Merge branch 'develop' into 351-lack-of-data-enforcement-in-syntax-no…

…de-is-showing-up-again

.github/ISSUE_TEMPLATE/bug_report.md

@@ -2,36 +2,78 @@
 name: Bug report
 about: Create a report to help us improve
 title: ''
-labels: bug
+labels: bugs
 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. 
+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.
+A short code snippet of what you have ran. Please change or remove any specific values or anything that can't be public. For example:
+
+``` python
+problem = montepy.read_input("foo.imcnp")
+```
+
+**Error Message (if any)**
+
+If an error message was printed please include the entire stacktrace. If it includes any specific values please change or remove them. For example:
+
+``` python
+In [6]: problem.cells.append(copy.deepcopy(cell))
+---------------------------------------------------------------------------
+NumberConflictError                       Traceback (most recent call last)
+Cell In[6], line 1
+----> 1 problem.cells.append(copy.deepcopy(cell))
+
+File ~/dev/montepy/montepy/numbered_object_collection.py:202, in NumberedObjectCollection.append(self, obj)
+    200     raise TypeError(f"object being appended must be of type: {self._obj_class}")
+    201 if obj.number in self.numbers:
+--> 202     raise NumberConflictError(
+    203         (
+    204             "There was a numbering conflict when attempting to add "
+    205             f"{obj} to {type(self)}. Conflict was with {self[obj.number]}"
+    206         )
+    207     )
+    208 else:
+    209     self.__num_cache[obj.number] = obj
 
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
+NumberConflictError: There was a numbering conflict when attempting to add CELL: 3, mat: 3, DENS: 1.0 g/cm3 to <class 'montepy.cells.Cells'>. Conflict was with CELL: 3, mat: 3, DENS: 1.0 g/cm3
+```
+
+**MCNP input file snippet**
+
+If applicable, please include a small section of the input file you were working on. If it includes any specific values please change or remove them. For example:
+
+```
+1 1 20
+         -1000  $ dollar comment
+        imp:n,p=1 U=350 trcl=5
+
+C surfaces
+1000 SO 1
+
+C data
+C materials
+C UO2 5 atpt enriched
+m1        92235.80c           5 &
+92238.80c          95
+```
+
+**Version**
 
-**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/pull_request_template.md

@@ -0,0 +1,21 @@
+<!--
+If you are a first-time contributor to MontePy,
+refer the developing guidelines at:
+https://idaholab.github.io/MontePy/developing.html
+-->
+
+# Description
+
+Please include a summary of the change and which issue is fixed if applicable. Please also include relevant motivation and context.
+
+Fixes # (issue)
+
+# Checklist
+
+- [ ] I have performed a self-review of my own code
+- [ ] I have made corresponding changes to the documentation (if applicable)
+- [ ] I have added tests that prove my fix is effective or that my feature works (if applicable)
+<!--
+While tests will automatically be checked by CI, it is good practice to
+ensure that they pass locally first. 
+-->

.github/workflows/deploy.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches: [main]
 
+
 jobs:
   last-minute-test:
     runs-on: ubuntu-latest    
@@ -13,13 +14,12 @@ jobs:
         uses: actions/setup-python@v4
         with: 
           python-version: 3.8
-      - run: pip install --user -r requirements/dev.txt
+      - run: pip install . montepy[develop]
       - run: python -m pytest
 
   build-pages:
     environment:
       name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
     runs-on: ubuntu-latest
     steps:
       - name: Configure git
@@ -30,13 +30,67 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: 3.8
-      - run: pip install --user montepy[doc]
+      - 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/
+
+  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  3.8
+        uses: actions/setup-python@v4
+        with: 
+          python-version: 3.8
+      - run: pip install . montepy[build]
+      - name: GitHub Actions Create Tag
+        id: tag_version
+        uses: mathieudutour/[email protected]
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+       # ensure tags are up to date
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          fetch-tags: true
+      - run: python -m build .
+      - name: Sign the dists with Sigstore
+        uses: sigstore/[email protected]
+        with:
+          inputs: >-
+            ./dist/*.tar.gz
+            ./dist/*.whl
+      - name: Create a GitHub release
+        uses: ncipollo/release-action@v1
+        with:
+          tag: ${{ steps.tag_version.outputs.new_tag }}
+          name: Release ${{ steps.tag_version.outputs.new_tag }}
+          body: ${{ steps.tag_version.outputs.changelog }}
+          draft: true
+      - run: >-
+          gh release upload
+          '${{ steps.tag_version.outputs.new_tag }}' dist/**
+          --repo '${{ github.repository }}'
+      - uses: actions/upload-artifact@v4
+        with: 
+           name: build
+           path: |
+               dist/*.tar.gz 
+               dist/*.whl
 
