chore: use mypy (MODFLOW-ORG#194)

Add mypy to lint deps, fix some typing issues, type check in CI

.github/workflows/ci.yml

@@ -30,18 +30,21 @@ jobs:
         with:
           cache-dependency-glob: "**/pyproject.toml"
 
-      - name: Install project
+      - name: Install
         run: uv sync --group lint
 
-      - name: Run ruff check
+      - name: Lint
         run: uvx ruff check
 
-      - name: Run ruff format
+      - name: Format
         run: uvx ruff format --check
 
-      - name: Check spelling
+      - name: Spelling
         run: uvx codespell
 
+      - name: Typing
+        run: uv run mypy modflow_devtools
+
   build:
     name: Build
     runs-on: ubuntu-latest

README.md

@@ -38,7 +38,6 @@ Python development tools for MODFLOW 6 and related projects.
   - [`MODFLOW-ORG/modflow6-examples`](https://github.com/MODFLOW-ORG/modflow6-examples)
   - [`MODFLOW-ORG/modflow6-testmodels`](https://github.com/MODFLOW-ORG/modflow6-testmodels)
   - [`MODFLOW-ORG/modflow6-largetestmodels`](https://github.com/MODFLOW-ORG/modflow6-largetestmodels)
-* a parser for MODFLOW 6 [definition files](https://modflow6.readthedocs.io/en/stable/_dev/dfn.html)
 
 ## Requirements
 

modflow_devtools/dfn.py

@@ -24,6 +24,10 @@
 
 from modflow_devtools.download import download_and_unzip
 
+# TODO: use dataclasses instead of typed dicts, static
+# methods on typed dicts are evidently not allowed
+# mypy: ignore-errors
+
 
 def _try_literal_eval(value: str) -> Any:
     """

modflow_devtools/dfn2toml.py

@@ -9,6 +9,8 @@
 
 from modflow_devtools.dfn import Dfn
 
+# mypy: ignore-errors
+
 
 def convert(indir: PathLike, outdir: PathLike):
     indir = Path(indir).expanduser().absolute()

modflow_devtools/download.py

@@ -146,7 +146,6 @@ def get_release(repo, tag="latest", retries=3, verbose=False) -> dict:
         else f"{req_url}/releases/tags/{tag}"
     )
     request = get_request(req_url)
-    releases = None
     num_tries = 0
 
     while True:
@@ -169,12 +168,7 @@ def get_release(repo, tag="latest", retries=3, verbose=False) -> dict:
                     f"use GITHUB_TOKEN env to bypass rate limit ({err})"
                 ) from err
             elif err.code == 404:
-                if releases is None:
-                    releases = get_releases(repo, verbose=verbose)
-                if tag not in releases:
-                    raise ValueError(
-                        f"Release {tag} not found (choose from {', '.join(releases)})"
-                    )
+                raise ValueError(f"Release {tag} not found")
             elif err.code == 503 and num_tries < retries:
                 # GitHub sometimes returns this error for valid URLs, so retry
                 warn(f"URL request {num_tries} failed ({err})")

modflow_devtools/fixtures.py

@@ -86,7 +86,8 @@ def session_tmpdir(tmpdir_factory, request) -> Generator[Path, None, None]:
 @pytest.fixture
 def repos_path() -> Path | None:
     """Path to directory containing test model and example repositories"""
-    return environ.get("REPOS_PATH", None)
+    path = environ.get("REPOS_PATH", None)
+    return Path(path) if path else None
 
 
 @pytest.fixture

modflow_devtools/imports.py

@@ -42,6 +42,9 @@
 
 from packaging.version import Version
 
+# mypy: ignore-errors
+
+
 VERSIONS = {}
 
 

modflow_devtools/latex.py

@@ -1,4 +1,4 @@
-from collections.abc import Iterable
+from collections.abc import Iterable, Sequence
 from os import PathLike
 from pathlib import Path
 
@@ -7,8 +7,8 @@ def build_table(
     caption: str,
     fpth: str | PathLike,
     arr,
-    headings: Iterable[str] | None = None,
-    col_widths: Iterable[float] | None = None,
+    headings: Sequence[str] | None = None,
+    col_widths: Sequence[float] | None = None,
 ):
     """
     Build a LaTeX table from the given NumPy array.
@@ -55,7 +55,7 @@ def build_table(
 def get_header(
     caption: str,
     label: str,
-    headings: Iterable[str],
+    headings: Sequence[str],
     col_widths: Iterable[float] | None = None,
     center: bool = True,
     firsthead: bool = False,

modflow_devtools/make_registry.py

@@ -30,7 +30,7 @@ def write_registry(
     if not registry_path.exists():
         registry_path.parent.mkdir(parents=True, exist_ok=True)
 
