Release version 3.4.2

COPYRIGHT.md

@@ -1,9 +1,9 @@
-TractoR, its constituent R packages and command-line interface system, are copyright (C) 2005-2007 Jon Clayden, and (C) 2007-2023 University College London.
+TractoR, its constituent R packages and command-line interface system, are copyright (C) 2005-2007 Jon Clayden, and (C) 2007-2024 University College London.
 
 Copyright on all dependency packages (within the `lib` directory) is owned by their respective authors, as described in each package's `DESCRIPTION` file.
 
 Standardised brain images in MNI space are copyright (C) 1993-2004 Louis Collins, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.
 
-TractoR as a whole is licensed under the [GNU General Public Licence, version 2](http://www.gnu.org/licenses/gpl-2.0.html). Individual package licence terms are given in their respective `DESCRIPTION` files.
+TractoR as a whole is licensed under the [GNU General Public Licence, version 2](http://www.gnu.org/licenses/gpl-2.0.html). Individual package licence terms are given in their respective `DESCRIPTION` and/or `LICENSE` files.
 
 This copyright notice, or an equivalent one, must be retained in any redistribution of the software.

VERSION

@@ -1 +1 @@
-3.4.1
+3.4.2

md5.txt

@@ -2,13 +2,13 @@
 fc0a10d7644b8c5d7ec0769d72236ba1 .nova/Artwork
 bbd3afbfd9a8f9f948f1a4e3b45aea85 .nova/Configuration.json
 d654c028827567e62ddbde4fa5b100d8 CITATION.cff
-d22a188c6bc052caa9bae61decec207f COPYRIGHT.md
+78970d5be0b8f494301086b5c5b61ee9 COPYRIGHT.md
 a5391c7555bd912343ae34a4ebf8ba89 Dockerfile
 6df8bfd02fd1dd8e238c7525eccbb8f5 INSTALL.md
 10b634d9e14144c8b6aa3562b4877ede LICENSE
-d3607bb7d2db0ccd7419b1aab489b3d4 Makefile
-8141723e4c647b8603aeffb381ffc7f1 README.md
-65455ebe4e5708535fba3a41d96e8acc VERSION
+557f2c428f5ce3e7848ee9337e537ad0 Makefile
+4f35cdd9c87b6d7b766823a4ee3a9a59 README.md
+a04a1335aea3f7a6ce9e0595b404f7c7 VERSION
 f13a73bd17fbe0f54870413c386c301a bin/extra/tractor_Rinstall
 5493da6482c836e47652578590daa718 bin/furrow
 87c38f3730a914abe1738c8c52679e4c bin/plough
@@ -21,7 +21,7 @@ a09a862f22f56b5a661c3d9ad22d2c94 share/doc/TractoR-for-R-users.html
 ce088d53ef9561c4dd85577f4c4e10ba share/doc/assets/prism.css
 cdca90be556c2e5f8dfb1482e0fc09e9 share/doc/assets/prism.js
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 a819a5c58a57f1f317888c4037b82a7b share/doc/diffusion-processing.html
@@ -33,7 +33,7 @@ cd8cec91833ffa792d4ad33729f8acbf share/doc/graph-brain.png
 fd0b3ec2dc56fcc4ad96953aab138c0e share/doc/graph-matrix.png
 aa9d14c499979d80fdff28dfbf0db5d5 share/doc/guidelines-for-contributors.html
 3c11235b2bef0c0b296fc0482a9d6e4b share/doc/home.html
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 f200f315d515320dc4e8c1fe13f52a59 share/doc/nitrc.png
 614b517b59fcee58ec3e0365c5db0d47 share/doc/paper/index.html
 b34a574652afa4baf8b594b9262b8c4c share/doc/principal-directions.png
@@ -290,7 +290,7 @@ c158a0811f6bd9b4000a3c549072b473 tests/25_Tractography/025_dti.sh
 3567531385b1c1116c9e4ad8d2111ea4 tests/25_Tractography/030_map.save
 ad08175cc7b4379da176cfeed10638d0 tests/25_Tractography/030_map.sh
 55aa082182f74bc6a2adb1547cc4a2c0 tests/35_PNT/005_ref.save
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 681478ce8ebbe30fb7f9eb41f5f519de tests/35_PNT/010_data.sh
 21b1819ce792fa4e1504857e44933742 tests/35_PNT/015_train.save
@@ -432,24 +432,24 @@ cbf8b8883ecb0eaeb70b826d9a4c97d9 tests/scripts/check-md5.R
 ea710301bda7777fc785e7bd130ee0f8 tests/scripts/hello-interactive.R
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@@ -459,7 +459,7 @@ e887b0bdd3b2be0b6bf7467fe8766a3a tractor.base/R/png.R
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 f7e442ddf61b4098a074d98d2e1d2dff tractor.base/R/viz.R
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@@ -473,6 +473,15 @@ b88a0b97d6e70e36d8b78682dbc149e3 tractor.base/inst/extdata/mrtrix/maskedb0_lia.m
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+5292d2707946454d33d09efae20413f6 tractor.base/inst/tinytest/test-20-serialisation.R
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@@ -508,16 +517,9 @@ c9213dd711d72ad45f53a19c24a8e9cc tractor.base/man/threadSafeTempFile.Rd
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@@ -581,8 +577,8 @@ ba5ada9bd8b65b5a302900f1a438d176 tractor.graph/tests/testthat/test-30-disconnect
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@@ -645,12 +641,12 @@ eed09bff91a83d067277af0e714cfc70 tractor.track/src/Trackvis.h
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share/doc/changelog.html

