update various issues in preparation for release

Author: rcannood

.github/workflows/R-CMD-check.yaml

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -29,7 +30,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v5
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -47,3 +48,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/test-coverage.yaml

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,36 +16,47 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v5
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v5
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -5,21 +5,21 @@ Description: Provides functionality to infer trajectories from single-cell data,
   represent them into a common format, and adapt them. Other biological information
   can also be added, such as cellular grouping, RNA velocity and annotation.
   Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.
-Version: 1.2.4
+Version: 1.2.5
 Authors@R: c(
     person(
       "Robrecht", 
       "Cannoodt", 
       email = "rcannood@gmail.com", 
       role = c("aut", "cre"),
-      comment = c(ORCID = "0000-0003-3641-729X", github = "rcannood")
+      comment = c(ORCID = "0000-0003-3641-729X")
     ),
     person(
       "Wouter", 
       "Saelens", 
       email = "wouter.saelens@gmail.com", 
       role = c("aut"), 
-      comment = c(ORCID = "0000-0002-7114-6248", github = "zouter")
+      comment = c(ORCID = "0000-0002-7114-6248")
     )
   )
 URL: https://github.com/dynverse/dynwrap

README.Rmd

@@ -14,7 +14,7 @@ library(tidyverse)
 ```
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/dynverse/dynwrap/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/dynverse/dynwrap/actions/workflows/R-CMD-check.yaml)
-[![Codecov test coverage](https://codecov.io/gh/dynverse/dynwrap/branch/master/graph/badge.svg)](https://app.codecov.io/gh/dynverse/dynwrap?branch=master)
+[![Codecov test coverage](https://codecov.io/gh/dynverse/dynwrap/graph/badge.svg)](https://app.codecov.io/gh/dynverse/dynwrap)
 [**Tutorials**](https://dynverse.org)
 [**Reference documentation**](https://dynverse.org/reference/dynwrap/)
 <!-- badges: end -->

README.md

@@ -6,7 +6,7 @@ dynwrap: Representing and Inferring Single-Cell Trajectories
 
 [![R-CMD-check](https://github.com/dynverse/dynwrap/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/dynverse/dynwrap/actions/workflows/R-CMD-check.yaml)
 [![Codecov test
-coverage](https://codecov.io/gh/dynverse/dynwrap/branch/master/graph/badge.svg)](https://app.codecov.io/gh/dynverse/dynwrap?branch=master)
+coverage](https://codecov.io/gh/dynverse/dynwrap/graph/badge.svg)](https://app.codecov.io/gh/dynverse/dynwrap)
 [**Tutorials**](https://dynverse.org) [**Reference
 documentation**](https://dynverse.org/reference/dynwrap/)
 <!-- badges: end -->
@@ -16,15 +16,15 @@ documentation**](https://dynverse.org/reference/dynwrap/)
 **dynwrap** contains the code for a common model of single-cell
 trajectories. The package can:
 
--   Wrap the input data of a trajectory inference method, such as
-    expression and prior information
--   Run a trajectory inference method in R, in a docker container or a
-    singularity container
--   Wrap the output of a trajectory inference method, such as the
-    pseudotime, a clustering or a branch network, and convert it into a
-    common trajectory model
--   Further postprocess and adapt the trajectory model, such as
-    labelling the milestones and rooting the trajectory
+- Wrap the input data of a trajectory inference method, such as
+  expression and prior information
+- Run a trajectory inference method in R, in a docker container or a
+  singularity container
+- Wrap the output of a trajectory inference method, such as the
+  pseudotime, a clustering or a branch network, and convert it into a
+  common trajectory model
+- Further postprocess and adapt the trajectory model, such as labelling
+  the milestones and rooting the trajectory
 
 ![](man/figures/trajectory_model.png)
 
@@ -38,13 +38,13 @@ containers in [dynmethods](https://github.com/dynverse/dynmethods).
 
 The advantage of using a common model is that it allows:
 
--   Comparison between a prediction and a gold standard, eg. using
-    [dyneval](https://github.com/dynverse/dyneval)
--   Comparing two predictions
--   Easily visualise the trajectory, eg. using
-    [dynplot](https://github.com/dynverse/dynplot)
--   Extracting relevant features/genes, eg. using
-    [dynfeature](https://github.com/dynverse/dynfeature)
+- Comparison between a prediction and a gold standard, eg. using
+  [dyneval](https://github.com/dynverse/dyneval)
+- Comparing two predictions
+- Easily visualise the trajectory, eg. using
+  [dynplot](https://github.com/dynverse/dynplot)
+- Extracting relevant features/genes, eg. using
+  [dynfeature](https://github.com/dynverse/dynfeature)
 
 ## Latest changes
 
@@ -53,34 +53,16 @@ list of changes.
 
 <!-- This section gets automatically generated from inst/NEWS.md -->
 
-### Recent changes in dynwrap 1.2.3
+### Recent changes in dynwrap 1.2.5
 
--   MINOR CHANGE: Fixes to metadata (documentation, citation entry,
-    broken links).
+- BUG FIX `convert_definition()`: Fix for purrr having deprecated
+  `invoke` in favour of `exec` (PR \#166).
 
-### Recent changes in dynwrap 1.2.2
+### Recent changes in dynwrap 1.2.4
 
--   MAJOR CHANGE `convert_milestone_percentages_to_progressions()`:
-    Rewrite implementation to attain significant speedup.
+- Resubmission after babelwhale was removed from CRAN.
 
--   MINOR CHANGE `infer_trajectory()`: Infer command (Rscript/python)
-    from file extension if possible and avoid using shebang to execute
-    script, because R CMD check for R 4.0 puts Rscript and R dummy
-    executables on the path before R CMD check. This means
-    `#!/usr/bin/env Rscript` does not work anymore.
-
--   MINOR CHANGE `add_feature_importance()`: Add a function for adding
-    feature importance scores to a trajectory.
-
--   BUG FIX `project_waypoints()`: Rename milestone waypoints such that
-    the names are unique.
-
--   BUG FIX `infer_trajectory()`: Fix error message printing.
-
--   BUG FIX: `dyndimred` is used conditionally.
-
--   BUG FIX: `wrap_expression()` and `add_expression()`: Do not override
-    feature_info when it already exists in dataset.
+- MINOR CHANGE: Added `@return` documentation to all functions.
 
 ## Dynverse dependencies