add some test scripts from matHELICS

.github/workflows/ci.yml

@@ -0,0 +1,49 @@
+name: Test matHELICS
+
+on:
+  push:
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+  #schedule:
+  #  - cron: "35 10 * * 1,3,5 # running early in the morning (UTC)
+
+jobs:
+  ci-test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [windows-2019,macos-11,ubuntu-20.04]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+      - name: Install latest HELICS release
+        uses: gmlc-tdc/helics-action/install@main
+      - name: Set up MATLAB
+        uses: matlab-actions/[email protected]
+        with:
+          release: R2021a
+      - name: Set up MEX
+        uses: matlab-actions/run-command@v1
+        with:
+          command: mex -setup
+      - name: Build matHELICS
+        uses: matlab-actions/run-command@v1
+        with:
+          command: buildHelicsInterface('helics',true)
+      - name: store package
+        uses: actions/upload-artifact@v3
+        with:
+          name: ${{ matrix.os }}-matHELICS
+          path: matHELICS.*
+      - name: run startup
+        uses: matlab-actions/run-command@v1
+        with:
+          command: addpath('helics'), helicsStartup
+      - name: run tests
+        uses: matlab-actions/run-command@v1
+        with:
+          command: addpath('tests'),addpath('helics'),runAllTests
+

.github/workflows/update-helics.yml

@@ -0,0 +1,51 @@
+name: Update HELICS Version
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'HELICS version number'
+        required: true
+        type: string
+      dryrun:
+        description: 'Do a dry run of the update process, without making the commit'
+        required: false
+        type: boolean
+
+
+jobs:
+  update-helics-version:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set git config for commits
+      run: |
+        git config --global user.name "github-actions[bot]"
+        git config --global user.email "github-actions[bot]@users.noreply.github.com"
+
+    - name: Update HELICS version number
+      run: |
+        # Update lines in the package file
+        version_line="HelicsVersion='${{ inputs.version }}';"
+        echo "::group::buildHelicsInterface.m version line"
+        echo "$version_line"
+        echo "::endgroup::"
+        sed -i "/HelicsVersion=/c ${version_line}" buildHelicsInterface.m
+
+        git add buildHelicsInterface.m
+
+        echo "::group::git diff --staged"
+        git diff --staged
+        echo "::endgroup::"
+
+        git commit -m "Bump HELICS download version to ${{ inputs.version }}"
+
+        echo "::group::git show"
+        git show
+        echo "::endgroup::"
+
+        if [ "${{ inputs.dryrun }}" = "false" ]; then
+          echo "Pushing changes"
+          git push
+        fi

.gitignore

@@ -316,7 +316,8 @@ venv*
 .LSOverride
 
 # Icon must end with two \r
-Icon
+Icon
+
 
 # Thumbnails
 ._*

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 exclude: ^(ThirdParty/|test/files/|.github/workflows/|.github/actions/)
 repos:
   - repo: https://github.com/jumanjihouse/pre-commit-hooks
-    rev: 2.1.6
+    rev: 3.0.0
     hooks:
       - id: markdownlint
         args: [-s, ./config/.markdownlintrc]
@@ -11,20 +11,27 @@ repos:
     hooks:
       - id: cmake-format
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v2.6.1
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
   - repo: https://github.com/Lucas-C/pre-commit-hooks
-    rev: v1.1.13
+    rev: v1.5.5
     hooks:
       - id: remove-tabs
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.1.0
+    rev: v2.3.0
     hooks:
       - id: codespell
         exclude: ^(test/)
+        args:
+          [
+            "-w",
+            "--skip=*.csv",
+            "--ignore-words=./config/spelling_whitelist.txt",
+            "--exclude-file=./config/spelling_ignorelines.txt",
+          ]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v4.6.0
     hooks:
       - id: mixed-line-ending
       - id: trailing-whitespace
@@ -35,15 +42,8 @@ repos:
       - id: end-of-file-fixer
       - id: check-shebang-scripts-are-executable
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v13.0.1
+    rev: v19.1.0
     hooks:
       - id: clang-format
         types:
-          - c++
-  - repo: local
-    hooks:
-      - id: disallow-caps
-        name: Disallow improper capitalization
-        language: pygrep
-        entry: PyBind|Numpy|Cmake|CCache|PyTest|Github
-        exclude: .pre-commit-config.yaml
+          - c

