ci: add all the github scripts

Signed-off-by: Ali Sajid Imami <[email protected]>

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/create_github_release.yaml

@@ -0,0 +1,89 @@
+on:
+  push:
+    branches:
+      - devel
+      - RELEASE*
+
+name: Create Github Release
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  optimize_ci:
+      runs-on: ubuntu-latest
+      outputs:
+        skip: ${{ steps.check_skip.outputs.skip }}
+      steps:
+        - name: Optimize CI
+          id: check_skip
+          uses: withgraphite/graphite-ci-action@main
+          with:
+            graphite_token: ${{secrets.GRAPHITE_TOKEN}}
+  create-release:
+    runs-on: ubuntu-latest
+    needs: [optimize_ci]
+    if: needs.optimize_ci.outputs.skip == 'false'
+    permissions:
+      contents: write
+    outputs:
+      tag_version: ${{ steps.create_release.outputs.tag_version }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
+        with:
+          fetch-depth: 0
+      - name: Get most recent tag
+        id: get_tag
+        run: echo "TAG_VERSION=$(git describe --tags $(git rev-list --tags --max-count=1))" >> "$GITHUB_ENV"
+      - name: Create Release
+        id: create_release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: |
+          echo "Creating release for tag $TAG_VERSION"
+          gh release create $TAG_VERSION --title "Release $TAG_VERSION" --notes "Release $TAG_VERSION" --target ${{ github.ref }}
+          echo "tag_version=$TAG_VERSION" >> "$GITHUB_OUTPUT"
+  create_release_artifacts:
+    needs: [create-release]
+    permissions:
+      contents: write
+    strategy:
+      fail-fast: false
+      matrix:
+        r_version: ['release', 'devel']
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
+      - name: Update system repositories
+        run: sudo apt-get update
+      - name: Install system dependencies
+        run: |
+          sudo apt-get install -y libxml2-dev \
+          libssl-dev libcurl4-openssl-dev \
+          libharfbuzz-dev libfribidi-dev \
+          pandoc
+      - name: Setup R
+        uses: r-lib/actions/setup-r@e6be4b3706e0f39bc7a4cf4496a5f2c4cb840040 # v2.10.1
+        with:
+          r-version: ${{ matrix.r_version }}
+          use-public-rspm: true
+        id: r
+      - name: Install dependencies
+        uses: r-lib/actions/setup-renv@e6be4b3706e0f39bc7a4cf4496a5f2c4cb840040 # v2.10.1
+      - name: Build Package
+        run: R CMD build .
+      - name: Rename Package
+        run: echo "NEWNAME=$(./utilities/rename-package.R *.tar.gz)" >> "$GITHUB_ENV"
+      - name: debug
+        run: |
+          echo "R version: ${{ steps.r.outputs.installed-r-version }}"
+          echo "Current Tag: ${{ needs.create-release.outputs.tag_version }}"
+          echo "Release File Name: ${{ env.NEWNAME }}"
+      - name: Upload Release Artifact
+        env:
+          RELEASE_TAG: ${{ needs.create-release.outputs.tag_version }}
+          GH_TOKEN: ${{ github.token }}
+        run: gh release upload ${{ env.RELEASE_TAG }} ${{ env.NEWNAME }}

.github/workflows/rworkflows.yml

@@ -0,0 +1,68 @@
+name: Continuous Integration / R Workflows
+on:
+  workflow_dispatch:
+  push:
+    branches-ignore:
+    - master
+    - main
+    - RELEASE_**
+    - graphite-**
+  pull_request:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  optimize_ci:
+      runs-on: ubuntu-latest
+      outputs:
+        skip: ${{ steps.check_skip.outputs.skip }}
+      steps:
+        - name: Optimize CI
+          id: check_skip
+          uses: withgraphite/graphite-ci-action@main
+          with:
+            graphite_token: ${{secrets.GRAPHITE_TOKEN}}
+  rworkflows:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    needs: [optimize_ci]
+    if: needs.optimize_ci.outputs.skip == 'false'
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: bioconductor/bioconductor_docker:devel
+          rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release
+        - os: macOS-latest
+          bioc: devel
+          r: auto
+        - os: windows-latest
+          bioc: devel
+          r: auto
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ true }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ false }}
+        run_pkgdown: ${{ false }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN:  ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1

.github/workflows/test-coverage.yaml

@@ -0,0 +1,62 @@
+# 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, devel]
+  pull_request:
+    branches: [main, master, devel]
+
+name: test-coverage
+
+jobs:
+  optimize_ci:
+      runs-on: ubuntu-latest
+      outputs:
+        skip: ${{ steps.check_skip.outputs.skip }}
+      steps:
+        - name: Optimize CI
+          id: check_skip
+          uses: withgraphite/graphite-ci-action@main
+          with:
+            graphite_token: ${{secrets.GRAPHITE_TOKEN}}
+  test-coverage:
+    runs-on: ubuntu-latest
+    needs: [optimize_ci]
+    if: needs.optimize_ci.outputs.skip == 'false'
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4
+
+      - uses: r-lib/actions/setup-r@e6be4b3706e0f39bc7a4cf4496a5f2c4cb840040 # v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@e6be4b3706e0f39bc7a4cf4496a5f2c4cb840040 # v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - 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: always()
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.pre-commit-config.yaml

@@ -39,7 +39,7 @@ repos:
           data/.*|
           .*\.(gz|xz|bz2)|
           (.*/|)codemeta.json|
-          COMMIT_EDITMSG
+          (.*)COMMIT_EDITMSG|
           )$
     -   id: readme-rmd-rendered
     -   id: parsable-R

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: PCSF
 Title: Network-based interpretation of highthroughput data
-Version: 0.99.67
+Version: 0.99.68
 Date: 2017-02-01
 Author: Murodzhon Akhmedov, Amanda Kedaigle, Renan Escalante, Roberto
     Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee

codemeta.json

@@ -5,7 +5,7 @@
   "description": "The PCSF package performs an integrated analysis of highthroughput data using the interaction networks as a template, and interprets the biological landscape of interaction networks with respect to the data, which potentially leads to predictions of functional units. It also interactively visualize the resulting subnetwork with functional enrichment analysis.",
   "name": "PCSF: Network-based interpretation of highthroughput data",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.99.67",
+  "version": "0.99.68",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -181,7 +181,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "7741.971KB",
+  "fileSize": "7741.975KB",
   "codeRepository": "https://github.com/CogDisResLab/PCSF",
   "readme": "https://github.com/CogDisResLab/PCSF/blob/master/README.md"
 }

inst/WORDLIST

@@ -13,6 +13,7 @@ biomolecule
 biomolecules
 BMC
 CBL
+ci
 CMake
 config
 downregulation