…et by default in build mode

* use dotenv for compatibility

* declare dotenv a dependency

* use older version due to python version requirements

* use optional dependecies

* fix typo

* install test dependencies for deployment

* use test extras instead of test requires

* Add pyfiction documentation to read the docs

* revert change in conf.py for local doc building

* add removed empty line

* Update requirements.txt

* Add docs

* change Mathjax commands to also work in pyfiction docs

* try to order members by source

* exclude mkdoc script from clang-tidy-review

* fix documentation for cartesian layout

* exclude documentation.hpp in clang-tidy review

* update exclude pattern in clang-tidy-review

* move header inside tab

* move header inside individual tabs

* change version requirement for Z3

* override hexagonal layout Python docs

* update hexagonal layout Python docs

---------

Co-authored-by: Marcel Walter <[email protected]>

…n its current form

… in pyfiction

# Conflicts:
#	.github/workflows/clang-tidy-review.yml
#	.github/workflows/codeql-analysis.yml
#	.github/workflows/coverage.yml
#	.github/workflows/ubuntu.yml
#	README.md
#	include/fiction/algorithms/simulation/sidb/quicksim.hpp
#	include/fiction/technology/charge_distribution_surface.hpp

# Conflicts:
#	docs/layouts/coordinates.rst

* expose bounding box to pyfiction

# Conflicts:
#	include/fiction/layouts/cartesian_layout.hpp
#	include/fiction/layouts/coordinates.hpp
#	include/fiction/layouts/hexagonal_layout.hpp

… to pyfiction

* 🎨 test added for several functions.

* 🎨 constructor added to use layout as input in charge_distribution_surface.hpp.

* 🎨 add test for the simulators.

* 🎨 add test for the simulators.

…are still failing though.

…_distribution_surface

# Conflicts:
#	.clang-format
#	README.md
#	docs/algorithms/path_finding.rst
#	docs/algorithms/sidb_simulation.rst
#	docs/getting_started.rst
#	docs/technology/simulation.rst
#	include/fiction/algorithms/path_finding/a_star.hpp
#	include/fiction/algorithms/path_finding/k_shortest_paths.hpp
#	include/fiction/algorithms/physical_design/orthogonal.hpp
#	include/fiction/algorithms/properties/critical_path_length_and_throughput.hpp
#	include/fiction/algorithms/simulation/sidb/critical_temperature.hpp
#	include/fiction/algorithms/simulation/sidb/sidb_simulation_parameters.hpp
#	include/fiction/layouts/cartesian_layout.hpp
#	include/fiction/layouts/hexagonal_layout.hpp
#	include/fiction/layouts/obstruction_layout.hpp
#	include/fiction/technology/charge_distribution_surface.hpp
#	include/fiction/technology/physical_constants.hpp
#	libs/CMakeLists.txt
#	test/algorithms/simulation/sidb/critical_temperature.cpp
#	test/layouts/cartesian_layout.cpp

… `main`

…on to pyfiction

* Update pyfiction-docstring-generator.yml

* expose post layout optimization algorithm

* Update pyfiction-docstring-generator.yml

* fix post layout optimiztaion binding

* Update pyfiction-docstring-generator.yml

* clang-format

# Conflicts:
#	bindings/pyfiction/include/pyfiction/algorithms/physical_design/hexagonalization.hpp
#	bindings/pyfiction/include/pyfiction/algorithms/physical_design/post_layout_optimization.hpp
#	bindings/pyfiction/test/algorithms/physical_design/test_hexagonalization.py
#	bindings/pyfiction/test/algorithms/physical_design/test_post_layout_optimization.py

# Conflicts:
#	.gitignore
#	.gitmodules
#	CMakeLists.txt
#	README.md
#	docs/algorithms/sidb_simulation.rst
#	docs/requirements.txt
#	include/fiction/algorithms/physical_design/exact.hpp
#	libs/CMakeLists.txt
#	libs/pybind11

* expose gate-level layout reader and writer

* clang-format

* fix tests and add docs

* add naming utils to logic network

* add po to index functions

… packaging

… pyfiction