README.md

@@ -7,9 +7,9 @@ For HELICS documentation see [HELICS.org](www.helics.org)
 
 For other platforms the installation is as simple as downloading this repository and inside matlab executing the `buildSimHELICS` Matlab script.
 
-This should download the required HELICS binary files and compile the platform specific mex file.  This does require a compiler be installed on the system and executing inside matlab
+This should download the required HELICS binary files and compile the platform specific mex file. This does require a compiler be installed on the system and executing inside matlab
 
-``` matlab
+```matlab
 >> mex -setup
 ```
 
@@ -20,21 +20,21 @@ This setup is only once on any given Matlab installation and does not need to be
 >> buildSimHELICS('../helics');
 ```
 
-this will generate the helics interface in a folder 1 level above the simHELICS directory.  If desired it can also be built in the simHELICS directory for example:
+this will generate the helics interface in a folder 1 level above the simHELICS directory. If desired it can also be built in the simHELICS directory for example:
 
 ```matlabs
 >> cd simHELICS
 >> buildSimHELICS();
 ```
 
-The `buildSimHELICS` function also has an option to generate the package file.  This can be used to generate a package that can be transfered to a similar system.
+The `buildSimHELICS` function also has an option to generate the package file. This can be used to generate a package that can be transferred to a similar system.
 
 This is a new process for building a simulink interface, it is tested but not extensively and not on a large variety of platforms if you run into issues please let us know.
 
 ### Requirements
 
 Matlab 2018a or greater.
-intalled compatible compiler to build the mex file
+installed compatible compiler to build the mex file
 
 ### building with custom HELICS version
 
@@ -53,40 +53,44 @@ These simulink blocks are in a simHELICS.slx library object and can be loaded or
 
 ### federate block
 
-The federate block takes 1 parameter which is the name of a config file.   This config file is typically json, but other formats including a direct string input is allowed.   This configuration json is the only means of configuring the federate in simulink.  All interfaces should be specified in this configuraiton file.
+The federate block takes 1 parameter which is the name of a config file. This config file is typically json, but other formats including a direct string input is allowed. This configuration json is the only means of configuring the federate in simulink. All interfaces should be specified in this configuration file.
 
 ### input block
 
-The input block is used to retreive data from HELICS.  It takes two parameters.  The first is an integer or string with the input index(zero based) or name resepectively, and some arguments as a string as the second argument.   Allowed arguments are 'output_size=X',  and 'output_type=XXXX'.  These define the size and type of the simulink output on the block.  Default for an empty string is 1, and double. 'double','int', 'bool', and 'complex' are supported along with 'vector' and 'complex_vector'.   The HELICS interface type is defined in the configuration.  This is defining the desired output type in simulink. 
+The input block is used to retrieve data from HELICS. It takes two parameters. The first is an integer or string with the input index(zero based) or name respectively, and some arguments as a string as the second argument. Allowed arguments are 'output_size=X', and 'output_type=XXXX'. These define the size and type of the simulink output on the block. Default for an empty string is 1, and double. 'double','int', 'bool', and 'complex' are supported along with 'vector' and 'complex_vector'. The HELICS interface type is defined in the configuration. This is defining the desired output type in simulink.
 
-The input_block is wired to the helics_federate block.  
+The input_block is wired to the helics_federate block.
 
