Merge branch 'develop' into pickle_tallies

.github/workflows/main.yml

@@ -129,8 +129,38 @@ jobs:
           python-version: 3.12
       - run: pip install . montepy[format]
       - run: black --check montepy/ tests/
-
+
+  profile:
+    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[test]
+      - run: pytest --profile
+        name: Profile test suite
+      - run: python prof/dump_results.py
+        name: Display pytest profiling data
+      - run: python prof/profile_big_model.py
+        name: Profile against big model
+
+  benchmark:
+    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[test]
+      - run: python benchmark/benchmark_big_model.py  
+        name: Benchmark against big model
 
+
   changelog-test:
     runs-on: ubuntu-latest
     if: github.ref != 'refs/heads/main'

.gitignore

@@ -7,6 +7,7 @@ dist/*
 .coverage
 .idea/*
 *.*.sw*
+*.prof
 doc/build/*
 .coverage
 .idea/

README.md

@@ -8,7 +8,7 @@
 [![PyPI version](https://badge.fury.io/py/montepy.svg)](https://badge.fury.io/py/montepy)
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 
-MontePy is a python library to read, edit, and write MCNP input files. 
+MontePy is the most user friendly Python library for reading, editing, and writing MCNP input files. 
 
 ## Installing
 
@@ -24,35 +24,56 @@ see the [Installing section in the user guide](https://www.montepy.org/starting.
 
 ## User Documentation
 
-MontePy has a [sphinx website](https://www.montepy.org/). 
-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.
+MontePy has a website [documenting how to work with MCNP in python with MontePy](https://www.montepy.org/). 
+The website contains a user's guide for getting started, 
+a developer's guide covering the design and approach of MontePy,
+instructions for contributing, 
+and the Python API documentation.
 
 ## 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 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 the original user formatting. 
-* 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 
+* Handles almost all MCNP input syntax.
+* Parses Cells, Surfaces, Materials, and Transforms very well.	
+* Can parse all surface types except macrobody facets ([Issue #354](https://github.com/idaholab/MontePy/issues/354)).
+* Can read and write out all other MCNP inputs, even if it doesn't not understand them	
+* Attempts to write out the MCNP problem verbatim, even matching the original user formatting. (See some of the [open issues](https://github.com/idaholab/MontePy/issues).)
+* Can quickly [access cells, surfaces, and materials by their numbers](https://www.montepy.org/starting.html#collections-are-accessible-by-number). For example: `cell = problem.cells[105]`.
+* Can quickly update cell parameters, [such as importances](https://www.montepy.org/starting.html#setting-cell-importances). For example `cell.importance.neutron = 2.0`.
+* Can easily [create universes, and fill other cells with universes](https://www.montepy.org/starting.html#universes).
+* Currently has over 430 test cases.
 
 
-Quick example for renumbering all of the cells in a problem:
+Here is a quick example showing multiple tasks in MontePy:
 
 ```python
 import montepy
-foo = montepy.read_input("foo.imcnp")
-i = 9500
-for cell in foo.cells:
-  cell.number = i
-  i = i + 5
+# read in file
+problem = montepy.read_input("foo.imcnp")
 
-foo.write_to_file("foo_update.imcnp")
+# set photon importance for multiple cells
+importances = {1: 0.005,
+    2: 0.1,
+    3: 1.0,
+    99: 1.235
+}
+for cell_num, importance in importances.items():
+    problem.cells[cell_num].importance.photon = importance
+
+#create a universe and fill another cell with it
+universe = montepy.Universe(123)
+problem.univeres.append(universe)
+# add all cells with numbers between 1 and 4
+universe.claim(problem.cells[1:5])
+# fill cell 99 with universe 123
+problem.cells[99].fill.universe = universe
+
+# update all surfaces numbers by adding 1000 to them
+for surface in problem.surfaces:
+    surface.number += 1000
+# all cells using these surfaces will be automatically updated as well
+
+#write out an updated file
+problem.write_problem("foo_update.imcnp")
 
 ```
 
@@ -62,16 +83,16 @@ 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.
+* Does not support editing tallies in a user-friendly way.
+* Does not support editing source definition in a user-friendly 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). 
+So MontePy doesn't do what you want? 
+Add an issue here with the "feature request" tag. 
 The system is very modular and you should be able to develop it pretty quickly.
-Also read the [developer's guide](https://www.montepy.org/developing.html).
+Read the [developer's guide](https://www.montepy.org/developing.html) for more details.
+If you have any questions feel free to ask [@micahgale](mailto:mgale@montepy.org).
 
 
-# Finally: make objects not regexes!
+# Finally: make objects, not regexes!

benchmark/benchmark_big_model.py

@@ -0,0 +1,21 @@
+import montepy
+
+import time
+import tracemalloc
+
+FAIL_THRESHOLD = 30
+
+tracemalloc.start()
+start = time.time()
+
+problem = montepy.read_input("benchmark/big_model.imcnp")
+
+stop = time.time()
+
+print(f"Took {stop - start} seconds")
+print(f"Memory usage report: {tracemalloc.get_traced_memory()}")
+
+if (stop - start) > FAIL_THRESHOLD:
+    raise RuntimeError(
+        f"Benchmark took too long to complete. It must be faster than: {FAIL_THRESHOLD} s."
+    )