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* bugfix: pinning cartopy and proj dependency versions as this was causing some issue with proj versions on systems that did not already have proj * bugfixing manager.write not able to write windows and adjoint sources if config.save_to_ds is set to False. This is unintended because write() is called explicitely and should force write, whereas save_to_ds is used to stop passive writing during the processing phase. Also threw in a check for ASDFDataSets opened in read-only during write() which would throw an error * bugfix changing a print statement in read_sem to a logger warning * removed pyaflowa from core objects, removed its tests and docs pages/references. Pyaflowa functionality has been completely shifted to SeisFlows * moved docs up to highest level directory to remove it from main dir and to match seisflows structure changed docs conf to point to the correct location updated changelog with most recent changes * Update README.md * udpating readthedocs.yaml to point to new docs location in package * pinning SciPy<=1.8.0 because SciPy==1.9.0 causes 'ValueErro: Unknown window type' because they changed name 'Hanning' -> 'Hann' causing errors in ObsPy * fixing setup procedure to avoid installing unnecessary requirements via pip * unpinning lowest scipy version due to Conda UnsatisfiedError package dependency conflicts during requirements installation * bugfixing time offset and waveform misfit naming * critical bug fix with filtering behavior for highpass and lowpass flipped from expected behavior. i.e., setting only min period used to set a highpass which is NOT what we want. This has been fixed * Remove external data gathering and I/O routines from Pyatoa (#23) * stripped away all moment tensor related functionality from the gatherer and plugins * further removed moment tensor related functionality and moved into pysep * stripped out I/O read and write functions related to SPECFEM which were redundant with respect to PySEP. replaced internal import statements with imports to pysep * stripped out all references to FDSN client in Pyatoa and all gathering that queried FDSN. This functionality will be shifted into PySEP * Removed now defunct docs related to gathering, updated changelog to reflect major changes made in this branch, removed failing tests that relied on removed functionality * update readme to remove reference of data fetchign * fixed missing comma in setup file * Update docs and install (#28) * removed setup.py and .cfg, implemented new pyproject.toml file replacing setup.py. pointed readthedocs to only requirements.txt file in docs directory. removed changelog in preference to set changelog in docs page * removed requirements.txt file * fixed missing suffixes in git dependencies of pyproject.toml file * docs added readme, moved notebooks into own directory, updated convert script. updating docs wording * updated overview page (slimmed down considerably) and bumped version number in conf * setting default filter periods to None and removing float requirement on input * pyflex requires a min period so setting to 1-100 rather than previous 10-30 * moved unused plot scripts out of repo (into simutil), removed unnecessary mgmt plot and moved into manager.plot() function * updated docs environment and main environment * update readme to match seisflows readme * removed manager and config notebooks and converted to a direct rst document added first glance to replace getting started * throws in a '*' on synthetic data gathering to deal with specfem3d_globe synthetics which suffix with 'ascii' * added data discovery rst doc page which is meant to replace the gatherer notebook and page * removed gatherer notebook and rst page * renames storage notebook * manually edited inspector rst doc file to be shorter and remove the notebook dependence. figures will be moved into the gallery * changed core_func name to misfit, for misfit quantifictaion * removed inspector notebook in favor of hand edited inspector doc page * updated naming standards page * cleaned out the scripts directory which had a lot of scripts that were unfinished or not used. ones that were important were moved into docs * bugfix inspector raypath plot checking incorrect logic * fixed bugfix * removed old image files from notebooks that are no longer required added an inspector gallery notebook and added rst to gallery page further cleaned up script repository added a load example inspector script * removed logging docs page and notebook, moved a short section into the misfit docs page * manually edited the storage rst file to be more concise and to move away from the notebook configuration. * removed storage notebook in favor of new .rst storage file * added outputs to code cells in inspector doc where relevant, changed ASDFDataSet example reading function to read only to not affect test data * added inspector figure text into gallery and removed text from inspector rst file * removing warnings from insp_gallery * renamed insp gallery notebook to avoid conversion deleting the manually edited version * condensed changelog to remove 0.3.0 changelog since we haven't even bumped to 0.2.0 removed make figures scripts directory * added github relevant files including different issue templates added contributing page modfieid from Pygmt * editing contributing document added cross-referencing into the misfit docs page * fixing typos misfit doc page * added cross-referencing to the storage docs page * finished adding cross-referencing into all docs pages of relevance * removed unnused 'read_seisflows_yaml' from Config class * major config and preprocessing reworking to allow for data-data misfit: removed unnused parameters 'start_pad', 'end_pad' from config, as well as filter corners removed seisflows_yaml and _par reading functionality from config, not necessary preprocess function now written more generally, does not take manager as input but rather takes stream and a few other arguments. manager preprocessing function changed to match * finished updating preprocessing function cleaned up logging statements, shortened and exchanged some 'info' for 'debug' statments * working data data example with some TA array data * renamed some files, cleaned up some docs text * last minute doc fixes * update changelog * fix tests which changed due to a change in default config parameters, removed some ununused test data, upated baseline images * bumping version number 0.2.0 for soft release Co-authored-by: Bryant Chow <[email protected]>
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