Add resume option and update docstrings in run_chain.py #42
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mjaehn
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Nov 11, 2023
* Remove `variants` key and use `features` instead (#30) * Remove variants from models.yaml * Remove spinup variant and use the spinup variable instead * GitHub Action: Apply Pep8-formatting * Remove variant check * Install specific icontools version --------- Co-authored-by: github-actions <[email protected]> * Convert config files to yaml format (#36) * Remove variants from models.yaml * Remove spinup variant and use the spinup variable instead * GitHub Action: Apply Pep8-formatting * Remove variant check * Install specific icontools version * Starting to work on cosmo case * GitHub Action: Apply Pep8-formatting * GitHub Action: Apply Pep8-formatting * Add cases and paths * Create cfg object from Config class * GitHub Action: Apply Pep8-formatting * Format output of configuration * Add email and simplify print function * GitHub Action: Apply Pep8-formatting * Improve output * GitHub Action: Apply Pep8-formatting * Make cams a dict and adapt prepare_data * GitHub Action: Apply Pep8-formatting * Adapt emissions * GitHub Action: Apply Pep8-formatting * Adapt biofluxes * Change user variable naming * GitHub Action: Apply Pep8-formatting * Fix path * Adapt oem * GitHub Action: Apply Pep8-formatting * Modify whole config.yaml * Adapt online_vprm * Work on int2lm, some restructuring * GitHub Action: Apply Pep8-formatting * Move times to config file * GitHub Action: Apply Pep8-formatting * Further work on int2lm * GitHub Action: Apply Pep8-formatting * Finish int2lm * GitHub Action: Apply Pep8-formatting * Fix post_int2lm * GitHub Action: Apply Pep8-formatting * Use correct config variable in post_int2lm * Work on cosmo job/config * GitHub Action: Apply Pep8-formatting * Make cosmo job run * GitHub Action: Apply Pep8-formatting * Fix hstart and hstop for spinup * GitHub Action: Apply Pep8-formatting * Fix post_cosmo and add functions to set config variables * GitHub Action: Apply Pep8-formatting * Rename cosmo-ghg test case and reduce simulation time * Minor fixes for other jobs * Fix cosmo job * Remove config.py * Change time interval * Remove cosmo_spec * Fix inidates for spinup runs * GitHub Action: Apply Pep8-formatting * Set correct inidate for int2lm job * Fix and unify post_int2lm * GitHub Action: Apply Pep8-formatting * Fix hstart and hstop for spinup runs * Remove unnecessary inidate variables * GitHub Action: Apply Pep8-formatting * Add cosmo-ghg restart test case * Create separate inidate variable for int2lm * GitHub Action: Apply Pep8-formatting * Work on icon case * Further work on ICON and make job_id and chain_root config variables * GitHub Action: Apply Pep8-formatting * Input files for ICON * GitHub Action: Apply Pep8-formatting * Add class function for easy-access variables * Further work on ICON * GitHub Action: Apply Pep8-formatting * Print config variables before duplicating dict variables * ICON: prepare_data * Remove icon_spec * Add class function to convert relative to absolute paths * Further work on prepare_data * GitHub Action: Apply Pep8-formatting * Add prefix to meteo nameformat * GitHub Action: Apply Pep8-formatting * Fix time variable for xarray * GitHub Action: Apply Pep8-formatting * Remove print * Further work on icon job * GitHub Action: Apply Pep8-formatting * Better naming for variables and restart setting * GitHub Action: Apply Pep8-formatting * Add GEOSP file for restart simulations * GitHub Action: Apply Pep8-formatting * Set procs for restart etc. in config * Set correct endtime in prepare_data * Set correct nodes for icon (cpu + gpu) * Fix error * Further work on icon restart * GitHub Action: Apply Pep8-formatting * Fix restart and finish icon-test case * Remove print * Update jenkins tests * Fix cosmo-ghg test * fix int2lm job script * Fix for GEOSP data copy * Fix jobid date * GitHub Action: Apply Pep8-formatting * Add ISO 8601 duration converter * Fix icon test jenkins files * GitHub Action: Apply Pep8-formatting * Modify comment in config file to match case --------- Co-authored-by: github-actions <[email protected]> * Use `cfg.enddate` instead of `hstart` and `hstop` (#39) * Remove variants from models.yaml * Remove spinup variant and use the spinup variable instead * GitHub Action: Apply Pep8-formatting * Remove variant check * Install specific icontools version * Starting to work on cosmo case * GitHub Action: Apply Pep8-formatting * GitHub Action: Apply Pep8-formatting * Add cases and paths * Create cfg object from Config class * GitHub Action: Apply Pep8-formatting * Format output of configuration * Add email and simplify print function * GitHub Action: Apply Pep8-formatting * Improve output * GitHub Action: Apply Pep8-formatting * Make cams a dict and adapt prepare_data * GitHub Action: Apply Pep8-formatting * Adapt emissions * GitHub Action: Apply Pep8-formatting * Adapt biofluxes * Change user variable naming * GitHub Action: Apply Pep8-formatting * Fix path * Adapt oem * GitHub Action: Apply Pep8-formatting * Modify whole config.yaml * Adapt online_vprm * Work on int2lm, some restructuring * GitHub Action: Apply Pep8-formatting * Move times to config file * GitHub Action: Apply Pep8-formatting * Further work on int2lm * GitHub Action: Apply Pep8-formatting * Finish int2lm * GitHub Action: Apply Pep8-formatting * Fix post_int2lm * GitHub Action: Apply Pep8-formatting * Use correct config variable in post_int2lm * Work on cosmo job/config * GitHub Action: Apply Pep8-formatting * Make cosmo job run * GitHub Action: Apply Pep8-formatting * Fix hstart and hstop for spinup * GitHub Action: Apply Pep8-formatting * Fix post_cosmo and add functions to set config variables * GitHub Action: Apply Pep8-formatting * Rename cosmo-ghg test case and reduce simulation time * Minor fixes for other jobs * Fix cosmo job * Remove config.py * Change time interval * Remove cosmo_spec * Fix inidates for spinup runs * GitHub Action: Apply Pep8-formatting * Set correct inidate for int2lm job * Fix and unify post_int2lm * GitHub Action: Apply Pep8-formatting * Fix hstart and hstop for spinup runs * Remove unnecessary inidate variables * GitHub Action: Apply Pep8-formatting * Add cosmo-ghg restart test case * Create separate inidate variable for int2lm * GitHub Action: Apply Pep8-formatting * Work on icon case * Further work on ICON and make job_id and chain_root config variables * GitHub Action: Apply Pep8-formatting * Input files for ICON * GitHub Action: Apply Pep8-formatting * Add class function for easy-access variables * Further work on ICON * GitHub Action: Apply Pep8-formatting * Print config variables before duplicating dict variables * ICON: prepare_data * Remove icon_spec * Add class function to convert relative to absolute paths * Further work on prepare_data * GitHub Action: Apply Pep8-formatting * Add prefix to meteo nameformat * GitHub Action: Apply Pep8-formatting * Fix time variable for xarray * GitHub Action: Apply Pep8-formatting * Remove print * Further work on icon job * GitHub Action: Apply Pep8-formatting * Better naming for variables and restart setting * GitHub Action: Apply Pep8-formatting * Add GEOSP file for restart simulations * GitHub Action: Apply Pep8-formatting * Set procs for restart etc. in config * Set correct endtime in prepare_data * Set correct nodes for icon (cpu + gpu) * Fix error * Further work on icon restart * GitHub Action: Apply Pep8-formatting * Fix restart and finish icon-test case * Remove print * Update jenkins tests * Fix cosmo-ghg test * fix int2lm job script * Fix for GEOSP data copy * Fix jobid date * GitHub Action: Apply Pep8-formatting * Add ISO 8601 duration converter * Fix icon test jenkins files * GitHub Action: Apply Pep8-formatting * Use startdate and enddate in iter_hours * Merge init * Work on startdate, enddate, etc. * GitHub Action: Apply Pep8-formatting * Some cleanup for startdates * GitHub Action: Apply Pep8-formatting * Set jobid based on enddate * Provide restart step in iso format (icon-test) * GitHub Action: Apply Pep8-formatting * Adapt run_chain for enddate * GitHub Action: Apply Pep8-formatting * Remove obsolete time occurences * GitHub Action: Apply Pep8-formatting * Fix last commit * GitHub Action: Apply Pep8-formatting * Set missing variables * Remove hstop in prepare_data * GitHub Action: Apply Pep8-formatting * Adapt namelist templates * fix for namelist templates * Remove config.py * Further fixes * Adapt main function parameters for all jobs * Adapt function parameters for other jobs and cfg_variables * Correct function arguments when called * Fix icon job * GitHub Action: Apply Pep8-formatting * Don't pass startdate and enddate anymore * GitHub Action: Apply Pep8-formatting * Further removal of startdate and enddate * GitHub Action: Apply Pep8-formatting * Remove check at the end of int2lm runscript * Sync int2lm scripts * Remove unused imports * Fix cosmo-ghg jobs * GitHub Action: Apply Pep8-formatting * Modify docstring for iter_hours function * Fix chain for spinup * Remove print from post_int2lm * Fix spinup * Fix for second simulation in spinup * GitHub Action: Apply Pep8-formatting * Some docstring cleanup --------- Co-authored-by: github-actions <[email protected]> * Add icon-art-oem-test (#40) * Add config.yaml * Replace inidate with startdate_sim * Fix icontools scripts * Fix chem file names * Set correct input file names * Small fix for latbc grid file name * Add prefix to chem file * GitHub Action: Apply Pep8-formatting * Fix for chem file * GitHub Action: Apply Pep8-formatting * More corrections for chem file * GitHub Action: Apply Pep8-formatting * Fix art namelist * Fix art input folder * Update on how to build icon(-art) * Update .gitignore * Correcting case name in comment * Use config variables for num_procs in namelist * Fix ICON namelists * Remove config.py * Only process initial file if present * GitHub Action: Apply Pep8-formatting * Add start of icontools runscript to logger --------- Co-authored-by: github-actions <[email protected]> * Add icon-art-global-test (#41) * Add config.yaml and modify icon_runjob * Change variables to scratch input files * Further modify variable names * GitHub Action: Apply Pep8-formatting * Fix restart file and disable create_oh_for_restart() * GitHub Action: Apply Pep8-formatting * Full log from runscript --------- Co-authored-by: github-actions <[email protected]> * GitHub Pages (#44) * Initial setup * Deploy only rc branch * Modify docs.yml * New preview action * Cleanup * GitHub Action: Apply Pep8-formatting * Remove PSphinxTheme * Deploy preview for PR 43 🛫 * Fix docs.yml * Remove pr-preview * Remove autodoc * GitHub Action: Apply Pep8-formatting * Select correct branch * Remvoe autofunctions * Formatting --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: mjaehn <[email protected]> * Update docs.yml * Add resume option and update docstrings in run_chain.py (#42) * Add resume option * GitHub Action: Apply Pep8-formatting * Add and modify docstrings in run_chain.py * Change some wording --------- Co-authored-by: github-actions <[email protected]> * Update README (#45) * Remove readthedocs yaml file * Update README * Fix link * Deploy docs to latest and tags (#47) * Deploy docs to latest and tags * Fix syntax error --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: mjaehn <[email protected]>
mjaehn
added a commit
that referenced
this pull request
Nov 29, 2023
* Remove `variants` key and use `features` instead (#30) * Remove variants from models.yaml * Remove spinup variant and use the spinup variable instead * GitHub Action: Apply Pep8-formatting * Remove variant check * Install specific icontools version --------- Co-authored-by: github-actions <[email protected]> * Convert config files to yaml format (#36) * Remove variants from models.yaml * Remove spinup variant and use the spinup variable instead * GitHub Action: Apply Pep8-formatting * Remove variant check * Install specific icontools version * Starting to work on cosmo case * GitHub Action: Apply Pep8-formatting * GitHub Action: Apply Pep8-formatting * Add cases and paths * Create cfg object from Config class * GitHub Action: Apply Pep8-formatting * Format output of configuration * Add email and simplify print function * GitHub Action: Apply Pep8-formatting * Improve output * GitHub Action: Apply Pep8-formatting * Make cams a dict and adapt prepare_data * GitHub Action: Apply Pep8-formatting * Adapt emissions * GitHub Action: Apply Pep8-formatting * Adapt biofluxes * Change user variable naming * GitHub Action: Apply Pep8-formatting * Fix path * Adapt oem * GitHub Action: Apply Pep8-formatting * Modify whole config.yaml * Adapt online_vprm * Work