Merge pull request #633 from cole-trapnell-lab/develop

Develop

.github/CODEOWNERS

@@ -0,0 +1,3 @@
+/.github/CODEOWNERS @ctrapnell @hpliner @brgew
+/.github/workflows/* @ctrapnell @hpliner @brgew
+/src/docker/* @ctrapnell @hpliner @brgew

.github/workflows/check_on_push.yml

@@ -0,0 +1,125 @@
+#
+# Check Monocle3 repository on push event.
+# 
+# There is information on Docker container security at
+#   URL: https://docs.docker.com/engine/security/
+#   URL: https://cheatsheetseries.owasp.org/cheatsheets/Docker_Security_Cheat_Sheet.html
+#   Note: I don't see how one can specify the 'user' for the
+#         Actions runs so I don't see the value of creating
+#         a non-root user when the container is built.
+# There is information on Github Actions security at
+#   URL: https://docs.github.com/en/actions/security-guides/security-hardening-for-github-actions
+#   URL: https://blog.gitguardian.com/github-actions-security-cheat-sheet/
+# This Github Actions page notes:
+#   o  Using CODEOWNERS to monitor changes: specifically changes to.github/workflows/*
+#   o  Preventing GitHub Actions from creating or approving pull requests
+# Security notes:
+#   o  secure the docker container against meddling
+#   o  secure the monocle3 repository against meddling
+#
+name: Monocle3 check on push
+run-name: Check branch ${{ github.ref_name }} on push by ${{ github.actor }}
+
+on: [push]
+
+jobs:
+  monocle3_check_on_push:
+
+    # Notes: ubuntu.
+    #   o use Ubuntu - there are messages on line about needing to use Ubuntu
+    #                  for use with Github Actions.
+    #   o use a Docker container that has the Monocle3 dependencies installed.
+    #     see 'github.com:cole-trapnell-lab/monocle3/src/docker/NOTES' and
+    #         'github.com:cole-trapnell-lab/Docker//monocle3_depend/NOTES'.
+    #   o Github Actions has a limited variety of Linux runners. See
+    #       URL: https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
+    runs-on: ubuntu-latest
+
+    # One can add fine-grain-control over GITHUB_TOKEN permissions but
+    # I have not found authoratative descriptions of the permissions
+    # targets. www pages have some information
+    #   URL: https://github.blog/changelog/2021-04-20-github-actions-control-permissions-for-github_token/
+    #   URL: https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#permissions
+    # permissions:
+    #   actions: read|write|none
+    #   checks: read|write|none
+    #   contents: read|write|none
+    #   deployments: read|write|none
+    #   id-token: read|write|none
+    #   issues: read|write|none
+    #   discussions: read|write|none
+    #   packages: read|write|none
+    #   pages: read|write|none
+    #   pull-requests: read|write|none
+    #   repository-projects: read|write|none
+    #   security-events: read|write|none
+    #   statuses: read|write|none
+
+    container:
+      # Note:
+      #   in order for the GITHUB_TOKEN to work as a credential one must
+      #   allow the Monocle3 repository to access the container 'package'.
+      #   Navigate to the Packages tab -> <repository> tab -> Package settings ->
+      #   Manage Actions access: click on Add Repository; give repository name
+      #
+      # The following Docker image was pushed initially to the Docker container
+      # but we use now the Github container registry. The following image and
+      # credential lines are here for documentation, if require in the future.
+      # image: docker.io/brgew/monocle3_depend:v1.3.0
+      #
+      # The following three (commented out) lines give credentials for a docker
+      # image stored at the Docker container registry.
+      # credentials:
+      #   username: brgew
+      #   password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN_READ }}
+      #
+
+
+      # The following Docker image was pushed to the Github container registry,
+      # which is found at the Github Packages tab.
+      # image: ghcr.io/cole-trapnell-lab/monocle3_depend.v1.3.0_20221103:v1 # old and replaced
+      image: ghcr.io/cole-trapnell-lab/monocle3_depend:v1.3.0_1
+
+      #
+      #
+      # The following three uncommented lines give credentials for a Github
+      # container registry. There is information about github.ACTOR at
+      #   URL: https://docs.github.com/en/actions/learn-github-actions/contexts
+      # where there is the statement
+      # github.actor	string	The username of the user that triggered the
+      #                         initial workflow run. If the workflow run is
+      #                         a re-run, this value may differ from
+      #                         github.triggering_actor. Any workflow re-runs
+      #                         will use the privileges of github.actor, even
+      #                         if the actor initiating the re-run
+      #                         (github.triggering_actor) has different
+      #                         privileges.
+      credentials:
+        username: ${{ github.ACTOR }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+
+    # TRAVIS: the testthat scripts check for the TRAVIS environment variable
+    # in order to choose the correct set of target values and to avoid
+    # running interactive code. For convenience, I keep the name TRAVIS after
+    # switching to  Actions CI.
+    # _R_CHECK_TESTS_NLINES_: instruct the devtools::test scripts to output all
+    # error lines rather than the last 13. See
+    # https://yihui.org/en/2017/12/last-13-lines-of-output/
+    env:
+      TRAVIS: true
+      _R_CHECK_TESTS_NLINES_: 0
+
+    steps:
+      # Get current repository contents.
+      - uses: actions/checkout@v3
+      # Run tests.
+      # Notes:
+      #   o  the RCMD check command appears to not output the regression tests
+      #      output unless an error occurs, in which case, the output of all
+      #       regressions tests is output.
+      - name: Run R CMD build and R CMD check
+        run: |
+          R CMD build .
+          R CMD check monocle3*tar.gz
+        shell: bash
+

