Merge pull request #367 from oscarbenjamin/pr_typing

Full test and typing coverage

Author: oscarbenjamin

bin/build_dependencies_unix.sh

@@ -22,6 +22,7 @@ SKIP_MPFR=no
 USE_GMP=gmp
 PATCH_GMP_ARM64=no
 BUILD_ARB=no
+USE_GMP_GITHUB_MIRROR=no
 
 while [[ $# -gt 0 ]]
 do
@@ -124,15 +125,15 @@ cd src
 #                                                                           #
 # ------------------------------------------------------------------------- #
 
-if [ $USE_GMP = "gmp" ]; then
+if [ "$USE_GMP" = "gmp" ]; then
 
   # ----------------------------------------------------------------------- #
   #                                                                         #
   #                            GMP                                          #
   #                                                                         #
   # ----------------------------------------------------------------------- #
 
-  if [ $SKIP_GMP = "yes" ]; then
+  if [ "$SKIP_GMP" = "yes" ]; then
     echo
     echo --------------------------------------------
     echo "           skipping GMP"
@@ -145,7 +146,7 @@ if [ $USE_GMP = "gmp" ]; then
     echo --------------------------------------------
     echo
 
-    if [ $USE_GMP_GITHUB_MIRROR = "yes" ]; then
+    if [ "$USE_GMP_GITHUB_MIRROR" = "yes" ]; then
       # Needed in GitHub Actions because it is blocked from gmplib.org
       git clone https://github.com/oscarbenjamin/gmp_mirror.git
       cp gmp_mirror/gmp-$GMPVER.tar.xz .
@@ -163,7 +164,7 @@ if [ $USE_GMP = "gmp" ]; then
       # from the GMP repo but was applied after the release of GMP 6.2.1.
       # This patch is no longer needed for GMP 6.3.0.
       #
-      if [ $PATCH_GMP_ARM64 = "yes" ]; then
+      if [ "$PATCH_GMP_ARM64" = "yes" ]; then
         echo
         echo --------------------------------------------
         echo "           patching GMP"
@@ -260,7 +261,7 @@ fi
 #                                                                           #
 # ------------------------------------------------------------------------- #
 
-if [ $SKIP_MPFR = "yes" ]; then
+if [ "$SKIP_MPFR" = "yes" ]; then
   echo
   echo --------------------------------------------
   echo "           skipping MPFR"
@@ -326,7 +327,7 @@ cd ..
 #                                                                           #
 # ------------------------------------------------------------------------- #
 
-if [ $BUILD_ARB = "yes" ]; then
+if [ "$BUILD_ARB" = "yes" ]; then
 
   echo
   echo --------------------------------------------
@@ -369,7 +370,7 @@ echo $PREFIX
 echo
 echo Versions:
 
-if [ $SKIP_GMP = "yes" ]; then
+if [ "$SKIP_GMP" = "yes" ]; then
   echo GMP: skipped
 else
   if [[ $USE_GMP = "gmp" ]]; then
@@ -379,15 +380,15 @@ else
   fi
 fi
 
-if [ $SKIP_MPFR = "yes" ]; then
+if [ "$SKIP_MPFR" = "yes" ]; then
   echo MPFR: skipped
 else
   echo MPFR: $MPFRVER
 fi
 
 echo Flint: $FLINTVER
 
-if [ $BUILD_ARB = "yes" ]; then
+if [ "$BUILD_ARB" = "yes" ]; then
   echo Arb: $ARBVER
 fi
 echo

coverage_plugin.py

@@ -62,7 +62,7 @@ def get_cython_build_rules():
 
 
 @cache
-def parse_all_cfile_lines():
+def parse_all_cfile_lines(excluded_line_patterns=()):
     """Parse all generated C files from the build directory."""
     #
     # Each .c file can include code generated from multiple Cython files (e.g.
@@ -77,6 +77,14 @@ def parse_all_cfile_lines():
     # expensive.
     #
     all_code_lines = {}
+    all_excluded_lines = defaultdict(set)
+    if excluded_line_patterns:
+        pattern = re.compile("|".join([f"(?:{regex})" for regex in excluded_line_patterns]))
+        line_is_excluded = pattern.search
+    else:
+        line_is_excluded = lambda line: False
+
+    source_cache = {}
 
     for c_file, _ in get_cython_build_rules():
 
