From 21ef9cfc0f20a7f72c6f47311d29afc79a995598 Mon Sep 17 00:00:00 2001 From: Jim Downie Date: Wed, 10 Dec 2025 08:58:11 +0000 Subject: [PATCH 1/4] feat: bump version to 0.0.8 --- dependency-reduced-pom.xml | 2 +- docs/index.md | 2 +- docs/index.md-e | 52 ++++++++++++++++++++ pom.xml | 2 +- src/main/resources/META-INF/nf-test-plugin | 2 +- src/main/resources/META-INF/nf-test-plugin-e | 4 ++ 6 files changed, 60 insertions(+), 4 deletions(-) create mode 100644 docs/index.md-e create mode 100644 src/main/resources/META-INF/nf-test-plugin-e diff --git a/dependency-reduced-pom.xml b/dependency-reduced-pom.xml index 71779fa..673f68f 100644 --- a/dependency-reduced-pom.xml +++ b/dependency-reduced-pom.xml @@ -4,7 +4,7 @@ com.nf-core nft-utils nft-utils - 0.0.7 + 0.0.8 nf-test plugin that adds commonly used utility functions https://github.com/nf-core/nft-utils diff --git a/docs/index.md b/docs/index.md index 1b45761..d5155ff 100644 --- a/docs/index.md +++ b/docs/index.md @@ -10,7 +10,7 @@ To start using the plugin please add it to your `nf-test.config` file: ```groovy title="nf-test.config" config { plugins { - load "nft-utils@0.0.7" + load "nft-utils@0.0.8" } } ``` diff --git a/docs/index.md-e b/docs/index.md-e new file mode 100644 index 0000000..d5155ff --- /dev/null +++ b/docs/index.md-e @@ -0,0 +1,52 @@ +# nft-utils + +nft-utils is an nf-test plugin to provide additional functions and assertions that fall outside of the typical nf-test features. +They were primarily developed by the nf-core community but should be applicable to any nf-tests. + +## Start using the plugin + +To start using the plugin please add it to your `nf-test.config` file: + +```groovy title="nf-test.config" +config { + plugins { + load "nft-utils@0.0.8" + } +} +``` + +Have a look at the [usage documentation](./usage.md) for more information on how to start working with the plugin. + +## Use a development version + +To use the development version, please do the following steps: + +- Clone the [nft-utils repository](https://github.com/nf-core/nft-utils) + +### SSH + +```bash +git clone git@github.com:nf-core/nft-utils.git +``` + +### HTTPS + +```bash +git clone https://github.com/nf-core/nft-utils.git +``` + +- Run the build script + +```bash +./build.sh +``` + +- Add the jar location (visible at the end of the build script output) to the `nf-test.config` file + +```groovy title="nf-test.config" +config { + plugins { + loadFromFile "full/path/to/the/plugin/jar" + } +} +``` diff --git a/pom.xml b/pom.xml index 1c9d883..fd625ba 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ com.nf-core nft-utils - 0.0.7 + 0.0.8 jar nft-utils diff --git a/src/main/resources/META-INF/nf-test-plugin b/src/main/resources/META-INF/nf-test-plugin index d517664..d996c03 100644 --- a/src/main/resources/META-INF/nf-test-plugin +++ b/src/main/resources/META-INF/nf-test-plugin @@ -1,4 +1,4 @@ moduleName=nft-utils -moduleVersion=0.0.7 +moduleVersion=0.0.8 moduleAuthors=nf-core extensionMethods=nf_core.nf.test.utils.Methods diff --git a/src/main/resources/META-INF/nf-test-plugin-e b/src/main/resources/META-INF/nf-test-plugin-e new file mode 100644 index 0000000..d996c03 --- /dev/null +++ b/src/main/resources/META-INF/nf-test-plugin-e @@ -0,0 +1,4 @@ +moduleName=nft-utils +moduleVersion=0.0.8 +moduleAuthors=nf-core +extensionMethods=nf_core.nf.test.utils.Methods From 98a75d04b8b78303b3b89382886f620cf59470ad Mon Sep 17 00:00:00 2001 From: Jim Downie Date: Wed, 10 Dec 2025 09:00:12 +0000 Subject: [PATCH 2/4] fix: remove temp files --- docs/index.md-e | 52 -------------------- src/main/resources/META-INF/nf-test-plugin-e | 4 -- 2 files changed, 56 deletions(-) delete mode 100644 docs/index.md-e delete mode 100644 src/main/resources/META-INF/nf-test-plugin-e diff --git a/docs/index.md-e b/docs/index.md-e deleted file mode 100644 index d5155ff..0000000 --- a/docs/index.md-e +++ /dev/null @@ -1,52 +0,0 @@ -# nft-utils - -nft-utils is an nf-test plugin to provide additional functions and assertions that fall outside of the typical nf-test features. -They were primarily developed by the nf-core community but should be applicable to any nf-tests. - -## Start using the plugin - -To start using the plugin