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* Add NaN check

* Add a custom exception for nan and add the check for all corrections

* use pandas builtin functions as suggested in the review

* Allow database to not be initialized (XENONnT#636)

* new plot_pmts (XENONnT#637)

* change plotting of dead pmts.

Co-authored-by: GiovanniVolta <gvolta@dali-login1.rcc.local>
Co-authored-by: Joran Angevaare <jorana@nikhef.nl>

* First nVeto monitor plugin (XENONnT#634)

* 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>

* Speed up event pattern fit (XENONnT#625)

* 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>

* Peak event veto tagging (XENONnT#618)

* Add peak and event veto tagging plugins + tests

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

* kwargs for saver (XENONnT#639)

* Add a plugin for external trigger run on nVeto calibration (XENONnT#630)

* 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>

* Fix veto event positions (XENONnT#641)

* Fixed floating point issue

* Renamed function update test

* bumped version

Co-authored-by: Evan Shockley <eshockley@physics.ucsd.edu>

* Fix peaklet area bias (XENONnT#601)

* 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>

* Bump tensorflow from 2.5.0 to 2.5.1 in /extra_requirements (XENONnT#643)

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)

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* Add lone hit information to merged S2s. (XENONnT#623)

* 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>

* Use rucio from straxen & nest RucioRemote imports (XENONnT#592)

* 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

* Update README.md

* create pre-release

* Update requirements for strax (XENONnT#644)

* 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

* Delete preinstall_requirements.sh

* Update requirements.txt

* Fix n hits (XENONnT#646)

* Fixed +1 in n_hits

* merge s2 without s1 (XENONnT#645)

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

* Updated history

* Bump version: '1.0.0-rc0' -> '1.0.0' (set str manually)

* Use query by index

* few tweaks from review

* Bump tqdm from 4.62.0 to 4.62.2 in /extra_requirements (XENONnT#658)

Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.62.0 to 4.62.2.
- [Release notes](https://github.com/tqdm/tqdm/releases)
- [Commits](tqdm/tqdm@v4.62.0...v4.62.2)

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* Bump dask from 2021.7.2 to 2021.8.1 in /extra_requirements (XENONnT#657)

Bumps [dask](https://github.com/dask/dask) from 2021.7.2 to 2021.8.1.
- [Release notes](https://github.com/dask/dask/releases)
- [Changelog](https://github.com/dask/dask/blob/main/docs/release-procedure.md)
- [Commits](dask/dask@2021.07.2...2021.08.1)

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* Bump pandas from 1.2.5 to 1.3.2 in /extra_requirements (XENONnT#653)

Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.2.5 to 1.3.2.
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Changelog](https://github.com/pandas-dev/pandas/blob/master/RELEASE.md)
- [Commits](pandas-dev/pandas@v1.2.5...v1.3.2)

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* Bump hypothesis from 6.14.5 to 6.17.4 in /extra_requirements (XENONnT#651)

Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.14.5 to 6.17.4.
- [Release notes](https://github.com/HypothesisWorks/hypothesis/releases)
- [Commits](HypothesisWorks/hypothesis@hypothesis-python-6.14.5...hypothesis-python-6.17.4)

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* Bump matplotlib from 3.4.2 to 3.4.3 in /extra_requirements (XENONnT#656)

Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.4.2 to 3.4.3.
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](matplotlib/matplotlib@v3.4.2...v3.4.3)

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* Bump scipy from 1.7.0 to 1.7.1 in /extra_requirements (XENONnT#647)

Bumps [scipy](https://github.com/scipy/scipy) from 1.7.0 to 1.7.1.
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.7.0...v1.7.1)

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* Bump jupyter-client from 6.1.12 to 7.0.2 in /extra_requirements (XENONnT#649)

Bumps [jupyter-client](https://github.com/jupyter/jupyter_client) from 6.1.12 to 7.0.2.
- [Release notes](https://github.com/jupyter/jupyter_client/releases)
- [Changelog](https://github.com/jupyter/jupyter_client/blob/master/CHANGELOG.md)
- [Commits](jupyter/jupyter_client@6.1.12...v7.0.2)

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  update-type: version-update:semver-major
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* Bump ipywidgets from 7.6.3 to 7.6.4 in /extra_requirements (XENONnT#650)

Bumps [ipywidgets](http://ipython.org) from 7.6.3 to 7.6.4.

---
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* Bump tensorflow from 2.5.1 to 2.6.0 in /extra_requirements (XENONnT#655)

Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 2.5.1 to 2.6.0.
- [Release notes](https://github.com/tensorflow/tensorflow/releases)
- [Changelog](https://github.com/tensorflow/tensorflow/blob/master/RELEASE.md)
- [Commits](tensorflow/tensorflow@v2.5.1...v2.6.0)

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- dependency-name: tensorflow
  dependency-type: direct:production
  update-type: version-update:semver-minor
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* Bump pytest from 6.2.4 to 6.2.5 in /extra_requirements (XENONnT#654)

Bumps [pytest](https://github.com/pytest-dev/pytest) from 6.2.4 to 6.2.5.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@6.2.4...6.2.5)

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* Fix minianalyses from apply_selection (XENONnT#666)

* Fix minianalyses from apply_selection

* Update mini_analysis.py

* Add small feature for printing versions of git (XENONnT#665)

* add small feature for printing versions of git

* allow detached heads

* Update misc.py

* Update bootstrax

* Update test_misc.py

* fix some warnings from testing (XENONnT#667)

* fix some warnings from testing

* Update rundb.py

* warn by default

* import typing

* Add posdiff plugin (XENONnT#669)

* Add posdiff plugin

Co-authored-by: Shengchao Li <scli@dali-login2.rcc.local>
Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
Co-authored-by: Evan Shockley <eshockley@physics.ucsd.edu>

* Bump jupyter-client from 7.0.2 to 7.0.5 in /extra_requirements (XENONnT#675)

Bumps [jupyter-client](https://github.com/jupyter/jupyter_client) from 7.0.2 to 7.0.5.
- [Release notes](https://github.com/jupyter/jupyter_client/releases)
- [Changelog](https://github.com/jupyter/jupyter_client/blob/master/CHANGELOG.md)
- [Commits](jupyter/jupyter_client@v7.0.2...v7.0.5)

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* Bump scikit-learn from 0.24.2 to 1.0 in /extra_requirements (XENONnT#676)

Bumps [scikit-learn](https://github.com/scikit-learn/scikit-learn) from 0.24.2 to 1.0.
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@0.24.2...1.0)

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* Bump hypothesis from 6.17.4 to 6.23.1 in /extra_requirements (XENONnT#680)

Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.17.4 to 6.23.1.
- [Release notes](https://github.com/HypothesisWorks/hypothesis/releases)
- [Commits](HypothesisWorks/hypothesis@hypothesis-python-6.17.4...hypothesis-python-6.23.1)

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* use strax notebook pbar if applicible (XENONnT#685)

* Implement SDSC as a local RSE for Expanse (XENONnT#687)

* Implement SDSC for rucio frontend / local backend

* Fix typo in comment

* Update contexts.py (XENONnT#673)

* Skips superruns in rucio frontend (XENONnT#689)

* Skips superruns in rucio frontend

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

* Previous S2 Shadow Plugin draft (XENONnT#664)

* Plugin which computes S2 shadows

Co-authored-by: Kexin Liu <kexinliu@dali-login1.rcc.local>
Co-authored-by: Shingo Kazama <kazama@isee.nagoya-u.ac.jp>
Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com>

* Warn about non-loadable loggers (XENONnT#693)

* Warn about non-loadable loggers

* Update bootstrax

* Add n saturated channels (XENONnT#691)

* Add n_saturated channels, makes peaklets explicit.

* Extend tight coincidence by channels

* Propagate info to peak basics

* Bump peaklet versions

* Bump peak_basics versions

* Propagate information to event_baiscs and bump version.

* Updated function call and return

* Add test for tight coincidence

* Some review dog things

* Move buffer cleaning

* Fixed field help

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

* add small tool to extract run comments from database (XENONnT#692)

* add small tool to extract run comments from database

* fix review comments

* Update misc.py

* Update pytest.yml

* Update online_monitor_nv to v0.0.3 (XENONnT#696)

* Added events_nv_area_per_chunk

* updated S2 corrected area (XENONnT#686)

* updated S2 corrected area

Co-authored-by: Jingqiang Ye <jyy2139@columbia.edu>
Co-authored-by: Shingo Kazama <kazama@isee.nagoya-u.ac.jp>
Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
Co-authored-by: Daniel Wenz <dwenz@kabelmail.de>

* Use admix in straxen (XENONnT#688)

* Implement SDSC for rucio frontend / local backend

* Fix typo in comment

* Have RucioRemoteBackend select RSEs in smart way

* Bug fix in cases where RucioLocalBackend is not appended to the backends list

* Update straxen/rucio.py

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

* Use admix

* Use admix now in remote plugin

* Dont require admix

* Update contexts.py and rucio.py to address Joran's comments

* small tweaks to XENONnT#688

* use strax#541

* fix bug

* fix docstring

Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com>

* Add RunDb read/write-test (XENONnT#695)

* add read write test for rundb

* cleanup

* remove pprint

* important if

* review comments

* fix non-utilx test

* remove _list_available??

* hack utilix

* hack it gooood

* Version bump of hitlets (XENONnT#690)

* Version bump of hitlets

* Changed path to new peak data

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

* Implemented channel range to support he channel plugins

* Fix bug in rucio frontend (XENONnT#699)

* Make release v1 1 0 (XENONnT#698)

* Updated history

* Bump version: 1.0.0 → 1.1.0

* Update test_database_frontends.py

* ready for patch release

* Bump version: 1.1.0 → 1.1.1

* Set default drift time as nan (XENONnT#700)

* change default drift time to nan

* change drift time to float to avoid convert nan into integer

* Test new numba (XENONnT#702)

* Revert auto inclusion of rucio remote XENONnT#688 (XENONnT#701)

* Revert auto inclusion of rucio remote XENONnT#688

* allow other frontends to have the data

* Also don't mark things available if not allowed

* Revert "Also don't mark things available if not allowed"

This reverts commit d6fb67a.

* Plugin for afterpulse processing (XENONnT#549)

* add plugin for APs

Co-authored-by: Luisa Hoetzsch <hoetzsch@dali-login1.rcc.local>
Co-authored-by: Luisa Hoetzsch <luisa.hoetzsch@mpi-hd.mpg.de>
Co-authored-by: Joran Angevaare <jorana@nikhef.nl>
Co-authored-by: Evan Shockley <eshockley@physics.ucsd.edu>
Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com>
Co-authored-by: Shingo Kazama <kazama@isee.nagoya-u.ac.jp>

* Refactor straxen tests (XENONnT#703)

* use a small test data file

* Bump dask from 2021.8.1 to 2021.10.0 in /extra_requirements (XENONnT#712)

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)

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* fix bug in CMT (XENONnT#710)

* fix bug in CMT

* remove nv&mv chaining plugins

* Revert "remove nv&mv chaining plugins"

This reverts commit 08bb8f4.

* Fix one year querries (XENONnT#711)

* 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>

* small codefactor patch (XENONnT#714)

* test nv with nv data (XENONnT#709)

* test nv with nv data

* remove tagging plugins

* test them here

* Update test_utils.py

* Update test_nveto_recorder.py

* WFSim registry as argument for simulations context (XENONnT#713)

* 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>

* Veto monitor (XENONnT#707)

* 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>

* Update S1 AFT map in event pattern fit (XENONnT#697)

* 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>

* Refactor s2 correction (XENONnT#704)

* 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>

* Unify CMT call in contexts (XENONnT#717)

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

* Remove old bootstrax argument

* add small test for wfsim (XENONnT#716)

* 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

* new version

* Bump version: 1.1.1 → 1.1.2

* Track typing_extensions==3.7.4.3 (XENONnT#722)

* Process afterpulses on ebs (XENONnT#727)

* Update test_misc.py

* test_widgets is broken? (XENONnT#726)

* test_widgets is broken?

* Update test_misc.py

* Update test_misc.py

* Bump scikit-learn from 1.0 to 1.0.1 in /extra_requirements (XENONnT#737)

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
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* Bump utilix from 0.6.1 to 0.6.5 in /extra_requirements (XENONnT#736)

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
...

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* Bump jupyter-client from 7.0.5 to 7.0.6 in /extra_requirements (XENONnT#734)

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)

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- dependency-name: jupyter-client
  dependency-type: direct:production
  update-type: version-update:semver-patch
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* Bump flake8 from 3.9.2 to 4.0.1 in /extra_requirements (XENONnT#730)

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)

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updated-dependencies:
- dependency-name: flake8
  dependency-type: direct:production
  update-type: version-update:semver-major
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* Bump blosc from 1.10.4 to 1.10.6 in /extra_requirements (XENONnT#728)

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:
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  dependency-type: direct:production
  update-type: version-update:semver-patch
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* Fix deprecation warning (XENONnT#723)

