Started on AminoAcid class #28

okkevaneck · 2021-05-21T14:24:29Z

Closes #25

…ments. 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

…dency

…ged' variable to 'solutions_found'-like variable

…for 2d and 3d depth_first tests

* 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 * Update build_deploy.yml * Fix compressing core and installed pre-commit (#15) * 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 * Fix datasets (#17) * 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 (#18) * 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 * Added enter to README * Release v0.2a2 (#20) * 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 * Changed version number * Add PyTest to repo and CI (#21) * 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 * Add CI caching for python environments (#23) * 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 * Add documentation to project (#24) * 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 (#28) * 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 * Temp commit to switch branch * Update core merge (#33) * 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

* Develop merge into master to sync commits. (#41) * 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 * Update build_deploy.yml * Fix compressing core and installed pre-commit (#15) * 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 * Fix datasets (#17) * 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 (#18) * 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 * Added enter to README * Release v0.2a2 (#20) * 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 * Changed version number * Add PyTest to repo and CI (#21) * 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 * Add CI caching for python environments (#23) * 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 * Add documentation to project (#24) * 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 (#28) * 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 * Temp commit to switch branch * Update core merge (#33) * 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 * Splitted visualization function to allow for multiple styles * Fixed function for plotting proteins * Fixed bug where no bonds would form * Fixed paper style * V1 paper style plots * Fixed first paper visualization. Added visualization to test set * Ran pre-commit

* 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 * Update build_deploy.yml * Fix compressing core and installed pre-commit (#15) * 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 * Fix datasets (#17) * 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 (#18) * 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 * Added enter to README * Release v0.2a2 (#20) * 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 * Changed version number * Add PyTest to repo and CI (#21) * 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 * Add CI caching for python environments (#23) * 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 * Add documentation to project (#24) * 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 (#28) * 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 * Temp commit to switch branch * Update core merge (#33) * 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 * Merge visualization updates (#41) (#42) * Develop merge into master to sync commits. (#41) * 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 * Update build_deploy.yml * Fix compressing core and installed pre-commit (#15) * 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 * Fix datasets (#17) * 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 (#18) * 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 * Added enter to README * Release v0.2a2 (#20) * 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 * Changed version number * Add PyTest to repo and CI (#21) * 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 * Add CI caching for python environments (#23) * 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 * Add documentation to project (#24) * 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 (#28) * 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 * Temp commit to switch branch * Update core merge (#33) * 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 * Splitted visualization function to allow for multiple styles * Fixed function for plotting proteins * Fixed bug where no bonds would form * Fixed paper style * V1 paper style plots * Fixed first paper visualization. Added visualization to test set * Ran pre-commit * Increased version to make new visualizations available

* 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 * Update build_deploy.yml * Fix compressing core and installed pre-commit (#15) * 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 * Fix datasets (#17) * 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 (#18) * 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 * Added enter to README * Release v0.2a2 (#20) * 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 * Changed version number * Add PyTest to repo and CI (#21) * 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 * Add CI caching for python environments (#23) * 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 * Add documentation to project (#24) * 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 (#28) * 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 * Temp commit to switch branch * Update core merge (#33) * 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 * Merge visualization updates (#41) (#42) * Develop merge into master to sync commits. (#41) * 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 * Update build_deploy.yml * Fix compressing core and installed pre-commit (#15) * 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 * Fix datasets (#17) * 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 (#18) * 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 * Added enter to README * Release v0.2a2 (#20) * 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 * Changed version number * Add PyTest to repo and CI (#21) * 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 * Add CI caching for python environments (#23) * 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 * Add documentation to project (#24) * 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 (#28) * 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 * Temp commit to switch branch * Update core merge (#33) * 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 * Splitted visualization function to allow for multiple styles * Fixed function for plotting proteins * Fixed bug where no bonds would form * Fixed paper style * V1 paper style plots * Fixed first paper visualization. Added visualization to test set * Ran pre-commit * Increased version to make new visualizations available * Add beam (#47) * V1 (untested) of a beam_search function * Compiles and runs, does not work * In mids of debug * Small changes * Changed wrong author usage in toml. Fixing copy issues with proteins and amino acids * Fixed copy operators for Protein and AminoAcid * Fixed bug in assignment and copy operators. New try for testing beam, which is also semi fixed * Fixed beam_search bugs * Added a more specific heuristic function for beam search and removed unnescessary branching in reach_prune * Solved bug in beam_search and add protein length to print * Finished beam search tests * Extended AminoAcid with << and = operator overloads * Added ptests for beam search and naive prune * Fixed typo for beam search class * Trying other pytest approach for mac * Trying run-on conditional from matrix * Removed file specifier for pytest * Added Windows runner check to linux * Enabled windows runner again * ALso removed big beam width * Removing dir slash in setuptools for windows buil * Removed windows due to Pybind11 bug

