RecSec improved customization (#170)

* recsec adds ability to change the colors of the axes (frame, labels etc.). Kwarg 'frame_color' will change all together

* adds option to change title color with 'title_c' and bugfixes 'y_label_c' not being propagated to all plotting options for the y label

* allow setting background color with 'bg_color' which colors both face of frame and the figure outside the axis
dpi is now controllable through parameter dpi

* bump patch and update changelog

PySEP v0.7.0 (#167)

* Bugfix RecSec zeropad introduces artifical timeshift (#150)

* recsec now properly accounting for zero pad when calculating time offsets.
* added a visual test for catching zero pad issue #149, this is a manual test for now so it's skipped

* RecordSection allow export traces and ignore locations (#148)

* new feature for exporting processed traces from recsec

* started test function for mismatched location case
added better error checking in check parameters to catch when subsetting removes all streams

* small updates to text

* remove debugger statement

* allow command line input of xlim_s be float

* Bugfix SAC header NZMSEC overflow causing incorrect SAC header origin time (#153)

* forcing microsecond to millisecond conversion in sac header

* turning off test debugging

* typo fix in sac header append

* updating a test to cover nzmsec issue

* no warning for missing sac header if list is empty

* bugfixing sac header nzmsec was overflowing causing incorrect sac header times

* removing debug statements

* hotfix recsec: synthetic amplitude scaling was referencing the incorrect start and end times leading to incorrectly scaled data-synthetic record sections when combining scale_by normalize and xlim_s #156

* hotfix recsec: trimming was not applied the same to obs and syn data and was locked behind the preprocessing flags. moved out and now trimming occurs on the global start and end times represented by both data and synthetics #157

* adding cmdline help message for how to set kwargs to False on the command line since all kwargs are input as strings

* bugfix when only plotting data with trim

* General Improvements (#164)

* adding kwargs and plot aesthetics to documentation #119

* adding write_files and plot_file to the pysep doc page

* #162 adds new recsec scale_by option 'rel_norm' which now normalizes pairs of traces to the largest amplitude between the both of them, preserving relative amplitudes per pair of traces

* rearranging recsec parameter input order to match docstring #163

* #163 rearranging PySEP input parameters to match docstring

* adding rel_norm to recsec docstring

* bugfix recsec caused by trim fix that was expanding st and causing certain sort types to fail due to index errors

* fixing failing tests

* hotfix recsec rel_norm scaling was not taking into account shortened indexing arrays when only selecting specific components

* adding kwarg definitions into recsec docstring for easier readability and inclusion in the AutoAPI #119 #163

* RecSec feature time_shift_s_syn + update docs (#166)

* adding 'time_shift_s_syn' as a way for user to time shift synthetics separately from data, if has the same traits as 'time_shift_s' but if not given it will take on values of 'time_shift_s' to retain original functionality
adding tests to cover time_shift_s_syn and expand coverage over use cases of time_shift_s

* two more tests to cover the use cases of time_shift_s_syn

* added recsec kwargs obs_zorder and syn_zorder to allow user to set order of plotting,
added more tests to cover time_shift_s and time_shift_s_syn
updated docs to cover zorder parameters

* all tests passing

* updating time_shift_s_syn behavior so that if time shifts are the same for both obs and syn, no new labels need to be plottedto keep clutter down

* small bugfix in logic

* fixing implementation of recsec debug log messages when using time_shift_s_syn
small bugfix time_shift_s_syn by default wasn't taking the properly formatted copy of time_shift_s

* rearrange sac header writer (#154)

* rearrange sac header writer

move sac header writer after preprocess (trim rewrite b, e, and origin time)

* update cap_sac.py with the nzmsec conversion

reinstate the nzmsec conversion

* bugfix time_shift_s_syn took on wrong value at init when a list

* modifying recsec docstring 'time_shift_s' to let user know that inputting a list requires a list of certain length

* makes minor modifications for #154 for slightly cleaner code, no chagne to functionality

