From c217286fcb3dbeadfb30bed63092a100673d54cd Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Fri, 14 May 2021 22:37:01 -0400 Subject: [PATCH 1/3] Changed version to v1.9. --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index c36eeb4..8264153 100644 --- a/pom.xml +++ b/pom.xml @@ -15,7 +15,7 @@ com.ggvaidya TaxonDNA - 1.9-SNAPSHOT + 1.9 TaxonDNA Taxonomy-aware DNA sequence processing toolkit. From 1be8189ae7d81247ba7f60ca870c0ddb6c4d6316 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Fri, 14 May 2021 22:40:24 -0400 Subject: [PATCH 2/3] Deleted defunct build.xml file. --- build.xml | 241 ------------------------------------------------------ 1 file changed, 241 deletions(-) delete mode 100644 build.xml diff --git a/build.xml b/build.xml deleted file mode 100644 index 6bbd997..0000000 --- a/build.xml +++ /dev/null @@ -1,241 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From ae52f5e4b5b81e6696e43126188d747b15504492 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Fri, 14 May 2021 22:56:35 -0400 Subject: [PATCH 3/3] Replaced Changes.txt with CHANGELOG.md. --- Changes.txt => CHANGELOG.md | 96 +++++++++++++++++++++++-------------- 1 file changed, 59 insertions(+), 37 deletions(-) rename Changes.txt => CHANGELOG.md (54%) diff --git a/Changes.txt b/CHANGELOG.md similarity index 54% rename from Changes.txt rename to CHANGELOG.md index d3c2c7f..f982d2d 100644 --- a/Changes.txt +++ b/CHANGELOG.md @@ -1,37 +1,59 @@ -Changelog -========== - -- 1.8: June 22, 2015 - - Used 'codesign' to sign "Sequence Matrix.app" as this might prevent - it from being recognized on MacOS X systems. - - Thanks to Shiyu Phan for this suggestion! - -- 1.7.9 - - Turned off displaying 'N's in the display, as we don't re-export - those anyway. - - Fixed a bug in the Cluster tool reported by Michael Balke: single - species without conspecific sequences in the dataset were being - reported as 'Split'. - -- 1.7.8 - - Added DOI to the citation for Sequence Matrix. - -- 1.7.7-dev4 - - Naked Nexus now replaces all non-alphanumeric characters with underscores. - -- 1.7.7-dev3 - - Fixed a minor bug with clustering in which the "% of valid comparisons - above the threshold" number was always 0%. - - Fixed a bug in which multiple "Cluster" analyses in the same session - caused the ProgressDialog to never close, resulting in the program - getting "stuck" and a forced quit becoming necessary. - -- 1.7.7-dev2 - - Rewrote SpeciesDetails to remove the old, bug-ridden algorithm. - The new one will probably actually work. - - Added discrimination between "Split only", "Lumped/Split" and - "Lumped" for clusters in Cluster. - -- 1.7.6 (June 6, 2010) - - Added code to detect overlapping codonsets on input (#19). - - Fixed a bug relating to TNT files exported into directory (#55). +# Changelog + +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), +and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +## [Unreleased] + +## [v1.9]: May 14, 2021 +- Replaced Ant-based build process with Maven build. +- Changed minimum Java version from 1.8 to 11. +- Consolidated all shared code into TaxonDNA.Common. +- Added memory information in the SequenceMatrix About dialog box. +- Added Spotless for code style checking. + +- [v1.8.2]: April 17, 2020 +- Updated Java version from 1.5 to 1.8. No Mac application is available for this release, but I'll try to fix that in #70 before the next release. You can run the JAR file on macOS by opening the Terminal and running: + +- [v1.8.1]: April 17, 2020 + +- [v1.8]: June 22, 2015 + - Used 'codesign' to sign "Sequence Matrix.app" as this might prevent + it from being recognized on MacOS X systems. + - Thanks to Shiyu Phan for this suggestion! + +- 1.7.9 + - Turned off displaying 'N's in the display, as we don't re-export + those anyway. + - Fixed a bug in the Cluster tool reported by Michael Balke: single + species without conspecific sequences in the dataset were being + reported as 'Split'. + +- 1.7.8 + - Added DOI to the citation for Sequence Matrix. + +- 1.7.7-dev4 + - Naked Nexus now replaces all non-alphanumeric characters with underscores. + +- 1.7.7-dev3 + - Fixed a minor bug with clustering in which the "% of valid comparisons + above the threshold" number was always 0%. + - Fixed a bug in which multiple "Cluster" analyses in the same session + caused the ProgressDialog to never close, resulting in the program + getting "stuck" and a forced quit becoming necessary. + +- 1.7.7-dev2 + - Rewrote SpeciesDetails to remove the old, bug-ridden algorithm. + The new one will probably actually work. + - Added discrimination between "Split only", "Lumped/Split" and + "Lumped" for clusters in Cluster. + +- 1.7.6 (June 6, 2010) + - Added code to detect overlapping codonsets on input (#19). + - Fixed a bug relating to TNT files exported into directory (#55). + +[Unreleased]: https://github.com/gaurav/taxondna/compare/v1.9...HEAD +[v1.9]: https://github.com/gaurav/taxondna/compare/v1.8.2...v1.9 +[v1.8.2]: https://github.com/gaurav/taxondna/compare/v1.8.1...v1.8.2 +[v1.8.1]: https://github.com/gaurav/taxondna/compare/v1.8...v1.8.1 +[1.8]: https://github.com/gaurav/taxondna/releases/tag/1.8