From 2070a53397ef6265ea21352f34e9b2f4403d746e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tomasz=20=C5=BBok?= Date: Tue, 5 Feb 2019 11:03:17 +0100 Subject: [PATCH 01/14] Set version to *-SNAPSHOT --- mcq-cli | 2 +- mcq-clustering | 2 +- mcq-core | 2 +- mcq-gui | 2 +- pom.xml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/mcq-cli b/mcq-cli index c4b701b8..4c8598df 160000 --- a/mcq-cli +++ b/mcq-cli @@ -1 +1 @@ -Subproject commit c4b701b8af90e837662209f7c894e8a5604f48d7 +Subproject commit 4c8598dfda6abd9959345700c49689e8cda1cb53 diff --git a/mcq-clustering b/mcq-clustering index 48314627..521b6982 160000 --- a/mcq-clustering +++ b/mcq-clustering @@ -1 +1 @@ -Subproject commit 483146274502a9cc6c1fe00b7b6eaccc2cd55a73 +Subproject commit 521b698250df454804363dae5c65e468ea0f2cfb diff --git a/mcq-core b/mcq-core index 1715948a..6c833f14 160000 --- a/mcq-core +++ b/mcq-core @@ -1 +1 @@ -Subproject commit 1715948ac4aae372b7ed015531483c343848bcf7 +Subproject commit 6c833f146c043c454b4d8b89cf848909807e2f50 diff --git a/mcq-gui b/mcq-gui index 86a844f4..a5648a2e 160000 --- a/mcq-gui +++ b/mcq-gui @@ -1 +1 @@ -Subproject commit 86a844f41923f17775e9ac8e1aaad232d074b980 +Subproject commit a5648a2ed10cd8cb472c7e235ba5aada6a5f4fbb diff --git a/pom.xml b/pom.xml index a851d33d..6fa13040 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ pl.poznan.put mcq-parent - 1.5.1 + 1.6-SNAPSHOT pom From 568062736ea0143e080f287e862a6d1926d7c9a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tomasz=20=C5=BBok?= Date: Wed, 13 Feb 2019 15:37:52 +0100 Subject: [PATCH 02/14] Testing Jenkins --- Jenkinsfile | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 Jenkinsfile diff --git a/Jenkinsfile b/Jenkinsfile new file mode 100644 index 00000000..87061d6e --- /dev/null +++ b/Jenkinsfile @@ -0,0 +1,10 @@ +pipeline { + agent { docker { image 'maven' } } + stages { + stage('build') { + steps { + sh 'mvn --version' + } + } + } +} From 55c2ec2b1ed2cbc8e42375c3cc88b0b997abdce3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tomasz=20=C5=BBok?= Date: Wed, 13 Feb 2019 16:17:19 +0100 Subject: [PATCH 03/14] Improve Jenkinsfile --- Jenkinsfile | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/Jenkinsfile b/Jenkinsfile index 87061d6e..031550cb 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -3,8 +3,24 @@ pipeline { stages { stage('build') { steps { - sh 'mvn --version' + sh 'mvn compile' } } + stage('test') { + steps { + sh 'mvn test' + } + } + stage('package') { + steps { + sh 'mvn package' + } + } + } + post { + always { + archiveArtifacts artifacts: '*/target/*.jar', fingerprint: true + junit '*/target/surefire-reports/*.xml' + } } } From a1a3463516d1790503505c6151de05edc1123dfa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tomasz=20=C5=BBok?= Date: Wed, 13 Feb 2019 16:34:49 +0100 Subject: [PATCH 04/14] Accept changes in TzokCommons --- pom.xml | 2 +- tzok-commons | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index 6fa13040..f3b652aa 100644 --- a/pom.xml +++ b/pom.xml @@ -205,7 +205,7 @@ pl.poznan.put TzokCommons - 1.5.1 + 1.6-SNAPSHOT diff --git a/tzok-commons b/tzok-commons index bb3ab889..ae3ec000 160000 --- a/tzok-commons +++ b/tzok-commons @@ -1 +1 @@ -Subproject commit bb3ab889d34b87f66a6d131d97f0742a3276e206 +Subproject commit ae3ec000e6989359721fa4971f00325320c50b3c From ede6e9a17998a18635e83ea615e7edddc0ba4592 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tomasz=20=C5=BBok?