Simplify test input files using AMReX FILE directive

.clang-tidy

@@ -1,25 +1,25 @@
 ---
 Checks: 'bugprone-*,
          -bugprone-easily-swappable-parameters,
-         -bugprone-exception-escape,
          clang-diagnostic-*,
          clang-analyzer-*,
          corecppguidelines-*,
          modernize-*,
-         -modernize-avoid-c-arrays,
          -modernize-use-trailing-return-type,
-         -modernize-make-unique,
-         -modernize-use-nodiscard,
+         mpi-*,
+         performance-*,
+         -performance-inefficient-string-concatenation,
+         portability-*,
+         -portability-template-virtual-member-function,
          readability-*,
          -readability-magic-numbers,
-         -readability-identifier-naming,
          -readability-isolate-declaration,
-         -readability-avoid-const-params-in-decls,
          -readability-identifier-length,
-         -readability-function-cognitive-complexity'
+         -readability-function-cognitive-complexity,
+         -readability-avoid-nested-conditional-operator'
 WarningsAsErrors: ''
 HeaderFilterRegex: '.*'
-AnalyzeTemporaryDtors: false
+HeaderFileExtensions: ['', "H", 'h', 'hh', 'hpp', 'hxx']
 FormatStyle:     none
 User:            user
 CheckOptions:
@@ -59,12 +59,18 @@ CheckOptions:
     value:           llvm
   - key:             modernize-use-nullptr.NullMacros
     value:           'NULL'
-  - { key: readability-identifier-naming.NamespaceCase,       value: lower_case }
-  - { key: readability-identifier-naming.ClassCase,           value: CamelCase  }
-  - { key: readability-identifier-naming.PrivateMemberPrefix, value: m_         }
-  - { key: readability-identifier-naming.ProtectedMemberPrefix, value: m_         }
-  - { key: readability-identifier-naming.StructCase,          value: CamelCase  }
-  - { key: readability-identifier-naming.FunctionCase,        value: lower_case }
-  - { key: readability-identifier-naming.VariableCase,        value: lower_case }
-  - { key: readability-identifier-naming.GlobalConstantCase,  value: UPPER_CASE }
+  - { key: readability-identifier-naming.NamespaceCase, value: lower_case }
+  - { key: readability-identifier-naming.ClassCase, value: CamelCase }
+  - { key: readability-identifier-naming.PrivateMemberPrefix, value: m_ }
+  - { key: readability-identifier-naming.ProtectedMemberPrefix, value: m_ }
+  - { key: readability-identifier-naming.StructCase, value: CamelCase }
+  - { key: readability-identifier-naming.FunctionCase, value: lower_case }
+  - { key: readability-identifier-naming.VariableCase, value: lower_case }
+  - { key: readability-identifier-naming.GlobalConstantCase, value: UPPER_CASE }
+  - { key: readability-identifier-naming.ClassIgnoredRegexp, value: "incflo"}
+  - { key: readability-identifier-naming.FunctionIgnoredRegexp, value: "(CheckAndSetUpDryRun|Godunov_|setVal|ApplyPredictor|ApplyCorrector|ApplyPrescribeStep|ApplyProjection|UpdateGradP|ReadCheckpointFile|Factory|ReadParameters|InitialProjection|InitialIterations|PrintMax|CheckForNans|InitData|Evolve|buildInfoGet|FAST_|SetMultiBlockPointer).*"}
+  - { key: readability-identifier-naming.GlobalConstantIgnoredRegexp, value: "^.*"}
+  - { key: readability-identifier-naming.NamespaceIgnoredRegexp, value: "Hydro"}
+  - { key: readability-identifier-naming.StructIgnoredRegexp, value: "(SC_DX|OpFM).*"}
+  - { key: readability-identifier-naming.VariableIgnoredRegexp, value: "^.*"}
 ...

