todos to issues (#51)

* remove todo
#42

* remove todo
#42

* remove todos
#47 and #42

* remove todo
#42

* remove todos
#49 and #42

* remove todos
#50 and #42

* improve code validation

* adapt code validation code duplication is allowed

.github/workflows/pylint.yml

@@ -23,5 +23,4 @@ jobs:
         pip install pylint
     - name: Analysing the code with pylint
       run: |
-        # TODO: code duplication should be allowed for unittest
-        pylint src
+        pylint --disable=R0801 src

src/nerte/geometry/cylindircal_swirl_geometry_unittest.py

@@ -349,7 +349,7 @@ def geodesic_equation(
             ray: TangentialVectorDelta,
         ) -> TangentialVectorDelta:
             # pylint: disable=C0103
-            # TODO: revert when mypy bug was fixed
+            # MYPY-BUG: revert when mypy bug was fixed
             #       see https://github.com/python/mypy/issues/2220
             # r, _, z = ray.point_delta
             # v_r, v_phi, v_z = ray.vector_delta

src/nerte/values/linalg.py

@@ -234,7 +234,7 @@ def dot(
     return np.dot(
         vec1._v,
         np.dot(metric.matrix()._m, vec2._v),  # type: ignore[no-untyped-call]
-    )  # TODO: optimize
+    )  # POSSIBLE-OPTIMIZATION: hard code
 
 
 def cross(
@@ -270,8 +270,9 @@ def length(vec: AbstractVector, metric: Optional[Metric] = None) -> float:
     Returns the length of the vector (with respect to an orthonormal basis).
     """
     if metric is None:
+        # POSSIBLE-OPTIMIZATION: hard code
         return np.linalg.norm(vec._v)  # type: ignore[no-untyped-call]
-    return dot(vec, vec, metric) ** 0.5  # TODO: optimize
+    return dot(vec, vec, metric) ** 0.5
 
 
 def normalized(
@@ -285,7 +286,7 @@ def normalized(
         return _abstract_vector_from_numpy(vec._v * (dot(vec, vec) ** -0.5))
         # NOTE: DON'T use this:
         # return Vector.__from_numpy((1 / np.linalg.norm(vec._v)) * vec._v)
-    return vec / length(vec, metric)  # TODO: optimize
+    return vec / length(vec, metric)  # POSSIBLE-OPTIMIZATION: hard code
 
 
 def are_linear_dependent(vectors: tuple[AbstractVector, ...]) -> bool:

src/nerte/values/manifold.py

@@ -15,7 +15,7 @@ class OutOfDomainError(ValueError):
     pass
 
 
-# TODO: Implement when type families are supported in python.
+# FUTURE: Implement when type families are supported in python.
 
 # class ManifoldTypeFamily[N:int]():
 #     # pylint: disable=W0107

src/nerte/values/manifolds/cartesian_swirl.py

@@ -234,7 +234,7 @@ def _christoffel_1(
     sin_2alpha = math.sin(2 * alpha)
     cos_3alpha = math.cos(3 * alpha)
     sin_3alpha = math.sin(3 * alpha)
-    # TODO: potential speed-up: symmetric matrices
+    # POSSIBLE-OPTIMIZATION: symmetric matrices
     return (
         AbstractMatrix(
             AbstractVector(

src/nerte/values/manifolds/cylindrical_swirl_unittest.py

@@ -97,7 +97,6 @@ def test_metric(self) -> None:
             )
 
 
-# TODO: edge case + non-edge case
 class CylindircSwirlGeodesicEquationTest(BaseTestCase):
     def setUp(self) -> None:
         self.swirl = 0.0
@@ -149,7 +148,6 @@ def cylin_next(x: TangentialVectorDelta) -> TangentialVectorDelta:
         )
 
 
-# TODO: edge case + non-edge case
 class CylindricalCoordinatesTransfomrationTest(BaseTestCase):
     def setUp(self) -> None:
         self.swirl = 0.0
@@ -198,7 +196,6 @@ def test_cylindric_swirl_to_carthesian_coords(self) -> None:
                 cylindric_swirl_to_carthesian_coords(self.swirl, coords)
 