= Date: Wed, 13 Feb 2019 16:38:21 +0100 Subject: [PATCH 05/14] Use dependencies in *-SNAPSHOT versions --- bio-commons | 2 +- circular | 2 +- pom.xml | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/bio-commons b/bio-commons index 9d92c0ad..0b97285e 160000 --- a/bio-commons +++ b/bio-commons @@ -1 +1 @@ -Subproject commit 9d92c0adadaead3b6535a59772afa88fce085023 +Subproject commit 0b97285ec3eeec932e01e362aea7381dd197ed25 diff --git a/circular b/circular index 44a599d2..baa8fcf1 160000 --- a/circular +++ b/circular @@ -1 +1 @@ -Subproject commit 44a599d2b5ce610da0a776080b355b5ef9d09c88 +Subproject commit baa8fcf111f4464161c37a7e3fc0bf8b26d5537e diff --git a/pom.xml b/pom.xml index f3b652aa..274b485d 100644 --- a/pom.xml +++ b/pom.xml @@ -193,13 +193,13 @@ pl.poznan.put BioCommons - 2.2.1 + 2.3-SNAPSHOT pl.poznan.put circular - 1.3.2 + 1.4-SNAPSHOT From 8e9d5cc6ff6f9f6787c13beab777a09b02d17f9f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tomasz=20=C5=BBok?= Date: Wed, 13 Feb 2019 16:40:58 +0100 Subject: [PATCH 06/14] Accept changes upstream --- bio-commons | 2 +- circular | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bio-commons b/bio-commons index 0b97285e..c6882366 160000 --- a/bio-commons +++ b/bio-commons @@ -1 +1 @@ -Subproject commit 0b97285ec3eeec932e01e362aea7381dd197ed25 +Subproject commit c688236681443f4730990d122e8b9cf9dd318a7d diff --git a/circular b/circular index baa8fcf1..0bf15e35 160000 --- a/circular +++ b/circular @@ -1 +1 @@ -Subproject commit baa8fcf111f4464161c37a7e3fc0bf8b26d5537e +Subproject commit 0bf15e359ade44cc2b8b322aaef292947ca7f626 From 96400ef97b6f4e1e0f918b0eb9602df416e71970 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tomasz=20=C5=BBok?= Date: Fri, 22 Feb 2019 14:23:56 +0100 Subject: [PATCH 07/14] Accept changes upstream --- mcq-cli | 2 +- mcq-core | 2 +- tzok-commons | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/mcq-cli b/mcq-cli index 4c8598df..fa2f6d07 160000 --- a/mcq-cli +++ b/mcq-cli @@ -1 +1 @@ -Subproject commit 4c8598dfda6abd9959345700c49689e8cda1cb53 +Subproject commit fa2f6d075659ebb778c38a66a7c17b65fa06e470 diff --git a/mcq-core b/mcq-core index 6c833f14..f5fa3317 160000 --- a/mcq-core +++ b/mcq-core @@ -1 +1 @@ -Subproject commit 6c833f146c043c454b4d8b89cf848909807e2f50 +Subproject commit f5fa3317e21a8c3eff46c741159f205816e8fbd8 diff --git a/tzok-commons b/tzok-commons index ae3ec000..ee00a33d 160000 --- a/tzok-commons +++ b/tzok-commons @@ -1 +1 @@ -Subproject commit ae3ec000e6989359721fa4971f00325320c50b3c +Subproject commit ee00a33d78d4e7375e494a23cb0f5033af0ffefc From b14bc859203330592e1d40a5a71426d86a40a236 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tomasz=20=C5=BBok?= Date: Fri, 22 Feb 2019 14:38:09 +0100 Subject: [PATCH 08/14] Accept changes upstream --- bio-commons | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bio-commons b/bio-commons index c6882366..ff95bb89 160000 --- a/bio-commons +++ b/bio-commons @@ -1 +1 @@ -Subproject commit c688236681443f4730990d122e8b9cf9dd318a7d +Subproject commit ff95bb89116942d08441fd509e806b3033cd8f79 From 136f50412163e7109bac146917398d9ec52c8f6a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tomasz=20=C5=BBok?= Date: Fri, 22 Feb 2019 14:38:18 +0100 Subject: [PATCH 09/14] Improve documentation --- README.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 0a327584..946f0f06 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,14 @@ Mean of Circular Quantities (MCQ) is a dissimilarity measure useful in comparison of 3D protein and/or RNA structures. It calculates an average difference between corresponding torsion angle values (rotations around bonds). More information can be found in: > Zok, T., Popenda, M., & Szachniuk, M. (2014). MCQ4Structures to compute similarity of molecule structures. Central European Journal of Operations Research, 22(3), 457–473. https://doi.org/10.1007/s10100-013-0296-5 +## Installation + +```sh +git clone