Merge pull request #6 from jefferis/fix/datetime

.Rbuildignore

@@ -9,3 +9,5 @@
 ^revdep$
 ^_pkgdown\.yml$
 ^docs$
+^\.github$
+^pkgdown$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,52 @@
+# 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]
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -0,0 +1,50 @@
+# 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]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -2,3 +2,4 @@
 private/
 .Rproj.user
 .Rhistory
+docs

DESCRIPTION

@@ -10,13 +10,14 @@ Authors@R: c(
 Description: Provides function to read data from the 'Igor Pro' data analysis
     program by Wavemetrics. The data formats supported are 'Igor' packed 
     experiment format (pxp) and 'Igor' binary wave (ibw). See: 
-    https://www.wavemetrics.com/ for details. Also includes functions to load 
+    <https://www.wavemetrics.com/> for details. Also includes functions to load 
     special pxp files produced by the 'Igor Pro' 'Neuromatic' and 'Nclamp' 
     packages for recording and analysing neuronal data. See 
-    https://github.com/SilverLabUCL/NeuroMatic for details.
+    <https://github.com/SilverLabUCL/NeuroMatic> for details.
 Imports:
     bitops,
-    tools
+    tools,
+    timechange
 Suggests:
     spelling,
     testthat
@@ -25,3 +26,5 @@ LazyLoad: yes
 RoxygenNote: 7.3.2
 Language: en-GB
 Encoding: UTF-8
+URL: https://github.com/jefferis/IgorR, https://jefferis.github.io/IgorR/
+BugReports: https://github.com/jefferis/IgorR/issues

R/ReadIgorBinary.R

@@ -338,12 +338,16 @@ read.pxp<-function(pxpfile,regex,ReturnTimeSeries=FALSE,Verbose=FALSE,
   i
 }
 
-igor_date_origin<-as.numeric(ISOdate(1904,1,1,hour=0,tz=""))
-
-.convertIgorDate<-function(dateval){
-  dateval=dateval+igor_date_origin
-  class(dateval)<-"POSIXct"
-  dateval
+# internal function to convert Igor dates
+# these are expressed in seconds since 1904-01-01 in the local timezone
+# note that we provide a tz argument to ensure that tests give the same
+# results regardless of the local timezone of the test machine
+.convertIgorDate<-function(dateval, tz=""){
+  igor_origin=ISOdatetime(1904,1,1,hour=0,min = 0, sec=0, tz=tz)
+  # this takes care of tz offset differences between the actual date and the origin
+  # e.g. because date is during daylight savings (but origin was not)
+  res=timechange::time_add(igor_origin, second = dateval)
+  res
 }
 
 # enum PackedFileRecordType {
@@ -402,24 +406,30 @@ NULL
   x
 }
 
+# private function to read a null terminated string
+.read_nt_string <- function(con, strlen) {
+  rawchars=readBin(con, what=raw(), n = strlen)
+  readBin(rawchars, what = 'character', n = 1)
+}
+
 .ReadPackedFile<-function(con, recordSize, encoding, Verbose){
 
   # discard first header part
   numBytes   = 32
-  readChar(con, numBytes)
+  res=readBin(con, what=raw(), n = numBytes)
   recordSize = recordSize - numBytes
 
   # read the filename
   file       = list()
-  file$name  = readChar(con, numBytes)
+  file$name  = .read_nt_string(con, numBytes)
   recordSize = recordSize - numBytes
 
   # discard last header part
   numBytes   = 90
-  readChar(con, numBytes)
+  readBin(con, what = raw(), n = numBytes)
   recordSize = recordSize - numBytes
 
-  file$data  = .readCharsWithEnc(con, recordSize, encoding)
+  file$data  = suppressWarnings(.readCharsWithEnc(con, recordSize, encoding))
 
   if(nchar(file$data) <= 1) { # assume it is a formatted notebook with custom binary header
 
@@ -763,21 +773,18 @@ if(R.version$major>2) {
     attr(WaveData,"Note")=.readCharsWithEnc(con,BinHeader5$noteSize,encoding)
   }
 
-  if(BinHeader5$dataEUnitsSize>0) {
-    attr(WaveData,"dataUnits")=.readNullTermString(con,BinHeader5$dataEUnitsSize,encoding)
-  }
+  # ignore dataEUnitsSize
+  if(BinHeader5$dataEUnitsSize>0)
+    readBin(con,what=raw(), n = BinHeader5$dataEUnitsSize)
+
+  if(any(BinHeader5$dimEUnitsSize>0))
+    readBin(con,what=raw(), n = sum(BinHeader5$dimEUnitsSize))
 
-  if(any(BinHeader5$dimEUnitsSize>0)) {
-    x=.readCharsWithEnc(con,BinHeader5$dimEUnitsSize,encoding)
-    attr(WaveData,"dimUnits")[BinHeader5$dimEUnitsSize>0]=x[BinHeader5$dimEUnitsSize>0]
-  }
   # Trim units down to active dimensions
   attr(WaveData,"dimUnits")=attr(WaveData,"dimUnits")[WaveHeader5$nDim>0]
 
-  if(any(BinHeader5$dimLabelsSize>0)) {
-    x=.readCharsWithEnc(con,BinHeader5$dimLabelsSize,encoding)
-    attr(WaveData,"dimLabels")=x[WaveHeader5$nDim>0]
-  }
+  if(any(BinHeader5$dimLabelsSize>0))
+    readBin(con,what=raw(), n = sum(BinHeader5$dimLabelsSize))
 
   # Finish up
   # Re-dimension

README.md

@@ -1,8 +1,11 @@
 # IgorR
+<!-- badges: start -->
 [![DOI](https://img.shields.io/badge/doi-10.5281%2Fzenodo.10230-blue.svg)](http://dx.doi.org/10.5281/zenodo.10230) 
 [![Release Version](https://img.shields.io/github/release/jefferis/IgorR.svg)](https://github.com/jefferis/IgorR/releases/latest) 
-[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/IgorR)](https://cran.r-project.org/package=IgorR) 
-[![Build Status](https://travis-ci.org/jefferis/IgorR.svg?branch=master)](https://travis-ci.org/jefferis/IgorR)
+[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/IgorR)](https://cran.r-project.org/package=IgorR)
+[![R-CMD-check](https://github.com/jefferis/IgorR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jefferis/IgorR/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->
+
 
 Introduction
 ============

_pkgdown.yml

@@ -1,3 +1,6 @@
+url: https://jefferis.github.io/IgorR/
+template:
+  bootstrap: 5
 reference:
 - title: Package Help
   contents: