FIX: Fixes

.github/pull_request_template.md

@@ -1,3 +1,3 @@
 ### Before merging …
 
-- [ ] Changelog has been updated (`docs/source/changes.md`)
+- [ ] Changelog has been updated (`docs/source/vX.Y.md.inc`)

.gitignore

@@ -19,3 +19,4 @@ build/
 .hypothesis/
 .coverage*
 junit-results.xml
+.cache/

docs/source/examples/gen_examples.py

@@ -7,8 +7,9 @@
 import shutil
 import sys
 from collections import defaultdict
-from collections.abc import Iterable
+from collections.abc import Generator, Iterable
 from pathlib import Path
+from typing import Any
 
 from tqdm import tqdm
 
@@ -23,15 +24,15 @@
 logger = logging.getLogger()
 
 
-def _bool_to_icon(x: bool | Iterable) -> str:
+def _bool_to_icon(x: bool | Iterable[Any]) -> str:
     if x:
         return "✅"
     else:
         return "❌"
 
 
 @contextlib.contextmanager
-def _task_context(task):
+def _task_context(task: str | None) -> Generator[None, None, None]:
     old_argv = sys.argv
     if task:
         sys.argv = [sys.argv[0], f"--task={task}"]
@@ -41,7 +42,7 @@ def _task_context(task):
         sys.argv = old_argv
 
 
-def _gen_demonstrated_funcs(example_config_path: Path) -> dict:
+def _gen_demonstrated_funcs(example_config_path: Path) -> dict[str, bool]:
     """Generate dict of demonstrated functionality based on config."""
     # Here we use a defaultdict, and for keys that might vary across configs
     # we should use an `funcs[key] = funcs[key] or ...` so that we effectively

docs/source/features/gen_steps.py

@@ -196,7 +196,6 @@
             if not isinstance(a_b, str):
                 all_steps_list.extend(a_b)
         all_steps = set(all_steps_list)
-        assert len(all_steps) == len(all_steps_list)
         assert mapped == all_steps, all_steps.symmetric_difference(mapped)
     overview_lines.append("```\n\n</details>\n")
 

docs/source/v1.9.md.inc

@@ -58,3 +58,4 @@
 
 - Use GitHub's `dependabot` service to automatically keep GitHub Actions up-to-date. (#893 by @hoechenberger)
 - Clean up some strings that our autoformatter failed to correctly merge. (#965 by @drammock)
+- Type hints are now checked using `mypy`. (#995 by @larsoner)

mne_bids_pipeline/_docs.py

@@ -3,6 +3,8 @@
 import re
 from collections import defaultdict
 from pathlib import Path
+from types import FunctionType
+from typing import Any
 
 from tqdm import tqdm
 
@@ -104,11 +106,11 @@
 
 
 class _ParseConfigSteps:
-    def __init__(self, force_empty=None):
+    def __init__(self, force_empty: tuple[str, ...] | None = None) -> None:
         self._force_empty = _FORCE_EMPTY if force_empty is None else force_empty
-        self.steps = defaultdict(list)
+        self.steps: dict[str, Any] = defaultdict(list)
         # Add a few helper functions
-        for func in (
+        for func_extra in (
             _config_utils.get_eeg_reference,
             _config_utils.get_all_contrasts,
             _config_utils.get_decoding_contrasts,
@@ -117,15 +119,16 @@ def __init__(self, force_empty=None):
             _config_utils.get_mf_cal_fname,
             _config_utils.get_mf_ctc_fname,
         ):
-            this_list = []
-            for attr in ast.walk(ast.parse(inspect.getsource(func))):
+            this_list: list[str] = []
+            assert isinstance(func_extra, FunctionType)
+            for attr in ast.walk(ast.parse(inspect.getsource(func_extra))):
                 if not isinstance(attr, ast.Attribute):
                     continue
                 if not (isinstance(attr.value, ast.Name) and attr.value.id == "config"):
                     continue
                 if attr.attr not in this_list:
                     this_list.append(attr.attr)
-            _MANUAL_KWS[func.__name__] = tuple(this_list)
+            _MANUAL_KWS[func_extra.__name__] = tuple(this_list)
 
