[Git][java-team/libbeam-java][master] 5 commits: New upstream version 1.3.6
Andrius Merkys (@merkys)
gitlab at salsa.debian.org
Tue Sep 10 14:52:35 BST 2024
Andrius Merkys pushed to branch master at Debian Java Maintainers / libbeam-java
Commits:
2f8a82f5 by Andrius Merkys at 2024-09-10T09:18:58-04:00
New upstream version 1.3.6
- - - - -
349acd96 by Andrius Merkys at 2024-09-10T09:18:59-04:00
Update upstream source from tag 'upstream/1.3.6'
Update to upstream version '1.3.6'
with Debian dir f1423cfce9d4a14c7b1e91d99a5c5bb017aaf679
- - - - -
0e01bb8e by Andrius Merkys at 2024-09-10T09:21:08-04:00
Bump copyright years.
- - - - -
bfa2cd07 by Andrius Merkys at 2024-09-10T09:28:32-04:00
Drop ${maven:CompileDepends} from Depends.
- - - - -
91a5ce3a by Andrius Merkys at 2024-09-10T09:28:57-04:00
Update changelog for 1.3.6-1 release
- - - - -
14 changed files:
- core/pom.xml
- core/src/main/java/uk/ac/ebi/beam/Bond.java
- core/src/main/java/uk/ac/ebi/beam/Localise.java
- core/src/main/java/uk/ac/ebi/beam/Parser.java
- debian/changelog
- debian/control
- debian/copyright
- exec/pom.xml
- func/pom.xml
- func/src/main/java/uk/ac/ebi/beam/AddDirectionalLabels.java
- func/src/main/java/uk/ac/ebi/beam/NormaliseDirectionalLabels.java
- func/src/main/java/uk/ac/ebi/beam/RemoveUpDownBonds.java
- func/src/main/java/uk/ac/ebi/beam/ToTrigonalTopology.java
- pom.xml
Changes:
=====================================
core/pom.xml
=====================================
@@ -5,7 +5,7 @@
<parent>
<artifactId>beam</artifactId>
<groupId>uk.ac.ebi.beam</groupId>
- <version>1.3.5</version>
+ <version>1.3.6</version>
</parent>
<modelVersion>4.0.0</modelVersion>
=====================================
core/src/main/java/uk/ac/ebi/beam/Bond.java
=====================================
@@ -106,6 +106,34 @@ public enum Bond {
return UP;
}
+ @Override boolean directional() {
+ return true;
+ }
+ },
+ /**
+ * This is an internal quirk to allow the aromaticity of input to be preserved when
+ * we kekulize. The up/down bonds may be between aromatic atoms:
+ * {@code O=c1cccc\c1=C/C} Since the double bond is exo, the / \ must be aromatic.
+ */
+ UP_AROMATIC("/", 1) {
+ @Override public Bond inverse() {
+ return DOWN_AROMATIC;
+ }
+
+ @Override boolean directional() {
+ return true;
+ }
+ },
+ /**
+ * This is an internal quirk to allow the aromaticity of input to be preserved when
+ * we kekulize. The up/down bonds may be between aromatic atoms:
+ * {@code O=c1cccc\c1=C/C} Since the double bond is exo, the / \ must be aromatic.
+ */
+ DOWN_AROMATIC("\\", 1) {
+ @Override public Bond inverse() {
+ return UP_AROMATIC;
+ }
+
@Override boolean directional() {
return true;
}
=====================================
core/src/main/java/uk/ac/ebi/beam/Localise.java
=====================================
@@ -95,6 +95,20 @@ final class Localise {
int v = e.other(u);
if (v < u) {
switch (e.bond()) {
+ case UP:
+ case UP_AROMATIC:
+ if (aromatic.get(u) && aromatic.get(v))
+ e.bond(Bond.UP_AROMATIC);
+ else
+ e.bond(Bond.UP);
+ break;
+ case DOWN:
+ case DOWN_AROMATIC:
+ if (aromatic.get(u) && aromatic.get(v))
+ e.bond(Bond.DOWN_AROMATIC);
+ else
+ e.bond(Bond.DOWN);
+ break;
case SINGLE:
if (aromatic.get(u) && aromatic.get(v)) {
e.bond(Bond.SINGLE);
=====================================
core/src/main/java/uk/ac/ebi/beam/Parser.java
=====================================
@@ -46,26 +46,38 @@ import static java.util.Map.Entry;
*/
final class Parser {
- /** Keep track of branching. */
+ /**
+ * Keep track of branching.
