remove utils. some minor cleanups

OpenMS · Aug 11, 2023 · d34e558 · d34e558
1 parent d9544b5
commit d34e558
Show file tree

Hide file tree

Showing 14 changed files with 12 additions and 258 deletions.
diff --git a/docs/contribute-to-openms/adding-new-tool-to-topp.md b/docs/contribute-to-openms/adding-new-tool-to-topp.md
@@ -30,15 +30,6 @@ add `-test` to the call of your TOPP tool and also create the expected output th
 flag active. The flag ensures that UniqueId's, dates etc are equal no matter where and when the tool is run.
 ```
 
-## What do I have to do to add a new UTILS tool?
-
-- Add the code to `src/utils/` and register it in `src/utils/executables.cmake`.
-- Add your tool to `getUtilList()` in `src/openms/source/APPLICATIONS/ToolHandler.cpp`. This creates a doxygen page with
- the `–help` output of the tool (using `TOPPDocumenter`). This page must be included at the end of the doxygen
- documentation of your tool (see other tools for an example).
-- Add it to the UTILS docu page (in `doc/doxygen/public/UTILS.doxygen`)
-- Write a test (this is optional for UTILS). See TOPP tools above and add the test to the bottom of `src/tests/topp/CMakeLists.txt`.
-
 ## I want to implement a new file adapter. What is to be done?
 
 First, add a file adapter class to the `include/OpenMS/FORMAT/` and `source/FORMAT/` folders. The file adapter should

diff --git a/docs/develop-with-openms/link-external-code-to-openms.md b/docs/develop-with-openms/link-external-code-to-openms.md
@@ -1,7 +1,7 @@
 External Code using OpenMS
 ==========================
 
-If OpenMS' TOPP and UTILS tools are not enough in a certain scenario, you can either request a change to OpenMS, if you
+If OpenMS' TOPP tools are not enough in a certain scenario, you can either request a change to OpenMS, if you
 feel this functionality is useful for others as well, or modify/extend OpenMS privately. For the latter, there are 
 multiple ways to do this:
 
@@ -100,7 +100,7 @@ installer for your platform (see our internal FAQ which is built using "make doc
 machine.
 
 If you've used an external project and have a new executable (+ an optional new library), use the installer approach as
-well, and manually copy the new executable to the `TOPP/UTILS` binary directory (e.g. on Windows this could be
+well, and manually copy the new executable to the `TOPP` binary directory (e.g. on Windows this could be
 `c:/program files/OpenMS/bin`, on Linux it could be `/bin`.
 
 If you do not use the installer, copy all required files manually, plus a few extra steps, see below. What needs to be

diff --git a/docs/index.rst b/docs/index.rst
@@ -52,7 +52,6 @@ Contents
  openms-applications-and-tools/installation.md
  openms-applications-and-tools/openms-graphical-user-interfaces.md
  openms-applications-and-tools/topp-tools.md
- openms-applications-and-tools/utils-tools.md
  openms-applications-and-tools/command-line-interface.md
  openms-applications-and-tools/visualize-with-openms.md
 

diff --git a/docs/openms-applications-and-tools/openms-applications/swathwizard.md b/docs/openms-applications-and-tools/openms-applications/swathwizard.md
@@ -7,7 +7,7 @@ SwathWizard
 SwathWizard is an assistant for Swath analysis.
 
 The Wizard takes the user through the whole analysis pipeline for SWATH proteomics data analysis, i.e. the
-[TOPP Documentation: OpenSwathWorkflow](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_OpenSwathWorkflow.html) tool, including downstream tools such as [GitHub:PyProphet/pyProphet](https://github.com/PyProphet/pyprophet) and the [GitHub:msproteomicstools/TRIC alignment](https://github.com/msproteomicstools/msproteomicstools) tool.
+[TOPP Documentation: OpenSwathWorkflow](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_OpenSwathWorkflow.html) tool, including downstream tools such as [GitHub:PyProphet/pyProphet](https://github.com/PyProphet/pyprophet) and the [GitHub:msproteomicstools/TRIC alignment](https://github.com/msproteomicstools/msproteomicstools) tool.
 
 Since the downstream tools require Python and the respective modules, the Wizard will check their proper installation
