Skip to content

Bump the development version to 7.3.0-SNAPSHOT #1142

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
aalhossary wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Bump the development version to 7.3.0-SNAPSHOT #1142

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
a203e67
Bump the development version to 7.3.0-SNAPSHOT
aalhossary Aug 15, 2026
c39c285
Draft the 7.3.0 changelog section
aalhossary Aug 30, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
49 changes: 49 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,55 @@
BioJava Changelog
-----------------

BioJava 7.3.0
==============================
### Added
* Fetching, caching and display of electron density and cryo-EM maps #1134
* Checksum verification (MD5, SHA-1, SHA-256) in `FileDownloadUtils`, replacing the previous
stub. Downloads from `files.wwpdb.org` and `files.rcsb.org` are checksummed from their `ETag`
without a second request #1133
* `HttpStatusException`, so callers can tell "not there" from a transport failure #1133
* `FileDownloadUtils.downloadFileWithValidation()`, which downloads and validates over a single
connection #1133
* `LocalPDBDirectory.getMiddleHash(String)`, computing the two-character directory from the
right so that it is correct for both short and extended PDB IDs #1133
* Support for the ECOD distribution format introduced at v294.1 #1141 #1139

### Performance
* Contact calculation is about 1.5x faster: squared distances compared against a squared cutoff,
primitive arrays in `GridCell` instead of boxed lists, and a pre-sized `AtomContactSet` #1147
* ASA calculation is about 1.2-1.3x faster, by the same replacement of objects with flat
primitive arrays in the hot loops #1148
* `EcodInstallation.getVersion()` reads the file header instead of parsing every domain. The
current release is 653 MB and holds nearly three million records #1141

### Fixed
* CATH downloads use https and check the response before caching it. The previous http URL began
redirecting, and the redirect body was cached as classification data #1133 #1138
* CATH parsing no longer throws `ArrayIndexOutOfBoundsException` on blank or truncated lines, and
cached files are validated before being used #1145
* Chemical component downloads reject redirects and error responses rather than caching them #1133
* Redirects that `HttpURLConnection` does not follow by itself - 307, 308, and any that change
http to https - are now followed #1151 #1149
* `FileDownloadUtils`: the `hash` argument was ignored by one overload; downloads could be
silently truncated; temporary files leaked on failure; `validateFile` threw on a file with no
parent directory and on an empty `.size` sidecar #1133
* mmCIF writer emits the entry identifier as a data item, so `getPdbId()` survives a
write-then-read round trip #1144 #1143
* The ECOD read lock is left balanced when a download fails, so the original error is no longer
replaced by `IllegalMonitorStateException` #1150
* Resolution parsing warns only when the values actually differ

### Changed
* `createValidationFiles()` now defaults to `ETagPolicy.USE_IF_HEX_DIGEST`, so existing callers
begin recording checksums where the server offers one #1133
* Integration tests run nightly rather than on every pull request #1137 #1135
* Tests migrated to JUnit 5 #1125 #1126 #1038
* Library upgrades #1130 #1132

### Removed
* The `junit-addons` test dependency, no longer needed after the JUnit 5 migration #1126

BioJava 7.2.6
==============================
### Fixed
Expand Down
6 changes: 3 additions & 3 deletions biojava-aa-prop/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
<parent>
<artifactId>biojava</artifactId>
<groupId>org.biojava</groupId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>biojava-aa-prop</artifactId>
Expand Down Expand Up @@ -70,12 +70,12 @@
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-structure</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</dependency>

