From 255c749c6d3143203a98a44bdd296fe501678bbf Mon Sep 17 00:00:00 2001 From: Mario Frank Date: Thu, 22 Jan 2026 09:32:38 +0100 Subject: [PATCH 1/7] [Prepare] Bump to v2.6.0, add developer, update group id --- pom.xml | 24 +++++++++++++++--------- 1 file changed, 15 insertions(+), 9 deletions(-) diff --git a/pom.xml b/pom.xml index 2024029..63089ce 100644 --- a/pom.xml +++ b/pom.xml @@ -2,11 +2,11 @@ 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 - io.github.sanctuuary + org.workflomics APE - 2.5.3 + 2.6.0 jar - io.github.sanctuuary:APE + org.workflomics:APE APE is a command line tool and an API for the automated exploration of possible computational pipelines (workflows) from large collections of computational tools. https://github.com/workflomics/ape @@ -23,6 +23,12 @@ Netherlands eScience Center https://www.esciencecenter.nl/ + + Mario Frank + mario.frank@uni-potsdam.de + University of Potsdam + https://www.uni-potsdam.de + scm:git:git://github.com/workflomics/ape.git @@ -31,8 +37,8 @@ UTF-8 - 17 - 17 + 21 + 21 @@ -41,8 +47,8 @@ maven-compiler-plugin 3.8.1 - 17 - 17 + 21 + 21 -Xlint:all @@ -67,8 +73,8 @@ implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer"> nl.uu.cs.ape.Main - 17 - 17 + 21 + 21 From e3e04ecee23ca1546dd8f9d7ab65df81aea4fe73 Mon Sep 17 00:00:00 2001 From: Mario Frank Date: Thu, 22 Jan 2026 09:43:29 +0100 Subject: [PATCH 2/7] [Update] Set Java version to 17 for Github workflow --- pom.xml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/pom.xml b/pom.xml index 63089ce..37b52f6 100644 --- a/pom.xml +++ b/pom.xml @@ -37,8 +37,8 @@ UTF-8 - 21 - 21 + 17 + 17 @@ -47,8 +47,8 @@ maven-compiler-plugin 3.8.1 - 21 - 21 + 17 + 17 -Xlint:all @@ -73,8 +73,8 @@ implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer"> nl.uu.cs.ape.Main - 21 - 21 + 17 + 17 From 82554dc2e8634e2e5623cbab93941fd158af0193 Mon Sep 17 00:00:00 2001 From: Mario Frank Date: Thu, 22 Jan 2026 16:13:59 +0100 Subject: [PATCH 3/7] [Update] Add Charlotte Grunert as developer --- pom.xml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/pom.xml b/pom.xml index 37b52f6..de1f3e2 100644 --- a/pom.xml +++ b/pom.xml @@ -29,6 +29,12 @@ University of Potsdam https://www.uni-potsdam.de + + Charlotte Grunert + charlotte.grunert@uni-potsdam.de + University of Potsdam + https://www.uni-potsdam.de + scm:git:git://github.com/workflomics/ape.git From c062c3ffeb9ea885b127c9c63910bc1c68833f86 Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Mon, 26 Jan 2026 23:34:22 +0100 Subject: [PATCH 4/7] Updated Vedran's info --- pom.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pom.xml b/pom.xml index de1f3e2..ca1d670 100644 --- a/pom.xml +++ b/pom.xml @@ -19,9 +19,9 @@ Vedran Kasalica - v.kasalica@esciencecenter.nl - Netherlands eScience Center - https://www.esciencecenter.nl/ + vedran.kasalica@health-ri.nl + Health-RI + https://www.health-ri.nl/ Mario Frank From 4b37d760e1cfce4cd9e5d81ed0f669f747a14545 Mon Sep 17 00:00:00 2001 From: Mario Frank Date: Tue, 27 Jan 2026 11:21:17 +0100 Subject: [PATCH 5/7] [Update] Make CITATION.cff consistent to POM concerning information of @vedran-kasalica --- CITATION.cff | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index ede79a0..6747a53 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -7,8 +7,8 @@ type: software authors: - given-names: Vedran family-names: Kasalica - email: v.kasalica@esciencecenter.nl - affiliation: Netherlands eScience Center, Netherlands + email: vedran.kasalica@health-ri.nl + affiliation: Health-RI, Netherlands orcid: 'https://orcid.org/0000-0002-0097-1056' - given-names: Anna-Lena family-names: Lamprecht From 533490674698b0897e4f5be88ea78d9a8722f91e Mon Sep 17 00:00:00 2001 From: Mario Frank Date: Tue, 27 Jan 2026 12:17:09 +0100 Subject: [PATCH 6/7] [Update] Update README.md referring to both the old and new group id. Also update main contacts. --- README.md | 57 ++++++++++++++++++++++++++++++++----------------------- 1 file changed, 33 insertions(+), 24 deletions(-) diff --git a/README.md b/README.md index 5084578..4166f46 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ | Badges | | |:----:|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | **Fairness** | [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu) [![OpenSSF Best Practices](https://bestpractices.coreinfrastructure.org/projects/5749/badge)](https://www.bestpractices.dev/projects/5749) | -| **Packages and Releases** | [![Latest release](https://img.shields.io/github/release/workflomics/ape.svg)](https://github.com/workflomics/ape/releases/latest) [![Maven