+ */
private final IntStack stack = new IntStack(10);
- /** Molecule being loaded. */
+ /**
+ * Molecule being loaded.
+ */
private final Graph g;
- /** Keep track of ring information. */
+ /**
+ * Keep track of ring information.
+ */
private RingBond[] rings = new RingBond[10];
- /** Local arrangement for ring openings. */
+ /**
+ * Local arrangement for ring openings.
+ */
private Map<Integer, LocalArrangement> arrangement
= new HashMap<Integer, LocalArrangement>(5);
private Map<Integer, Configuration> configurations
= new HashMap<Integer, Configuration>(5);
- /** Current bond. */
+ /**
+ * Current bond.
+ */
private Bond bond = Bond.IMPLICIT;
- /** Current configuration. */
+ /**
+ * Current configuration.
+ */
private Configuration configuration = Configuration.UNKNOWN;
@@ -76,16 +88,20 @@ final class Parser {
*/
private Set<Integer> start = new TreeSet<Integer>();
- /** Number of open rings - all rings should be closed. */
+ /**
+ * Number of open rings - all rings should be closed.
+ */
private int openRings = 0;
- /** Strict parsing. */
+ /**
+ * Strict parsing.
+ */
private final boolean strict;
private BitSet checkDirectionalBonds = new BitSet();
private int lastBondPos = -1;
- private Map<Edge,Integer> bondStrPos = new HashMap<>();
+ private Map<Edge, Integer> bondStrPos = new HashMap<>();
private List<String> warnings = new ArrayList<>();
@@ -116,7 +132,7 @@ final class Parser {
int nArom = 0;
for (Edge e : g.edges(i)) {
if (e.bond() == Bond.AROMATIC ||
- e.bond() == Bond.IMPLICIT && g.atom(e.other(i)).aromatic())
+ e.bond() == Bond.IMPLICIT && g.atom(e.other(i)).aromatic())
nArom++;
}
if (nArom >= 2) {
@@ -124,13 +140,13 @@ final class Parser {
g.setAtom(i, AtomImpl.AromaticSubset.Any);
else
g.setAtom(i,
- new AtomImpl.BracketAtom(-1,
- Element.Unknown,
- atom.label(),
- atom.hydrogens(),
- atom.charge(),
- atom.atomClass(),
- true));
+ new AtomImpl.BracketAtom(-1,
+ Element.Unknown,
+ atom.label(),
+ atom.hydrogens(),
+ atom.charge(),
+ atom.atomClass(),
+ true));
}
}
}
@@ -190,6 +206,7 @@ final class Parser {
// create topologies (stereo configurations)
for (Entry<Integer, Configuration> e : configurations.entrySet()) {
addTopology(e.getKey(),
+ e.getValue(),
Topology.toExplicit(g, e.getKey(), e.getValue()));
}
@@ -244,8 +261,8 @@ final class Parser {
offset2 = bondStrPos.get(e);
}
String errorPos = InvalidSmilesException.display(buffer,
- offset1-buffer.length(),
- offset2-buffer.length());
+ offset1 - buffer.length(),
+ offset2 - buffer.length());
if (strict)
throw new InvalidSmilesException("Ignored invalid Cis/Trans specification: " + errorPos);
else
@@ -261,8 +278,8 @@ final class Parser {
offset2 = bondStrPos.get(e);
}
String errorPos = InvalidSmilesException.display(buffer,
- offset1-buffer.length(),
- offset2-buffer.length());
+ offset1 - buffer.length(),
+ offset2 - buffer.length());
if (strict)
throw new InvalidSmilesException("Ignored invalid Cis/Trans specification: " + errorPos);
else
@@ -311,22 +328,25 @@ final class Parser {
return new int[]{prevEnd1, prevEnd2};
}
- /** Access the local edges in order. */
+ /**
+ * Access the local edges in order.
+ */
private List<Edge> getLocalEdges(int end) {
return getEdges(arrangement.get(end), end);
}
/**
* Complicated process to get correct Allene neighbors.
+ *
* @param focus the focus (central cumualted atom)
* @return the carrier list
*/
public int[] getAlleneCarriers(int focus) {
int[] carriers = new int[4];
- int i = 0;
- int[] ends = findExtendedTetrahedralEnds(focus);
- int beg = ends[0];
- int end = ends[1];
+ int i = 0;
+ int[] ends = findExtendedTetrahedralEnds(focus);
+ int beg = ends[0];
+ int end = ends[1];
boolean begh = g.implHCount(beg) == 1;
boolean endh = g.implHCount(end) == 1;
List<Edge> begEdges = new ArrayList<>(getLocalEdges(beg));
@@ -372,52 +392,56 @@ final class Parser {
* @param c explicit configuration of that vertex
* @see Topology#toExplicit(Graph, int, Configuration)
*/
- private void addTopology(int u, Configuration c) throws
- InvalidSmilesException {
-
+ private void addTopology(int u, Configuration input, Configuration c) throws
+ InvalidSmilesException {
// stereo on ring closure - use local arrangement
if (arrangement.containsKey(u)) {
int[] us = arrangement.get(u).toArray();
List<Edge> es = getLocalEdges(u);
- if (c.type() == Configuration.Type.Tetrahedral)
+ if (c.type() == Configuration.Type.Tetrahedral) {
us = insertThImplicitRef(u, us); // XXX: temp fix
- else if (c.type() == Configuration.Type.DoubleBond)
+ } else if (c.type() == Configuration.Type.DoubleBond) {
us = insertDbImplicitRef(u, us); // XXX: temp fix
- else if (c.type() == Configuration.Type.ExtendedTetrahedral) {
+ } else if (c.type() == Configuration.Type.ExtendedTetrahedral) {
g.addFlags(Graph.HAS_EXT_STRO);
if ((us = getAlleneCarriers(u)) == null) {
- if (strict)
- throw new InvalidSmilesException("Invalid Allene stereo");
- else
- warnings.add("Ignored invalid Allene stereochemistry");
- return;
+ if (strict)
+ throw new InvalidSmilesException("Invalid Allene stereo");
+ else
+ warnings.add("Ignored invalid Allene stereochemistry");
+ return;
}
+ } else if (input.type() == Configuration.Type.SquarePlanar) {
+ us = insertMultipleImplicitRefs(u, us, 4);
+ } else if (input.type() == Configuration.Type.TrigonalBipyramidal) {
+ us = insertMultipleImplicitRefs(u, us, 5);
+ } else if (input.type() == Configuration.Type.Octahedral) {
+ us = insertMultipleImplicitRefs(u, us, 6);
} else if (c.type() == Configuration.Type.SquarePlanar &&
us.length != 4) {
- if (strict)
- throw new InvalidSmilesException("SquarePlanar without 4 explicit neighbours");
- else
- warnings.add("SquarePlanar without 4 explicit neighbours");
- return;
+ if (strict)
+ throw new InvalidSmilesException("SquarePlanar without 4 explicit neighbours");
+ else
+ warnings.add("SquarePlanar without 4 explicit neighbours");
+ return;
} else if (c.type() == Configuration.Type.TrigonalBipyramidal &&
us.length != 5) {
- if (strict)
- throw new InvalidSmilesException("SquarePlanar without 5 explicit neighbours");
- else
- warnings.add("SquarePlanar without 5 explicit neighbours");
- return;
+ if (strict)
+ throw new InvalidSmilesException("TrigonalBipyramidal without 5 explicit neighbours");
+ else
+ warnings.add("SquarePlanar without 5 explicit neighbours");
