Merge pull request #507 from idaholab/mat_redesign

Mat redesign

.github/scripts/check_version.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+
+import argparse
+import re
+import sys
+from setuptools_scm import get_version
+
+parser = argparse.ArgumentParser()
+parser.add_argument("-a", "--alpha", action="store_true")
+DEPLOY_VERSION = r"\d+\.\d+\.\d+"
+ALPHA_VERSION = DEPLOY_VERSION + r"a\d+"
+args = parser.parse_args()
+if args.alpha:
+    print("checking alpha release")
+    parser = ALPHA_VERSION
+else:
+    print("checking Final release.")
+    parser = DEPLOY_VERSION
+
+version = get_version()
+print(f"version = {version}")
+if not re.fullmatch(parser, version):
+    exit(1)
+exit(0)

.github/workflows/deploy-alpha.yml

@@ -0,0 +1,107 @@
+name: Deploy
+
+on: 
+  push:
+    branches: [alpha-test]
+
+
+jobs:
+  last-minute-test:
+    runs-on: ubuntu-latest    
+    steps:
+      - uses: actions/checkout@v4
+      - name: set up python  3.12
+        uses: actions/setup-python@v5
+        with: 
+          python-version: 3.12
+      - run: pip install . montepy[develop]
+      - run: python -m pytest
+
+  build-packages:
+    name: Build, sign, and release packages on github
+    runs-on: ubuntu-latest
+    needs: [last-minute-test]
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write  # IMPORTANT: mandatory for sigstore
+    env:
+      GH_TOKEN: ${{ github.token }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          fetch-tags: true
+      - name: set up python  3.12
+        uses: actions/setup-python@v5
+        with: 
+          python-version: 3.12
+      - run: pip install . montepy[build]
+      - name: Get Version
+        id: get_version
+        run: echo "version=`python -m setuptools_scm`" >> $GITHUB_OUTPUT
+      - name: Verify that this is a non-dev alpha release
+        run: .github/scripts/check_version.py --alpha 
+      - run: python -m build .
+      - name: Sign the dists with Sigstore
+        uses: sigstore/gh-action-sigstore-python@v2.1.1
+        with:
+          inputs: >-
+            ./dist/*.tar.gz
+            ./dist/*.whl
+      - name: Create a GitHub release
+        uses: ncipollo/release-action@v1
+        with:
+          tag: v${{ steps.get_version.outputs.version }}
+          name: Release ${{ steps.get_version.outputs.version }}
+          draft: true
+      - run: >-
+          gh release upload
+          'v${{ steps.get_version.outputs.version }}' dist/**
+          --repo '${{ github.repository }}'
+      - uses: actions/upload-artifact@v4
+        with: 
+           name: build
+           path: |
+               dist/*.tar.gz 
+               dist/*.whl
+
+
+  deploy-test-pypi: 
+    environment:
+      name: test-pypi
+      url: https://test.pypi.org/p/montepy  # Replace <package-name> with your PyPI project name
+    needs: [build-packages]
+    permissions:
+      contents: read
+      id-token: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: build
+          path: dist/
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  deploy-pypi: 
+    environment:
+      name: pypi
+      url: https://pypi.org/p/montepy  # Replace <package-name> with your PyPI project name
+    needs: [deploy-pages, deploy-test-pypi, build-packages]
+    permissions:
+      contents: read
+      id-token: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: build
+          path: dist/
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+
+
+

.github/workflows/deploy.yml

@@ -62,7 +62,7 @@ jobs:
         id: get_version
         run: echo "version=`python -m setuptools_scm`" >> $GITHUB_OUTPUT
       - name: Verify that this is a non-dev release
-        run: .github/scripts/check_version.sh ${{ steps.get_version.outputs.version }}
+        run: .github/scripts/check_version.py
       - run: python -m build .
       - name: Sign the dists with Sigstore
         uses: sigstore/gh-action-sigstore-python@v2.1.1

.gitignore

@@ -17,3 +17,8 @@ doc/build/*
 .idea/
 .ipynb_checkpoints/
 montepy/_version.py
+
+# various testing results
+htmlcov
+.hypothesis
+.mutmut-cache

benchmark/benchmark_big_model.py

@@ -1,25 +1,41 @@
 import gc
-import montepy
 
 import time
 import tracemalloc
 
-FAIL_THRESHOLD = 30
-
 tracemalloc.start()
+
+import montepy
+
+FAIL_THRESHOLD = 40
+MEMORY_FRACTION = 0.50
+
+starting_mem = tracemalloc.get_traced_memory()[0]
+print(f"starting memory with montepy. {starting_mem/1024/1024} MB")
 start = time.time()
 
 problem = montepy.read_input("benchmark/big_model.imcnp")
 
 stop = time.time()
 
+problem_mem = tracemalloc.get_traced_memory()[0]
 print(f"Took {stop - start} seconds")
-print(f"Memory usage report: {tracemalloc.get_traced_memory()[0]/1024/1024} MB")
+print(f"Memory usage report: {problem_mem/1024/1024} MB")
 del problem
 gc.collect()
-print(f"Memory usage report after GC: {tracemalloc.get_traced_memory()[0]/1024/1024} MB")
+ending_mem = tracemalloc.get_traced_memory()[0]
+print(f"Memory usage report after GC: {ending_mem/1024/1024} MB")
 
 if (stop - start) > FAIL_THRESHOLD:
     raise RuntimeError(
         f"Benchmark took too long to complete. It must be faster than: {FAIL_THRESHOLD} s."
     )
+
+prob_gc_mem = problem_mem - ending_mem
+prob_actual_mem = problem_mem - starting_mem
+gc_ratio = prob_gc_mem / prob_actual_mem
+print(f"{gc_ratio:.2%} of the problem's memory was garbage collected.")
+if (prob_gc_mem / prob_actual_mem) < MEMORY_FRACTION:
+    raise RuntimeError(
+        f"Benchmark had too many memory leaks. Only {gc_ratio:.2%} of the memory was collected."
+    )