.travis.yml → 00travis.yml

@@ -15,18 +15,18 @@ cache: packages
 sudo: required
 warnings_are_errors: true
 os: linux
-dist: xenial
+dist: focal
 language: r
 before_install:
  - sudo apt-get install -y libnlopt-dev
  - sudo apt-get install -y libudunits2-dev
  - sudo apt-get install -y gdal-bin
- - sudo apt-get install -y libgdal1-dev
+ - sudo apt-get install -y libgdal-dev
  - sudo apt-get install -y libharfbuzz-dev
  - sudo apt-get install -y libfribidi-dev
  - sudo apt-get install -y libgit2-dev
  - sudo wget -qO - https://apt.kitware.com/keys/kitware-archive-latest.asc | sudo apt-key add -
- - sudo apt-add-repository 'deb https://apt.kitware.com/ubuntu/ xenial main'
+ - sudo apt-add-repository 'deb https://apt.kitware.com/ubuntu/ jammy main'
  - sudo apt-get update
  - sudo apt-get install -y cmake
 r:
@@ -50,6 +50,7 @@ script:
     export _R_CHECK_DONTTEST_EXAMPLES_=false
     R CMD build .
     export PKG_TARBALL=$(Rscript -e 'pkg <- devtools::as.package("."); cat(paste0(pkg$package,"_",pkg$version,".tar.gz"))')
+    export TESTTHAT_MAX_FAILS=Inf
     if [ ! -f "$PKG_TARBALL" ]; then exit 1; fi
     travis_wait 20 R CMD check monocle3*tar.gz
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: monocle3
-Title: Clustering, differential expression, and trajectory analysis for single-
-    cell RNA-Seq
-Version: 1.2.9
+Title: Clustering, Differential Expression, and Trajectory Analysis for
+    Single-Cell RNA-Seq
+Version: 1.3.1
 Authors@R: c(
     person(given = "Hannah",
            family = "Pliner",
@@ -46,7 +46,7 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: false
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 LinkingTo: 
     Rcpp
 Depends:
@@ -76,7 +76,6 @@ Imports:
     lmtest (>= 0.9-36),
     MASS (>= 7.3-51.4),
     Matrix (>= 1.2-17),
-    Matrix.utils,
     methods,
     openssl,
     pbapply (>= 1.4-0),
@@ -108,7 +107,6 @@ Imports:
     uwot (>= 0.1.8),
     terra (>= 1.4-17),
     tibble (>= 2.1.1),
-    tictoc,
     tidyr (>= 0.8.3),
     viridis (>= 0.5.1)
 Suggests: 
@@ -120,3 +118,6 @@ Suggests:
     scran
 VignetteBuilder: knitr
 Language: en-US
+NeedsCompilation: yes
+Packaged: 2022-05-10 17:21:53 UTC; brent
+Maintainer: Brent Ewing <bge@uw.edu>

NAMESPACE

@@ -102,6 +102,7 @@ importFrom(SummarizedExperiment,Assays)
 importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,rowRanges)
 importFrom(dplyr,"%>%")
+importFrom(dplyr,n)
 importFrom(future,value)
 importFrom(igraph,dfs)
 importFrom(lme4,glmer)

NEWS.md

@@ -1,3 +1,13 @@
+# Monocle3 1.3.0
+
+### Changes
+
+* Work around conflict between SingleCellExperiment and tictoc packages.
+* Fix missing DelayedArray conversion in sparse_prcomp_irlba().
+* Relax test for rowname consistency in transfer_cell_labels().
+* Update URLs in load_worm_*() functions.
+* Minor bug fixes.
+
 # Monocle3 1.2.9
 
 ### Changes

R/cluster_cells.R

@@ -61,7 +61,7 @@
 #'   Cell, 2015.
 #'
 #' @examples
-#'   \donttest{ 
+#'   \donttest{
 #'     cell_metadata <- readRDS(system.file('extdata',
 #'                                          'worm_embryo/worm_embryo_coldata.rds',
 #'                                          package='monocle3'))
@@ -71,7 +71,7 @@
 #'     expression_matrix <- readRDS(system.file('extdata',
 #'                                  'worm_embryo/worm_embryo_expression_matrix.rds',
 #'                                  package='monocle3'))
-#'    
+#'
 #'     cds <- new_cell_data_set(expression_data=expression_matrix,
 #'                              cell_metadata=cell_metadata,
 #'                              gene_metadata=gene_metadata)
@@ -354,7 +354,7 @@ louvain_clustering <- function(data,
                                            weight=weight,
                                            cell_names=cell_names,
                                            nn_index,
-                                           k=k, 
+                                           k=k,
                                            nn_control=nn_control,
                                            verbose=verbose)
 
@@ -471,7 +471,7 @@ leiden_clustering <- function(data,
     stop("Phenotype and row name from the data don't match")
 
   graph_result <- cluster_cells_make_graph(data=data,
-                                           weight=weight, 
+                                           weight=weight,
                                            cell_names=cell_names,
                                            nn_index,
                                            k=k,
@@ -622,6 +622,7 @@ compute_partitions <- function(g,
                         ncol=length(louvain_modules))
 
   sig_links <- as.matrix(num_links)
+  row.names(sig_links) = colnames(sig_links) = louvain_modules
   sig_links[cluster_mat > qval_thresh] = 0
   diag(sig_links) <- 0