Merge pull request #89 from LeaSeep/develop

release 0.1.3

.github/workflows/pages.yml

@@ -0,0 +1,84 @@
+# 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.
+
+# Sample workflow for building and deploying a Jekyll site to GitHub Pages
+name: Deploy Jekyll site to Pages
+
+on:
+  push:
+    branches: 
+         - main
+         - develop   
+    paths:
+      - "docs/**"
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: docs
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '3.3' # Not needed with a .ruby-version file
+          cache-version: 0 # Increment this number if you need to re-download cached gems
+
+      - name: Configure Bundler
+        run: |
+          bundle config --local path vendor/bundle
+          bundle config --local deployment true
+          bundle lock --add-platform x86_64-linux
+
+      - name: Install dependencies
+        run: bundle install --jobs 4
+
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v5
+
+      - name: Build with Jekyll
+        # Outputs to the './_site' directory by default
+        run: bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
+        env:
+          JEKYLL_ENV: production
+          PAGES_REPO_NWO: leaseep/OmicShiny
+
+      - name: Upload artifact
+        # Automatically uploads an artifact from the './_site' directory by default
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: "docs/_site/"
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/start_check.yaml

@@ -0,0 +1,118 @@
+name: Test Shiny App Startup
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    env:
+      RENV_PATHS_ROOT: ~/.cache/R/renv
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: 4.2.0
+
+    - name: Restore Renv package cache
+      uses: actions/cache@v3
+      with:
+        path: |
+          ${{ env.RENV_PATHS_ROOT }}
+          ./renv/library
+        key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ inputs.cache-version }}-${{ hashFiles('renv.lock') }}
+        restore-keys: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ inputs.cache-version }}-
+
+    - name: Install system dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev libsqlite3-dev libglu1-mesa-dev default-jdk libmagick++-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev
+        sudo apt install curl
+    
+    - name: Install and activate renv
+      shell: Rscript {0}
+      run: |
+        install.packages("renv")
+        renv::restore()
+        
+    # - name: Get R and OS version
+    #   id: get-version
+    #   run: |
+    #     cat("##[set-output name=os-version;]", sessionInfo()$running, "\n", sep = "")
+    #     cat("##[set-output name=r-version;]", R.Version()$version.string, sep = "")
+    #   shell: Rscript {0}
+
+
+#    - name: Setup renv
+#      uses: r-lib/actions/setup-renv@v2
+
+    # - name: Restore packages
+    #   shell: Rscript {0}
+    #   run: |
+    #     renv::restore()
+
+#    - name: test specific packages
+#      run: |
+#        Rscript -e 'install.packages("Rcpp")'
+#          Rscript -e 'install.packages("RcppArmadillo")'
+#          Rscript -e 'install.packages("DESeq2")'
+
+    - name: Test if Shiny app starts
+      timeout-minutes: 2
+      shell: Rscript {0}
+      run: |
+        install.packages('processx')
+        library(processx)
+        
+        execute_shiny_app <- function() {
+          tryCatch(
+            {
+              # Start the Shiny app in a separate process
+              app_process <- process$new(
+                "Rscript",
+                c("-e", "shiny::runApp('program/shinyApp', launch.browser = FALSE, port = 3838)"),
+                stdout = "|", stderr = "|"
+              )
+              
+              # Wait for a few seconds to allow the app to start
+              Sys.sleep(15)
+              
+              # Check if the process is still running
+              if (app_process$is_alive()) {
+                # Terminate the app if it started successfully
+                app_process$kill()
+                return("Success")
+              } else {
+                # Capture and return the error message if the app failed to start
+                error_message <- app_process$read_error()
+                return(paste("Error:", error_message))
+              }
+            },
+            error = function(e) {
+              return(paste("Error:", e$message))
+            }
+          )
+        }
+        
+        
+        result <- execute_shiny_app()
+        
+            # Check if the result is "failure"
+        if (result == "Success") {
+          cat("Test passed")
+        } else {
+           cat("Test failed: Output is 'failure'\n")
+          quit(status = 1)
+        }
+        
+    - name: Save cache
+      uses: actions/cache@v3
+      with:
+        path: |
+          ~/.local/share/renv
+          ./renv/library
+        key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ inputs.cache-version }}-${{ hashFiles('renv.lock') }}
+
+
+

.gitignore

@@ -17,3 +17,8 @@ program/shinyApp/*.png
 program/shinyApp/*.xml
 program/shinyApp/*.log
 program/shinyApp/www/*md
+!.github/
+!./renv/cellar
+program/shinyApp/www/*/
+program/shinyApp/www/*.png
+docs/_site/*

CHANGELOG.md

@@ -6,6 +6,17 @@ Release notes
 ..........
 
 
+0.1.3 (2022-12-02)
+-------------------
+* General
+   * Fix various bugs (#78, #76, #84, #80, #85, #86, #91)
+* Significance Panel (#81)
+    * allows for significance analysis of two conditions, multiple times
+    * choice of test, adjustment
+    * summary of each significance testing
+    * visualisations of summaries via VennDiagramm and UpSetR
+
+
 0.1.2 (2022-11-23)
 -------------------
 * General:

DESCRIPTION

@@ -0,0 +1,2 @@
+Author: AG Hasenauer, Lea Seep & Paul Jonas Jost
+Version: 0.1.3 (2022-12-02)

README.md

@@ -1,4 +1,13 @@
 # Data Input Notes:
+## Status Quo
+General Test:
+![example workflow](https://github.com/LeaSeep/OmicShiny/actions/workflows/run-tests.yaml/badge.svg)
+
+Develop-Version Test-Status:
+![develop status](https://github.com/LeaSeep/OmicShiny/actions/workflows/run-tests.yaml/badge.svg?branch=develop)
+
+Main-Version Test-Status:
+![main status](https://github.com/LeaSeep/OmicShiny/actions/workflows/run-tests.yaml/badge.svg?branch=main)
 
 3 tables are needed:
 1. data-table (e.g. counts or intensitites)

docs/Gemfile

@@ -0,0 +1,11 @@
+source "https://rubygems.org"
+
+gem "rails"
+gem "puma"
+gem "nokogiri"
+gem "jekyll"
+gem "jekyll-remote-theme"
+gem "jekyll-seo-tag"
+gem "github-pages", group: :jekyll_plugins
+gem "webrick"
+gem "just-the-docs"