Fixed #1059 missing fastmath (#1060)

* add function to  check fastmath

* revise fastmath script and add support for reading arg from command line

* minor fixes

* rename function to improve readability

* simplify code by passing boolean value

* fix to catch njit functions with decorator

* use regex to find njit functions

* minor change

* revise code to detect bare njit decorator

* minor fix

* fix path

* add missing fastmath

* revise fastmath flag

* Improve ValueError msg

* fix format

* enable function to accept path as input

* pass param via CLI, and some minor changes

* adapt changes in test script

* use type str for the param pkg_dir

* minor changes

* Revised string concatenation in error message

Author: NimaSarajpoor

fastmath.py

@@ -0,0 +1,100 @@
+#!/usr/bin/env python
+
+import argparse
+import ast
+import importlib
+import pathlib
+
+
+def get_njit_funcs(pkg_dir):
+    """
+    Identify all njit functions
+
+    Parameters
+    ----------
+    pkg_dir : str
+       The path to the directory containing some .py files
+
+    Returns
+    -------
+    njit_funcs : list
+        A list of all njit functions, where each element is a tuple of the form
+        (module_name, func_name)
+    """
+    ignore_py_files = ["__init__", "__pycache__"]
+    pkg_dir = pathlib.Path(pkg_dir)
+
+    module_names = []
+    for fname in pkg_dir.iterdir():
+        if fname.stem not in ignore_py_files and not fname.stem.startswith("."):
+            module_names.append(fname.stem)
+
+    njit_funcs = []
+    for module_name in module_names:
+        filepath = pkg_dir / f"{module_name}.py"
+        file_contents = ""
+        with open(filepath, encoding="utf8") as f:
+            file_contents = f.read()
+        module = ast.parse(file_contents)
+        for node in module.body:
+            if isinstance(node, ast.FunctionDef):
+                func_name = node.name
+                for decorator in node.decorator_list:
+                    decorator_name = None
+                    if isinstance(decorator, ast.Name):
+                        # Bare decorator
+                        decorator_name = decorator.id
+                    if isinstance(decorator, ast.Call) and isinstance(
+                        decorator.func, ast.Name
+                    ):
+                        # Decorator is a function
+                        decorator_name = decorator.func.id
+
+                    if decorator_name == "njit":
+                        njit_funcs.append((module_name, func_name))
+
+    return njit_funcs
+
+
+def check_fastmath(pkg_dir, pkg_name):
+    """
+    Check if all njit functions have the `fastmath` flag set
+
+    Parameters
+    ----------
+    pkg_dir : str
+        The path to the directory containing some .py files
+
+    pkg_name : str
+        The name of the package
+
+    Returns
+    -------
+    None
+    """
+    missing_fastmath = []  # list of njit functions with missing fastmath flags
+    for module_name, func_name in get_njit_funcs(pkg_dir):
+        module = importlib.import_module(f".{module_name}", package=pkg_name)
+        func = getattr(module, func_name)
+        if "fastmath" not in func.targetoptions.keys():
+            missing_fastmath.append(f"{module_name}.{func_name}")
+
+    if len(missing_fastmath) > 0:
+        msg = (
+            "Found one or more `@njit` functions that are missing the `fastmath` flag. "
+            + f"The functions are:\n {missing_fastmath}\n"
+        )
+        raise ValueError(msg)
+
+    return
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--check", dest="pkg_dir")
+    args = parser.parse_args()
+
+    if args.pkg_dir:
+        pkg_dir = pathlib.Path(args.pkg_dir)
+        pkg_name = pkg_dir.name
+        check_fastmath(str(pkg_dir), pkg_name)

stumpy/cache.py

@@ -5,7 +5,6 @@
 import ast
 import importlib
 import pathlib
-import pkgutil
 import site
 import warnings
 
@@ -28,13 +27,17 @@ def get_njit_funcs():
     out : list
         A list of (`module_name`, `func_name`) pairs
     """
+    ignore_py_files = ["__init__", "__pycache__"]
+
     pkg_dir = pathlib.Path(__file__).parent
-    module_names = [name for _, name, _ in pkgutil.iter_modules([str(pkg_dir)])]
+    module_names = []
+    for fname in pkg_dir.iterdir():
+        if fname.stem not in ignore_py_files and not fname.stem.startswith("."):
+            module_names.append(fname.stem)
 
