Add GitHub CI workflows

.gitattributes

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+*.xls filter=lfs diff=lfs merge=lfs -text
+*.xlsx filter=lfs diff=lfs merge=lfs -text
+*.parquet filter=lfs diff=lfs merge=lfs -text
+*.geojson filter=lfs diff=lfs merge=lfs -text
+*.csv filter=lfs diff=lfs merge=lfs -text
+*.bz2 filter=lfs diff=lfs merge=lfs -text
+*.pdf filter=lfs diff=lfs merge=lfs -text
+DESCRIPTION text eol=lf

.github/workflows/R-CMD-check.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:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  prepare-ptaxsim:
+    uses: ./.github/workflows/prepare-ptaxsim.yaml
+    secrets: inherit
+
+  R-CMD-check:
+    needs: prepare-ptaxsim
+    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 }}
+      PTAXSIM_DB_PATH: ${{ github.workspace }}/ptaxsim.db
+      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
+
+      - name: Restore database cache
+        uses: actions/cache/[email protected]
+        with:
+          path: ptaxsim.db.bz2
+          key: ${{ format('{0}-{1}', needs.prepare-ptaxsim.outputs.PTAXSIM_VERSION, hashFiles('DESCRIPTION')) }}
+          fail-on-cache-miss: true
+          enableCrossOsArchive: true
+
+      - name: Unpack database
+        run: |
+          bzip2 -d ${{ github.workspace }}/ptaxsim.db.bz2
+        shell: bash
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/lint.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:
+  pull_request:
+  push:
+    branches: [main, master]
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.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:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches: [main, master]
+  release:
+    types: [published]
+
+name: pkgdown
+
+jobs:
+  prepare-ptaxsim:
+    uses: ./.github/workflows/prepare-ptaxsim.yaml
+    secrets: inherit
+
+  pkgdown:
+    needs: prepare-ptaxsim
+    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 }}
+      PTAXSIM_DB_PATH: ${{ github.workspace }}/ptaxsim.db
+    permissions:
+      contents: write
+    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: Restore database cache
+        uses: actions/cache/restore@v3
+        with:
+          path: ptaxsim.db.bz2
+          key: ${{ format('{0}-{1}', needs.prepare-ptaxsim.outputs.PTAXSIM_VERSION, hashFiles('DESCRIPTION')) }}
+          fail-on-cache-miss: true
+
+      - name: Unpack database
+        run: |
+          bzip2 -d ${{ github.workspace }}/ptaxsim.db.bz2
+        shell: bash
+
+      - 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

.github/workflows/pre-commit.yaml

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+on:
+  pull_request:
+  push:
+    branches: [main, master]
+
+name: pre-commit
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      RENV_CONFIG_CACHE_ENABLED: false
+      R_CACHE_ROOTPATH: ~/.cache/pre-commit
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, any::styler, local::.
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+
+      - uses: pre-commit/[email protected]

.github/workflows/prepare-ptaxsim.yaml

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+on:
+  workflow_call:
+    inputs:
+      PTAXSIM_DB_BASE_URL:
+        required: false
+        type: string
+        default: "s3://ccao-data-public-us-east-1/ptaxsim"
+    outputs:
+      PTAXSIM_VERSION:
+        description: "PTAXSIM database version"
+        value: ${{ jobs.download-db.outputs.output1 }}
+
+jobs:
+  download-db:
+    runs-on: ubuntu-latest
+    env:
+      AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+      AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+      AWS_REGION: ${{ secrets.AWS_REGION }}
+    outputs:
+      output1: ${{ steps.version_db.outputs.PTAXSIM_VERSION }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - id: version_db
+        name: Get database version
+        run: |
+          echo "PTAXSIM_VERSION=$(grep -Po "(?<=Wants_DB_Version: )[0-9]*\.[0-9]*\.[0-9]*" ${{ github.workspace }}/DESCRIPTION)" >> $GITHUB_ENV
+          echo "PTAXSIM_VERSION=$(grep -Po "(?<=Wants_DB_Version: )[0-9]*\.[0-9]*\.[0-9]*" ${{ github.workspace }}/DESCRIPTION)" >> $GITHUB_OUTPUT
+
+      - id: check_db
+        name: Check database cache
+        uses: actions/cache/restore@v3
+        with:
+          path: ptaxsim.db.bz2
+          key: ${{ format('{0}-{1}', env.PTAXSIM_VERSION, hashFiles('DESCRIPTION')) }}
+          lookup-only: true
+
+      - id: fetch_db
+        name: Fetch database file
+        if: steps.check_db.outputs.cache-hit != 'true'
+        run: |
+          aws s3 cp ${{ inputs.PTAXSIM_DB_BASE_URL }}/ptaxsim-${{ env.PTAXSIM_VERSION }}.db.bz2 ${{ github.workspace }}/ptaxsim.db.bz2
+        shell: bash
+
+      - id: save_db
+        name: Save database cache
+        uses: actions/cache/save@v3
+        if: steps.check_db.outputs.cache-hit != 'true'
+        with:
+          path: ptaxsim.db.bz2
+          key: ${{ format('{0}-{1}', env.PTAXSIM_VERSION, hashFiles('DESCRIPTION')) }}
+          enableCrossOsArchive: true

.github/workflows/test-coverage.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:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  prepare-ptaxsim:
+    uses: ./.github/workflows/prepare-ptaxsim.yaml
+    secrets: inherit
+
+  test-coverage:
+    needs: prepare-ptaxsim
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      PTAXSIM_DB_PATH: ${{ github.workspace }}/ptaxsim.db
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Restore database cache
+        uses: actions/cache/restore@v3
+        with:
+          path: ptaxsim.db.bz2
+          key: ${{ format('{0}-{1}', needs.prepare-ptaxsim.outputs.PTAXSIM_VERSION, hashFiles('DESCRIPTION')) }}
+          fail-on-cache-miss: true
+
+      - name: Unpack database
+        run: |
+          bzip2 -d ${{ github.workspace }}/ptaxsim.db.bz2
+        shell: bash
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package