.codespell-ignore-words

@@ -7,4 +7,6 @@ vell
 nd
 fo
 ue
-structed
+structed
+acount
+abl

.codespellrc

@@ -1,3 +1,3 @@
 [codespell]
-skip = .git,*.ipynb,*.bib,*.ps,*.patch,spack-build-*,*/build,*/submods,plt*,chk*,__pycache__,.ccls,.ccls-cache,*.pdf,DU21_A17.txt,inspect_abl_io.html
+skip = .git,*.ipynb,*.bib,*.ps,*.patch,spack-build-*,*/build,*/submods,plt*,chk*,__pycache__,.ccls,.ccls-cache,*.pdf,DU21_A17.txt,inspect_abl_io.html,*.dat,*.yaml
 ignore-words = .codespell-ignore-words

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,75 @@
+---
+name: Bug report
+about: Report a bug to help us improve
+title: 'Bug report'
+labels: "bug:amr-wind"
+---
+
+## Bug description
+<!-- A clear and concise description of the bug. -->
+
+## Steps to reproduce
+<!-- Update the following list with your specific information. -->
+
+Steps to reproduce the behavior:
+1. Compiler used
+   - [ ] GCC
+   - [ ] LLVM
+   - [ ] oneapi (Intel)
+   - [ ] nvcc (NVIDIA)
+   - [ ] rocm (AMD)
+   - [ ] with MPI
+   - [ ] other:
+2. Operating system
+   - [ ] Linux
+   - [ ] OSX
+   - [ ] Windows
+   - [ ] other (do tell ;)):
+3. Hardware:
+   - [ ] CPU
+   - [ ] GPU
+4. Machine details ():
+```
+<!-- name, modules loaded, environment variables, etc -->
+```
+5. Input file attachments <!-- Please upload the input files in a zip or point to a public branch. -->
+6. Error (paste or attach):
+```
+<!-- error output -->
+```
+7. If this is a segfault, a stack trace from a debug build (paste or attach):
+```
+<!-- stack trace -->
+```
+
+## Expected behavior
+<!-- A clear and concise description of what is expected behavior. -->
+
+## AMR-Wind information
+<!-- Please provide as much detail as possible including git commit. The best information is a snapshot of the AMR-Wind header. -->
+
+```
+==============================================================================
+                AMR-Wind (https://github.com/exawind/amr-wind)
+
+  AMR-Wind version :: v1.4.0-17-g250778a3-DIRTY
+  AMR-Wind Git SHA :: 250778a3306e96b46afc117fc722491acaeb6176-DIRTY
+  AMReX version    :: 24.03-36-g748f8dfea597
+
+  Exec. time       :: Fri May 10 09:51:15 2024
+  Build time       :: May  8 2024 20:36:21
+  C++ compiler     :: Clang 17.0.6
+
+  MPI              :: OFF
+  GPU              :: OFF
+  OpenMP           :: OFF
+
+  No additional third-party libraries enabled
+
+           This software is released under the BSD 3-clause license.
+ See https://github.com/Exawind/amr-wind/blob/development/LICENSE for details.
+------------------------------------------------------------------------------
+```
+
+## Additional context
+<!-- Screenshots, related issues, etc -->

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,15 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: 'Feature request'
+labels: 'enhancement'
+---
+
+## Is this feature request related to a problem? Please describe.
+<!-- A clear and concise description of the problem. -->
+
+## Describe the preferred solution
+<!-- A clear and concise description of what you want to happen. -->
+
+## Additional context
+<!-- Add any other context or screenshots about the feature request here. -->

.github/dependabot.yml

@@ -3,7 +3,8 @@ version: 2
 updates:
   - package-ecosystem: gitsubmodule
     schedule:
-        interval: "weekly"
+        interval: "monthly"
+        day: "tuesday"
     directory: /
     allow:
       - dependency-name: "submods/amrex"

.github/pull_request_template.md

@@ -0,0 +1,40 @@
+## Summary
+
+<!--- Please provide a one sentence summary of your changes  -->
+
+## Pull request type
+
+<!-- Please try to limit your pull request to one type, submit multiple pull requests if needed. -->
+
+Please check the type of change introduced:
+
+- [ ] Bugfix
+- [ ] Feature
+- [ ] Code style update (formatting, renaming)
+- [ ] Refactoring (no functional changes, no api changes)
+- [ ] Build related changes
+- [ ] Documentation content changes
+- [ ] Other (please describe):
+
+## Checklist
+
+The following is included:
+
+- [ ] new unit-test(s)
+- [ ] new regression test(s)
+- [ ] documentation for new capability
+
+This PR was tested by running:
+
+- the unit tests
+  - [ ] on GPU <!-- note the OS and compiler -->
+  - [ ] on CPU <!-- note the OS and compiler -->
+- the regression tests
+  - [ ] on GPU <!-- note the OS and compiler -->
+  - [ ] on CPU <!-- note the OS and compiler -->
+
+## Additional background
+
+<!-- Any other information that is important to this PR such as screenshots of how the component looks before and after the change. -->
+
+Issue Number: <!-- Note related issues -->