gemd 2.1.1__tar.gz → 2.1.4__tar.gz

{gemd-2.1.1 → gemd-2.1.4}/PKG-INFO

@@ -1,9 +1,11 @@
 Metadata-Version: 2.1
 Name: gemd
-Version: 2.1.1
+Version: 2.1.4
 Summary: Python binding for Citrine's GEMD data model
 Home-page: http://github.com/CitrineInformatics/gemd-python
 Author: Citrine Informatics
+License: UNKNOWN
+Platform: UNKNOWN
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
@@ -11,15 +13,11 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 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: scripts
 Provides-Extra: tests
-Requires-Dist: pytest<9,>=8.0.0; extra == "tests"
-Provides-Extra: tests-demo
-Requires-Dist: pandas<3,>=2.0.3; extra == "tests-demo"
-Provides-Extra: tests-entity-bounds
-Requires-Dist: numpy<2,>=1.24.4; extra == "tests-entity-bounds"
-Requires-Dist: pandas<3,>=2.0.3; extra == "tests-entity-bounds"
+Provides-Extra: tests.demo
+Provides-Extra: tests.entity.bounds
+License-File: LICENSE
+
+UNKNOWN
+

{gemd-2.1.1 → gemd-2.1.4}/README.md

@@ -1,5 +1,5 @@
 # GEMD-python 
-Python binding for Citrine's nextgen data model, GEMD. 
+Python binding for Citrine's data model, GEMD. 
 
 This package provides a framework for storing information about the processes that create materials, the materials themselves, and measurements performed on those materials. 
 

gemd-2.1.4/gemd/__version__.py

@@ -0,0 +1 @@
+__version__ = "2.1.4"

{gemd-2.1.1 → gemd-2.1.4}/gemd/demo/strehlow_and_cook.py

@@ -48,7 +48,7 @@ def import_table(filename=SMALL_TABLE):
     from importlib_resources import files
     import json
 
-    return json.loads(files("gemd.demo").joinpath(filename).read_text())
+    return json.loads(files("gemd.demo").joinpath(filename).read_text(encoding='utf-8'))
 
 
 def _fingerprint(row):

{gemd-2.1.1 → gemd-2.1.4}/gemd/units/impl.py

@@ -35,7 +35,7 @@ def _deploy_default_files() -> Tuple[Path, Path]:
     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")
+        target.write_bytes(source.read_bytes())
 
     return target_paths
 

{gemd-2.1.1 → gemd-2.1.4}/gemd.egg-info/PKG-INFO

@@ -1,9 +1,11 @@
 Metadata-Version: 2.1
 Name: gemd
-Version: 2.1.1
+Version: 2.1.4
 Summary: Python binding for Citrine's GEMD data model
 Home-page: http://github.com/CitrineInformatics/gemd-python
 Author: Citrine Informatics
+License: UNKNOWN
+Platform: UNKNOWN
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
@@ -11,15 +13,11 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 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: scripts
 Provides-Extra: tests
-Requires-Dist: pytest<9,>=8.0.0; extra == "tests"
-Provides-Extra: tests-demo
-Requires-Dist: pandas<3,>=2.0.3; extra == "tests-demo"
-Provides-Extra: tests-entity-bounds
-Requires-Dist: numpy<2,>=1.24.4; extra == "tests-entity-bounds"
-Requires-Dist: pandas<3,>=2.0.3; extra == "tests-entity-bounds"
+Provides-Extra: tests.demo
+Provides-Extra: tests.entity.bounds
+License-File: LICENSE
+
+UNKNOWN
+

{gemd-2.1.1 → gemd-2.1.4}/gemd.egg-info/SOURCES.txt

@@ -108,4 +108,8 @@ gemd/units/constants_en.txt
 gemd/units/impl.py
 gemd/util/__init__.py
 gemd/util/impl.py
-tests/test_examples.py
+tests/__init__.py
+tests/test_examples.py
+tests/units/__init__.py
+tests/units/test_parser.py
+tests/units/test_units.txt

