Merge branch 'develop' into 476-parsing-of-transformations-on-fill-ke…

…ywords-appears-to-be-failing

README.md

@@ -6,6 +6,7 @@
 [![JOSS article status](https://joss.theoj.org/papers/e5b5dc8cea19605a1507dd4d420d5199/status.svg)](https://joss.theoj.org/papers/e5b5dc8cea19605a1507dd4d420d5199)
 [![Coverage Status](https://coveralls.io/repos/github/idaholab/MontePy/badge.svg?branch=develop)](https://coveralls.io/github/idaholab/MontePy?branch=develop)
 [![PyPI version](https://badge.fury.io/py/montepy.svg)](https://badge.fury.io/py/montepy)
+[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 
 MontePy is a python library to read, edit, and write MCNP input files. 
 

doc/source/changelog.rst

@@ -10,6 +10,11 @@ MontePy Changelog
 * Fixed bug with appending and renumbering numbered objects from other MCNP problems (:issue:`466`).
 * Fixed bug with dynamic typing and the parsers that only appear in edge cases (:issue:`461`).
 * Fixed parser bug with having spaces in the start of the transform input for the fill of a cell (:pull:`479`).
+* Fixed bug with trying to get trailing comments from non-existant parts of the syntax tree (:pull:`480`).
+
+**Code Quality**
+
+* Simpler ``Isotope`` representation (:issue:`473`).
 
 
 0.3.2

doc/source/conf.py

@@ -36,12 +36,16 @@
     "sphinx.ext.napoleon",
     "sphinx.ext.intersphinx",
     "sphinx.ext.extlinks",
+    "sphinx_sitemap",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 html_favicon = "monty.svg"
 html_logo = "monty.svg"
+
+html_baseurl = "https://www.montepy.org/"
+html_extra_path = ["robots.txt"]
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.

doc/source/robots.txt

@@ -0,0 +1,4 @@
+User-agent: *
+Allow: /
+
+Sitemap: https://www.montepy.org/sitemap.xml

montepy/data_inputs/isotope.py

@@ -168,8 +168,8 @@ def library(self, library):
             raise TypeError("library must be a string")
         self._library = library
 
-    def __str__(self):
-        return f"{self.element.symbol:>2}-{self.A:<3} ({self._library})"
+    def __repr__(self):
+        return f"{self.__class__.__name__}({repr(self.nuclide_str())})"
 
     def mcnp_str(self):
         """
@@ -182,6 +182,10 @@ def mcnp_str(self):
         """
         return f"{self.ZAID}.{self.library}" if self.library else self.ZAID
 
+    def nuclide_str(self):
+        suffix = f".{self._library}" if self._library else ""
+        return f"{self.element.symbol}-{self.A}{suffix}"
+
     def get_base_zaid(self):
         """
         Get the ZAID identifier of the base isotope this is an isomer of.
@@ -193,8 +197,9 @@ def get_base_zaid(self):
         """
         return self.Z * 1000 + self.A
 
-    def __repr__(self):
-        return f"ZAID={self.ZAID}, Z={self.Z}, A={self.A}, element={self.element}, library={self.library}"
+    def __str__(self):
+        suffix = f" ({self._library})" if self._library else ""
+        return f"{self.element.symbol:>2}-{self.A:<3}{suffix}"
 
     def __hash__(self):
         return hash(self._ZAID)

montepy/input_parser/syntax_node.py

@@ -193,8 +193,9 @@ def comments(self):
     def get_trailing_comment(self):
         if len(self.nodes) == 0:
             return
-        tail = next(reversed(self.nodes.items()))
-        return tail[1].get_trailing_comment()
+        for node in reversed(self.nodes.values()):
+            if node is not None:
+                return node.get_trailing_comment()
 
     def _delete_trailing_comment(self):
         tail = next(reversed(self.nodes.items()))

