v0.6.1 release branch #185

wsavran · 2022-02-10T17:11:25Z

No description provided.

* quadtree csv reader * included depth columns in reader * reader name change * cartesian_grid.bounds added * check for zero area

* Added new functions that compute and plot 95% and 97.5% confidence ranges, as well as p values for CSEP consistency tests.

…to v0.6.1-release-branch

added proper imports for plot_pvalues_and_intervals minor code formatting fixed issue incorrect percentile in plot_pvalues_and_intervals

wsavran · 2022-07-26T18:00:21Z

csep/utils/plots.py

+    return ax
+
+
+def plot_pvalues_and_intervals(test_results, ax, var=None):


@bayonato89 i had to make some modifications here to work within pycsep. can you test this new function out and make sure that it's working properly?

It does work properly @wsavran

minor code formatting updates update tests for python 3.10: failing absolute assertion changing to numpy.testing.all_close in csep1 t-test

codecov-commenter · 2022-07-26T18:23:26Z

Codecov Report

Base: 55.84% // Head: 54.55% // Decreases project coverage by -1.28% ⚠️

Coverage data is based on head (09e2769) compared to base (ad217ed).
Patch coverage: 27.33% of modified lines in pull request are covered.

❗ Current head 09e2769 differs from pull request most recent head 76844eb. Consider uploading reports for the commit 76844eb to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #185      +/-   ##
==========================================
- Coverage   55.84%   54.55%   -1.29%     
==========================================
  Files          20       20              
  Lines        3560     3668     +108     
  Branches      568      540      -28     
==========================================
+ Hits         1988     2001      +13     
- Misses       1452     1550      +98     
+ Partials      120      117       -3

Impacted Files	Coverage Δ
csep/core/binomial_evaluations.py	`14.48% <14.48%> (ø)`
csep/utils/readers.py	`46.44% <20.00%> (-1.39%)`	⬇️
csep/utils/comcat.py	`83.74% <27.77%> (-2.85%)`	⬇️
csep/core/regions.py	`47.04% <38.88%> (+0.32%)`	⬆️
csep/core/catalogs.py	`60.95% <60.00%> (-0.15%)`	⬇️
csep/core/forecasts.py	`57.57% <73.33%> (+0.18%)`	⬆️
csep/utils/calc.py	`54.78% <85.71%> (ø)`
csep/utils/basic_types.py	`89.28% <100.00%> (ø)`
csep/__init__.py

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* Changed np for numpy in the poisson_evaluations.py file * Added non-Poissonian comparative and consistency tests. * format docstrings * Rename non_poissonian_evaluations.py to binomial_evaluations.py * Update binomial_evaluations.py removed unused imports Co-authored-by: wsavran <35315438+wsavran@users.noreply.github.com>

Added NZ collection and testing regions, and parser to csep region object. Added test for NZ testing regions

fix: region border plot. Now uses shapely that merges all cells and gets the boundary of the total region. Bypasses floating point issues by rounding down to 2 decimals fix: load_ascii now creates cell polygons clockwise fix: tight_bbox has option for precision. It is not necessary for lat_lon, but explicited the argument, in case cartesian coordinates were implemented. build: added shapely as requirement

* Added some documentation on new binary CSEP tests.

added proper imports for plot_pvalues_and_intervals minor code formatting fixed issue incorrect percentile in plot_pvalues_and_intervals

minor code formatting updates update tests for python 3.10: failing absolute assertion changing to numpy.testing.all_close in csep1 t-test

* Changed np for numpy in the poisson_evaluations.py file * Added non-Poissonian comparative and consistency tests. * format docstrings * Rename non_poissonian_evaluations.py to binomial_evaluations.py * Update binomial_evaluations.py removed unused imports Co-authored-by: wsavran <35315438+wsavran@users.noreply.github.com>

* Added some documentation on new binary CSEP tests.

…to v0.6.1-release-branch

…orbar changes

wsavran · 2022-09-23T20:38:10Z

@khawajasim, @bayonato89, I'm writing some docs and reviewing the binomial_tests.py, and i have a couple of questions.

It seems we are missing the function _simulate_catalog(). is this from poisson_evaluations.py? if not, can you add the binomial _simulate_catalog() to this pull request?
This also makes me think we should have a test case for this function. Can you give me a worked example that we could implement like this, for one of the binomial tests with simulation?

bayonato89 · 2022-09-28T17:55:48Z

Just added the _simulate_catalog function (although I think I sent it to the wrong branch). Let me know if I should resubmit @wsavran. The function was written by @khawajasim. We should be careful when calling it, because the _simulate_catalog functions for Poisson and non Poisson consistency tests share the same name.

