funT

.Rbuildignore

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+## R system cruft
+^.*\.Rproj$
+^hector.Rproj$
+^\.Rproj\.user$
+
+## GitHub config, license, CI, etc.
+^CONTRIBUTING.md$
+^LICENSE.md$
+^changelog.txt$
+^.travis.yml$
+^appveyor.yml$
+^.github$
+^wiki/
+^_pkgdown.yml$
+
+## Files supporting stand-alone hector.
+^Makefile$
+^project_files$
+^output$
+^scripts$
+^scripts/
+^logs$
+^test_hector.sh$
+^src/hector$
+^src/.*\.txt$
+^src/.*\.a$
+^src/.*\.d$
+^.*\.o$
+^src/main.*$
+^src/makefile.standalone$
+^src/testing$
+^misc$
+^data-raw$
+^.vscode$
+
+# pkgdown config and output
+_pkgdown.yml
+^docs/
+^\.github$
+
+# lintr config
+.lintr
+^doc$
+^Meta$
+^vignettes/articles$
+
+# README and similar files
+^CITATION\.cff$
+^CODE_OF_CONDUCT\.md$
+^README\.Rmd$

.github/.gitignore

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+*.html

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve Hector
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Explain how to reproduce the behavior:
+1. Attach the hector input file to the bug report (you will have to add `.txt` to the end of the filename to get GitHub to accept the attachment).
+2. Briefly describe the scenario you were trying to run, if it is not one of the standard scenarios.
+3. Tell us how you were running Hector (e.g., stand-alone, R interface, pyhector)
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Actual behavior**
+  - Describe what actually happened.
+  - If applicable, copy and paste any error messages that were produced (please do not include screenshots of terminal output).
+  - Attach the global log (`hector.log`) and any additional log files that may be relevant (e.g., if the error message refers to a component, the log file for that component).
+
+**Runtime and build environment (please complete the following information):**
+ - OS: [Linux, OS-X, Windows]
+ - Boost version you used to build Hector
+ - If running from R, output of `SessionInfo()`.
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/development.md

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+---
+name: Development
+about: Create an issue for a  Hector PR
+
+---
+
+**Describe development**
+
+A clear and concise description of the Hector development. 
+
+
+**Type of development** 
+
+The Hector team uses [semantic versioning](https://semver.org/), please let us know what type of changes have been made, this will help us determine if we need additional information. 
+
+* MAJOR: potential code-breaking changes or Hector behavior changes
+* MINOR: some functionality is added but backward compatible
+* PATCH: minor changes (e.g., documentation or bug fixes)
+
+**Checklist**
+- [ ] [Roxygen](https://roxygen2.r-lib.org/) where applicable but also thorough and coherent inline documentation 
+- [ ] [Unit tests](https://r-pkgs.org/tests.html) when applicable
+- [ ] Complies with the [Hector code style guide](https://jgcri.github.io/hector/articles/manual/StyleGuide.html)
+- [ ] The PR passes automated testing suite

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/R-CMD-check.yaml

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+name: R-CMD-check
+# Controls when the action will run.
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - '**' # matches every branch
+
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    # Launch run at 6am the 1st of every month.
+    - cron:  '0 6 1 * *'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          args: 'c("--no-manual", "--as-cran")'
+          error-on: '"error"'
+          check-dir: '"check"'

.github/workflows/codecov.yaml

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+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - '**' # matches every branch
+  schedule:
+   # * is a special character in YAML so you have to quote this string, it is set up to run at 6am
+   # on the first day of the month, this is helpful for periods of time when PRs are not being merged.
+    - cron:  '0 6 1 * *'
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: macOS-r-4.0-2-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: macOS-r-4.0-2-
+
+      - name: Install libcurl
+        run: sudo apt-get install libcurl4-openssl-dev
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

.github/workflows/command-line.yaml

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+# This is a basic workflow to help you get started with Actions
+# based on https://github.com/JGCRI/hector/new/master?filename=.github%2Fworkflows%2Fmain.yml&workflow_template=blank
+
+name: Command Line Hector
+
+# Controls when the action will run.
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - '**' # matches every branch
+
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    # Launch run at 6am the 1st of every month.
+    - cron:  '0 6 1 * *'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  # This workflow contains two jobs, one that builds hector on ubuntu and the second
+  # builds and tests Hector on macos. The purpose of this work for is to make sure that Hector
+  # can be built from the command line.
+  ubuntu:
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+      - name: build and run
+        run: |
+          sudo apt-get update
+          sudo apt install libboost-dev
+          make hector
+          bash ./test_hector.sh ./src/hector

.github/workflows/leeyabot.yml

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+name: leeyabot
+on:
+  pull_request:
+    branches:
+      - '**' # matches every branch
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: iterative/setup-cml@v1
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+
+      - name: Install libcurl
+        run: sudo apt-get install libcurl4-openssl-dev
+
+      - name: Install dependencies
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          install.packages(c("ggplot2", "rmarkdown", "dplyr", "remotes", "here"))
+          remotes::install_github("hadley/emo")
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Generate report
+        run: |
+          rmarkdown::render("./scripts/OutputDifferences.Rmd", run_pandoc = FALSE)
+        shell: Rscript {0}
+
+      - name: Post comment
+        env:
+          REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+            # Post reports as comments in GitHub PRs
+            cd scripts/
+            if [ -f "diff_plot.png" ]
+            then
+                cat OutputDifferences.knit.md >> report.md
+                echo "![](./diff_plot.png)" >> report.md
+                echo "![](./comp_plot.png)" >> report.md
+            elif [ -f "same_plot.png" ]
+            then
+                cat OutputDifferences.knit.md >> report.md
+            else
+                cat OutputDifferences.knit.md >> report.md
+                echo "leeyabot down :(" > report.md
+            fi
+            cml comment create report.md

.github/workflows/pkgdown.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches:
+      - '**' # matches every branch
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs