From 8158f35cb3e149ba8079f798fe5688da632ea8de Mon Sep 17 00:00:00 2001 From: John Mayfield Date: Wed, 22 Dec 2021 12:46:13 +0000 Subject: [PATCH] Significant dependency cleanup in the descriptor/qsar modules. --- descriptor/cip/pom.xml | 16 --- descriptor/fingerprint/pom.xml | 25 +--- descriptor/ionpot/pom.xml | 114 +---------------- descriptor/qsar/pom.xml | 95 -------------- descriptor/qsaratomic/pom.xml | 76 +----------- descriptor/qsarbond/pom.xml | 87 ------------- descriptor/qsarcml/pom.xml | 21 ---- descriptor/qsarionpot/pom.xml | 205 +------------------------------ descriptor/qsarmolecular/pom.xml | 76 ++---------- descriptor/qsarprotein/pom.xml | 81 +----------- descriptor/qsarsubstance/pom.xml | 6 +- descriptor/signature/pom.xml | 48 -------- 12 files changed, 26 insertions(+), 824 deletions(-) diff --git a/descriptor/cip/pom.xml b/descriptor/cip/pom.xml index 3e6fe0280e1..443cb5c2363 100644 --- a/descriptor/cip/pom.xml +++ b/descriptor/cip/pom.xml @@ -28,16 +28,6 @@ hamcrest test - - uk.ac.ebi.beam - beam-core - test - - - uk.ac.ebi.beam - beam-func - test - ${project.groupId} cdk-interfaces @@ -78,12 +68,6 @@ ${project.parent.version} test - - ${project.groupId} - cdk-valencycheck - ${project.parent.version} - test - ${project.groupId} cdk-io diff --git a/descriptor/fingerprint/pom.xml b/descriptor/fingerprint/pom.xml index b5d950f1d48..aa8b5661e73 100644 --- a/descriptor/fingerprint/pom.xml +++ b/descriptor/fingerprint/pom.xml @@ -23,18 +23,6 @@ commons-math3 3.6.1 - - com.google.guava - guava - - - uk.ac.ebi.beam - beam-core - - - uk.ac.ebi.beam - beam-func - org.hamcrest hamcrest @@ -85,12 +73,6 @@ cdk-formula ${project.parent.version} - - ${project.groupId} - cdk-io - ${project.parent.version} - test - ${project.groupId} cdk-test @@ -123,9 +105,14 @@ ${project.parent.version} test + + org.openscience.cdk + cdk-ctab + ${project.parent.version} + ${project.groupId} - cdk-extra + cdk-atomtype ${project.parent.version} test diff --git a/descriptor/ionpot/pom.xml b/descriptor/ionpot/pom.xml index 3d269cd3ce4..8b1d22f8d1b 100644 --- a/descriptor/ionpot/pom.xml +++ b/descriptor/ionpot/pom.xml @@ -3,124 +3,12 @@ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> 4.0.0 - cdk-descriptor org.openscience.cdk 2.7-SNAPSHOT - cdk-ionpot - cdk-ionpot - - - junit - junit - test - - - org.hamcrest - hamcrest - test - - - gov.nist.math - jama - test - - - javax.vecmath - vecmath - test - - - xom - xom - test - - - ${project.groupId} - cdk-interfaces - ${project.parent.version} - - - ${project.groupId} - cdk-core - ${project.parent.version} - - - ${project.groupId} - cdk-standard - ${project.parent.version} - - - ${project.groupId} - cdk-libiocml - ${project.parent.version} - - - ${project.groupId} - cdk-valencycheck - ${project.parent.version} - - - ${project.groupId} - cdk-isomorphism - ${project.parent.version} - - - ${project.groupId} - cdk-dict - ${project.parent.version} - - - ${project.groupId} - cdk-charges - ${project.parent.version} - - - ${project.groupId} - cdk-reaction - ${project.parent.version} - - - ${project.groupId} - cdk-data - ${project.parent.version} - test - - - ${project.groupId} - cdk-silent - ${project.parent.version} - test - - - ${project.groupId} - cdk-extra - ${project.parent.version} - test - - - ${project.groupId} - cdk-io - ${project.parent.version} - test - - - ${project.groupId} - cdk-smiles - ${project.parent.version} - test - - - ${project.groupId} - cdk-test - ${project.parent.version} - test-jar - test - - - + Deprecated - Functionality moved to cdk-legacy diff --git a/descriptor/qsar/pom.xml b/descriptor/qsar/pom.xml index f48054bb4ba..852880a1d3d 100644 --- a/descriptor/qsar/pom.xml +++ b/descriptor/qsar/pom.xml @@ -14,38 +14,16 @@ cdk-qsar - - gov.nist.math - jama - - - javax.vecmath - vecmath - - - xom - xom - junit junit test - - org.hamcrest - hamcrest - test - ${project.groupId} cdk-interfaces ${project.parent.version} - - ${project.groupId} - cdk-core - ${project.parent.version} - ${project.groupId} cdk-standard @@ -57,54 +35,6 @@ ${project.parent.version} test - - ${project.groupId} - cdk-silent - ${project.parent.version} - test - - - ${project.groupId} - cdk-io - ${project.parent.version} - test - - - ${project.groupId} - cdk-pdb - ${project.parent.version} - test - - - ${project.groupId} - cdk-valencycheck - ${project.parent.version} - test - - - ${project.groupId} - cdk-extra - ${project.parent.version} - test - - - ${project.groupId} - cdk-reaction - ${project.parent.version} - test - - - ${project.groupId} - cdk-charges - ${project.parent.version} - test - - - ${project.groupId} - cdk-smiles - ${project.parent.version} - test - ${project.groupId} cdk-test @@ -112,31 +42,6 @@ test-jar test - - ${project.groupId} - cdk-builder3d - ${project.parent.version} - test - - - ${project.groupId} - cdk-forcefield - ${project.parent.version} - test - - - ${project.groupId} - cdk-sdg - ${project.parent.version} - test - - - ${project.groupId} - cdk-testdata - ${project.parent.version} - test-jar - test - diff --git a/descriptor/qsaratomic/pom.xml b/descriptor/qsaratomic/pom.xml index 1f6dde794cb..55d704bea90 100644 --- a/descriptor/qsaratomic/pom.xml +++ b/descriptor/qsaratomic/pom.xml @@ -14,29 +14,14 @@ cdk-qsaratomic - - gov.nist.math - jama - javax.vecmath vecmath - xom - xom - - - com.google.guava - guava - - - uk.ac.ebi.beam - beam-core - - - uk.ac.ebi.beam - beam-func + org.openscience.cdk + cdk-ctab + ${project.parent.version} junit @@ -63,16 +48,6 @@ cdk-standard ${project.parent.version} - - ${project.groupId} - cdk-valencycheck - ${project.parent.version} - - - ${project.groupId} - cdk-isomorphism - ${project.parent.version} - ${project.groupId} cdk-reaction @@ -93,11 +68,6 @@ cdk-qsar ${project.parent.version} - - ${project.groupId} - cdk-dict - ${project.parent.version} - ${project.groupId} cdk-data @@ -110,24 +80,6 @@ ${project.parent.version} test - - ${project.groupId} - cdk-io - ${project.parent.version} - test - - - ${project.groupId} - cdk-pdb - ${project.parent.version} - test - - - ${project.groupId} - cdk-extra - ${project.parent.version} - test - ${project.groupId} cdk-smiles @@ -141,12 +93,6 @@ test-jar test - - ${project.groupId} - cdk-builder3d - ${project.parent.version} - test - ${project.groupId} cdk-qsar @@ -154,12 +100,6 @@ test-jar test - - ${project.groupId} - cdk-ionpot - ${project.parent.version} - test - ${project.groupId} cdk-diff @@ -171,14 +111,8 @@ cdk-testdata ${project.parent.version} test-jar - test + test - - ${project.groupId} - cdk-inchi - ${project.parent.version} - test - - + diff --git a/descriptor/qsarbond/pom.xml b/descriptor/qsarbond/pom.xml index e8518fefb8b..c6664129083 100644 --- a/descriptor/qsarbond/pom.xml +++ b/descriptor/qsarbond/pom.xml @@ -14,40 +14,15 @@ cdk-qsarbond - - gov.nist.math - jama - javax.vecmath vecmath - - xom - xom - - - com.google.guava - guava - - - uk.ac.ebi.beam - beam-core - - - uk.ac.ebi.beam - beam-func - junit junit test - - org.hamcrest - hamcrest - test - ${project.groupId} cdk-interfaces @@ -63,21 +38,6 @@ cdk-standard ${project.parent.version} - - ${project.groupId} - cdk-valencycheck - ${project.parent.version} - - - ${project.groupId} - cdk-reaction - ${project.parent.version} - - - ${project.groupId} - cdk-isomorphism - ${project.parent.version} - ${project.groupId} cdk-charges @@ -88,41 +48,12 @@ cdk-qsar ${project.parent.version} - - ${project.groupId} - cdk-dict - ${project.parent.version} - ${project.groupId} cdk-data ${project.parent.version} test - - ${project.groupId} - cdk-silent - ${project.parent.version} - test - - - ${project.groupId} - cdk-io - ${project.parent.version} - test - - - ${project.groupId} - cdk-pdb - ${project.parent.version} - test - - - ${project.groupId} - cdk-extra - ${project.parent.version} - test - ${project.groupId} cdk-smiles @@ -134,18 +65,6 @@ cdk-test ${project.parent.version} test-jar - test - - - ${project.groupId} - cdk-builder3d - ${project.parent.version} - test - - - ${project.groupId} - cdk-forcefield - ${project.parent.version} test @@ -155,12 +74,6 @@ test-jar test - - ${project.groupId} - cdk-ionpot - ${project.parent.version} - test - ${project.groupId} cdk-testdata diff --git a/descriptor/qsarcml/pom.xml b/descriptor/qsarcml/pom.xml index e13984addc4..d6bb32547a6 100644 --- a/descriptor/qsarcml/pom.xml +++ b/descriptor/qsarcml/pom.xml @@ -39,21 +39,6 @@ junit test - - org.hamcrest - hamcrest - test - - - javax.vecmath - vecmath - test - - - ${project.groupId} - cdk-core - ${project.parent.version} - ${project.groupId} cdk-interfaces @@ -81,12 +66,6 @@ test-jar test - - ${project.groupId} - cdk-io - ${project.parent.version} - test - ${project.groupId} cdk-testdata diff --git a/descriptor/qsarionpot/pom.xml b/descriptor/qsarionpot/pom.xml index 9c966626fe5..330737af03a 100644 --- a/descriptor/qsarionpot/pom.xml +++ b/descriptor/qsarionpot/pom.xml @@ -3,215 +3,12 @@ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> 4.0.0 - cdk-descriptor org.openscience.cdk 2.7-SNAPSHOT - cdk-qsarionpot - cdk-qsarionpot - - - junit - junit - test - - - org.hamcrest - hamcrest - test - - - javax.vecmath - vecmath - test - - - gov.nist.math - jama - test - - - xom - xom - test - - - com.google.guava - guava - test - - - uk.ac.ebi.beam - beam-core - test - - - uk.ac.ebi.beam - beam-func - test - - - ${project.groupId} - cdk-interfaces - ${project.parent.version} - - - ${project.groupId} - cdk-core - ${project.parent.version} - - - ${project.groupId} - cdk-standard - ${project.parent.version} - - - ${project.groupId} - cdk-valencycheck - ${project.parent.version} - - - ${project.groupId} - cdk-reaction - ${project.parent.version} - - - ${project.groupId} - cdk-charges - ${project.parent.version} - - - ${project.groupId} - cdk-qsar - ${project.parent.version} - - - ${project.groupId} - cdk-qsaratomic - ${project.parent.version} - - - ${project.groupId} - cdk-qsarbond - ${project.parent.version} - - - ${project.groupId} - cdk-qsarmolecular - ${project.parent.version} - - - ${project.groupId} - cdk-smiles - ${project.parent.version} - - - ${project.groupId} - cdk-smarts - ${project.parent.version} - - - ${project.groupId} - cdk-formula - ${project.parent.version} - - - ${project.groupId} - cdk-isomorphism - ${project.parent.version} - - - ${project.groupId} - cdk-dict - ${project.parent.version} - - - ${project.groupId} - cdk-ionpot - ${project.parent.version} - - - ${project.groupId} - cdk-data - ${project.parent.version} - test - - - ${project.groupId} - cdk-atomtype - ${project.parent.version} - test - - - ${project.groupId} - cdk-silent - ${project.parent.version} - test - - - ${project.groupId} - cdk-io - ${project.parent.version} - test - - - ${project.groupId} - cdk-extra - ${project.parent.version} - test - - - ${project.groupId} - cdk-test - ${project.parent.version} - test-jar - test - - - ${project.groupId} - cdk-qsar - ${project.parent.version} - test-jar - test - - - ${project.groupId} - cdk-qsaratomic - ${project.parent.version} - test-jar - test - - - ${project.groupId} - cdk-qsarbond - ${project.parent.version} - test-jar - test - - - ${project.groupId} - cdk-qsarmolecular - ${project.parent.version} - test-jar - test - - - ${project.groupId} - cdk-testdata - ${project.parent.version} - test-jar - test - - - ${project.groupId} - cdk-diff - ${project.parent.version} - test - - - + Deprecated - Functionality moved to cdk-legacy diff --git a/descriptor/qsarmolecular/pom.xml b/descriptor/qsarmolecular/pom.xml index 541caa502c3..f7622e6a68d 100644 --- a/descriptor/qsarmolecular/pom.xml +++ b/descriptor/qsarmolecular/pom.xml @@ -23,20 +23,13 @@ vecmath - xom - xom - - - com.google.guava - guava - - - uk.ac.ebi.beam - beam-core + org.openscience.cdk + cdk-ctab + ${project.parent.version} - uk.ac.ebi.beam - beam-func + xom + xom junit @@ -123,11 +116,6 @@ cdk-fingerprint ${project.parent.version} - - ${project.groupId} - cdk-hash - ${project.parent.version} - ${project.groupId} cdk-data @@ -146,30 +134,6 @@ ${project.parent.version} test - - ${project.groupId} - cdk-extra - ${project.parent.version} - test - - - ${project.groupId} - cdk-qsaratomic - ${project.parent.version} - test - - - ${project.groupId} - cdk-qsarbond - ${project.parent.version} - test - - - ${project.groupId} - cdk-builder3d - ${project.parent.version} - test - ${project.groupId} cdk-test @@ -191,23 +155,15 @@ test-jar test - - ${project.groupId} - cdk-qsarbond - ${project.parent.version} - test-jar - test - ${project.groupId} cdk-qsaratomic ${project.parent.version} - test-jar - test + test ${project.groupId} - cdk-ionpot + cdk-qsarbond ${project.parent.version} test @@ -224,24 +180,6 @@ ${project.parent.version} test - - ${project.groupId} - cdk-sdg - ${project.parent.version} - test - - - ${project.groupId} - cdk-forcefield - ${project.parent.version} - test - - - ${project.groupId} - cdk-ioformats - ${project.parent.version} - test - ${project.groupId} cdk-pdb diff --git a/descriptor/qsarprotein/pom.xml b/descriptor/qsarprotein/pom.xml index c286ff20084..516623ed0a8 100644 --- a/descriptor/qsarprotein/pom.xml +++ b/descriptor/qsarprotein/pom.xml @@ -14,28 +14,11 @@ cdk-qsarprotein - - gov.nist.math - jama - - - javax.vecmath - vecmath - - - xom - xom - junit junit test - - org.hamcrest - hamcrest - test - ${project.groupId} cdk-interfaces @@ -53,11 +36,6 @@ test test-jar - - ${project.groupId} - cdk-core - ${project.parent.version} - ${project.groupId} cdk-standard @@ -68,11 +46,6 @@ cdk-qsar ${project.parent.version} - - ${project.groupId} - cdk-pdb - ${project.parent.version} - ${project.groupId} cdk-silent @@ -87,37 +60,13 @@ ${project.groupId} - cdk-io - ${project.parent.version} - test - - - ${project.groupId} - cdk-valencycheck - ${project.parent.version} - test - - - ${project.groupId} - cdk-extra - ${project.parent.version} - test - - - ${project.groupId} - cdk-reaction - ${project.parent.version} - test - - - ${project.groupId} - cdk-charges + cdk-pdb ${project.parent.version} test ${project.groupId} - cdk-smiles + cdk-io ${project.parent.version} test @@ -128,30 +77,12 @@ test-jar test - - ${project.groupId} - cdk-builder3d - ${project.parent.version} - test - - - ${project.groupId} - cdk-forcefield - ${project.parent.version} - test - - - ${project.groupId} - cdk-sdg - ${project.parent.version} - test - ${project.groupId} cdk-qsar ${project.parent.version} test-jar - test + test ${project.groupId} @@ -167,12 +98,6 @@ test-jar test - - ${project.groupId} - cdk-dict - ${project.parent.version} - test - diff --git a/descriptor/qsarsubstance/pom.xml b/descriptor/qsarsubstance/pom.xml index ee0e4673869..9a0bdd5d092 100644 --- a/descriptor/qsarsubstance/pom.xml +++ b/descriptor/qsarsubstance/pom.xml @@ -20,9 +20,9 @@ test - org.hamcrest - hamcrest - test + org.openscience.cdk + cdk-standard + ${project.parent.version} ${project.groupId} diff --git a/descriptor/signature/pom.xml b/descriptor/signature/pom.xml index be5229c1b07..2c5052f80ab 100644 --- a/descriptor/signature/pom.xml +++ b/descriptor/signature/pom.xml @@ -19,34 +19,11 @@ signatures 1.1 - - uk.ac.ebi.beam - beam-core - - - uk.ac.ebi.beam - beam-func - junit junit test - - org.mockito - mockito-core - test - - - org.hamcrest - hamcrest - test - - - javax.vecmath - vecmath - test - ${project.groupId} cdk-interfaces @@ -74,30 +51,12 @@ ${project.parent.version} test - - ${project.groupId} - cdk-valencycheck - ${project.parent.version} - test - - - ${project.groupId} - cdk-io - ${project.parent.version} - test - ${project.groupId} cdk-smiles ${project.parent.version} test - - ${project.groupId} - cdk-extra - ${project.parent.version} - test - ${project.groupId} cdk-test @@ -118,13 +77,6 @@ ${project.parent.version} test - - ${project.groupId} - cdk-test-standard - ${project.parent.version} - test-jar - test -