Merge pull request #195 from omnideconv/fix-conda-ci

Switch to rattler-build for testing conda recipe

Author: grst

.conda/meta.yaml .conda/recipe.yaml.conda/meta.yaml renamed to .conda/recipe.yaml

@@ -1,26 +1,21 @@
-{% set name = "r-immunedeconv" %}
-
 package:
-  name: {{ name }}
+  name: immunedeconv
   version: "develop"
 
 source:
   path: ".."
 
 build:
-  script: $R CMD INSTALL --build .
+  script: R CMD INSTALL --build .
   number: 0
   noarch: generic
-  rpaths:
-    - lib/R/lib/
-    - lib/
 
 requirements:
   host:
     - r-base >=4.1
     - r-dplyr >=0.7
     - r-magrittr >=1.5
-    - r-readr >=1.1
+    - r-readr >=1.4
     - r-readxl >=1.0
     - r-testit >=0.7
     - r-tibble >=1.4.2
@@ -43,7 +38,7 @@ requirements:
     - r-base >=4.1
     - r-dplyr >=0.7
     - r-magrittr >=1.5
-    - r-readr >=1.1
+    - r-readr >=1.4
     - r-readxl >=1.0
     - r-testit >=0.7
     - r-tibble >=1.4.2
@@ -63,19 +58,19 @@ requirements:
     - r-consensustme
     - r-mmcpcounter
 
-test:
-  commands:
-    - '$R -e "library(''immunedeconv'')"'
+tests:
+  - r:
+      libraries:
+        - immunedeconv
 
 about:
-  home: https://github.com/omnideconv/immunedeconv
-  license: BSD_3_clause
+  repository: https://github.com/omnideconv/immunedeconv
+  homepage: https://omnideconv.org/immunedeconv/
+  license: GPL-2.0-only
   summary: "collection of methods for immune cell deconvolution of bulk RNA-seq samples."
-  license_family: BSD
   license_file: LICENSE
+  description: Collection of methods for immune cell deconvolution of bulk RNA-seq samples.
 
 extra:
-  recipe-maintainers:
-    - grst
   identifiers:
     - doi:10.1101/463828

.github/workflows/conda.yml

@@ -10,36 +10,37 @@ on:
   pull_request:
     branches: [master]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   tests:
     runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -el {0} # -l for login shell (conda), -e to fail on error
     name: conda ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest", "macos-latest"]
+        os: ["ubuntu-latest"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Setup Minoconda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          auto-update-conda: true
-          miniforge-version: latest
-          use-mamba: true
+          mamba-version: "*"
           channels: conda-forge,bioconda
-          channel-priority: true
-          python-version: 3.9
+          channel-priority: strict
+          python-version: ${{ matrix.python }}
 
-      - name: Set-up channels and install conda build
+      - name: install rattler-build
         run: |
-          mamba install -y conda-build conda-verify
-        shell: bash
+          mamba install -y rattler-build
 
       - name: build and test package
         run: |
-          set -euxo pipefail
-          test -f .conda/meta.yaml
-          conda build .conda --no-anaconda-upload
-        shell: bash
+          cd .conda && rattler-build build -c conda-forge -c bioconda

.github/workflows/test.yml

@@ -52,6 +52,33 @@ jobs:
           cd preprocessCore
           R CMD INSTALL --configure-args="--disable-threading"  .
 
-      - uses: r-lib/actions/check-r-package@v2
+      # Simpler version – re-enable once the "stack imbalance" dependency bug is fixed:
+      # - uses: r-lib/actions/check-r-package@v2
+      #   with:
+      #     upload-snapshots: true
+
+      - name: R CMD check
+        run: |
+          results <- rcmdcheck::rcmdcheck(
+            args = c("--no-manual"),
+            build_args = c("--no-manual"),
+            error_on = "never",
+            check_dir = "check"
+          )
+          # Filter out known dependency bug (stack imbalance in '::' / '<-')
+          real_warnings <- Filter(
+            function(w) !grepl("stack imbalance", w),
+            results$warnings
+          )
+          if (length(results$errors) > 0 || length(real_warnings) > 0) {
+            print(results)
+            stop("R CMD check found errors or warnings.")
+          }
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
         with:
-          upload-snapshots: true
+          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
+          path: check

DESCRIPTION

@@ -14,7 +14,7 @@ Imports:
     purrr (>= 1.0.2),
     dplyr (>= 0.7),
     magrittr (>= 1.5),
-    readr (>= 1.1),
+    readr (>= 1.4),
     readxl (>= 1.0),
     testit (>= 0.7),
     tibble (>= 1.4.2),

R/custom_deconvolution_methods.R

@@ -64,8 +64,8 @@ deconvolute_cibersort_custom <- function(gene_expression_matrix, signature_matri
 
   temp.expression.file <- tempfile()
   temp.signature.file <- tempfile()
-  write_tsv(as_tibble(gene_expression_matrix, rownames = "gene_symbol"), path = temp.expression.file)
-  write_tsv(as_tibble(signature_matrix, rownames = "gene_symbol"), path = temp.signature.file)
+  write_tsv(as_tibble(gene_expression_matrix, rownames = "gene_symbol"), file = temp.expression.file)
+  write_tsv(as_tibble(signature_matrix, rownames = "gene_symbol"), file = temp.signature.file)
 
 
   arguments <- dots_list(temp.signature.file, temp.expression.file,

R/mouse_deconvolution_methods.R

@@ -95,7 +95,7 @@ deconvolute_seqimmucc <- function(gene_expression_matrix,
 
     temp.expression.file <- tempfile()
 
-    write_tsv(as_tibble(gene_expression_matrix, rownames = "gene_symbol"), path = temp.expression.file)
+    write_tsv(as_tibble(gene_expression_matrix, rownames = "gene_symbol"), file = temp.expression.file)
     perm <- 100
     # results = CIBERSORT(signature.path, temp.expression.file, perm, QN=FALSE, ...)
     # results = results %>%