https://github.com/RNA-Puzzles/mcq-parent +git submodule update --init +mvn install +``` + ## Contents This project consists of a few subprojets: @@ -21,4 +29,4 @@ This project consists of a few subprojets: - Use `pl.poznan.put.clustering.hierarchical.Clusterer` to construct dendrograms from a distance matrix (with `COMPLETE`, `SINGLE` or `AVERAGE` linkage option) - Use `pl.poznan.put.clustering.partitional.KMedoids` to perform partitional clustering based on distance matrix -- Use `pl.poznan.put.clustering.partitional.KScanner#parallelScan` to find optimum number of clusters with respect to silhouette score \ No newline at end of file +- Use `pl.poznan.put.clustering.partitional.KScanner#parallelScan` to find optimum number of clusters with respect to silhouette score From f52aa6e4ba718c76b3535c410b1b4fac50d408fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tomasz=20=C5=BBok?= Date: Fri, 22 Feb 2019 14:39:33 +0100 Subject: [PATCH 10/14] Fix documentation --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 946f0f06..610321db 100644 --- a/README.md +++ b/README.md @@ -7,6 +7,7 @@ Mean of Circular Quantities (MCQ) is a dissimilarity measure useful in compariso ```sh git clone https://github.com/RNA-Puzzles/mcq-parent +cd mcq-parent git submodule update --init mvn install ``` From 77367eccfbba36e094e95de836a574377fbcd863 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tomasz=20=C5=BBok?= Date: Wed, 5 Jun 2019 15:30:39 +0200 Subject: [PATCH 11/14] Accept new commits in subprojects --- Jenkinsfile | 26 -------------------------- bio-commons | 2 +- mcq-cli | 2 +- mcq-clustering | 2 +- mcq-core | 2 +- mcq-gui | 2 +- 6 files changed, 5 insertions(+), 31 deletions(-) delete mode 100644 Jenkinsfile diff --git a/Jenkinsfile b/Jenkinsfile deleted file mode 100644 index 031550cb..00000000 --- a/Jenkinsfile +++ /dev/null @@ -1,26 +0,0 @@ -pipeline { - agent { docker { image 'maven' } } - stages { - stage('build') { - steps { - sh 'mvn compile' - } - } - stage('test') { - steps { - sh 'mvn test' - } - } - stage('package') { - steps { - sh 'mvn package' - } - } - } - post { - always { - archiveArtifacts artifacts: '*/target/*.jar', fingerprint: true - junit '*/target/surefire-reports/*.xml' - } - } -} diff --git a/bio-commons b/bio-commons index ff95bb89..f3d6c7f4 160000 --- a/bio-commons +++ b/bio-commons @@ -1 +1 @@ -Subproject commit ff95bb89116942d08441fd509e806b3033cd8f79 +Subproject commit f3d6c7f45fd9b00c6d8020b90064025fede4b9c3 diff --git a/mcq-cli b/mcq-cli index fa2f6d07..3370a144 160000 --- a/mcq-cli +++ b/mcq-cli @@ -1 +1 @@ -Subproject commit fa2f6d075659ebb778c38a66a7c17b65fa06e470 +Subproject commit 3370a1448f1b195c349cd25aedbe114a3795beae diff --git a/mcq-clustering b/mcq-clustering index 521b6982..8353fde4 160000 --- a/mcq-clustering +++ b/mcq-clustering @@ -1 +1 @@ -Subproject commit 521b698250df454804363dae5c65e468ea0f2cfb +Subproject commit 8353fde40ecc7cd7bd136ee6f5f3fd5827bef52c diff --git a/mcq-core b/mcq-core index f5fa3317..ffd97a18 160000 --- a/mcq-core +++ b/mcq-core @@ -1 +1 @@ -Subproject commit f5fa3317e21a8c3eff46c741159f205816e8fbd8 +Subproject commit ffd97a18a07acbadaddc633456d48146b416fca9 diff --git a/mcq-gui b/mcq-gui index a5648a2e..f15d11a5 160000 --- a/mcq-gui +++ b/mcq-gui @@ -1 +1 @@ -Subproject commit a5648a2ed10cd8cb472c7e235ba5aada6a5f4fbb +Subproject commit f15d11a5df4117c38ffa4bf659cd09d341b4f502 From 477de09fde769c2e3afe772b495869a329e1274e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tomasz=20=C5=BBok?