 
-# TODO: edge case + non-edge case
 class CylindricSwirlVectorTransfomrationTest(BaseTestCase):
     def setUp(self) -> None:
         self.swirl = 0.0
@@ -307,7 +304,6 @@ def test_vector_length_preservation(self) -> None:
             self.assertAlmostEqual(cylin_len, carth_len)
 
 
-# TODO: edge case + non-edge case
 class CylindricalTangentialVectorTransfomrationTest(BaseTestCase):
     def setUp(self) -> None:
         self.swirl = 0.0
@@ -519,7 +515,6 @@ def test_plane_tangential_space_domain(self) -> None:
             self.infinite_plane.tangential_space(coords)
 
 
-# TODO: edge case + non-edge case
 class PlanePropertiesTest(BaseTestCase):
     # pylint: disable=R0902
     def setUp(self) -> None:

validate_for_commit.py

@@ -38,12 +38,12 @@ def __exit__(self, exc_type, exc_val, exc_tb) -> None:  # type: ignore
 
 # src must exist
 if not os.path.isdir("src"):
-    print("Code base invalid. No directory 'src' found.")
+    print("ERROR: Code base invalid. No directory 'src' found.")
     sys.exit(1)
 
 # src must be readable
 if not os.access("src", os.R_OK):
-    print("Code base invalid. Cannot read directory 'src'.")
+    print("ERROR: Code base invalid. Cannot read directory 'src'.")
     sys.exit(1)
 
 
@@ -59,27 +59,53 @@ def run_mypy() -> None:
             stderr=sys.stderr,
         )
         if res.returncode != 0:
-            print("Code base invalid. Mypy failed.")
+            print("ERROR: Code base invalid. Mypy failed.")
             sys.exit(1)
 
 
-def run_pylint(disable: Optional[list[str]] = None) -> None:
+def _pylint_disable_str(disable: list[str]) -> str:
+    if disable is None:
+        return ""
+    dis = ",".join(disable)
+    return f" --disable={dis}"
+
+
+def _pylint_ignnore_patterns_str(exclude_unittests: bool) -> str:
+    if exclude_unittests:
+        return ' --ignore-patterns=".*_unittest.py"'
+    return ""
+
+
+def run_pylint(
+    disable: Optional[list[str]] = None,
+    exclude_unittests: bool = False,
+) -> None:
     """Runs pylint on src."""
+
+    if disable is None:
+        disable = []
+    disable_str = _pylint_disable_str(disable)
+    ignore_patterns_str = _pylint_ignnore_patterns_str(exclude_unittests)
+
     print("running pylint ...")
     with ChangeDirecory("."):
-        if disable is None:
-            dis = ""
-        else:
-            dis = ",".join(disable)
         res = subprocess.run(
-            f"pylint --disable={dis} src",
+            f"pylint{disable_str}{ignore_patterns_str} src",
             shell=True,
             check=False,
             stdout=sys.stdout,
             stderr=sys.stderr,
         )
+        if exclude_unittests:
+            print("INFO: Unit tests were excluded.")
+        if len(disable) > 0:
+            print(
+                "INFO: The following codes were disabled: "
+                + ", ".join(disable)
+                + "."
+            )
         if res.returncode != 0:
-            print("Code base invalid. Pylint failed.")
+            print("ERROR: Code base invalid. Pylint failed.")
             sys.exit(1)
 
 
@@ -95,14 +121,14 @@ def run_tests() -> None:
             stderr=sys.stderr,
         )
         if res.returncode != 0:
-            print("Code base invalid. Tests failed.")
+            print("ERROR: Code base invalid. Tests failed.")
             sys.exit(1)
 
 
 def run_all() -> None:
     """Full run of checks."""
     run_mypy()
-    run_pylint()
+    run_pylint(disable=["R0801"])
     run_tests()
     print("Code base is valid!")
     sys.exit(0)  # must be 0
@@ -114,7 +140,9 @@ def run_light() -> None:
     run_mypy()
     run_tests()
     # do pylint last as it often fails in pre-checks
-    run_pylint(disable=["R0801", "W0511"])
+    # fix me: W0511
+    # code duplication: R0801
+    run_pylint(disable=["R0801"])
     print(
         "WARNING: Results were obtained in light mode."
         " Therefore the code base may not be valid!"