Merge branch 'openmc-dev:develop' into develop

.clang-format

@@ -84,6 +84,7 @@ PenaltyBreakTemplateDeclaration: 10
 PenaltyExcessCharacter: 1000000
 PenaltyReturnTypeOnItsOwnLine: 200
 PointerAlignment: Left
+QualifierAlignment: Left
 ReflowComments:  true
 SortIncludes:    true
 SortUsingDeclarations: true

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,29 @@
+---
+name: Bug report
+about: Report a bug that is preventing proper operation
+title: ''
+labels: Bugs
+assignees: ''
+
+---
+
+<!--
+If you are a user of OpenMC and are running into trouble with the code or are
+seeking general user support, we highly recommend posting on the OpenMC
+discourse forum first. GitHub issues should be used specifically for bug reports
+and feature requests.
+
+https://openmc.discourse.group/
+
+-->
+
+## Bug Description
+<!--A clear and concise description of the problem (Note: A missing feature is not a bug).-->
+
+
+## Steps to Reproduce
+<!--Steps to reproduce the behavior (input file, or modifications to an existing input file, etc.)-->
+
+
+## Environment
+<!--Operating system, OpenMC version, how OpenMC was installed, nuclear data being used, etc.-->

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Troubleshooting and User Support
+    url: https://openmc.discourse.group/
+    about: For user support and troubleshooting, please use our Discourse forum

.github/ISSUE_TEMPLATE/documentation.md

@@ -0,0 +1,10 @@
+---
+name: Documentation improvement
+about: Found something incomplete or incorrect in our documentation?
+title: ''
+labels: Documentation
+assignees: ''
+
+---
+
+<!--Describe the issue with the documentation and include a URL to the corresponding page-->

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,19 @@
+---
+name: Feature request
+about: Suggest a new feature or enhancement to existing capabilities
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+## Description
+<!--What is the feature or enhancement?-->
+
+
+## Alternatives
+<!--If alternative solutions have been considered, describe them here and the reasoning for the chosen solution --->
+
+
+## Compatibility
+<!--Will the enhancement change existing APIs or add something new?-->

.github/pull_request_template.md

@@ -0,0 +1,24 @@
+<!--
+If you are a first-time contributor to OpenMC, please have a look at our
+contributing guidelines:
+https://github.com/openmc-dev/openmc/blob/develop/CONTRIBUTING.md
+-->
+
+# 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 run [clang-format](https://docs.openmc.org/en/latest/devguide/styleguide.html#automatic-formatting) on any C++ source files (if applicable)
+- [ ] I have followed the [style guidelines](https://docs.openmc.org/en/latest/devguide/styleguide.html#python) for Python source files (if applicable)
+- [ ] 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. See instructions here:
+https://docs.openmc.org/en/latest/devguide/tests.html
+-->

.github/workflows/format-check.yml

@@ -0,0 +1,25 @@
+name: C++ Format Check
+
+on: pull_request
+
+jobs:
+  cpp-linter:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: cpp-linter/cpp-linter-action@v2
+        id: linter
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          style: file
+          files-changed-only: true
+          tidy-checks: '-*'
+          version: '15' # clang-format version
+          file-annotations: true
+          step-summary: true
+          extensions: 'cpp,h'
+
+      - name: Failure Check
+        if: steps.linter.outputs.checks-failed > 0
+        run: echo "Some files failed the formatting check! See job summary and file annotations for more info" && exit 1

CMakeLists.txt

@@ -292,7 +292,7 @@ endif()
 