* adding some comments

* bump version number and update changelog. reverse order in changelog, done with copilot so hopefully it's right

---------

Co-authored-by: emanuele casarotti <casarotti@tiscali.it>

Hotfix: CAP weight file sorting (#145)

* removed pypi version documentation, moved to adjdocs
bump patch version number
remove annoying warning log when specfem source does not have origin time

* added docstring for recsec taper parameter

* fixed sorting issue related to #144 and extended test to cover this function

* update changelog

PySEP v0.6.0 (#143)

* added read function for asdfdatasets and allow RecSec to plot windows on top of record section (#136)

* added test to check zero division error, (#137)

added logger warning about zero amplitude scaling
feature: user can now set kwargs for obs_color and syn_color

* Improve SAC header append functions (#138)

* extending read_sem_cartesian test to check for evdp related to #132
adding warning messages to sac header append when evdp or mag not
present

* extended cartesian sac headers to match all normal sac header values except for cmpinc and cmpaz
added better warning message for missing sac header values in normal sac header reading
extended tests to cover new functionalities

* Improve RecSec preprocessing architecture (#139)

* reorganizing docstring, restructuring preprocess flag
default value for overwrite is now set True so User does not have to unset
changed default preprocess flag to True, removed 'both' option

* fixed up check function to reflect new preprocess flag

* restructuring preprocessing function to put each individual feature behind a boolean flag so that they can be turned on/off at will
also expose some key arguments as keyword arguments so the User has more control

* all preprocessing now behind tunable knobs

* moved kwargs to args of process_st
reorganized init parameter input to organize a bit better
added new parameters to main docstring

* allow preprocess=True to be more flexible and just take st and st_syn if available, removed hard check on preprocess=True requireing st_syn to be more intutive by users
bugfix move fill value to after assignment of trace in loop

* moved parameters back to internal kwargs to match recsec structure and allow passing them in through command line

* bump version 0.6.0 and bump copyright year in docs

* update changelog

* slim down changelog to include only most recent

bumping ->0.5.1 and updating changelog

PySEP v0.5.0 (#130)

* FEATURE: improves FORCESOLUTION read function to deal with SPECFEM3D_GLOBE format, previously could only handle 3D_CARTESIAN. adds more detailed docstring for the function

* utils.io.read_forcesolution changed input variable 'default_time' -> 'origin_time' to match other read functions and be slightly more intuitive

* REFORMAT read_forcesolution to return an ObsPy Event object rather than a PySEP SOURCE object, so that it can be parsed and used by Pyflex which is expecting ObsPy Event or Catalog objects to define sources

* added function 'read_events_plus' (originally defined in Pyatoa) which provides additional file format support to ObsPy's read_events function

* removed Source class from io.mt which was an old holdover for reading in FORCESOLUTION and SOURCE files from SPECFEM2D/3D. the revised method simply returns barebones ObsPy Event objects which is much cleaner and avoids requiring having to define an entirely new class. Does not affect PySEP routines, these were mainly used by external libraries calling PySEP

* General Improvements: improve recsec log, single-source version, bugfix zero trace length (#121)

* bumping version numbers to 0.5.0-dev to signify backwards-incompatible changes and that this is the 'dev' version of the code

* Issue #120 single-sourcing version number from pyproject.toml and sourcing version number in docs and __init__ directly from this value

* code fix conf finding version number,
update 'how_to_version_release' to only bump pyproject.toml version number

* #117 added a new pre-preprocessing curtail function that removes Traces whose trace lenght is 0

* #116 RecSec now logs amplitude and amplitude ratios if both obs and syn are plotted together

* amp ratio log messages now for abs max

* update CHANGELOG

* updates RTD Yaml file to comply with build.image deprecation

* attempt fix failing RTD build by swapping Python for Mamba

* removed 'read_sem' logger warning about not providing an origin time by setting default origin time to 1970-01-01T00:00:00 directly in the input variables

* added read functions to main package imports (read_sem, read_stations, read_events_plus)

