Release 0.2.5

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,37 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Reminders**
+1. This is not a place to debug your MCNP models
+1. MCNP is export controlled and only its 6.2 and 6.3 user manuals are public. Don't include any information about MCNP which is not in those manuals.
+1. Your model may be export controlled, or proprietary. Please change specific numbers (e.g., dimensions, material compositions, etc.) in your minimum working examples. 
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Version [e.g. 0.2.5]
+
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,23 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: 'feature request'
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.
+
+**Reminder**
+Only the MCNP 6.2 and 6.3 user manuals are public. If this discusses a feature of MCNP you could only know by running MCNP please do not include it.

.github/workflows/deploy.yml

@@ -0,0 +1,105 @@
+name: Deploy
+
+on: 
+ push:
+ branches: [main]
+
+jobs:
+ last-minute-test:
+ runs-on: ubuntu-latest 
+ steps:
+ - uses: actions/checkout@v4
+ - name: set up python 3.8
+ uses: actions/setup-python@v4
+ with: 
+ python-version: 3.8
+ - run: pip install --user -r requirements/dev.txt
+ - run: python -m pytest
+
+ build-pages:
+ environment:
+ name: github-pages
+ url: ${{ steps.deployment.outputs.page_url }}
+ runs-on: ubuntu-latest
+ steps:
+ - name: Configure git
+ env:
+ TOKEN: ${{ secrets.ACCESS_TOKEN }}
+ run: git config --global url."https://${TOKEN}:x-oauth-basic@github.com/".insteadOf "https://github.com/"
+ - uses: actions/checkout@v4
+ - uses: actions/setup-python@v4
+ with:
+ python-version: 3.8
+ - run: pip install --user montepy[doc]
+ - run: cd doc && make html
+ - uses: actions/configure-pages@v4
+ - uses: actions/upload-pages-artifact@v3
+ with: 
+ name: deploy-pages
+ path: doc/build/html/
+
+ deploy-pages:
+ permissions:
+ contents: read
+ pages: write # to deploy to Pages
+ id-token: write # to verify the deployment originates from an appropriate source
+ environment:
+ name: github-pages
+ url: ${{ steps.deployment.outputs.page_url }}
+ needs: [build-pages, last-minute-test]
+ runs-on: ubuntu-latest
+ steps:
+ - run: ls -l
+ - uses: actions/download-artifact@v4
+ with: 
+ name: deploy-pages
+ - run: ls -l
+ - name: Deploy to GitHub Pages
+ id: deployment 
+ uses: actions/deploy-pages@v4
+ with: 
+ artifact_name: deploy-pages
+
+
+ deploy-test-pypi: 
+ environment:
+ name: test-pypi
+ url: https://test.pypi.org/p/montepy # Replace <package-name> with your PyPI project name
+ needs: [deploy-pages]
+ permissions:
+ contents: read
+ id-token: write
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v4
+ - uses: actions/setup-python@v4
+ with:
+ python-version: 3.8
+ - run: python -m pip install build
+ - run: python -m build --sdist --wheel
+ - 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]
+ permissions:
+ contents: read
+ id-token: write
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v4
+ - uses: actions/setup-python@v4
+ with:
+ python-version: 3.8
+ - run: python -m pip install build
+ - run: python -m build --sdist --wheel
+ - name: Publish distribution 📦 to PyPI
+ uses: pypa/gh-action-pypi-publish@release/v1
+
+
+

