Update downloads.md (#188)

* Update downloads.md

* cleaned up

* removed releases section

* fix broken link

* fix broken link part 2

* get rid of twitter

* Update downloads.md

* Update downloads.md

* Update openms-user-tutorial.md

* Update downloads.md

* Update contributors-quickstart-guide.md

* Update contributors-quickstart-guide.md

* Update tutorial.md

* Update downloads.md

docs/downloads.md

@@ -1,12 +1,27 @@
 # OpenMS Installers
+::::{tab-set}
 
+:::{tab-item} Release
+:sync: Release
 | Platform | Name |
 |----------|------|
 | Windows   | {{ '[OpenMS-{0}-Win64.exe](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/{0}/OpenMS-{0}-Win64.exe)'.format(version) }} |
-| macOS | {{ '[OpenMS-{0}-macOS.dmg](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/{0}/OpenMS-{0}-macOS.dmg)'.format(version) }} |
+| macOS | {{ '[OpenMS-{0}-macOS.dmg](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/{0}/OpenMS-{0}-macOS-Intel.dmg)'.format(version) }} |
 | GNU/Linux | {{ '[OpenMS-{0}-Debian-Linux-x86_64.deb](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/{0}/OpenMS-{0}-Debian-Linux-x86_64.deb)'.format(version) }} | `d203985c7042b885ac1085c30a2d9f36d7609b47` |
 | Source | {{ '[OpenMS-{0}-src.tar.gz](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/{0}/OpenMS-{0}-src.tar.gz)'.format(version) }} |
+:::
 
+:::{tab-item} Nightly
+:sync: Nightly
+| Platform | Name |
+|----------|------|
+| Windows   | {{ '[OpenMS-3.1.0-Win64.exe](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/OpenMS-3.1.0-pre-nightly-latest-Win64.exe)'.format(version) }} |
+| macOS | [OpenMS-3.1.0-macOS.dmg](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/OpenMS-3.1.0-pre-nightly-latest-macOS-Intel.dmg) |
+| GNU/Linux | [OpenMS-3.1.0-Linux-x86_64.deb](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/OpenMS-3.1.0-pre-nightly-latest-Linux-x86_64.deb) |
+| Source | [OpenMS-3.1.0-src.tar.gz](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/OpenMS-3.1.0-src.tar.gz) |
+:::
+
+::::
 
 # Workflows
 
@@ -25,14 +40,6 @@
 |`OpenSWATH` | Targeted extraction and scoring of transitions in DIA data based on an (iRT) assay library. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/OpenSWATH.knwf?raw=true) |
 |`Phosphoproteomics_ID` | Identification of Phosphorilation sites. | [Download](https://github.com/OpenMS/Tutorials/blob/master/Workflows/Phosphoproteomics_ID.knwf?raw=true) |
 
-# OpenMS Releases
-
-| Release                                                |  Installers |
-|--------------------------------------------------------|-------------|
-| Stable release     | [Archive Link](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/) |
-| Release candidates | [Archive Link](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/RC/) |
-| Nightly release    | [Archive Link](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/) |
-
 # Other Resources
 
 | Name | Description | Download Link |

docs/quick-reference/contact-us.md

@@ -11,6 +11,3 @@ You can also contact us:
 3. To stay updated of new versions of OpenMS and releases, subscribe to 
    [openms-announcements mailing list](https://sourceforge.net/projects/open-ms/lists/open-ms-announcements).
 4. To report a new bug, create an issue on GitHub [OpenMS](https://github.com/OpenMS/OpenMS/issues) repository.
-
-
-Say hi on [OpenMS Twitter](https://twitter.com/openmsteam)!

docs/run-workflows-with-openms-tools/knime/tutorial.md

@@ -453,7 +453,7 @@ Those *knwf* files can again be imported by selecting: **File** > **Import KNIME
 
 ```{note}
 For your convenience we added all workflows discussed in this tutorial to the **Workflows** folder on the USB Stick.
- Additionally, the workflow files can be found on <a href="../downloads.html#workflows">workflow downloads</a>. If you want to check
+ Additionally, the workflow files can be found on <a href="../../downloads.html#workflows">workflow downloads</a>. If you want to check
  your own workflow by comparing it to the solution or got stuck, simply import the full workflow from the corresponding
  *knwf* file and after that double-click it in your KNIME Workflow repository to open it.
 ```

docs/tutorials-and-quickstart-guides/guides/contributors-quickstart-guide.md

@@ -5,7 +5,7 @@ To contribute to OpenMS:
 
 - Familiarise yourself with the [OpenMS online documentation](../../index.rst).
 - Learn how to [build OpenMS](../../develop-with-openms/build-openms-from-source.md).
-- Check out the [OpenMS tutorial for developers](https://openms.readthedocs.io/en/latest/develop-with-openms/developer-tutorial.html#developer-tutorial).
+- Check out the [OpenMS tutorial for developers](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/tutorial.html#tutorial_developing).
 
 For any questions, please [contact us](/quick-reference/contact-us.md).
 

docs/tutorials-and-quickstart-guides/openms-user-tutorial.md

@@ -54,8 +54,24 @@ On Linux, you can extract KNIME to a folder of your choice and for TOPPView you
 [build instructions](/openms-applications-and-tools/installation/installation-on-gnu-linux.md#build-openms-from-source).
 
 :::
-
 ::::
+```{note}
+If you have installed OpenMS on Linux or macOS via your package
+manager (for instance by installing the {{ '`OpenMS-{0}-Linux.deb`'.format(version) }} package),
+then you need to set the `OPENMS_DATA_PATH` variable to the directory containing the shared data (normally `/usr/share/OpenMS`). This must be done prior to running any TOPP tool.
+```
+#### Installation from the internet
+
+If you are working through this tutorial at home, you can get the installers under the following links:
+
+- [OpenMS](https://openms.readthedocs.io/en/latest/downloads.html)
+- [KNIME](https://www.knime.org/downloads/overview)
+- OpenMS prerequisites (Windows-only): After installation, before your first use
+of the OpenMS plugin in KNIME you will be asked to download it automatically
+if certain requirements are not found in your Windows registry. Alternatively,
+you can get a bundled version here.
+
+Choose the installers for the platform you are working on.
 
 ### Data conversion
 
@@ -1797,6 +1813,7 @@ Run the workflow and inspect the output.
 In metabolomics, matches between tandem spectra and spectral libraries are manually validated. Several commercial and free online resources exist which help in that task. Some examples are:
 
 - mzCloud contains only spectra from Thermo Orbitrap instruments. The webpage requires Microsoft Silverlight which currently does not work in modern browsers (see the following [link](https://www.mzcloud.org/DataViewer).
+
 - MassBank North America (MoNA) has spectra from different instruments but falls short in the number of spectra (compared to Metlin and mzCloud). See the following [link](http://mona.fiehnlab.ucdavis.edu/spectra/display/KNA00122).
 - METLIN includes 961,829 molecules ranging from lipids, steroids, metabolites, small peptides, carbohydrates, exogenous drugs, and toxicants. In total over 14,000 metabolites.