* Bugfix: incorrect RecSec xlim_s indexing (#123)

* bugfix: xlim_s was using time and not sample to index the waveform when selecting max amplitudes for normalization, causing incorrect normalization to occur

* tests caught edge case where indicies were None and could not be converted to integer samples. fixing

* Update RecordSection data reading (#124)

* BUGFIX: in read_events_plus, read_specfem3d_cmtsolution_cartesian was returning an Event and not a catalog object. This was probably fine but not consistent with the other returns

* new recsec.read_data function that replaces the old generate_synthetic_data function, contains logic for taking paths and return streams and can handle both obs and syn data as well as SAC formatted syn data (#122)
bugfix: added a catch in recsec to kill the object if no stream data are found

* API CHANGE: RecSec parameter 'cmtsolution' has been changed to 'source' for generality because the file does not need to be a cmtsolution, can be a forcesolution or source as well

* small bugfixes to get synthetic stream reading working

* adding Cartesian generated synthetics to test data and added new test data to make sure read_sem can handle these appropriately

* removing some of the test data, only need a few traces

* update API recsec cmtsolution -> source

* update changelog

* BUGFIX: RecSec was unable to read different source file formats. New parameter added '--srcfmt' which allows the User to set the file format manually. If srcfmt is not provided, RecSec will attempt to guess the file format based on the file name, checking against a list of common SPECFEM source file format types

* BUGFIX: function 'read_specfem3d_cmtsolution_cartesian' can is now less strict about how it expects the incoming file to be formatted

* removing debug statement left in read forcesolution function

* #126 updating example config files to fix inconsistencies

* BUGFIX: RecordSection was incorrectly using indices in units of time, and not samples, to index the visible portion of the waveform for use in determining the local max amplitude within the time window. This would have led to incorrectly scaled waveforms when using the option 'xlim_s'. This bugfix sets the correct index unit, and ensures that all indices coming out of getter function 'get_xlim' are integers so that they directly be used to index waveform data

* Update recsec.rst

Accommodating parameter name change from 'cmtsolution' to 'source' in the docs to match recent update in #124

* pysep internal variable _legacy_naming -> legacy_naming so that it can be used in parameter file

* recsec #127 added parameters 'obs_wildcard' and 'syn_wildcard' to allow user to determine which files are read in

* change feature so that 'syn_wildcard' defaults to 'wildcard' unless explicitely provided

* removed parameters 'log_level' and 'legacy_naming' from the default config writing function, remade the template config, added new test to check the example config files are still in order and removed some unncessary parameters from example configs

* update changelog

PySEP v0.4.1 (#115)

* Update docs w GEOS626 Lab (#114)

* adding IPython to docs environment and conf to allow coloring lab notebook with ipython color scheme

* adding 626 lab converted notebook, manually reformatted to remove unncessary jupyter notebook output cells, renamed all figures to follow indexing order and not cell count, reformatted some text. still some text to sort out

* cleaning up lab record section docs

* incrementing PATCH number in semver to v0.4.1

* updates docs link in pyproject.toml file

* updating maps in recsec lab to remove unnecessary figure axis

* update changelog, add version release documentation

* Update how_to_version_release.md

PySEP v0.4.0 (#112)

* Fix various bugs and adds features to code (#60)

* renamed specfem station writing function, and added an ordering component

* bumping version in setup and changing url and author

* small mt typo change

* added an example config that gathers a small amount of data for testing/dev purposes

* added a new kwarg 'order_stations_list_by' which sets the order of the output stations list, related to #36

* bugfix typo parameter call

* bugfix rotating was not actually rotating streams in place for arbitrary components ->ENZ

* bugfix fixed rotation testing, which was not actually evaluating as expected. some confusion about editing streams and inventories in place which was not actually happening. Fixed and now rotate test works as expected

* added 12Z test data for rotating 12Z -> ENZ which works now, added test to cover this case

* moved 2012 central alaska IU gather script (which gathers 12Z component) into examples

* bugfix pysep was not setting log level properly from the config file. now in the load() function, config log level is allowed to override logger level

