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fix master #25

Merged
merged 108 commits into from
Nov 1, 2021
Merged

fix master #25

merged 108 commits into from
Nov 1, 2021

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JoranAngevaare
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Before you submit this PR: make sure to put all operations-related information in a wiki-note, a PR should be about code and is publicly accessible

What does the code in this PR do / what does it improve?

Can you briefly describe how it works?

Can you give a minimal working example (or illustrate with a figure)?

Please include the following if applicable:

  • Update the docstring(s)
  • Update the documentation
  • Tests to check the (new) code is working as desired.
  • Does it solve one of the open issues on github?

Notes on testing

  • Until the automated tests pass, please mark the PR as a draft.
  • On the XENONnT fork we test with database access, on private forks there is no database access for security considerations.

All italic comments can be removed from this template.

ahiguera-mx and others added 30 commits August 4, 2021 16:34
Add NaN check
5e950d2
@JoranAngevaare
Merge branch 'master' into master
172d318
@JoranAngevaare
Merge branch 'master' into master
40489bd
@ahiguera-mx
Merge branch 'XENONnT:master' into master
b64fc70
Add a custom exception for nan and add the check for all corrections
6de627d
@ahiguera-mx
Merge branch 'XENONnT:master' into master
29ff1d9
use pandas builtin functions as suggested in the review
3564ac2
@JoranAngevaare
Allow database to not be initialized (#636)
5261253
@GiovanniVolta @JoranAngevaare
new plot_pmts (#637)
b471fa7 
* change plotting of dead pmts.

Co-authored-by: GiovanniVolta <gvolta@dali-login1.rcc.local>
Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@WenzDaniel
Merge branch 'master' into master
7e0b2c3
@tuankhaibui @JoranAngevaare
First nVeto monitor plugin (#634)
fc10bde 
* I added first nVeto monitor plugin

* Update straxen/plugins/online_monitor.py

I modified as suggestion from @jorana

Co-authored-by: Joran Angevaare <jorana@nikhef.nl>

* Update straxen/plugins/online_monitor.py

I modified as suggestion

Co-authored-by: Joran Angevaare <jorana@nikhef.nl>

* Update straxen/plugins/online_monitor.py

I modified as suggestion

Co-authored-by: Joran Angevaare <jorana@nikhef.nl>

* Update straxen/plugins/online_monitor.py

I modified as suggestion

Co-authored-by: Joran Angevaare <jorana@nikhef.nl>

* Update straxen/plugins/online_monitor.py

I modified as suggestion at line 235 in new version

Co-authored-by: Joran Angevaare <jorana@nikhef.nl>

* Update online_monitor.py

Update online_monitor.py with the

* Add online_monitor_nv to contexts.py

Add 'online_monitor_nv' at line 196 to contexts.py 
to produce data to monitor nVeto detector

Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@WenzDaniel
Merge branch 'master' into master
50943ea
@WenzDaniel
Speed up event pattern fit (#625)
a106733 
* Numbafy binomial_test

* Small changes in neg2ll_modpoisson

* fix bug on binomial test

* update binomial test considering that the mean is not the maximum

Co-authored-by: GiovanniVolta <gvolta@dali-login1.rcc.local>
@ahiguera-mx
Merge branch 'XENONnT:master' into master
d9e6282
@WenzDaniel @JoranAngevaare
Peak event veto tagging (#618)
86669ac 
* Add peak and event veto tagging plugins + tests

Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@JoranAngevaare
kwargs for saver (#639)
8faa8f0
@mzks @JoranAngevaare
Add a plugin for external trigger run on nVeto calibration (#630)
5586d61 
* Add a plugin for external trigger run on nVeto calibration plus tests

Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com>

Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@WenzDaniel @ershockley
Fix veto event positions (#641)
9d8bce7 
* Fixed floating point issue

* Renamed function update test

* bumped version

Co-authored-by: Evan Shockley <eshockley@physics.ucsd.edu>
@WenzDaniel @JoranAngevaare
Fix peaklet area bias (#601)
bc35a32 
* Modified peaklet building to remove baseline bias

* Forgot to updated desaturation

* test

* Fix record_i in overlapping peaks

* Updated peaklets building according to change in strax

* Minor fixes

* Addressed some review dog comments.

* Added test for new function

* Fixed test

* Add empty peaklets support

* Update splitting inputs in veto plugins

* Add time shift to get correct maximum

* Update peaklet_processing.py

* Rename startegy alias

* Update straxen/plugins/peaklet_processing.py

Co-authored-by: Joran Angevaare <jorana@nikhef.nl>

* Change naming conventions

* fix test

Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@JoranAngevaare
Merge branch 'master' into master
ba721f3
@dependabot
Bump tensorflow from 2.5.0 to 2.5.1 in /extra_requirements (#643)
a9ec90f 
Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 2.5.0 to 2.5.1.
- [Release notes](https://github.com/tensorflow/tensorflow/releases)
- [Changelog](https://github.com/tensorflow/tensorflow/blob/master/RELEASE.md)
- [Commits](tensorflow/tensorflow@v2.5.0...v2.5.1)

---
updated-dependencies:
- dependency-name: tensorflow
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@WenzDaniel @JoranAngevaare
Add lone hit information to merged S2s. (#623)
c25acdf 
* Add lone hit information to merged S2s.