@@ -85,13 +93,33 @@ def parse_all_cfile_lines():
         for cython_file, line_map in cfile_lines.items():
             if cython_file == '(tree fragment)':
                 continue
-            elif cython_file in all_code_lines:
+            src_lines = source_cache.get(cython_file)
+            if src_lines is None:
+                src_path = src_dir / cython_file
+                if src_path.exists():
+                    with open(src_path, encoding="utf8") as src:
+                        src_lines = src.read().splitlines()
+                else:
+                    src_lines = []
+                source_cache[cython_file] = src_lines
+
+            excluded = set()
+            filtered_line_map = {}
+            for lineno, line in line_map.items():
+                source_line = src_lines[lineno - 1] if 0 < lineno <= len(src_lines) else ""
+                if line_is_excluded(source_line) or line_is_excluded(line):
+                    excluded.add(lineno)
+                else:
+                    filtered_line_map[lineno] = line
+            if cython_file in all_code_lines:
                 # Possibly need to merge the lines?
-                assert all_code_lines[cython_file] == line_map
+                assert all_code_lines[cython_file] == filtered_line_map
+                all_excluded_lines[cython_file].update(excluded)
             else:
-                all_code_lines[cython_file] = line_map
+                all_code_lines[cython_file] = filtered_line_map
+                all_excluded_lines[cython_file] = excluded
 
-    return all_code_lines
+    return all_code_lines, all_excluded_lines
 
 
 def parse_cfile_lines(c_file):
@@ -102,6 +130,11 @@ def parse_cfile_lines(c_file):
 
 class Plugin(CoveragePlugin):
     """A coverage plugin for a spin/meson project with Cython code."""
+    _excluded_line_patterns = ()
+
+    def configure(self, config):
+        # Match Cython's plugin behavior and respect coverage's exclusion regexes.
+        self._excluded_line_patterns = tuple(config.get_option("report:exclude_lines"))
 
     def file_tracer(self, filename):
         """Find a tracer for filename to handle trace events."""
@@ -121,7 +154,7 @@ def file_tracer(self, filename):
     def file_reporter(self, filename):
         """Return a file reporter for filename."""
         srcfile = Path(filename).relative_to(src_dir)
-        return CyFileReporter(srcfile)
+        return CyFileReporter(srcfile, self._excluded_line_patterns)
 
 
 class CyFileTracer(FileTracer):
@@ -157,14 +190,15 @@ def get_source_filename(filename):
 class CyFileReporter(FileReporter):
     """File reporter for Cython or Python files (.pyx,.pxd,.py)."""
 
-    def __init__(self, srcpath):
+    def __init__(self, srcpath, excluded_line_patterns):
         abspath = (src_dir / srcpath)
         assert abspath.exists()
 
         # filepath here needs to match dynamic_source_filename
         super().__init__(str(abspath))
 
         self.srcpath = srcpath
+        self.excluded_line_patterns = excluded_line_patterns
 
     def relative_filename(self):
         """Path displayed in the coverage reports."""
@@ -173,10 +207,15 @@ def relative_filename(self):
     def lines(self):
         """Set of line numbers for possibly traceable lines."""
         srcpath = str(self.srcpath)
-        all_line_maps = parse_all_cfile_lines()
+        all_line_maps, _ = parse_all_cfile_lines(self.excluded_line_patterns)
         line_map = all_line_maps[srcpath]
         return set(line_map)
 
+    def excluded_lines(self):
+        srcpath = str(self.srcpath)
+        _, all_excluded_lines = parse_all_cfile_lines(self.excluded_line_patterns)
+        return set(all_excluded_lines.get(srcpath, ()))
+
 
 def coverage_init(reg, options):
     plugin = Plugin()

pyproject.toml

@@ -87,6 +87,9 @@ package = "flint"
     "spin.cmds.meson.run",
 ]
 