* changed config examples dir name to test, to be used as a test bed for checking specific data gathering features such as data gap removal

* bugfix #57, reading event origin time from sac header was shifting times unexpectedly

* added utility function to convert obspy catalog to event input list

* Bugfix missing rotation metadata throwing TypeError (#63)

* bugfix clipped amplitude check was not properly checking the data array

* added error catch and release during rotate code to avoid processing breakdown. also rotate now goes by channel rather than the entire stream at once

* rearranged rotation algorithm to be a bit cleaner, previously too many different streams floating around and being fed to one another.

* pysep rotation now has additional checks for station metadata and error catching to get around any rotation bugs that used to cause the rotation to fail
added new tests to cover rotation and fixed a rotation test that was failing due to change
added a config for testing the rotation bug, providing station info

* updating bug config file

* feature mass download (#64)

* fixed exclude string making and added a bool check for deleting tmpdir in mass download function

* removed accidental debug statement

* Remove llnl_db_client hard dependency (#65)

* moved llnl_db_client as a hard dep of pysep and moved it into an optional dependency
hid llnl_db_client import statement behind a try-except block and threw a check in the init of pysep only requiring this dep if the client choice is LLNL

* Added setup.py legacy file

* removed llnl dep from conda env yml file

* tested install with and without llnl dep and tested check statement for missing llnl import

* Feature: event declustering and source receiver weighting (#66)

* started adding declustering rewrite with test and test data

* finished cartesian gridding decluster script, added radial gridding decluster script, added tests to cover both and plotting

* decluster catalog added feature to threshold events by min magnitude and data availability separate from declustering
added plot feture to connect source receiver pairs based on data availability
added feature to allow sorting by data availability

* adjusting default figure names for declust plotting scripts

* cleaned up plotting functions into functions to avoid repeat plotting calls, added removed events to
plotting routines

* small typo updte declust

* moved some declustering functions into util

* declust started srcrcv weighting function

* individual source or receiver list weighting working with the smart scan feature
next up is to implement the entire weighting scheme with normalization and based on data availability

* declust slow progression

* finished srcrcv weighting scheme

* finished declustering and weighting algos with additional plotting and text file writing for weights

* added basic test for srcrcv weight calc

* clean up docstrings of pysep/recsec, bugfix pysep restrictions (#68)

* reformatted PySEP init docstring, added missing parameters and categorized parameters to make things easier to find

* removed hard requirement that user provides event depth and magnitude if event selection is default

* added boolean flag to toggle insufficient length checker
bugfix: added remove_clipped boolean toggle on the actual processing step, which was not there before

* bugfix phase list passed from pysep into util function for phase getting

* last minute touch ups on docstring

* recsec removed unneeded myround function from top of script

* categorized recsec init docstring for easier readability

* bugfix: rotate parameter check function was setting rotate parameter as an empty list, but it was expected as NoneType within the main processing function. removed this type conversion

* bugfix: log message failing when magnitude or depth set to NoneType

* bugfix allow NoneType event magnitude and depth, ass
ign dummy values to cap header because these are required by record section

* Update docs (#69)

* moved docstring of pysep into class description for autoapi

* instantiated sphinx for doc creation and autoapi building,  reorganized pysep and recsec docstrings to be well formatted for autoapi

* migrated wiki docs into docs directory

* fixed docstrings and corrected links for API references in docs

* fixed up typos and cleaned up docs

* Delete jekyll-gh-pages.yml

* Bugfix: unable to set event_depth_km or event_magnitude as NoneType (#72)

* allow taup arrival time get to be skipped if event depth not provided

* sac header functions that required 'evdp' are now skipped over if 'evdp' is not present in the sac header

* Update pysep.py

bugfix: removing debug statement left in pysep

* Feature recsec tmarks (#73)

* replace plotw_rs with record section run command in pysep plotting,
sets default sorting to 'distance' and not 'distance_r' for pysep-generated record section