Central](https://badgen.net/maven/v/maven-central/io.github.sanctuuary/APE)](https://mvnrepository.com/artifact/io.github.sanctuuary/APE) [![Static Badge](https://img.shields.io/badge/RSD-APE-ape)](https://research-software-directory.org/software/ape-automated-pipeline-explorer) +| **Packages and Releases** | [![Latest release](https://img.shields.io/github/release/workflomics/ape.svg)](https://github.com/workflomics/ape/releases/latest) [![Maven Central](https://badgen.net/maven/v/maven-central/org.workflomics/APE)](https://mvnrepository.com/artifact/org.workflomics/APE) [![Static Badge](https://img.shields.io/badge/RSD-APE-ape)](https://research-software-directory.org/software/ape-automated-pipeline-explorer) | **Build Status** | [![Build](https://github.com/workflomics/ape/actions/workflows/mvnbuild.yml/badge.svg)](https://github.com/workflomics/ape/actions/workflows/mvnbuild.yml) [![CodeQL Analysis](https://github.com/workflomics/ape/actions/workflows/codeql.yml/badge.svg)](https://github.com/workflomics/ape/actions/workflows/codeql.yml) | | **Documentation** | [![Documentation Status](https://readthedocs.org/projects/ape-framework/badge/?version=latest)](https://ape-framework.readthedocs.io/en/latest/?badge=latest) | | **DOI** | [![DOI](https://zenodo.org/badge/227861653.svg)](https://zenodo.org/badge/latestdoi/227861653) | @@ -33,7 +33,7 @@ To [run](https://github.com/workflomics/ape#how-to-run-ape-from-the-command-line To [build](https://github.com/workflomics/ape#build-ape-from-source-using-maven) APE from source, [Maven 3.3+](https://maven.apache.org/download.cgi) has to be installed as well (use the command `$ mvn -version` to check your local version). -> **_Note:_** Building APE from source is not required to run it, as the latest stable version is available at [maven repository](https://mvnrepository.com/artifact/io.github.sanctuuary/APE/latest). +> **_Note:_** Building APE from source is not required to run it, as the latest stable version is available at [maven repository](https://mvnrepository.com/artifact/org.workflomics/APE/latest). ### Releases @@ -45,6 +45,19 @@ To [build](https://github.com/workflomics/ape#build-ape-from-source-using-maven) To add a dependency on APE using Maven, use the following: +```xml + + + org.workflomics + APE + 2.6.x + +``` + +For information regarding **Gradle**, **Ivy**, etc. we refer to the [APE mvn repository](https://mvnrepository.com/artifact/org.workflomics/APE/latest). + +To add a dependency on older versions of APE using Maven, use the following: + ```xml @@ -60,17 +73,18 @@ For information regarding **Gradle**, **Ivy**, etc. we refer to the [APE mvn rep | Date | Version | Download | |------------|---------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| 15-07-2020 | 1.0.1 | [jar](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.0.1/APE-1.0.1.jar), [executable](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.0.1/APE-1.0.1-executable.jar), [javadoc](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.0.1/APE-1.0.1-javadoc.jar), [sources](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.0.1/APE-1.0.1-sources.jar) | -| 02-05-2021 | 1.1.7 | [jar](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.1.7/APE-1.1.7.jar), [executable](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.1.7/APE-1.1.7-executable.jar), [javadoc](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.1.7/APE-1.1.7-javadoc.jar), [sources](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.1.7/APE-1.1.7-sources.jar) | -| 20-12-2021 | 1.1.12 | [jar](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.1.12/APE-1.1.12.jar), [executable](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.1.12/APE-1.1.12-executable.jar), [javadoc](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.1.12/APE-1.1.12-javadoc.jar), [sources](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.1.12/APE-1.1.12-sources.jar) | -| 17-05-2022 | 2.0.0 | [jar](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.0.0/APE-2.0.0.jar), [executable](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.0.0/APE-2.0.0-executable.jar), [javadoc](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.0.0/APE-2.0.0-javadoc.jar), [sources](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.0.0/APE-2.0.0-sources.jar) | -| 19-02-2024 | 2.3.0 | [jar](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.3.0/APE-2.3.0.jar), [executable](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.3.0/APE-2.3.0-executable.jar), [javadoc](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.3.0/APE-2.3.0-javadoc.jar), [sources](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.3.0/APE-2.3.0-sources.jar) | -| 09-06-2025 | 2.5.0 | [jar](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.0/APE-2.5.0.jar), [executable](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.0/APE-2.5.0-executable.jar), [javadoc](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.0/APE-2.5.0-javadoc.jar), [sources](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.0/APE-2.5.0-sources.jar) | -| 10-06-2025 | 2.5.2 | [jar](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.2/APE-2.5.2.jar), [executable](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.2/APE-2.5.2-executable.jar), [javadoc](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.2/APE-2.5.2-javadoc.jar), [sources](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.2/APE-2.5.2-sources.jar) | | 29-09-2025 | 2.5.3 | [jar](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.3/APE-2.5.3.jar), [executable](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.3/APE-2.5.3-executable.jar), [javadoc](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.3/APE-2.5.3-javadoc.jar), [sources](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.3/APE-2.5.3-sources.jar) | +| 10-06-2025 | 2.5.2 | [jar](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.2/APE-2.5.2.jar), [executable](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.2/APE-2.5.2-executable.jar), [javadoc](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.2/APE-2.5.2-javadoc.jar), [sources](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.2/APE-2.5.2-sources.jar) | +| 09-06-2025 | 2.5.0 | [jar](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.0/APE-2.5.0.jar), [executable](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.0/APE-2.5.0-executable.jar), [javadoc](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.0/APE-2.5.0-javadoc.jar), [sources](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.5.0/APE-2.5.0-sources.jar) | +| 19-02-2024 | 2.3.0 | [jar](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.3.0/APE-2.3.0.jar), [executable](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.3.0/APE-2.3.0-executable.jar), [javadoc](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.3.0/APE-2.3.0-javadoc.jar), [sources](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.3.0/APE-2.3.0-sources.jar) | +| 17-05-2022 | 2.0.0 | [jar](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.0.0/APE-2.0.0.jar), [executable](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.0.0/APE-2.0.0-executable.jar), [javadoc](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.0.0/APE-2.0.0-javadoc.jar), [sources](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/2.0.0/APE-2.0.0-sources.jar) | +| 20-12-2021 | 1.1.12 | [jar](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.1.12/APE-1.1.12.jar), [executable](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.1.12/APE-1.1.12-executable.jar), [javadoc](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.1.12/APE-1.1.12-javadoc.jar), [sources](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.1.12/APE-1.1.12-sources.jar) | +| 02-05-2021 | 1.1.7 | [jar](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.1.7/APE-1.1.7.jar), [executable](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.1.7/APE-1.1.7-executable.jar), [javadoc](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.1.7/APE-1.1.7-javadoc.jar), [sources](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.1.7/APE-1.1.7-sources.jar) | +| 15-07-2020 | 1.0.1 | [jar](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.0.1/APE-1.0.1.jar), [executable](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.0.1/APE-1.0.1-executable.jar), [javadoc](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.0.1/APE-1.0.1-javadoc.jar), [sources](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/1.0.1/APE-1.0.1-sources.jar) | -The complete list of releases can be found on the [MVN Repository](https://mvnrepository.com/artifact/io.github.sanctuuary/APE). +The complete list of releases can be found on the [MVN Repository](https://mvnrepository.com/artifact/org.workflomics/APE). +Older releases (`< 2.6`), can be found in the previous [MVN Repository](https://mvnrepository.com/artifact/io.github.sanctuuary/APE). ### Build APE from source (using Maven) @@ -88,7 +102,7 @@ Automated workflow composition