires-Dist: pylint; extra == "lint"
+Requires-Dist: ruff; extra == "lint"
 Provides-Extra: test
 Requires-Dist: modflow-devtools[lint]; extra == "test"
 Requires-Dist: coverage; extra == "test"
@@ -37,11 +33,13 @@ Requires-Dist: filelock; extra == "test"
 Requires-Dist: meson!=0.63.0; extra == "test"
 Requires-Dist: ninja; extra == "test"
 Requires-Dist: numpy; extra == "test"
-Requires-Dist: pytest; extra == "test"
+Requires-Dist: pandas; extra == "test"
+Requires-Dist: pytest!=8.1.0; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
 Requires-Dist: pytest-dotenv; extra == "test"
 Requires-Dist: pytest-xdist; extra == "test"
 Requires-Dist: PyYaml; extra == "test"
+Requires-Dist: syrupy; extra == "test"
 Provides-Extra: docs
 Requires-Dist: sphinx; extra == "docs"
 Requires-Dist: sphinx-rtd-theme; extra == "docs"
@@ -105,6 +103,7 @@ 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
 
@@ -114,7 +113,7 @@ 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]"
@@ -122,7 +121,7 @@ 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" ]

{modflow-devtools-1.4.0 → modflow_devtools-1.6.0}/modflow_devtools.egg-info/SOURCES.txt

@@ -13,6 +13,7 @@ modflow_devtools/latex.py
 modflow_devtools/markers.py
 modflow_devtools/misc.py
 modflow_devtools/ostags.py
+modflow_devtools/snapshots.py
 modflow_devtools/zip.py
 modflow_devtools.egg-info/PKG-INFO
 modflow_devtools.egg-info/SOURCES.txt

{modflow-devtools-1.4.0 → modflow_devtools-1.6.0}/modflow_devtools.egg-info/requires.txt

@@ -5,11 +5,7 @@ sphinx-rtd-theme
 myst-parser
 
 [lint]
-black
-cffconvert
-flake8
-isort
-pylint
+ruff
 
 [test]
 modflow-devtools[lint]
@@ -19,8 +15,10 @@ filelock
 meson!=0.63.0
 ninja
 numpy
-pytest
+pandas
+pytest!=8.1.0
 pytest-cov
 pytest-dotenv
 pytest-xdist
 PyYaml
+syrupy

{modflow-devtools-1.4.0 → modflow_devtools-1.6.0}/pyproject.toml

@@ -44,11 +44,7 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 lint = [
-    "black",
-    "cffconvert",
-    "flake8",
-    "isort",
-    "pylint"
+    "ruff"
 ]
 test = [
     "modflow-devtools[lint]",
@@ -58,11 +54,13 @@ test = [
     "meson!=0.63.0",
     "ninja",
     "numpy",
-    "pytest",
+    "pandas",
+    "pytest!=8.1.0",
     "pytest-cov",
     "pytest-dotenv",
     "pytest-xdist",
-    "PyYaml"
+    "PyYaml",
+    "syrupy"
 ]
 docs = [
     "sphinx",
@@ -75,19 +73,19 @@ docs = [
 "Bug Tracker" = "https://github.com/MODFLOW-USGS/modflow-devtools/issues"
 "Source Code" = "https://github.com/MODFLOW-USGS/modflow-devtools"
 
+[tool.ruff]
+target-version = "py38"
+include = [
+    "pyproject.toml",
+    "modflow_devtools/**/*.py",
+    "autotest/**/*.py",
+    "docs/**/*.py",
+    "scripts/**/*.py",
+    ".github/**/*.py",
+]
 
-[tool.black]
-line-length = 79
-target_version = ["py37"]
-
-[tool.flynt]
-line-length = 79
-verbose = true
-
-[tool.isort]
-profile = "black"
-src_paths = ["modflow_devtools"]
-line_length = 79
+[tool.ruff.lint]
+select = ["F", "E", "I001"]
 
 [tool.setuptools]
 packages = ["modflow_devtools"]

modflow_devtools-1.6.0/version.txt

@@ -0,0 +1 @@
+1.6.0

modflow-devtools-1.4.0/version.txt

@@ -1 +0,0 @@
-1.4.0