Merge pull request #142 from alan-turing-institute/test-travis

Fix CI (/migrate to GitHub actions)

.github/workflows/main.yml

@@ -0,0 +1,54 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  schedule:
+    - cron: "5 5 5 * *"  # run at 05:05 on 5th day of each month
+
+name: Build
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel'}
+          - {os: ubuntu-latest,   r: 'devel'}
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-tinytex@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::devtools
+            any::covr
+
+      - name: Check package
+        run: devtools::document();devtools::check()
+        shell: Rscript {0}
+
+      - name: Check coverage
+        run: covr::codecov(quiet = FALSE)
+        shell: Rscript {0}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: netdist
 Title: An implementation of the NetEMD alignment-free network distance measure
-Version: 0.4.9000
+Version: 0.4.9100
 Authors@R: person("Martin", "O'Reilly",email = "[email protected]", 
                   role = c("aut", "cre"))
 Description: An implementation of the NetEMD alignment-free network
@@ -20,15 +20,15 @@ Imports:
     purrr,
     lpSolve,
     plyr,
-    dplyr,
     pheatmap,
     Rcpp,
-    phangorn
 Suggests:
+    dplyr,
+    phangorn,
     testthat,
     knitr,
     rmarkdown,
     roxygen2
-RoxygenNote: 7.1.0
+RoxygenNote: 7.2.0
 VignetteBuilder: knitr
 Encoding: UTF-8

R/measures_net_dis.R

@@ -380,7 +380,6 @@ netdis_one_to_many <- function(graph_1 = NULL,
 #' 3) NULL (default) - Expected counts will be calculated based on the properties of the
 #' query graphs themselves. (Geometric-Poisson approximation).
 #'
-#' 
 #' @param comparisons Which comparisons to perform between graphs.
 #' Can be "many-to-many" (all pairwise combinations) or "one-to-many"
 #' (compare first graph in graphs to all other graphs.)
@@ -394,18 +393,17 @@ netdis_one_to_many <- function(graph_1 = NULL,
 #'
 #' @param min_ego_edges Filter ego networks which have fewer
 #' than min_ego_edges edges (default 1).
-#'
-#'  @param binning_fn Function used to bin ego network densities. Takes edge \code{densities}
+#' 
+#' @param binning_fn Function used to bin ego network densities. Takes edge \code{densities}
 #' as its single argument, and returns a named list including, the input \code{densities}, the resulting bin \code{breaks} (vector of density bin limits), and the vector \code{interval_indexes} which states to what bin each of the individual elements in \code{densities} belongs to.
 #' ego network). If \code{NULL}, then the method \code{binned_densities_adaptive} with
-#' \code{min_counts_per_interval = 5} and \code{num_intervals = 100} is used
-#' (Default: NULL).
+#' \code{min_counts_per_interval = 5} and \code{num_intervals = 100} is used (default: NULL).
 #'
 #' @param bin_counts_fn Function used to calculate expected graphlet counts in
 #' each density bin. Takes \code{graphlet_counts}, \code{interval_indexes}
 #' (bin indexes) and \code{max_graphlet_size} as arguments. If \code{bin_counts_fn} is \code{NULL}, (default),
-#'  it will apply either the approach from the original Netdis paper, or the respective Geometric-Poisson
-#'   approximation; depending on the values of \code{ref_graph} and \code{graphlet_counts_ref}.
+#' it will apply either the approach from the original Netdis paper, or the respective Geometric-Poisson
+#' approximation; depending on the values of \code{ref_graph} and \code{graphlet_counts_ref}.
 #'
 #' @param exp_counts_fn Function used to map from binned reference counts to
 #' expected counts for each graphlet in each ego network of the query graphs.
@@ -414,7 +412,7 @@ netdis_one_to_many <- function(graph_1 = NULL,
 #' If \code{exp_counts_fn} is \code{NULL}, (default), it will apply
 #' either the approach from the original Netdis paper, or the respective Geometric-Poisson approximation; depending on the
 #' values of \code{ref_graph} and \code{graphlet_counts_ref}.
-#' 
+#'
 #' @param graphlet_counts Pre-generated graphlet counts (default: NULL). If the
 #' \code{graphlet_counts} argument is defined then \code{graphs} will not be
 #' used.
@@ -433,7 +431,7 @@ netdis_one_to_many <- function(graph_1 = NULL,
 #' each ego network. 
 #' If the \code{graphlet_counts_ref} argument is defined then \code{ref_graph} will not
 #' be used.
-
+#' 
 #' @return Netdis statistics between query graphs for graphlet sizes
 #' up to and including max_graphlet_size.
 #'

README.md

@@ -6,8 +6,7 @@ Until this package hits release 1.0 anything can change with no notice.
 
 [![Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](http://www.repostatus.org/badges/latest/wip.svg)](http://www.repostatus.org/#wip)
 [![GitHub release](https://img.shields.io/github/release/alan-turing-institute/network-comparison.svg)](https://github.com/alan-turing-institute/network-comparison/releases/latest)
-[![Travis](https://img.shields.io/travis/alan-turing-institute/network-comparison/master.svg)](https://travis-ci.org/alan-turing-institute/network-comparison/branches)
-[![Appveyor](https://ci.appveyor.com/api/projects/status/jn1a36c22vjw1l4d/branch/master?svg=true)](https://ci.appveyor.com/project/alan-turing-institute/network-comparison/branch/master)
+[![Build](https://github.com/alan-turing-institute/network-comparison/actions/workflows/main.yml/badge.svg)](https://github.com/alan-turing-institute/network-comparison/actions/workflows/main.yml)
 
 [![Codecov](https://img.shields.io/codecov/c/github/alan-turing-institute/network-comparison/master.svg)](https://codecov.io/gh/alan-turing-institute/network-comparison?branch=master)
 [![license](https://img.shields.io/github/license/alan-turing-institute/network-comparison.svg)](https://github.com/alan-turing-institute/network-comparison/edit/master/LICENSE)