please add it to your `nf-test.config` file: - -```groovy title="nf-test.config" -config { - plugins { - load "nft-utils@0.0.8" - } -} -``` - -Have a look at the [usage documentation](./usage.md) for more information on how to start working with the plugin. - -## Use a development version - -To use the development version, please do the following steps: - -- Clone the [nft-utils repository](https://github.com/nf-core/nft-utils) - -### SSH - -```bash -git clone git@github.com:nf-core/nft-utils.git -``` - -### HTTPS - -```bash -git clone https://github.com/nf-core/nft-utils.git -``` - -- Run the build script - -```bash -./build.sh -``` - -- Add the jar location (visible at the end of the build script output) to the `nf-test.config` file - -```groovy title="nf-test.config" -config { - plugins { - loadFromFile "full/path/to/the/plugin/jar" - } -} -``` diff --git a/src/main/resources/META-INF/nf-test-plugin-e b/src/main/resources/META-INF/nf-test-plugin-e deleted file mode 100644 index d996c03..0000000 --- a/src/main/resources/META-INF/nf-test-plugin-e +++ /dev/null @@ -1,4 +0,0 @@ -moduleName=nft-utils -moduleVersion=0.0.8 -moduleAuthors=nf-core -extensionMethods=nf_core.nf.test.utils.Methods From 280b5cedbb8b23b234c532137bf2cd0ebcd35ed7 Mon Sep 17 00:00:00 2001 From: Jim Downie Date: Thu, 11 Dec 2025 16:50:56 +0000 Subject: [PATCH 3/4] feat: write changelog file using GH release changes --- CHANGELOG.md | 103 +++++++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 99 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2b140e4..a77eef6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,11 +1,106 @@ # Changelog -## dev +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) +and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +## 0.0.8 ### New features -- Added the `listToMD5` function +- Added the `curlAndExtract` function to download and extract `tar` and `zip` files during the nf-test setup stage. + +## 0.0.7 + +### Added + +- Added the OutputSanitizer class with the sanitizeOutput() method to process and clean output channels, supporting options like unstableKeys to handle unstable file outputs by @nvnieuwk + +### Fixed + +- nfcoreLibraryLinker: exit gracefully when directories don't exist by @prototaxites + +## 0.0.6 + +### Added + +- Add stdout and stderr helper function for better snapshot by @maxulysse + +### Fixed + +- improve docs by @maxulysse + +## 0.0.5 + +### Added + +- Add functions for managing dependencies on nf-core modules by @prototaxites + +### Fixed + +- Fix rendering of cloning code blocks by @TCLamnidis + +New Contributors + +- @prototaxites +- @TCLamnidis + +## 0.0.4 + +### Added + +- Add listToMD5 by @nvnieuwk in #26 + +### Fixed + +- Improve user eligibility for getAllFilesInDir() docs by @jfy133 +- fix missing ',' in docs code by @Joon-Klaps +- fix listToMD5 by @maxulysse +- Improve remove from yaml map by @maxulysse + +### New Contributors + +- @jfy133 +- @Joon-Klaps +- @itrujnara + +## 0.0.3 + +### Added + +- Add wrapper functions for getAllFilesFromDir with named parameters by @lukfor +- add include in getAllFilesFromDir by @maxulysse +- add removeFromYamlMap by @maxulysse + +### Fixed + +- Move all docs in its own folder by @maxulysse + +### New Contributors + +- @lukfor + +## 0.0.2 + +### Added + +- Add maven to gitpod install by @nvnieuwk +- Add getRelativePath() function by @maxulysse + +### New Contributors + +- @nvnieuwk + +## 0.0.1 + +First release of nft-utils 🍏🚀 + +### Added + +- add removeNextflowVersion function by @maxulysse +- Add getAllFilesFromDir function by @maxulysse +- Add docs by @maxulysse -### Fixes +### New Contributors -Fixes are written here +- @adamrtalbot +- @maxulysse From cb3938b137cc8c7d913ed564fd5a3fad7573c0c5 Mon Sep 17 00:00:00 2001 From: Jim Downie <19718667+prototaxites@users.noreply.github.com> Date: Fri, 12 Dec 2025 09:29:40 +0000 Subject: [PATCH 4/4] fix: typo --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a77eef6..46c681b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -39,7 +39,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fix rendering of cloning code blocks by @TCLamnidis -New Contributors +### New Contributors - @prototaxites - @TCLamnidis