         for module in tqdm(
             sum(_config_utils._get_step_modules().values(), tuple()),
@@ -147,6 +150,7 @@ def __init__(self, force_empty=None):
                         for keyword in call.keywords:
                             if not isinstance(keyword.value, ast.Attribute):
                                 continue
+                            assert isinstance(keyword.value.value, ast.Name)
                             if keyword.value.value.id != "config":
                                 continue
                             if keyword.value.attr in ("exec_params",):
@@ -165,6 +169,7 @@ def __init__(self, force_empty=None):
                         for attr in ast.walk(cond.test):
                             if not isinstance(attr, ast.Attribute):
                                 continue
+                            assert isinstance(attr.value, ast.Name)
                             if attr.value.id != "config":
                                 continue
                             self._add_step_option(step, attr.attr)
@@ -175,6 +180,7 @@ def __init__(self, force_empty=None):
                 for call in ast.walk(func):
                     if not isinstance(call, ast.Call):
                         continue
+                    assert isinstance(call.func, ast.Name)
                     if call.func.id != "SimpleNamespace":
                         continue
                     break
@@ -183,6 +189,7 @@ def __init__(self, force_empty=None):
                 assert call.args == []
                 for keyword in call.keywords:
                     if isinstance(keyword.value, ast.Call):
+                        assert isinstance(keyword.value.func, ast.Name)
                         key = keyword.value.func.id
                         if key in _MANUAL_KWS:
                             for option in _MANUAL_KWS[key]:
@@ -191,6 +198,7 @@ def __init__(self, force_empty=None):
                         if keyword.value.func.id == "_sanitize_callable":
                             assert len(keyword.value.args) == 1
                             assert isinstance(keyword.value.args[0], ast.Attribute)
+                            assert isinstance(keyword.value.args[0].value, ast.Name)
                             assert keyword.value.args[0].value.id == "config"
                             self._add_step_option(step, keyword.value.args[0].attr)
                             continue
@@ -213,6 +221,7 @@ def __init__(self, force_empty=None):
                         for func_name in _EXTRA_FUNCS.get(key, ()):
                             funcs.append(getattr(_config_utils, func_name))
                         for fi, func in enumerate(funcs):
+                            assert isinstance(func, FunctionType), func
                             source = inspect.getsource(func)
                             assert "config: SimpleNamespace" in source, key
                             if fi == 0:
@@ -240,6 +249,7 @@ def __init__(self, force_empty=None):
                     option = keyword.value.attr
                     if option in _IGNORE_OPTIONS:
                         continue
+                    assert isinstance(keyword.value.value, ast.Name)
                     assert keyword.value.value.id == "config", f"{where} {keyword.value.value.id}"  # noqa: E501  # fmt: skip
                     self._add_step_option(step, option)
             if step in _NO_CONFIG:

mne_bids_pipeline/steps/sensor/_05_decoding_csp.py

@@ -223,7 +223,6 @@ def one_subject_decoding(
         ignore_index=True,
     )
     del freq_decoding_table_rows
-    assert isinstance(freq_decoding_table, pd.DataFrame)
 
     def _fmt_contrast(cond1, cond2, fmin, fmax, freq_range_name, tmin=None, tmax=None):
         msg = (
@@ -235,16 +234,12 @@ def _fmt_contrast(cond1, cond2, fmin, fmax, freq_range_name, tmin=None, tmax=Non
         return msg
 
     for idx, row in freq_decoding_table.iterrows():
-        assert isinstance(row["f_min"], pd.Series)
-        fmin = row["f_min"].item()
-        assert isinstance(row["f_max"], pd.Series)
-        fmax = row["f_max"].item()
-        assert isinstance(row["cond_1"], pd.Series)
-        cond1 = row["cond_1"].item()
-        assert isinstance(row["cond_2"], pd.Series)
-        cond2 = row["cond_2"].item()
-        assert isinstance(row["freq_range_name"], pd.Series)
-        freq_range_name = row["freq_range_name"].item()
+        assert isinstance(row, pd.Series)
+        fmin = row["f_min"]
+        fmax = row["f_max"]
+        cond1 = row["cond_1"]
+        cond2 = row["cond_2"]
+        freq_range_name = row["freq_range_name"]
 
         msg = _fmt_contrast(cond1, cond2, fmin, fmax, freq_range_name)
         logger.info(**gen_log_kwargs(msg))
@@ -268,6 +263,7 @@ def _fmt_contrast(cond1, cond2, fmin, fmax, freq_range_name, tmin=None, tmax=Non
         )
         freq_decoding_table.loc[idx, "mean_crossval_score"] = cv_scores.mean()
         freq_decoding_table.at[idx, "scores"] = cv_scores
+        del fmin, fmax, cond1, cond2, freq_range_name
 
     # Loop over times x frequencies
     #
@@ -308,6 +304,7 @@ def _fmt_contrast(cond1, cond2, fmin, fmax, freq_range_name, tmin=None, tmax=Non
     for idx, row in tf_decoding_table.iterrows():
         if len(row) == 0:
             break  # no data
+        assert isinstance(row, pd.Series)
         tmin = row["t_min"]
         tmax = row["t_max"]
         fmin = row["f_min"]
@@ -339,6 +336,7 @@ def _fmt_contrast(cond1, cond2, fmin, fmax, freq_range_name, tmin=None, tmax=Non
         msg = _fmt_contrast(cond1, cond2, fmin, fmax, freq_range_name, tmin, tmax)
         msg += f": {cfg.decoding_metric}={score:0.3f}"
         logger.info(**gen_log_kwargs(msg))
+        del tmin, tmax, fmin, fmax, cond1, cond2, freq_range_name
 