* Bump pytest-cov from 2.12.1 to 3.0.0 in /extra_requirements (XENONnT#732)

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)

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  dependency-type: direct:production
  update-type: version-update:semver-major
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* Bump hypothesis from 6.23.1 to 6.24.1 in /extra_requirements (XENONnT#738)

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)

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* Test installation without extra requirements (XENONnT#725)

* 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

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2 changes: 1 addition & 1 deletion .bumpversion.cfg
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
[bumpversion]
current_version = 0.19.3
current_version = 1.1.2
files = setup.py straxen/__init__.py
commit = True
tag = True
3 changes: 3 additions & 0 deletions .github/scripts/filter_strax_from_requirements.sh
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
echo `pwd`
cat requirements.txt | grep -v 'strax' &> requirements.txt
cat requirements.txt
11 changes: 0 additions & 11 deletions .github/scripts/preinstall_requirements.sh

This file was deleted.

35 changes: 21 additions & 14 deletions .github/workflows/pytest.yml
Original file line number Diff line number Diff line change
Expand Up @@ -18,21 +18,17 @@ on:
release:
types: [created]
pull_request:
branches:
- master
- stable
- joran_master
push:
branches:
- master
- joran_master
- stable

jobs:
update:
name: "${{ matrix.test }}_py${{ matrix.python-version }}"
runs-on: ubuntu-latest
strategy:
fail-fast: True
fail-fast: False
matrix:
python-version: [3.7, 3.8, 3.9]
test: ['coveralls', 'pytest', 'pytest_no_database']
Expand All @@ -54,11 +50,21 @@ jobs:
python-version: ${{ matrix.python-version }}
- name: Checkout repo
uses: actions/checkout@v2
- name: Remove strax from reqs.
if: matrix.test == 'coveralls' && env.HAVE_ACCESS_TO_SECTETS != null
env:
HAVE_ACCESS_TO_SECTETS: ${{ secrets.RUNDB_API_URL }}
run: |
bash .github/scripts/filter_strax_from_requirements.sh
- name: Install requirements for tests and latest strax
run: |
pip install -r extra_requirements/requirements-tests.txt
pip install git+https://github.com/AxFoundation/strax.git
git clone https://github.com/AxFoundation/strax ../strax
pip install -e ../strax
- name: Start MongoDB
uses: supercharge/mongodb-github-action@1.6.0
with:
mongodb-version: 4.2
# Secrets and required files
- name: patch utilix file
# Patch this file if we want to have access to the database
Expand All @@ -85,18 +91,20 @@ jobs:
env:
HAVE_ACCESS_TO_SECTETS: ${{ secrets.RUNDB_API_URL }}
if: env.HAVE_ACCESS_TO_SECTETS == null || matrix.test == 'pytest_no_database'
run: |
bash .github/scripts/create_pre_apply_function.sh $HOME
# Run tests
run: bash .github/scripts/create_pre_apply_function.sh $HOME
- name: Test package
# This is running a normal test
if: matrix.test == 'pytest_no_database' || matrix.test == 'pytest'
env:
ALLOW_WFSIM_TEST: 1
TEST_MONGO_URI: 'mongodb://localhost:27017/'
run: |
python setup.py test -v
pytest -rsxv --durations 0
- name: Coveralls
# Make the coverage report and upload
env:
TEST_MONGO_URI: 'mongodb://localhost:27017/'
ALLOW_WFSIM_TEST: 1
NUMBA_DISABLE_JIT: 1
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# We need to check if we had access to the secrets, otherwise coveralls
Expand All @@ -107,7 +115,6 @@ jobs:
run: |
coverage run --source=straxen setup.py test -v
coveralls --service=github
# Done
- name: goodbye
run: echo "tests done, bye bye"
36 changes: 36 additions & 0 deletions .github/workflows/test_install.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,36 @@
# Test if we can actually install strax by installing
name: Installation test

on:
workflow_dispatch:
release:
types: [created]
pull_request:
branches:
- master
- stable
push:
branches:
- master

jobs:
update:
name: "py${{ matrix.python-version }}"
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
python-version: [3.8]
steps:
- name: Setup python
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Checkout repo
uses: actions/checkout@v2
- name: Install straxen
run: python setup.py install
- name: Test import
run: python -c "import straxen; straxen.print_versions()"
- name: goodbye
run: echo goodbye
91 changes: 91 additions & 0 deletions HISTORY.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,94 @@
1.1.2 / 2021-10-27
-------------------
minor / patches:
- Plugin for afterpulse processing (#549)
- Veto online monitor (#707)
- Refactor straxen tests (#703)
- WFSim registry as argument for simulations context (#713)
- Update S1 AFT map in event pattern fit (#697)

fixes/tests:
- Set default drift time as nan (#700)
- Revert auto inclusion of rucio remote #688 (#701)
- fix bug in CMT (#710)
- Fix one year querries (#711
- Test new numba (#702)
- Unify CMT call in contexts (#717)
- Small codefactor patch (#714)
- test nv with nv data (#709)
- Add small test for wfsim (#716)


