Add Core zFPKM Tests

main/como/approx.py

@@ -1,30 +1,64 @@
 from __future__ import annotations
 
 from collections.abc import Callable, Sequence
-from typing import Any
+from typing import Literal, NamedTuple
 
 import numpy as np
+import numpy.typing as npt
 
 
-def _coerce_to_float_array(a):
-    """Helper to ensure input is a 1D float array."""
+class RegularizedArray(NamedTuple):
+    x: npt.NDArray[np.number]
+    y: npt.NDArray[np.number]
+    not_na: npt.NDArray[bool]
+    kept_na: bool
+
+
+class Approx(NamedTuple):
+    x: npt.NDArray[float]
+    y: npt.NDArray[float]
+
+
+def _coerce_to_float_array(a: Sequence[int | float | np.number]):
+    """Coerce input to a 1D float array.
+
+    Args:
+        a: the array to coerce
+
+    Returns:
+        A floating point 1D array.
+    """
     arr = np.asarray(a, dtype=float)
     if arr.ndim != 1:
         arr = arr.ravel()
     return arr
 
 
-def _regularize_values(x: np.ndarray, y: np.ndarray, ties, na_rm: bool) -> dict[str, Any]:
-    """Minimal reimplementation of R's regularize.values() used by approx().
+def _regularize_values(
+    x: npt.NDArray[np.number],
+    y: npt.NDArray[np.number],
+    *,
+    na_rm: bool,
+    ties: Callable[[np.ndarray], float] | Literal["mean", "first", "last", "min", "max", "median", "sum"] = "mean",
+) -> RegularizedArray:
+    """Reimplementation of R's regularize.values() used by approx().
 
       - Removes NA pairs if na_rm is True (else requires x to have no NA).
       - Sorts by x (stable).
       - Collapses duplicate x via `ties` aggregator.
-    Returns dict with:
-      x: sorted unique x
-      y: aggregated y aligned with x
-      not_na: boolean mask of y that are not NaN
-      kept_na: True iff any NaN remained in y after regularization
+
+    Args:
+        x: the x values to regularize
+        y: ties: the corresponding y values
+        na_rm: should NA values be removed?
+        ties: how to handle duplicate x values; can be a string or a callable
+
+    Returns:
+        A NamedTuple with:
+          - x: sorted unique x
+          - y: aggregated y aligned with x
+          - not_na: boolean mask of y that are not NaN
+          - kept_na: True iff any NaN remained in y after regularization
     """
     if na_rm:
         # Remove pairs where x or y is NA
@@ -39,8 +73,7 @@ def _regularize_values(x: np.ndarray, y: np.ndarray, ties, na_rm: bool) -> dict[
         kept_na = np.isnan(y).any()
 
     if x.size == 0:
-        # THIS IS THE CORRECTED LINE:
-        return {"x": x, "y": y, "not_na": np.array([], dtype=bool), "kept_na": kept_na}
+        return RegularizedArray(x=x, y=y, not_na=np.array([], dtype=bool), kept_na=kept_na)
 
     # Use a stable sort (mergesort) to match R's order()
     order = np.argsort(x, kind="mergesort")
@@ -51,27 +84,26 @@ def _regularize_values(x: np.ndarray, y: np.ndarray, ties, na_rm: bool) -> dict[
     if callable(ties):
         agg_fn = ties
     else:
-        ties_str = "mean" if ties is None else str(ties).lower()
-        if ties_str in ("mean", "avg", "average"):
+        # fmt: off
+        if ties in ("mean", "avg", "average"):
             agg_fn = np.mean
-        elif ties_str in ("first", "left"):
-
+        elif ties in ("first", "left"):
             def agg_fn(a):
                 return a[0]
-        elif ties_str in ("last", "right"):
-
+        elif ties in ("last", "right"):
             def agg_fn(a):
                 return a[-1]
-        elif ties_str == "min":
+        elif ties == "min":
             agg_fn = np.min
-        elif ties_str == "max":
+        elif ties == "max":
             agg_fn = np.max
-        elif ties_str == "median":
+        elif ties == "median":
             agg_fn = np.median
-        elif ties_str == "sum":
+        elif ties == "sum":
             agg_fn = np.sum
         else:
             raise ValueError("Unsupported `ties`; use a callable or one of 'mean', 'first', 'last', 'min', 'max', 'median', 'sum'.")
+        # fmt: on
 