* working on ordering of multiple pages

* added feature tmark to add static lines at given time values, does not address time shifts or move out

* Bugfix: plotw rs sort (#76)

* reformatting plotw_rs page separation logic

* sort order of multi-page record sections is now reversed to be more natural

* Update CHANGELOG.md

* version bump v0.3.0

* Bugfix trace merge (#81)

* added a try-except block over trace merging to avoid errors caused by incompatible sampling rates

* re-ordered processing steps, resample now occurs before merge and start/endtime trims to avoid sampling rate inconsistency during merge process

* added comment for merge command

* Feature: fill data gaps and bug fix trim start end times (#84)

* pysep new parameter  which allows users to fill gappy data with a given value
process function 'merge_and_trim_start_end_times' now takes fill value in order to fill in gappy data
added test to test gap filling

* added gap_fraction parameter which allows selecting the overall percentage length of allowable data gaps. defaults to 1 (100%). added test to cover this

* added gap_fraction to pysep docstring and parameters

* cleaned up docstrings for new parameters

* split up processing function 'merge_and_trim...' into merge function and trim function
trim function now takes actual expected start and end times rather than inferring from the data
bugfix gap percentage not accurately determinig total trace length

* bugfix merge gapped data not returning any data

* remove debugger statement

* added a check in trim function for late starttimes and early endtimes which would create incomplete data

* changed default 'fill_data_gaps' value as False to be more intuitive

* added new hidden variable 'extra_download_pct' which allows downloading an additional x% of data from data center because downloading the exact time bounds may lead to shorter waveforms after resampling or preprocessing. the extra downloaded data is trimmed away before being saved

* fixing tests, trim start and end times ignored if no origin time given to allow for direct preprocessing of streams without event ifnormation

* bugfix: location code hardcoded for bulk waveform request
bugfix: debugger left in test suite

* Bugfix: stations removed insufficient time  (#88)

* bugfix: seconds before and after ref were allowed to be integers which caused floating point rounding errors when trimming start and end times
curtail remove for insufficient lenght now checks for streams with time less than the mode rather than no equal, to not kick out streams with sufficient data

* check statement forces time buggers to be floats
obspy trim function set nearest sample to False to ensure we are taking inner samples and getting same sampling rate

* remove last data gap check from merge gapped data

* allow user to fill boundary data gaps with parameter 'fill_data_gaps' which sidesteps rejection for late starttimes and early endtimes

* update changelog

* added another postprocessing check to remove masked data from array which has a flag toggle in PySEP to turn on or off, on by default

* fixed merging tests

* moved remove masked data check into end of preprocessing because it affects the rotation operations if not done prior to rotation.
fixed tests

* bugfix insufficient length check remove '=' which was causing all traces to be thrown out and not just ones with shorter lengths

* bugfix-xticks

* Bugfix: plotw_rs sort order and multi-page order (#90)

* reverse sort on absolute sorting to get smallest values on top

* absolute sorting default y-axis label now plots on the y-axis rather than inside the figure, co-existing with distance labels

* fixing docstrings with new parameters

* added option y_axis_abs_right for absolute scale plotting which places waveform text labels outside the right border of the figure, with the normal y axis showing distance or azimuth values. this is the default option for absolute sorting

* bugfix azimuth bins now recognize multi-page azimuth sorting and do not show azimuth bins if no data are available at those azimiuths on a given page'

* bugfix azimuth bin divider was not searching properly causing no bins to be plotted

* typo fix: missing space in log message

* bugfix bool check on fill value during trim was skipping over when fill was 0, even though that was a requested value

* source reciver map plot plots event before stations to center on epicenter

* fixed broken preprocessing test, minor break, still working as expected

* improve source receiver map plotting (#91)

* moved figure generation attributes into catalog plotting which comes first

* srcrv map was not ever plotting global projection even though ortho was not useful for global scales
now has an internal check for projection and also resizes for local scales
also contains a subsetting feature to pick certain stations based on event id

* Update CHANGELOG.md

* improve TauP theoretical arrival usage (#94)

