Merge pull request #374 from marouenbg/optimize-package-2026

Optimize netZooR package dependency and loading

Author: taraeicher

.Rbuildignore

@@ -32,3 +32,6 @@ vignettes/yarn.Rmd
 notes.md
 R/createDiffPandaStyle.R
 R/visDiffPandaInCytoscape.R
+^env$
+^\.venv$
+netZooR\.code-workspace$

.github/workflows/bioc-check.yml

@@ -0,0 +1,157 @@
+## Bioconductor-style R CMD check + BiocCheck
+## Mirrors the checks run on the Bioconductor build system (BBS)
+## https://contributions.bioconductor.org/bioconductor-package-submissions.html
+
+name: BioC Check
+
+on:
+  push:
+    branches: [master, devel]
+  pull_request:
+    branches: [master, devel]
+
+env:
+  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+jobs:
+  bioc-check:
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 120
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          # Bioconductor devel tracks the latest R release
+          - os: ubuntu-latest
+            r-version: "devel"
+            bioc-version: "devel"
+          # Bioconductor release tracks the current R release
+          - os: ubuntu-latest
+            r-version: "release"
+            bioc-version: "release"
+          - os: macos-latest
+            r-version: "release"
+            bioc-version: "release"
+          - os: windows-latest
+            r-version: "release"
+            bioc-version: "release"
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.r-version }}
+          use-public-rspm: true
+
+      - name: Setup Pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      # System dependencies (Linux)
+      - name: Install system dependencies (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update -qq
+          sudo apt-get install -y --no-install-recommends \
+            libcurl4-openssl-dev \
+            libssl-dev \
+            libxml2-dev \
+            libglpk-dev
+
+      # Install dependencies using r-lib/actions (uses pak, handles R-devel well)
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::BiocCheck
+            any::rcmdcheck
+
+      # Setup Python for reticulate (cross-platform)
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Install Python packages
+        run: |
+          pip install --upgrade pip
+          pip install numpy scipy pandas
+        shell: bash
+
+      - name: Set RETICULATE_PYTHON
+        run: |
+          echo "RETICULATE_PYTHON=$(python -c 'import sys; print(sys.executable)')" >> $GITHUB_ENV
+        shell: bash
+
+      # R CMD build (mirrors BBS: build step)
+      - name: Build package
+        run: |
+          R CMD build . --no-build-vignettes
+        shell: bash
+
+      # R CMD check (mirrors BBS: check step with --no-vignettes)
+      - name: R CMD check
+        run: |
+          pkg=$(ls -1 netZooR_*.tar.gz)
+          R CMD check "$pkg" \
+            --no-manual \
+            --no-vignettes \
+            --timings \
+            --install-args="--build"
+        shell: bash
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+          _R_CHECK_FORCE_SUGGESTS_: false
+
+      - name: Show check results
+        if: always()
+        run: |
+          cat netZooR.Rcheck/00check.log
+        shell: bash
+
+      # BiocCheck (mirrors BBS: BiocCheck step)
+      - name: BiocCheck
+        run: |
+          library(BiocCheck)
+          BiocCheck(".", `no-check-vignettes` = TRUE, `new-package` = FALSE)
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: check-results-${{ matrix.os }}-R${{ matrix.r-version }}
+          path: netZooR.Rcheck/
+
+  # Separate test job with coverage
+  test-coverage:
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: "release"
+          use-public-rspm: true
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update -qq
+          sudo apt-get install -y --no-install-recommends \
+            libcurl4-openssl-dev libssl-dev libxml2-dev libglpk-dev
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::covr
+
+      - name: Test coverage
+        run: |
+          covr::codecov(quiet = FALSE)
+        shell: Rscript {0}
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/main.yml

@@ -9,7 +9,6 @@
 name: netZooR
 
 env:
-    ACTIONS_ALLOW_UNSECURE_COMMANDS: 'true'
     GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
@@ -28,8 +27,9 @@ jobs:
     runs-on: ${{ matrix.os }}
     timeout-minutes: 300
     strategy:
+      fail-fast: false
       matrix:
-        os: [ubuntu-latest]
+        os: [ubuntu-latest, macos-latest, windows-latest]
         r-version: [4.4]
 
     steps:
@@ -50,35 +50,27 @@ jobs:
         with:
           cache-version: 2
           extra-packages: |
-             any::reticulate
              any::rcmdcheck
              any::covr
           needs: |
              website
              coverage
 
-      - name: Install blas/lapack
-        run: |
-            La_library()
-            extSoftVersion()["BLAS"]
-        shell: Rscript {0}
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
 
