dynverse · rcannood · Feb 23, 2021 · Jul 17, 2020 · Aug 8, 2020 · Aug 8, 2020
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,22 +1,22 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^\.travis
 ^\.git$
 ^_pkgdown\.yml$
 ^data-raw$
 ^docs$
-^appveyor\.yml$
 ^README\.Rmd$
-^example_script\.R$
-^scripts_tmp
-^LICENSE\.md$
 ^LICENSE\.md$
 ^man/figures/logo\.svg$
 ^man/figures/Arte_De_athletica_2b\.jpg$
 ^man/figures/dependencies\.png$
 ^\.github$
 ^docker$
+^vignettes/advanced_topics$
 ^vignettes/.*\.md$
-^vignettes/.*/.*\.png$
-^vignettes/getting_started.Rmd$
-^vignettes/showcase_backbones.Rmd$
+^vignettes/.*_files$
+^vignettes/.*.Rmd$
+^vignettes/.*.R$
+^vignettes/scalability_and_runtime_runs$
+^vignettes/showcase_backbones
+^cran-comments\.md$
+^pkgdown$
diff --git a/.github/.gitignore b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/docker_build.yml b/.github/workflows/docker_build.yml
@@ -0,0 +1,38 @@
+on:
+  push:
+    branches:
+      - master
+      - devel
+  schedule:
+    - cron: "0 0 * * 1"
+
+name: docker_build
+
+jobs:
+  build_containers:
+    runs-on: 'ubuntu-latest'
+    if: "!contains(github.event.head_commit.message, 'ci skip')"
+    name: build container
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Build
+        run: |
+          VERSION=`cat DESCRIPTION | grep Version | sed 's#.*: ##'`
+          BRANCH="${GITHUB_REF#refs/heads/}"
+          docker build -t $GITHUB_REPOSITORY:$BRANCH -f docker/Dockerfile .
+          if [[ $BRANCH == "master" ]] ; then
+            docker tag $GITHUB_REPOSITORY:$BRANCH $GITHUB_REPOSITORY:$VERSION
+            docker tag $GITHUB_REPOSITORY:$BRANCH $GITHUB_REPOSITORY:latest
+          fi
+
+      - name: Push
+        run: |
+          docker login -u ${{ secrets.DOCKER_USERNAME }} -p ${{ secrets.DOCKER_PASSWORD }}
+          BRANCH="${GITHUB_REF#refs/heads/}"
+          docker push $GITHUB_REPOSITORY:$BRANCH
+          if [[ $BRANCH == "master" ]] ; then
+            docker push $GITHUB_REPOSITORY:$VERSION
+            docker push $GITHUB_REPOSITORY:latest
+          fi
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,51 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          install.packages("pkgdown", type = "binary")
+          install.packages("tidyverse", type = "binary")
+          remotes::install_github('dynverse/dyno')
+          remotes::install_bioc('countsimQC')
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
diff --git a/.github/workflows/r_cmd_check.yml b/.github/workflows/r_cmd_check.yml
@@ -21,8 +21,8 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macos-latest, r: 'release'}
-          - {os: ubuntu-16.04, r: '3.5', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04, r: '3.6', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+          # - {os: ubuntu-16.04, r: '3.5', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"} # disable 3.5 due to SCE
+          # - {os: ubuntu-16.04, r: '3.6', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"} # disable 3.6 due to Seurat >_>
           - {os: ubuntu-16.04, r: 'release', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
 
     env:
@@ -64,6 +64,8 @@ jobs:
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
+          reticulate::install_miniconda()
+          anndata::install_anndata()
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 

diff --git a/.github/workflows/test_coverage.yml b/.github/workflows/test_coverage.yml
@@ -45,6 +45,8 @@ jobs:
         run: |
           install.packages(c("remotes"))
           remotes::install_deps(dependencies = TRUE)
+          reticulate::install_miniconda()
+          anndata::install_anndata()
           remotes::install_cran("covr")
         shell: Rscript {0}
 