     # Write each DataFrame to a different Excel worksheet.
     a_vs_b = f"{condition1}+{condition2}".replace(op.sep, "")
@@ -441,14 +439,15 @@ def _fmt_contrast(cond1, cond2, fmin, fmax, freq_range_name, tmin=None, tmax=Non
             )
             results = all_csp_tf_results[contrast]
             mean_crossval_scores: list[float] = list()
-            tmin, tmax, fmin, fmax = list(), list(), list(), list()
+            tmin_list, tmax_list = list(), list()
+            fmin_list, fmax_list = list(), list()
             mean_crossval_scores.extend(
                 results["mean_crossval_score"].to_numpy().ravel().tolist()
             )
-            tmin.extend(results["t_min"].to_numpy().ravel())
-            tmax.extend(results["t_max"].to_numpy().ravel())
-            fmin.extend(results["f_min"].to_numpy().ravel())
-            fmax.extend(results["f_max"].to_numpy().ravel())
+            tmin_list.extend(results["t_min"].to_numpy().ravel())
+            tmax_list.extend(results["t_max"].to_numpy().ravel())
+            fmin_list.extend(results["f_min"].to_numpy().ravel())
+            fmax_list.extend(results["f_max"].to_numpy().ravel())
             mean_crossval_scores_array = np.array(mean_crossval_scores, float)
             del mean_crossval_scores
             fig, ax = plt.subplots(constrained_layout=True)
@@ -466,10 +465,10 @@ def _fmt_contrast(cond1, cond2, fmin, fmax, freq_range_name, tmin=None, tmax=Non
             img = _imshow_tf(
                 mean_crossval_scores_array,
                 ax,
-                tmin=tmin,
-                tmax=tmax,
-                fmin=fmin,
-                fmax=fmax,
+                tmin=tmin_list,
+                tmax=tmax_list,
+                fmin=fmin_list,
+                fmax=fmax_list,
                 vmin=vmin,
                 vmax=vmax,
             )
@@ -478,16 +477,16 @@ def _fmt_contrast(cond1, cond2, fmin, fmax, freq_range_name, tmin=None, tmax=Non
             )
             for freq_range_name, bins in freq_name_to_bins_map.items():
                 ax.text(
-                    tmin[0],
+                    tmin_list[0],
                     0.5 * bins[0][0] + 0.5 * bins[-1][1],
                     freq_range_name,
                     transform=offset,
                     ha="left",
                     va="center",
                     rotation=90,
                 )
-            ax.set_xlim([np.min(tmin), np.max(tmax)])
-            ax.set_ylim([np.min(fmin), np.max(fmax)])
+            ax.set_xlim([np.min(tmin_list), np.max(tmax_list)])
+            ax.set_ylim([np.min(fmin_list), np.max(fmax_list)])
             ax.set_xlabel("Time (s)")
             ax.set_ylabel("Frequency (Hz)")
             cbar = fig.colorbar(

mne_bids_pipeline/tests/test_documented.py

@@ -5,6 +5,7 @@
 import re
 import sys
 from pathlib import Path
+from types import CodeType
 
 import yaml
 
@@ -22,11 +23,13 @@ def test_options_documented():
     with open(root_path / "_config.py") as fid:
         contents = fid.read()
     contents = ast.parse(contents)
-    in_config = [
+    assert isinstance(contents, CodeType)
+    in_config_list = [
         item.target.id for item in contents.body if isinstance(item, ast.AnnAssign)
     ]
-    assert len(set(in_config)) == len(in_config)
-    in_config = set(in_config)
+    assert len(set(in_config_list)) == len(in_config_list)
+    in_config = set(in_config_list)
+    del in_config_list
     # ensure we clean our namespace correctly
     config = _get_default_config()
     config_names = set(d for d in dir(config) if not d.startswith("_"))
@@ -156,7 +159,7 @@ def test_datasets_in_doc():
         assert n_found == count, f"{cp} ({n_found} != {count})"
 
     # 3. Read examples from docs (being careful about tags we can't read)
-    class SafeLoaderIgnoreUnknown(yaml.SafeLoader):
+    class SafeLoaderIgnoreUnknown(yaml.SafeLoader):  # type: ignore[misc]
         def ignore_unknown(self, node):
             return None
 

pyproject.toml

@@ -133,12 +133,27 @@ convention = "numpy"
 ignore_errors = false
 scripts_are_modules = true
 ignore_missing_imports = true
-strict = false
 modules = ["mne_bids_pipeline"]
 disable_error_code = [
     "import-untyped",
 ]
 
+# TODO: Add these
+[[tool.mypy.overrides]]
+module = [
+  "mne_bids_pipeline.steps.*",
+  "mne_bids_pipeline.tests.*",
+  "docs.source.examples.*",
+]
+disable_error_code = [
+  "assignment",
+  "no-untyped-call",
+  "no-untyped-def",
+  "union-attr",
+  "type-arg",
+  "no-any-return",
+]
+
 [[tool.mypy.overrides]]
 module = ["mne_bids_pipeline.steps.freesurfer.contrib.*"]
 ignore_errors = true
@@ -147,11 +162,11 @@ ignore_errors = true
 module = ['mne_bids_pipeline.tests.configs.*']
 # Ignare: Need type annotation for "plot_psd_for_runs" [var-annotated]
 disable_error_code = [
-    "var-annotated",
+  "var-annotated",
 ]
 
 [[tool.mypy.overrides]]
 module = ["mne_bids_pipeline.tests.configs.config_ERP_CORE"]
 disable_error_code = [
-    "assignment",
-]
+  "assignment",
+]