Update maaslin2 to latest version

.github/pull_request_template.md

@@ -0,0 +1,14 @@
+We welcome feedback and issue reporting for all bioBakery tools through our [Discourse site](https://forum.biobakery.org/c/pull-request/featurepull-request/). For users that would like to directly contribute to the [tools](https://github.com/biobakery/) we are happy to field PRs to address **bug fixes**. Please note the turn around time on our end might be a bit long to field these but that does not mean we don't value the contribution! We currently **don't** accept PRs to add **new functionality** to tools but we would be happy to receive your feedback on [Discourse](https://forum.biobakery.org/c/pull-request/featurepull-request/).
+
+Also, we will make sure to attribute your contribution in our User’s manual(README.md) and in any associated paper Acknowledgements.
+
+
+## Description
+<!--- Describe your changes in detail -->
+
+## Related Issue
+<!--- If fixing a bug, there should be an issue describing it with steps to reproduce -->
+<!--- Please link to the issue here: -->
+
+
+## Screenshots (if appropriate):

.github/workflows/main.yml

@@ -1,42 +1,180 @@
+## Read more about GitHub actions the features of this GitHub Actions workflow
+## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action
+##
+## For more details, check the biocthis developer notes vignette at
+## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html
+##
+## You can add this workflow to other packages using:
+## > biocthis::use_bioc_github_action()
+##
+## Using GitHub Actions exposes you to many details about how R packages are
+## compiled and installed in several operating system.s
+### If you need help, please follow the steps listed at
+## https://github.com/r-lib/actions#where-to-find-help
+##
+## If you found an issue specific to biocthis's GHA workflow, please report it
+## with the information that will make it easier for others to help you.
+## Thank you!
 
-name: build and test
+## Acronyms:
+## * GHA: GitHub Action
+## * OS: operating system
 
-# Controls when the action will run. Triggers the workflow on push or pull request
-# events but only for the master branch
 on:
   push:
-    branches: [ master ]
   pull_request:
-    branches: [ master ]
+
+name: build and test
+
+env:
+  has_testthat: 'true'
 
 jobs:
-  build:
-    runs-on: ubuntu-latest
-    container:
-      image: biobakery/maaslin2:latest
+  build-check:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    ## Environment variables unique to this job.
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: ubuntu-latest, cont: "bioconductor/bioconductor_docker" }
+          - { os: macOS-latest }
+          - { os: windows-latest }
+          ## Check https://github.com/r-lib/actions/tree/master/examples
+          ## for examples using the http-user-agent
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      NOT_CRAN: true
+      TZ: UTC
 
     steps:
-    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-    - uses: actions/checkout@v2
+      ## Most of these steps are the same as the ones in
+      ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
+      ## If they update their steps, we will also need to update ours.
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+
+      ## R is already included in the Bioconductor docker images
+      - name: Setup R from r-lib
+        if: runner.os != 'Linux'
+        uses: r-lib/actions/setup-r@v2
+
+      ## pandoc is already included in the Bioconductor docker images
+      - name: Setup pandoc from r-lib
+        if: runner.os != 'Linux'
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Install Linux system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          apt-get update -y && apt-get install -y make cmake libicu-dev zlib1g-dev pandoc
+
+      - name: Install macOS system dependencies
+        if: matrix.config.os == 'macOS-latest'
+        run: |
+          ## Enable installing XML from source if needed
+          brew install libxml2
+          echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
+
+          ## Required to install magick as noted at
+          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
+          brew install imagemagick@6
+
+          ## For textshaping, required by ragg, and required by pkgdown
+          brew install harfbuzz fribidi
+
+          ## For installing usethis's dependency gert
+          brew install libgit2
+
+          ## Required for tcltk
+          brew install xquartz --cask
+
+      - name: Install Windows system dependencies
+        if: runner.os == 'Windows'
+        run: |
+          ## Edit below if you have any Windows system dependencies
+        shell: Rscript {0}
+
+      - name: Install BiocManager
+        run: |
+          message(paste('****', Sys.time(), 'installing BiocManager ****'))
+          remotes::install_cran("BiocManager")
+        shell: Rscript {0}
+
+      - name: Set BiocVersion
+        run: |
+          BiocManager::install(force = TRUE, ask = FALSE)
+        shell: Rscript {0}
+
+      - name: Install dependencies pass 1
+        run: |
+          ## Try installing the package dependencies in steps. First the local
+          ## dependencies, then any remaining dependencies to avoid the
+          ## issues described at
+          ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
+          ## https://github.com/r-lib/remotes/issues/296
+          ## Ideally, all dependencies should get installed in the first pass.
+
+          ## For running the checks
+          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
+          install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())
 