* 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 * Update build_deploy.yml * Fix compressing core and installed pre-commit (#15) * 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 * Fix datasets (#17) * 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 (#18) * 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 * Added enter to README * Release v0.2a2 (#20) * 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 * Changed version number * Add PyTest to repo and CI (#21) * 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 * Add CI caching for python environments (#23) * 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 * Add documentation to project (#24) * 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 (#28) * 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 * Temp commit to switch branch * Update core merge (#33) * 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 * Merge visualization updates (#41) (#42) * Develop merge into master to sync commits. (#41) * 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 * Update build_deploy.yml * Fix compressing core and installed pre-commit (#15) * 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 * Fix datasets (#17) * 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 (#18) * 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 * Added enter to README * Release v0.2a2 (#20) * 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 * Changed version number * Add PyTest to repo and CI (#21) * 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 * Add CI caching for python environments (#23) * 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 * Add documentation to project (#24) * 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 (#28) * 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 * Temp commit to switch branch * Update core merge (#33) * 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 * Splitted visualization function to allow for multiple styles * Fixed function for plotting proteins * Fixed bug where no bonds would form * Fixed paper style * V1 paper style plots * Fixed first paper visualization. Added visualization to test set * Ran pre-commit * Increased version to make new visualizations available * Add beam (#47) * V1 (untested) of a beam_search function * Compiles and runs, does not work * In mids of debug * Small changes * Changed wrong author usage in toml. Fixing copy issues with proteins and amino acids * Fixed copy operators for Protein and AminoAcid * Fixed bug in assignment and copy operators. New try for testing beam, which is also semi fixed * Fixed beam_search bugs * Added a more specific heuristic function for beam search and removed unnescessary branching in reach_prune * Solved bug in beam_search and add protein length to print * Finished beam search tests * Extended AminoAcid with << and = operator overloads * Added ptests for beam search and naive prune * Fixed typo for beam search class * Trying other pytest approach for mac * Trying run-on conditional from matrix * Removed file specifier for pytest * Added Windows runner check to linux * Enabled windows runner again * ALso removed big beam width * Removing dir slash in setuptools for windows buil * Removed windows due to Pybind11 bug * 32 change documentation to match core functionality (#53) * Made abstraction for version identification. Changed docs style to Furo. Updated internal contents to match core more. Visualization and Datasets still need to be done, as well as more visualizations * Wrote more on visualization and datasets. Only need to add correct figures, and fix pipeline issue when generating the core * Fixed versioning and importing for compilation. Added new figures for quickstart docs * Added last missing method * Added AminoAcid class to the API focs * Added beam search to the docs api * Added furo to docs requirements.txt * Trying different configuration for building readthedocs * Removed versioning * Exended and pinned requirements for docs * Changed python version to make readthedocs work. Also changed some small things * More minimal setup for furo * Upped versioning and new try for dong data reading * Removed commented code * Trying Windows build again * Trying full pytest on MacOS * Different Pip upgrade line for window * Excluded Windows again because it wants to be a special snowflake.. * Upped pybind in setup

