* Renamed actions and added badges to readme

* Switched slash for dash

* Fixed import structure

* Removed pull_request target as push also seems to trigger on pull request?

* Fixed bugs

* Added pull_request again as trigger for workflow

* Pre-commit test

* Added local hook for zipping core

* Added .zip and .tar.gz autozips into core_archives folder

* Zip test

* tar.gz test

* Compressing works, only really ugly workaround for moving files

* Refered to the archives in the README

* Release v0.2a1 (#14)

* Rework readme (#6)

* Renamed actions and added badges to readme

* Switched slash for dash

* Fix import structure (#10)

* Fixed import structure

* Removed pull_request target as push also seems to trigger on pull request?

* Fix visualization helpers (#13)

* Fixed bugs

* Added pull_request again as trigger for workflow

* Deleted old log file and changed setup version

* Restructured dataset files and added package_data to setup.py, also changed max-line-length for black to 79

* New setup for loading datasets

* Added dataset inclusion

* Added archiving for datasets

* Test for matrix include

* Added runOns variable

* Changed to a custom action

* Added inputFile

* Copied literal line

* Changed strategy order

* Check only ubuntu

* Extended matrix with all OS and extra CIBW_BUILD ENV flag

* Added default of only python 3.6 builds for 64-bit if push is not to master

* Release v0.2a1 (#14)

* Rework readme (#6)

* Renamed actions and added badges to readme

* Switched slash for dash

* Fix import structure (#10)

* Fixed import structure

* Removed pull_request target as push also seems to trigger on pull request?

* Fix visualization helpers (#13)

* Fixed bugs

* Added pull_request again as trigger for workflow

* Deleted old log file and changed setup version

* Changed master trigger to release trigger

* Moved wildcard

* Moved wildcard of JMESPath

* Added dot

* Trying starts_with

* Switched arguments

* Excluded python 2.7 pypy

* New jmespath filter test

* Added first pytest script for protein class and a script for performing local tests.

* Added pytest in CI

* Forgot -r for file

* Version of pytest with pytest at end of pipeline

* New pytest CI where pip installs local package

* Fixed tabs and added caching of python/pip environment

* Removed dot and added removal of build dirs to manage clean command

* Added cache ignores for env setup and ids for the caches

* Fixed cache IDs

* Renamed cache because GitHub does not allow for clearing caches...

* Moved python setup to be before cache loading

* Run that will install the dependencies

* Uncommented the cache-hit detection for installing dependencies

* Updated pre-commit version in hope that runner will create new cache

* Added more tests and added flake8 incompatability

* Other flake8 config try

* Reset to .flake8 file

* Downgrade of pre-commit to force dep. installation in CI

* Different pre-commit version

* Added depth_first tests

* Added depth_first_bnb tests

* Push to try and install all dependencies correctly

* Added back cache check for installing dependencies. New way of calling flake8, added class dependencies on tests

* Removed ls

* Core change test

* Core change test - new correctly

* Core archiving works

* Fixed pytest ordering and upgraded pandas version to trigger new cache

* Upgraded pandas

* Changed pandas version to 1.1.0

* Removed caching of CI and moved code to new PR

* Added first pytest script for protein class and a script for performing local tests.

* Added pytest in CI

* Forgot -r for file

* Version of pytest with pytest at end of pipeline

* New pytest CI where pip installs local package

* Fixed tabs and added caching of python/pip environment

* Removed dot and added removal of build dirs to manage clean command

* Added cache ignores for env setup and ids for the caches

* Fixed cache IDs

* Renamed cache because GitHub does not allow for clearing caches...

* Moved python setup to be before cache loading

* Run that will install the dependencies

* Uncommented the cache-hit detection for installing dependencies

* Updated pre-commit version in hope that runner will create new cache

* Added more tests and added flake8 incompatability

* Other flake8 config try

* Reset to .flake8 file

* Downgrade of pre-commit to force dep. installation in CI

* Different pre-commit version

* Added depth_first tests

* Added depth_first_bnb tests

* Push to try and install all dependencies correctly

* Added back cache check for installing dependencies. New way of calling flake8, added class dependencies on tests

* Removed ls

* Core change test

* Core change test - new correctly

* Core archiving works

* Fixed pytest ordering and upgraded pandas version to trigger new cache

* Upgraded pandas

* Changed pandas version to 1.1.0

* Dependency check

* new flake8 installation

* Flake8 action

* Added pip update flag

* Cleaned up the flake8 action usage

* Trying to install new deps

* Removed caching, only using dependencies during pytest

* Ran the sphinx quickstart, ignored mypy on docs

* First version of docs

* Added installation instructions for python

* Finished installation page and added quickstart info (not done yet)