with APE can be performed through its command lin ### How to run APE from the command line -**APE-[latest]-executable.jar** is available in [maven repository](https://mvnrepository.com/artifact/io.github.sanctuuary/APE/latest). +**APE-[latest]-executable.jar** is available in [maven repository](https://mvnrepository.com/artifact/org.workflomics/APE/latest). When running APE-[latest]-executable.jar from the command line, it requires a JSON configuration file given as a parameter and executes the automated workflow composition process accordingly: @@ -113,7 +127,7 @@ or git clone https://github.com/sanctuuary/APE_UseCases.git ``` -Download the latest version of [`APE-[latest]-executable.jar`](https://repo.maven.apache.org/maven2/io/github/sanctuuary/APE/) and add it to the APE_UseCases directory (`~/git/APE_UseCases`) +Download the latest version of [`APE-[latest]-executable.jar`](https://repo.maven.apache.org/maven2/org/workflomics/APE/) and add it to the APE_UseCases directory (`~/git/APE_UseCases`) ```shell cd ~/git/APE_UseCases @@ -160,7 +174,8 @@ runConfig.setUseWorkflowInput(ConfigEnum.ONE); SATsolutionsList solutions2 = ape.runSynthesis(runConfig); ``` -For more information see [APE javadoc.io](https://javadoc.io/doc/io.github.sanctuuary/APE/latest/nl/uu/cs/ape/sat/APE.html) page. +For more information see [APE javadoc.io](https://javadoc.io/doc/org.workflomics/APE/latest/nl/uu/cs/ape/sat/APE.html) or +the [APE (< 2.6) javadoc.io](https://javadoc.io/doc/io.github.sanctuuary/APE/latest/nl/uu/cs/ape/sat/APE.html) page. ## APE v2 architecture @@ -171,27 +186,21 @@ The architecture of the APE v2 library is presented in the following figure. Com ## APE Web -Graphical Web Interface for the APE library is available at [APE Web](https://github.com/sanctuuary/APE-Web). +Graphical Web Interface for the APE library is available at [APE Web](https://github.com/Workflomics/APE-Web). ## Use Cases and Demos Our use cases are motivated by practical problems in various domains (e.g. bioinformatics, GIS [[3]](#3)). Different examples are available at the [APE Use Cases Repository](https://github.com/sanctuuary/APE_UseCases). - -## The APE team - -* Vedran Kasalica (v.kasalica[at]esciencecenter.nl), lead developer -* Maurin Voshol, student developer -* Koen Haverkort, student developer -* Anna-Lena Lamprecht (anna-lena.lamprecht[at]uni-potsdam.de), project initiator and principal investigator - ## Contact -For any questions concerning APE please get in touch with Vedran Kasalica (v.kasalica[at]esciencecenter.nl.nl). +For any questions concerning APE please get in touch with Anna-Lena Lamprecht (anna-lena.lamprecht[at]uni-potsdam.de). ## Contributions -We welcome all contributions (bug reports, bug fixes, feature requests, extensions, use cases, etc.) to APE. Please get in touch with Vedran Kasalica (v.kasalica[at]esciencecenter.nl.nl) to coordinate your contribution. We expect all contributors to follow our [Code of Conduct](https://github.com/workflomics/ape/blob/master/CODE_OF_CONDUCT.md). +We welcome all contributions (bug reports, bug fixes, feature requests, extensions, use cases, etc.) to APE. +Please get in touch with Anna-Lena Lamprecht (anna-lena.lamprecht[at]uni-potsdam.de) to coordinate your contribution. +We expect all contributors to follow our [Code of Conduct](https://github.com/workflomics/ape/blob/master/CODE_OF_CONDUCT.md). In case you have a specific request, want to report a bug or suggest a new constraint template please make an issue [here](https://github.com/workflomics/ape/issues/new). From deafab3b355d0596f64c8b1d7b12c971c300b08a Mon Sep 17 00:00:00 2001 From: Mario Frank Date: Mon, 9 Feb 2026 12:14:43 +0100 Subject: [PATCH 7/7] [Update] Update SECURITY.md and CHANGELOG.md --- CHANGELOG.md | 89 ++++++++++++++++++++++++++++++++++++++++++++++++++++ SECURITY.md | 13 ++++---- 2 files changed, 95 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f84f905..e066785 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,92 @@ +### APE 2.6.0 - Snakemake, Partial Workflows and Major Refactorings + +- Maven Group change to `org.workflomics` +- Snakemake output support by @CGru21 +- Added configuration for explicitly accepting or skipping `partial` outputs, i.e. outputs where the executed command is unknown by @eladrion +- Major refactoring +- Test resources improvements +- Markdown documentation updates (Releases, Maven Bundles, Security contacts, general contacts) + +### APE 2.5.3 - CWL Support Improvements, Bugfixes + +- Introduce a new CWL