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Major Revision of database and distributed #472

Merged
merged 81 commits into from
Jan 16, 2024
+9,450 −8,313
Merged

Major Revision of database and distributed #472

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c4ddef9
Prototype revisions to save methods - incomplete posted for group dis…
pavlis Jul 10, 2023
9a0110d
Add mummify method and make several changes to allow use in Database …
pavlis Jul 10, 2023
cc432e5
Add clear method for ErrorLogger for use in parallel writer
pavlis Jul 10, 2023
293f5b7
Improve error messages
pavlis Jul 11, 2023
bc988a1
Change handling of dead data for ensembles to be more robust
pavlis Jul 11, 2023
f04e185
Major revision to readers
pavlis Jul 28, 2023
0ff2bf8
Add code for new concept of abortion
pavlis Jul 28, 2023
ec6558b
Changes to fix circular dependence errors
pavlis Jul 30, 2023
e5bda33
Restore read_to_dataframe cut by mistake
pavlis Jul 30, 2023
0afdda2
Disable test that is no longer valid
pavlis Jul 30, 2023
d4b8389
Fix bugs found with pytest test_ensembles
pavlis Aug 1, 2023
ec4e97c
Fix bugs found in initial round with pytest
pavlis Aug 2, 2023
fb17529
Modify tests to mesh with changes for new Database implementation
pavlis Aug 2, 2023
a484e3f
Fix bug that would not handle foff==0 correctly unless the list was s…
pavlis Aug 3, 2023
23e11e1
Fix same issue for TimeSeriesEnemble - missed in previous commit
pavlis Aug 3, 2023
f4de76b
Add new implementation to read ensembles more efficiently stored in b…
pavlis Aug 4, 2023
508be1e
Implement exclude_objects option for deprecated ensemble methods
pavlis Aug 4, 2023
980cc81
Fix several bugs - incomplete debug. Intermediate commit
pavlis Aug 7, 2023
0695e8f
Change isinstance to pymongo base class to resolve inconsistent behavior
pavlis Aug 7, 2023
6606773
Numerous fixes found in testing - intermediate save for backup while …
pavlis Aug 9, 2023
0d14e30
Add some attributes to Seismogram metadata that were missing and caus…
pavlis Aug 9, 2023
eeaac1c
Changes to get test_save_read_data to run
pavlis Aug 20, 2023
8ae21c1
Modify test scripts to mate with changes in Database detailed behavior.
pavlis Aug 21, 2023
cd83986
Bug fixes found with current round of pytest - incomplete. Pushing t…
pavlis Aug 21, 2023
b584385
Add attributes to Metadata to prevent bad behavior in cautions and pe…
pavlis Aug 21, 2023
b42669b
Add binding code to handle live in ensembles consistent with atomic d…
pavlis Aug 26, 2023
9b67484
Changes for ensemble using live as a property
pavlis Aug 26, 2023
95cb6e5
Bug fixes from working through pytest suite
pavlis Aug 26, 2023
038e678
Modify tests for new database features and comments to clarify them
pavlis Aug 26, 2023
f454beb
Modify this test to handle ensemble live as a property
pavlis Aug 26, 2023
4f13970
Revert "Modify this test to handle ensemble live as a property"
pavlis Sep 23, 2023
2a2f3a8
Assorted bug fixes found from pytest runs
pavlis Sep 25, 2023
0234097
Numerous changes from running pytest
pavlis Oct 26, 2023
fe9becb
Revise tests to mesh with new implementation of Database
pavlis Oct 26, 2023
690b016
Update and improve docstrings
pavlis Oct 26, 2023
a449e49
Fix bug in failing to call set_live for bring_out_your_dead
pavlis Oct 29, 2023
9ab2770
Fix bug in gridfs section of update_data
pavlis Oct 29, 2023
2a66f69
Several errors fixed in initial testing with pytest - incomplete vers…
pavlis Nov 1, 2023
7e87767
Fix bug in exclude_data feature
pavlis Nov 2, 2023
669f3fd
Several fixes found from initial testing - intermediate commit
pavlis Nov 2, 2023
9f0f7a1
Use fixtures and parameters to produce standardized test - incomplete…
pavlis Nov 2, 2023
b561ebd
New test for Database class - supercedes two previous test files that…
pavlis Nov 2, 2023
9586b78
Remove old test files superceded by test_database.py
pavlis Nov 2, 2023
2bb7d94
Fix bug from api change for ensembles
pavlis Nov 2, 2023
290c40a
Major revision to writer to implement return_data option
pavlis Nov 10, 2023
84efafe
Commit partially completed test script before major additions
pavlis Nov 11, 2023
3e699be
Several bug fixes found with pytest new test runs. This version has …
pavlis Nov 14, 2023
f246e53
Bug fixes found with distributed io testing - mostly in cremate method
pavlis Nov 14, 2023
363ac29
Docstring corrections
pavlis Nov 14, 2023
cc09a2a
Intermediate save before adding a set of new stuff
pavlis Nov 14, 2023
41b779a
Remove return_data options from writer and add docstring instruction …
pavlis Nov 15, 2023
832cbb8
Several fixes found from pytest initial tests.
pavlis Nov 17, 2023
af2d0a8
Fix bug in failing to handle nonexistent directory specified thorugh …
pavlis Nov 17, 2023
2eeddc7
Mostly completed test for distributed module - full of print statment…
pavlis Nov 17, 2023
8350dad
Enable spark tests.
pavlis Nov 17, 2023
ea22439
Fix small bug in error handler
pavlis Nov 17, 2023
45f27c2
Many changes to both distributed module and related pytest script to …
pavlis Nov 20, 2023
9cd14d8
Fix typo in an exception message
pavlis Nov 20, 2023
9ef643f
Remove print scaffolding from debugging parallel tests
pavlis Nov 20, 2023
b23b1f9
Add handler to assure ensemble marked dead has all members marked dead
pavlis Nov 20, 2023
15cd24e
Minor fixes of typos and wording in schema file
pavlis Nov 20, 2023
0f739c5
Reformat with black
pavlis Nov 21, 2023
49cae24
fixing python setup error due to wrong application of debug option to…
wangyinz Dec 3, 2023
f096c7d
another attempt
wangyinz Dec 3, 2023
bf5af35
Fix bug from not handling formatted data with nbytes set 0 - common w…
pavlis Dec 4, 2023
601dc33
Merge branch 'cleanup_database' of github.com:mspass-team/mspass into…
pavlis Dec 4, 2023
d46fb3e
Fix spark setup problem and section to cleanup files created in data …
pavlis Dec 4, 2023
baac626
Disable problematic import
pavlis Dec 12, 2023
d4feac4
Add delete to spark fixture
pavlis Dec 12, 2023
e900559
Changes to resolve git conflicts with master
pavlis Dec 12, 2023
264340c
Fix spark setup to use pytest-spark consistent with other spark tests
pavlis Dec 13, 2023
2106fcc
Minor fix required by save_data api change
pavlis Dec 13, 2023
58e36fa
Restore DatetimeConverstion - needed for master but caused local prob…
pavlis Dec 13, 2023
83af3d5
Cleanup handling of normalizing data.
pavlis Dec 15, 2023
667629e
Fix two typos that caused serious bugs
pavlis Dec 16, 2023
1230dd2
Fix bug in mishandling relative time stardard
pavlis Dec 21, 2023
ef0e703
Disable two test lines of dubious value to get a clean build
pavlis Jan 4, 2024
6f03b64
Allow subclasses of Metadata as input to read_data
pavlis Jan 4, 2024
ed21cac
Disable failing test that seems no longer correct
pavlis Jan 4, 2024
c790098
Black format patches
pavlis Jan 4, 2024
565da0b
Fix bug in reversed coords values and add geoJSON format version with…
pavlis Jan 15, 2024
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Modify tests to mesh with changes for new Database implementation
@pavlis
pavlis committed Aug 2, 2023

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commit fb17529e360c65e88f78a266878a5661ddf79232
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