 status and warn the user if a component is missing.

diff --git a/docs/openms-applications-and-tools/topp-tools/types-of-topp-tools.md b/docs/openms-applications-and-tools/topp-tools/types-of-topp-tools.md
@@ -41,9 +41,7 @@ The following tools are offered:
 - **Protein/Peptide identification**
 - **Protein/Peptide processing**
 - **Targeted experiments and OpenSWATH**
-- **Peptide property prediction**
 
- For more information, view the [Peptide property prediction](types-of-topp-tools/peptide-property-prediction.md) section.
 - **Cross-linking**
 
  Cross-linking is a technique where substances are chemically treated to create covalent bonds between different molecules. The strength of the covalent bonds can be quantified to indicate the proximity of certain molecules within a 3D structure.

diff --git a/...cations-and-tools/topp-tools/types-of-topp-tools/peptide-property-prediction.md b/...cations-and-tools/topp-tools/types-of-topp-tools/peptide-property-prediction.md
diff --git a/docs/openms-applications-and-tools/utils-tools.md b/docs/openms-applications-and-tools/utils-tools.md
diff --git a/docs/quick-reference/contributor-faq.md b/docs/quick-reference/contributor-faq.md
@@ -17,11 +17,6 @@ The following section provides general information to new contributors.
 * Subscribe to the [open-ms-general](https://sourceforge.net/projects/open-ms/lists/open-ms-general) 
 or [contact us](/quick-reference/contact-us.md).
 
-### What is the difference between an OpenMS tool and util?
-
-A tool starts its lifecycle in `UTILS` and may exist without being thoroughly tested. Tools may be promoted from `UTILS`
-to `TOOLS` if they are stable enough, are fully tested, fully documented, and a test workflow exists.
-
 ### I have written a class for OpenMS. What should I do?
 
 Follow the [OpenMS coding conventions](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/coding_conventions.html).
@@ -167,7 +162,7 @@ Find a definition of the main page [here](https://github.com/OpenMS/OpenMS/edit/
 Add a new module [here](https://github.com/OpenMS/OpenMS/edit/develop/doc/doxygen/public/Modules.doxygen).
 
 
-### How is the command line documentation for TOPP/UTILS tools created?
+### How is the command line documentation for TOPP tools created?
 
 The program `OpenMS/doc/doxygen/parameters/TOPPDocumenter.cpp` creates the command line documentation for all classes
 that are included in the static `ToolHandler.cpp` tools list. It can be included in the documentation using 

diff --git a/docs/quick-reference/developer-faq.md b/docs/quick-reference/developer-faq.md
@@ -17,11 +17,6 @@ The following section provides general information to new contributors.
 * Subscribe to the [open-ms-general](https://sourceforge.net/projects/open-ms/lists/open-ms-general) 
  or [contact-us](/quick-reference/contact-us.md).
 
-### What is the difference between an OpenMS tool and util?
-
-A tool starts its lifecycle in `UTILS` and may exist without being thoroughly tested. Tools may be promoted from `UTILS`
-to `TOOLS` if they are stable enough, are fully tested, fully documented, and a test workflow exists.
-
 ### I have written a class for OpenMS. What should I do?
 
 Follow the [OpenMS coding conventions](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/coding_conventions.html).
@@ -204,10 +199,10 @@ to learn more about contributing to releases.
 
 ## Working in Integrated Development Environments (IDEs)
 
-### Why are there no `source/TEST` and `source/APPLICATIONS/TOPP|UTILS` folder?
+### Why are there no `source/TEST` and `source/APPLICATIONS/TOPP` folder?
 
 All source files added to an IDE are associated with their targets. Find the source files for each test within
-its own subproject. The same is true for the `TOPP` and `UTILS` classes.
+its own subproject. The same is true for the `TOPP` classes.
 
 ### I'm getting the error "Error C2471: cannot update program database"
 
@@ -347,22 +342,17 @@ generates a html table with the parameters. This table can then be included in t
 following `doxygen` command:`@htmlinclude OpenMS_<class name>.parameters`.
 
