Merge branch 'main' into dependabot/pip/lxml-5.3.0

.Renviron

@@ -1 +1 @@
-_R_CHECK_FORCE_SUGGESTS_=false
+_R_CHECK_FORCE_SUGGESTS_=TRUE

.dockerignore

@@ -0,0 +1,12 @@
+.git/
+.gitignore
+
+.Rhistory
+.RData
+.Rproj.user
+*.tar.gz
+*.Rcheck/
+tests/testthat/_snaps/
+docs/
+.DS_Store
+Thumbs.db

.github/workflows/docker-publish.yml

@@ -0,0 +1,101 @@
+name: flaiR-Docker
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+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'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@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-pandoc@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.9'
+
+      - name: Check Python Version
+        run: python --version
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flair
+
+      - name: Install R dependencies
+        run: |
+          install.packages('remotes')
+          remotes::install_github("davidycliao/flaiR", force = TRUE)
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: rcmdcheck
+
+      - name: Setup Python (Only on ubuntu-latest)
+        if: matrix.config.os == 'ubuntu-latest'
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.10.13'
+
+      - name: Install Python venv and dependencies (Only on ubuntu-latest)
+        if: matrix.config.os == 'ubuntu-latest'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y python3-venv
+          python -m venv ~/.venv
+          echo "RETICULATE_PYTHON=~/.venv/bin/python" >> $GITHUB_ENV
+          source ~/.venv/bin/activate
+          pip install scipy==1.12.0
+
+      - name: Install Pandoc (Only on Windows)
+        if: matrix.config.os == 'windows-latest'
+        run: choco install pandoc
+
+      - name: Install Python dependencies (Only on Windows)
+        if: matrix.config.os == 'windows-latest'
+        run: |
+          python -m pip install --upgrade pip
+          pip install scipy==1.12.0
+          pip install flair
+
+      - name: Install Python dependencies (Only on macOS)
+        if: matrix.config.os == 'macos-latest'
+        run: |
+          python -m pip install --upgrade pip
+          pip install scipy==1.12.0
+          pip install flair
+
+      - name: Build and push Docker image (Only on ubuntu-latest)
+        if: matrix.config.os == 'ubuntu-latest'
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file:  ./Dockerfile
+          push: true
+          tags: ghcr.io/davidycliao/flair:latest

.github/workflows/r.yml

@@ -5,82 +5,17 @@
 #
 # See https://github.com/r-lib/actions/tree/master/examples#readme for
 # additional example workflows available for the R community.
-# on:
-#   push:
-#     branches: [main, master]
-#   pull_request:
-#     branches: [main, master]
-#
-# name: R-CMD-check
-#
-# 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'}
-#     env:
-#       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-#       R_KEEP_PKG_SOURCE: yes
-#
-#     steps:
-#       - uses: actions/checkout@v2
-#
-#       - uses: r-lib/actions/setup-pandoc@v2
-#
-#
-#       - name: Setup Python (Only on ubuntu-latest)
-#         if: matrix.config.os == 'ubuntu-latest'
-#         uses: actions/setup-python@v2
-#         with:
-#           python-version: '3.x'
-#
-#       - name: Install Python venv and dependencies (Only on ubuntu-latest)
-#         if: matrix.config.os == 'ubuntu-latest'
-#         run: |
-#           sudo apt-get update
-#           sudo apt-get install -y python3-venv
-#           python -m venv ~/.venv
-#           echo "RETICULATE_PYTHON=~/.venv/bin/python" >> $GITHUB_ENV
-#           source ~/.venv/bin/activate
-#       - 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
-#
-#       - name: Install reticulate (Only on ubuntu-latest)
-#         if: matrix.config.os == 'ubuntu-latest'
-#         run: |
-#           Rscript -e "install.packages('reticulate', repos = 'https://cloud.r-project.org/')"
-#
-#       - 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
-#
-
-on:
-  push:
-    branches: [main, master]
-  pull_request:
-    branches: [main, master]
 
 name: R-CMD-check
 
+on:
+ push:
+   branches: [main, master]
+ pull_request:
+   branches: [main, master]
+
 jobs:
+
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
 
@@ -92,8 +27,7 @@ jobs:
         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'}
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
@@ -166,6 +100,3 @@ jobs:
         with:
           extra-packages: rcmdcheck
 
-      # - uses: r-lib/actions/check-r-package@v2
-      #   with:
-      #     upload-snapshots: true