 if(OPENMC_BUILD_TESTS)
   find_package_write_status(Catch2)
-  if (NOT Catch2)
+  if (NOT Catch2_FOUND)
     add_subdirectory(vendor/Catch2)
   endif()
 endif()
@@ -334,10 +334,10 @@ list(APPEND libopenmc_SOURCES
   src/bank.cpp
   src/boundary_condition.cpp
   src/bremsstrahlung.cpp
-  src/dagmc.cpp
   src/cell.cpp
   src/cmfd_solver.cpp
   src/cross_sections.cpp
+  src/dagmc.cpp
   src/distribution.cpp
   src/distribution_angle.cpp
   src/distribution_energy.cpp
@@ -347,11 +347,12 @@ list(APPEND libopenmc_SOURCES
   src/endf.cpp
   src/error.cpp
   src/event.cpp
-  src/initialize.cpp
+  src/file_utils.cpp
   src/finalize.cpp
   src/geometry.cpp
   src/geometry_aux.cpp
   src/hdf5_interface.cpp
+  src/initialize.cpp
   src/lattice.cpp
   src/material.cpp
   src/math_functions.cpp
@@ -393,15 +394,15 @@ list(APPEND libopenmc_SOURCES
   src/tallies/derivative.cpp
   src/tallies/filter.cpp
   src/tallies/filter_azimuthal.cpp
-  src/tallies/filter_cellborn.cpp
-  src/tallies/filter_cellfrom.cpp
   src/tallies/filter_cell.cpp
   src/tallies/filter_cell_instance.cpp
+  src/tallies/filter_cellborn.cpp
+  src/tallies/filter_cellfrom.cpp
+  src/tallies/filter_collision.cpp
   src/tallies/filter_delayedgroup.cpp
   src/tallies/filter_distribcell.cpp
-  src/tallies/filter_energyfunc.cpp
   src/tallies/filter_energy.cpp
-  src/tallies/filter_collision.cpp
+  src/tallies/filter_energyfunc.cpp
   src/tallies/filter_legendre.cpp
   src/tallies/filter_material.cpp
   src/tallies/filter_mesh.cpp
@@ -418,8 +419,8 @@ list(APPEND libopenmc_SOURCES
   src/tallies/tally.cpp
   src/tallies/tally_scoring.cpp
   src/tallies/trigger.cpp
-  src/timer.cpp
   src/thermal.cpp
+  src/timer.cpp
   src/track_output.cpp
   src/universe.cpp
   src/urr.cpp

README.md

@@ -15,7 +15,8 @@ project started under the Computational Reactor Physics Group at MIT.
 Complete documentation on the usage of OpenMC is hosted on Read the Docs (both
 for the [latest release](https://docs.openmc.org/en/stable/) and
 [developmental](https://docs.openmc.org/en/latest/) version). If you are
-interested in the project, or would like to help and contribute, please get in touch on the OpenMC [discussion forum](https://openmc.discourse.group/).
+interested in the project, or would like to help and contribute, please get in
+touch on the OpenMC [discussion forum](https://openmc.discourse.group/).
 
 ## Installation
 
@@ -36,20 +37,21 @@ citing the following publication:
 ## Troubleshooting
 
 If you run into problems compiling, installing, or running OpenMC, first check
-the [Troubleshooting section](https://docs.openmc.org/en/stable/usersguide/troubleshoot.html) in
-the User's Guide. If you are not able to find a solution to your problem there,
+the [Troubleshooting
+section](https://docs.openmc.org/en/stable/usersguide/troubleshoot.html) in the
+User's Guide. If you are not able to find a solution to your problem there,
 please post to the [discussion forum](https://openmc.discourse.group/).
 
 ## Reporting Bugs
 
 OpenMC is hosted on GitHub and all bugs are reported and tracked through the
-[Issues](https://github.com/openmc-dev/openmc/issues) feature on GitHub. However,
-GitHub Issues should not be used for common troubleshooting purposes. If you are
-having trouble installing the code or getting your model to run properly, you
-should first send a message to the User's Group mailing list. If it turns out
-your issue really is a bug in the code, an issue will then be created on
-GitHub. If you want to request that a feature be added to the code, you may
-create an Issue on github.
+[Issues](https://github.com/openmc-dev/openmc/issues) feature on GitHub.
+However, GitHub Issues should not be used for common troubleshooting purposes.
+If you are having trouble installing the code or getting your model to run
+properly, you should first send a message to the [discussion
+forum](https://openmc.discourse.group/). If it turns out your issue really is a
+bug in the code, an issue will then be created on GitHub. If you want to request
+that a feature be added to the code, you may create an Issue on github.
 
 ## License
 

docs/requirements-rtd.txt

@@ -10,3 +10,4 @@ h5py
 pandas
 uncertainties
 matplotlib
+lxml

docs/source/devguide/docbuild.rst

@@ -5,21 +5,14 @@ Building Sphinx Documentation
 =============================
 
 In order to build the documentation in the ``docs`` directory, you will need to
-have the `Sphinx <https://www.sphinx-doc.org/en/master/>`_ third-party Python
-package. The easiest way to install Sphinx is via pip:
+have the several third-party Python packages installed, including `Sphinx
+<https://www.sphinx-doc.org/en/master/>`_. To install the necessary
+prerequisites, provide the optional "docs" dependencies when installing OpenMC's
+Python API. That is, from the root directory of the OpenMC repository:
 
 .. code-block:: sh
 
-    pip install sphinx
-
-Additionally, you will need several Sphinx extensions that can be installed
-directly with pip:
-
-.. code-block:: sh
-
-    pip install sphinx-numfig
-    pip install sphinxcontrib-katex
-    pip install sphinxcontrib-svg2pdfconverter
+    python -m pip install .[docs]
 
 -----------------------------------
 Building Documentation as a Webpage

docs/source/devguide/tests.rst

@@ -23,11 +23,7 @@ Prerequisites
   OpenMC in development/editable mode. With setuptools, this is accomplished by
   running::
 
-      python setup.py develop
-
-  or using pip (recommended)::
-
-      pip install -e .[test]
+      python -m pip install -e .[test]
 
 - The test suite requires a specific set of cross section data in order for
   tests to pass. A download URL for the data that OpenMC expects can be found
@@ -83,13 +79,13 @@ does not exist run::
 
     touch test_<name-of-header-file>.cpp
 
-The file must be added to the CMake build system in 
-``tests/cpp_unit_tests/CMakeLists.txt``. ``test_<name-of-header-file>`` should 
-be added to ``TEST_NAMES``. 
+The file must be added to the CMake build system in
+``tests/cpp_unit_tests/CMakeLists.txt``. ``test_<name-of-header-file>`` should
+be added to ``TEST_NAMES``.
 
-To add a test case to ``test_<name-of-header-file>.cpp`` ensure 
-``catch2/catch_test_macros.hpp`` is included. A unit test can then be added 
-using the ``TEST_CASE`` macro and the ``REQUIRE`` assertion from Catch2. 
+To add a test case to ``test_<name-of-header-file>.cpp`` ensure
+``catch2/catch_test_macros.hpp`` is included. A unit test can then be added
+using the ``TEST_CASE`` macro and the ``REQUIRE`` assertion from Catch2.
 
 Adding Tests to the Regression Suite
 ------------------------------------

docs/source/devguide/workflow.rst

@@ -116,7 +116,7 @@ pip_. From the root directory of the OpenMC repository, run:
 
 .. code-block:: sh
 
-    pip install -e .[test]
+    python -m pip install -e .[test]
 
 This installs the OpenMC Python package in `"editable" mode
 <https://pip.pypa.io/en/stable/cli/pip_install/#editable-installs>`_ so that 1)

docs/source/io_formats/depletion_results.rst

@@ -47,10 +47,3 @@ The current version of the depletion results file format is 1.1.
 **/reactions/<name>/**
 
 :Attributes: - **index** (*int*) -- Index user in results for this reaction
-
-.. note::
-
-    The reaction rates for some isotopes not originally present may
-    be non-zero, but should be negligible compared to other atoms.
-    This can be controlled by changing the
-    :class:`openmc.deplete.Operator` ``dilute_initial`` attribute.

docs/source/io_formats/index.rst

@@ -51,3 +51,4 @@ Output Files
    track
    voxel
    volume
+   weight_windows

docs/source/io_formats/particle_restart.rst

@@ -26,6 +26,8 @@ The current version of the particle restart file format is 2.0.
            - **run_mode** (*char[]*) -- Run mode used, either 'fixed source',
              'eigenvalue', or 'particle restart'.
            - **id** (*int8_t*) -- Unique identifier of the particle.
+           - **type** (*int*) -- Particle type (0=neutron, 1=photon, 2=electron,
+             3=positron)
            - **weight** (*double*) -- Weight of the particle.
            - **energy** (*double*) -- Energy of the particle in eV for
              continuous-energy mode, or the energy group of the particle for