* Update README.md

Update readme with better description of PySEP

* remove hardcode phase list for getting TauP arrival times

* change phase_list default value NoneType -> ('ttall',) to match ObsPy default which gets all phase arrivals

* REMOVED function 'get_taup_arrival_w_sac_headers' which was merged into
'get_taup_arrivals' to avoid redundant code. 'get_taup_arrivals' now
either takes a Stream or Inventory + Event object"

* changed the keys of the phase dict outputted by TauP arrival getting to be more uniform, and better warning messages when phase arrivals can not be found for a station.
arrival time fetching now finds earliest arriving P and S wave, rather than just the P or S arrival

* removed 'model' from SAC header TauP arrival time labels because SAC cuts off the values for long phase names (ie pdiff_ak135 -> pdiff_ak), which seems more confusing than its worht

* allowed SAC header value 'a' to be earliest arriving phase regardless of P or S derived. P and S are still hardcoded later

* removed s and p phase names from incident angle and takeoff angle names in SAC header because long phase names were cutting them off (8 char max), hardcoded to string that sorta looks like the words'

* BUGFIX: SAC header incident angle was being incorrectly set to takeoff angle value, causing no takeoff angle name and incorrect incidient angle name to be attributed

* added 'earliest arrival' to SAC DICT for use in record section

* RecSec now accepts phase arrival times as an acceptable time shift value to align on specific phases

* add log message about how time shift is applied in RecSec

* flip tshift value for phase arrivals to align rather than space out

* fixed failing test for sac header

* related to #93, remove hard no-NoneType restriction on 'output_unit' and 'water_level' during pysep checks because 1. ObsPy allows NoneType water level and 2. there is already a check for valid output units earlier in the check function

* Update CHANGELOG.md

* add readthedocs yaml file to shift docs to RTD, and bumped docs version number and trimmed down doc environment to bare essentials (holdovers from previous docs builds not required)

* General updates and bugfixes (#97)

* added kwarg parameters  and  to let user determine if they want to show figures during pysep processing. defaults to false
bugfix: pysep load was not retaining keyword arguments for command line usage of pysep

* added version number to __init__ so that its accessible. bumped version number of 0.3.2 so that it is uniquely identifiable from the master version 0.3.1

* related to #95 display pysep version in debug log

* playing around with aspect ratio on maps

* changing default value of 'remove_clipped' parameter to True to be more restrictive by default, related to #80

* map plotting at local scales now auto scales based on the figure size, using obspy internal logic, which fixes the problem of having very narrow map plots or not showing the event, or not showing all the stations

* Bugfix: RecSec abs sorting and y-tick scaling (#100)

* fixed the polarity of waveforms for the yabsolute y-axis sorting by inverting waveforms when inverting the y-axis, #99

* added automatic y-axis tick mark scaling for absolute sorting based on total distance span shown on record section

* bugfix ytick implementation was conflicting with absolute plotting, merged the two operations together

* bugfix allow abs_backazimuth as an option for recsec sorting

* Update documentation (#102)

* changing recsec doc page to .rst to get relative linking working
util.plot.set_plot_aesthetic, changed kwargs to args and added all options to docstring

* bugfix addresses #101 allow RecSec 'save' to be None

* added plotw_rs to init

* Added source receiver map plotting to cookbook and added a link to it in the recsec documentation

* convert pysep doc from md-> rst for better internal file linking

* added general error catching to pysep plotting because these are non-critical tasks #71 (comment)

* addresses #71 comment about maps not plotting when no depth or magnitude information provided. This was used in the title of the map, so added some if statements to avoid these quantities if they are nto rpesent

* General bugfixing and updates (#105)

* API change, parameters 'mindistance' -> 'mindistance_km', 'maxdistance' -> 'maxdistance_km'

* related to #98 allow list of station ids as input
updated docs to reflect station id parameter
starting script to update example config files

* formatting

* moved default phase list value into init and out of hard set parameter since its a list (avoiding mutable input values)