* Copy lone hit as it is read only

* Add dummy lone hits for he channel

* Modify tests to avoid deadlock

* Revert "Add dummy lone hits for he channel"

This reverts commit 4710419.

* Revert "Revert "Add dummy lone hits for he channel""

This reverts commit 4cbfb3c.

* Revert "Modify tests to avoid deadlock"

This reverts commit 271e7cf.

* Update straxen/plugins/peaklet_processing.py

Co-authored-by: Joran Angevaare <jorana@nikhef.nl>

Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@JoranAngevaare
Use rucio from straxen & nest RucioRemote imports (#592)
0620126 
* use nested imports for RucioRemote

* use the right imports

* fix none/import error

* add simple test

* test loading runs

* if no utilix there is no sense in testing

* make faster

* test find

* Update test_rucio.py

* Update test_rucio.py

* comment on the tests

* Update test_rucio.py
@JoranAngevaare
Update README.md
9acbc9e
@JoranAngevaare
create pre-release
0bbf3b9
@JoranAngevaare
Update requirements for strax (#644)
8befa20 
* Update requirements for strax

* Update pytest.yml

* Update pytest.yml

* Update pytest.yml

* Update pytest.yml

* Update pytest.yml

* Update pytest.yml

* Update pytest.yml

* Update pytest.yml

* Create filter_strax_from_requirements.sh

* Update pytest.yml

* Update pytest.yml
@JoranAngevaare
Delete preinstall_requirements.sh
6205853
@JoranAngevaare
Update requirements.txt
f51e4fb
@WenzDaniel
Fix n hits (#646)
dea6aa3 
* Fixed +1 in n_hits
@zhut19 @WenzDaniel
merge s2 without s1 (#645)
1037fc6 
Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com>
dependabot bot and others added 28 commits October 27, 2021 23:21
@dependabot
Bump dask from 2021.8.1 to 2021.10.0 in /extra_requirements (#712)
d8d669f 
Bumps [dask](https://github.com/dask/dask) from 2021.8.1 to 2021.10.0.
- [Release notes](https://github.com/dask/dask/releases)
- [Changelog](https://github.com/dask/dask/blob/main/docs/release-procedure.md)
- [Commits](dask/dask@2021.08.1...2021.10.0)

---
updated-dependencies:
- dependency-name: dask
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@JoranAngevaare
fix bug in CMT (#710)
d4b17d6 
* fix bug in CMT

* remove nv&mv chaining plugins

* Revert "remove nv&mv chaining plugins"

This reverts commit 08bb8f4.
@WenzDaniel @JoranAngevaare
Fix one year querries (#711)
f0f52be 
* Fix querries which last longer than one year

* Changed querring to support >1 year queries

* Reviewdog comments

Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@JoranAngevaare
small codefactor patch (#714)
395d69e
@JoranAngevaare
test nv with nv data (#709)
983e122 
* test nv with nv data

* remove tagging plugins

* test them here

* Update test_utils.py

* Update test_nveto_recorder.py
@ramirezdiego @JoranAngevaare
WFSim registry as argument for simulations context (#713)
74a7dee 
* WFSim registry as argument for sims context

* Copypasting Joran's function

* Shame on me

* use new func

Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@tuankhaibui @WenzDaniel @JoranAngevaare
Veto monitor (#707)
742d9c4 
* add data kinds to monitor neutron and muon Veto

add online_monitor_nv and online_monitor_mv

* Update contexts.py

* Update online_monitor.py

* Update contexts.py

* Update online_monitor.py

I update OnlineMonitorNV (to v.0.0.4) and OnlineMonitorMV. 
OnlineMonitorMV is a child plugin of OnlineMonitorNV.

* Update contexts.py

* Update online_monitor.py

* Update online_monitor.py

* small editorial changes

Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com>
Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@GiovanniVolta @JoranAngevaare
Update S1 AFT map in event pattern fit (#697)
cf868e7 
* Update S1 AFT map in event pattern fit

* Update event_patternfit.py

* test s1 aft map unity

* Update test_utils.py

* Update test_utils.py

Co-authored-by: GiovanniVolta <gvolta@dali-login1.rcc.local>
Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@jingqiangye @JoranAngevaare
Refactor s2 correction (#704)
1e9b592 
* refactor fields for correctedareas

* add corrected s2 with s2xy correction only

* fix dtype

* use infer_dtype

* remove redundant variables

* remove elife_corr from infer_dtype

* line break after operator

* use strax.to_str_tuple

* remove cs2_bottom_wo_elifecorr

* fix bug

Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@ramirezdiego @JoranAngevaare
Unify CMT call in contexts (#717)
8c2eea9 
Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@JoranAngevaare
Remove old bootstrax argument
9795bbf
@JoranAngevaare
add small test for wfsim (#716)
32dac79 
* Update test_contexts.py