 ```{note}
-Parameter documentation is automatically generated for `TOPP/UTILS` included in the static `ToolHandler.cpp` tools list.
+Parameter documentation is automatically generated for `TOPP` included in the static `ToolHandler.cpp` tools list.
 ```
 
-To include TOPP/UTILS parameter documentation use following `doxygen` command:
-
+To include TOPP parameter documentation use following `doxygen` command:
 
 `@htmlinclude TOPP_<tool name>.parameters`
 
-or
-
-`@htmlinclude UTILS_<tool name>.parameters`
-
 Test if everything worked by calling `make doc_param_internal`. The parameters documentation is written to
 `OpenMS/doc/doxygen/parameters/output/`.
 
-### How is the command line documentation for TOPP/UTILS tools created?
+### How is the command line documentation for TOPP tools created?
 
 The program `OpenMS/doc/doxygen/parameters/TOPPDocumenter.cpp` creates the command line documentation for all classes
 that are included in the static `ToolHandler.cpp` tools list. It can be included in the documentation using the 

diff --git a/docs/quick-reference/glossary.md b/docs/quick-reference/glossary.md
@@ -88,9 +88,6 @@ pyOpenMS
 TOPP Tools
  OpenMS provides a number of functions that process mass spectrometry data called TOPP tools. More information on TOPP tools can be found in the [OpenMS API reference documentation](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html).
 
-UTILS
- Besides {term}`TOPP`, OpenMS offers a range of other tools. They are not included in {term}`TOPP` as they are not part of typical analysis pipelines. More information is present in [OpenMS UTILS Documentation](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_documentation.html).
-
 TOPPView
  TOPPView is a viewer for MS and HPLC-MS data. More information is available in [TOPPView documentation](../openms-applications-and-tools/visualize-with-openms.md).
 

diff --git a/docs/research/whitepapers/OpenMS-2.0-kernel-whitepaper.md b/docs/research/whitepapers/OpenMS-2.0-kernel-whitepaper.md
diff --git a/docs/run-workflows-with-openms-tools/openms-in-knime.md b/docs/run-workflows-with-openms-tools/openms-in-knime.md
@@ -1,7 +1,7 @@
 OpenMS in KNIME
 ===============
 
-KNIME is a free graphical application for creating and executing workflows. OpenMS provides a plugin, which exposes TOPP and UTILS tools to the KNIME interface.
+KNIME is a free graphical application for creating and executing workflows. OpenMS provides a plugin, which exposes TOPP tools to the KNIME interface.
 
 
 ```{toctree}

diff --git a/docs/topp-and-utils/swathwizard.md b/docs/topp-and-utils/swathwizard.md
@@ -7,7 +7,7 @@ SwathWizard
 An assistant for Swath analysis.
 
 The Wizard takes the user through the whole analysis pipeline for SWATH proteomics data analysis, i.e. the
-[TOPP Documentation: OpenSwathWorkflow](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_OpenSwathWorkflow.html) tool, including downstream tools such as [GitHub:PyProphet/pyProphet](https://github.com/PyProphet/pyprophet) and the [GitHub:msproteomicstools/TRIC alignment](https://github.com/msproteomicstools/msproteomicstools) tool.
+[TOPP Documentation: OpenSwathWorkflow](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_OpenSwathWorkflow.html) tool, including downstream tools such as [GitHub:PyProphet/pyProphet](https://github.com/PyProphet/pyprophet) and the [GitHub:msproteomicstools/TRIC alignment](https://github.com/msproteomicstools/msproteomicstools) tool.
 
 Since the downstream tools require Python and the respective modules, the Wizard will check their proper installation
 status and warn the user if a component is missing.