-      - if: matrix.os == 'ubuntu-latest'
+      - name: Install Python packages
         run: |
-          sudo apt-get install python3-venv
           pip install --upgrade pip
-          python3 -m venv env
-          source env/bin/activate
-          echo "VIRTUAL ENV:" $VIRTUAL_ENV
-  
-      - name: Install reticulate
+          pip install numpy scipy pandas joblib
+        shell: bash
+
+      - name: Set RETICULATE_PYTHON
         run: |
-            library("reticulate")
-            py_install("numpy")
-            py_install("scipy")
-            py_install("pandas")
-            py_install("joblib")
-        shell: Rscript {0}
+          echo "RETICULATE_PYTHON=$(python -c 'import sys; print(sys.executable)')" >> $GITHUB_ENV
+        shell: bash
 
       - name: Check
         uses: r-lib/actions/check-r-package@v2.11.3

.gitignore

@@ -36,3 +36,4 @@ docs/*.npy
 docs/reference/*.npy
 bladder.rdata
 skin.rdata
+netZooR.code-workspace

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: netZooR
 Type: Package
-Title: A menagerie of Methods for the inference and analysis of gene regulatory networks
+Title: A Menagerie of Methods for the Inference and Analysis of Gene Regulatory Networks
 Version: 1.6.3
-Date: 2024-11-26
+Date: 2026-02-19
 Authors@R: c(person("Tara", "Eicher",
                         email = "teicher@hsph.harvard.edu", role = c("aut"), comment = c(ORCID = "0000-0003-1809-4458")),
              person("Marouen", "Ben Guebila",
@@ -23,15 +23,23 @@ Authors@R: c(person("Tara", "Eicher",
                         email = "",role = "aut", comment = c(ORCID = "0000-0002-8042-7201")),
              person("Kate", "Shutta",
                         email = "",role = "aut", comment = c(ORCID = "0000-0003-0402-3771")))
-Description: netZooR unifies the implementations of several Network Zoo methods (netzoo, netzoo.github.io) into a single package by creating interfaces between network inference and network analysis methods. Currently, the package has 3 methods for network inference including PANDA and its optimized implementation OTTER (network reconstruction using mutliple lines of biological evidence), LIONESS (single-sample network inference), and EGRET (genotype-specific networks). Network analysis methods include CONDOR (community detection), ALPACA (differential community detection), CRANE (significance estimation of differential modules), MONSTER (estimation of network transition states). In addition, YARN allows to process gene expresssion data for tissue-specific analyses and SAMBAR infers missing mutation data based on pathway information.
+Description: Unifies the implementations of several Network Zoo methods
+    (netzoo, netzoo.github.io) into a single package by creating interfaces
+    between network inference and network analysis methods. Currently, the
+    package has 3 methods for network inference including PANDA and its
+    optimized implementation OTTER (network reconstruction using multiple
+    lines of biological evidence), LIONESS (single-sample network inference),
+    and EGRET (genotype-specific networks). Network analysis methods include
+    CONDOR (community detection), ALPACA (differential community detection),
+    CRANE (significance estimation of differential modules), MONSTER
+    (estimation of network transition states). In addition, YARN allows to
+    process gene expression data for tissue-specific analyses and SAMBAR
+    infers missing mutation data based on pathway information.
 Depends: R (>= 4.2.0),
    igraph,
-	 reticulate,
-	 pandaR,
+   reticulate,
+   pandaR,
    Biobase
-Remotes: 
-	 stan-dev/cmdstanr,
-	 jnpaulson/pandaR, 
 biocViews:
 	 NetworkInference,
 	 Network,
@@ -41,36 +49,44 @@ biocViews:
          Microarray,   
          GraphAndNetwork
 Imports:
+    matrixStats,
+    Matrix,
+    stats,
+    utils,
+    methods,
+    graphics,
+    parallel,
+    doParallel,
+    foreach,
+    reshape,
+    MASS,
+    data.table
+License: GPL-3
+Encoding: UTF-8
+LazyData: false
+Suggests: 
+    testthat (>= 2.1.0),
+    knitr,
+    rmarkdown,
+    pkgdown,
     viridisLite,
     STRINGdb,
     GOstats,
     AnnotationDbi,
-    matrixStats,
     GO.db,
     org.Hs.eg.db,
-    Matrix,
     matrixTests,
     gplots,
     nnet,
-    data.table,
     vegan,
-    stats,
-    utils,
-    reshape,
     reshape2,
     penalized,
-    parallel,
-    doParallel,
-    foreach,
     ggplot2,
     ggdendro,
     grid,
-    MASS,
     assertthat,
     tidyr,
-    methods,
     dplyr,
-    graphics,
     GeneNet,
     loo,
     rARPACK,
@@ -83,19 +99,8 @@ Imports:
     readr,
     RColorBrewer,
     quantro,
-    matrixcalc,
     fgsea
-License: GPL-3
-Encoding: UTF-8
-LazyData: false
-Suggests: 
-    testthat (>= 2.1.0),
-    knitr,
-    rmarkdown,
-    pkgdown,
-    dorothea,
-    cmdstanr
-VignetteEngine: knitr
+Remotes: jnpaulson/pandaR
 VignetteBuilder: knitr
 RoxygenNote: 7.3.3
 BugReports: https://github.com/netZoo/netZooR/issues