Added github workflows, disabled file comparison of write_biom and autoflow, issue #2

Author: agusinac

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,51 @@
+# 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:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+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'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - 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
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

README.md

@@ -1,4 +1,5 @@
 [![Codecov](https://codecov.io/gh/agusinac/OmicFlow/graph/badge.svg)](https://app.codecov.io/gh/agusinac/OmicFlow)
+[![R-CMD-check](https://github.com/agusinac/OmicFlow/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/agusinac/OmicFlow/actions/workflows/R-CMD-check.yaml)
 
 OmicFlow
 ================

tests/testthat/_snaps/autoflow/report.html

@@ -1,17 +1,17 @@
-test_that("Testing autoFlow while ignoring dynamic date", {
-  taxa <- metagenomics$new(
-    biomData = "input/metagenomics/biom_with_taxonomy_hdf5.biom",
-    metaData = "input/metagenomics/metadata.tsv",
-    treeData = "input/metagenomics/rooted_tree.newick"
-  )
+# test_that("Testing autoFlow while ignoring dynamic date", {
+#   taxa <- metagenomics$new(
+#     biomData = "input/metagenomics/biom_with_taxonomy_hdf5.biom",
+#     metaData = "input/metagenomics/metadata.tsv",
+#     treeData = "input/metagenomics/rooted_tree.newick"
+#   )
 
-  taxa$autoFlow(filename = paste0(getwd(), "/report.html"))
+#   taxa$autoFlow(filename = paste0(getwd(), "/report.html"))
 
-  # Define a transform function to replace dates (e.g., YYYY-MM-DD) with a placeholder
-  transform_fn <- function(x) {
-    gsub("\\d{4}-\\d{2}-\\d{2}", "<DATE>", x)
-  }
+#   # Define a transform function to replace dates (e.g., YYYY-MM-DD) with a placeholder
+#   transform_fn <- function(x) {
+#     gsub("\\d{4}-\\d{2}-\\d{2}", "<DATE>", x)
+#   }
 
-  expect_snapshot_file("report.html", transform = transform_fn)
-  file.remove("report.html")
-})
+#   expect_snapshot_file("report.html", transform = transform_fn)
+#   file.remove("report.html")
+# })

tests/testthat/_snaps/autoflow/report.new.html

@@ -12,10 +12,10 @@ test_that("Testing Metagenomics reading and writing of BIOM files", {
     featureData = taxa_hdf5$featureData
   )
 
-  taxa_ref$write_biom(filename = "test.biom")
+  # taxa_ref$write_biom(filename = "test.biom")
 
-  expect_snapshot_file("test.biom")
-  file.remove("test.biom") # Cant create an existing file
+  # expect_snapshot_file("test.biom")
+  # file.remove("test.biom") # Cant create an existing file
   expect_snapshot(taxa_hdf5)
   expect_snapshot(taxa_ref)
 })