-    - name: Install build and test dependencies from dist
-      run: apt-get update -y && apt-get install -y libssl-dev libxml2-dev libcurl4-openssl-dev texlive
+          ## Pass #1 at installing dependencies
+          message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
+        continue-on-error: true
+        shell: Rscript {0}
 
-    - name: install build and test dependencies from bioconductor
-      run: R -q -e "BiocManager::install('BiocCheck')"
+      - name: Install dependencies pass 2
+        run: |
+          ## Pass #2 at installing dependencies
+          message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
+        shell: Rscript {0}
 
-    - name: Install build and test dependencies from CRAN
-      run: R -q -e "install.packages(c('knitr','glmmTMB'), repos='http://cran.r-project.org')" 
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
 
-    - name: Build
-      run: cd $GITHUB_WORKSPACE && R CMD build .
+      - name: Run CMD check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+          DISPLAY: 99.0
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(
+              args = c("--no-manual", "--no-vignettes", "--timings"),
+              build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
+              error_on = "warning",
+              check_dir = "check"
+          )
+        shell: Rscript {0}
 
-    - name: Install maaslin2
-      run: VERSION=$(grep Version DESCRIPTION | cut -d" " -f2) && R CMD INSTALL "Maaslin2_${VERSION}.tar.gz"
+      ## Might need an to add this to the if:  && runner.os == 'Linux'
+      - name: Reveal testthat details
+        if:  env.has_testthat == 'true'
+        run: find . -name testthat.Rout -exec cat '{}' ';'
 
-    - name: R test
-      run: VERSION=$(grep Version DESCRIPTION | cut -d" " -f2) && R CMD check "Maaslin2_${VERSION}.tar.gz"
-
-    - name: Bioc test
-      run: VERSION=$(grep Version DESCRIPTION | cut -d" " -f2) && R CMD BiocCheck "Maaslin2_${VERSION}.tar.gz"
-
+      - name: Run BiocCheck
+        env:
+          DISPLAY: 99.0
+        run: |
+          BiocCheck::BiocCheck(
+              dir('check', 'tar.gz$', full.names = TRUE),
+              `quit-with-status` = TRUE,
+              `no-check-R-ver` = TRUE,
+              `no-check-bioc-help` = TRUE
+          )
+        shell: Rscript {0}

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Maaslin2
 Title: "Multivariable Association Discovery in Population-scale Meta-omics Studies"
 Year: 2021
-Version: 1.15.0
+Version: 1.7.4
 Authors@R: c(
   person("Himel", "Mallick", email = "[email protected]", role = "aut"), 
   person("Ali", "Rahnavard", email = "[email protected]", role = "aut"),
@@ -11,11 +11,12 @@ Depends: R (>= 3.6)
 Description: MaAsLin2 is comprehensive R package for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. MaAsLin2 is the next generation of MaAsLin.
 License: MIT + file LICENSE
 LazyData: false
-Imports: robustbase, biglm, pcaPP, edgeR, metagenomeSeq, lpsymphony, pbapply, car, dplyr, vegan, chemometrics, ggplot2, pheatmap, logging, data.table, lmerTest, hash, optparse, grDevices, stats, utils, glmmTMB, MASS, cplm, pscl, lme4
+Imports: robustbase, biglm, pcaPP, edgeR, metagenomeSeq, pbapply, car, dplyr, vegan, chemometrics, ggplot2, pheatmap, logging, data.table, lmerTest, hash, optparse, grDevices, stats, utils, glmmTMB, MASS, cplm, pscl, lme4, tibble
 Suggests: 
     knitr,
     testthat (>= 2.1.0),
-    rmarkdown
+    rmarkdown, 
+    markdown
 VignetteBuilder: knitr
 Collate: fit.R utility_scripts.R viz.R  Maaslin2.R
 URL: http://huttenhower.sph.harvard.edu/maaslin2

NAMESPACE

@@ -3,11 +3,11 @@ export(Maaslin2)
 import("robustbase")
 import("biglm")
 import("pcaPP")
-import("lpsymphony")
 import("optparse")
 importFrom("grDevices", "colorRampPalette", "dev.off", "pdf", "jpeg","png")
 importFrom("stats", "as.formula", "coef", "glm", "lm", "na.exclude",
-    "p.adjust", "update")
+    "p.adjust", "update", "relevel")
 importFrom("utils", "capture.output", "read.table", "write.table")
 importFrom("dplyr", "%>%")
 importFrom("stats", "sd", "na.omit")
+importFrom("utils","type.convert")

NEWS

@@ -1,3 +1,10 @@
+Changes in version 1.7.3 (11-02-2021):
+* Update sourcing R scripts 
+* Update reference level handling
+* Update example files
+* Fix saved plots to allow for runs with less then N plots per metadata
+* Convert strings to numeric when needed for metadata
+* Fix actions to build with latest version of dependencies
 
 Changes in version 1.7.1 (07-27-2021):
 * Update tutorial data files