gemd 2.0.0__tar.gz → 2.1.1__tar.gz

{gemd-2.0.0 → gemd-2.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gemd
-Version: 2.0.0
+Version: 2.1.1
 Summary: Python binding for Citrine's GEMD data model
 Home-page: http://github.com/CitrineInformatics/gemd-python
 Author: Citrine Informatics
@@ -14,6 +14,8 @@ Requires-Python: >=3.8
 License-File: LICENSE
 Requires-Dist: pint<0.24,>=0.20
 Requires-Dist: deprecation<3,>=2.1.0
+Requires-Dist: typing_extensions<5,>=4.8
+Requires-Dist: importlib-resources<7,>=5.3
 Provides-Extra: tests
 Requires-Dist: pytest<9,>=8.0.0; extra == "tests"
 Provides-Extra: tests-demo

gemd-2.1.1/gemd/__version__.py

@@ -0,0 +1 @@
+__version__ = "2.1.1"

{gemd-2.0.0 → gemd-2.1.1}/gemd/demo/cake.py

@@ -1,4 +1,5 @@
 """Bake a cake."""
+from importlib_resources import files
 from io import BytesIO
 import random
 
@@ -67,10 +68,7 @@ def get_template_scope():
 
 def import_toothpick_picture() -> BytesIO:
     """Return the stream of the toothpick picture."""
-    from importlib.resources import read_binary
-    resource = read_binary("gemd.demo", "toothpick.jpg")
-
-    return BytesIO(resource)
+    return files("gemd.demo").joinpath("toothpick.jpg").open("rb")
 
 
 def make_cake_templates():

{gemd-2.0.0 → gemd-2.1.1}/gemd/demo/strehlow_and_cook.py

@@ -45,11 +45,10 @@ __all__ = [
 
 def import_table(filename=SMALL_TABLE):
     """Return the deserialized JSON table."""
-    from importlib.resources import read_text
+    from importlib_resources import files
     import json
-    table = json.loads(read_text("gemd.demo", filename))
 
-    return table
+    return json.loads(files("gemd.demo").joinpath(filename).read_text())
 
 
 def _fingerprint(row):

{gemd-2.0.0 → gemd-2.1.1}/gemd/units/impl.py

@@ -1,13 +1,14 @@
 """Implementation of units."""
+from deprecation import deprecated
 import functools
-from importlib.resources import read_text
+from importlib_resources import files
 import os
 from pathlib import Path
 import re
 from tempfile import TemporaryDirectory
 from typing import Union, List, Tuple, Generator, Any
 
-from pint import UnitRegistry, Unit, register_unit_format
+from pint import UnitRegistry, register_unit_format
 try:  # Pint 0.23 migrated the location of this method, and augmented it
     from pint.pint_eval import tokenizer
 except ImportError:  # pragma: no cover
@@ -27,18 +28,19 @@ __all__ = [
 ]
 
 
-def _deploy_default_files() -> str:
+def _deploy_default_files() -> Tuple[Path, Path]:
     """Copy the units & constants file into a temporary directory."""
-    units_path = Path(_TEMP_DIRECTORY.name) / "citrine_en.txt"
-    units_path.write_text(read_text("gemd.units", "citrine_en.txt"), encoding="utf-8")
+    resources = files("gemd.units")
+    target_dir = Path(_TEMP_DIRECTORY.name)
+    target_paths = tuple(target_dir / f for f in ("citrine_en.txt", "constants_en.txt"))
+    for target in target_paths:
+        source = resources.joinpath(target.name)
+        target.write_text(source.read_text(), encoding="utf-8")
 
-    constants_path = Path(_TEMP_DIRECTORY.name) / "constants_en.txt"
-    constants_path.write_text(read_text("gemd.units", "constants_en.txt"), encoding="utf-8")
+    return target_paths
 
-    return str(units_path)
 
-
-DEFAULT_FILE = _deploy_default_files()
+DEFAULT_FILE, DEFAULT_CONSTANTS = _deploy_default_files()
 _ALLOWED_OPERATORS = {".", "+", "-", "*", "/", "//", "^", "**", "(", ")"}
 
