initial commit

.github/pages.yml

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+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# Sample workflow for building and deploying a Jekyll site to GitHub Pages
+name: Deploy Jekyll site to Pages
+
+on:
+  push:
+    branches: ["main"]
+    paths: ["./*"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: .
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '3.3' # Not needed with a .ruby-version file
+          bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+          cache-version: 0 # Increment this number if you need to re-download cached gems
+          working-directory: '${{ github.workspace }}'
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v5
+      - name: Build with Jekyll
+        # Outputs to the './_site' directory by default
+        run: bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
+        env:
+          JEKYLL_ENV: production
+      - name: Upload artifact
+        # Automatically uploads an artifact from the './_site' directory by default
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: "./_site/"
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

Gemfile

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+source 'https://rubygems.org'
+
+gem "jekyll", "~> 4.3.3" # installed by `gem jekyll`
+# gem "webrick"        # required when using Ruby >= 3 and Jekyll <= 4.2.2
+
+gem "just-the-docs", "0.10.0" # pinned to the current release
+# gem "just-the-docs"        # always download the latest release

Gemfile.lock

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+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
+    bigdecimal (3.1.8)
+    colorator (1.1.0)
+    concurrent-ruby (1.3.4)
+    em-websocket (0.5.3)
+      eventmachine (>= 0.12.9)
+      http_parser.rb (~> 0)
+    eventmachine (1.2.7)
+    ffi (1.17.0-arm64-darwin)
+    ffi (1.17.0-x86_64-linux-gnu)
+    forwardable-extended (2.6.0)
+    google-protobuf (4.28.0-arm64-darwin)
+      bigdecimal
+      rake (>= 13)
+    google-protobuf (4.28.0-x86_64-linux)
+      bigdecimal
+      rake (>= 13)
+    http_parser.rb (0.8.0)
+    i18n (1.14.5)
+      concurrent-ruby (~> 1.0)
+    jekyll (4.3.3)
+      addressable (~> 2.4)
+      colorator (~> 1.0)
+      em-websocket (~> 0.5)
+      i18n (~> 1.0)
+      jekyll-sass-converter (>= 2.0, < 4.0)
+      jekyll-watch (~> 2.0)
+      kramdown (~> 2.3, >= 2.3.1)
+      kramdown-parser-gfm (~> 1.0)
+      liquid (~> 4.0)
+      mercenary (>= 0.3.6, < 0.5)
+      pathutil (~> 0.9)
+      rouge (>= 3.0, < 5.0)
+      safe_yaml (~> 1.0)
+      terminal-table (>= 1.8, < 4.0)
+      webrick (~> 1.7)
+    jekyll-include-cache (0.2.1)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-sass-converter (3.0.0)
+      sass-embedded (~> 1.54)
+    jekyll-seo-tag (2.8.0)
+      jekyll (>= 3.8, < 5.0)
+    jekyll-watch (2.2.1)
+      listen (~> 3.0)
+    just-the-docs (0.10.0)
+      jekyll (>= 3.8.5)
+      jekyll-include-cache
+      jekyll-seo-tag (>= 2.0)
+      rake (>= 12.3.1)
+    kramdown (2.4.0)
+      rexml
+    kramdown-parser-gfm (1.1.0)
+      kramdown (~> 2.0)
+    liquid (4.0.4)
+    listen (3.9.0)
+      rb-fsevent (~> 0.10, >= 0.10.3)
+      rb-inotify (~> 0.9, >= 0.9.10)
+    mercenary (0.4.0)
+    pathutil (0.16.2)
+      forwardable-extended (~> 2.6)
+    public_suffix (6.0.1)
+    rake (13.2.1)
+    rb-fsevent (0.11.2)
+    rb-inotify (0.11.1)
+      ffi (~> 1.0)
+    rexml (3.3.7)
+    rouge (4.3.0)
+    safe_yaml (1.0.5)
+    sass-embedded (1.78.0-arm64-darwin)
+      google-protobuf (~> 4.27)
+    sass-embedded (1.78.0-x86_64-linux-gnu)
+      google-protobuf (~> 4.27)
+    terminal-table (3.0.2)
+      unicode-display_width (>= 1.1.1, < 3)
+    unicode-display_width (2.5.0)
+    webrick (1.8.1)
+
+PLATFORMS
+  arm64-darwin
+  x86_64-linux-gnu
+
+DEPENDENCIES
+  jekyll (~> 4.3.3)
+  just-the-docs (= 0.10.0)
+
+BUNDLED WITH
+   2.5.9