pyproject.toml

@@ -37,7 +37,12 @@ dependencies = [
 [project.optional-dependencies]
 test = ["coverage[toml]>=6.3.2", "pytest"]
 # This is needed for a sphinx bug. See #414.
-doc = ["sphinx>=7.4.0", "sphinxcontrib-apidoc", "sphinx_rtd_theme"]
+doc = [
+	"sphinx>=7.4.0", 
+	"sphinxcontrib-apidoc", 
+	"sphinx_rtd_theme",
+	"sphinx-sitemap"
+]
 format = ["black>=23.3.0"]
 build = [
 	"build",

tests/inputs/test_missing_mat_for_mt.imcnp

@@ -6,4 +6,7 @@ c surfaces
 1 so 0.5
 
 c data
+m5      8016.71c  2.6999999-02
+        8017.71c  9.9999998-01
+        plib=84p
 MT1 lwtr.01t

tests/test_material.py

@@ -15,62 +15,6 @@
 
 
 class testMaterialClass(TestCase):
-    def test_material_init(self):
-        # test invalid material number
-        input_card = Input(["Mfoo"], BlockType.DATA)
-        with self.assertRaises(MalformedInputError):
-            Material(input_card)
-        input_card = Input(["M-20"], BlockType.DATA)
-        with self.assertRaises(MalformedInputError):
-            Material(input_card)
-
-        in_str = "M20 1001.80c 0.5 8016.710nc 0.5"
-        input_card = Input([in_str], BlockType.DATA)
-        material = Material(input_card)
-        self.assertEqual(material.number, 20)
-        self.assertEqual(material.old_number, 20)
-        self.assertTrue(material.is_atom_fraction)
-        for component in material.material_components:
-            self.assertEqual(material.material_components[component].fraction, 0.5)
-
-        # test implicit library with syntax tree errors
-        in_str = """m1 1001 0.33
-    8016 0.666667"""
-        input_card = Input(in_str.split("\n"), BlockType.DATA)
-        material = Material(input_card)
-        # test implicit library
-        in_str = "M20 1001 0.5 2001 0.5 8016.710nc 0.5"
-        input_card = Input([in_str], BlockType.DATA)
-        material = Material(input_card)
-        self.assertEqual(material.number, 20)
-        self.assertEqual(material.old_number, 20)
-        self.assertTrue(material.is_atom_fraction)
-        for component in material.material_components:
-            self.assertEqual(material.material_components[component].fraction, 0.5)
-
-        # test weight fraction
-        in_str = "M20 1001.80c -0.5 8016.80c -0.5"
-        input_card = Input([in_str], BlockType.DATA)
-        material = Material(input_card)
-        self.assertFalse(material.is_atom_fraction)
-        for component in material.material_components:
-            self.assertEqual(material.material_components[component].fraction, 0.5)
-
-        # test bad fraction
-        in_str = "M20 1001.80c foo"
-        input_card = Input([in_str], BlockType.DATA)
-        with self.assertRaises(MalformedInputError):
-            material = Material(input_card)
-        # test mismatch fraction
-        in_str = "M20 1001.80c 0.5 8016.80c -0.5"
-        input_card = Input([in_str], BlockType.DATA)
-        with self.assertRaises(MalformedInputError):
-            material = Material(input_card)
-        # test parameters
-        in_str = "M20 1001.80c 0.5 8016.80c 0.5 Gas=1"
-        input_card = Input([in_str], BlockType.DATA)
-        material = Material(input_card)
-        self.assertEqual(material.parameters["gas"]["data"][0].value, 1.0)
 
     def test_material_parameter_parsing(self):
         for line in ["M20 1001.80c 1.0 gas=0", "M20 1001.80c 1.0 gas = 0 nlib = 00c"]:
@@ -99,16 +43,17 @@ def test_material_str(self):
         in_str = "M20 1001.80c 0.5 8016.80c 0.4 94239.80c 0.1"
         input_card = Input([in_str], BlockType.DATA)
         material = Material(input_card)
-        answers = """MATERIAL: 20 fractions: atom
+        answers = """\
+MATERIAL: 20 fractions: atom
  H-1   (80c) 0.5
  O-16  (80c) 0.4
 Pu-239 (80c) 0.1
 """
         output = repr(material)
         print(output)
-        self.assertEqual(output, answers)
+        assert output == answers
         output = str(material)
-        self.assertEqual(output, "MATERIAL: 20, ['hydrogen', 'oxygen', 'plutonium']")
+        assert output == "MATERIAL: 20, ['hydrogen', 'oxygen', 'plutonium']"
 