parser and related classes to support APE semantic annotations embedded into the CWL files. +- Bugfixes in CNF handling output numbering +- Bump commons-lang3 to 3.19.0 +- Documentation Updates + +### APE 2.4.0 - CLI Extensions, Template Enhancements + +- CLI is extended. It now allows users to automatically convert tools from bioinformatics domain (specifically `bio.tools`), using methods: `pull-a-tool`, `convert-tools` and `bio.tools` (The previous interface only allowed workflow synthesis while we are now using the command synthesis). +- Included more constraint templates +- Migrate to Java 17 + +### APE 2.3.0 - CWL Improvements and General Code Improvements + +#### CWL Support Enhancements + +- Removed full CWL implementation support within the annotation file due to maintainability challenges and insufficient examples. +- Introduced a `cwl_reference` field for direct linkage to CWL implementation files of tools, facilitating easier access and usability. + +#### Code and Documentation Improvements + +- Conducted a comprehensive refactor of the codebase, including improvements in naming conventions to enhance code clarity and quality. +- Updated the project's security guidelines to ensure compliance with current best practices. + +#### Minor Fixes and Updates + +- Implemented small fixes to address issues and improve overall functionality. +- Updated the releases list to keep users informed of new versions and available features. + +### APE 2.2.6 - General Enhancements + +- Added `SECURITY.md` +- Build process updates +- Enhancements of Badges (e.g. `fair-software`) +- API methods improvements + +### APE 2.2.0 - Code refactor and Taverna style workflow outputs + +- Fix `CITATION.cff` formatting and update the file +- Refactor code and implement the Taverna style workflow outputs +- Fix JavaDoc error +- Update `README.md` - remove a badge + +### APE 2.1.8 - Improved CWL generation and code refactor + +- Create `codeql.yml` +- Update constraint formats and annotation labels +- Introduce constraints APERunConfig tag & refactor +- Update `README.md` +- Fix build badge +- CWL fixes and dependencies update +- Create `CITATION.cff` + +### APE 2.1.5 - Support executable CWL outputs + +- Configuration files can be provided as URLs and can contain URLs +- CWL files are now executable +- CWL input file (`.yml`) is also provided +- Tests are improved +- Refactoring + + +### APE 2.0.3 - Improved SLTLx Templates and direct encoding + +- Added new NL templates for SLTLx +- Added encoding runtime message +- Fixed issue with cache of SLTLx specified constraints on synthesis re-run + +### APE 2.0.2 - New SLTLx Templates, added workflow output dependency + +- Added new constraint templates +- Workflows no longer use provided inputs as outputs + +### APE 2.0.0 - Support for SLTLx + +APE formalism is extended to support the SLTLx logic. The solving engine is still a SAT solver. +The project is restructured and it includes a parser for the underlying logic. +Problem constraints can now be specified using constraints as well as directly in SLTLx. + ### APE 1.1.12 - log4j version fix Latest - Changed log4j version dependency to 2.17.0, due to security issues. - Updated other mvn dependencies diff --git a/SECURITY.md b/SECURITY.md index 2fe19b6..df117ac 100644 --- a/SECURITY.md +++ b/SECURITY.md @@ -5,15 +5,14 @@ The following versions of APE are currently supported with security updates: | Version | Supported | -| ------- | ------------------ | -| 2.2.x | :white_check_mark: | -| 2.1.x | :x: | -| 2.0.x | :x: | -| < 2.0 | :x: | +|---------| ------------------ | +| 2.6.x | :white_check_mark: | +| 2.5.x | :white_check_mark: | +| < 2.5 | :x: | ## Reporting a Vulnerability -If you discover a security vulnerability in APE, please report it by sending an email to v.kasalica[at]esciencecenter.nl. We ask that you do not publicly disclose the issue until it has been addressed. +If you discover a security vulnerability in APE, please report it by sending an email to anna-lena.lamprecht[at]uni-potsdam.de. We ask that you do not publicly disclose the issue until it has been addressed. In your report, please provide the following information: @@ -27,7 +26,7 @@ We are committed to responding promptly to security reports. We will acknowledge Our security response team consists of the following individuals: -- Vedran Kasalica (v.kasalica[at]esciencecenter.nl) +- Anna-Lena Lamprecht (anna-lena.lamprecht[at]uni-potsdam.de) Please contact the team directly for security-related matters.