1.1.1 / 2021-10-19
-------------------
- Fix to test for RunDB frontend when no test DB is sourced (6da2233)


1.1.0 / 2021-10-18
-------------------
major / minor:

- Previous S2 Shadow Plugin draft (#664)
- Use admix in straxen (#688)
- Add posdiff plugin (#669)
- updated S2 corrected area (#686)
- Version bump of hitlets (#690)
- Add n saturated channels (#691)
- add small tool to extract run comments from database (#692)
- Update online_monitor_nv to v0.0.3 (#696)


patches and fixes:

- Use read by index and check for NaNs (#661)
- Add small feature for printing versions of git (#665)
- Fix minianalyses from apply_selection (#666)
- fix some warnings from testing (#667)
- Add source to runs table (#673)
- Pbar patch for rundb query (#685)
- Implement SDSC as a local RSE for Expanse (#687)
- Skips superruns in rucio frontend (#689)
- Warn about non-loadable loggers (#693)
- Add RunDb read/write-test (#695)
- Fix bug in rucio frontend (#699)



1.0.0 / 2021-09-01
-------------------
major / minor:

- merge s2 without s1 (#645)
- First nVeto monitor plugin (#634)
- Peak event veto tagging (#618)
- Fix peaklet area bias (#601)
- Add lone hit information to merged S2s. (#623)


patches and fixes:

- Fix n_hits of peaks (#646)
- Update requirements for strax (#644)
- Modifications of nT simulation context (#602)
- Straxer for other packages (#595)
- [Bug fix] alt_s{i}_delay computation (#598)
- Bump version refactor code for cleanliness. (#597)
- Increase buffer size (#604)
- Stop testing py3.6 (#621)
- Remove online event monitor (#620)
- Add matplotlib to test requirements (#626)
- Fix rundb select runs with superruns (#627)
- Change EventInfo to save when explicit (#628)
- Update test data (#631)
- Allow database to not be initialized (#636)
- new plot_pmts (#637)
- Speed up event pattern fit (#625)
- kwargs for saver (#639)
- Add a plugin for external trigger run on nVeto calibration (#630)
- Fix veto event positions (#641)
- Use rucio from straxen & nest RucioRemote imports (#592)


0.19.3 / 2021-07-16
-------------------
- Rewrite EventBasics, set event level S1 tight coincidence (#569)
Expand Down
1 change: 0 additions & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -18,4 +18,3 @@ For installation instructions and usage information, please see the [straxen doc

[![Update context collection](https://github.com/XENONnT/straxen/workflows/Update%20context%20collection/badge.svg)](https://github.com/XENONnT/straxen/actions/workflows/contexts.yml)
[![Python style](https://github.com/XENONnT/straxen/actions/workflows/code_style.yml/badge.svg)](https://github.com/XENONnT/straxen/actions/workflows/code_style.yml)
[![Coveralls](https://github.com/XENONnT/straxen/actions/workflows/coveralls.yml/badge.svg?branch=master)](https://github.com/XENONnT/straxen/actions/workflows/coveralls.yml)
38 changes: 22 additions & 16 deletions bin/bootstrax
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ How to use
For more info, see the documentation:
https://straxen.readthedocs.io/en/latest/bootstrax.html
"""
__version__ = '1.1.8'
__version__ = '1.1.9'

import argparse
from datetime import datetime, timedelta, timezone
Expand All @@ -38,6 +38,7 @@ import straxen
import threading
import pandas as pd
import typing as ty
import daqnt

parser = argparse.ArgumentParser(
description="XENONnT online processing manager")
Expand Down Expand Up @@ -203,31 +204,30 @@ max_queue_new_runs = 2
# this many times. If high level data is hitting some edge case, we
# might want to be able to keep the intermediate level data.
# NB: string match so events applies e.g. to event_basics, peak to e.g. peaklets
remove_target_after_fails = dict(events=2,
remove_target_after_fails = dict(event=2,
hitlets=2,
peaks=4,
online=5,
peak_basics=5,
peaklets=6,
online=5,
ALL=7)