+ return;
} else if (c.type() == Configuration.Type.Octahedral &&
us.length != 6) {
- if (strict)
- throw new InvalidSmilesException("SquarePlanar without 6 explicit neighbours");
- else
- warnings.add("SquarePlanar without 6 explicit neighbours");
- return;
+ if (strict)
+ throw new InvalidSmilesException("Octahedral without 6 explicit neighbours");
+ else
+ warnings.add("SquarePlanar without 6 explicit neighbours");
+ return;
}
g.addTopology(Topology.create(u, us, es, c));
- }
- else {
+ } else {
int[] us = new int[g.degree(u)];
List<Edge> es = g.edges(u);
for (int i = 0; i < us.length; i++)
@@ -425,35 +449,78 @@ final class Parser {
if (c.type() == Configuration.Type.Tetrahedral) {
us = insertThImplicitRef(u, us); // XXX: temp fix
- }
- else if (c.type() == Configuration.Type.DoubleBond) {
+ } else if (c.type() == Configuration.Type.DoubleBond) {
us = insertDbImplicitRef(u, us); // XXX: temp fix
- }
- else if (c.type() == Configuration.Type.ExtendedTetrahedral) {
+ } else if (c.type() == Configuration.Type.ExtendedTetrahedral) {
g.addFlags(Graph.HAS_EXT_STRO);
if ((us = getAlleneCarriers(u)) == null)
return;
+ } else if (input.type() == Configuration.Type.SquarePlanar) {
+ us = insertMultipleImplicitRefs(u, us, 4);
+ } else if (input.type() == Configuration.Type.TrigonalBipyramidal) {
+ us = insertMultipleImplicitRefs(u, us, 5);
+ } else if (input.type() == Configuration.Type.Octahedral) {
+ us = insertMultipleImplicitRefs(u, us, 6);
+ } else if (c.type() == Configuration.Type.SquarePlanar &&
+ us.length != 4) {
+ if (strict)
+ throw new InvalidSmilesException("SquarePlanar without 4 explicit neighbours");
+ else
+ warnings.add("SquarePlanar without 4 explicit neighbours");
+ return;
+ } else if (c.type() == Configuration.Type.TrigonalBipyramidal &&
+ us.length != 5) {
+ if (strict)
+ throw new InvalidSmilesException("TrigonalBipyramidal without 5 explicit neighbours");
+ else
+ warnings.add("SquarePlanar without 5 explicit neighbours");
+ return;
+ } else if (c.type() == Configuration.Type.Octahedral &&
+ us.length != 6) {
+ if (strict)
+ throw new InvalidSmilesException("Octahedral without 6 explicit neighbours");
+ else
+ warnings.add("SquarePlanar without 6 explicit neighbours");
+ return;
}
g.addTopology(Topology.create(u, us, es, c));
}
}
- // XXX: temporary fix for correcting configurations
private int[] insertThImplicitRef(int u, int[] vs) throws
- InvalidSmilesException {
+ InvalidSmilesException {
if (vs.length == 4)
return vs;
if (vs.length != 3)
- throw new InvalidSmilesException("Invaid number of verticies for TH1/TH2 stereo chemistry");
+ throw new InvalidSmilesException("Invalid number of vertices for TH1/TH2 stereo chemistry");
if (start.contains(u))
return new int[]{u, vs[0], vs[1], vs[2]};
else
return new int[]{vs[0], u, vs[1], vs[2]};
}
+ private int[] insertMultipleImplicitRefs(int u, int[] vs, int n) throws
+ InvalidSmilesException {
+ if (vs.length == n)
+ return vs;
+ if (vs.length <= 1)
+ throw new InvalidSmilesException("Cannot have <= 1 vertices for high-order stereo chemistry");
+ int cnt = n - vs.length;
+ int srcIdx = 0;
+ int dstIdx = 0;
+ int[] padded = new int[n];
