Convert ramp fitting Cython .pyx files into annotated .py files

.gitignore

@@ -139,9 +139,9 @@ dmypy.json
 
 # Cython debug symbols
 cython_debug/
-src/stcal/ramp_fitting/ols_cas22/*.c
-src/stcal/ramp_fitting/ols_cas22/*.cpp
-src/stcal/ramp_fitting/ols_cas22/*.html
+src/stcal/ramp_fitting/_ols_cas22/*.c
+src/stcal/ramp_fitting/_ols_cas22/*.cpp
+src/stcal/ramp_fitting/_ols_cas22/*.html
 
 # setuptools-scm generated module
 src/stcal/_version.py

CHANGES.rst

@@ -5,6 +5,10 @@ jump
 ----
 - Fix the code to at least always flag the group with the shower and the requested
   groups after the primary shower. [#237]
+
+  ramp
+  ----
+- Convert Cython code to using annotated .py files. [#232]
 
 1.5.2 (2023-12-13)
 ==================

pyproject.toml

@@ -47,7 +47,7 @@ test = [
 requires = [
     'setuptools >=61',
     'setuptools_scm[toml] >=3.4',
-    'Cython >=0.29.21',
+    'Cython >=3.0.0',
     'numpy >=1.18',
 ]
 build-backend = 'setuptools.build_meta'
@@ -81,6 +81,7 @@ testpaths = [
     "docs",
 ]
 norecursedirs = [
+    'src/stcal/ramp_fitting/_ols_cas22',
     'benchmarks',
     '.asv',
     '.eggs',
@@ -146,7 +147,6 @@ extend-select = [
     'FLY',    # flynt (f-string conversion where possible)
     'NPY',    # NumPy-specific checks (recommendations from NumPy)
     'PERF',   # Perflint (performance linting)
-    'LOG',
     'RUF',    # ruff specific checks
 ]
 ignore = [

setup.py

@@ -8,20 +8,8 @@
 
 extensions = [
     Extension(
-        "stcal.ramp_fitting.ols_cas22._ramp",
-        ["src/stcal/ramp_fitting/ols_cas22/_ramp.pyx"],
-        include_dirs=[np.get_include()],
-        language="c++",
-    ),
-    Extension(
-        "stcal.ramp_fitting.ols_cas22._jump",
-        ["src/stcal/ramp_fitting/ols_cas22/_jump.pyx"],
-        include_dirs=[np.get_include()],
-        language="c++",
-    ),
-    Extension(
-        "stcal.ramp_fitting.ols_cas22._fit",
-        ["src/stcal/ramp_fitting/ols_cas22/_fit.pyx"],
+        "stcal.ramp_fitting._ols_cas22._fit",
+        ["src/stcal/ramp_fitting/_ols_cas22/_fit.py"],
         include_dirs=[np.get_include()],
         language="c++",
     ),

src/stcal/ramp_fitting/_ols_cas22/__init__.py

@@ -0,0 +1,14 @@
+"""
+This subpackage exists to hold the Cython implementation of the OLS cas22 algorithm
+    This subpackage is private, and should not be imported directly by users. Instead,
+    import from stcal.ramp_fitting.ols_cas22.
+"""
+from ._fit import FixedOffsets, Parameter, PixelOffsets, Variance, fit_ramps
+
+__all__ = [
+    "fit_ramps",
+    "Parameter",
+    "Variance",
+    "PixelOffsets",
+    "FixedOffsets",
+]

src/stcal/ramp_fitting/_ols_cas22/_fit.pxd

@@ -0,0 +1,32 @@
+# cython: language_level=3str
+
+
+cpdef enum Parameter:
+    intercept
+    slope
+    n_param
+
+
+cpdef enum Variance:
+    read_var
+    poisson_var
+    total_var
+    n_var
+
+
+cpdef enum:
+    JUMP_DET = 4
+
+
+cpdef enum FixedOffsets:
+    t_bar_diff
+    t_bar_diff_sqr
+    read_recip
+    var_slope_val
+    n_fixed_offsets
+
+
+cpdef enum PixelOffsets:
+    local_slope
+    var_read_noise
+    n_pixel_offsets