     # Find unique x values and their indices/counts
     unique_x, start_idx, counts = np.unique(x_sorted, return_index=True, return_counts=True)
@@ -86,8 +118,8 @@ def agg_fn(a):
 
     not_na = ~np.isnan(y_agg)
     # Check if any NaNs remain in the *aggregated* y values
-    kept_na_final = np.any(~not_na) if np.any(np.isnan(y_agg)) else False
-    return {"x": unique_x, "y": y_agg, "not_na": not_na, "kept_na": kept_na_final}
+    kept_na_final = bool(np.any(~not_na) if np.any(np.isnan(y_agg)) else False)
+    return RegularizedArray(x=unique_x, y=y_agg, not_na=not_na, kept_na=kept_na_final)
 
 
 def approx(
@@ -98,11 +130,11 @@ def approx(
     n: int = 50,
     yleft: float | None = None,
     yright: float | None = None,
-    rule: int | Sequence[int] = 1,
+    rule: int | Sequence[int] | npt.NDArray[int] = 1,
     f: float = 0.0,
-    ties: str | Callable[[np.ndarray], float] = "mean",
+    ties: Callable[[np.ndarray], float] | Literal["mean", "first", "last", "min", "max", "median", "sum"] = "mean",
     na_rm: bool = True,
-) -> dict[str, np.ndarray]:
+) -> Approx:
     """Faithful Python port of R's `approx` function.
 
     This implementation aims to replicate the behavior of R's `approx`
@@ -114,26 +146,18 @@ def approx(
         y: y-coordinates. If None, `x` is treated as `y` and `x` becomes `1..n`.
         xout: Points at which to interpolate.
         method: Interpolation method. "linear" (1) or "constant" (2).
-        n: If `xout` is not provided, interpolation happens at `n`
-             equally spaced points spanning the range of `x`.
-        yleft: Value to use for extrapolation to the left.
-               Defaults to `NA` (np.nan) if `rule` is 1.
-        yright: Value to use for extrapolation to the right.
-                Defaults to `NA` (np.nan) if `rule` is 1.
+        n: If `xout` is not provided, interpolation happens at `n` equally spaced points spanning the range of `x`.
+        yleft: Value to use for extrapolation to the left. Defaults to `NA` (np.nan) if `rule` is 1.
+        yright: Value to use for extrapolation to the right. Defaults to `NA` (np.nan) if `rule` is 1.
         rule: Extrapolation rule.
               - 1: Return `np.nan` for points outside the `x` range.
               - 2: Use `yleft` and `yright` for points outside the range.
-        f: For `method="constant"`, determines the split point.
-           `f=0` is left-step, `f=1` is right-step, `f=0.5` is midpoint.
-        ties: How to handle duplicate `x` values.
-              Can be 'mean', 'first', 'last', 'min', 'max', 'median', 'sum',
-              or a callable function.
-        na_rm: If True, `NA` pairs are removed before interpolation.
-               If False, `NA`s in `x` cause an error, `NA`s in `y`
-               are propagated.
+        f: For `method="constant"`, determines the split point. `f=0` is left-step, `f=1` is right-step, `f=0.5` is midpoint.
+        ties: How to handle duplicate `x` values. Can be 'mean', 'first', 'last', 'min', 'max', 'median', 'sum', or a callable function.
+        na_rm: If True, `NA` pairs are removed before interpolation. If False, `NA`s in `x` cause an error, `NA`s in `y` are propagated.
 
     Returns:
-        dict with:
+        `Approx` class with:
           - 'x': numpy array of xout used
           - 'y': numpy array of interpolated values
     """
@@ -164,25 +188,24 @@ def approx(
             raise ValueError("invalid interpolation method")
 
     # --- Rule normalization ---
-    if isinstance(rule, list | tuple | np.ndarray):
-        rlist = list(rule)
-        if not (1 <= len(rlist) <= 2):
+    if isinstance(rule, Sequence | np.ndarray):
+        rule_list: list[int] = list(rule)  # type: ignore[invalid-argument-type]  # This is a valid argument type, not sure why ty is upset
+        if not (1 <= len(rule_list) <= 2):
             raise ValueError("`rule` must have length 1 or 2")
-        if len(rlist) == 1:
-            rlist = [rlist[0], rlist[0]]
+        if len(rule_list) == 1:
+            rule_list = [rule_list[0], rule_list[0]]
     else:
-        rlist = [rule, rule]
+        rule_list = [rule, rule]
 