-    models = {}
+    models: dict[str, list[str]] = {}
     exclude = [".DS_Store"]
     with registry_path.open("a+" if append else "w") as f:
         if not path.is_dir():

modflow_devtools/misc.py

@@ -162,7 +162,7 @@ def get_packages(namefile_path: PathLike) -> list[str]:
         a list of packages used by the simulation or model
     """
 
-    packages = []
+    packages: list[str] = []
     path = Path(namefile_path).expanduser().resolve()
     lines = path.read_text().splitlines()
     gwf_lines = [ln for ln in lines if ln.strip().lower().startswith("gwf6 ")]
@@ -188,22 +188,22 @@ def parse_model_namefile(line):
 
     for line in lines:
         # Skip over blank and commented lines
-        line = line.strip().split()
-        if len(line) < 2:
+        words = line.strip().split()
+        if len(words) < 2:
             continue
 
-        line = line[0].lower()
-        if any(line.startswith(c) for c in ["#", "!", "data", "list"]) or line in [
+        word = words[0].lower()
+        if any(word.startswith(c) for c in ["#", "!", "data", "list"]) or word in [
             "begin",
             "end",
             "memory_print_option",
         ]:
             continue
 
         # strip "6" from package name
-        line = line.replace("6", "")
+        word = word.replace("6", "")
 
-        packages.append(line.lower())
+        packages.append(word.lower())
 
     return list(set(packages))
 
@@ -293,6 +293,7 @@ def keyfunc(v):
         else:
             return 1
 
+    path = Path(path).expanduser().absolute()
     model_paths = []
     globbed = path.rglob(f"{prefix if prefix else ''}*")
     example_paths = [p for p in globbed if p.is_dir()]
@@ -499,7 +500,8 @@ def get_env(name: str, default: object = None) -> object | None:
     otherwise the default value if the environment variable is not set.
     """
     try:
-        v = environ.get(name)
+        if (v := environ.get(name, None)) is None:
+            return default
         if isinstance(default, bool):
             v = v.lower().title()
         v = literal_eval(v)

modflow_devtools/models.py

@@ -1,4 +1,5 @@
 import importlib.resources as pkg_resources
+from collections.abc import Callable
 from io import IOBase
 from pathlib import Path
 
@@ -29,13 +30,13 @@
 )
 
 try:
-    with pkg_resources.open_text(DATA_ANCHOR, REGISTRY_NAME) as f:
-        FETCHER.load_registry(f)
+    with pkg_resources.open_text(DATA_ANCHOR, REGISTRY_NAME) as rf:
+        FETCHER.load_registry(rf)
 except:  # noqa: E722
     print(f"Could not load registry from {DATA_PATH}/{REGISTRY_NAME}.")
 
 
-def _generate_function(model_name, files) -> callable:
+def _generate_function(model_name, files) -> Callable:
     def model_function():
         return [Path(FETCHER.fetch(file)) for file in files]
 
@@ -59,7 +60,7 @@ def model_map() -> dict[str, list[Path]]:
 
 
 try:
-    with pkg_resources.open_binary(DATA_ANCHOR, MODELMAP_NAME) as f:
-        _attach_functions(f)
+    with pkg_resources.open_binary(DATA_ANCHOR, MODELMAP_NAME) as mf:
+        _attach_functions(mf)
 except:  # noqa: E722
     print(f"Could not load model mapping from {DATA_PATH}/{MODELMAP_NAME}.")

modflow_devtools/snapshots.py

@@ -1,5 +1,5 @@
 from io import BytesIO, StringIO
-from typing import Optional
+from typing import Optional, Union
 
 from modflow_devtools.imports import import_optional_dependency
 
@@ -107,7 +107,7 @@ def snapshot_disable(pytestconfig) -> bool:
 
 
 @pytest.fixture
-def snapshot(request, snapshot_disable) -> "SnapshotAssertion":
+def snapshot(request, snapshot_disable) -> Union[MatchAnything, "SnapshotAssertion"]:
     return (
         MatchAnything()
         if snapshot_disable

pyproject.toml

@@ -45,7 +45,8 @@ build = [
 ]
 lint = [
     "codespell[toml]",
-    "ruff"
+    "ruff",
+    "mypy"
 ]
 test = [
     "modflow-devtools[lint]",
@@ -87,7 +88,8 @@ build = [
 ]
 lint = [
     "codespell[toml]",
-    "ruff"
+    "ruff",
+    "mypy",
 ]
 test = [
     "modflow-devtools[lint]",
@@ -178,3 +180,8 @@ select = [
 
 [tool.pytest.ini_options]
 addopts = ["--import-mode=importlib"]
+
+[tool.mypy]
+mypy_path = "modflow_devtools"
+ignore_missing_imports = true
+warn_unreachable = true