Require Documenter for docs

.github/workflows/ci.yml

@@ -18,10 +18,6 @@ jobs:
           - ubuntu-latest
         arch:
           - x64
-        include:
-          - os: windows-latest
-            version: '1'
-            arch: x86
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
@@ -34,7 +30,7 @@ jobs:
         env:
           JULIA_NUM_THREADS: 4
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v2
         with:
           file: lcov.info
   docs:

Project.toml

@@ -14,7 +14,7 @@ XAM = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
 DataFrames = "^0.22.0"
 GenomicFeatures = "^2.0.0"
 OrderedCollections = "~1.3.0"
-RLEVectors = "^0.9.0"
+RLEVectors = "^0.9.9"
 Requires = "~1.1.0"
 XAM = "^0.2.1"
 julia = "1"

docs/#make.jl#

@@ -0,0 +1,12 @@
+using Documenter, GenomicVectors
+
+makedocs(
+         modules = [GenomicVectors],
+         format = :html,
+         sitename = "GenomicVectors"
+         )
+
+deploydocs(
+           repo = "github.com/phaverty/GenomicVectors.jl.git",
+           julia = "release"
+           )

docs/Project.toml

@@ -0,0 +1,5 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+
+[compat]
+Documenter = "0.27"

docs/make.jl

@@ -1,10 +1,9 @@
 using Documenter, GenomicVectors
 
 makedocs(
-         modules = [GenomicVectors]
+         sitename = "GenomicVectors"
          )
 
 deploydocs(
-           repo = "github.com/phaverty/GenomicVectors.jl.git",
-           julia = "release"
+           repo = "github.com/phaverty/GenomicVectors.jl.git"
            )

src/rcall.jl

@@ -1,11 +1,11 @@
 using .RCall
 
 function RCall.sexp(f::GenomeInfo)
-    RCall.R"library(GenomicRanges)"
+    @rlibrary GenomicRanges
     s = [string(x) for x in chr_names(f)]
     l = collect(chr_lengths(f))
     g = genome(f)
-    RCall.R"Seqinfo($s, $l, NA, $g)"
+    RCall.reval("Seqinfo($s, $l, NA, $g)")
 end
 
 function RCall.rcopy(::Type{GenomeInfo}, s::Ptr{RCall.S4Sxp})
@@ -17,7 +17,7 @@ function RCall.rcopy(::Type{GenomeInfo}, s::Ptr{RCall.S4Sxp})
 end
 
 function RCall.sexp(f::GenomicRanges)
-    RCall.R"library(GenomicRanges)"
+    @rlibrary GenomicRanges
     s = starts(f)
     e = ends(f)
     c = [string(x) for x in chromosomes(f)]
@@ -26,11 +26,11 @@ function RCall.sexp(f::GenomicRanges)
 #    RCall.R"GRanges($c, IRanges($s, $e), $r, seqinfo = $i)"
 #    RCall.R"GRanges($c, IRanges($s, $e), seqinfo = $i)
 #    RCall.R"GRanges($c, IRanges($s, $e), $r)
-    RCall.R"GRanges($c, IRanges($s, $e))
+    RCall.reval("GRanges($c, IRanges($s, $e))")
 end
 
 #function RCall.sexp(f::GenomicDataFrame)
-#    RCall.R"library(GenomicRanges)"
+#    @rlibrary GenomicRanges
 #    s = starts(f)
 #    e = ends(f)
 #    c = [string(x) for x in chromosomes(f)]