Resolve merge conflicts.

README.md

@@ -100,7 +100,7 @@ If you want to build plotID yourself, follow these steps:
 1. Download the source code from [Gitlab](https://git.rwth-aachen.de/plotid/plotid_python):  
 `git clone https://git.rwth-aachen.de/plotid/plotid_python.git`  
 `cd plotid_python`  
-2. *[Optional]* Create a virtual environment (see [Installation](#Installation)).  
+2. *[Optional]* Create a virtual environment (see [Installation](#installation)).  
 3. *[Optional]* Run unittests and coverage:  
 `python3 tests/runner_tests.py`
 4. Build the package
@@ -114,4 +114,4 @@ To install all optional dependencies use `pip install .[test,docs]` or `pip inst
 
 ## Documentation
 If you have more questions about plotID, please have a look at the [documentation](https://plotid.pages.rwth-aachen.de/plotid_python).  
-Also have a look at the [examples](./examples) that are shipped with plotID.
+Also have a look at the [examples](https://git.rwth-aachen.de/plotid/plotid_python/-/tree/main/examples) that are shipped with plotID.

docs/source/about.rst

@@ -4,6 +4,6 @@ About plotID
 plotID is developed at the Institut Fluidsystemtechnik within nfdi4ing at the Technische Universität Darmstadt.
 
 Acknowledgements
----------------
+----------------
 
 The authors would like to thank the Federal Government and the Heads of Government of the Länder, as well as the Joint Science Conference (GWK), for their funding and support within the framework of the NFDI4Ing consortium. Funded by the German Research Foundation (DFG) - project number 442146713.
\ No newline at end of file

docs/source/conf.py

@@ -38,6 +38,8 @@ release = __version__
 extensions = ["sphinx.ext.napoleon", "autoapi.extension", "myst_parser"]
 autoapi_type = "python"
 autoapi_dirs = ["../../plotid", "../../tests"]
+# autoapi_keep_files = True
+myst_heading_anchors = 2
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]

docs/source/dependencies.rst

@@ -8,6 +8,7 @@ The plotID package depends on other software for its full funcionality. Since pl
 - `qrcode <https://github.com/lincolnloop/python-qrcode>`_: Creates QR codes from input data. qrcode is used to create the QR code which is printed on the plot in the end.
 - `numpy <https://numpy.org/doc/stable/>`_: Package for scientific computing. Right now it is only used to generate sample data in the examples. Since it is a dependency of matplotlib, it has to be installed anyway.
 
+
 Optional dependencies that are not necessary to run plotID but more to contribute to the code quality are the following:
 
 - `coverage <https://coverage.readthedocs.io/en/6.5.0/#>`_: Program to measure the code coverage. It is used in the development of plotID to monitor the coverage of the code when the unit tests are run.

docs/source/modules.rst

-plotid
-======
-
-.. toctree::
-   :maxdepth: 4
-
-   plotid

docs/source/readme_link.md

+```{include} ../../README.md
+:relative-docs: docs/
+:relative-images: 
+```
\ No newline at end of file

docs/source/readme_link.rst

-Overview
-========
-
-README file
------------
-
-.. include:: ../../README.md
-   :parser: myst_parser.sphinx_
\ No newline at end of file

docs/source/structure.rst

 Structure and architecture of plotID
-==================================
+====================================
 
 A visualization of the internal structure of plotID is provided here. The structure tries to follow Object Oriented Programming (OOP) principles. First tagplot() is depicted with matplotlib as example plot engine:
 

plotid/publish.py

@@ -245,7 +245,6 @@ def publish(figs_and_ids, src_datapath, dst_path, **kwargs):
         Path to data that should be published.
     dst_path : str
         Path to the destination directory.
-
     **kwargs : dict, optional
         Extra arguments for additional publish options.