 
@@ -131,6 +133,7 @@ def _scaling_identify_factors(
     """
     todo = []
     for block in blocks:
+        # Note: while Python does not recognize ^ as exponentiation, pint does
         i_exp = next((i for i, t in enumerate(block) if t.string in {"**", "^"}), len(block))
         i_name = next((i for i, t in enumerate(block) if t.type == NAME), None)
         numbers = [(i, t.string) for i, t in enumerate(block) if t.type == NUMBER and i < i_exp]
@@ -168,10 +171,14 @@ def _scaling_store_and_mangle(input_string: str, todo: List[Tuple[str, str, str]
     """
     for scaled_term, number_string, unit_string in todo:
         regex = rf"(?<![-+0-9.]){re.escape(scaled_term)}(?![0-9.])"
-        stripped = re.sub(r"[+\s]+", "", scaled_term).replace("--", "")
+        stripped = re.sub(
+            r"(?<=\d)_(?=\d)", "", re.sub(r"[+\s]+", "", scaled_term).replace("--", "")
+        )
 
         if unit_string is not None:
-            stripped_unit = re.sub(r"[+\s]+", "", unit_string).replace("--", "")
+            stripped_unit = re.sub(
+                r"(?<!0)(?=\.)", "0", re.sub(r"[+\s]+", "", unit_string)
+            ).replace("--", "")
             long_unit = f"{_REGISTRY.parse_units(stripped_unit)}"
             short_unit = f"{_REGISTRY.parse_units(stripped_unit):~}"
             long = stripped.replace(stripped_unit, "_" + long_unit)
@@ -201,7 +208,58 @@ def _scaling_preprocessor(input_string: str) -> str:
     return _scaling_store_and_mangle(input_string, todo)
 
 
-_REGISTRY: UnitRegistry = None  # global requires it be defined in this scope
+def _unmangle_scaling(input_string: str) -> str:
+    """Convert mangled scaling values into a pint-compatible expression."""
+    number_re = r'\b_(_)?(\d+)(_\d+)?([eE]_?\d+)?(_(?=[a-zA-Z]))?'
+    while match := re.search(number_re, input_string):
+        replacement = '' if match.group(1) is None else '-'
+        replacement += match.group(2)
+        replacement += '' if match.group(3) is None else match.group(3).replace('_', '.')
+        replacement += '' if match.group(4) is None else match.group(4).replace('_', '-')
+        replacement += '' if match.group(5) is None else match.group(5).replace('_', ' ')
+        input_string = input_string.replace(match.group(0), replacement)
+    return input_string
+
+
+try:  # pragma: no cover
+    # Pint 0.23 modified the preferred way to derive a custom class
+    # https://pint.readthedocs.io/en/0.23/advanced/custom-registry-class.html
+    from pint.registry import GenericUnitRegistry
+    from typing_extensions import TypeAlias
+
+    class _ScaleFactorUnit(UnitRegistry.Unit):
+        """Child class of Units for generating units w/ clean scaling factors."""
+
+        def __format__(self, format_spec):
+            result = super().__format__(format_spec)
+            return _unmangle_scaling(result)
+
+    class _ScaleFactorQuantity(UnitRegistry.Quantity):
+        """Child class of Quantity for generating units w/ clean scaling factors."""
+
+        pass
+
+    class _ScaleFactorRegistry(GenericUnitRegistry[_ScaleFactorQuantity, _ScaleFactorUnit]):
+        """UnitRegistry class that uses _GemdUnits."""
+
+        Quantity: TypeAlias = _ScaleFactorQuantity
+        Unit: TypeAlias = _ScaleFactorUnit
+
+except ImportError:  # pragma: no cover
+    # https://pint.readthedocs.io/en/0.21/advanced/custom-registry-class.html
+    class _ScaleFactorUnit(UnitRegistry.Unit):
+        """Child class of Units for generating units w/ clean scaling factors."""
+
+        def __format__(self, format_spec):
+            result = super().__format__(format_spec)
+            return _unmangle_scaling(result)
+
+    class _ScaleFactorRegistry(UnitRegistry):
+        """UnitRegistry class that uses _GemdUnits."""
+
+        _unit_class = _ScaleFactorUnit
+
+_REGISTRY: _ScaleFactorRegistry = None  # global requires it be defined in this scope
 
 
 @functools.lru_cache(maxsize=1024 * 1024)
@@ -244,38 +302,23 @@ def convert_units(value: float, starting_unit: str, final_unit: str) -> float:
 
 
 @register_unit_format("clean")
+@deprecated(deprecated_in="2.1.0", removed_in="3.0.0", details="Scaling factor clean-up ")
 def _format_clean(unit, registry, **options):
-    """Formatter that turns scaling-factor-units into numbers again."""
-    numerator = []
-    denominator = []
-    for u, p in unit.items():
-        if re.match(r"_[\d_]+", u):
-            # Munged scaling factor; grab symbol, which is the prettier
-            u = registry.get_symbol(u)
-
-        if p == 1:
-            numerator.append(u)
-        elif p > 0:
-            numerator.append(f"{u} ** {p}")
-        elif p == -1:
-            denominator.append(u)
-        elif p < 0:
-            denominator.append(f"{u} ** {-p}")
-
-    if len(numerator) == 0:
-        numerator = ["1"]
-
-    if len(denominator) > 0:
-        return " / ".join((" * ".join(numerator), " / ".join(denominator)))
-    else:
-        return " * ".join(numerator)
+    """
+    DEPRECATED Formatter that turns scaling-factor-units into numbers again.
+
+    Responsibility for this piece of clean-up has been shifted to a custom class.
+
+    """
+    from pint.formatting import _FORMATTERS
+    return _FORMATTERS["D"](unit, registry, **options)
 
 
 @functools.lru_cache(maxsize=1024)
-def parse_units(units: Union[str, Unit, None],
+def parse_units(units: Union[str, UnitRegistry.Unit, None],
                 *,
                 return_unit: bool = False
-                ) -> Union[str, Unit, None]:
+                ) -> Union[str, UnitRegistry.Unit, None]:
     """
     Parse a string or Unit into a standard string representation of the unit.
 
@@ -298,19 +341,20 @@ def parse_units(units: Union[str, Unit, None],
         else:
             return None
     elif isinstance(units, str):
-        parsed = _REGISTRY.parse_units(units)
+        # SPT-1311 Protect against leaked mangled strings
+        parsed = _REGISTRY.parse_units(_unmangle_scaling(units))
         if return_unit:
             return parsed
         else:
-            return f"{parsed:clean}"
-    elif isinstance(units, Unit):
+            return f"{parsed}"
+    elif isinstance(units, UnitRegistry.Unit):
         return units
     else:
         raise UndefinedUnitError("Units must be given as a recognized unit string or Units object")
 
 
 @functools.lru_cache(maxsize=1024)
-def get_base_units(units: Union[str, Unit]) -> Tuple[Unit, float, float]:
+def get_base_units(units: Union[str, UnitRegistry.Unit]) -> Tuple[UnitRegistry.Unit, float, float]:
     """
     Get the base units and conversion factors for the given unit.
 
@@ -350,21 +394,20 @@ def change_definitions_file(filename: str = None):
     if filename is None:
         target = DEFAULT_FILE
     else:
-        # TODO: Handle case where user provides a units file but no constants file
         target = Path(filename).expanduser().resolve(strict=True)
 
     current_dir = Path.cwd()
     try:
-        path = Path(target)
-        os.chdir(path.parent)
-        # Need to re-verify path because of some slippiness around tmp on MacOS
-        _REGISTRY = UnitRegistry(filename=Path.cwd() / path.name,
-                                 preprocessors=[_space_after_minus_preprocessor,
-                                                _scientific_notation_preprocessor,
-                                                _scaling_preprocessor
-                                                ],
-                                 autoconvert_offset_to_baseunit=True
-                                 )
+        os.chdir(target.parent)
+        # Need to re-verify path because of some slippiness around tmp on macOS
+        updated = (Path.cwd() / target.name).resolve(strict=True)
+        _REGISTRY = _ScaleFactorRegistry(filename=updated,
+                                         preprocessors=[_space_after_minus_preprocessor,
+                                                        _scientific_notation_preprocessor,
+                                                        _scaling_preprocessor
+                                                        ],
+                                         autoconvert_offset_to_baseunit=True
+                                         )
     finally:
         os.chdir(current_dir)
 

{gemd-2.0.0 → gemd-2.1.1}/gemd.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gemd
-Version: 2.0.0
+Version: 2.1.1
 Summary: Python binding for Citrine's GEMD data model
 Home-page: http://github.com/CitrineInformatics/gemd-python
 Author: Citrine Informatics
@@ -14,6 +14,8 @@ Requires-Python: >=3.8
 License-File: LICENSE
 Requires-Dist: pint<0.24,>=0.20
 Requires-Dist: deprecation<3,>=2.1.0
+Requires-Dist: typing_extensions<5,>=4.8
+Requires-Dist: importlib-resources<7,>=5.3
 Provides-Extra: tests
 Requires-Dist: pytest<9,>=8.0.0; extra == "tests"
 Provides-Extra: tests-demo

{gemd-2.0.0 → gemd-2.1.1}/gemd.egg-info/requires.txt

@@ -1,5 +1,7 @@
 pint<0.24,>=0.20
 deprecation<3,>=2.1.0
+typing_extensions<5,>=4.8
+importlib-resources<7,>=5.3
 
 [tests]
 pytest<9,>=8.0.0

{gemd-2.0.0 → gemd-2.1.1}/setup.py

@@ -37,7 +37,9 @@ setup(name='gemd',
       },
       install_requires=[
           "pint>=0.20,<0.24",
-          "deprecation>=2.1.0,<3"
+          "deprecation>=2.1.0,<3",
+          "typing_extensions>=4.8,<5",
+          "importlib-resources>=5.3,<7"
       ],
       extras_require={
           "tests": [

gemd-2.0.0/gemd/__version__.py

@@ -1 +0,0 @@
-__version__ = "2.0.0"