* update all example config files with updated API

* bugfix recsec spines not showing by default and bugfix allow command line users ability to input spine flags which are input as strings

* typo incorrect default inventory name in cookbook docs

* overhaul file writing system plus general updates (#106)

* #75 turn OFF azimuth bins when sorting by absolute (back)azimuth

* typo fixing, adding 'event_depth_km' and 'event_magnitude' to pysep docstring

* replaced 'stations_list' -> 'station_list' throughout package for consistentcy'

* one more stations -> station

* slightly modified how the plot and write functions check for validity of file selection, same outward behavior but internally a little cleaner

* removed unncessary 'cha' aprameter in RTZ rotation
updating rotation implementation

* updated write system to be able to write out individual channel SAC files
completed intermediate writing so that files are written as the program progresses

* overwrite_event_tag new behavior, allow users to dump files directly into output directory with no event tags'

* allow SAC sub directory bypass

* added file logger to pysep

* pysep added ability to write out specific components for SAC files
added docs page for explaining how to ignore event tag and sac sub directory

* fixing up docs page for output control

* cleanup docs

* bump version number for easier version tracking

* bump version in toml and docs files

* adjusting log behavior, allow turning off log with 'save_log' kwarg, and move created log to output directory after run has completed

* #107 incorrect directory name for pysep doc page

* #107 add overwrite catch for '-W' option

* #109 allow log file creation to create the output directory if specified by the user but not already existing.
Bump devel version number for debug checking

* added a -v/--version option to pysep command line tool to check pysep version number

* removing debugger statement

* bugfix: multi-page record section was using the incorrect number of traces to traverse through the list causing index errors

* bugfix: avoid silently skipping nonexistent pysep path or syn path in recsec initialization

* bugfix: read_sem_cartesian was incorrectly defining azimuth based for two points in cartesian space

* bugfix: implemented separate amplitude scaling arrays tfor data (st) and synthetics (st_syn) because originally all scaling was done w.r.t data array which would cause incorrect normalizations for per-trace normalizing

* fixing broken tests due to indexing errors

* bump dev version number

* bugfix typo

* bugfix: read sem cartesian azimuth calculation takes sign of coordinate into account

* bugfix: checking bool of max amplitudes for recsec syn check

* feature: kwarg 'title' allows user to overwrite default recsec title

* recsec docstring typo fix type -> param

* bugfix: subsetting routine in source receiver map plot had the ability to ignore repeat stations even if they came from different networks, due to exclusion based on station name only. Now it excludes based on a NN.SSS (network + station), which is assumed to be unique for all seismic stations

* typo fix recsec docstring parameter: x_min -> x_max

* add warning log message to alert User if Config file parameter is not explicitely used by PySEP to help debug argument mispelling or future API changes not registering. Related to #110

bump docs version 0.3.1 and add furo as pip dependency for docs theme

PySEP v0.3.0 (#78)

* Fix various bugs and adds features to code (#60)

* renamed specfem station writing function, and added an ordering component

* bumping version in setup and changing url and author

* small mt typo change

* added an example config that gathers a small amount of data for testing/dev purposes

* added a new kwarg 'order_stations_list_by' which sets the order of the output stations list, related to #36

* bugfix typo parameter call

* bugfix rotating was not actually rotating streams in place for arbitrary components ->ENZ

* bugfix fixed rotation testing, which was not actually evaluating as expected. some confusion about editing streams and inventories in place which was not actually happening. Fixed and now rotate test works as expected

* added 12Z test data for rotating 12Z -> ENZ which works now, added test to cover this case

* moved 2012 central alaska IU gather script (which gathers 12Z component) into examples

* bugfix pysep was not setting log level properly from the config file. now in the load() function, config log level is allowed to override logger level

* changed config examples dir name to test, to be used as a test bed for checking specific data gathering features such as data gap removal

* bugfix #57, reading event origin time from sac header was shifting times unexpectedly

* added utility function to convert obspy catalog to event input list

* Bugfix missing rotation metadata throwing TypeError (#63)

* bugfix clipped amplitude check was not properly checking the data array

* added error catch and release during rotate code to avoid processing breakdown. also rotate now goes by channel rather than the entire stream at once

* rearranged rotation algorithm to be a bit cleaner, previously too many different streams floating around and being fed to one another.