* Develop (#55) * 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 * Update build_deploy.yml * Fix compressing core and installed pre-commit (#15) * 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 * Fix datasets (#17) * 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 (#18) * 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 * Added enter to README * Release v0.2a2 (#20) * 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 * Changed version number * Add PyTest to repo and CI (#21) * 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 * Add CI caching for python environments (#23) * 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 * Add documentation to project (#24) * 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 (#28) * 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 * Temp commit to switch branch * Update core merge (#33) * 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 * Merge visualization updates (#41) (#42) * Develop merge into master to sync commits. (#41) * 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 * Update build_deploy.yml * Fix compressing core and installed pre-commit (#15) * 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 * Fix datasets (#17) * 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 (#18) * 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 * Added enter to README * Release v0.2a2 (#20) * 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 * Changed version number * Add PyTest to repo and CI (#21) * 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 * Add CI caching for python environments (#23) * 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 * Add documentation to project (#24) * 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 (#28) * 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 * Temp commit to switch branch * Update core merge (#33) * 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 * Splitted visualization function to allow for multiple styles * Fixed function for plotting proteins * Fixed bug where no bonds would form * Fixed paper style * V1 paper style plots * Fixed first paper visualization. Added visualization to test set * Ran pre-commit * Increased version to make new visualizations available * Add beam (#47) * V1 (untested) of a beam_search function * Compiles and runs, does not work * In mids of debug * Small changes * Changed wrong author usage in toml. Fixing copy issues with proteins and amino acids * Fixed copy operators for Protein and AminoAcid * Fixed bug in assignment and copy operators. New try for testing beam, which is also semi fixed * Fixed beam_search bugs * Added a more specific heuristic function for beam search and removed unnescessary branching in reach_prune * Solved bug in beam_search and add protein length to print * Finished beam search tests * Extended AminoAcid with << and = operator overloads * Added ptests for beam search and naive prune * Fixed typo for beam search class * Trying other pytest approach for mac * Trying run-on conditional from matrix * Removed file specifier for pytest * Added Windows runner check to linux * Enabled windows runner again * ALso removed big beam width * Removing dir slash in setuptools for windows buil * Removed windows due to Pybind11 bug * 32 change documentation to match core functionality (#53) * Made abstraction for version identification. Changed docs style to Furo. Updated internal contents to match core more. Visualization and Datasets still need to be done, as well as more visualizations * Wrote more on visualization and datasets. Only need to add correct figures, and fix pipeline issue when generating the core * Fixed versioning and importing for compilation. Added new figures for quickstart docs * Added last missing method * Added AminoAcid class to the API focs * Added beam search to the docs api * Added furo to docs requirements.txt * Trying different configuration for building readthedocs * Removed versioning * Exended and pinned requirements for docs * Changed python version to make readthedocs work. Also changed some small things * More minimal setup for furo * Upped versioning and new try for dong data reading * Removed commented code * Trying Windows build again * Trying full pytest on MacOS * Different Pip upgrade line for window * Excluded Windows again because it wants to be a special snowflake.. * Upped pybind in setup * Resolved import error of '_version.py' --------- Co-authored-by: Ruben Horn <>

@rubenhorn

* Added manual function for running github actions and added pipeline execution for pull requests * Forget variable sign * Another try * Another one * Different appraoch * Changed usage * Removed brackets to don't reploy on push for non-master branches * Removed condition statements, as they might already be added by the if clause * Changed to string eval of true as github actions is possibly broken by design * Removed string eval as it appearently works * Fix/locate version module from @rubenhorn (#58) * Develop (#55) * 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 * Update build_deploy.yml * Fix compressing core and installed pre-commit (#15) * 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 * Fix datasets (#17) * 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 (#18) * 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 * Added enter to README * Release v0.2a2 (#20) * 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 * Changed version number * Add PyTest to repo and CI (#21) * 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 * Add CI caching for python environments (#23) * 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 * Add documentation to project (#24) * 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 (#28) * 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 * Temp commit to switch branch * Update core merge (#33) * 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 * Merge visualization updates (#41) (#42) * Develop merge into master to sync commits. (#41) * 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 * Update build_deploy.yml * Fix compressing core and installed pre-commit (#15) * 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 * Fix datasets (#17) * 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 (#18) * 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 * Added enter to README * Release v0.2a2 (#20) * 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 * Changed version number * Add PyTest to repo and CI (#21) * 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 * Add CI caching for python environments (#23) * 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 * Add documentation to project (#24) * 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 (#28) * 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 * Temp commit to switch branch * Update core merge (#33) * 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 * Splitted visualization function to allow for multiple styles * Fixed function for plotting proteins * Fixed bug where no bonds would form * Fixed paper style * V1 paper style plots * Fixed first paper visualization. Added visualization to test set * Ran pre-commit * Increased version to make new visualizations available * Add beam (#47) * V1 (untested) of a beam_search function * Compiles and runs, does not work * In mids of debug * Small changes * Changed wrong author usage in toml. Fixing copy issues with proteins and amino acids * Fixed copy operators for Protein and AminoAcid * Fixed bug in assignment and copy operators. New try for testing beam, which is also semi fixed * Fixed beam_search bugs * Added a more specific heuristic function for beam search and removed unnescessary branching in reach_prune * Solved bug in beam_search and add protein length to print * Finished beam search tests * Extended AminoAcid with << and = operator overloads * Added ptests for beam search and naive prune * Fixed typo for beam search class * Trying other pytest approach for mac * Trying run-on conditional from matrix * Removed file specifier for pytest * Added Windows runner check to linux * Enabled windows runner again * ALso removed big beam width * Removing dir slash in setuptools for windows buil * Removed windows due to Pybind11 bug * 32 change documentation to match core functionality (#53) * Made abstraction for version identification. Changed docs style to Furo. Updated internal contents to match core more. Visualization and Datasets still need to be done, as well as more visualizations * Wrote more on visualization and datasets. Only need to add correct figures, and fix pipeline issue when generating the core * Fixed versioning and importing for compilation. Added new figures for quickstart docs * Added last missing method * Added AminoAcid class to the API focs * Added beam search to the docs api * Added furo to docs requirements.txt * Trying different configuration for building readthedocs * Removed versioning * Exended and pinned requirements for docs * Changed python version to make readthedocs work. Also changed some small things * More minimal setup for furo * Upped versioning and new try for dong data reading * Removed commented code * Trying Windows build again * Trying full pytest on MacOS * Different Pip upgrade line for window * Excluded Windows again because it wants to be a special snowflake.. * Upped pybind in setup * Resolved import error of '_version.py' --------- Co-authored-by: Ruben Horn <> * Added specific typing for the pull_request workflow * Fixed typo * Added dependencies with develop as root branch (#59) * Upped version

