From 365bf895817c51c9ed6b0e510880e90958d09313 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 30 Oct 2025 09:49:09 +0000 Subject: [PATCH 1/4] Initial plan From c74ca5582eef1268212c9445f16be57a58c928c8 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 30 Oct 2025 09:53:27 +0000 Subject: [PATCH 2/4] Update installer download links from deprecated abibuilder URLs to GitHub releases Co-authored-by: timosachsenberg <5803621+timosachsenberg@users.noreply.github.com> --- docs/about/installation/installation-on-gnu-linux.md | 2 +- docs/about/installation/installation-on-macos.md | 2 +- docs/about/installation/installation-on-windows.md | 2 +- docs/manual/develop.md | 2 +- docs/manual/develop/developer-faq.md | 5 ++--- 5 files changed, 6 insertions(+), 7 deletions(-) diff --git a/docs/about/installation/installation-on-gnu-linux.md b/docs/about/installation/installation-on-gnu-linux.md index ca4f31d6..17e62d5b 100644 --- a/docs/about/installation/installation-on-gnu-linux.md +++ b/docs/about/installation/installation-on-gnu-linux.md @@ -25,7 +25,7 @@ Some thirdparty software used via adapter tools in OpenMS might also require an ## Install via the provided Debian package -For Debian-based Linux users, it is suggested to use the [deb-package](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/) provided. It is most easily installed with **[gdebi](https://launchpad.net/gdebi)** +For Debian-based Linux users, it is suggested to use the [deb-package](https://github.com/OpenMS/OpenMS/releases/latest) provided. It is most easily installed with **[gdebi](https://launchpad.net/gdebi)** which automatically resolves the dependencies available in the PPA Repositories. ```bash diff --git a/docs/about/installation/installation-on-macos.md b/docs/about/installation/installation-on-macos.md index 100e5f0d..1ac80ede 100644 --- a/docs/about/installation/installation-on-macos.md +++ b/docs/about/installation/installation-on-macos.md @@ -9,7 +9,7 @@ macOS To install OpenMS on macOS, run the following steps: -1. Download and install the macOS drag-and-drop installer from the [archive](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/). +1. Download and install the macOS drag-and-drop installer from the [GitHub releases page](https://github.com/OpenMS/OpenMS/releases/latest). 2.Double click on the downloaded file. It will start to open the `OpenMS--macOS.pkg` installer file. ```{image} /_images/installations/macos/Warning-openMS-3.3.0-macOS-Silicon.pkg-Not-Opened.png diff --git a/docs/about/installation/installation-on-windows.md b/docs/about/installation/installation-on-windows.md index 21aef1e8..86cb3535 100644 --- a/docs/about/installation/installation-on-windows.md +++ b/docs/about/installation/installation-on-windows.md @@ -5,7 +5,7 @@ Windows To Install the binary package of OpenMS & {term}`TOPP`: -1. Download the installer `OpenMS--Win64.exe` from the [archive](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/) +1. Download the installer `OpenMS--Win64.exe` from the [GitHub releases page](https://github.com/OpenMS/OpenMS/releases/latest) 2. Execute the installer under the user account that later runs OpenMS and follow its instructions. You may see a Windows Defender Warning, since our installer is not digitally signed. diff --git a/docs/manual/develop.md b/docs/manual/develop.md index 67b8298c..1937735c 100644 --- a/docs/manual/develop.md +++ b/docs/manual/develop.md @@ -69,7 +69,7 @@ Consider the following resources for further information: - **Guidelines for adding new dependency libraries**: View the guidelines for [adding new dependency libraries](/manual/develop/developer-guidelines-for-adding-new-dependent-libraries.md). - **Experimental installers**: We automatically build installers for different platforms. These usually contain unstable or partially untested code. - The nightly (unstable) installers are available at the [build archive](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/). + The latest stable installers are available on the [GitHub releases page](https://github.com/OpenMS/OpenMS/releases/latest). - **Developer FAQ**: Visit the [Developer FAQ](/manual/develop/developer-faq.md) to get answers to frequently asked questions. ```{toctree} diff --git a/docs/manual/develop/developer-faq.md b/docs/manual/develop/developer-faq.md index b9cdd854..a256fbd0 100644 --- a/docs/manual/develop/developer-faq.md +++ b/docs/manual/develop/developer-faq.md @@ -46,9 +46,8 @@ Insert round brackets around the method declaration. ### Where can I find the binary installers created? -View the binary installers at the [build archive](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/). -Please verify the creation date of the individual installers, as there may have been an error while