Revert @jpfeuffer [10 - 11] Jun, 2022 +0200 recent commits

conf.py

@@ -30,7 +30,6 @@
   'sphinx_copybutton',
   'sphinx.ext.autodoc',
   'sphinx.ext.autosummary',
-  'sphinx.ext.autosectionlabel',
   'myst_parser',
   'notfound.extension',
   'sphinxcontrib.images',
@@ -47,9 +46,6 @@
   "linkify_fuzzy_links",
 ]
 
-# Generate header anchors for cross-linking in markdown until depth n
-myst_heading_anchors = 3
-
 autosummary_generate = True
 autosummary_imported_members = True
 

docs/installations/installation-on-gnu-linux.md

@@ -3,17 +3,17 @@ Installation on GNU/Linux
 
 ## Install via Conda
 
-You can use conda to install the OpenMS library and tools without user interface. Depending on the conda channel, you can
-obtain release versions (`bioconda` channel) and nightly versions (`openms` channel).
+Use conda or bioconda to install OpenMS.
 
 1. Follow the instructions to [install conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html).
-2. Add channels for dependencies:
-   ```bash
-    conda config --add channels defaults
-    conda config --add channels bioconda
-    conda config --add channels conda-forge
+2. Install OpenMS using conda:
+   `conda install -c openms openms`
+3. Other OpenMS packages can be installed using:
+   ```
+   conda install -c openms pyopenms
+   conda install -c openms openms-thirdparty
+   conda install -c openms libopenms
    ```
-3. Install any of the following packages related to OpenMS
 
 ```{tab} openms
 openms contains OpenMS C++ Tools.
@@ -32,57 +32,13 @@ openms-thirdparty are external tools that are wrapped in OpenMS with adapters. T
 the openms package.
 ```
 
-via `bioconda` for release versions
-
-````{tab} openms
-```bash
-conda install openms
-```
-````
-
-````{tab} libopenms
-```bash
-conda install libopenms
-```
-````
-
-````{tab} pyopenms
-```bash
-conda install pyopenms
-```
-````
-
-````{tab} openms-thirdparty
-```bash
-conda install openms-thirdparty
-```
-````
-
-or our own `openms` channel for nightly snapshots (which are build based on the same bioconda dependencies)
-
-````{tab} openms
-```bash
-conda install -c openms openms
-```
-````
-
-````{tab} libopenms
-```bash
-conda install -c openms libopenms
-```
-````
+To install using bioconda:
 
-````{tab} pyopenms
-```bash
-conda install -c openms pyopenms
 ```
-````
-
-````{tab} openms-thirdparty
-```bash
-conda install -c openms openms-thirdparty
+conda install -c bioconda openms
+conda install -c bioconda libopenms
+conda install -c bioconda openms-thirdparty
 ```
-````
 