+[tool.mypy]
+files = ["src"]
+
 [tool.pytest.ini_options]
 addopts = "--import-mode=importlib"
 

src/flint/__init__.py

@@ -50,6 +50,23 @@
 
 __version__ = "0.8.0"
 
+
+def _flint_version_at_least(major: int, minor: int) -> bool:
+    version_parts = __FLINT_VERSION__.split(".")
+    if len(version_parts) < 2:
+        return False
+    try:
+        current_major = int(version_parts[0])
+        current_minor = int(version_parts[1])
+    except ValueError:
+        return False
+    return (current_major, current_minor) >= (major, minor)
+
+
+def _has_acb_theta() -> bool:
+    return _flint_version_at_least(3, 1)
+
+
 __all__ = [
     "ctx",
     "fmpz",

src/flint/flint_base/flint_base.pyi

@@ -80,13 +80,23 @@ class flint_poly(flint_elem, Generic[Telem]):
     def is_one(self) -> bool: ...
     def is_constant(self) -> bool: ...
     def is_gen(self) -> bool: ...
-    def roots(self) -> list[tuple[Telem, int]]: ...
+    def roots(self) -> list[tuple[Telem, int]] | list[Telem]: ...
     # Should be list[arb]:
     def real_roots(self) -> list[Any]: ...
     # Should be list[acb]:
     def complex_roots(self) -> list[Any]: ...
     def derivative(self) -> Self: ...
 
+class flint_mat(flint_elem, Generic[Telem]):
+    def nrows(self) -> int: ...
+    def ncols(self) -> int: ...
+    def __getitem__(self, index: tuple[int, int], /) -> Telem: ...
+    def __setitem__(self, index: tuple[int, int], value: Telem | int, /) -> None: ...
+    def entries(self) -> list[Telem]: ...
+    def table(self) -> list[list[Telem]]: ...
+    def tolist(self) -> list[list[Telem]]: ...
+    def __iter__(self) -> Iterator[Telem]: ...
+
 class Ordering(enum.Enum):
     lex = "lex"
     deglex = "deglex"

src/flint/flint_base/flint_context.pyi

@@ -0,0 +1,50 @@
+from __future__ import annotations
+
+from typing import Callable, ParamSpec, TypeVar
+
+
+_P = ParamSpec("_P")
+_R = TypeVar("_R")
+
+
+class FlintContext:
+    pretty: bool
+    unicode: bool
+
+    def __init__(self) -> None: ...
+    def default(self) -> None: ...
+
+    @property
+    def prec(self) -> int: ...
+    @prec.setter
+    def prec(self, prec: int) -> None: ...
+
+    @property
+    def dps(self) -> int: ...
+    @dps.setter
+    def dps(self, prec: int) -> None: ...
+
+    @property
+    def cap(self) -> int: ...
+    @cap.setter
+    def cap(self, cap: int) -> None: ...
+
+    @property
+    def threads(self) -> int: ...
+    @threads.setter
+    def threads(self, num: int) -> None: ...
+
+    def extraprec(self, n: int) -> PrecisionManager: ...
+    def extradps(self, n: int) -> PrecisionManager: ...
+    def workprec(self, n: int) -> PrecisionManager: ...
+    def workdps(self, n: int) -> PrecisionManager: ...
+
+    def __repr__(self) -> str: ...
+    def cleanup(self) -> None: ...
+
+
+class PrecisionManager:
+    def __init__(self, ctx: FlintContext, eprec: int = -1, edps: int = -1) -> None: ...
+    def __call__(self, func: Callable[_P, _R]) -> Callable[_P, _R]: ...
+    def __enter__(self) -> None: ...
+    def __exit__(self, exc_type: object, value: object, traceback: object) -> None: ...

src/flint/flint_base/meson.build

@@ -3,6 +3,7 @@ pkgdir = 'flint/flint_base'
 pyfiles = [
   '__init__.py',
   'flint_base.pyi',
+  'flint_context.pyi',
 ]
 
 exts = [

src/flint/flintlib/functions/arf.pxd

@@ -16,6 +16,7 @@ from flint.flintlib.types.fmpq cimport fmpq_t
 # .. macro:: ARF_PREC_EXACT
 
 cdef extern from "flint/arf.h":
+    cdef const slong ARF_PREC_EXACT
     void arf_init(arf_t x)
     void arf_clear(arf_t x)
     slong arf_allocated_bytes(const arf_t x)

src/flint/meson.build

@@ -4,6 +4,7 @@ pyfiles = [
   '__init__.py',
   'typing.py',
   'py.typed',
+  'pyflint.pyi',
 ]
 
 exts = [

src/flint/pyflint.pyi

@@ -0,0 +1,4 @@
+from .flint_base.flint_context import FlintContext
+
+
+ctx: FlintContext