* feat: Added query_bsi, based on comcat query functions. Can be called from csep.__init__, wrapping the readers._query_bsi. This is based in csep.utils.comcat.search functions. mods: (i) Exception catchs for Hostname mismatch in SSL verification (the bsi does not go through https). (ii) in comcat and bsi, ids are set different. SummaryEvent now handles this with try/except. (iii) bsi returns datetimes as utc strings, instead of timestamp as comcat. * docs: added query_bsi to api reference and mentioned it in tutorial/catalog_filtering styl: modified query_comcat docstring * fix: added maxdepth to query_comcat and query_bsi wrappers at top and bottom level. default=1000. Maybe these functions should have the arguments to completely define an experiment catalog (perhaps just max_mag and its ready)

* added to unit test for binary_joint_LL

* Added non-Poissonian comparative and consistency tests. * Added a _simulate_catalog function for binary likelihood tests Co-authored-by: wsavran <35315438+wsavran@users.noreply.github.com>

* style: formatted function plot_consistency_test to use original dependencies aliases * fix: changed errorbar to be defined from the test distribution mean. * feat: added option to plot test distribution's mean. * styl: homogenized plot_poisson_consistency_test and plot_consistency_test * build: removed matplotlib pin

style: changed variable names in simulation function to keep it consistent style: updated named of tests in test_evaluations.py to better reflect the test

Added verbose option to get_event_counts() Added additional test case to CatalogForecast creation

style: changed names of functions in test_evaluations.py

…to v0.6.1-release-branch

* testing_likelihood * name correction * fixing imports

Update setup.py

664f508

wsavran mentioned this pull request Feb 10, 2022

warnings with numpy 1.20.1 #72

Closed

wsavran changed the title ~~Update setup.py~~ v0.6.1 release branch Feb 10, 2022

khawajasim and others added 7 commits February 23, 2022 08:37

quadtree csv reader (#186)

d13f74f

* quadtree csv reader * included depth columns in reader * reader name change * cartesian_grid.bounds added * check for zero area

New plotting routines (#190)

74106b9

* Added new functions that compute and plot 95% and 97.5% confidence ranges, as well as p values for CSEP consistency tests.

Update setup.py

f75861f

Merge branch 'v0.6.1-release-branch' of github.com:SCECcode/pycsep in…

da4a51d

…to v0.6.1-release-branch

unpinned numpy version for security issues

380c7fc

added docstrings to plot_pvalues_and_intervals

29d0733

added proper imports for plot_pvalues_and_intervals minor code formatting fixed issue incorrect percentile in plot_pvalues_and_intervals

fixed failing test with python 3.10 due to floating point rounding issue

8624724

wsavran commented Jul 26, 2022

View reviewed changes

fixed warnings from numpy np.int -> np.int64

1a507f9

minor code formatting updates update tests for python 3.10: failing absolute assertion changing to numpy.testing.all_close in csep1 t-test

bayonato89 and others added 13 commits August 18, 2022 11:01

Added NZ testing and collection regions, parser and test (#198)

518e750

Added NZ collection and testing regions, and parser to csep region object. Added test for NZ testing regions

Notebook documentation (#202)

4a2e926

* Added some documentation on new binary CSEP tests.

Update setup.py

8678a73

unpinned numpy version for security issues

9cf5e0e

added docstrings to plot_pvalues_and_intervals

ddca684

added proper imports for plot_pvalues_and_intervals minor code formatting fixed issue incorrect percentile in plot_pvalues_and_intervals

fixed failing test with python 3.10 due to floating point rounding issue

f7ad419

fixed warnings from numpy np.int -> np.int64

0ef85ed

minor code formatting updates update tests for python 3.10: failing absolute assertion changing to numpy.testing.all_close in csep1 t-test

Notebook documentation (#202)

81b177a

* Added some documentation on new binary CSEP tests.

Merge branch 'v0.6.1-release-branch' of github.com:SCECcode/pycsep in…

08a4ef5

…to v0.6.1-release-branch

pinned matplotlib version until we implement a workaround for the err…

920b366

…orbar changes

pabloitu and others added 2 commits November 14, 2022 10:59

Binomial testing (#208)

ec78dd0

* added to unit test for binary_joint_LL

bayonato89 and others added 8 commits November 14, 2022 11:55

Non poissonian tests (#205)

94dee18

* Added non-Poissonian comparative and consistency tests. * Added a _simulate_catalog function for binary likelihood tests Co-authored-by: wsavran <35315438+wsavran@users.noreply.github.com>

style: updated comment formats in binomial evaluations

7142fbb

style: changed variable names in simulation function to keep it consistent style: updated named of tests in test_evaluations.py to better reflect the test

Updated docstrings in catalogs.py

985aad8

Added verbose option to get_event_counts() Added additional test case to CatalogForecast creation

style: updated variable names to better reflect the binomial evaluation

09e2769

style: changed names of functions in test_evaluations.py

Merge branch 'v0.6.1-release-branch' of github.com:SCECcode/pycsep in…

76844eb

…to v0.6.1-release-branch

unit test for sim_cat (#209)

53bbd1a

* testing_likelihood * name correction * fixing imports

bumped version numbers

8010dbc

wsavran merged commit 48bddff into master Dec 12, 2022

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v0.6.1 release branch #185

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wsavran commented Feb 10, 2022

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bayonato89 commented Sep 28, 2022

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		return ax


		def plot_pvalues_and_intervals(test_results, ax, var=None):

v0.6.1 release branch #185

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