= Date: Wed, 5 Jun 2019 16:09:37 +0200 Subject: [PATCH 12/14] Accept changes in subprojects --- bio-commons | 2 +- circular | 2 +- mcq-gui | 2 +- pom.xml | 11 ++--------- tzok-commons | 2 +- 5 files changed, 6 insertions(+), 13 deletions(-) diff --git a/bio-commons b/bio-commons index f3d6c7f4..9d29498d 160000 --- a/bio-commons +++ b/bio-commons @@ -1 +1 @@ -Subproject commit f3d6c7f45fd9b00c6d8020b90064025fede4b9c3 +Subproject commit 9d29498d5a3c632e0b46828dba6a41e7c0a9b84c diff --git a/circular b/circular index 0bf15e35..44a599d2 160000 --- a/circular +++ b/circular @@ -1 +1 @@ -Subproject commit 0bf15e359ade44cc2b8b322aaef292947ca7f626 +Subproject commit 44a599d2b5ce610da0a776080b355b5ef9d09c88 diff --git a/mcq-gui b/mcq-gui index f15d11a5..51933793 160000 --- a/mcq-gui +++ b/mcq-gui @@ -1 +1 @@ -Subproject commit f15d11a5df4117c38ffa4bf659cd09d341b4f502 +Subproject commit 51933793c5ef750148ff26f4fb9b0d39315ed3ca diff --git a/pom.xml b/pom.xml index 274b485d..0600479b 100644 --- a/pom.xml +++ b/pom.xml @@ -21,7 +21,6 @@ 1.10 5.2.0 - 2.9.8 UTF-8 1.7.25 @@ -34,12 +33,6 @@ 1.2.3 - - com.fasterxml.jackson.core - jackson-databind - ${jackson.version} - - commons-cli commons-cli @@ -199,13 +192,13 @@ pl.poznan.put circular - 1.4-SNAPSHOT + 1.3.2 pl.poznan.put TzokCommons - 1.6-SNAPSHOT + 1.6 diff --git a/tzok-commons b/tzok-commons index ee00a33d..e1e26918 160000 --- a/tzok-commons +++ b/tzok-commons @@ -1 +1 @@ -Subproject commit ee00a33d78d4e7375e494a23cb0f5033af0ffefc +Subproject commit e1e269189772cdba984500981b336cf198a978c9 From 362805528c7f91af215906c1941fdb9220d3045d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tomasz=20=C5=BBok?= Date: Wed, 5 Jun 2019 16:10:09 +0200 Subject: [PATCH 13/14] Accept changes --- mcq-cli | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mcq-cli b/mcq-cli index 3370a144..0dcf91fd 160000 --- a/mcq-cli +++ b/mcq-cli @@ -1 +1 @@ -Subproject commit 3370a1448f1b195c349cd25aedbe114a3795beae +Subproject commit 0dcf91fd4efa7e3c69350fe02f65d1703fb60bd4 From 2bb55e45e0ea452fafc8be62b72e3eb55f519635 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tomasz=20=C5=BBok?= Date: Wed, 5 Jun 2019 16:57:19 +0200 Subject: [PATCH 14/14] All subprojects are set up correctly --- bio-commons | 2 +- mcq-cli | 2 +- mcq-clustering | 2 +- mcq-core | 2 +- mcq-gui | 2 +- pom.xml | 8 ++++++-- 6 files changed, 11 insertions(+), 7 deletions(-) diff --git a/bio-commons b/bio-commons index 9d29498d..d601b4f4 160000 --- a/bio-commons +++ b/bio-commons @@ -1 +1 @@ -Subproject commit 9d29498d5a3c632e0b46828dba6a41e7c0a9b84c +Subproject commit d601b4f47f56f13db8e4931b003e9a121377dc1f diff --git a/mcq-cli b/mcq-cli index 0dcf91fd..1f771adf 160000 --- a/mcq-cli +++ b/mcq-cli @@ -1 +1 @@ -Subproject commit 0dcf91fd4efa7e3c69350fe02f65d1703fb60bd4 +Subproject commit 1f771adfeab04995ac9c8298411cf557a2f60e9d diff --git a/mcq-clustering b/mcq-clustering index 8353fde4..73a592de 160000 --- a/mcq-clustering +++ b/mcq-clustering @@ -1 +1 @@ -Subproject commit 8353fde40ecc7cd7bd136ee6f5f3fd5827bef52c +Subproject commit 73a592de52b5961f4944aeb42e0dd19cddeb8420 diff --git a/mcq-core b/mcq-core index ffd97a18..9d82d724 160000 --- a/mcq-core +++ b/mcq-core @@ -1 +1 @@ -Subproject commit ffd97a18a07acbadaddc633456d48146b416fca9 +Subproject commit 9d82d724587f87a0b69aefa894ed50dc38e41e4a diff --git a/mcq-gui b/mcq-gui index 51933793..e39fefe0 160000 --- a/mcq-gui +++ b/mcq-gui @@ -1 +1 @@ -Subproject commit 51933793c5ef750148ff26f4fb9b0d39315ed3ca +Subproject commit e39fefe05b435e179a65863edbd2c730392aa425 diff --git a/pom.xml b/pom.xml index 0600479b..48374b26 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ pl.poznan.put mcq-parent - 1.6-SNAPSHOT + 1.6 pom @@ -126,6 +126,10 @@ log4j-slf4j-impl org.apache.logging.log4j + + jackson-databind + com.fasterxml.jackson.core + @@ -186,7 +190,7 @@ pl.poznan.put BioCommons - 2.3-SNAPSHOT + 2.3.2