creating -the installer. +View the binary installers on the [GitHub releases page](https://github.com/OpenMS/OpenMS/releases/latest). +Please check the release date to ensure you are getting the most recent stable version. ## Troubleshooting From 10b344ee4e72794f26896117f77c56a391121ac5 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 30 Oct 2025 09:55:20 +0000 Subject: [PATCH 3/4] Fix text clarity and formatting issues in installer documentation Co-authored-by: timosachsenberg <5803621+timosachsenberg@users.noreply.github.com> --- docs/about/installation/installation-on-macos.md | 2 +- docs/manual/develop.md | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/docs/about/installation/installation-on-macos.md b/docs/about/installation/installation-on-macos.md index 1ac80ede..f24f25a8 100644 --- a/docs/about/installation/installation-on-macos.md +++ b/docs/about/installation/installation-on-macos.md @@ -10,7 +10,7 @@ macOS To install OpenMS on macOS, run the following steps: 1. Download and install the macOS drag-and-drop installer from the [GitHub releases page](https://github.com/OpenMS/OpenMS/releases/latest). -2.Double click on the downloaded file. It will start to open the `OpenMS--macOS.pkg` installer file. +2. Double click on the downloaded file. It will start to open the `OpenMS--macOS.pkg` installer file. ```{image} /_images/installations/macos/Warning-openMS-3.3.0-macOS-Silicon.pkg-Not-Opened.png :alt: macOS warning message when opening OpenMS--macOS.pkg diff --git a/docs/manual/develop.md b/docs/manual/develop.md index 1937735c..1cf089c6 100644 --- a/docs/manual/develop.md +++ b/docs/manual/develop.md @@ -67,8 +67,7 @@ Nightly tests: [CDASH](https://cdash.seqan.de/index.php?project=OpenMS). Consider the following resources for further information: - **Guidelines for adding new dependency libraries**: View the guidelines for [adding new dependency libraries](/manual/develop/developer-guidelines-for-adding-new-dependent-libraries.md). -- **Experimental installers**: We automatically build installers for different platforms. These usually contain - unstable or partially untested code. +- **Binary installers**: We provide pre-built binary installers for different platforms. The latest stable installers are available on the [GitHub releases page](https://github.com/OpenMS/OpenMS/releases/latest). - **Developer FAQ**: Visit the [Developer FAQ](/manual/develop/developer-faq.md) to get answers to frequently asked questions. From 55f7b4ec8f0e8df63e8479257fac75ac7073ab2a Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 30 Oct 2025 10:01:08 +0000 Subject: [PATCH 4/4] Revert developer docs to use nightly installer links Co-authored-by: timosachsenberg <5803621+timosachsenberg@users.noreply.github.com> --- docs/manual/develop.md | 5 +++-- docs/manual/develop/developer-faq.md | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/docs/manual/develop.md b/docs/manual/develop.md index 1cf089c6..67b8298c 100644 --- a/docs/manual/develop.md +++ b/docs/manual/develop.md @@ -67,8 +67,9 @@ Nightly tests: [CDASH](https://cdash.seqan.de/index.php?project=OpenMS). Consider the following resources for further information: - **Guidelines for adding new dependency libraries**: View the guidelines for [adding new dependency libraries](/manual/develop/developer-guidelines-for-adding-new-dependent-libraries.md). -- **Binary installers**: We provide pre-built binary installers for different platforms. - The latest stable installers are available on the [GitHub releases page](https://github.com/OpenMS/OpenMS/releases/latest). +- **Experimental installers**: We automatically build installers for different platforms. These usually contain + unstable or partially untested code. + The nightly (unstable) installers are available at the [build archive](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/). - **Developer FAQ**: Visit the [Developer FAQ](/manual/develop/developer-faq.md) to get answers to frequently asked questions. ```{toctree} diff --git a/docs/manual/develop/developer-faq.md b/docs/manual/develop/developer-faq.md index a256fbd0..b9cdd854 100644 --- a/docs/manual/develop/developer-faq.md +++ b/docs/manual/develop/developer-faq.md @@ -46,8 +46,9 @@ Insert round brackets around the method declaration. ### Where can I find the binary installers created? -View the binary installers on the [GitHub releases page](https://github.com/OpenMS/OpenMS/releases/latest). -Please check the release date to ensure you are getting the most recent stable version. +View the binary installers at the [build archive](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/). +Please verify the creation date of the individual installers, as there may have been an error while creating +the installer. ## Troubleshooting