Update README.md

Update `# Using` section.
Several updates in PR #47

README.md

@@ -1,20 +1,19 @@
 # TdVisu
+
 ![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)
 [![PyPI license](https://img.shields.io/pypi/l/tdvisu.svg)](https://pypi.python.org/pypi/tdvisu/)
-![Tests](https://github.com/VaeterchenFrost/tdvisu/workflows/Tests/badge.svg) 
+![Tests](https://github.com/VaeterchenFrost/tdvisu/workflows/Tests/badge.svg)
 [![codecov](https://codecov.io/gh/VaeterchenFrost/tdvisu/branch/master/graph/badge.svg)](https://codecov.io/gh/VaeterchenFrost/tdvisu)
 
-
 ![GitHub release (latest SemVer including pre-releases)](https://img.shields.io/github/v/release/vaeterchenfrost/tdvisu?include_prereleases)
 [![PyPI version fury.io](https://badge.fury.io/py/tdvisu.svg)](https://pypi.python.org/pypi/tdvisu/)
+![GitHub commits since latest release (by SemVer)](https://img.shields.io/github/commits-since/VaeterchenFrost/tdvisu/latest)
 [![PyPI status](https://img.shields.io/pypi/status/tdvisu.svg)](https://pypi.python.org/pypi/tdvisu/)
 [![PyPI pyversions](https://img.shields.io/pypi/pyversions/tdvisu.svg)](https://pypi.python.org/pypi/tdvisu/)
 ![PyPI - Wheel](https://img.shields.io/pypi/wheel/tdvisu)
-![GitHub repo size](https://img.shields.io/github/repo-size/VaeterchenFrost/tdvisu)
 ![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/VaeterchenFrost/tdvisu)
-![GitHub commits since latest release (by SemVer)](https://img.shields.io/github/commits-since/VaeterchenFrost/tdvisu/latest)
 
-----------
+---
 
 Visualization for [dynamic programming](https://en.wikipedia.org/wiki/Dynamic_programming) on [tree decompositions](https://en.wikipedia.org/wiki/Tree_decomposition).
 
@@ -28,173 +27,200 @@ For the portable and light weight '.svg' format, all graphs for a timestep can b
 
 With the '.svg' format the images are highly customizable, and even combining several timesteps together using svg [animate](https://developer.mozilla.org/en-US/docs/Web/SVG/Element/animate) would be an option in the future.
 
-----------
+---
 
 # Using
-[Alubbock:Graphviz](https://anaconda.org/alubbock/graphviz) (or [Graphviz (>=2.38)](https://graphviz.gitlab.io/download/))
 
-[python-benedict](https://pypi.org/project/python-benedict/)
+> Note: see also the steps prepared in the CI/CD [.github/workflows/python-app.yml](https://github.com/VaeterchenFrost/tdvisu/actions/workflows/python-app.yml):
+
+[Graphviz (>=2.38)](https://graphviz.gitlab.io/download/). Be aware of changes in default layouts over different major versions of Graphviz. The project currently tests with `graphviz-version: "12.2.1"`.
 
-[for dpdb: psycopg2 (2.8.5)](https://www.psycopg.org/docs/index.html)
+[python-benedict[xml]](https://pypi.org/project/python-benedict/)
 
-----------
+PostgreSQL adapter for Python: [psycopg (3)](https://www.psycopg.org/docs/index.html)
+
+---
 
 # To register the graphviz plugins
+
 https://gitlab.com/graphviz/graphviz/-/issues/1352
+
 ```shell
 dot.exe -c
 ```
 
 # To install
 
-In a command prompt with pip (to get *pip* see: https://pip.pypa.io/en/stable/) installed:
+In a command prompt with pip (to get _pip_ see: https://pip.pypa.io/en/stable/) installed:
 Just run
+
 ```shell
 pip install -h (for more information on install options)
 pip install tdvisu
 ```
 
 To download the latest version from the default branch:
+
 ```shell
 git clone --depth 1 --single https://github.com/VaeterchenFrost/tdvisu
 ```
 