-    # --- Regularize values ---
     # Sort by x, collapse ties, and handle NAs like R's regularize.values()
-    r = _regularize_values(x_arr, y_arr, ties, na_rm)
-    x_reg = r["x"]
-    y_reg = r["y"]
-    not_na_mask = r["not_na"]
+    r: RegularizedArray = _regularize_values(x_arr, y_arr, na_rm=na_rm, ties=ties)
+    x_reg: npt.NDArray[float] = r.x
+    y_reg: npt.NDArray[float] = r.y
+    not_na_mask: npt.NDArray[bool] = r.not_na
     # no_na is True if we don't have to worry about NAs in y_reg
-    no_na = na_rm or (not r["kept_na"])
+    no_na: bool = na_rm or (not r.kept_na)
     # nx is the number of *valid* (non-NA) points for interpolation
-    nx = x_reg.size if no_na else int(np.count_nonzero(not_na_mask))
+    nx: int = x_reg.size if no_na else int(np.count_nonzero(not_na_mask))
 
     if np.isnan(nx):
         raise ValueError("invalid length(x)")
@@ -194,98 +217,98 @@ def approx(
         if nx == 0:
             raise ValueError("zero non-NA points")
 
-    # --- Set extrapolation values (yleft/yright) ---
+    # set extrapolation values (yleft/yright)
     # This logic matches R's C code (R_approxtest)
     if no_na:
-        y_first = y_reg[0]
-        y_last = y_reg[-1]
+        y_first: float = y_reg[0]
+        y_last: float = y_reg[-1]
     else:
         # Find first and last non-NA y values
-        y_valid = y_reg[not_na_mask]
-        y_first = y_valid[0]
-        y_last = y_valid[-1]
+        y_valid: npt.NDArray[float] = y_reg[not_na_mask]
+        y_first: float = y_valid[0]
+        y_last: float = y_valid[-1]
 
-    yleft_val = (np.nan if int(rlist[0]) == 1 else y_first) if yleft is None else float(yleft)
-    yright_val = (np.nan if int(rlist[1]) == 1 else y_last) if yright is None else float(yright)
+    yleft_val: float = (np.nan if int(rule_list[0]) == 1 else y_first) if yleft is None else float(yleft)
+    yright_val: float = (np.nan if int(rule_list[1]) == 1 else y_last) if yright is None else float(yright)
 
-    # --- Fabricate xout if missing ---
+    # fabricate xout if it is missing
     if xout is None:
         if n <= 0:
             raise ValueError("'approx' requires n >= 1")
         if no_na:
-            x_first = x_reg[0]
-            x_last = x_reg[nx - 1]
+            x_first: float = x_reg[0]
+            x_last: float = x_reg[nx - 1]
         else:
-            x_valid = x_reg[not_na_mask]
-            x_first = x_valid[0]
-            x_last = x_valid[-1]
-        xout_arr = np.linspace(x_first, x_last, num=int(n), dtype=float)
+            x_valid: npt.NDArray[float] = x_reg[not_na_mask]
+            x_first: float = x_valid[0]
+            x_last: float = x_valid[-1]
+        xout_arr: npt.NDArray[float] = np.linspace(x_first, x_last, num=int(n), dtype=float)
     else:
-        xout_arr = _coerce_to_float_array(xout)
+        xout_arr: npt.NDArray[float] = _coerce_to_float_array(xout)
 
-    # --- C_ApproxTest checks ---
+    # replicate R's C_ApproxTest checks
     if method_code == 2 and (not np.isfinite(f) or f < 0.0 or f > 1.0):
-        raise ValueError("approx(): invalid f value")
+        raise ValueError("approx(): invalid f value; with `method=2`, `f` must be in the range [0,1] (inclusive) or NA")
     if not no_na:
         # R re-filters x and y here if NAs remained
-        x_reg = x_reg[not_na_mask]
-        y_reg = y_reg[not_na_mask]
+        x_reg: npt.NDArray[float] = x_reg[not_na_mask]
+        y_reg: npt.NDArray[float] = y_reg[not_na_mask]
 
-    # --- Interpolation ---
-    # This section vectorized the logic from R's approx1 and R_approxfun
-    yout = np.empty_like(xout_arr, dtype=float)
-    mask_nan_xout = np.isnan(xout_arr)
+    # perform interpolation
+    # this section is a vectorized form of the logic from R's approx1 and R_approxfun
+    yout: npt.NDArray[float] = np.empty_like(xout_arr, dtype=float)
+    mask_nan_xout: npt.NDArray[bool] = np.isnan(xout_arr)
     yout[mask_nan_xout] = np.nan
-    mask_valid = ~mask_nan_xout
+    mask_valid: npt.NDArray[bool] = ~mask_nan_xout
 
     if x_reg.size == 0:
         # No valid points to interpolate against
         yout[mask_valid] = np.nan
-        return {"x": xout_arr, "y": yout}
+        return Approx(x=xout_arr, y=yout)
 
