Merge pull request #1 from idaholab/develop

Merging disjoint histories for public release.

.gitignore

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+__pycache__/
+build/*
+dist/*
+*egg-info/*
+*.mcnp
+.coverage
+.idea/*
+*.*.sw*
+doc/build/*
+.coverage
+.idea/
+.ipynb_checkpoints/

.gitlab-ci.yml

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+image: python:latest
+
+include: 
+  - templates/install.yml
+  - templates/test.yml
+
+variables:
+  PYTHON_VER: "3.8"
+  CONDA_BASE_NAME: experiment_analysis_montepy
+
+default:
+  artifacts:
+    expire_in: 7 day
+
+after_script:
+  - export PATH=$(echo "$PATH" | sed -e 's/:\/data\/gitlab-runner\/.conda\/envs\/experiment_analysis_mcnpy\/$//')
+  - echo $PATH
+  - conda deactivate
+
+.job_template: &install-boiler
+  stage: build
+  extends: .install
+  when: delayed
+  start_in: 1 minutes
+  variables:
+    PYTHON_VER: "3.8"
+
+install-3.8:
+  stage: build
+  extends: .install
+  variables:
+    PYTHON_VER: "3.8"
+
+install-3.9:
+  <<: *install-boiler 
+  variables:
+    PYTHON_VER: "3.9"
+
+
+install-3.10:
+  <<: *install-boiler 
+  variables:
+    PYTHON_VER: "3.10"
+
+install-3.11:
+  <<: *install-boiler 
+  variables:
+    PYTHON_VER: "3.11"
+
+install-3.12:
+  <<: *install-boiler 
+  variables:
+    PYTHON_VER: "3.12"
+
+coverage_unit_test:
+  stage: test
+  coverage: '/TOTAL.+ ([0-9\.]{1,5}%)/'
+  script:
+    - conda activate $CONDA_BASE_NAME-$PYTHON_VER
+    - export PATH="~/.local/bin/:/data/gitlab-runner/.conda/envs/$CONDA_BASE_NAME-$PYTHON_VER/bin:$PATH"
+    - echo $PATH
+    - echo "Executing unit tests"
+    - which python
+    - pip freeze
+    - coverage run -m pytest --junitxml=test_report.xml
+    - coverage report 
+    - coverage xml
+  artifacts:
+    reports:
+      junit: test_report.xml
+      coverage_report:
+         coverage_format: cobertura
+         path: coverage.xml
+  needs: ["install-3.8"]
+
+# skip 3.8 because of coverage test
+
+.job_template: &test_config
+  stage: test
+  extends: .test_no_cover
+
+unit_test-3.9:
+  <<: *test_config
+  variables:
+    PYTHON_VER: "3.9"
+  needs: ["coverage_unit_test","install-3.9"]
+
+unit_test-3.10:
+  <<: *test_config
+  variables:
+    PYTHON_VER: "3.10"
+  needs: ["coverage_unit_test","install-3.10"]
+
+unit_test-3.11:
+  <<: *test_config
+  variables:
+    PYTHON_VER: "3.11"
+  needs: ["coverage_unit_test","install-3.11"]
+
+unit_test-3.12:
+  <<: *test_config
+  variables:
+    PYTHON_VER: "3.12"
+  needs: ["coverage_unit_test","install-3.12"]
+
+doc_test:
+   stage: test
+   script:
+      - conda activate $CONDA_BASE_NAME-$PYTHON_VER
+      - export PATH="~/.local/bin/:/data/gitlab-runner/.conda/envs/$CONDA_BASE_NAME-$PYTHON_VER/bin:$PATH"
+      - echo "Executing Sphinx build to detect syntax errors"
+      - sphinx-build doc/source/ doc/build/ -W --keep-going -E
+      - sphinx-build -b html doc/source/ doc/build/html
+      - mv doc/build/html html
+   needs: ["install-3.8"]
+   artifacts:
+     expose_as: 'Updated Documentation'
+     paths: 
+       - html
+     expire_in: 1 day
+
+format_test:
+  stage: test
+  script: 
+    - conda activate $CONDA_BASE_NAME-$PYTHON_VER
+    - export PATH="~/.local/bin/:/data/gitlab-runner/.conda/envs/$CONDA_BASE_NAME-$PYTHON_VER/bin:$PATH"
+    - echo "Testing if anything is unformatted"
+    - echo "If error occurs changes were not formatted using black"
+    - black --check montepy/ tests/
+  needs: ["install-3.8"]
+
+
+
+pages:
+  stage: deploy
+  script:
+    - conda activate $CONDA_BASE_NAME-$PYTHON_VER
+    - export PATH="~/.local/bin/:/data/gitlab-runner/.conda/envs/$CONDA_BASE_NAME-$PYTHON_VER/bin:$PATH"
+    - echo "Building documentation with Sphinx."
+    - cd doc/
+    - make html
+    - cd ..
+    - mv doc/build/html public
+    - python -m build --sdist --wheel
+    - mv dist/ public/dist
+  artifacts:
+    paths:
+      - public
+  only:
+    - master
+    - main
+    - doc
+
+
+packaging:
+  stage: deploy
+  script:
+    - rm dist/*
+    - conda activate $CONDA_BASE_NAME-$PYTHON_VER
+    - export PATH="~/.local/bin/:/data/gitlab-runner/.conda/envs/$CONDA_BASE_NAME-$PYTHON_VER/bin:$PATH"
+    - pip install build twine
+    - python -m build --sdist --wheel
+    - TWINE_PASSWORD=${CI_JOB_TOKEN} TWINE_USERNAME=gitlab-ci-token python -m twine upload --repository-url ${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/pypi dist/*
+
+  only:
+    - master
+    - main

AUTHORS

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+Micah D. Gale <micah.gale@inl.gov>
+Travis J. Labossiere-Hickman <Travis.LabossiereHickman@inl.gov>
+Brenna A. Carbno <brenna.carbno@inl.gov>

README.md

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+# MontePy
+
+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).
+
+
+## User Documentation
+
+MontePy has a [sphinx website](https://experiment_analysis_all.pages.hpc.inl.gov/software/montepy/). 
+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.
+
+## Features
+
+* 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 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 
+
+
+Quick example for renumbering all of the cells in a problem:
+
+```python
+import montepy
+foo = montepy.read_input("foo.imcnp")
+i = 9500
+for cell in foo.cells:
+  cell.number = i
+  i = i + 5
+
+foo.write_to_file("foo_update.imcnp")
+
+```
+
+## Limitations
+
+Here a few of the known bugs and limitations:
+
+
+* Cannot handle vertical input mode.
+* Does not support tallies in an easy way.
+* Does not support source definition in an easy way.
+
+## Bugs, Requests and Development
+
+So MontePy doesn't do what you want? Right now development is done with a  Just-In-Time development approach, as in features are added JIT for a developer to use them on my current projects. 
+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).
+
+# Version Numbering Scheme
+
+* Software on `develop` and feature branches are subject to change without a version number increment. These version
+  may be suffixed as dev (e.g., `0.1.0.dev2`) and may change as features and bug fixes are implemented.
+
+* Versions are official if and only if they are:
+   1. on the branch `main`.
+   1. has a release git tag assigned
+   1. has distribution packages created and released
+   Official shall not change. New merges to main shall have a version number incremented.
+
+
+# Finally: make objects not regexs!