{gemd-2.1.1 → gemd-2.1.4}/gemd.egg-info/requires.txt

@@ -1,7 +1,12 @@
-pint<0.24,>=0.20
 deprecation<3,>=2.1.0
-typing_extensions<5,>=4.8
 importlib-resources<7,>=5.3
+pint<0.24,>=0.20
+typing_extensions<5,>=4.8
+
+[scripts]
+packagingsphinx==5.0.0
+sphinx-rtd-theme==1.0.0
+sphinxcontrib-apidoc==0.3.0
 
 [tests]
 pytest<9,>=8.0.0

gemd-2.1.4/gemd.egg-info/top_level.txt

@@ -0,0 +1,2 @@
+gemd
+tests

{gemd-2.1.1 → gemd-2.1.4}/setup.py

@@ -1,23 +1,20 @@
 from setuptools import setup, find_packages
-from os import path
-from packaging.version import Version
+from pathlib import Path
 import re
 
 packages = find_packages()
 
-this_directory = path.abspath(path.dirname(__file__))
-version_file = path.join(this_directory, 'gemd', '__version__.py')
-version_re = r'''^__version__\s*=\s*(['"])([\w\.]+)\1$'''
-with open(version_file, 'r') as f:
-    mo = re.search(version_re, f.read(), re.M)
-    if mo:
-        version = Version(mo.group(2))
-    else:
-        raise RuntimeError(f"Unable to find version string in {version_file}")
+this_directory = Path(__file__).parent.absolute()
+version_file = this_directory / 'gemd' / '__version__.py'
+version_re = r'''^\s*__version__\s*=\s*(['"])([\w\.]+)\1$'''
+if mo := re.search(version_re, version_file.read_text(), re.M):
+    version = mo.group(2)
+else:
+    raise RuntimeError(f"Unable to find version string in {version_file}")
 
 setup(name='gemd',
       # Update this in gemd/__version__.py
-      version=str(version),
+      version=version,
       python_requires='>=3.8',
       url='http://github.com/CitrineInformatics/gemd-python',
       description="Python binding for Citrine's GEMD data model",
@@ -42,6 +39,12 @@ setup(name='gemd',
           "importlib-resources>=5.3,<7"
       ],
       extras_require={
+          "scripts": [
+              "packaging"
+              "sphinx==5.0.0",
+              "sphinx-rtd-theme==1.0.0",
+              "sphinxcontrib-apidoc==0.3.0",
+          ],
           "tests": [
               "pytest>=8.0.0,<9"
           ],