* Update requirements-tests.txt

* Update test_contexts.py

* Update pytest.yml

* Update pytest.yml

* Update pytest.yml

* Update pytest.yml

* Update pytest.yml

* this is so confusing

* Update pytest.yml

* Update test_contexts.py

* Update test_contexts.py

* Update pytest.yml

* Update requirements.txt

* Update requirements-tests.txt
@JoranAngevaare
new version
ce55224
@JoranAngevaare
Bump version: 1.1.1 → 1.1.2
63a1561
@JoranAngevaare
Track typing_extensions==3.7.4.3 (#722)
c003ee1
@JoranAngevaare
Process afterpulses on ebs (#727)
105eca0
@JoranAngevaare
Update test_misc.py
90f2fc3
@JoranAngevaare
test_widgets is broken? (#726)
cf26112 
* test_widgets is broken?

* Update test_misc.py

* Update test_misc.py
@dependabot @JoranAngevaare
Bump scikit-learn from 1.0 to 1.0.1 in /extra_requirements (#737)
17a3b01 
Bumps [scikit-learn](https://github.com/scikit-learn/scikit-learn) from 1.0 to 1.0.1.
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@1.0...1.0.1)

---
updated-dependencies:
- dependency-name: scikit-learn
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@dependabot @JoranAngevaare
Bump utilix from 0.6.1 to 0.6.5 in /extra_requirements (#736)
50e6a1a 
Bumps [utilix](https://github.com/XENONnT/utilix) from 0.6.1 to 0.6.5.
- [Release notes](https://github.com/XENONnT/utilix/releases)
- [Changelog](https://github.com/XENONnT/utilix/blob/master/HISTORY.md)
- [Commits](XENONnT/utilix@v0.6.1...v0.6.5)

---
updated-dependencies:
- dependency-name: utilix
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@dependabot @JoranAngevaare
Bump jupyter-client from 7.0.5 to 7.0.6 in /extra_requirements (#734)
a5b5834 
Bumps [jupyter-client](https://github.com/jupyter/jupyter_client) from 7.0.5 to 7.0.6.
- [Release notes](https://github.com/jupyter/jupyter_client/releases)
- [Changelog](https://github.com/jupyter/jupyter_client/blob/master/CHANGELOG.md)
- [Commits](jupyter/jupyter_client@v7.0.5...v7.0.6)

---
updated-dependencies:
- dependency-name: jupyter-client
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@dependabot @JoranAngevaare
Bump flake8 from 3.9.2 to 4.0.1 in /extra_requirements (#730)
af34b02 
Bumps [flake8](https://github.com/pycqa/flake8) from 3.9.2 to 4.0.1.
- [Release notes](https://github.com/pycqa/flake8/releases)
- [Commits](PyCQA/flake8@3.9.2...4.0.1)

---
updated-dependencies:
- dependency-name: flake8
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@dependabot @JoranAngevaare
Bump blosc from 1.10.4 to 1.10.6 in /extra_requirements (#728)
f6228e0 
Bumps [blosc](https://github.com/blosc/python-blosc) from 1.10.4 to 1.10.6.
- [Release notes](https://github.com/blosc/python-blosc/releases)
- [Changelog](https://github.com/Blosc/python-blosc/blob/master/RELEASE_NOTES.rst)
- [Commits](Blosc/python-blosc@v1.10.4...v1.10.6)

---
updated-dependencies:
- dependency-name: blosc
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@JoranAngevaare
Fix deprecation warning (#723)
59ac610
@dependabot
Bump pytest-cov from 2.12.1 to 3.0.0 in /extra_requirements (#732)
5cd75ab 
Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 2.12.1 to 3.0.0.
- [Release notes](https://github.com/pytest-dev/pytest-cov/releases)
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](pytest-dev/pytest-cov@v2.12.1...v3.0.0)

---
updated-dependencies:
- dependency-name: pytest-cov
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@dependabot @JoranAngevaare
Bump hypothesis from 6.23.1 to 6.24.1 in /extra_requirements (#738)
f752739 
Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.23.1 to 6.24.1.
- [Release notes](https://github.com/HypothesisWorks/hypothesis/releases)
- [Commits](HypothesisWorks/hypothesis@hypothesis-python-6.23.1...hypothesis-python-6.24.1)

---
updated-dependencies:
- dependency-name: hypothesis
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
@JoranAngevaare
Test installation without extra requirements (#725)
193a703 
* Test installation without extra requirements

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt
@JoranAngevaare
Merge branch 'joran_master' into test_fix
39f36e0
@JoranAngevaare JoranAngevaare merged commit 0cc3f57 into JoranAngevaare:joran_master Nov 1, 2021
@JoranAngevaare JoranAngevaare deleted the test_fix branch November 1, 2021 11:29
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