Merge branch '105-make-sphinx-and-readme-compatible' into 'dev'

Draft: Fix documentation build

See merge request !51

README.md

@@ -96,7 +96,7 @@ 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
@@ -110,4 +110,4 @@ 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

+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

@@ -8,7 +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 depedencies that are not necessary to run plotID but more to contribute to the code are the following:
+Optional dependencies that are not necessary to run plotID but more to contribute to the code 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.
 - `sphinx <https://www.sphinx-doc.org/en/master/>`_: Program to build documentation. For example, this documentatio is generated with the help of sphinx.

docs/source/index.rst

@@ -10,9 +10,11 @@ Welcome to plotID's documentation!
    :maxdepth: 2
    :caption: Contents:
 
-    README <readme_link.rst>
-    Structure and architecture <structure.rst>
+    Overview <readme_link.rst>
+    Installation <installation.rst>
     Dependencies <dependencies.rst>
+    Structure and architecture <structure.rst>
+    About <about.rst>
 
 
 Indices and tables

docs/source/installation.rst

+Installation of plotID
+==================================
+
+For installation instructions, first have a look at the general :doc:`readme_link` or the `README.md <https://git.rwth-aachen.de/plotid/plotid_python/-/blob/main/README.md>`_ file. More detailed information about the installation process can then be found here.
+
+Wrong python version
+--------------------
+To install and run plotID a python version ≥ 3.10 is required. If your linux distribution is shipped with a python version < 3.10, you still can install a newer python version. Intalling python 3.10 on Debian or Ubuntu would look like this
+
+.. code:: bash
+
+    sudo apt install python3.10 python3.10-venv
+
+You can then create a virtual environment "venv" to run plotID inside it
+
+.. code:: bash
+
+    python3.10 -m venv venv
+
+Now activate the venv
+
+.. code:: bash
+
+    source venv/bin/activate
+
+The virtual environment now runs with python 3.10 and plotID can be installed the usual way as described in :doc:`Overview`.
+
+
+Installation on Windows via pip
+-------------------------------
+If you're trying
+
+.. code:: cmd
+
+    pip install .
+
+and following error is thrown
+
+.. code:: cmd
+
+    Fatal error in launcher: Unable to create process using '"...env\Scripts\python.exe"  "..\venv\Scripts\pip.exe" install .': The system cannot find the specified file.
+
+Try to forcefully reinstall pip
+
+.. code:: cmd
+
+    python -m pip install --upgrade --force pip
+
+Or use 
+
+.. code:: cmd
+
+    python -m pip install .
+
+instead.

docs/source/modules.rst

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

docs/source/plotid.rst

-plotid package
-==============
-
-Submodules
-----------
-
-plotid.create\_id module
-------------------------
-
-.. automodule:: plotid.create_id
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-plotid.example module
----------------------
-
-.. automodule:: plotid.example
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-plotid.filecompare module
--------------------------
-
-.. automodule:: plotid.filecompare
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-plotid.hdf5\_external\_link module
-----------------------------------
-
-.. automodule:: plotid.hdf5_external_link
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-plotid.plotoptions module
--------------------------
-
-.. automodule:: plotid.plotoptions
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-plotid.publish module
----------------------
-
-.. automodule:: plotid.publish
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-plotid.save\_plot module
-------------------------
-
-.. automodule:: plotid.save_plot
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-plotid.tagplot module
----------------------
-
-.. automodule:: plotid.tagplot
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-plotid.tagplot\_matplotlib module
----------------------------------
-
-.. automodule:: plotid.tagplot_matplotlib
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: plotid
-   :members:
-   :undoc-members:
-   :show-inheritance:

docs/source/readme_link.md

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

docs/source/readme_link.rst

-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: