update popsyn unit test branch with development updates#616
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elizabethteng wants to merge 20 commits into
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update popsyn unit test branch with development updates#616elizabethteng wants to merge 20 commits into
elizabethteng wants to merge 20 commits into
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* add versioning + automatic fetching of docs * comment out deploy action * remove git fetch * cleanup * remove PATH_TO_POSYDON * add MESA_DIR and PATH_TO_POSYDON_DATA * add reinstall for autodoc * do v1 generation * add v2 + install wheel for python 3.9 * positive grep * add wheel install v1 + remove from v2 * remove development for now * use as path * change out folder * add * change build_path * change build_path again * change checkout + path * add v1 & v2 make documentation * update _build for v1 documentation * show current version in documentation instead of latest * rename folder * remove old unused unstable workflow * Update docs/_source/conf.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * typo * fix typo * remove development doc make from release * remove v2.0.0-dev tag from version TAG list * remove dry-run commands * add v1 and v2 distinction + treat v2.0.0-dev as an indicator for development creation * force remove dirty for current version doc build, because copying files into version necessary * fix * link cleanup * add injection grab * move subprocess * add current version * change old_tags name * change posydon_version old tag version * posydon cleanup too * only apply injection to old v2 verions * add dry-run back in * template -> templates * add symlink process to latest release version * check for all dev tags of v2.X.X versions Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * implement comments * check for latest non-pre-release version * Update .github/workflows/deploy-github-pages-release.yml Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * Update .github/workflows/deploy-github-pages-release.yml Co-authored-by: Seth Gossage <sethg45@gmail.com> * remove dry-run --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> Co-authored-by: Seth Gossage <sethg45@gmail.com>
* Add fetch-tags:true Currently, not all the tags from Github are correctly pulled in this workflow, as such the code fails. * add v for folders + links to make all consistent * Add v for folder creation and in linkage
If multiple population synthesis reruns are present, the jobID check was returning a list of one. This should have just been the jobID. This corrects that selection.
Another fix to the building of the development version. This time, entering the git folder I don't understand why this worked locally with Local Github Actions (act) and not on the actual Github Actions. Is the workflow different?
* bump miniconda version to v3 and add proper bash shell initiation * clean up * remove sourcing conda; already done with bash -el * add pip upgrade back * Update install_extras.yml * remove check on PR
* change ECSN default and comment defaults in MODELS * function: get_MODEL; update tests * Update population_params_default.ini Add allow_spin_None to default ini file. * Update posydon-popsyn add verbose_on_fail * get at least mass in get_initial_BH_properties * update docs * adopt pre defined SN models; rename MODEL to SN_MODEL * adjust test mass to give BHs; rename prop * update population_params_default.ini to default SN model * change values for Farag matching * refer to v2 interpolators * add back Sukhbold+16-engine
* Update SN_MODELS.py Add S19.8 engine, rename SN_models for easier addition of more changes * update docs and ini files * rename SN_models
* update absolute imports and default ini with some docs * Changed grids.io to parse mesa grid dirs with changing eccentricity * Removed hotfix comments for PR * remove spurious spacing * Updating unit test to correspond to initial eccentricity in filename * Update posydon/unit_tests/grids/test_io.py Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> --------- Co-authored-by: astroJeff <andrews.jeff@gmail.com> Co-authored-by: Jeff Andrews <jeffrey.andrews@ufl.edu> Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com>
* Update 10_binaries_pop_syn.ipynb Fix typos * Update bbh_analysis.ipynb * Update bbh_analysis.ipynb * Update bbh_analysis.ipynb test * Update lgrb_pop_syn.ipynb * Update pop_syn.ipynb * Update pop_syn.ipynb * Update bbh_analysis.ipynb * Update custom_step_and_flow.ipynb * Update docs/_source/tutorials-examples/population-synthesis/bbh_analysis.ipynb Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * Update docs/_source/tutorials-examples/population-synthesis/bbh_analysis.ipynb Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * Update pop_syn.ipynb * Update bbh_analysis.ipynb - more verbose * Update bbh_analysis.ipynb - clarity * Update bbh_analysis.ipynb * Update bbh_analysis.ipynb clarity * Update bbh_analysis.ipynb addressing a few typos and clarity * Update lgrb_pop_syn.ipynb clarity * Update one_met_pop_syn.ipynb addressed typos and consistency with code updates * Update bbh_analysis.ipynb argument name update * Update one_met_pop_syn.ipynb typo * typo * Update evolve_single_binaries.ipynb typo * Update custom_step_and_flow.ipynb; adding clarity * Update custom_step_and_flow.ipynb small addition to last commit * Update custom_step_and_flow.ipynb * Update custom_step_and_flow.ipynb * some variables are not defined so I removed them. one is introduced later in the tutorial * maybe this change is wrong but I was unable to pip install .[vis] * Update - all but the last cell works with v2 population * added --account argument to posydon-popsyn Quest example. Without this, job submission will fail * Small typo fixes * add pending review changes --------- Co-authored-by: Monica Gallegos-Garcia <monicagallegosgarcia2024@u.northwestern.edu> Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> Co-authored-by: Seth Gossage <sethg45@gmail.com> Co-authored-by: mkruckow <Matthias.Kruckow@unige.ch>