     def test_material_sort(self):
         in_str = "M20 1001.80c 0.5 8016.80c 0.5"
@@ -190,6 +135,46 @@ def test_material_update_format():
     assert "8016" in material.format_for_mcnp_input((6, 2, 0))[0]
 
 
+@pytest.mark.parametrize(
+    "line, mat_number, is_atom, fractions",
+    [
+        ("M20 1001.80c 0.5 8016.710nc 0.5", 20, True, [0.5, 0.5]),
+        ("m1 1001 0.33 8016 0.666667", 1, True, [0.33, 0.666667]),
+        ("M20 1001 0.5 8016 0.5", 20, True, [0.5, 0.5]),
+        ("M20 1001.80c -0.5 8016.80c -0.5", 20, False, [0.5, 0.5]),
+        ("M20 1001.80c -0.5 8016.710nc -0.5", 20, False, [0.5, 0.5]),
+        ("M20 1001.80c 0.5 8016.80c 0.5 Gas=1", 20, True, [0.5, 0.5]),
+        (
+            "m1      8016.71c  2.6999999-02 8017.71c  9.9999998-01 plib=84p",
+            1,
+            True,
+            [2.6999999e-2, 9.9999998e-01],
+        ),
+    ],
+)
+def test_material_init(line, mat_number, is_atom, fractions):
+
+    input = Input([line], BlockType.DATA)
+    material = Material(input)
+    assert material.number == mat_number
+    assert material.old_number == mat_number
+    assert material.is_atom_fraction == is_atom
+    for component, gold in zip(material.material_components.values(), fractions):
+        assert component.fraction == pytest.approx(gold)
+    if "gas" in line:
+        assert material.parameters["gas"]["data"][0].value == pytest.approx(1.0)
+
+
+@pytest.mark.parametrize(
+    "line", ["Mfoo", "M-20", "M20 1001.80c foo", "M20 1001.80c 0.5 8016.80c -0.5"]
+)
+def test_bad_init(line):
+    # test invalid material number
+    input = Input([line], BlockType.DATA)
+    with pytest.raises(MalformedInputError):
+        Material(input)
+
+
 class TestIsotope(TestCase):
     def test_isotope_init(self):
         isotope = Isotope("1001.80c")
@@ -245,14 +230,18 @@ def test_isotope_library_setter(self):
 
     def test_isotope_str(self):
         isotope = Isotope("1001.80c")
-        self.assertEqual(isotope.mcnp_str(), "1001.80c")
-        self.assertEqual(str(isotope), " H-1   (80c)")
-        self.assertEqual(
-            repr(isotope), "ZAID=1001, Z=1, A=1, element=hydrogen, library=80c"
-        )
+        assert isotope.mcnp_str() == "1001.80c"
+        assert isotope.nuclide_str() == "H-1.80c"
+        assert repr(isotope) == "Isotope('H-1.80c')"
+        assert str(isotope) == " H-1   (80c)"
         isotope = Isotope("94239.80c")
-        self.assertEqual(isotope.mcnp_str(), "94239.80c")
-        self.assertEqual(str(isotope), "Pu-239 (80c)")
+        assert isotope.nuclide_str() == "Pu-239.80c"
+        assert isotope.mcnp_str() == "94239.80c"
+        assert repr(isotope) == "Isotope('Pu-239.80c')"
+        isotope = Isotope("95642")
+        assert isotope.nuclide_str() == "Am-242"
+        assert isotope.mcnp_str() == "95642"
+        assert repr(isotope) == "Isotope('Am-242')"
 
 
 class TestThermalScattering(TestCase):