* Finished v1 of the quickstart guide

* Removed heterogeneous setup page and added todo for creating example

* Added manpages for the datasets and algorithms

* Added helpers and visualize documentation

* Added placeholders for the Protein properties

* Added methods of Protein to the documentation

* Small changes

* Reworked the README

* Added whitespace for enter

* Added github star and filler-logo

* Starting on logo

* Added logo

* Removed github fork banner

* Logo test

* Changed logo loading

* New test

* Trying image tag

* Trying image tag 2.0

* Trying image tag 2.0

* Trying relative link

* New size

* New logo test

* New logo try

* New logo

* Reworked logo

* Downgraded matplotlib to alllow CI pipeline

* Added edittable logo, fixed small rst things, fixed compression of cores

* Added some figures, added reference to license, added license

* Started on AminoAcid class

* Added comments in core, still bugs to sort out

* Fixed more bugs in the core when adding AminoAcid class

* Moved part of bind

* Integrated AminoAcid class and fixed Protein tests

* Mid way testing for new depth-first approach

* Added local check script and depth_first works for HPPH

* Fixed depth_first search new version

* Fixed depth_first_bnb algorithm using new system

* Fixed small core bugs, working on new logo

* Mid-way of changing bond_value  structure

* Cleaned up bugs from intermediate version. Bumped versions of requirements. Introduced max_weights string for keeping track of possible future scores. Merged bond_semetry model setup with the else model setup. Fixed bug with cur_len of protein always being 1. Fixed getting the weight of a amino bond

* Bumbed python version in github workflow for matplotlib version dependency

* Bumped workflow python version to 3.9 as numpy 1.23 requires so

* Removed h_idxs from prune function. Nothing has been tested

* Fixed Protein signature for pybind build

* Setup for debugging current protein issues

* Introduced core testing code

* Finished test script for amino acids

* Started on Protein core tests

* Fixed protein test compilation

* Fixed first couple protein generation checks

* Added more debug statements for core tests

* Fixed bugs with bond checks

* Fixed generation of weighted amino maps

* Finished all protein generation test

* Added debug options in script to run core tests with gdb

* Added removal of amino tests

* Updated some pytest asserts. Added pytest and core_test asserts for score updates

* Updated reference for black in pre-commit

* Try adding core build in github actions pipeline

* Fixed local algorithm core tests

* Fixed dfs_bnb

* Fixed pybind11 change to providing protein pointers

* Added special compilation case for MacOS

* Changed minimum Python version to 3.9 as 3.11 will release soon

* Changed always build to only build python 3.9 versions

* Changed CIwheel builds to be specific instead of exlcuding based

* Leaving documentation as is and adding issue for the future

* Added more licensing references

* Added config file for rtfd to set python version to 3.9

* Started on AminoAcid class

* Added comments in core, still bugs to sort out

* Fixed more bugs in the core when adding AminoAcid class

* Moved part of bind

* Integrated AminoAcid class and fixed Protein tests

* Mid way testing for new depth-first approach

* Added local check script and depth_first works for HPPH

* Fixed depth_first search new version

* Fixed depth_first_bnb algorithm using new system

* Fixed small core bugs, working on new logo

* Mid-way of changing bond_value  structure

* Cleaned up bugs from intermediate version. Bumped versions of requirements. Introduced max_weights string for keeping track of possible future scores. Merged bond_semetry model setup with the else model setup. Fixed bug with cur_len of protein always being 1. Fixed getting the weight of a amino bond

* Bumbed python version in github workflow for matplotlib version dependency

* Bumped workflow python version to 3.9 as numpy 1.23 requires so

* Removed h_idxs from prune function. Nothing has been tested

* Fixed Protein signature for pybind build

* Setup for debugging current protein issues

* Introduced core testing code

* Finished test script for amino acids

* Started on Protein core tests

* Fixed protein test compilation

* Fixed first couple protein generation checks

* Added more debug statements for core tests

* Fixed bugs with bond checks

* Fixed generation of weighted amino maps

* Finished all protein generation test

* Added debug options in scriptn to run core tests with gdb

* Fixed the last_pos indexing error from place_amino. Changed the 'changed' variable to 'solutions_found'-like variable

* Solved typing issues

* Finished protein movement tests

* Added removal of amino tests

* Updated some pytest asserts. Added pytest and core_test asserts for score updates

* Updated reference for black in pre-commit

* Fixed score generation of core_test

* Fixed score update through removal

* Try adding core build in github actions pipeline

* Started on algorithm code

* Changed signature of depth_first to use pointers. Added testing code for 2d and 3d depth_first tests

* Fixed local algorithm core tests

* Fixed dfs_bnb

* Fixed pybind11 change to providing protein pointers

* Added dynamic_lookup for linking python in case of undefined symbols

* New way of setting -undefined flag

* Updated the way of passing -undefined setting for macos

* Added special compilation case for MacOS

* Saving Furo update for issue

* Changed minimum Python version to 3.9 as 3.11 will release soon

* Updated versions for wheel deployment

* Changed always build to only build python 3.9 versions

* Changed CIwheel builds to be specific instead of exlcuding based

* Leaving documentation as is and adding issue for the future

* Added more licensing references

* Added config file for rtfd to set python version to 3.9

* Removed commented code