.github/workflows/main.yml

@@ -0,0 +1,91 @@
+name: Test package
+
+on: [push]
+
+jobs:
+ build:
+ runs-on: ubuntu-latest
+ strategy:
+ matrix:
+ python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+ steps:
+ - uses: actions/checkout@v4
+ - name: set up python ${{ matrix.python-version }}
+ uses: actions/setup-python@v4
+ with: 
+ python-version: ${{ matrix.python-version }}
+ - run: pip install --upgrade pip build
+ - run: pip install -r requirements/common.txt
+ - run: python -m build --sdist --wheel
+ - run: pip install .
+ - run: pip uninstall -y montepy
+ - run: pip install --user dist/*.whl
+ - run: pip uninstall -y montepy
+ - run: pip install --user dist/*.tar.gz
+ - run: pip install --user montepy[test]
+ - run: pip install --user montepy[doc]
+ - run: pip freeze
+ - name: Upload build artifacts
+ uses: actions/upload-artifact@v3
+ with: 
+ name: build
+ path: dist/*
+
+ test:
+ runs-on: ubuntu-latest
+ strategy:
+ matrix:
+ python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+ steps:
+ - uses: actions/checkout@v4
+ - name: set up python ${{ matrix.python-version }}
+ uses: actions/setup-python@v4
+ with: 
+ python-version: ${{ matrix.python-version }}
+ - run: pip install --user -r requirements/dev.txt
+ - run: coverage run -m pytest --junitxml=test_report.xml
+ - run: coverage report
+ - run: coverage xml
+ - name: Upload test report
+ uses: actions/upload-artifact@v3
+ with:
+ name: test
+ path: test_report.xml
+ - name: Upload coverage report
+ uses: actions/upload-artifact@v3
+ with:
+ name: coverage
+ path: coverage.xml
+
+ doc-test:
+ runs-on: ubuntu-latest
+
+ steps:
+ - uses: actions/checkout@v4
+ - name: set up python 3.8
+ uses: actions/setup-python@v4
+ with: 
+ python-version: 3.8
+ - run: pip install montepy[doc]
+ - run: sphinx-build doc/source/ doc/build/ -W --keep-going -E
+ - run: sphinx-build -b html doc/source/ doc/build/html
+ - uses: actions/upload-artifact@v3
+ with:
+ name: website
+ path: doc/build/html
+
+ format-test:
+ runs-on: ubuntu-latest
+
+ steps:
+ - uses: actions/checkout@v4
+ - name: set up python 3.8
+ uses: actions/setup-python@v4
+ with: 
+ python-version: 3.8
+ - run: pip install --user -r requirements/dev.txt
+ - run: black --check montepy/ tests/
+
+

README.md

@@ -1,15 +1,17 @@
 # MontePy
 
+<img src="https://raw.githubusercontent.com/idaholab/MontePy/develop/graphics/monty.svg" width="180" alt="MontePY: a cute snek on a red over white circle"/>
+
 A python library to read, edit, and write MCNP input files. 
 
 ## Installing
 
-See the [Installing section in the user guide](https://experiment_analysis_all.pages.hpc.inl.gov/software/montepy/starting.html#installing).
+See the [Installing section in the user guide](https://idaholab.github.io/MontePy/starting.html#installing).
 
 
 ## User Documentation
 
-MontePy has a [sphinx website](https://experiment_analysis_all.pages.hpc.inl.gov/software/montepy/). 
+MontePy has a [sphinx website](https://idaholab.github.io/MontePy/index.html). 
 This has a getting started guide for users,
 as well as API documentation. 
 There is also a developer's guide covering the design and approach of MontePy, and how to contribute.
@@ -19,9 +21,9 @@ There is also a developer's guide covering the design and approach of MontePy, a
 * Handles almost all MCNP input syntax including: message blocks, & continue, comments, etc.
 * Parses Cells, surfaces, materials, and transforms very well. 
 * Can parse the following surfaces exactly P(X|Y|Z), C(X|Y|Z), C/(X|Y|Z) (I mean it can do PX, and PY, etc.)
-* Can read in all other cards but not understand them 
-* Can write out full MCNP problem even if it doesn't fully understand a card. 
-* Can write out the MCNP problem verbatim, if it has not been modified at all.
+* Can read in all other inputs but not understand them 
+* Can write out full MCNP problem even if it doesn't fully understand an input. 
+* Can write out the MCNP problem verbatim, and try to match 
 * Can quickly access cells, surfaces, and materials by their numbers. For example: `cell = problem.cells[105]`.
 * Can quickly update cell importances. For example `cell.importance.neutron = 2.0`.
 * Has over 240 test cases right now 
@@ -56,7 +58,7 @@ So MontePy doesn't do what you want? Right now development is done with a Just-
 If there's a feature you want add an issue here with the feature request tag. 
 If you want to add a feature on your own talk to Micah Gale (but still add the issue). 
 The system is very modular and you should be able to develop it pretty quickly.
-Also read the [developer's guide](https://experiment_analysis_all.pages.hpc.inl.gov/software/montepy/developing.html).
+Also read the [developer's guide](https://idaholab.github.io/MontePy/developing.html).
 