* Update SN_MODELS.py change S19.8 to W20 * Update population_params_default.ini * Update population_params_end.ini
* combine SFR_Z_fraction and star_formation_rate into a single function call, which pre-calculate the multiplication for speed improvemen * add correct select_one_met in function * move SFH into separate classes with abstract inheritance * Move SFH to classes (with abstract treatments) + Add Chruslinska+21 SFH models * fix fSFR. Now sums correctly to 1 at each redshift. * add fSFR unit tests * add additional basic tests * fix double naming of SFR * add tests for new SFRs * remove old SFH code; not used anywhere * move std_log_metallicity_history * add dosctring for abstract class * add docstrings * rename variables * add more doc strings * add even more docs * more doc strings * add checks for required parameters in MadauBase * docstrings: * change name of SFR_per_met_per_z function * alter unit tests to adapt to previous changes * change ' to " * cleanup line lengths * change output fSFR and _call__ dosctring to ndarray * add check for model parameters required * restructure + integrate only between Z_min and Z_max + add option normalise * Z_max check * update the SFH to use Z_min and Z_max and normalise. Move the splitting per metallicity bin to its own function. Additionally, revamp the unit tests to be more in style with the other unit tests and adapt them for the new functions and treatment of the metallicity bins. * fix name typo * remove Z_max requirement for Chruslinska * implement Matthias comments * change to rates.MODEL * change comment * add test for get_SFR_per_met_at_z * make sure to test branches * add SFH tests * add space * remove duplicate lines in IllustrisTNG class * move ConcreteSFH into a fixture * Add support for Zmin and Zmax inside bins and inside the same bin. * add doc string + remove select_one_met * replace MODEL with SFH_MODEL * change DEFAULT_MODEL to DEFAULT_SFH_MODEL * add to default Zmin,Zmax=None + normalise=True * update docstrings: * clean up star_formation_history file * update unit tests + implement comments * update call method test * add std_log_metallicity_dist integer support * make explicit regex expression * update unit tests & implement remainder of comments Matthias * cleanup * warning cleanup * add SFHModelWarning + add sort check * change to sphinx reference style * add reference * add check for None output in error * add unit test for unsorted Metalicity bins * suggested change * add new warning class to test * Update posydon/unit_tests/popsyn/test_star_formation_history.py Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> --------- Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com>
* Update README.md * Apply suggestions from Seth Co-authored-by: Seth Gossage <sethg45@gmail.com> --------- Co-authored-by: Seth Gossage <sethg45@gmail.com>
* minor text change in 'I. Running your first MESA simulation using POSYDON' * changes up to 'Run one binary on your laptop for debugging' where I had error with work_dir * partial changes to the tutorial * small last changes in the documentation * adding matthias comment on work dir * Update docs/_source/tutorials-examples/MESA-grids/laptop.ipynb typo Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> --------- Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com>
* change the core radius for the stableMT option * Updating step_CEE.py * Re-writing step_CEE alpha_lambda prescription code * Updating code * updating common_functions list of functions to test * Apply suggestions from code review Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * Removing core_not_replaced_noMT option from documentation * Apply suggestions from code review Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * Updating mass loss due to merger in CEE * Update common_functions.py * Apply suggestions from code review Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * Update step_CEE.py * Update step_CEE.py * Apply suggestions from code review Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * Updated due to code review comments and changing CE function names * Missed this previous update * Updating documentation * Update docs/_source/components-overview/pop_syn/population_params.rst Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * Update posydon/unit_tests/utils/test_common_functions.py Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * Moving from double quotes to single quotes * Update posydon/binary_evol/CE/step_CEE.py Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * fix option names as Zepei reported * Update docs/_source/components-overview/pop_syn/population_params.rst Co-authored-by: Max <14039563+maxbriel@users.noreply.github.com> * add compt_type to CEE_adjust_binary_upon_merger as requested by me and Max --------- Co-authored-by: ZepeiX <Zepei.Xing@unige.ch> Co-authored-by: astroJeff <andrews.jeff@gmail.com> Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> Co-authored-by: mkruckow <Matthias.Kruckow@unige.ch> Co-authored-by: Max <14039563+maxbriel@users.noreply.github.com>