diff --git a/.gitignore b/.gitignore
@@ -6,3 +6,4 @@
 .httr-oauth
 inst/doc
 scripts_tmp
+docs
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,11 +2,11 @@ Type: Package
 Package: dyngen
 Title: A Multi-Modal Simulator for Spearheading Single-Cell
     Omics Analyses
-Version: 0.4.0
+Version: 1.0.0
 Authors@R: 
     c(person(given = "Robrecht",
              family = "Cannoodt",
-             role = c("aut", "cre"),
+             role = c("aut", "cre", "cph"),
              email = "rcannood@gmail.com",
              comment = c(ORCID = "0000-0003-3641-729X")),
       person(given = "Wouter",
@@ -15,21 +15,20 @@ Authors@R:
              email = "wouter.saelens@ugent.be",
              comment = c(ORCID = "0000-0002-7114-6248")))
 Description: A novel, multi-modal simulation engine for
-    studying dynamic cellular processes at single-cell resolution. dyngen
+    studying dynamic cellular processes at single-cell resolution. 'dyngen'
     is more flexible than current single-cell simulation engines. It
     allows better method development and benchmarking, thereby stimulating
     development and testing of novel computational methods. Cannoodt et
     al. (2020) <doi:10.1101/2020.02.06.936971>.
 License: MIT + file LICENSE
-URL: https://github.com/dynverse/dyngen
+URL: https://dyngen.dynverse.org, https://github.com/dynverse/dyngen
 BugReports: https://github.com/dynverse/dyngen/issues
 Depends:
     R (>= 3.5.0)
 Imports:
     assertthat,
     dplyr,
     dynutils (>= 1.0.4),
-    furrr,
     ggplot2,
     ggraph (>= 2.0),
     ggrepel,
@@ -51,15 +50,18 @@ Imports:
     utils,
     viridis
 Suggests:
+    anndata,
     covr,
     dynwrap (>= 1.2.0),
-    knitr,
     R.rsp,
     rmarkdown,
+    Seurat,
+    SingleCellExperiment (>= 1.5.3),
+    SummarizedExperiment,
     testthat
 VignetteBuilder: 
-    knitr,
     R.rsp
+biocViews:
 Encoding: UTF-8
 LazyData: TRUE
 Roxygen: list(markdown = TRUE)

diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2014-2020
-COPYRIGHT HOLDER: Robrecht Cannoodt, Wouter Saelens
+YEAR: 2014-2021
+COPYRIGHT HOLDER: Robrecht Cannoodt
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2014-2020 Robrecht Cannoodt, Wouter Saelens
+Copyright (c) 2014-2021 Robrecht Cannoodt
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
+export("%>%")
+export(as_anndata)
+export(as_dyno)
+export(as_list)
+export(as_sce)
+export(as_seurat)
 export(backbone)
 export(backbone_bifurcating)
 export(backbone_bifurcating_converging)
@@ -20,6 +26,7 @@ export(bblego_branching)
 export(bblego_end)
 export(bblego_linear)
 export(bblego_start)
+export(combine_models)
 export(experiment_snapshot)
 export(experiment_synchronised)
 export(feature_network_default)
@@ -30,6 +37,7 @@ export(generate_feature_network)
 export(generate_gold_standard)
 export(generate_kinetics)
 export(generate_tf_network)
+export(get_timings)
 export(gold_standard_default)
 export(initialise_model)
 export(kinetics_default)
@@ -40,6 +48,7 @@ export(list_experiment_samplers)
 export(ode_em)
 export(plot_backbone_modulenet)
 export(plot_backbone_statenet)
+export(plot_experiment_dimred)
 export(plot_feature_network)
 export(plot_gold_expression)
 export(plot_gold_mappings)
@@ -67,6 +76,7 @@ importFrom(Matrix,summary)
 importFrom(Matrix,t)
 importFrom(assertthat,"%has_name%")
 importFrom(assertthat,assert_that)
+importFrom(dplyr,.data)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
@@ -100,10 +110,12 @@ importFrom(dynutils,add_class)
 importFrom(dynutils,extend_with)
 importFrom(dynutils,extract_row_to_list)
 importFrom(dynutils,is_sparse)
-importFrom(furrr,future_map)
 importFrom(ggplot2,aes)
+importFrom(ggplot2,aes_string)
 importFrom(ggplot2,coord_equal)
+importFrom(ggplot2,coord_flip)
 importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,geom_bar)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_path)
 importFrom(ggplot2,geom_point)
@@ -113,8 +125,12 @@ importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggsave)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,scale_colour_manual)
+importFrom(ggplot2,scale_fill_brewer)
+importFrom(ggplot2,scale_linetype_manual)
 importFrom(ggplot2,scale_size_manual)
+importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
+importFrom(ggplot2,theme_classic)
 importFrom(ggraph,circle)
 importFrom(ggraph,geom_edge_fan)
 importFrom(ggraph,geom_edge_loop)
@@ -139,7 +155,9 @@ importFrom(lmds,lmds)
 importFrom(methods,as)
 importFrom(methods,is)
 importFrom(patchwork,plot_annotation)
+importFrom(patchwork,plot_layout)
 importFrom(patchwork,wrap_plots)
+importFrom(pbapply,pblapply)
 importFrom(pbapply,setTimerProgressBar)
 importFrom(pbapply,timerProgressBar)
 importFrom(purrr,"%>%")
@@ -153,6 +171,7 @@ importFrom(purrr,map_int)
 importFrom(purrr,pmap)
 importFrom(purrr,set_names)
 importFrom(rlang,"%|%")
+importFrom(rlang,"%||%")
 importFrom(stats,approx)
 importFrom(stats,approxfun)
 importFrom(stats,density)
@@ -164,6 +183,7 @@ importFrom(stats,rmultinom)
 importFrom(stats,rnorm)
 importFrom(stats,runif)
 importFrom(tibble,as_tibble)
+importFrom(tibble,column_to_rownames)
 importFrom(tibble,deframe)
 importFrom(tibble,enframe)
 importFrom(tibble,lst)