update af_st and add helpers.py

- Reduce the number of lines in each test by setting hypothesis settings
by defining callable functions in helpers.py
- Simplify generation of valid characters by adding strategy for
  generating valid characters

afids_utils/afids.py

@@ -54,18 +54,6 @@ class AfidPosition:
     z: float = attrs.field()
     desc: str = attrs.field(validator=_validate_desc)
 
-    def __sub__(self, other: AfidPosition) -> tuple[float, float, float]:
-        # Check if computation performed on corresponding AFIDs
-        if not self.label == other.label or not self.desc == other.desc:
-            raise ValueError("Non-corresponding AFIDs")
-
-        # Compute distances
-        x_dist = self.x - other.x
-        y_dist = self.y - other.y
-        z_dist = self.z - other.z
-
-        return x_dist, y_dist, z_dist
-
 
 def _validate_afids(
     instance: AfidSet,

afids_utils/tests/helpers.py

@@ -0,0 +1,24 @@
+from __future__ import annotations
+
+from datetime import timedelta
+from typing import Callable, TypeVar
+
+from hypothesis import HealthCheck, settings
+
+_T = TypeVar("_T")
+
+
+def allow_function_scoped(callable: _T, /) -> _T:
+    """Allow function_scoped fixtures in tests"""
+    return settings(
+        suppress_health_check=[HealthCheck.function_scoped_fixture]
+    )(callable)
+
+
+def deadline(time: int | float | timedelta | None) -> Callable[[_T], _T]:
+    """Change hypothesis deadline"""
+
+    def inner(callable: _T, /) -> _T:
+        return settings(deadline=time)(callable)
+
+    return inner

afids_utils/tests/strategies.py

@@ -18,6 +18,14 @@
     HUMAN_PROTOCOL_MAP = json.load(json_fpath)["human"]
 
 
+def gen_chars():
+    return st.text(
+        min_size=2,
+        max_size=5,
+        alphabet=st.characters(min_codepoint=ord("A"), max_codepoint=ord("z")),
+    )
+
+
 def valid_labels():
     return st.integers(min_value=1, max_value=32)
 

afids_utils/tests/test_afids.py

@@ -8,13 +8,14 @@
 from pathlib import Path
 
 import pytest
-from hypothesis import HealthCheck, assume, example, given, settings
+from hypothesis import assume, example, given
 from hypothesis import strategies as st
 from more_itertools import pairwise
 
 import afids_utils.tests.strategies as af_st
 from afids_utils.afids import AfidPosition, AfidSet
 from afids_utils.exceptions import InvalidFiducialError, InvalidFileError
+from afids_utils.tests.helpers import allow_function_scoped
 
 
 @pytest.fixture
@@ -158,10 +159,8 @@ def test_repeated_incomplete_afid_set(
 
 
 class TestAfidsIO:
-    @given(label=st.integers(min_value=0, max_value=31))
-    @settings(
-        suppress_health_check=[HealthCheck.function_scoped_fixture],
-    )
+    @given(label=af_st.valid_labels())
+    @allow_function_scoped
     def test_valid_load(
         self,
         valid_fcsv_file: PathLike[str],
@@ -177,25 +176,15 @@ def test_valid_load(
         assert isinstance(afids_set.slicer_version, str)
         assert isinstance(afids_set.coord_system, str)
         assert isinstance(afids_set.afids, list)
-        assert isinstance(afids_set.afids[label], AfidPosition)
+        assert isinstance(afids_set.afids[label - 1], AfidPosition)
 
     def test_invalid_fpath(self):
         with pytest.raises(FileNotFoundError, match=".*does not exist"):
             AfidSet.load("invalid/fpath.fcsv")
 
-    @given(
-        ext=st.text(
-            min_size=2,
-            max_size=5,
-            alphabet=st.characters(
-                min_codepoint=ord("A"), max_codepoint=ord("z")
-            ),
-        )
-    )
-    @settings(
-        suppress_health_check=[HealthCheck.function_scoped_fixture],
-    )
-    def test_invalid_ext(self, valid_fcsv_file: PathLike[str], ext: str):
+    @given(ext=af_st.gen_chars())
+    @allow_function_scoped
+    def test_invalid_ext(self, ext: str):
         assume(not ext == "fcsv" or not ext == "json")
 
         with tempfile.NamedTemporaryFile(
@@ -224,19 +213,8 @@ def test_invalid_label_range(self, valid_fcsv_file: PathLike[str]):
             with pytest.raises(InvalidFileError, match="Unexpected number.*"):
                 AfidSet.load(out_fcsv_file.name)
 