     njit_funcs = []
-
     for module_name in module_names:
-        filepath = pathlib.Path(__file__).parent / f"{module_name}.py"
+        filepath = pkg_dir / f"{module_name}.py"
         file_contents = ""
         with open(filepath, encoding="utf8") as f:
             file_contents = f.read()
@@ -43,11 +46,18 @@ def get_njit_funcs():
             if isinstance(node, ast.FunctionDef):
                 func_name = node.name
                 for decorator in node.decorator_list:
+                    decorator_name = None
+                    if isinstance(decorator, ast.Name):
+                        # Bare decorator
+                        decorator_name = decorator.id
                     if isinstance(decorator, ast.Call) and isinstance(
                         decorator.func, ast.Name
                     ):
-                        if decorator.func.id == "njit":
-                            njit_funcs.append((module_name, func_name))
+                        # Decorator is a function
+                        decorator_name = decorator.func.id
+
+                    if decorator_name == "njit":
+                        njit_funcs.append((module_name, func_name))
 
     return njit_funcs
 

stumpy/core.py

@@ -2356,6 +2356,7 @@ def _count_diagonal_ndist(diags, m, n_A, n_B):
 
 @njit(
     # "i8[:, :](i8[:], i8, b1)"
+    fastmath=True
 )
 def _get_array_ranges(a, n_chunks, truncate):
     """
@@ -2404,6 +2405,7 @@ def _get_array_ranges(a, n_chunks, truncate):
 
 @njit(
     # "i8[:, :](i8, i8, b1)"
+    fastmath=True
 )
 def _get_ranges(size, n_chunks, truncate):
     """
@@ -3256,7 +3258,7 @@ def _select_P_ABBA_value(P_ABBA, k, custom_func=None):
     return MPdist
 
 
-@njit()
+@njit(fastmath={"nsz", "arcp", "contract", "afn", "reassoc"})
 def _merge_topk_PI(PA, PB, IA, IB):
     """
     Merge two top-k matrix profiles `PA` and `PB`, and update `PA` (in place).
@@ -3329,7 +3331,7 @@ def _merge_topk_PI(PA, PB, IA, IB):
             IA[i] = tmp_I
 
 
-@njit()
+@njit(fastmath={"nsz", "arcp", "contract", "afn", "reassoc"})
 def _merge_topk_ρI(ρA, ρB, IA, IB):
     """
     Merge two top-k pearson profiles `ρA` and `ρB`, and update `ρA` (in place).
@@ -3403,7 +3405,7 @@ def _merge_topk_ρI(ρA, ρB, IA, IB):
             IA[i] = tmp_I
 
 
-@njit()
+@njit(fastmath={"nsz", "arcp", "contract", "afn", "reassoc"})
 def _shift_insert_at_index(a, idx, v, shift="right"):
     """
     If `shift=right` (default), all elements in `a[idx:]` are shifted to the right by
@@ -4379,7 +4381,7 @@ def get_ray_nworkers(ray_client):
     return int(ray_client.cluster_resources().get("CPU"))
 
 
-@njit
+@njit(fastmath={"nsz", "arcp", "contract", "afn", "reassoc"})
 def _update_incremental_PI(D, P, I, excl_zone, n_appended=0):
     """
     Given the 1D array distance profile, `D`, of the last subsequence of T,

test.sh

@@ -93,6 +93,13 @@ check_print()
     fi
 }
 
+check_fastmath()
+{
+    echo "Checking Missing fastmath flags in njit functions"
+    ./fastmath.py --check stumpy
+    check_errs $?
+}
+
 check_naive()
 {
     # Check if there are any naive implementations not at start of test file
@@ -146,14 +153,14 @@ set_ray_coveragerc()
 show_coverage_report()
 {
     set_ray_coveragerc
-    coverage report -m --fail-under=100 --skip-covered --omit=docstring.py,min_versions.py,ray_python_version.py,stumpy/cache.py $fcoveragerc
+    coverage report -m --fail-under=100 --skip-covered --omit=fastmath.py,docstring.py,min_versions.py,ray_python_version.py,stumpy/cache.py $fcoveragerc
 }
 
 gen_coverage_xml_report()
 {
     # This function saves the coverage report in Cobertura XML format, which is compatible with codecov
     set_ray_coveragerc
-    coverage xml -o $fcoveragexml --fail-under=100 --omit=docstring.py,min_versions.py,ray_python_version.py,stumpy/cache.py $fcoveragerc
+    coverage xml -o $fcoveragexml --fail-under=100 --omit=fastmath.py,docstring.py,min_versions.py,ray_python_version.py,stumpy/cache.py $fcoveragerc
 }
 
 test_custom()
@@ -333,6 +340,12 @@ check_print
 check_naive
 check_ray
 
+
+if [[ -z $NUMBA_DISABLE_JIT || $NUMBA_DISABLE_JIT -eq 0 ]]; then
+  check_fastmath
+fi
+
+
 if [[ $test_mode == "notebooks" ]]; then
     echo "Executing Tutorial Notebooks Only"
     convert_notebooks