Merge pull request #5 from idaholab/develop

Release 0.2.5
idaholab · Jan 16, 2024 · 5cf1e1e · 5cf1e1e
2 parents b323df3 + 720b2cd
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.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.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.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.
diff --git a/.github/workflows/deploy.yml b/.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}:[email protected]/".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
+
+
+
diff --git a/.github/workflows/main.yml b/.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/
+
+
diff --git a/README.md b/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!
diff --git a/doc/source/conf.py b/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")

diff --git a/doc/source/developing.rst b/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.

diff --git a/doc/source/index.rst b/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

diff --git a/montepy/__init__.py b/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

diff --git a/montepy/errors.py b/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):

diff --git a/montepy/input_parser/syntax_node.py b/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):