 # Version Numbering Scheme
 
@@ -70,4 +72,4 @@ Also read the [developer's guide](https://experiment_analysis_all.pages.hpc.inl.
  Official shall not change. New merges to main shall have a version number incremented.
 
 
-# Finally: make objects not regexs!
+# Finally: make objects not regexes!

doc/source/conf.py

@@ -21,8 +21,8 @@
 # -- Project information -----------------------------------------------------
 
 project = "MontePy"
-copyright = "2021 – 2023, Battelle Energy Alliance LLC."
-author = "Micah D. Gale (@galemica), Travis J. Labossiere-Hickman (@tjlaboss)"
+copyright = "2021 – 2024, Battelle Energy Alliance LLC."
+author = "Micah D. Gale (@micahgale), Travis J. Labossiere-Hickman (@tjlaboss)"
 
 
 release = importlib.metadata.version("montepy")

doc/source/developing.rst

@@ -322,7 +322,7 @@ How to __str__ vs __repr__
 """"""""""""""""""""""""""
 All objects must implement ``__str__`` (called by ``str()``), 
 and ``__repr__`` (called by ``repr()``).
-See `this issue <https://hpcgitlab.hpc.inl.gov/experiment_analysis/montepy/-/issues/41>`_ for a more detailed discussion.
+See `this issue <https://github.com/idaholab/MontePy/issues/82>`_ for a more detailed discussion.
 In general ``__str__`` should return a one line string with enough information to uniquely identify the object.
 For numbered objects this should include their number, and a few high level details.
 For ``__repr__`` this should include debugging information.

doc/source/index.rst

@@ -22,7 +22,7 @@ See Also
 ========
 
 * `MontePy github Repository <https://github.com/idaholab/montepy>`_ 
-* `MCNP 6.2 User Manual <https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/la-ur-17-29981.pdf>`_
+* `MCNP 6.2 User Manual <https://mcnp.lanl.gov/pdf_files/TechReport_2017_LANL_LA-UR-17-29981_WernerArmstrongEtAl.pdf>`_
 * `MCNP 6.3 User Manual <https://mcnp.lanl.gov/pdf_files/TechReport_2022_LANL_LA-UR-22-30006Rev.1_KuleszaAdamsEtAl.pdf>`_
 
 Indices and tables

montepy/__init__.py

@@ -23,7 +23,8 @@
 from montepy.universe import Universe
 import sys
 
-__version__ = "0.2.4"
+__version__ = "0.2.5"
+
 # enable deprecated warnings for users
 if not sys.warnoptions:
  import os, warnings

montepy/errors.py

@@ -10,8 +10,7 @@ def __init__(self, message):
 
 class MalformedInputError(ValueError):
  """
- <<<<<<< HEAD
- Raised when there is an error with the MCNP input not related to the parser.
+ Raised when there is an error with the MCNP input not related to the parser.
  """
 
  def __init__(self, input, message):

montepy/input_parser/syntax_node.py

@@ -241,8 +241,19 @@ def format(self):
 
  @property
  def comments(self):
- for node in self.nodes.values():
- yield from node.comments
+ for key, node in self.nodes.items():
+ if isinstance(node, SyntaxNodeBase):
+ yield from node.comments
+ elif isinstance(node, dict):
+ yield from GeometryTree._recurse_comments(node)
+
+ @staticmethod
+ def _recurse_comments(tree):
+ for node in tree.values():
+ if isinstance(node, SyntaxNodeBase):
+ yield from node.comments
+ elif isinstance(node, dict):
+ yield from GeometryTree._recurse_comments(node)
 
  @property
  def left(self):