-    xv = xout_arr[mask_valid]
-    left_mask = xv < x_reg[0]
-    right_mask = xv > x_reg[-1]
-    mid_mask = ~(left_mask | right_mask)
+    xv: npt.NDArray[float] = xout_arr[mask_valid]
+    left_mask: npt.NDArray[bool] = xv < x_reg[0]
+    right_mask: npt.NDArray[bool] = xv > x_reg[-1]
+    mid_mask: npt.NDArray[bool] = ~(left_mask | right_mask)
 
-    res = np.empty_like(xv)
+    res: npt.NDArray[float] = np.empty_like(xv, dtype=float)
     res[left_mask] = yleft_val
     res[right_mask] = yright_val
 
     if np.any(mid_mask):
-        xm = xv[mid_mask]
+        xm: npt.NDArray[float] = xv[mid_mask]
 
         # Find indices
         # j_right[k] = index of first x_reg > xm[k]
-        j_right = np.searchsorted(x_reg, xm, side="right")
+        j_right: npt.NDArray[int] = np.searchsorted(x_reg, xm, side="right")
         # j_left[k] = index of first x_reg >= xm[k]
-        j_left = np.searchsorted(x_reg, xm, side="left")
+        j_left: npt.NDArray[int] = np.searchsorted(x_reg, xm, side="left")
 
         # Points that exactly match an x_reg value
-        eq_mask = j_left != j_right
+        eq_mask: npt.NDArray[bool] = j_left != j_right
         # Points that fall between x_reg values
-        in_interval_mask = ~eq_mask
+        in_interval_mask: npt.NDArray[bool] = ~eq_mask
 
-        res_mid = np.empty_like(xm)
+        res_mid: npt.NDArray[float] = np.empty_like(xm, dtype=float)
 
         if np.any(eq_mask):
             # For exact matches, use the corresponding y_reg value
             # R's C code uses the 'j_left' index here
-            res_mid[eq_mask] = y_reg[j_left[eq_mask]]
+            res_mid[eq_mask] = y_reg[j_left[eq_mask]]  # type: ignore[non-subscriptable]  # we know this is of type npt.NDArray[float], not sure why ty is upset
 
         if np.any(in_interval_mask):
             # R's C code sets i = j-1, where j is the 'right' index
-            j = j_right[in_interval_mask]
-            i = j - 1
+            j: npt.NDArray[float] = j_right[in_interval_mask]  # type: ignore[non-subscriptable]  # we know this is of type npt.NDArray[float], not sure why ty is upset
+            i: npt.NDArray[float] = j - 1
 
             # Get the surrounding x and y values
-            xi = x_reg[i]
-            xj = x_reg[j]
-            yi = y_reg[i]
-            yj = y_reg[j]
+            xi: npt.NDArray[float] = x_reg[i]
+            xj: npt.NDArray[float] = x_reg[j]
+            yi: npt.NDArray[float] = y_reg[i]
+            yj: npt.NDArray[float] = y_reg[j]
 
             if method_code == 1:  # linear
-                t = (xm[in_interval_mask] - xi) / (xj - xi)
+                t: npt.NDArray[float] = (xm[in_interval_mask] - xi) / (xj - xi)
                 res_mid[in_interval_mask] = yi + (yj - yi) * t
             else:  # constant
                 # This matches R_approxfun's constant logic
@@ -294,17 +317,17 @@ def approx(
                 elif f == 1.0:
                     res_mid[in_interval_mask] = yj
                 else:
-                    # R computes (1-f)*yi + f*yj, but carefully
-                    f1 = 1.0 - f
-                    f2 = f
-                    part = np.zeros_like(yi)
+                    # computes R's (1-f)*yi + f*yj
+                    f1: float = float(1.0 - f)
+                    f2: float = float(f)
+                    part: npt.NDArray[float] = np.zeros_like(yi, dtype=float)
                     if f1 != 0.0:
-                        part = part + yi * f1
+                        part: npt.NDArray[float] = part + yi * f1
                     if f2 != 0.0:
-                        part = part + yj * f2
+                        part: npt.NDArray[float] = part + yj * f2
                     res_mid[in_interval_mask] = part
 
         res[mid_mask] = res_mid
 
     yout[mask_valid] = res
-    return {"x": xout_arr, "y": yout}
+    return Approx(x=xout_arr, y=yout)