@@ -48,14 +48,23 @@ <h1>Changelog</h1>
 
 <p>The significant user-visible changes in each release of TractoR are documented below.</p>
 
+<h2 id="342-2024-03-01">3.4.2 (2024-03-01)</h2>
+
+<ul>
+<li>Package unit tests have been moved from the <code>testthat</code> to the <code>tinytest</code> framework.</li>
+<li>Several tweaks have been made to improve compatibility with R 4.3.x and the upcoming R 4.4.0, as well as <code>divest</code> 1.0 and <code>igraph</code> 2.0.</li>
+<li>The minimum required version of R has been updated in the documentation to 3.5.0. This was already the case, but the documentation was out of date. TractoR’s continuous integration tests now also run on old versions of R to help ensure the minimum version specified is accurate.</li>
+<li>Two spurious errors that could arise during an interactive run of the <code>dpreproc</code> script have been corrected.</li>
+</ul>
+
 <h2 id="341-2023-06-30">3.4.1 (2023-06-30)</h2>
 
 <ul>
 <li>Several tweaks have been made to better support paths containing spaces, particularly for session paths in workflows. In support of this, two small new features have been added: the new <code>TRACTOR_WORKING_DIR</code> environment variable is now used as a default working directory by <code>tractor</code>, <code>plough</code> and <code>furrow</code>, if it is set, and <code>furrow</code> gains a <code>-r</code> flag to request relative paths be substituted rather than absolute ones. This is used in certain workflows to work around third-party tools’ own difficulties with paths containing spaces.</li>
 <li>When writing an image to file, any existing “tags” file with the corresponding name is now always overwritten, to avoid the auxiliary file getting out of sync with the image file.</li>
 <li>Relative paths should now be correct when the reference path is a directory.</li>
 <li>The working directory should no longer be erroneously prepended to image paths beginning with a tilde (<code>~</code>), which indicates a home directory on Unix-like systems.</li>
-<li>The <code>bids</code> would sometimes attempt to copy an image file with no extension, leading to an error. This has been corrected.</li>
+<li>The <code>bids</code> script would sometimes attempt to copy an image file with no extension, leading to an error. This has been corrected.</li>
 <li>Decomposition applied to a transformation object containing only one transform now works as expected.</li>
 </ul>
 

share/doc/install.html

@@ -50,14 +50,14 @@ <h1>Installation</h1>
 
 <h2 id="system-requirements">System requirements</h2>
 
-<p>In its basic form, TractoR is a set of packages written for the <a href="http://www.r-project.org">R language and environment</a>. R (version 3.0.0 or later) is therefore an absolute prerequisite unless you want to use Docker to run TractoR fully containerised. R is an open-source package that is easy to install. Precompiled binaries are available from a number of <a href="https://cran.r-project.org/mirrors.html">CRAN mirror sites</a>, along with the source code.</p>
+<p>In its basic form, TractoR is a set of packages written for the <a href="http://www.r-project.org">R language and environment</a>. R (version 3.5.0 or later) is therefore an absolute prerequisite unless you want to use Docker to run TractoR fully containerised. R is an open-source package that is easy to install. Precompiled binaries are available from a number of <a href="https://cran.r-project.org/mirrors.html">CRAN mirror sites</a>, along with the source code.</p>
 
 <p>A C/C++ compiler, such as <code>gcc</code>/<code>g++</code> or <code>clang</code>/<code>clang++</code>, is also required to install TractoR from source, although R handles all the details of actually compiling code.</p>
 
 <h2 id="downloads">Downloads</h2>
 
 <div id="download-box">
-  <p>The latest version of TractoR is <span id="version">v3.4.0</span>.</p>
+  <p>The latest version of TractoR is <span id="version">v3.4.1</span>.</p>
   <img src="download.png" alt="Download icon">
   <p>Download <a href="#" onclick="gtag('event','download_tarball'); window.location.href='http://www.tractor-mri.org.uk/tractor.tar.gz'">tractor.tar.gz</a> or <a href="#" onclick="gtag('event','download_zipball'); window.location.href='http://www.tractor-mri.org.uk/tractor.zip'">tractor.zip</a>.</p>
 </div>

tractor.base/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tractor.base
-Version: 3.4.1
-Date: 2023-06-30
+Version: 3.4.2
+Date: 2024-02-27
 Title: Read, Manipulate and Visualise Magnetic Resonance Images
 Author: Jon Clayden
 Maintainer: Jon Clayden <code@clayden.org>

tractor.graph/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tractor.graph
-Version: 3.4.0
-Date: 2023-05-17
+Version: 3.4.2
+Date: 2024-02-22
 Title: Functions for working with connectivity graphs
 Author: Jon Clayden, Lena Dorfschmidt and Fani Deligianni
 Maintainer: Jon Clayden <code@clayden.org>