   deploy-pages:
     permissions:
@@ -65,18 +119,16 @@ jobs:
     environment:
       name: test-pypi
       url: https://test.pypi.org/p/montepy  # Replace <package-name> with your PyPI project name
-    needs: [deploy-pages]
+    needs: [deploy-pages, build-packages]
     permissions:
       contents: read
       id-token: write
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/download-artifact@v4
         with:
-          python-version: 3.8
-      - run: python -m pip install build
-      - run: python -m build --sdist --wheel
+          name: build
+          path: dist/
       - name: Publish distribution 📦 to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
@@ -86,20 +138,19 @@ jobs:
     environment:
       name: pypi
       url: https://pypi.org/p/montepy  # Replace <package-name> with your PyPI project name
-    needs: [deploy-pages, deploy-test-pypi]
+    needs: [deploy-pages, deploy-test-pypi, build-packages]
     permissions:
       contents: read
       id-token: write
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/download-artifact@v4
         with:
-          python-version: 3.8
-      - run: python -m pip install build
-      - run: python -m build --sdist --wheel
+          name: build
+          path: dist/
       - name: Publish distribution 📦 to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
 
+
 
 

.github/workflows/main.yml

@@ -1,6 +1,9 @@
-name: Test package
+name: CI testing
 
-on: [push]
+on: 
+  pull_request:
+  push: 
+     branches: [develop, main, alpha-test]
 
 jobs:
   build:
@@ -16,7 +19,7 @@ jobs:
         with: 
           python-version: ${{ matrix.python-version }}
       - run: pip install --upgrade pip build
-      - run: pip install -r requirements/common.txt
+      - run: pip install build
       - run: python -m build --sdist --wheel
       - run: pip install .
       - run: pip uninstall -y montepy
@@ -25,8 +28,11 @@ jobs:
       - run: change_to_ascii -h
       - 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 install --user . montepy[test]
+      - run: pip install --user . montepy[doc]
+      - run: pip install --user . montepy[format]
+      - run: pip install --user . montepy[build]
+      - run: pip install --user . montepy[develop]
       - run: pip freeze
       - name: Upload build artifacts
         uses: actions/upload-artifact@v3
@@ -36,6 +42,7 @@ jobs:
 
   test:
     runs-on: ubuntu-latest
+    permissions: write-all
     strategy:
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
@@ -46,20 +53,35 @@ jobs:
         uses: actions/setup-python@v4
         with: 
           python-version: ${{ matrix.python-version }}
-      - run: pip install --user -r requirements/dev.txt
+      - run: pip install --user . montepy[test]
       - run: coverage run -m pytest --junitxml=test_report.xml
       - run: coverage report
       - run: coverage xml
       - name: Upload test report
-        uses: actions/upload-artifact@v3
+        if: ${{ matrix.python-version == '3.9' }}
+        uses: actions/upload-artifact@v4
         with:
           name: test
           path: test_report.xml
       - name: Upload coverage report
-        uses: actions/upload-artifact@v3
+        if: ${{ matrix.python-version == '3.9' }}
+        uses: actions/upload-artifact@v4
         with:
           name: coverage
           path: coverage.xml
+      - name: Test Reporter
+        if: ${{ matrix.python-version == '3.9' }}
+        uses: dorny/[email protected]
+        with:
+          name: CI-test-report
+          path: test_report.xml
+          reporter: java-junit
+      - name: Coveralls GitHub Action
+        if: ${{ matrix.python-version == '3.9' }}
+        uses: coverallsapp/[email protected]
+        with:
+          file: coverage.xml
+
 
   doc-test:
     runs-on: ubuntu-latest
@@ -70,13 +92,17 @@ jobs:
         uses: actions/setup-python@v4
         with: 
           python-version: 3.8
-      - run: pip install montepy[doc]
+      - 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
+      - name: Test for missing API documentation  
+        run: | 
+             cd doc/source
+             python _test_for_missing_docs.py  
 
   format-test:
     runs-on: ubuntu-latest
@@ -87,7 +113,7 @@ jobs:
         uses: actions/setup-python@v4
         with: 
           python-version: 3.8
-      - run: pip install --user -r requirements/dev.txt
+      - run: pip install . montepy[format]
       - run: black --check montepy/ tests/
 
 

.gitignore

@@ -10,3 +10,4 @@ doc/build/*
 .coverage
 .idea/
 .ipynb_checkpoints/
+montepy/_version.py