demo/Pin_cell.ipynb

@@ -9,6 +9,7 @@
    "source": [
     "import montepy\n",
     "import os\n",
+    "\n",
     "montepy.__version__"
    ]
   },
@@ -95,7 +96,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#make folder\n",
+    "# make folder\n",
     "os.mkdir(\"parametric\")\n",
     "\n",
     "fuel_wall = problem.surfaces[1]\n",

doc/source/_test_for_missing_docs.py

@@ -9,6 +9,7 @@
     "_version.py",
     "__main__.py",
     "_cell_data_control.py",
+    "_singleton.py"
 }
 
 base = os.path.join("..", "..")

doc/source/api/montepy.data_inputs.nuclide.rst

@@ -0,0 +1,10 @@
+montepy.data_inputs.nuclide module
+==================================
+
+
+.. automodule:: montepy.data_inputs.nuclide
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+

doc/source/api/montepy.data_inputs.rst

@@ -23,6 +23,7 @@ montepy.data\_inputs package
    montepy.data_inputs.lattice_input
    montepy.data_inputs.material
    montepy.data_inputs.material_component
+   montepy.data_inputs.nuclide
    montepy.data_inputs.mode
    montepy.data_inputs.thermal_scattering
    montepy.data_inputs.transform

doc/source/api/montepy.input_parser.material_parser.rst

@@ -0,0 +1,9 @@
+montepy.input\_parser.material\_parser module
+==============================================
+
+
+.. automodule:: montepy.input_parser.material_parser
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:

doc/source/api/montepy.input_parser.rst

@@ -17,12 +17,14 @@ montepy.input\_parser package
    montepy.input_parser.input_file
    montepy.input_parser.input_reader
    montepy.input_parser.input_syntax_reader
+   montepy.input_parser.material_parser
    montepy.input_parser.mcnp_input
    montepy.input_parser.parser_base
    montepy.input_parser.read_parser
    montepy.input_parser.shortcuts
    montepy.input_parser.surface_parser
    montepy.input_parser.syntax_node
    montepy.input_parser.tally_parser
+   montepy.input_parser.tally_seg_parser
    montepy.input_parser.thermal_parser
    montepy.input_parser.tokens

doc/source/api/montepy.input_parser.tally_seg_parser.rst

@@ -0,0 +1,9 @@
+montepy.input\_parser.tally\_seg\_parser module
+===============================================
+
+
+.. automodule:: montepy.input_parser.tally_seg_parser
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:

doc/source/changelog.rst

@@ -2,6 +2,61 @@
 MontePy Changelog
 *****************
 
+1.0.0 releases
+==============
+
+#Next Version#
+--------------
+
+**Features Added**
+
+* Redesigned how Materials hold Material_Components. See :ref:`migrate 0 1` (:pull:`507`). 
+
+* Made it easier to create an Isotope, or now Nuclide: ``montepy.Nuclide("H-1.80c")`` (:issue:`505`).
+* When a typo in an object attribute is made an Error is raised rather than silently having no effect (:issue:`508`).
+* Improved material printing to avoid very long lists of components (:issue:`144`).
+* Allow querying for materials by components (:issue:`95`).
+* Added support for getting and setting default libraries, e.g., ``nlib``, from a material (:issue:`369`).
+* 
+* Added most objects to the top level so they can be accessed like: ``montepy.Cell``.
+* Made ``Material.is_atom_fraction`` settable (:issue:`511`). 
+* Made NumberedObjectCollections act like a set (:issue:`138`).
+* Automatically added children objects, e.g., the surfaces in a cell, to the problem when the cell is added to the problem (:issue:`63`).
+
+**Bugs Fixed**
+
+* Made it so that a material created from scratch can be written to file (:issue:`512`).
+* Added support for parsing materials with parameters mixed throughout the definition (:issue:`182`).
+
+**Breaking Changes**
+
+* Removed :func:`~montepy.data_inputs.material.Material.material_components``. See :ref:`migrate 0 1` (:pull:`507`).
+* Removed :class:`~montepy.data_inputs.isotope.Isotope` and changed them to :class:`~montepy.data_inputs.nuclide.Nuclide`.
+* Removed :func:`~montepy.mcnp_problem.MCNP_Problem.add_cell_children_to_problem` as it is no longer needed. 
+
+**Deprecated code Removed**
+
+* ``montepy.Cell.geometry_logic_string``
+* ``montepy.data_inputs.cell_modifier.CellModifier.has_changed_print_style``
+* ``montepy.data_inputs.data_input.DataInputAbstract``
+
+  * ``class_prefix``
+  * ``has_number``
+  * ``has_classifier``
+
+* ``montepy.input_parser.mcnp_input.Card``
+* ``montepy.input_parser.mcnp_input.ReadCard``
+* ``montepy.input_parser.mcnp_input.Input.words``
+* ``montepy.input_parser.mcnp_input.Comment``
+* ``montepy.input_parser.mcnp_input.parse_card_shortcuts``
+* ``montepy.mcnp_object.MCNP_Object``
+
+  * ``wrap_words_for_mcnp``
+  * ``compress_repeat_values``
+  * ``compress_jump_values``
+  * ``words``
+  * ``allowed_keywords``
+
 0.5 releases
 ============
 
@@ -47,7 +102,7 @@ MontePy Changelog
 ============
 
 0.4.1
---------------
+----------------
 
 **Features Added**