+ if (!start.contains(u))
+ padded[dstIdx++] = vs[srcIdx++];
+ while (cnt-- > 0)
+ padded[dstIdx++] = u;
+ while (srcIdx < vs.length)
+ padded[dstIdx++] = vs[srcIdx++];
+ return padded;
+ }
+
// XXX: temporary fix for correcting configurations
private int[] insertDbImplicitRef(int u, int[] vs) throws
- InvalidSmilesException {
+ InvalidSmilesException {
if (vs.length == 3)
return vs;
if (vs.length != 2)
@@ -484,8 +551,7 @@ final class Parser {
g.addEdge(e);
if (arrangement.containsKey(u))
arrangement.get(u).add(v);
- }
- else {
+ } else {
start.add(v); // start of a new run
}
}
@@ -507,7 +573,7 @@ final class Parser {
* @throws InvalidSmilesException invalid grammar
*/
private void readSmiles(final CharBuffer buffer) throws
- InvalidSmilesException {
+ InvalidSmilesException {
// primary dispatch
while (buffer.hasRemaining()) {
char c = buffer.get();
@@ -733,7 +799,7 @@ final class Parser {
* specification.
*/
Atom readBracketAtom(final CharBuffer buffer) throws
- InvalidSmilesException {
+ InvalidSmilesException {
int start = buffer.position;
boolean arbitraryLabel = false;
@@ -770,8 +836,7 @@ final class Parser {
if (!arbitraryLabel && !buffer.getIf(']')) {
if (strict) {
throw InvalidSmilesException.invalidBracketAtom(buffer);
- }
- else {
+ } else {
arbitraryLabel = true;
}
}
@@ -852,10 +917,10 @@ final class Parser {
private static int readCharge(int acc, final CharBuffer buffer) {
if (buffer.getIf('+'))
return buffer.nextIsDigit() ? acc + buffer.getNumber()
- : readCharge(acc + 1, buffer);
+ : readCharge(acc + 1, buffer);
if (buffer.getIf('-'))
return buffer.nextIsDigit() ? acc - buffer.getNumber()
- : readCharge(acc - 1, buffer);
+ : readCharge(acc - 1, buffer);
return acc;
}
@@ -988,7 +1053,7 @@ final class Parser {
* Decide the bond to use for a ring bond. The bond symbol can be present on
* either or both bonded atoms. This method takes those bonds, chooses the
* correct one or reports an error if there is a conflict.
- *
+ * <p>
* Equivalent SMILES:
* <blockquote><pre>
* C=1CCCCC=1
@@ -996,9 +1061,9 @@ final class Parser {
* C1CCCCC=1
* </pre></blockquote>
*
- * @param a a bond
- * @param b other bond
- * @param pos the position in the string of bond a
+ * @param a a bond
+ * @param b other bond
+ * @param pos the position in the string of bond a
* @param buffer the buffer and it's current position
* @return the bond to use for this edge
* @throws InvalidSmilesException ring bonds did not match
@@ -1013,11 +1078,11 @@ final class Parser {
if (strict || a.inverse() != b)
throw new InvalidSmilesException("Ring closure bonds did not match, '" + a + "'!='" + b + "':" +
InvalidSmilesException.display(buffer,
- pos-buffer.position,
- lastBondPos-buffer.position));
+ pos - buffer.position,
+ lastBondPos - buffer.position));
warnings.add("Ignored invalid Cis/Trans on ring closure, should flip:" +
- InvalidSmilesException.display(buffer, pos-buffer.position,
- lastBondPos-buffer.position));
+ InvalidSmilesException.display(buffer, pos - buffer.position,
+ lastBondPos - buffer.position));
return Bond.IMPLICIT;
}
@@ -1035,6 +1100,7 @@ final class Parser {
/**
* Access any warning messages from parsing the SMILES.
+ *
* @return the warnings.
*/
public Collection<? extends String> getWarnings() {
@@ -1046,9 +1112,9 @@ final class Parser {
* specify the bond type.
*/
private static final class RingBond {
- int u;
+ int u;
Bond bond;
- int pos;
+ int pos;
private RingBond(int u, Bond bond, int pos) {
this.u = u;
@@ -1070,9 +1136,11 @@ final class Parser {
private static final class LocalArrangement {
int[] vs;
- int n;
+ int n;
- /** New local arrangement. */
+ /**
+ * New local arrangement.
+ */
private LocalArrangement() {
this.vs = new int[4];
}
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+libbeam-java (1.3.6-1) unstable; urgency=medium
+
+ * New upstream version 1.3.6
+ * Drop ${maven:CompileDepends} from Depends.
+
+ -- Andrius Merkys <merkys at debian.org> Tue, 10 Sep 2024 09:28:50 -0400
+
libbeam-java (1.3.5-2) unstable; urgency=medium
* Upload to unstable.
=====================================
debian/control
=====================================
@@ -21,7 +21,6 @@ Homepage: https://github.com/johnmay/beam/
Package: libbeam-java
Architecture: all
Depends:
- ${maven:CompileDepends},
${maven:Depends},
${misc:Depends},
Suggests:
=====================================
debian/copyright
=====================================
@@ -7,7 +7,7 @@ Copyright: 2013, European Bioinformatics Institute (EMBL-EBI)
License: BSD-2-clause
Files: debian/*
-Copyright: 2019-2023, Andrius Merkys <merkys at debian.org>
+Copyright: 2019-2024, Andrius Merkys <merkys at debian.org>
License: BSD-2-clause
License: BSD-2-clause
=====================================
exec/pom.xml
=====================================
@@ -5,7 +5,7 @@
<parent>
<artifactId>beam</artifactId>
<groupId>uk.ac.ebi.beam</groupId>
- <version>1.3.5</version>
+ <version>1.3.6</version>
</parent>
<modelVersion>4.0.0</modelVersion>
=====================================
func/pom.xml
=====================================
@@ -5,7 +5,7 @@
<parent>
<artifactId>beam</artifactId>
<groupId>uk.ac.ebi.beam</groupId>
- <version>1.3.5</version>
+ <version>1.3.6</version>
</parent>
<modelVersion>4.0.0</modelVersion>
=====================================
func/src/main/java/uk/ac/ebi/beam/AddDirectionalLabels.java
=====================================
@@ -246,14 +246,16 @@ final class AddDirectionalLabels
return Status.COMPLETED;
break;
case UP:
+ case UP_AROMATIC:
case DOWN:
+ case DOWN_AROMATIC:
if (explicit != null) {
if (acc.containsKey(explicit))
explicit = acc.get(explicit);
// original bonds are invalid
- if ((f.bond() == Bond.UP || f.bond() == Bond.DOWN) && explicit.bond(u).inverse() != f.bond(u)) {
+ if ((f.bond().directional()) && explicit.bond(u).inverse() != f.bond(u)) {
return Status.INVALID;
}
=====================================
func/src/main/java/uk/ac/ebi/beam/NormaliseDirectionalLabels.java
=====================================
@@ -182,7 +182,7 @@ final class NormaliseDirectionalLabels
if (first == null)
return;
if (ordering[first.other(u)] < ordering[u]) {
- if (first.bond(u) == Bond.UP)
+ if (first.bond(u) == Bond.UP || first.bond(u) == Bond.UP_AROMATIC)
invertExistingDirectionalLabels(g,
u,
new BitSet(),
@@ -198,7 +198,7 @@ final class NormaliseDirectionalLabels
u);
}
else {
- if (first.bond(u) == Bond.DOWN)
+ if (first.bond(u) == Bond.DOWN || first.bond(u) == Bond.DOWN_AROMATIC)
invertExistingDirectionalLabels(g,