 # To isolate the dependencies
 
-With [virtualenv](https://virtualenv.pypa.io/en/latest/installation.html ) on the system installed you can isolate the environment, for example
+With [virtualenv](https://virtualenv.pypa.io/en/latest/installation.html) on the system installed you can isolate the environment, for example
+
 ```shell
-virtualenv tdvisu_dir -p 3.8
+virtualenv tdvisu_dir -p 3.12
 cd tdvisu_dir/bin/
 source activate
+# Windows: ./tdvisu_dir/Scripts/activate
 ```
+
 With [Conda](https://docs.conda.io/en/latest/) on the system installed the dependencies for this project can be automatically installed in a new environment:
 
 Go to the projects base directory.
 
-Open a *conda-command-prompt* with admin privileges and run the commands from the project folder
+Open a _conda-command-prompt_ with admin privileges and run the commands from the project folder
+
 - to create a new environment with basic dependencies:
+
 ```shell
-conda env create -f .\environment.yml
+conda env create -f ./environment.yml
 ```
+
 - to activate the environment:
+
 ```shell
 conda activate tdvisu
 ```
 
 # Install from source
 
 To clone the complete repository:
+
 ```shell
 git clone https://github.com/VaeterchenFrost/tdvisu
 ```
 
 To download only the latest version from the default branch:
+
 ```shell
 git clone --depth 1 --single https://github.com/VaeterchenFrost/tdvisu
 ```
 
 To install the project from the source folder:
+
 ```shell
 pip install -h (for more information on install options)
 pip install .
 ```
+
 to confirm that the visualization finds all dependencies:
+
 ```shell
-python .\tdvisu\visualization.py -h
+python ./tdvisu/visualization.py -h
 ```
+
 to run all tests:
+
 ```shell
-pip install .[test] 
-pytest .\test\
+pip install .[test]
+pytest ./test/
 ```
 
-----------
+---
 
 # How to use
 
 The visualization needs input in the form of the [Json API](https://github.com/VaeterchenFrost/gpusat-VISU/blob/master/JsonAPI_v1.3.md).
-The creation of this file is exemplary implemented in *construct_dpdb_visu.py* or the fork [GPUSAT](https://github.com/VaeterchenFrost/GPUSAT) and *--visufile filename* (optionally disabling preprocessing with *-p*).
+The creation of this file is exemplary implemented in _construct_dpdb_visu.py_ or the fork [GPUSAT](https://github.com/VaeterchenFrost/GPUSAT) and _--visufile filename_ (optionally disabling preprocessing with _-p_).
 
 Run the python file with the above dependencies installed:
 [visualization.py](https://github.com/VaeterchenFrost/gpusat-VISU/blob/master/satvisualization_repo/satvisu/visualization.py)
 
 **visualization.py** takes two parameters, the json-**infile** to read from, and optionally one **outputfolder**.
-With both arguments a call from IPython might look like this:
+With both arguments a run might look like this:
 