on int2lm, some restructuring * GitHub Action: Apply Pep8-formatting * Move times to config file * GitHub Action: Apply Pep8-formatting * Further work on int2lm * GitHub Action: Apply Pep8-formatting * Finish int2lm * GitHub Action: Apply Pep8-formatting * Fix post_int2lm * GitHub Action: Apply Pep8-formatting * Use correct config variable in post_int2lm * Work on cosmo job/config * GitHub Action: Apply Pep8-formatting * Make cosmo job run * GitHub Action: Apply Pep8-formatting * Fix hstart and hstop for spinup * GitHub Action: Apply Pep8-formatting * Fix post_cosmo and add functions to set config variables * GitHub Action: Apply Pep8-formatting * Rename cosmo-ghg test case and reduce simulation time * Minor fixes for other jobs * Fix cosmo job * Remove config.py * Change time interval * Remove cosmo_spec * Fix inidates for spinup runs * GitHub Action: Apply Pep8-formatting * Set correct inidate for int2lm job * Fix and unify post_int2lm * GitHub Action: Apply Pep8-formatting * Fix hstart and hstop for spinup runs * Remove unnecessary inidate variables * GitHub Action: Apply Pep8-formatting * Add cosmo-ghg restart test case * Create separate inidate variable for int2lm * GitHub Action: Apply Pep8-formatting * Work on icon case * Further work on ICON and make job_id and chain_root config variables * GitHub Action: Apply Pep8-formatting * Input files for ICON * GitHub Action: Apply Pep8-formatting * Add class function for easy-access variables * Further work on ICON * GitHub Action: Apply Pep8-formatting * Print config variables before duplicating dict variables * ICON: prepare_data * Remove icon_spec * Add class function to convert relative to absolute paths * Further work on prepare_data * GitHub Action: Apply Pep8-formatting * Add prefix to meteo nameformat * GitHub Action: Apply Pep8-formatting * Fix time variable for xarray * GitHub Action: Apply Pep8-formatting * Remove print * Further work on icon job * GitHub Action: Apply Pep8-formatting * Better naming for variables and restart setting * GitHub Action: Apply Pep8-formatting * Add GEOSP file for restart simulations * GitHub Action: Apply Pep8-formatting * Set procs for restart etc. in config * Set correct endtime in prepare_data * Set correct nodes for icon (cpu + gpu) * Fix error * Further work on icon restart * GitHub Action: Apply Pep8-formatting * Fix restart and finish icon-test case * Remove print * Update jenkins tests * Fix cosmo-ghg test * fix int2lm job script * Fix for GEOSP data copy * Fix jobid date * GitHub Action: Apply Pep8-formatting * Add ISO 8601 duration converter * Fix icon test jenkins files * GitHub Action: Apply Pep8-formatting * Modify comment in config file to match case --------- Co-authored-by: github-actions <[email protected]> * Use `cfg.enddate` instead of `hstart` and `hstop` (#39) * Remove variants from models.yaml * Remove spinup variant and use the spinup variable instead * GitHub Action: Apply Pep8-formatting * Remove variant check * Install specific icontools version * Starting to work on cosmo case * GitHub Action: Apply Pep8-formatting * GitHub Action: Apply Pep8-formatting * Add cases and paths * Create cfg object from Config class * GitHub Action: Apply Pep8-formatting * Format output of configuration * Add email and simplify print function * GitHub Action: Apply Pep8-formatting * Improve output * GitHub Action: Apply Pep8-formatting * Make cams a dict and adapt prepare_data * GitHub Action: Apply Pep8-formatting * Adapt emissions * GitHub Action: Apply Pep8-formatting * Adapt biofluxes * Change user variable naming * GitHub Action: Apply Pep8-formatting * Fix path * Adapt oem * GitHub Action: Apply Pep8-formatting * Modify whole config.yaml * Adapt online_vprm * Work on int2lm, some restructuring * GitHub Action: Apply Pep8-formatting * Move times to config file * GitHub Action: Apply Pep8-formatting * Further work on int2lm * GitHub Action: Apply Pep8-formatting * Finish int2lm * GitHub Action: Apply Pep8-formatting * Fix post_int2lm * GitHub Action: Apply Pep8-formatting * Use correct config variable in post_int2lm * Work on cosmo job/config * GitHub Action: Apply Pep8-formatting * Make cosmo job run * GitHub Action: Apply Pep8-formatting * Fix hstart and hstop for spinup * GitHub Action: Apply Pep8-formatting * Fix post_cosmo and add functions to set config variables * GitHub Action: Apply Pep8-formatting * Rename cosmo-ghg test case and reduce simulation time * Minor fixes for other jobs * Fix cosmo job * Remove config.py * Change time interval * Remove cosmo_spec * Fix inidates for spinup runs * GitHub Action: Apply Pep8-formatting * Set correct inidate for int2lm job * Fix and unify post_int2lm * GitHub Action: Apply Pep8-formatting * Fix hstart and hstop for spinup runs * Remove unnecessary inidate variables * GitHub Action: Apply Pep8-formatting * Add cosmo-ghg restart test case * Create separate inidate variable for int2lm * GitHub Action: Apply Pep8-formatting * Work on icon case * Further work on ICON and make job_id and chain_root config variables * GitHub Action: Apply Pep8-formatting * Input files for ICON * GitHub Action: Apply Pep8-formatting * Add class function for easy-access variables * Further work on ICON * GitHub Action: Apply Pep8-formatting * Print config variables before duplicating dict variables * ICON: prepare_data * Remove icon_spec * Add class function to convert relative to absolute paths * Further work on prepare_data * GitHub Action: Apply Pep8-formatting * Add prefix to meteo nameformat * GitHub Action: Apply Pep8-formatting * Fix time variable for xarray * GitHub Action: Apply Pep8-formatting * Remove print * Further work on icon job * GitHub Action: Apply Pep8-formatting * Better naming for variables and restart setting * GitHub Action: Apply Pep8-formatting * Add GEOSP file for restart simulations * GitHub Action: Apply Pep8-formatting * Set procs for restart etc. in config * Set correct endtime in prepare_data * Set correct nodes for icon (cpu + gpu) * Fix error * Further work on icon restart * GitHub Action: Apply Pep8-formatting * Fix restart and finish icon-test case * Remove print * Update jenkins tests * Fix cosmo-ghg test * fix int2lm job script * Fix for GEOSP data copy * Fix jobid date * GitHub Action: Apply Pep8-formatting * Add ISO 8601 duration converter * Fix icon test jenkins files * GitHub Action: Apply Pep8-formatting * Use startdate and enddate in iter_hours * Merge init * Work on startdate, enddate, etc. * GitHub Action: Apply Pep8-formatting * Some cleanup for startdates * GitHub Action: Apply Pep8-formatting * Set jobid based on enddate * Provide restart step in iso format (icon-test) * GitHub Action: Apply Pep8-formatting * Adapt run_chain for enddate * GitHub Action: Apply Pep8-formatting * Remove obsolete time occurences * GitHub Action: Apply Pep8-formatting * Fix last commit * GitHub Action: Apply Pep8-formatting * Set missing variables * Remove hstop in prepare_data * GitHub Action: Apply Pep8-formatting * Adapt namelist templates * fix for namelist templates * Remove config.py * Further fixes * Adapt main function parameters for all jobs * Adapt function parameters for other jobs and cfg_variables * Correct function arguments when called * Fix icon job * GitHub Action: Apply Pep8-formatting * Don't pass startdate and enddate anymore * GitHub Action: Apply Pep8-formatting * Further removal of startdate and enddate * GitHub Action: Apply Pep8-formatting * Remove check at the end of int2lm runscript * Sync int2lm scripts * Remove unused imports * Fix cosmo-ghg jobs * GitHub Action: Apply Pep8-formatting * Modify docstring for iter_hours function * Fix chain for spinup * Remove print from post_int2lm * Fix spinup * Fix for second simulation in spinup * GitHub Action: Apply Pep8-formatting * Some docstring cleanup --------- Co-authored-by: github-actions <[email protected]> * Add icon-art-oem-test (#40) * Add config.yaml * Replace inidate with startdate_sim * Fix icontools scripts * Fix chem file names * Set correct input file names * Small fix for latbc grid file name * Add prefix to chem file * GitHub Action: Apply Pep8-formatting * Fix for chem file * GitHub Action: Apply Pep8-formatting * More corrections for chem file * GitHub Action: Apply Pep8-formatting * Fix art namelist * Fix art input folder * Update on how to build icon(-art) * Update .gitignore * Correcting case name in comment * Use config variables for num_procs in namelist * Fix ICON namelists * Remove config.py * Only process initial file if