* pysep rotation now has additional checks for station metadata and error catching to get around any rotation bugs that used to cause the rotation to fail
added new tests to cover rotation and fixed a rotation test that was failing due to change
added a config for testing the rotation bug, providing station info

* updating bug config file

* feature mass download (#64)

* fixed exclude string making and added a bool check for deleting tmpdir in mass download function

* removed accidental debug statement

* Remove llnl_db_client hard dependency (#65)

* moved llnl_db_client as a hard dep of pysep and moved it into an optional dependency
hid llnl_db_client import statement behind a try-except block and threw a check in the init of pysep only requiring this dep if the client choice is LLNL

* Added setup.py legacy file

* removed llnl dep from conda env yml file

* tested install with and without llnl dep and tested check statement for missing llnl import

* Feature: event declustering and source receiver weighting (#66)

* started adding declustering rewrite with test and test data

* finished cartesian gridding decluster script, added radial gridding decluster script, added tests to cover both and plotting

* decluster catalog added feature to threshold events by min magnitude and data availability separate from declustering
added plot feture to connect source receiver pairs based on data availability
added feature to allow sorting by data availability

* adjusting default figure names for declust plotting scripts

* cleaned up plotting functions into functions to avoid repeat plotting calls, added removed events to
plotting routines

* small typo updte declust

* moved some declustering functions into util

* declust started srcrcv weighting function

* individual source or receiver list weighting working with the smart scan feature
next up is to implement the entire weighting scheme with normalization and based on data availability

* declust slow progression

* finished srcrcv weighting scheme

* finished declustering and weighting algos with additional plotting and text file writing for weights

* added basic test for srcrcv weight calc

* clean up docstrings of pysep/recsec, bugfix pysep restrictions (#68)

* reformatted PySEP init docstring, added missing parameters and categorized parameters to make things easier to find

* removed hard requirement that user provides event depth and magnitude if event selection is default

* added boolean flag to toggle insufficient length checker
bugfix: added remove_clipped boolean toggle on the actual processing step, which was not there before

* bugfix phase list passed from pysep into util function for phase getting

* last minute touch ups on docstring

* recsec removed unneeded myround function from top of script

* categorized recsec init docstring for easier readability

* bugfix: rotate parameter check function was setting rotate parameter as an empty list, but it was expected as NoneType within the main processing function. removed this type conversion

* bugfix: log message failing when magnitude or depth set to NoneType

* bugfix allow NoneType event magnitude and depth, ass
ign dummy values to cap header because these are required by record section

* Update docs (#69)

* moved docstring of pysep into class description for autoapi

* instantiated sphinx for doc creation and autoapi building,  reorganized pysep and recsec docstrings to be well formatted for autoapi

* migrated wiki docs into docs directory

* fixed docstrings and corrected links for API references in docs

* fixed up typos and cleaned up docs

* Delete jekyll-gh-pages.yml

* Bugfix: unable to set event_depth_km or event_magnitude as NoneType (#72)

* allow taup arrival time get to be skipped if event depth not provided

* sac header functions that required 'evdp' are now skipped over if 'evdp' is not present in the sac header

* Update pysep.py

bugfix: removing debug statement left in pysep

* Feature recsec tmarks (#73)

* replace plotw_rs with record section run command in pysep plotting,
sets default sorting to 'distance' and not 'distance_r' for pysep-generated record section

* working on ordering of multiple pages

* added feature tmark to add static lines at given time values, does not address time shifts or move out

* Bugfix: plotw rs sort (#76)

* reformatting plotw_rs page separation logic

* sort order of multi-page record sections is now reversed to be more natural

* Update CHANGELOG.md

* version bump v0.3.0