…inaries (#580) * Update binarystar.py adding a check for array like data and pad w/ nans as before, but with the right data type * Update binarystar.py operate on column element rather than the column itself * Update binarystar.py rename data_len to element_len * initialize V_sys as numpy array, rather than list, to match subsequent data types * added new dtypes in popsyn/io.py: object.string and object.float64 to differentiate subtypes of objects. Dynamically determine filler values when extending failed binary data columns * remove debug print statements and also add in default case if somehow a data column key does not exist in dtype dictionary * remove max_ele_length initialization, superfluous * added new sub dtype dictionary in popsyn/io.py to hold specs on dtypes within an object, now default to NoneTypes in case a definition is not found, which is converted to nan in case of single values (not objects), also now nearest_neighbour_distance is initialized as a float array rather than a string array * added empty string definition for cases of missing dtype definitions * Update posydon/binary_evol/binarystar.py Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> * Update posydon/binary_evol/binarystar.py Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com> --------- Co-authored-by: mkruckow <122798003+mkruckow@users.noreply.github.com>
* cancel the signal alarm * typo fix * remove min m2
* clean up dead links * fix typos * fix more typos * more spelling/wording changes * spelling mistakes + update Collaboration team (name error + core dev team) * fix * more typos * 1_HMS_HMS checked * baic number * fix more typo's and grammar * fix pop_syn notebook * fix pop_syn notebook * collaboration link change + spelling * 10 binaries + custom_steps * revert POSYDON capitalisation * revert POSYDON capitalisation * remove team page and link to website page * typo fix * revert POSYDON accronym capitalisation. * Update docs/_source/index.rst Co-authored-by: Matthias <122798003+mkruckow@users.noreply.github.com> * Update index.rst Change papers to POSYDON ADS collection * Apply suggestions from code review Co-authored-by: Matthias <122798003+mkruckow@users.noreply.github.com> * Update docs/_source/tutorials-examples/population-synthesis/10_binaries_pop_syn.ipynb Co-authored-by: Matthias <122798003+mkruckow@users.noreply.github.com> * Update docs/_source/tutorials-examples/population-synthesis/10_binaries_pop_syn.ipynb Co-authored-by: Matthias <122798003+mkruckow@users.noreply.github.com> * change focus of contact * Adapt focus of contact info * remove old release notes info * fix link * remove verification post-installation instructions (were only AI generated not filled) * remove PATH_TO_POSYDON_DATA location recommendation * restructure installation instructions * rework titles * remove display_version; no longer supported * remove user guides. It only pointed other tutorials (already linked) * remove empty posydon-workflow files * fix bold issue * remove unneccesary installation issues * update tutorial population instructions * cleanup * fix tutorial * fix link to file * remove unused published-wors page * remove link to non-existent dynamic grid tutorial * exclude tests * Remove non-existing link + add a warning about the MESA inlist stacking * add comment * add temp link zenodo * change to shell instead of python * fix error plot_2d * clean-up references to roadmap * cleanup reference to flowchart * restucture headers * cleanup refs * fix cell type * fix typo * fix link * fix link * fix links * fix link * remove :ref: for external links * fix headers * fix headers * cleanup * fix code blocks + table * fix table * fix header errors * add empty line after file docstring * fix table * Update installation-guide.rst * remove code-style + move contributing to Support and contact * remove report issue page + reorder index.rst * Add capital * Apply suggestions from Seth's code review Co-authored-by: Seth Gossage <sethg45@gmail.com> * update code-questions 1. Add Github Discussions to support questions 2. Change memory usage question since the memory requirement have changed for DR2 with the increased low-mass resolution. * Update docs/_source/getting-started/installation-guide.rst Co-authored-by: Elizabeth Teng <41969755+elizabethteng@users.noreply.github.com> * Update docs/_source/components-overview/pop_syn/synthetic_population.rst Co-authored-by: Elizabeth Teng <41969755+elizabethteng@users.noreply.github.com> * Update docs/_source/components-overview/pop_syn/synthetic_population.rst Co-authored-by: Elizabeth Teng <41969755+elizabethteng@users.noreply.github.com> * Update docs/_source/components-overview/pop_syn/synthetic_population.rst Co-authored-by: Elizabeth Teng <41969755+elizabethteng@users.noreply.github.com> --------- Co-authored-by: Matthias <122798003+mkruckow@users.noreply.github.com> Co-authored-by: Seth Gossage <sethg45@gmail.com> Co-authored-by: Elizabeth Teng <41969755+elizabethteng@users.noreply.github.com>
…ary (#609) * fix rescue resubmit merge job + exit gracefully if no resubmit necessary * change subfunction name * fix rescue submission * raise warning * change multiple print statements into single ones
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