 ## Install via Debian package
 
@@ -135,60 +91,34 @@ Debian package.
 Some thirdparty software used via adapter tools in OpenMS might also require an installed JavaVM.
 ```
 
-## Run via a (Bio)Container
+## Run via a (Bio)Docker image
 
-Install a containerization software (e.g., [Docker](https://docs.docker.com/engine/install/) or [Singularity](https://sylabs.io/guides/3.0/user-guide/quick_start.html#quick-installation-steps))
+Make sure you have [Docker installed](https://docs.docker.com/engine/install/).
 
-Our container support is constantly updated. Docker images provided by us,
-can be obtained via [ghcr.io](https://ghcr.io).
+Our Docker support is constantly updated. Images can be obtained via [ghcr.io](https://ghcr.io).
 
-1. [openms-executables](https://ghcr.io/openms/openms-executables)
-2. [openms-library](https://ghcr.io/openms/openms-library)
+1. [openms-executables](https://ghcr.io/openms/openms-executables:latest)
+2. [openms-library](https://ghcr.io/openms/openms-library:latest)
 
-Otherwise, the [BioContainers Registries](https://biocontainers.pro/registry) and the associated Galaxy
-project provide native containers from our bioconda packages for both Docker and Singularity.
+Or via [BioContainers Registeries](https://biocontainers.pro/registry).
 
 1. [BioContainers libopenms](https://biocontainers.pro/tools/libopenms)
 2. [BioContainers openms](https://biocontainers.pro/tools/openms)
 3. [BioContainers openms-thirdparty](https://biocontainers.pro/tools/openms-thirdparty)
 4. [BioContainers pyOpenMS](https://biocontainers.pro/tools/pyopenms)
 
-Images of the containers can be pulled via or one of the following commands:
+Docker images can be pulled via or one of the following commands:
 
-````{tab} Docker
-```bash
-docker pull quay.io/biocontainers/libopenms
-docker pull quay.io/biocontainers/openms
-docker pull quay.io/biocontainers/pyopenms
-docker pull quay.io/biocontainers/openms-thirdparty
 ```
-````
-
-````{tab} Singularity
-```bash
-docker pull https://depot.galaxyproject.org/singularity/libopenms
-docker pull https://depot.galaxyproject.org/singularity/openms
-docker pull https://depot.galaxyproject.org/singularity/pyopenms
-docker pull https://depot.galaxyproject.org/singularity/openms-thirdparty
-```
-````
-
-If Singularity images fail to download or run, try to use the Docker images as Singularity will automatically convert them.
-
-Docker images from our own continuous integration can be installed via the following commands:
-
-```bash
-docker pull ghcr.io/openms/openms-library
-docker pull ghcr.io/openms/openms-executables
+docker pull biocontainers/openms
+docker pull openms/library
+docker pull openms/executables
+docker pull openms/pyopenms
 ```
 
-per default this results in the download of the latest nightly snapshot. Specify a release version to
-receive a stable version.
-
-Dockerfiles to build different kind of images (corresponding to build instructions, e.g. on ArchLinux) yourself can be found on
-GitHub in our [OpenMS/dockerfiles](https://github.com/OpenMS/dockerfiles) repository.
-
 ## Build OpenMS from source
 
 To build OpenMS from source, follow the build instructions for [Linux](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/install_linux.html).
 
+Dockerfiles to build different kind of images (corresponding to build instructions, e.g. on ArchLinux) can be found on
+GitHub in [OpenMS/dockerfiles](https://github.com/OpenMS/dockerfiles) repository.

docs/installations/installation-on-macos.md

@@ -37,27 +37,9 @@ source ${OPENMS_TOPP_PATH}/.TOPP_bash_profile
 
 Make sure `<OpenMS-PATH>` points to the folder where OpenMS is installed locally (e.g., `/Applications/OpenMS-<version>`)
 
-## Install via Conda with the Bioconda channel
+## Install via Conda or Bioconda
 
-Follow the instructions for {ref}`GNU/Linux <./installation-on-gnu-linux.md#install-via-conda>`. Use the Terminal.app or any
-terminal of your choice to run the commands.
-
-```{note}
-Due to unavailability of an exact copy of the macOS build machines used in bioconda, we currently cannot offer nightly
-builds for macOS on our own conda channel `openms`.
-```
-
-## Run via (Bio)Container
-
-Follow the instructions for{ref}`GNU/Linux <./installation-on-gnu-linux.md#run-via-a-bio-container>`. Make sure to
-follow specific installation instructions for macOS during the installation of the containerization software.
-Use the Terminal.app or any terminal of your choice to run the commands.
-
-```{note}
-Running OpenMS containers (currently built for Linux) on macOS involves
-running virtual machines (sometimes hidden from the user, e.g., with Docker).
-This comes with disadvantages in runtime and memory consumption.
-```
+Follow [these](installation-on-gnu-linux.md#install-via-conda) instructions.
 
 
 ## Build OpenMS from source