LICENSE

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+The text and multimedia in this repository retains the top-level Myna license, which
+can be found below and at https://github.com/ORNL-MDF/Myna/blob/main/LICENSE.md.
+
+This documentation is built on the Just The Docs template found
+at https://github.com/just-the-docs/just-the-docs-template/, which is licensed under the
+MIT License reproduced at the bottom of this license file.
+
+----------------------------------------------------------------------------------------
+BSD 3-Clause License
+
+Copyright (c) 2024, Oak Ridge National Laboratory
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software without
+   specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
+EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
+SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
+OF SUCH DAMAGE.
+
+----------------------------------------------------------------------------------------
+
+MIT License
+
+Copyright (c) 2022 just-the-docs
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

_config.yml

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+# General site settings
+title: Myna
+description: Documentation for Myna
+repository: ORNL-MDF/myna.github.io
+
+# Theme settings
+permalink: /:title
+theme: just-the-docs
+compress_html:
+  blanklines: true
+color_scheme: ornl_green
+
+# Navigation bar
+nav_enabled: true
+nav_external_links:
+  - title: Myna on GitHub
+    url: "https://github.com/ORNL-MDF/Myna"
+
+# Upper-right link bar
+aux_links:
+  Myna on GitHub:
+    - "https://github.com/ORNL-MDF/Myna"
+
+# Link settings
+aux_links_new_tab: false
+
+# Enable callouts in markdown, for example "{: .warning }"
+callouts:
+  highlight:
+    color: yellow
+  important:
+    title: Important
+    color: blue
+  new:
+    title: New
+    color: green
+  note:
+    title: Note
+    color: ornl_green
+  warning:
+    title: Warning
+    color: red
+
+# Update custom style assets
+assets:
+  stylesheets:
+    - /assets/css/custom.css

_sass/color_schemes/ornl_green.scss

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+$ornl-green: #007833;
+$link-color: $ornl-green;
+$btn-primary-color: $ornl-green;
+$sidebar-color: #ffffff;

_sass/custom/setup.scss

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+$ornl-green-000: #008542;
+$ornl-green-100: #008542;
+$ornl-green-200: #008542;
+$ornl-green-300: #008542;

cli.md

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+---
+title: Command Line Interfaces (CLIs)
+layout: default
+nav_order: 5
+---
+
+# Command Line Interfaces (CLIs)
+{: .no_toc }
+
+## Table of Contents
+{: .no_toc .text-delta }
+
+1. TOC
+{:toc}
+
+## Peregrine CLI
+
+A command line interface for interacting with the [ORNL-developed Peregrine software](https://www.ornl.gov/technology/90000077)
+enables Myna to receive commands to construct and execute simulation pipelines for
+a particular set of build, parts, and layers with minimal user input. The CLI is called
+via `myna launch_peregrine ...`. Instructions for how to setup and use the Myna tools in
+Peregrine are provided in the Peregrine user manual. The documentation here describes
+the general functionality of the CLI and how to develop additional functionality.
+
+The main parameter that is used to construct the input file for the specified pipeline
+is the `--mode <str>` argument passed to the CLI. This tells Myna which template input
+file to use, evaluated as `f"cli/peregrine_launcher/input_{mode}.yaml"`. These templates
+have to define the simulation steps to take, though many of the details of each step
+are defined by the `peregrine_default_workspace.yaml` file. Additional modes can be
+added, but they will only be accessible in Peregrine if corresponding changes are made
+within Peregrine.
+
+While this CLI was developed with the intention to interact with Peregrine, it can
+generally be used to run cases for specific builds, parts, and layers within a database.
+The following examples will run a case using the resources provided with the `myna`
+repository.
+
+```bash
+# set to the directory where Myna repository was cloned/downloaded
+MYNA_PATH="."
+
+# Launch the melt pool geometry simulation
+myna launch_peregrine --build "$MYNA_PATH/resources" --parts [P5] --layers [50,51,52] --workspace "$MYNA_PATH/cli/peregrine_launcher/peregrine_default_workspace.yaml" --mode "meltpool_geometry"
+```