gemd-2.1.4/tests/units/test_parser.py

@@ -0,0 +1,225 @@
+from contextlib import contextmanager
+from deprecation import DeprecatedWarning
+from importlib_resources import files
+import re
+from pint import UnitRegistry
+import pytest
+
+from gemd.units import parse_units, convert_units, get_base_units, change_definitions_file, \
+    UndefinedUnitError, DefinitionSyntaxError, IncompatibleUnitsError
+
+
+@pytest.mark.parametrize("return_unit", [True, False])
+def test_parse_expected(return_unit):
+    """Test that we can parse the units that we expect to be able to."""
+    # Pint's parse_units actually gets this wrong
+    assert parse_units("m^-1 * newton / meter", return_unit=return_unit) == \
+           parse_units("N / m^2", return_unit=return_unit)
+
+    expected = [
+        "degC", "degF", "K",
+        "g", "kg", "mg", "ton",
+        "L", "mL",
+        "inch", "ft", "mm", "um",
+        "second", "ms", "hour", "minute", "ns",
+        "g/cm^3", "g/mL", "kg/cm^3",
+        "", "1",
+        "amu",  # A line that was edited
+        "Seconds",  # Added support for some title-case units
+        "delta_Celsius / hour",  # Added to make sure pint version is right (>0.10)
+        "g / 2.5 cm",  # Scaling factors are acceptable
+        "g / -+-25e-1 m",  # Weird but fine
+        "ug / - -250 mL",  # Spaces between unaries is acceptable
+        "1 / 10**5 degC",  # Spaces between unaries is acceptable
+        "1 / 10_000 degC",  # Spaces between unaries is acceptable
+        "m ** - 1",  # Pint < 0.21 throws DefinitionSyntaxError
+        "gram / _10_minute",  # Stringified Unit object SPT-1311
+        "gram / __1_2e_3minute",  # Stringified Unit object SPT-1311
+    ]
+    for unit in expected:
+        parsed = parse_units(unit, return_unit=return_unit)
+        assert parsed == parse_units(parsed, return_unit=return_unit)
+    assert parse_units("") == 'dimensionless'
+    # Scaling factors bind tightly to trailing units
+    scaling = [
+        ("g / 2.5 cm", "g / (2.5 cm)"),
+        ("g / 2.5cm", "g / (2.5 cm)"),
+        ("g / 25.mm", "g / (25. mm)"),
+        ("g / 2.5 * cm", "g cm / 2.5")
+    ]
+    for left, right in scaling:
+        assert parse_units(left, return_unit=return_unit) == \
+               parse_units(right, return_unit=return_unit)
+
+
+def test_parse_unexpected():
+    """Test that we cannot parse the units that we do not expect to."""
+    unexpected = [
+        "gibberish",
+        5,
+        "cp",  # Removed because of risk of collision with cP
+        "chain",  # Survey units eliminated
+        "SECONDS",  # Not just case insensitivity
+        "lb : in^3",  # : is not a valid operator
+    ]
+    for unit in unexpected:
+        with pytest.raises(UndefinedUnitError):
+            parse_units(unit)
+
+    scaling = [
+        "3 rpm",  # No leading digits
+        "16",  # No values that are just integers
+        "16.2"  # No values that are just floats
+        "g * 0/ m",  # Zero scaling factor
+        "F * 1.1 3.5",  # numeric syntax error
+        "F m 1.1",  # scale follows unit
+        "F * 1.1 ** 2",  # numeric syntax error
+    ]
+    for unit in scaling:
+        with pytest.raises(ValueError, match=r"[sS]caling"):
+            parse_units(unit)
+
+    definition = [
+        "/gram",  # A leading operator makes no sense
+    ]
+    for unit in definition:
+        with pytest.raises(DefinitionSyntaxError):
+            parse_units(unit)
+
+    zero_division = [
+        "g / 0 m",  # Division by zero
+    ]
+    for unit in zero_division:
+        with pytest.raises(ZeroDivisionError):
+            parse_units(unit)
+
+
+def test_parse_none():
+    """Test that None parses as None."""
+    assert parse_units(None) is None
+    assert parse_units(None, return_unit=True) == parse_units("", return_unit=True)
+
+
+def test_parse_units_as_units():
+    """Test that Units in == Units out."""
+    from gemd.units.impl import _REGISTRY
+
+    expected = [
+        _REGISTRY("kg").u,
+    ]
+    for unit in expected:
+        parsed = parse_units(unit)
+        assert parsed == parse_units(parsed)
+
+
+def test_format():
+    """Test that custom formatting behaves as we hope."""
+    # use the default unit registry for now
+    reg = UnitRegistry()
+
+    result = parse_units("K^-2.0 m^-1e0 C^0 g^1 s^2")
+    assert "-" not in result
+    assert "[time]" in str(reg(result).dimensionality)