 ### Publication block
 
-The publication block is used to send data via HELICS.  The first is an integer or string with the publication index(zero based) or name resepectively, and some arguments as a string as the second argument.   Allowed arguments are 'input_size=X',  and 'input_type=XXXX'.  These define the size and type of the second simulink input on the block.  Default for an empty string argument is 1, and double. 'double','int', 'bool', and 'complex' are supported along with 'vector' and 'complex_vector'.   The HELICS interface type is defined in the configuration.  This is defining the desired input type and size in simulink.
+The publication block is used to send data via HELICS. The first is an integer or string with the publication index(zero based) or name respectively, and some arguments as a string as the second argument. Allowed arguments are 'input_size=X', and 'input_type=XXXX'. These define the size and type of the second simulink input on the block. Default for an empty string argument is 1, and double. 'double','int', 'bool', and 'complex' are supported along with 'vector' and 'complex_vector'. The HELICS interface type is defined in the configuration. This is defining the desired input type and size in simulink.
 
 The publication is block is wired to the helics_federate block and the data wishing to be published.
 
 ### Example
 
-A trivial example federate (test_fed.slx) is located in the example folder, along with a simple config file.   This federate sends data to itself using a inproc federate and plots the result.
+A trivial example federate (test_fed.slx) is located in the example folder, along with a simple config file. This federate sends data to itself using a inproc federate and plots the result.
 
 ## Building with older versions of Matlab
 
 If it is necessary to run on an older version of Matlab prior to 2018a, some minor modifications to the helicsMex.cpp may be possible to allow things to work fine, please contact the developers for specific instructions.
 
-Versions prior to Matlab 2015 will require more extensive modifications.  And may be better served by using the Swig based matlab build from Helics version 3.2 which should be compatible with other HELICS versions in the 3.X series.
+Versions prior to Matlab 2015 will require more extensive modifications. And may be better served by using the Swig based matlab build from Helics version 3.2 which should be compatible with other HELICS versions in the 3.X series.
 
 ## Source Repo
 
-The simHelics source code is hosted on GitHub: [https://github.com/GMLC-TDC/simHelics](https://github.com/GMLC-TDC/simHELICS) \[This may not be accurate\]
+The simHELICS source code is hosted on GitHub: [https://github.com/GMLC-TDC/simHelics](https://github.com/GMLC-TDC/simHELICS)
 
 ## Citation
 
 General citation for HELICS:
-T. Hardy, B. Palmintier, P. Top, D. Krishnamurthy and J. Fuller, "HELICS: A Co-Simulation Framework for Scalable Multi-Domain Modeling and Analysis," in IEEE Access, doi: 10.1109/ACCESS.2024.3363615, available at [https://ieeexplore.ieee.org/document/10424422](https://ieeexplore.ieee.org/document/10424422/
+T. Hardy, B. Palmintier, P. Top, D. Krishnamurthy and J. Fuller, "HELICS: A Co-Simulation Framework for Scalable Multi-Domain Modeling and Analysis," in IEEE Access, doi: 10.1109/ACCESS.2024.3363615, available at [<https://ieeexplore.ieee.org/document/10424422>](https://ieeexplore.ieee.org/document/10424422/)
 
 ## Release
 
 HELICS, simHELICS and many associated repositories are distributed under the terms of the BSD-3 clause license. All new
-contributions must be made under this license. [LICENSE](LICENSE)
+contributions must be made under this license. [LICENSE](LICENSE)
+
+SPDC-License-Identifier: BSD-3-Clause
+
+Portions of the code written by LLNL with release number LLNL-CODE-866414

buildSimHELICS.m

@@ -59,7 +59,7 @@ function buildSimHELICS(targetPath,makePackage)
     end
     %actually build the mex file
     fprintf('building helics mex target\n');
-   
+
    mex('-lhelics','-R2018a',['-I',basePath,'/include/'],['-L',basePath,'/lib'],['LDFLAGS=$LDFLAGS -Wl,-rpath,$ORIGIN/lib,-rpath,',basePath,'/lib',',-rpath,',basePath,'/lib64'],fullfile(inputPath,'helics_federate.c'),'-outdir',targetPath);
    mex('-lhelics','-R2018a',['-I',basePath,'/include/'],['-L',basePath,'/lib'],['LDFLAGS=$LDFLAGS -Wl,-rpath,$ORIGIN/lib,-rpath,',basePath,'/lib',',-rpath,',basePath,'/lib64'],fullfile(inputPath,'helics_input.c'),'-outdir',targetPath);
       mex('-lhelics','-R2018a',['-I',basePath,'/include/'],['-L',basePath,'/lib'],['LDFLAGS=$LDFLAGS -Wl,-rpath,$ORIGIN/lib,-rpath,',basePath,'/lib',',-rpath,',basePath,'/lib64'],fullfile(inputPath,'helics_publication.c'),'-outdir',targetPath);
@@ -108,7 +108,7 @@ function buildSimHELICS(targetPath,makePackage)
     %copy the needed dll file if on windows
     if ispc
       if (~exist(fullfile(targetPath,targetFile),'file'))
-        
+
           copyfile(fullfile(basePath,'bin',targetFile),fullfile(targetPath,targetFile));
           copyfile(fullfile(basePath,'bin','*.dll'),targetPath);
       end
@@ -118,7 +118,7 @@ function buildSimHELICS(targetPath,makePackage)
   end
   %% now build the interface directory and copy files
   fprintf('copying required files\n');
-  
+
   % copy the include directory with the C headers
   if (~exist(fullfile(targetPath,'include'),'dir'))
     mkdir(fullfile(targetPath,'include'));
@@ -137,7 +137,7 @@ function buildSimHELICS(targetPath,makePackage)
   else
     copyfile(fullfile(basePath,'bin'),fullfile(targetPath,'bin'));
   end
-  
+
   if (makePackage)
     fprintf('generating helics simulink binary package file\n');
     rmdir(basePath,'s');
@@ -150,6 +150,3 @@ function buildSimHELICS(targetPath,makePackage)
       warning('unrecognized platform for making package');
     end
   end
-
-
-

config/.markdownlintrc

@@ -0,0 +1,27 @@
+rule "MD001" # header levels increment by 1
+rule "MD003", :style => :atx # header style - atx
+rule "MD004", :style => :dash # unordered list style - dash
+#rule "MD005" # don't allow inconsistent indentation for list items managed by prettier
+#rule "MD007", :indent => 2 # unordered list indentation should be 4 spaces managed by prettier
+rule "MD009" # trailing spaces not allowed
+rule "MD010" # hard tabs not allowed
+rule "MD011" # alert on reversed link syntax
+rule "MD012" # alert on multiple consecutive blank lines
+#rule "MD013" # line length should be no more than 80 characters
+#rule "MD014" # dollars signs not before commands w/o showing output
+rule "MD018" # must have space after header style
+rule "MD019" # no multiple spaces after header style
+rule "MD022" # headers should be surrounded by blank lines
+rule "MD023" # headers must start at the beginning of the line
+rule "MD024", :allow_different_nesting => true # no multiple same level headers with same content
+rule "MD025" # only 1 level 1 header
+rule "MD026", :punctuation => '.,;:' # no trailing punctuation in headers
+rule "MD027" # no multiple spaces after blockquote symbol
+rule "MD028" # no blank lines within blockquote
+#rule "MD029", :style => :ordered # ordered list item prefix, shoulded be ordered
+#rule "MD030", :ul_single => 1, :ol_single => 1, :ul_multi => 1, :ol_multi => 3 # spaces after list markers, controlled by prettier
+rule "MD031" # fenced code blocks need line surrounding
+#rule "MD032" # lists should be surrounded by line # handled by prettier markdown formatting
+rule "MD034" # no raw url
+rule "MD040" # Fenced code blocks should have a language specified
+rule "MD046", :style => :fenced # code block style - fenced

config/spelling_ignorelines.txt

@@ -0,0 +1 @@
+- [Parth Bansal](https://github.com/parthb83)

config/spelling_whitelist.txt

@@ -0,0 +1,9 @@
+ans
+te
+stoll
+endwhile
+fo
+emiss
+ist
+copyable
+dur