-    @given(
-        label=st.integers(min_value=0, max_value=31),
-        desc=st.text(
-            min_size=2,
-            max_size=5,
-            alphabet=st.characters(
-                min_codepoint=ord("A"), max_codepoint=ord("z")
-            ),
-        ),
-    )
-    @settings(
-        suppress_health_check=[HealthCheck.function_scoped_fixture],
-    )
+    @given(label=af_st.valid_labels(), desc=af_st.gen_chars())
+    @allow_function_scoped
     def test_invalid_desc(
         self,
         valid_fcsv_file: PathLike[str],
@@ -247,16 +225,16 @@ def test_invalid_desc(
         assume(
             desc
             not in [
-                human_mappings[label]["desc"],
-                human_mappings[label]["acronym"],
+                human_mappings[label - 1]["desc"],
+                human_mappings[label - 1]["acronym"],
             ]
         )
 
         # Replace valid description with a mismatch
         with open(valid_fcsv_file) as valid_fcsv:
             fcsv_data = valid_fcsv.readlines()
-            fcsv_data[label + 3] = fcsv_data[label + 3].replace(
-                human_mappings[label]["desc"], desc
+            fcsv_data[label + 2] = fcsv_data[label + 2].replace(
+                human_mappings[label - 1]["desc"], desc
             )
 
         # Write to temp file
@@ -283,18 +261,8 @@ def test_valid_save(self, valid_fcsv_file: PathLike[str]):
 
             assert Path(out_fcsv_file.name).exists()
 
-    @given(
-        ext=st.text(
-            min_size=2,
-            max_size=5,
-            alphabet=st.characters(
-                min_codepoint=ord("A"), max_codepoint=ord("z")
-            ),
-        )
-    )
-    @settings(
-        suppress_health_check=[HealthCheck.function_scoped_fixture],
-    )
+    @given(ext=af_st.gen_chars())
+    @allow_function_scoped
     def test_invalid_ext_save(self, valid_fcsv_file: PathLike[str], ext: str):
         assume(not ext == "fcsv" or not ext == "json")
 
@@ -306,9 +274,7 @@ def test_invalid_ext_save(self, valid_fcsv_file: PathLike[str], ext: str):
                 afid_set.save(out_file.name)
 
     @given(afid_set=af_st.afid_sets())
-    @settings(
-        suppress_health_check=[HealthCheck.function_scoped_fixture],
-    )
+    @allow_function_scoped
     def test_save_invalid_coord_system(self, afid_set: AfidSet):
         afid_set.coord_system = "invalid"
 
@@ -323,9 +289,7 @@ def test_save_invalid_coord_system(self, afid_set: AfidSet):
     @given(
         afid_set=af_st.afid_sets(), coord_sys=st.sampled_from(["LPS", "RAS"])
     )
-    @settings(
-        suppress_health_check=[HealthCheck.function_scoped_fixture],
-    )
+    @allow_function_scoped
     def test_update_coord_system(self, afid_set: AfidSet, coord_sys: str):
         afid_set.coord_system = coord_sys
 
@@ -348,10 +312,8 @@ def test_update_coord_system(self, afid_set: AfidSet, coord_sys: str):
 
 
 class TestAfidsCore:
-    @given(label=st.integers(min_value=1, max_value=32))
-    @settings(
-        suppress_health_check=[HealthCheck.function_scoped_fixture],
-    )
+    @given(label=af_st.valid_labels())
+    @allow_function_scoped
     def test_valid_get_afid(self, valid_fcsv_file: PathLike[str], label: int):
         afid_set = AfidSet.load(valid_fcsv_file)
         afid_pos = afid_set.get_afid(label)
@@ -360,9 +322,7 @@ def test_valid_get_afid(self, valid_fcsv_file: PathLike[str], label: int):
         assert isinstance(afid_pos, AfidPosition)
 
