Develop #60
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Develop #60
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…xecution for pull requests
* 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 <>
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