##
# Initialize globals (e.g. rundb connection)
##
hostname = socket.getfqdn()

try:
import daqnt
log_name = 'bootstrax_' + hostname + ('' if args.production else '_TESTING')
log = daqnt.get_daq_logger(log_name, log_name, level=logging.DEBUG)
except ModuleNotFoundError:
logging.basicConfig(
level=logging.INFO,
format='%(asctime)s %(name)s %(levelname)-8s %(message)s',
datefmt='%m-%d %H:%M')
log = logging.getLogger()

log_name = 'bootstrax_' + hostname + ('' if args.production else '_TESTING')
log = daqnt.get_daq_logger(log_name, log_name, level=logging.DEBUG)
log.info(f'---\n bootstrax version {__version__}\n---')
log.info(
straxen.print_versions(
modules='strax straxen utilix daqnt numpy tensorflow numba'.split(),
include_git=True,
return_string=True,
))


# Set the output folder
output_folder = '/data/xenonnt_processed/' if args.production else test_data_folder
Expand Down Expand Up @@ -273,9 +273,10 @@ def new_context(cores=args.cores,
allow_multiprocess=cores > 1,
allow_shm=cores > 1,
allow_lazy=False,
use_rucio=False,
max_messages=max_messages,
timeout=timeout)
timeout=timeout,
_rucio_path=None,
)
if not args.production:
# Keep the rundb but set it to readonly and local only, delete
# all other storage frontends except fo the test folder.
Expand Down Expand Up @@ -522,7 +523,8 @@ def infer_target(rd: dict) -> dict:

# Special modes override target for these
led_modes = ['pmtgain']
diagnostic_modes = ['exttrig', 'noise', 'pmtap']
diagnostic_modes = ['exttrig', 'noise']
ap_modes = ['pmtap']
mode = str(rd.get('mode'))
detectors = list(rd.get('detectors'))

Expand All @@ -531,6 +533,10 @@ def infer_target(rd: dict) -> dict:
log.debug('led-mode')
targets = 'led_calibration'
post_process = 'raw_records'
elif np.any([m in mode for m in ap_modes]):
log.debug('afterpulse mode')
targets = 'afterpulses'
post_process = 'raw_records'
elif np.any([m in mode for m in diagnostic_modes]):
log.debug('diagnostic-mode')
targets = 'raw_records'
Expand Down
33 changes: 18 additions & 15 deletions extra_requirements/requirements-tests.txt
Original file line number Diff line number Diff line change
@@ -1,30 +1,33 @@
# File for the requirements of straxen with the automated tests
blosc==1.10.4 # Strax dependency
blosc==1.10.6 # Strax dependency
boltons==21.0.0
datashader==0.13.0
dask==2021.7.2
dask==2021.10.0
dill==0.3.4 # Strax dependency
coveralls==3.2.0
commentjson==0.9.0
coverage==5.5
flake8==3.9.2
flake8==4.0.1
gitpython==3.1.18
holoviews==1.14.5
ipywidgets==7.6.3
hypothesis==6.14.6
jupyter-client==6.1.12 # for ipywidgets
matplotlib==3.4.2
ipywidgets==7.6.4
hypothesis==6.24.1
jupyter-client==7.0.6 # for ipywidgets
matplotlib==3.4.3
multihist==0.6.4
npshmex==0.2.1 # Strax dependency
numba==0.53.1 # Strax dependency
numba==0.54.1 # Strax dependency
numpy==1.19.5
pandas==1.3.1 # Strax dependency
pandas==1.3.2 # Strax dependency
psutil==5.8.0 # Strax dependency
pytest==6.2.4
pytest-cov==2.12.1
scikit-learn==0.24.2
pytest==6.2.5
pytest-cov==3.0.0
scikit-learn==1.0.1
scipy==1.7.1 # Strax dependency
tensorflow==2.5.1
tqdm==4.62.0
tensorflow==2.6.0
typing_extensions==3.7.4.3 # Tensorflow depencency
tqdm==4.62.2
wfsim==0.5.9
xarray==0.19.0
utilix==0.6.1
utilix==0.6.5
zstd==1.5.0.2 # Strax dependency
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