Started on AminoAcid class

d3c67ff

okkevaneck self-assigned this May 21, 2021

okkevaneck added 28 commits June 11, 2021 18:42

Added comments in core, still bugs to sort out

3004562

Fixed more bugs in the core when adding AminoAcid class

4fe1ef0

Moved part of bind

0d60dd6

Integrated AminoAcid class and fixed Protein tests

dad30d0

Mid way testing for new depth-first approach

d9bfacb

Added local check script and depth_first works for HPPH

374cec8

Fixed depth_first search new version

5771c12

Fixed depth_first_bnb algorithm using new system

62d2373

Fixed small core bugs, working on new logo

120c998

Mid-way of changing bond_value structure

aaf1192

Bumbed python version in github workflow for matplotlib version depen…

aeba497

…dency

Bumped workflow python version to 3.9 as numpy 1.23 requires so

8e99f67

Removed h_idxs from prune function. Nothing has been tested

ac84d2c

Fixed Protein signature for pybind build

9b1e667

Setup for debugging current protein issues

11db2f6

Introduced core testing code

741d57e

Finished test script for amino acids

4b2d324

Started on Protein core tests

bdcaf82

Fixed protein test compilation

0c00ea6

Fixed first couple protein generation checks

b81ead6

Added more debug statements for core tests

b07ac00

Fixed bugs with bond checks

2fad7a5

Fixed generation of weighted amino maps

d67ef67

Finished all protein generation test

b6326ff

Added debug options in scriptn to run core tests with gdb

627c192

Fixed the last_pos indexing error from place_amino. Changed the 'chan…

bd03007

…ged' variable to 'solutions_found'-like variable

Solved typing issues

959390b

okkevaneck added 17 commits September 20, 2022 17:55

Changed signature of depth_first to use pointers. Added testing code …

a539ecd

…for 2d and 3d depth_first tests

Fixed local algorithm core tests

263c735

Fixed dfs_bnb

516f243

Fixed pybind11 change to providing protein pointers

991e8b4

Added dynamic_lookup for linking python in case of undefined symbols

8a91410

New way of setting -undefined flag

d998040

Updated the way of passing -undefined setting for macos

7b79d02

Added special compilation case for MacOS

169ef09

Saving Furo update for issue

d53c018

Changed minimum Python version to 3.9 as 3.11 will release soon

1cc85c0

Updated versions for wheel deployment

e948739

Changed always build to only build python 3.9 versions

aea9ba8

Changed CIwheel builds to be specific instead of exlcuding based

0460e7d

Leaving documentation as is and adding issue for the future

588d411

Added more licensing references

368f196

Added config file for rtfd to set python version to 3.9

5503043

Removed commented code

21c1e9d

okkevaneck merged commit 39be57a into develop Sep 28, 2022

okkevaneck deleted the update_core branch September 28, 2022 11:04

okkevaneck restored the update_core branch October 3, 2022 13:00

okkevaneck deleted the update_core branch October 3, 2022 13:55

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Started on AminoAcid class #28

Started on AminoAcid class #28

okkevaneck commented May 21, 2021

Started on AminoAcid class #28

Started on AminoAcid class #28

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okkevaneck commented May 21, 2021