+    assert "[current]" not in str(reg(result).dimensionality)
+    kelvin = str(reg("K").units)
+    gram = str(reg("g").units)
+    second = str(reg("s").units)
+    assert kelvin in str(result)
+    assert gram in str(result)
+    assert second in str(result)
+    assert result.index(gram) < result.index(kelvin)
+    assert result.index(gram) < result.index(second)
+
+    assert not re.search(r"\d", parse_units("m kg / s"))
+    assert "/" not in parse_units("m kg s")
+    assert "1" not in parse_units("s")
+    assert "1" in parse_units("s^-1")
+    assert "2.5" in parse_units("g / 2.5 cm")
+
+
+def test_conversion():
+    """Tests that check if particular units are interoperable."""
+    conversions = {"in_lb": "foot_pound"}
+    for source, dest in conversions.items():
+        assert convert_units(convert_units(1, source, dest), dest, source) == 1
+
+    # Verify that convert_units respects scaling factors
+    assert -1e-8 < convert_units(100, 'g / 100 mL', 'g/cc') - 1 < 1e-8
+    assert -1e-8 < convert_units(1, "g / 2.5 cm", "g / 25 mm") - 1 < 1e-8
+
+    # Verify that convert_units throws exceptions
+    with pytest.raises(IncompatibleUnitsError):
+        convert_units(1, 'mL', 'g')
+    with pytest.raises(IncompatibleUnitsError):
+        # https://pint.readthedocs.io/en/0.23/user/angular_frequency.html
+        convert_units(1, 'Hz', 'rpm')
+
+
+def test_get_base_units():
+    """Test that base units & conversions make sense."""
+    from gemd.units.impl import _REGISTRY
+    assert get_base_units("degC") == (_REGISTRY("kelvin"), 1, 273.15)
+    assert get_base_units("degC") == get_base_units(_REGISTRY("degC"))
+    assert get_base_units("km") == (_REGISTRY("meter"), 1000, 0)
+    assert get_base_units("g / 25 mm") == (_REGISTRY("kg / m"), 0.04, 0)
+
+
+@contextmanager
+def _change_units(filename):
+    try:
+        change_definitions_file(filename)
+        yield
+    finally:
+        change_definitions_file()
+
+
+def test_file_change(tmpdir):
+    """Test that swapping units files works."""
+    assert convert_units(1, 'm', 'cm') == 100
+    with pytest.raises(UndefinedUnitError):
+        assert convert_units(1, 'usd', 'USD') == 1
+
+    test_file = tmpdir / "test_units.txt"
+    test_file.write_binary(files("tests.units").joinpath("test_units.txt").read_bytes())
+    with _change_units(filename=test_file):
+        with pytest.raises(UndefinedUnitError):
+            assert convert_units(1, 'm', 'cm') == 100
+        assert convert_units(1, 'usd', 'USD') == 1
+    assert convert_units(1, 'm', 'cm') == 100  # And verify we're back to normal
+    with pytest.raises(UndefinedUnitError):
+        parse_units('mol : mol')  # Ensure the preprocessor is still there
+
+
+def test_punctuation():
+    """Test that punctuation parses reasonably."""
+    assert parse_units('mol.') == parse_units('moles')
+    assert parse_units('N.m') == parse_units('N * m')
+    with pytest.raises(UndefinedUnitError):
+        parse_units('mol : mol')
+
+
+def test_exponents():
+    """SPT-874 fractional exponents were being treated as zero."""
+    megapascals = parse_units("MPa")
+    sqrt_megapascals = parse_units('MPa^0.5')
+    assert megapascals in sqrt_megapascals
+    assert sqrt_megapascals == parse_units(f"{megapascals} / {sqrt_megapascals}")
+    assert parse_units('MPa^1.5') == parse_units(f"{megapascals} * {sqrt_megapascals}")
+
+
+def test__scientific_notation_preprocessor():
+    """Verify that numbers are converted into scientific notation."""
+    assert "1e2 kilogram" in parse_units("F* 10 ** 2 kg")
+    assert "1e2 kg" in f'{parse_units("F* 10 ** 2 kg", return_unit=True):~}'
+    assert "1e-5" in parse_units("F* mm*10**-5")
+    assert "1e" not in parse_units("F* kg * 10 cm")
+    assert "-3.07e2" in parse_units("F* -3.07 * 10 ** 2")
+    assert "11e2" in parse_units("F* 11*10^2")
+
+
+def test_deprecation():
+    """Make sure deprecated things warn correctly."""
+    megapascals = parse_units("MPa", return_unit=True)
+    with pytest.warns(DeprecatedWarning):
+        stringified = f"{megapascals:clean}"
+    assert megapascals == parse_units(stringified, return_unit=True)

gemd-2.1.4/tests/units/test_units.txt

@@ -0,0 +1,4 @@
+
+#### BASE UNITS ####
+
+usd = [currency] = USD

gemd-2.1.1/gemd/__version__.py

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

gemd-2.1.1/gemd.egg-info/top_level.txt

@@ -1 +0,0 @@
-gemd