     @given(label=st.integers(min_value=-100, max_value=100))
-    @settings(
-        suppress_health_check=[HealthCheck.function_scoped_fixture],
-    )
+    @allow_function_scoped
     def test_invalid_get_afid(
         self, valid_fcsv_file: PathLike[str], label: int
     ):

afids_utils/tests/test_ext.py

@@ -6,13 +6,14 @@
 from pathlib import Path
 
 import pytest
-from hypothesis import HealthCheck, assume, given, settings
+from hypothesis import assume, given
 from hypothesis import strategies as st
 
+import afids_utils.tests.strategies as af_st
 from afids_utils.afids import AfidPosition, AfidSet
 from afids_utils.exceptions import InvalidFileError
 from afids_utils.ext.fcsv import _get_afids, _get_metadata, save_fcsv
-from afids_utils.tests.strategies import afid_sets
+from afids_utils.tests.helpers import allow_function_scoped
 
 
 @pytest.fixture
@@ -24,9 +25,7 @@ def valid_fcsv_file() -> PathLike[str]:
 
 class TestLoadFcsv:
     @given(coord_num=st.integers(min_value=0, max_value=1))
-    @settings(
-        suppress_health_check=[HealthCheck.function_scoped_fixture],
-    )
+    @allow_function_scoped
     def test_get_valid_metadata(
         self, valid_fcsv_file: PathLike[str], coord_num: int
     ):
@@ -62,9 +61,7 @@ def test_get_valid_metadata(
             assert parsed_coord == "RAS"
 
     @given(coord_num=st.integers(min_value=2))
-    @settings(
-        suppress_health_check=[HealthCheck.function_scoped_fixture],
-    )
+    @allow_function_scoped
     def test_invalid_num_coord(
         self, valid_fcsv_file: PathLike[str], coord_num: int
     ):
@@ -89,17 +86,8 @@ def test_invalid_num_coord(
                 ):
                     _get_metadata(temp_in_fcsv.readlines())
 
-    @given(
-        coord_str=st.text(
-            min_size=3,
-            alphabet=st.characters(
-                min_codepoint=ord("A"), max_codepoint=ord("z")
-            ),
-        )
-    )
-    @settings(
-        suppress_health_check=[HealthCheck.function_scoped_fixture],
-    )
+    @given(coord_str=af_st.gen_chars())
+    @allow_function_scoped
     def test_invalid_str_coord(
         self, valid_fcsv_file: PathLike[str], coord_str: int
     ):
@@ -145,34 +133,28 @@ def test_invalid_header(self, valid_fcsv_file: PathLike[str]):
                 ):
                     _get_metadata(temp_in_fcsv.readlines())
 
-    @given(label=st.integers(min_value=0, max_value=31))
-    @settings(
-        suppress_health_check=[HealthCheck.function_scoped_fixture],
-    )
+    @given(label=af_st.valid_labels())
+    @allow_function_scoped
     def test_valid_get_afids(self, valid_fcsv_file: PathLike[str], label: int):
         with open(valid_fcsv_file) as valid_fcsv:
             afids_positions = _get_afids(valid_fcsv.readlines())
 
         assert isinstance(afids_positions, list)
-        assert isinstance(afids_positions[label], AfidPosition)
+        assert isinstance(afids_positions[label - 1], AfidPosition)
 
 
 class TestSaveFcsv:
-    @given(afid_set=afid_sets())
-    @settings(
-        suppress_health_check=[HealthCheck.function_scoped_fixture],
-    )
+    @given(afid_set=af_st.afid_sets())
+    @allow_function_scoped
     def test_save_fcsv_invalid_template(
         self,
         afid_set: AfidSet,
     ):
         with pytest.raises(FileNotFoundError):
             save_fcsv(afid_set, "/invalid/template/path.fcsv")
 
-    @given(afid_set=afid_sets(randomize_header=False))
-    @settings(
-        suppress_health_check=[HealthCheck.function_scoped_fixture],
-    )
+    @given(afid_set=af_st.afid_sets(randomize_header=False))
+    @allow_function_scoped
     def test_save_fcsv_valid_template(self, afid_set: AfidSet):
         with tempfile.NamedTemporaryFile(
             mode="w", prefix="sub-test_desc-", suffix="_afids.fcsv"