<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
Expand Down
4 changes: 2 additions & 2 deletions biojava-alignment/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
<parent>
<artifactId>biojava</artifactId>
<groupId>org.biojava</groupId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</parent>
<artifactId>biojava-alignment</artifactId>
<name>biojava-alignment</name>
Expand Down Expand Up @@ -47,7 +47,7 @@
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
Expand Down
2 changes: 1 addition & 1 deletion biojava-core/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<parent>
<artifactId>biojava</artifactId>
<groupId>org.biojava</groupId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>biojava-core</artifactId>
Expand Down
6 changes: 3 additions & 3 deletions biojava-genome/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<parent>
<artifactId>biojava</artifactId>
<groupId>org.biojava</groupId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>biojava-genome</artifactId>
Expand Down Expand Up @@ -73,13 +73,13 @@
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-alignment</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
Expand Down
4 changes: 2 additions & 2 deletions biojava-integrationtest/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
<parent>
<artifactId>biojava</artifactId>
<groupId>org.biojava</groupId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</parent>
<artifactId>biojava-integrationtest</artifactId>
<packaging>jar</packaging>
Expand Down Expand Up @@ -40,7 +40,7 @@
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-structure</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</dependency>
<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
<dependency>
Expand Down
4 changes: 2 additions & 2 deletions biojava-modfinder/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
<parent>
<artifactId>biojava</artifactId>
<groupId>org.biojava</groupId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</parent>
<artifactId>biojava-modfinder</artifactId>
<name>biojava-modfinder</name>
Expand All @@ -31,7 +31,7 @@
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-structure</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
<type>jar</type>
<scope>compile</scope>
</dependency>
Expand Down
2 changes: 1 addition & 1 deletion biojava-ontology/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
<parent>
<groupId>org.biojava</groupId>
<artifactId>biojava</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</parent>

<artifactId>biojava-ontology</artifactId>
Expand Down
10 changes: 5 additions & 5 deletions biojava-protein-comparison-tool/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
<parent>
<artifactId>biojava</artifactId>
<groupId>org.biojava</groupId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</parent>

<artifactId>biojava-protein-comparison-tool</artifactId>
Expand Down Expand Up @@ -36,23 +36,23 @@
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-alignment</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>

</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-structure</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-structure-gui</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>net.sourceforge.jmol</groupId>
Expand Down
4 changes: 2 additions & 2 deletions biojava-protein-disorder/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<parent>
<artifactId>biojava</artifactId>
<groupId>org.biojava</groupId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</parent>
<artifactId>biojava-protein-disorder</artifactId>
<packaging>jar</packaging>
Expand Down Expand Up @@ -63,7 +63,7 @@
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</dependency>
<!-- logging dependencies (managed by parent pom, don't set versions or
scopes here) -->
Expand Down
6 changes: 3 additions & 3 deletions biojava-structure-gui/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<parent>
<artifactId>biojava</artifactId>
<groupId>org.biojava</groupId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>biojava-structure-gui</artifactId>
Expand All @@ -27,13 +27,13 @@
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-structure</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
<scope>compile</scope>
</dependency>

Expand Down
6 changes: 3 additions & 3 deletions biojava-structure/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
<parent>
<artifactId>biojava</artifactId>
<groupId>org.biojava</groupId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</parent>
<artifactId>biojava-structure</artifactId>
<name>biojava-structure</name>
Expand Down Expand Up @@ -51,13 +51,13 @@
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-alignment</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
<scope>compile</scope>
</dependency>

Expand Down
2 changes: 1 addition & 1 deletion biojava-survival/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
<parent>
<groupId>org.biojava</groupId>
<artifactId>biojava</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</parent>

<artifactId>biojava-survival</artifactId>
Expand Down
4 changes: 2 additions & 2 deletions biojava-ws/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<parent>
<artifactId>biojava</artifactId>
<groupId>org.biojava</groupId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
</parent>
<artifactId>biojava-ws</artifactId>
<name>biojava-ws</name>
Expand All @@ -19,7 +19,7 @@
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
Expand Down
2 changes: 1 addition & 1 deletion pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
<groupId>org.biojava</groupId>
<artifactId>biojava</artifactId>
<packaging>pom</packaging>
<version>7.2.7-SNAPSHOT</version>
<version>7.3.0-SNAPSHOT</version>
<name>biojava</name>
<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
data. It provides analytical and statistical routines, parsers for common file formats and allows the
Expand Down
Loading