Merge pull request #820 from jiajic/suite

v4.0.0 - Suite Modular

.Rbuildignore

@@ -14,3 +14,5 @@
 ^pkgdown$
 .Rbuildignore.save
 ^\.github$
+^codecov\.yml$
+^vignettes$

.github/CONTRIBUTING.md

@@ -0,0 +1,4 @@
+# How to Contribute?
+
+We welcome contributions or suggestions from other developers. Please contact us if you have questions or would like to discuss an addition or major modifications to the Giotto main code.
+The source code for Giotto Suite may be found on our [GitHub repository](https://github.com/drieslab/Giotto/tree/suite_modular).

.github/workflows/covr.yml

@@ -0,0 +1,63 @@
+
+
+name: code coverage
+
+on:
+  push:
+    branches: [ "suite_modular" ]
+  # pull_request:
+  #   types: closed
+  #   branches: [ "main" ]
+  schedule:
+    - cron: '16 20 * * 2'
+
+jobs:
+  test-coverage:
+    name: Code coverage
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+
+      - name: Checkout repo for workflow access
+        uses: actions/checkout@v3
+
+      - name: Set up R environment
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Set up dependencies (general)
+        uses: r-lib/actions/setup-r-dependencies@v2
+        env:
+          _R_CHECK_FORCE_SUGGESTS: false
+          _R_CHECK_RD_XREFS: false
+        with:
+          dependencies: '"hard"' # do not use suggested dependencies
+          extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes, any::covr
+          needs: coverage
+
+      - name: Set up dependencies (GiottoData)
+        run: |
+          suppressWarnings({
+            remotes::install_github('drieslab/GiottoData@suite_modular', build = FALSE)
+          })
+        shell: Rscript {0}
+
+      - name: Generate coverage report
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          token: e6770448-c694-49d7-b83f-b6cb21c0e7ad
+          fail_ci_if_error: false
+          flags: unittests
+          verbose: true

.github/workflows/lintr.yml

@@ -0,0 +1,62 @@
+# 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.
+# lintr provides static code analysis for R.
+# It checks for adherence to a given style,
+# identifying syntax errors and possible semantic issues,
+# then reports them to you so you can take action.
+# More details at https://lintr.r-lib.org/
+
+name: lintr
+
+on:
+  push:
+    branches: [ "suite_modular" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "suite_modular" ]
+  schedule:
+    - cron: '16 20 * * 2'
+
+permissions:
+  contents: read
+
+jobs:
+  lintr:
+    name: Run lintr scanning
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read # for checkout to fetch code
+      security-events: write # for github/codeql-action/upload-sarif to upload SARIF results
+      actions: read # only required for a private repository by github/codeql-action/upload-sarif to get the Action run status
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up R environment
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Set up dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        env:
+          _R_CHECK_FORCE_SUGGESTS: false
+          _R_CHECK_RD_XREFS: false
+        with:
+          dependencies: '"hard"' # do not use suggested dependencies
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Run lintr
+        run: lintr::sarif_output(lintr::lint_dir("."), "lintr-results.sarif")
+        shell: Rscript {0}
+        continue-on-error: true
+
+      - name: Upload analysis results to GitHub
+        uses: github/codeql-action/upload-sarif@v2
+        with:
+          sarif_file: lintr-results.sarif
+          wait-for-processing: true

.github/workflows/main_check.yaml

@@ -0,0 +1,87 @@
+# 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
+
+
+name: R-CMD-check
+
+on:
+  push:
+    branches:
+      - 'ci-unittest'
+      - 'suite_modular'
+  # pull_request:
+  #   branches:
+  #     - 'suite'
+  #     - 'suite_dev'
+
+permissions:
+  contents: read
+
+jobs:
+  R-CMD-check:
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config: # matrix of system runners to run workflow on
+          - {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'}
+
+    steps:
+
+      - name: Remove vignettes dir
+        run: rm -rf 'vignettes/'
+        shell: bash
+
+      - name: Checkout repo for workflow access
+        uses: actions/checkout@v3
+
+      - name: Set up R environment
+        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: Set up dependencies (general)
+        uses: r-lib/actions/setup-r-dependencies@v2
+        env:
+          _R_CHECK_FORCE_SUGGESTS: false
+          _R_CHECK_RD_XREFS: false
+        with:
+          dependencies: '"hard"' # do not use suggested dependencies
+          extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes, any::covr, any::spdep
+
+      - name: Set up dependencies (GiottoData)
+        run: |
+          suppressWarnings({
+            remotes::install_github('drieslab/GiottoData@suite_modular', build = FALSE)
+          })
+        shell: Rscript {0}
+
+      - name: Test python env build
+        run: |
+          if (!GiottoClass::checkGiottoEnvironment()) {
+            GiottoClass::installGiottoEnvironment()
+          }
+        shell: Rscript {0}
+
+      - name: Run R CMD check
+        uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          error-on: '"error"' # workflow errors on error only, can change to include warnings
+
+      # show testthat output for ease of access
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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: [main, master]
+  pull_request:
+    branches: [main, master]
+  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 }}
+    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: 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/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -2,11 +2,11 @@
 .Rproj.user
 .Rhistory
 inst/doc
-.DS_Store
+*.DS_Store
 *.Rproj
 .git_old
 merfish_preoptic/
 .vscode/*
 .Rprofile
-inst/python/.ipynb_checkpoints/
+inst/python/.ipynb_checkpoints/ 
 docs