u,
new BitSet(),
@@ -220,7 +220,7 @@ final class NormaliseDirectionalLabels
final int d = g.degree(u);
for (int j = 0; j < d; ++j) {
final Edge f = g.edgeAt(u, j);
- if (f.bond() == Bond.UP || f.bond() == Bond.DOWN) {
+ if (f.bond().directional()) {
if (first == null || ordering[f.other(u)] < ordering[first.other(u)])
first = f;
}
=====================================
func/src/main/java/uk/ac/ebi/beam/RemoveUpDownBonds.java
=====================================
@@ -162,6 +162,8 @@ final class RemoveUpDownBonds extends AbstractFunction<Graph,Graph> {
break;
case UP:
case DOWN:
+ case UP_AROMATIC:
+ case DOWN_AROMATIC:
edges.add(f);
break;
}
=====================================
func/src/main/java/uk/ac/ebi/beam/ToTrigonalTopology.java
=====================================
@@ -63,8 +63,7 @@ final class ToTrigonalTopology extends AbstractFunction<Graph,Graph> {
// change edges (only changed added to replacement)
for (int u = 0; u < g.order(); u++) {
for (final Edge e : g.edges(u)) {
- if (e.other(u) > u && e.bond() == Bond.UP || e
- .bond() == Bond.DOWN) {
+ if (e.other(u) > u && e.bond().directional()) {
replacements.put(e,
new Edge(u, e.other(u), Bond.IMPLICIT));
}
@@ -181,11 +180,11 @@ final class ToTrigonalTopology extends AbstractFunction<Graph,Graph> {
}
static boolean isUp(Bond b) {
- return b == Bond.UP;
+ return b == Bond.UP || b == Bond.UP_AROMATIC;
}
static boolean isDown(Bond b) {
- return b == Bond.DOWN;
+ return b == Bond.DOWN || b == Bond.DOWN_AROMATIC;
}
private List<Edge> doubleBondLabelledEdges(Graph g) {
=====================================
pom.xml
=====================================
@@ -7,7 +7,7 @@
<description>SMILES parsing and generation library for cheminformatics</description>
<url>http://www.github.com/johnmay/beam/</url>
<packaging>pom</packaging>
- <version>1.3.5</version>
+ <version>1.3.6</version>
<modules>
<module>core</module>
<module>func</module>
@@ -93,8 +93,8 @@
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
- <version>1.6.3</version>
- <extensions>false</extensions>
+ <version>1.6.13</version>
+ <extensions>true</extensions>
<configuration>
<serverId>ossrh</serverId>
<nexusUrl>https://oss.sonatype.org/</nexusUrl>
@@ -104,7 +104,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
- <version>1.5</version>
+ <version>1.6</version>
<executions>
<execution>
<id>sign-artifacts</id>
@@ -112,13 +112,21 @@
<goals>
<goal>sign</goal>
</goals>
+ <configuration>
+ <executable>gpg</executable>
+ <gpgArguments>
+ <arg>--pinentry-mode</arg>
+ <arg>loopback</arg>
+ </gpgArguments>
+ <passphrase>${gpg.passphrase}</passphrase>
+ </configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
- <version>2.2.1</version>
+ <version>3.2.1</version>
<executions>
<execution>
<id>attach-sources</id>
@@ -131,7 +139,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
- <version>2.9.1</version>
+ <version>3.3.1</version>
<executions>
<execution>
<id>attach-javadocs</id>
View it on GitLab: https://salsa.debian.org/java-team/libbeam-java/-/compare/5501cc0ef5d55752496e525f8522c06815ab6a63...91a5ce3afe5fb0854fc3ed5d42e192165af06a9b
--
View it on GitLab: https://salsa.debian.org/java-team/libbeam-java/-/compare/5501cc0ef5d55752496e525f8522c06815ab6a63...91a5ce3afe5fb0854fc3ed5d42e192165af06a9b
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