present * GitHub Action: Apply Pep8-formatting * Add start of icontools runscript to logger --------- Co-authored-by: github-actions <[email protected]> * Add icon-art-global-test (#41) * Add config.yaml and modify icon_runjob * Change variables to scratch input files * Further modify variable names * GitHub Action: Apply Pep8-formatting * Fix restart file and disable create_oh_for_restart() * GitHub Action: Apply Pep8-formatting * Full log from runscript --------- Co-authored-by: github-actions <[email protected]> * GitHub Pages (#44) * Initial setup * Deploy only rc branch * Modify docs.yml * New preview action * Cleanup * GitHub Action: Apply Pep8-formatting * Remove PSphinxTheme * Deploy preview for PR 43 🛫 * Fix docs.yml * Remove pr-preview * Remove autodoc * GitHub Action: Apply Pep8-formatting * Select correct branch * Remvoe autofunctions * Formatting --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: mjaehn <[email protected]> * Update docs.yml * Add resume option and update docstrings in run_chain.py (#42) * Add resume option * GitHub Action: Apply Pep8-formatting * Add and modify docstrings in run_chain.py * Change some wording --------- Co-authored-by: github-actions <[email protected]> * Update README (#45) * Remove readthedocs yaml file * Update README * Fix link * Deploy docs to latest and tags (#47) * Deploy docs to latest and tags * Fix syntax error * Edit intro text * Reduce toc depth * Edit file structure * Futher modify file structure * Add environment section and move file structure * Add environment info * Format note * Add features * Add logo to README * Shorten title * Add logo to docs * Fix logo * Add favicon * Use small logo for docs * Add features * Update README.md * Update README * Add 'v' to version * Update README * Work on how-to-run * Add autodoc * Add syspath * GitHub Action: Apply Pep8-formatting * Add more paths * Test * Small fixes * Enable local html build * Add html baseurl * Remove baseurl * Install conda env before building docs * Fix for pr-preview * Update docs-pr-preview.yml * Update docs-pr-preview.yml * Update docs-pr-preview.yml * Update docs-pr-preview.yml * Adapt requirements files * Fix requirement file * Update gitignore * Remove python version * Remove shell env * Unify docs actions * Fix listing and remove autofunction * Add autofunctinos * Show command-line arguments * Add autofunctions * Update file structure * Fix indentation * Another small fix * Add lines * Rename src to externals * Add test cases section * Fix tree formatting * Remove obsolte file * Revise code structure * Update index for code structure * Add general table * Add more examples * Correct heading size * Fix typo * Add info for variables in namelist templates * List dict variables and job occurences * GitHub Action: Apply Pep8-formatting * Fix table * Edit namelist section * Fix colons * Fix autofunctions * Fix table * Settings for autofunctions * GitHub Action: Apply Pep8-formatting * Settings for autofunctions * Settings for toctree * Revert last commit * Add variable information * Fix table * Fix typo * Minor corrections * Minor corrections * Update jobs * Sort imports alphabetically * Update docstring for biofluxes * Rename externals -> ext * Update docstring for biofluxes * Update docstring for check_output * Update docstring for cosmo * Update docstring for emissions * Remove headers * Update docstring for icon * Update docstring for int2lm * Update docstring for obs_nudging and octe * Remove headers * Update docstring for oem * Update docstring for online_vprm * Update docstring for photo_rate * Update docstring for post_cosmo * Update docstring for post_int2lm * Update docstring for prepare_date * Update docstring for reduce_output * Update docstring for verify_chain * Change src to ext directory in scripts and config files * Add tools * Add autofunctions * Fix formatting * Fix formatting * Remove non-existing tool functions * Fix tool function * Change structure * Fix functions * restructuring * Unify docstrings * Fix directory structure formatting * Update README.md * Remove variant from config file and docs --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: mjaehn <[email protected]>
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Closes #29