-```python
-runfile('visualization.py', 
-args='visugpusat.json examplefolder')
+```shell
+python tdvisu/visualization.py visugpusat.json examplefolder
 ```
 
 For #SAT it produces for example three different graphs suffixed with a running integer to represent timesteps:
 
-+ *TDStep* the tree decomposition with solved nodes
-+ *PrimalGraphStep* the primal graph with currently active variables highlighted
-+ *IncidenceGraphStep* the bipartite incidence graph with active clauses/variables highlighted
+- _TDStep_ the tree decomposition with solved nodes
+- _PrimalGraphStep_ the primal graph with currently active variables highlighted
+- _IncidenceGraphStep_ the bipartite incidence graph with active clauses/variables highlighted
 
 The graphs are images encoded in resolution independent **.svg files** (see https://www.lifewire.com/svg-file-4120603)
 
 <p align="center"><img src="https://raw.githubusercontent.com/VaeterchenFrost/tdvisu/master/doc/images/combined6DA4.svg?sanitize=true" width="70%"/></p>
 
 ## How to use construct_dpdb_visu.py
+
 After installing the project [dp_on_dbs](https://github.com/hmarkus/dp_on_dbs) with the there listed [requirements](https://github.com/hmarkus/dp_on_dbs#requirements), we need to
+
 - edit the [database.ini](https://github.com/VaeterchenFrost/tdvisu/blob/master/tdvisu/database.ini) with our password to [postgresql](https://www.postgresql.org/)
 - Solve a problem with `python dpdb.py [GENERAL-OPTIONS] -f <INPUT-FILE> <PROBLEM> [PROBLEM-SPECIFIC-OPTIONS]`
-  - for the problem **VertexCover** 
+  - for the problem **VertexCover**
     - with flag `--gr-file` to store the htd Input (if the input was in a different format)
   - for the problem **SharpSat**
     - with flag `--store-formula` to store the formula in the database
-- Run 
+- Run
   - **Sat** / **SharpSat**: `python construct_dpdb_visu.py [PROBLEMNUMBER]`
-  - **VertexCover**: `python construct_dpdb_visu.py [PROBLEMNUMBER] --twfile [TWFILE]` 
-   with the file in DIMACS tw-format containing the edges of the graph.
+  - **VertexCover**: `python construct_dpdb_visu.py [PROBLEMNUMBER] --twfile [TWFILE]`
+    with the file in DIMACS tw-format containing the edges of the graph.
 
-# Installation of the psycopg2 package 
+# Installation of the psycopg package 
 
-See https://www.psycopg.org/docs/install.html#build-prerequisites
+See https://www.psycopg.org/psycopg3/docs/basic/install.html
 
-For example on linux today this might need
-`sudo apt install libpq-dev` 
-before completion.
+**Note** Whatever version of `libpq` psycopg is compiled with, it will be possible to connect to PostgreSQL servers of any [supported version](https://www.psycopg.org/docs/install.html#prerequisites): just install the most recent libpq version or the most practical, without trying to match it to the version of the PostgreSQL server you will have to connect to.
 
------------------
+---
 
 # New Release
 
 ## Version
+
 - Bump `/version.py` according to the changes made
-- Change date to the release day, keep format 
+- Change date to the release day, keep format
 
 ## Requirements
+
 In case dependencies have changed, or just to update some, check
-- *requirements.txt*
-- *stable-requirements.txt* (using `pip freeze`)
-- *setup.py*
+
+- _requirements.txt_
+- _stable-requirements.txt_ (using `pip freeze`)
+- _setup.py_
 
 ## Write Changelog.md
+
 - Add tag with link (see bottom for linking examples)
-- Add changes, maybe some are already in *Unreleased*
-- Update *Unreleased* with **(No) unreleased changes**
+- Add changes, maybe some are already in _Unreleased_
+- Update _Unreleased_ with **(No) unreleased changes**
 
 ## Review code
+
 - Run tests (pytest)
 - Check codestyle (pylint)
 
 ## Push
+
 - Push changes to master
 - Wait for all automated checks! (All checks have passed...)
 
 ## Create Release
-- On the GitHub page go to: Release, **[Draft a new release](https://github.com/VaeterchenFrost/tdvisu/releases/new )** 
+
+- On the GitHub page go to: Release, **[Draft a new release](https://github.com/VaeterchenFrost/tdvisu/releases/new)**
 - Enter v'YOUR VERSION NUMBER' as the tag.
 - Add a **Release Title** (could be just the version)
 - Add some description (like in the CHANGELOG.md)
 - Click on **Publish release** on the bottom
 
-## Should automatically release to [PyPI](https://pypi.org/project/tdvisu/ )
-- For details see: [Upload Python Package](https://github.com/VaeterchenFrost/tdvisu/blob/master/.github/workflows/python-publish.yml )
+## Should automatically release to [PyPI](https://pypi.org/project/tdvisu/)
 
-**Now you are set for the new release :tada:**
+- For details see: [Upload Python Package](https://github.com/VaeterchenFrost/tdvisu/blob/master/.github/workflows/python-publish.yml)
 
-----------
+**Now you are set for the new release :tada:**
 
+---