Remove RuntimeError in RucioFrontend #719
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Apparently codefactor doesn't like TODOs, but I think we should leave it because this really is a TODO we need to addresss. |
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Could we use something similar to Line 31 in 63a1561 |
JoranAngevaare
suggested changes
Oct 30, 2021
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I think it would be much better to not raise runtime errors in the Rucio Frontend, just that it cannot provide you data shouldn't prevent you from initializing the context (or event the frontend itself). For example, you can also initialize the storage front-ends without having the /dali/bla paths.
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Ok we can also do this. In my view it doesn't make much sense to register storage frontends that can't be used, but it would make this exception handling much better. |
ershockley
changed the title
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Thanks Evan |
JoranAngevaare
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Jan 23, 2022
* 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 * Use query by index * few tweaks from review * Bump tqdm from 4.62.0 to 4.62.2 in /extra_requirements (#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](https://github.com/tqdm/tqdm/compare/v4.62.0...v4.62.2) --- updated-dependencies: - dependency-name: tqdm 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> * Bump dask from 2021.7.2 to 2021.8.1 in /extra_requirements (#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](https://github.com/dask/dask/compare/2021.07.2...2021.08.1) --- updated-dependencies: - dependency-name: dask 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> * Bump pandas from 1.2.5 to 1.3.2 in /extra_requirements (#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](https://github.com/pandas-dev/pandas/compare/v1.2.5...v1.3.2) --- updated-dependencies: - dependency-name: pandas 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> * Bump hypothesis from 6.14.5 to 6.17.4 in /extra_requirements (#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](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.14.5...hypothesis-python-6.17.4) --- 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> * Bump matplotlib from 3.4.2 to 3.4.3 in /extra_requirements (#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](https://github.com/matplotlib/matplotlib/compare/v3.4.2...v3.4.3) --- updated-dependencies: - dependency-name: matplotlib 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> * Bump scipy from 1.7.0 to 1.7.1 in /extra_requirements (#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](https://github.com/scipy/scipy/compare/v1.7.0...v1.7.1) --- updated-dependencies: - dependency-name: scipy 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> * Bump jupyter-client from 6.1.12 to 7.0.2 in /extra_requirements (#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](https://github.com/jupyter/jupyter_client/compare/6.1.12...v7.0.2) --- updated-dependencies: - dependency-name: jupyter-client 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> * Bump ipywidgets from 7.6.3 to 7.6.4 in /extra_requirements (#650) Bumps [ipywidgets](http://ipython.org) from 7.6.3 to 7.6.4. --- updated-dependencies: - dependency-name: ipywidgets 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> * Bump tensorflow from 2.5.1 to 2.6.0 in /extra_requirements (#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](https://github.com/tensorflow/tensorflow/compare/v2.5.1...v2.6.0) --- updated-dependencies: - dependency-name: tensorflow 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> * Bump pytest from 6.2.4 to 6.2.5 in /extra_requirements (#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](https://github.com/pytest-dev/pytest/compare/6.2.4...6.2.5) --- updated-dependencies: - dependency-name: pytest 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> * Fix minianalyses from apply_selection (#666) * Fix minianalyses from apply_selection * Update mini_analysis.py * Add small feature for printing versions of git (#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 (#667) * fix some warnings from testing * Update rundb.py * warn by default * import typing * Add posdiff plugin (#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 (#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](https://github.com/jupyter/jupyter_client/compare/v7.0.2...v7.0.5) --- 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> * Bump scikit-learn from 0.24.2 to 1.0 in /extra_requirements (#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](https://github.com/scikit-learn/scikit-learn/compare/0.24.2...1.0) --- updated-dependencies: - dependency-name: scikit-learn 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> * Bump hypothesis from 6.17.4 to 6.23.1 in /extra_requirements (#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](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.17.4...hypothesis-python-6.23.1) --- 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> * use strax notebook pbar if applicible (#685) * Implement SDSC as a local RSE for Expanse (#687) * Implement SDSC for rucio frontend / local backend * Fix typo in comment * Update contexts.py (#673) * Skips superruns in rucio frontend (#689) * Skips superruns in rucio frontend Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Previous S2 Shadow Plugin draft (#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 (#693) * Warn about non-loadable loggers * Update bootstrax * Add n saturated channels (#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 (#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 (#696) * Added events_nv_area_per_chunk * updated S2 corrected area (#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 (#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 #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 (#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 (#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 (#699) * Make release v1 1 0 (#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 (#700) * change default drift time to nan * change drift time to float to avoid convert nan into integer * Test new numba (#702) * Revert auto inclusion of rucio remote #688 (#701) * Revert auto inclusion of rucio remote #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 d6fb67ad8c6338e4dc9a7773fd50549811f476e3. * Plugin for afterpulse processing (#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 (#703) * use a small test data file * Bump dask from 2021.8.1 to 2021.10.0 in /extra_requirements (#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](https://github.com/dask/dask/compare/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> * fix bug in CMT (#710) * fix bug in CMT * remove nv&mv chaining plugins * Revert "remove nv&mv chaining plugins" This reverts commit 08bb8f434a4658d117adca8c4393d70f2ce41546. * Fix one year querries (#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 (#714) * test nv with nv data (#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 (#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 (#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 (#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 (#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 (#717) Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Remove old bootstrax argument * add small test for wfsim (#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 (#722) * Process afterpulses on ebs (#727) * Update test_misc.py * test_widgets is broken? (#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 (#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](https://github.com/scikit-learn/scikit-learn/compare/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> * Bump utilix from 0.6.1 to 0.6.5 in /extra_requirements (#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](https://github.com/XENONnT/utilix/compare/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> * Bump jupyter-client from 7.0.5 to 7.0.6 in /extra_requirements (#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](https://github.com/jupyter/jupyter_client/compare/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> * Bump flake8 from 3.9.2 to 4.0.1 in /extra_requirements (#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](https://github.com/pycqa/flake8/compare/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> * Bump blosc from 1.10.4 to 1.10.6 in /extra_requirements (#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](https://github.com/blosc/python-blosc/compare/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> * Fix deprecation warning (#723) * Bump pytest-cov from 2.12.1 to 3.0.0 in /extra_requirements (#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](https://github.com/pytest-dev/pytest-cov/compare/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> * Bump hypothesis from 6.23.1 to 6.24.1 in /extra_requirements (#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](https://github.com/HypothesisWorks/hypothesis/compare/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> * Test installation without extra requirements (#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 * Update requirements-tests.txt (#739) * Fix history * Add a few special cases (#740) * Add a few special cases The renaming for variables starting with cs1/cs2 is made via explicitly written special cases. Those were not updated for a few added fields. * corrected syntax error * Increment plugin version Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Remove RuntimeError in RucioFrontend (#719) * Add try except for rucio frontend * remove runtime error in rucio Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * use alt z for alternative s1 binomial test (#724) * use alt z for alternative s1 binomial test Co-authored-by: GiovanniVolta <gvolta@dali-login1.rcc.local> Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Add zenodo (#742) * Add zenodo * Update README.md * Fix keras requirement (#748) * Bump tensorflow from 2.6.0 to 2.6.1 in /extra_requirements (#752) Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 2.6.0 to 2.6.1. - [Release notes](https://github.com/tensorflow/tensorflow/releases) - [Changelog](https://github.com/tensorflow/tensorflow/blob/master/RELEASE.md) - [Commits](https://github.com/tensorflow/tensorflow/compare/v2.6.0...v2.6.1) --- 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> * update docs (#743) * update docs * typo * Set check_broken=False for RucioFrontend.find (#749) Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Added resource exception (#755) * Added resource exception * Add perpendicular wires handling info and function (#756) * Add perpendicular wires handling info and function Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> * Track bokeh (#759) * Track bokeh * Update requirements-tests.txt * Adding code comments for corrected z position (#763) * Small fix in definition of buffer (#760) * Small fix in definition of buffer * Reactivate scada test (#764) * Reactivate scada * Trigger new run https://xenonnt.slack.com/archives/C016UJZ090B/p1637148920183500 * Update test_scada.py * Revert "Small fix in definition of buffer (#760)" (#766) This reverts commit fd34198df065f18a003dbb09c4b7589cd9ba1a5b. * cleanup bootstrax logic for target determiniation (#768) * cleanup bootstrax logic * just in case one uses capital letters * Add URL based configs (#758) * add optional pyroscope profiling * add URLConfig and basic protocol implementations * Update straxen/url_config.py Co-authored-by: Joran Angevaare <joranangevaare@gmail.com> * undo accidental change to bootstrax * docstring and explicit exeption catch * Update straxen/url_config.py Co-authored-by: Joran Angevaare <joranangevaare@gmail.com> Co-authored-by: Yossi Mosbacher <joe.mosbacher> Co-authored-by: Joran Angevaare <joranangevaare@gmail.com> Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Explicitly set infer_dtype=False for all Options (#750) * add infer_dtype to all options * rename infer_dtype to infer_type * pin strax version since not backward compatible Co-authored-by: Yossi Mosbacher <joe.mosbacher> Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * new release * Bump version: 1.1.2 → 1.1.3 * Update bootstrax * Implement peak-level shadow and event-level shadow refactor (#753) * Add PeakShadow plugin. * Separate event shadow and peak shadow Co-authored-by: chnlkx <lkx21@mails.tsinghua.edu.cn> * Bump supercharge/mongodb-github-action from 1.6.0 to 1.7.0 (#771) Bumps [supercharge/mongodb-github-action](https://github.com/supercharge/mongodb-github-action) from 1.6.0 to 1.7.0. - [Release notes](https://github.com/supercharge/mongodb-github-action/releases) - [Changelog](https://github.com/supercharge/mongodb-github-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/supercharge/mongodb-github-action/compare/1.6.0...1.7.0) --- updated-dependencies: - dependency-name: supercharge/mongodb-github-action 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> * Add main peaks' shadow for event shadow (#770) * Add main peaks' shadow for event shadow Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> * Cache dependencies (#772) * cache dependencies * Update pytest.yml * Update contexts.yml * order events * Bump wfsim tests (#773) * wipe the online monitor * Revert "wipe the online monitor" This reverts commit a945e75725c40d7661f90cb3032d20f15175d18d. * whipe online monitor data (#777) * whipe online monitor data * rever pycharm nonsense * revert it more * pycharm doesn't even allow me to copy past it back * Pin pymongo (#801) * Bump packaging from 20.8 to 21.3 in /extra_requirements (#794) Bumps [packaging](https://github.com/pypa/packaging) from 20.8 to 21.3. - [Release notes](https://github.com/pypa/packaging/releases) - [Changelog](https://github.com/pypa/packaging/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pypa/packaging/compare/20.8...21.3) --- updated-dependencies: - dependency-name: packaging 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> * Bump xarray from 0.19.0 to 0.20.1 in /extra_requirements (#799) Bumps [xarray](https://github.com/pydata/xarray) from 0.19.0 to 0.20.1. - [Release notes](https://github.com/pydata/xarray/releases) - [Changelog](https://github.com/pydata/xarray/blob/main/HOW_TO_RELEASE.md) - [Commits](https://github.com/pydata/xarray/compare/v0.19.0...v0.20.1) --- updated-dependencies: - dependency-name: xarray 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> * Bump wfsim from 0.5.10 to 0.5.11 in /extra_requirements (#798) Bumps [wfsim](https://github.com/XENONnT/wfsim) from 0.5.10 to 0.5.11. - [Release notes](https://github.com/XENONnT/wfsim/releases) - [Changelog](https://github.com/XENONnT/WFSim/blob/master/HISTORY.md) - [Commits](https://github.com/XENONnT/wfsim/compare/v0.5.10...v0.5.11) --- updated-dependencies: - dependency-name: wfsim 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> * Bump hypothesis from 6.24.1 to 6.29.0 in /extra_requirements (#797) Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.24.1 to 6.29.0. - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.24.1...hypothesis-python-6.29.0) --- 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> * Bump dask from 2021.10.0 to 2021.11.2 in /extra_requirements (#786) Bumps [dask](https://github.com/dask/dask) from 2021.10.0 to 2021.11.2. - [Release notes](https://github.com/dask/dask/releases) - [Changelog](https://github.com/dask/dask/blob/main/docs/release-procedure.md) - [Commits](https://github.com/dask/dask/compare/2021.10.0...2021.11.2) --- updated-dependencies: - dependency-name: dask 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> * Bump coveralls from 3.2.0 to 3.3.1 in /extra_requirements (#789) Bumps [coveralls](https://github.com/TheKevJames/coveralls-python) from 3.2.0 to 3.3.1. - [Release notes](https://github.com/TheKevJames/coveralls-python/releases) - [Changelog](https://github.com/TheKevJames/coveralls-python/blob/master/CHANGELOG.md) - [Commits](https://github.com/TheKevJames/coveralls-python/compare/3.2.0...3.3.1) --- updated-dependencies: - dependency-name: coveralls 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> * specified wfsim twice * Bump jupyter-client from 7.0.6 to 7.1.0 in /extra_requirements (#788) Bumps [jupyter-client](https://github.com/jupyter/jupyter_client) from 7.0.6 to 7.1.0. - [Release notes](https://github.com/jupyter/jupyter_client/releases) - [Changelog](https://github.com/jupyter/jupyter_client/blob/master/CHANGELOG.md) - [Commits](https://github.com/jupyter/jupyter_client/compare/v7.0.6...v7.1.0) --- updated-dependencies: - dependency-name: jupyter-client 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> * Bump coverage from 5.5 to 6.2 in /extra_requirements (#790) Bumps [coverage](https://github.com/nedbat/coveragepy) from 5.5 to 6.2. - [Release notes](https://github.com/nedbat/coveragepy/releases) - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst) - [Commits](https://github.com/nedbat/coveragepy/compare/coverage-5.5...6.2) --- updated-dependencies: - dependency-name: coverage 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> * Add refactor event building cut (#778) * Move le/re into setup for event building cut. * Add comment * Remove whitespace * Add types to plugin * Matplotlib changed requirements (#805) * fix shadow plugins * move to peaks/events * address review * make static * issue with the requirements? * URLConfig not in strax (#781) * URLConfig not in strax * add import to package init * add tests for URLConfig * replace deprecates pymongo Cursor.count * skip cmt test if utilix not configured * require pymongo<=3.12.0 to avoid breaking changes * add md5 to file documents for pymongo 4.0 support * add protocol description method * SecondaryPreferred read preference for OM tests * Update requirements-tests.txt * test fsspec protocol * formatting * fix typos and print_protocols-dummy test * add type hints to protocols Co-authored-by: Yossi Mosbacher <joe.mosbacher> Co-authored-by: Joran Angevaare <jorana@nikhef.nl> Co-authored-by: Yossi Mosbacher <joe.mosbacher@gmail.com> * Revert "URLConfig not in strax (#781)" (#807) This reverts commit b5f3d99344fe9f46eec8126338afce99fed92168. * Fix #781 (#808) * can we disable codefactor please (#809) * Update bokeh, panel, tensorflow and keras (#796) * Bump bokeh from 2.3.3 to 2.4.2 in /extra_requirements Bumps [bokeh](https://github.com/bokeh/bokeh) from 2.3.3 to 2.4.2. - [Release notes](https://github.com/bokeh/bokeh/releases) - [Changelog](https://github.com/bokeh/bokeh/blob/branch-3.0/CHANGELOG) - [Commits](https://github.com/bokeh/bokeh/compare/2.3.3...2.4.2) --- updated-dependencies: - dependency-name: bokeh dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * Update requirements-tests.txt * Update requirements-tests.txt * Update requirements-tests.txt * Update bokeh_waveform_plot.py Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Loose packaging requirement (#810) * Exclude S1 as triggering peak (#779) Co-authored-by: Shingo Kazama <kazama@isee.nagoya-u.ac.jp> Co-authored-by: Jingqiang Ye <jyy2139@columbia.edu> * fix dep. order * sort alphabetically * Restore #760 Patch peaks merging (#767) * Update definition array_valued (#757) * use channel tight coincidence level (#745) Co-authored-by: Evan Shockley <eshockley@physics.ucsd.edu> Co-authored-by: Shingo Kazama <kazama@isee.nagoya-u.ac.jp> Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> * Two manual boundaries (updated 11/24/2021) (#775) Updates classification boundaries for S1 and Se * S2 pattern fit (#780) * add neural tensorflow method chi2 * Revert "Update definition array_valued (#757)" (#812) This reverts commit 23e4eacb4191ae3444df2bdd483795bd93b28026. * Itp test (#813) * can we disable codefactor please * add itp test * Events synchronize (#761) *Add preliminary plugin for synchronized time stamps * Performance update for binomial test (#783) * update binom test * Fix broken matplotlib/minianalyses (#815) * fix broken matplotlib * fix some tests * update tests * remove asserts * Update test_mini_analyses.py * fix multihist syntax * Update matplotlib_utils.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/holoviews_waveform_display.py * Update straxen/analyses/posrec_comparison.py * Update straxen/analyses/posrec_comparison.py * Update straxen/analyses/posrec_comparison.py * Update straxen/analyses/posrec_comparison.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * fix codefactor * sorry sorry for this mess * assert is inverted * this is not log * fix more bugs * deprecate tight layout * add docs * review comments * stupid typo * Remove codefactor (#818) https://xenonnt.slack.com/archives/C016UJZ090B/p1639500799304900 * Rename tight coincidence (#825) * Rename tight coincidence -> tight_coincidence channel, remove previous tight coincidence. * Update help * Remove field * Remove n_hits computation * Update the test * URLConfig take protocol for nested keys (#826) * adjust take protocol for lists * one more test, thanks Yossi Co-authored-by: Yossi Mosbacher <joe.mosbacher> Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Restore #757 (#814) Co-authored-by: Johanna Jakob <56300925+jjakob03@users.noreply.github.com> Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> Co-authored-by: tianyu zhu <tz2263@columbia.edu> * Bump wemake-services/wemake-python-styleguide from 0.15.3 to 0.16.0 (#829) Bumps [wemake-services/wemake-python-styleguide](https://github.com/wemake-services/wemake-python-styleguide) from 0.15.3 to 0.16.0. - [Release notes](https://github.com/wemake-services/wemake-python-styleguide/releases) - [Changelog](https://github.com/wemake-services/wemake-python-styleguide/blob/master/CHANGELOG.md) - [Commits](https://github.com/wemake-services/wemake-python-styleguide/compare/0.15.3...0.16.0) --- updated-dependencies: - dependency-name: wemake-services/wemake-python-styleguide 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> * Unittest for DAQreader (#828) * add daq_reader_test * add review comments * remove the erease option, it absolutely is one big horrible idea * fix review comments * Fix nv testing data (#830) * Another try at codefactor (#831) Let's give it another try, other tools have their own issues too * Move URLConfig cache to global dictionary (#822) * Adds size_of function for cache Co-authored-by: Yossi Mosbacher <joe.mosbacher> Co-authored-by: Joran Angevaare <joranangevaare@gmail.com> Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Add test for filter_kwargs (#837) Co-authored-by: Yossi Mosbacher <joe.mosbacher> * Update CorrectedAreas (instead of EnergyEstimates) (#817) * Update CorrectedAreas (instead of EnergyEstimates) * Changed CorrectedAreas and EnergyEstimates to URL configs * Added new fields cs2_wo_elifecorr and cs2_wo_time_corr * Using bodega for EnergyEstimates option * Extend URL configs and CMT Co-authored-by: Yossi Mosbacher <joe.mosbacher@gmail.com> Co-authored-by: Yossi Mosbacher <joe.mosbacher> Co-authored-by: Joran Angevaare <jorana@nikhef.nl> Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> * Fix codefactor issues (#832) Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> * use URL configs for NeuralNets (#821) * use URL configs for NeuralNets * placeholders * whoops * add test * review comments * small bug * fix tests * remove scaffolding * 100% COVERAGE :tada: * one line more * Update test_plugins.py * review * Update test_utils.py * fix tests and todos * Update tests/test_posrec_plugins.py * git scrambelled commit * Update url_config.py * Normalized line endings (#833) (#838) * Bump panel from 0.12.5 to 0.12.6 in /extra_requirements (#842) Bumps [panel](https://github.com/holoviz/panel) from 0.12.5 to 0.12.6. - [Release notes](https://github.com/holoviz/panel/releases) - [Changelog](https://github.com/holoviz/panel/blob/master/CHANGELOG.md) - [Commits](https://github.com/holoviz/panel/compare/v0.12.5...v0.12.6) --- updated-dependencies: - dependency-name: panel 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> * Bump zstd from 1.5.0.2 to 1.5.0.4 in /extra_requirements (#844) Bumps [zstd](https://github.com/sergey-dryabzhinsky/python-zstd) from 1.5.0.2 to 1.5.0.4. - [Release notes](https://github.com/sergey-dryabzhinsky/python-zstd/releases) - [Commits](https://github.com/sergey-dryabzhinsky/python-zstd/compare/v1.5.0.2...v1.5.0.4) --- updated-dependencies: - dependency-name: zstd 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> * Make v1 2 0 (#849) * Up history * Bump version: 1.1.3 → 1.2.0 * Bump hypothesis from 6.29.0 to 6.31.6 in /extra_requirements (#846) Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.29.0 to 6.31.6. - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.29.0...hypothesis-python-6.31.6) --- 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> * Bump xarray from 0.20.1 to 0.20.2 in /extra_requirements (#847) Bumps [xarray](https://github.com/pydata/xarray) from 0.20.1 to 0.20.2. - [Release notes](https://github.com/pydata/xarray/releases) - [Changelog](https://github.com/pydata/xarray/blob/main/HOW_TO_RELEASE.md) - [Commits](https://github.com/pydata/xarray/compare/v0.20.1...v0.20.2) --- updated-dependencies: - dependency-name: xarray 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> * Bump wfsim from 0.5.11 to 0.5.12 in /extra_requirements (#843) Bumps [wfsim](https://github.com/XENONnT/wfsim) from 0.5.11 to 0.5.12. - [Release notes](https://github.com/XENONnT/wfsim/releases) - [Changelog](https://github.com/XENONnT/WFSim/blob/master/HISTORY.md) - [Commits](https://github.com/XENONnT/wfsim/compare/v0.5.11...v0.5.12) --- updated-dependencies: - dependency-name: wfsim 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> * Bump dask from 2021.11.2 to 2021.12.0 in /extra_requirements (#841) Bumps [dask](https://github.com/dask/dask) from 2021.11.2 to 2021.12.0. - [Release notes](https://github.com/dask/dask/releases) - [Changelog](https://github.com/dask/dask/blob/main/docs/release-procedure.md) - [Commits](https://github.com/dask/dask/compare/2021.11.2...2021.12.0) --- updated-dependencies: - dependency-name: dask 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> * Update requirements.txt (#852) * Bump scipy from 1.7.1 to 1.7.3 in /extra_requirements (#840) Bumps [scipy](https://github.com/scipy/scipy) from 1.7.1 to 1.7.3. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.7.1...v1.7.3) --- updated-dependencies: - dependency-name: scipy 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> * Bump packaging from 20.8 to 21.3 in /extra_requirements (#845) Bumps [packaging](https://github.com/pypa/packaging) from 20.8 to 21.3. - [Release notes](https://github.com/pypa/packaging/releases) - [Changelog](https://github.com/pypa/packaging/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pypa/packaging/compare/20.8...21.3) --- updated-dependencies: - dependency-name: packaging 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> * add read the docs config (#861) * add read the docs config * Update .readthedocs.yaml * one file * Pin documentation requirements (#862) * Add cmt tests and fix bug in apply_cmt_version (#860) * Add cmt tests and fix bug in apply_cmt_version * fix bug in url * Make dog happy * Add test for offline context * Skip offline text if no db * Implement Yossi's suggestion * Small typo in comment * just some bookkeeping * add comments Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * new release * Bump version: 1.2.0 → 1.2.1 * Tests for `common.py` fix #741 (#856) * Fix common.py test * simplify * solve #741 * also load from mem * Update common.py * Add `strax.Context` documentation, fix #439 (#851) * fix #439 * fix source * Update build_context_doc.py * add bokeh to wiki test (#857) * Test for rucio-documents in the rundb (#858) * add test for rucio docs * revert change * fix comments * reduce testing time * one small test * Test for Mongo-down/uploader (#859) * add down/uploader tests * fix last line * Bump psutil from 5.8.0 to 5.9.0 in /extra_requirements (#872) Bumps [psutil](https://github.com/giampaolo/psutil) from 5.8.0 to 5.9.0. - [Release notes](https://github.com/giampaolo/psutil/releases) - [Changelog](https://github.com/giampaolo/psutil/blob/master/HISTORY.rst) - [Commits](https://github.com/giampaolo/psutil/compare/release-5.8.0...release-5.9.0) --- updated-dependencies: - dependency-name: psutil 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> * Bump scikit-learn from 1.0.1 to 1.0.2 in /extra_requirements (#869) Bumps [scikit-learn](https://github.com/scikit-learn/scikit-learn) from 1.0.1 to 1.0.2. - [Release notes](https://github.com/scikit-learn/scikit-learn/releases) - [Commits](https://github.com/scikit-learn/scikit-learn/compare/1.0.1...1.0.2) --- 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> * Bump hypothesis from 6.31.6 to 6.34.1 in /extra_requirements (#868) Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.31.6 to 6.34.1. - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.31.6...hypothesis-python-6.34.1) --- 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> * Bump nbsphinx from 0.8.7 to 0.8.8 in /extra_requirements (#871) Bumps [nbsphinx](https://github.com/spatialaudio/nbsphinx) from 0.8.7 to 0.8.8. - [Release notes](https://github.com/spatialaudio/nbsphinx/releases) - [Changelog](https://github.com/spatialaudio/nbsphinx/blob/master/NEWS.rst) - [Commits](https://github.com/spatialaudio/nbsphinx/compare/0.8.7...0.8.8) --- updated-dependencies: - dependency-name: nbsphinx 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> * Bump peaklets version (#873) * Bump peaklets version * Update peaklet_processing.py Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * new version * Bump version: 1.2.1 → 1.2.2 * Bump numpy (#876) * Update requirements.txt * Update requirements.txt * Update requirements.txt * update test * typo * sort by alpha. * fix end * Update requirements-tests.txt * make new release for req. update * Bump version: 1.2.2 → 1.2.3 * fix action * Another WFSim `<->` CMT patch (#865) * just another hack for WFSim<3CMT * alternative suggestion * reveert * revert please * keep wfsim hack working as expected Co-authored-by: Yossi Mosbacher <joe.mosbacher> * introduce development branch * Tests for WFSim contexts (#855) * test for wfsim contexts * fix typo * how are you even supposed to pass these arguments?! * maybe this is the right syntax? Super convoluted.. * skip no db test * fix some leftovers * get ready for new release * Bump version: 1.2.3 → 1.2.4 * test with py3.10 (#878) * test with py3.10 * bump tf * Update pytest.yml * pin keras * fix test for wfsim * differently * Update pytest.yml * clean instructins * remove scaffolding * another try * simplify pandas * fix typo * skip HV * fix dtype * remove fixme error * bump numba (#880) * Tests for scada interface (#877) * Add additional tests * Add additional tests * Add additional tests * Update scada.py * add some more Co-authored-by: Joran R. Angevaare <jorana@nikhef.nl> * bumpversion * Bump version: 1.2.4 → 1.2.5 * Fix online monitor test (#882) * Update test_mongo_interactions.py * i love codefactor? * bumpversion * Bump version: 1.2.5 → 1.2.6 * fix typo * Delete update context collection (#883) * Delete update context collection * Delete create-utilix-config.sh * update zenodo * update github actions (#884) * URLConfig documentation (#863) * document urlconfigs * comment on URL argument order * change order Co-authored-by: Yossi Mosbacher <joe.mosbacher> Co-authored-by: Joran Angevaare <jorana@nikhef.nl> Co-authored-by: ahiguera-mx <ahiguera-mx@fried.rice.edu> Co-authored-by: Aaron Higuera <64651045+ahiguera-mx@users.noreply.github.com> Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> Co-authored-by: Shingo Kazama <kazama@isee.nagoya-u.ac.jp> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Evan Shockley <eshockley@physics.ucsd.edu> Co-authored-by: Shengchao Li <li4006@purdue.edu> Co-authored-by: Shengchao Li <scli@dali-login2.rcc.local> Co-authored-by: Kexin Liu <lkx21@mails.tsinghua.edu.cn> Co-authored-by: Kexin Liu <kexinliu@dali-login1.rcc.local> Co-authored-by: Tuan Khai Bui <82461188+tuankhaibui@users.noreply.github.com> Co-authored-by: Jianyu Long <38538701+Jianyu010@users.noreply.github.com> Co-authored-by: Jingqiang Ye <jyy2139@columbia.edu> Co-authored-by: Daniel Wenz <dwenz@kabelmail.de> Co-authored-by: Daniel Wenz <dwenz@students.uni-mainz.de> Co-authored-by: Luisa Hoetzsch <hoetzsch@mpi-hd.mpg.de> Co-authored-by: Luisa Hoetzsch <hoetzsch@dali-login1.rcc.local> Co-authored-by: Luisa Hoetzsch <luisa.hoetzsch@mpi-hd.mpg.de> Co-authored-by: Diego Ramírez García <diego.ramirez@physik.uni-freiburg.de> Co-authored-by: Giovanni Volta <38431109+GiovanniVolta@users.noreply.github.com> Co-authored-by: GiovanniVolta <gvolta@dali-login1.rcc.local> Co-authored-by: Johanna Jakob <56300925+jjakob03@users.noreply.github.com> Co-authored-by: Ricardo Peres <rperes@physik.uzh.ch> Co-authored-by: Lutz Althüser <account@l-althueser.de> Co-authored-by: Yossi Mosbacher <joe.mosbacher@gmail.com> Co-authored-by: Dacheng Xu <xdc17@mails.tsinghua.edu.cn> Co-authored-by: Dacheng Xu <xudctron@gmail.com> Co-authored-by: Knut Dundas Morå <kdm2160@columbia.edu> Co-authored-by: Yue Ma <3124558229@qq.com> Co-authored-by: Shenyang Shi <ss6109@columbia.edu> Co-authored-by: tianyu zhu <tz2263@columbia.edu>
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Jan 24, 2022
* 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 (#636) * new plot_pmts (#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 (#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 (#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 (#618) * Add peak and event veto tagging plugins + tests Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * kwargs for saver (#639) * Add a plugin for external trigger run on nVeto calibration (#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 (#641) * Fixed floating point issue * Renamed function update test * bumped version Co-authored-by: Evan Shockley <eshockley@physics.ucsd.edu> * Fix peaklet area bias (#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 (#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](https://github.com/tensorflow/tensorflow/compare/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> * Add lone hit information to merged S2s. (#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 4710419151b33639e4cdf7349cfa9afb0b3e31cd. * Revert "Revert "Add dummy lone hits for he channel"" This reverts commit 4cbfb3c23d0da764bb967323fca0d6272f39b494. * Revert "Modify tests to avoid deadlock" This reverts commit 271e7cfdb8b1d2d605fa9fb885d2142db860555a. * 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 (#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 (#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 (#646) * Fixed +1 in n_hits * merge s2 without s1 (#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 (#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](https://github.com/tqdm/tqdm/compare/v4.62.0...v4.62.2) --- updated-dependencies: - dependency-name: tqdm 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> * Bump dask from 2021.7.2 to 2021.8.1 in /extra_requirements (#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](https://github.com/dask/dask/compare/2021.07.2...2021.08.1) --- updated-dependencies: - dependency-name: dask 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> * Bump pandas from 1.2.5 to 1.3.2 in /extra_requirements (#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](https://github.com/pandas-dev/pandas/compare/v1.2.5...v1.3.2) --- updated-dependencies: - dependency-name: pandas 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> * Bump hypothesis from 6.14.5 to 6.17.4 in /extra_requirements (#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](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.14.5...hypothesis-python-6.17.4) --- 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> * Bump matplotlib from 3.4.2 to 3.4.3 in /extra_requirements (#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](https://github.com/matplotlib/matplotlib/compare/v3.4.2...v3.4.3) --- updated-dependencies: - dependency-name: matplotlib 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> * Bump scipy from 1.7.0 to 1.7.1 in /extra_requirements (#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](https://github.com/scipy/scipy/compare/v1.7.0...v1.7.1) --- updated-dependencies: - dependency-name: scipy 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> * Bump jupyter-client from 6.1.12 to 7.0.2 in /extra_requirements (#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](https://github.com/jupyter/jupyter_client/compare/6.1.12...v7.0.2) --- updated-dependencies: - dependency-name: jupyter-client 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> * Bump ipywidgets from 7.6.3 to 7.6.4 in /extra_requirements (#650) Bumps [ipywidgets](http://ipython.org) from 7.6.3 to 7.6.4. --- updated-dependencies: - dependency-name: ipywidgets 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> * Bump tensorflow from 2.5.1 to 2.6.0 in /extra_requirements (#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](https://github.com/tensorflow/tensorflow/compare/v2.5.1...v2.6.0) --- updated-dependencies: - dependency-name: tensorflow 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> * Bump pytest from 6.2.4 to 6.2.5 in /extra_requirements (#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](https://github.com/pytest-dev/pytest/compare/6.2.4...6.2.5) --- updated-dependencies: - dependency-name: pytest 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> * Fix minianalyses from apply_selection (#666) * Fix minianalyses from apply_selection * Update mini_analysis.py * Add small feature for printing versions of git (#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 (#667) * fix some warnings from testing * Update rundb.py * warn by default * import typing * Add posdiff plugin (#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 (#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](https://github.com/jupyter/jupyter_client/compare/v7.0.2...v7.0.5) --- 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> * Bump scikit-learn from 0.24.2 to 1.0 in /extra_requirements (#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](https://github.com/scikit-learn/scikit-learn/compare/0.24.2...1.0) --- updated-dependencies: - dependency-name: scikit-learn 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> * Bump hypothesis from 6.17.4 to 6.23.1 in /extra_requirements (#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](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.17.4...hypothesis-python-6.23.1) --- 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> * use strax notebook pbar if applicible (#685) * Implement SDSC as a local RSE for Expanse (#687) * Implement SDSC for rucio frontend / local backend * Fix typo in comment * Update contexts.py (#673) * Skips superruns in rucio frontend (#689) * Skips superruns in rucio frontend Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Previous S2 Shadow Plugin draft (#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 (#693) * Warn about non-loadable loggers * Update bootstrax * Add n saturated channels (#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 (#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 (#696) * Added events_nv_area_per_chunk * updated S2 corrected area (#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 (#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 #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 (#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 (#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 (#699) * Make release v1 1 0 (#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 (#700) * change default drift time to nan * change drift time to float to avoid convert nan into integer * Test new numba (#702) * Revert auto inclusion of rucio remote #688 (#701) * Revert auto inclusion of rucio remote #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 d6fb67ad8c6338e4dc9a7773fd50549811f476e3. * Plugin for afterpulse processing (#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 (#703) * use a small test data file * Bump dask from 2021.8.1 to 2021.10.0 in /extra_requirements (#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](https://github.com/dask/dask/compare/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> * fix bug in CMT (#710) * fix bug in CMT * remove nv&mv chaining plugins * Revert "remove nv&mv chaining plugins" This reverts commit 08bb8f434a4658d117adca8c4393d70f2ce41546. * Fix one year querries (#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 (#714) * test nv with nv data (#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 (#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 (#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 (#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 (#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 (#717) Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Remove old bootstrax argument * add small test for wfsim (#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 (#722) * Process afterpulses on ebs (#727) * Update test_misc.py * test_widgets is broken? (#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 (#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](https://github.com/scikit-learn/scikit-learn/compare/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> * Bump utilix from 0.6.1 to 0.6.5 in /extra_requirements (#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](https://github.com/XENONnT/utilix/compare/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> * Bump jupyter-client from 7.0.5 to 7.0.6 in /extra_requirements (#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](https://github.com/jupyter/jupyter_client/compare/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> * Bump flake8 from 3.9.2 to 4.0.1 in /extra_requirements (#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](https://github.com/pycqa/flake8/compare/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> * Bump blosc from 1.10.4 to 1.10.6 in /extra_requirements (#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](https://github.com/blosc/python-blosc/compare/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> * Fix deprecation warning (#723) * Bump pytest-cov from 2.12.1 to 3.0.0 in /extra_requirements (#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](https://github.com/pytest-dev/pytest-cov/compare/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> * Bump hypothesis from 6.23.1 to 6.24.1 in /extra_requirements (#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](https://github.com/HypothesisWorks/hypothesis/compare/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> * Test installation without extra requirements (#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 * Update requirements-tests.txt (#739) * Fix history * Add a few special cases (#740) * Add a few special cases The renaming for variables starting with cs1/cs2 is made via explicitly written special cases. Those were not updated for a few added fields. * corrected syntax error * Increment plugin version Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Remove RuntimeError in RucioFrontend (#719) * Add try except for rucio frontend * remove runtime error in rucio Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * use alt z for alternative s1 binomial test (#724) * use alt z for alternative s1 binomial test Co-authored-by: GiovanniVolta <gvolta@dali-login1.rcc.local> Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Add zenodo (#742) * Add zenodo * Update README.md * Fix keras requirement (#748) * Bump tensorflow from 2.6.0 to 2.6.1 in /extra_requirements (#752) Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 2.6.0 to 2.6.1. - [Release notes](https://github.com/tensorflow/tensorflow/releases) - [Changelog](https://github.com/tensorflow/tensorflow/blob/master/RELEASE.md) - [Commits](https://github.com/tensorflow/tensorflow/compare/v2.6.0...v2.6.1) --- 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> * update docs (#743) * update docs * typo * Set check_broken=False for RucioFrontend.find (#749) Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Added resource exception (#755) * Added resource exception * Add perpendicular wires handling info and function (#756) * Add perpendicular wires handling info and function Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> * Track bokeh (#759) * Track bokeh * Update requirements-tests.txt * Adding code comments for corrected z position (#763) * Small fix in definition of buffer (#760) * Small fix in definition of buffer * Reactivate scada test (#764) * Reactivate scada * Trigger new run https://xenonnt.slack.com/archives/C016UJZ090B/p1637148920183500 * Update test_scada.py * Revert "Small fix in definition of buffer (#760)" (#766) This reverts commit fd34198df065f18a003dbb09c4b7589cd9ba1a5b. * cleanup bootstrax logic for target determiniation (#768) * cleanup bootstrax logic * just in case one uses capital letters * Add URL based configs (#758) * add optional pyroscope profiling * add URLConfig and basic protocol implementations * Update straxen/url_config.py Co-authored-by: Joran Angevaare <joranangevaare@gmail.com> * undo accidental change to bootstrax * docstring and explicit exeption catch * Update straxen/url_config.py Co-authored-by: Joran Angevaare <joranangevaare@gmail.com> Co-authored-by: Yossi Mosbacher <joe.mosbacher> Co-authored-by: Joran Angevaare <joranangevaare@gmail.com> Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Explicitly set infer_dtype=False for all Options (#750) * add infer_dtype to all options * rename infer_dtype to infer_type * pin strax version since not backward compatible Co-authored-by: Yossi Mosbacher <joe.mosbacher> Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * new release * Bump version: 1.1.2 → 1.1.3 * Update bootstrax * Implement peak-level shadow and event-level shadow refactor (#753) * Add PeakShadow plugin. * Separate event shadow and peak shadow Co-authored-by: chnlkx <lkx21@mails.tsinghua.edu.cn> * Bump supercharge/mongodb-github-action from 1.6.0 to 1.7.0 (#771) Bumps [supercharge/mongodb-github-action](https://github.com/supercharge/mongodb-github-action) from 1.6.0 to 1.7.0. - [Release notes](https://github.com/supercharge/mongodb-github-action/releases) - [Changelog](https://github.com/supercharge/mongodb-github-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/supercharge/mongodb-github-action/compare/1.6.0...1.7.0) --- updated-dependencies: - dependency-name: supercharge/mongodb-github-action 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> * Add main peaks' shadow for event shadow (#770) * Add main peaks' shadow for event shadow Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> * Cache dependencies (#772) * cache dependencies * Update pytest.yml * Update contexts.yml * order events * Bump wfsim tests (#773) * wipe the online monitor * Revert "wipe the online monitor" This reverts commit a945e75725c40d7661f90cb3032d20f15175d18d. * whipe online monitor data (#777) * whipe online monitor data * rever pycharm nonsense * revert it more * pycharm doesn't even allow me to copy past it back * Pin pymongo (#801) * Bump packaging from 20.8 to 21.3 in /extra_requirements (#794) Bumps [packaging](https://github.com/pypa/packaging) from 20.8 to 21.3. - [Release notes](https://github.com/pypa/packaging/releases) - [Changelog](https://github.com/pypa/packaging/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pypa/packaging/compare/20.8...21.3) --- updated-dependencies: - dependency-name: packaging 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> * Bump xarray from 0.19.0 to 0.20.1 in /extra_requirements (#799) Bumps [xarray](https://github.com/pydata/xarray) from 0.19.0 to 0.20.1. - [Release notes](https://github.com/pydata/xarray/releases) - [Changelog](https://github.com/pydata/xarray/blob/main/HOW_TO_RELEASE.md) - [Commits](https://github.com/pydata/xarray/compare/v0.19.0...v0.20.1) --- updated-dependencies: - dependency-name: xarray 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> * Bump wfsim from 0.5.10 to 0.5.11 in /extra_requirements (#798) Bumps [wfsim](https://github.com/XENONnT/wfsim) from 0.5.10 to 0.5.11. - [Release notes](https://github.com/XENONnT/wfsim/releases) - [Changelog](https://github.com/XENONnT/WFSim/blob/master/HISTORY.md) - [Commits](https://github.com/XENONnT/wfsim/compare/v0.5.10...v0.5.11) --- updated-dependencies: - dependency-name: wfsim 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> * Bump hypothesis from 6.24.1 to 6.29.0 in /extra_requirements (#797) Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.24.1 to 6.29.0. - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.24.1...hypothesis-python-6.29.0) --- 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> * Bump dask from 2021.10.0 to 2021.11.2 in /extra_requirements (#786) Bumps [dask](https://github.com/dask/dask) from 2021.10.0 to 2021.11.2. - [Release notes](https://github.com/dask/dask/releases) - [Changelog](https://github.com/dask/dask/blob/main/docs/release-procedure.md) - [Commits](https://github.com/dask/dask/compare/2021.10.0...2021.11.2) --- updated-dependencies: - dependency-name: dask 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> * Bump coveralls from 3.2.0 to 3.3.1 in /extra_requirements (#789) Bumps [coveralls](https://github.com/TheKevJames/coveralls-python) from 3.2.0 to 3.3.1. - [Release notes](https://github.com/TheKevJames/coveralls-python/releases) - [Changelog](https://github.com/TheKevJames/coveralls-python/blob/master/CHANGELOG.md) - [Commits](https://github.com/TheKevJames/coveralls-python/compare/3.2.0...3.3.1) --- updated-dependencies: - dependency-name: coveralls 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> * specified wfsim twice * Bump jupyter-client from 7.0.6 to 7.1.0 in /extra_requirements (#788) Bumps [jupyter-client](https://github.com/jupyter/jupyter_client) from 7.0.6 to 7.1.0. - [Release notes](https://github.com/jupyter/jupyter_client/releases) - [Changelog](https://github.com/jupyter/jupyter_client/blob/master/CHANGELOG.md) - [Commits](https://github.com/jupyter/jupyter_client/compare/v7.0.6...v7.1.0) --- updated-dependencies: - dependency-name: jupyter-client 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> * Bump coverage from 5.5 to 6.2 in /extra_requirements (#790) Bumps [coverage](https://github.com/nedbat/coveragepy) from 5.5 to 6.2. - [Release notes](https://github.com/nedbat/coveragepy/releases) - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst) - [Commits](https://github.com/nedbat/coveragepy/compare/coverage-5.5...6.2) --- updated-dependencies: - dependency-name: coverage 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> * Add refactor event building cut (#778) * Move le/re into setup for event building cut. * Add comment * Remove whitespace * Add types to plugin * Matplotlib changed requirements (#805) * fix shadow plugins * move to peaks/events * address review * make static * issue with the requirements? * URLConfig not in strax (#781) * URLConfig not in strax * add import to package init * add tests for URLConfig * replace deprecates pymongo Cursor.count * skip cmt test if utilix not configured * require pymongo<=3.12.0 to avoid breaking changes * add md5 to file documents for pymongo 4.0 support * add protocol description method * SecondaryPreferred read preference for OM tests * Update requirements-tests.txt * test fsspec protocol * formatting * fix typos and print_protocols-dummy test * add type hints to protocols Co-authored-by: Yossi Mosbacher <joe.mosbacher> Co-authored-by: Joran Angevaare <jorana@nikhef.nl> Co-authored-by: Yossi Mosbacher <joe.mosbacher@gmail.com> * Revert "URLConfig not in strax (#781)" (#807) This reverts commit b5f3d99344fe9f46eec8126338afce99fed92168. * Fix #781 (#808) * can we disable codefactor please (#809) * Update bokeh, panel, tensorflow and keras (#796) * Bump bokeh from 2.3.3 to 2.4.2 in /extra_requirements Bumps [bokeh](https://github.com/bokeh/bokeh) from 2.3.3 to 2.4.2. - [Release notes](https://github.com/bokeh/bokeh/releases) - [Changelog](https://github.com/bokeh/bokeh/blob/branch-3.0/CHANGELOG) - [Commits](https://github.com/bokeh/bokeh/compare/2.3.3...2.4.2) --- updated-dependencies: - dependency-name: bokeh dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * Update requirements-tests.txt * Update requirements-tests.txt * Update requirements-tests.txt * Update bokeh_waveform_plot.py Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Loose packaging requirement (#810) * Exclude S1 as triggering peak (#779) Co-authored-by: Shingo Kazama <kazama@isee.nagoya-u.ac.jp> Co-authored-by: Jingqiang Ye <jyy2139@columbia.edu> * fix dep. order * sort alphabetically * Restore #760 Patch peaks merging (#767) * Update definition array_valued (#757) * use channel tight coincidence level (#745) Co-authored-by: Evan Shockley <eshockley@physics.ucsd.edu> Co-authored-by: Shingo Kazama <kazama@isee.nagoya-u.ac.jp> Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> * Two manual boundaries (updated 11/24/2021) (#775) Updates classification boundaries for S1 and Se * S2 pattern fit (#780) * add neural tensorflow method chi2 * Revert "Update definition array_valued (#757)" (#812) This reverts commit 23e4eacb4191ae3444df2bdd483795bd93b28026. * Itp test (#813) * can we disable codefactor please * add itp test * Events synchronize (#761) *Add preliminary plugin for synchronized time stamps * Performance update for binomial test (#783) * update binom test * Fix broken matplotlib/minianalyses (#815) * fix broken matplotlib * fix some tests * update tests * remove asserts * Update test_mini_analyses.py * fix multihist syntax * Update matplotlib_utils.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/holoviews_waveform_display.py * Update straxen/analyses/posrec_comparison.py * Update straxen/analyses/posrec_comparison.py * Update straxen/analyses/posrec_comparison.py * Update straxen/analyses/posrec_comparison.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * Update straxen/analyses/bokeh_waveform_plot.py * fix codefactor * sorry sorry for this mess * assert is inverted * this is not log * fix more bugs * deprecate tight layout * add docs * review comments * stupid typo * Remove codefactor (#818) https://xenonnt.slack.com/archives/C016UJZ090B/p1639500799304900 * Rename tight coincidence (#825) * Rename tight coincidence -> tight_coincidence channel, remove previous tight coincidence. * Update help * Remove field * Remove n_hits computation * Update the test * URLConfig take protocol for nested keys (#826) * adjust take protocol for lists * one more test, thanks Yossi Co-authored-by: Yossi Mosbacher <joe.mosbacher> Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Restore #757 (#814) Co-authored-by: Johanna Jakob <56300925+jjakob03@users.noreply.github.com> Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> Co-authored-by: tianyu zhu <tz2263@columbia.edu> * Bump wemake-services/wemake-python-styleguide from 0.15.3 to 0.16.0 (#829) Bumps [wemake-services/wemake-python-styleguide](https://github.com/wemake-services/wemake-python-styleguide) from 0.15.3 to 0.16.0. - [Release notes](https://github.com/wemake-services/wemake-python-styleguide/releases) - [Changelog](https://github.com/wemake-services/wemake-python-styleguide/blob/master/CHANGELOG.md) - [Commits](https://github.com/wemake-services/wemake-python-styleguide/compare/0.15.3...0.16.0) --- updated-dependencies: - dependency-name: wemake-services/wemake-python-styleguide 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> * Unittest for DAQreader (#828) * add daq_reader_test * add review comments * remove the erease option, it absolutely is one big horrible idea * fix review comments * Fix nv testing data (#830) * Another try at codefactor (#831) Let's give it another try, other tools have their own issues too * Move URLConfig cache to global dictionary (#822) * Adds size_of function for cache Co-authored-by: Yossi Mosbacher <joe.mosbacher> Co-authored-by: Joran Angevaare <joranangevaare@gmail.com> Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * Add test for filter_kwargs (#837) Co-authored-by: Yossi Mosbacher <joe.mosbacher> * Update CorrectedAreas (instead of EnergyEstimates) (#817) * Update CorrectedAreas (instead of EnergyEstimates) * Changed CorrectedAreas and EnergyEstimates to URL configs * Added new fields cs2_wo_elifecorr and cs2_wo_time_corr * Using bodega for EnergyEstimates option * Extend URL configs and CMT Co-authored-by: Yossi Mosbacher <joe.mosbacher@gmail.com> Co-authored-by: Yossi Mosbacher <joe.mosbacher> Co-authored-by: Joran Angevaare <jorana@nikhef.nl> Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> * Fix codefactor issues (#832) Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> * use URL configs for NeuralNets (#821) * use URL configs for NeuralNets * placeholders * whoops * add test * review comments * small bug * fix tests * remove scaffolding * 100% COVERAGE :tada: * one line more * Update test_plugins.py * review * Update test_utils.py * fix tests and todos * Update tests/test_posrec_plugins.py * git scrambelled commit * Update url_config.py * Normalized line endings (#833) (#838) * Bump panel from 0.12.5 to 0.12.6 in /extra_requirements (#842) Bumps [panel](https://github.com/holoviz/panel) from 0.12.5 to 0.12.6. - [Release notes](https://github.com/holoviz/panel/releases) - [Changelog](https://github.com/holoviz/panel/blob/master/CHANGELOG.md) - [Commits](https://github.com/holoviz/panel/compare/v0.12.5...v0.12.6) --- updated-dependencies: - dependency-name: panel 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> * Bump zstd from 1.5.0.2 to 1.5.0.4 in /extra_requirements (#844) Bumps [zstd](https://github.com/sergey-dryabzhinsky/python-zstd) from 1.5.0.2 to 1.5.0.4. - [Release notes](https://github.com/sergey-dryabzhinsky/python-zstd/releases) - [Commits](https://github.com/sergey-dryabzhinsky/python-zstd/compare/v1.5.0.2...v1.5.0.4) --- updated-dependencies: - dependency-name: zstd 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> * Make v1 2 0 (#849) * Up history * Bump version: 1.1.3 → 1.2.0 * Bump hypothesis from 6.29.0 to 6.31.6 in /extra_requirements (#846) Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.29.0 to 6.31.6. - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.29.0...hypothesis-python-6.31.6) --- 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> * Bump xarray from 0.20.1 to 0.20.2 in /extra_requirements (#847) Bumps [xarray](https://github.com/pydata/xarray) from 0.20.1 to 0.20.2. - [Release notes](https://github.com/pydata/xarray/releases) - [Changelog](https://github.com/pydata/xarray/blob/main/HOW_TO_RELEASE.md) - [Commits](https://github.com/pydata/xarray/compare/v0.20.1...v0.20.2) --- updated-dependencies: - dependency-name: xarray 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> * Bump wfsim from 0.5.11 to 0.5.12 in /extra_requirements (#843) Bumps [wfsim](https://github.com/XENONnT/wfsim) from 0.5.11 to 0.5.12. - [Release notes](https://github.com/XENONnT/wfsim/releases) - [Changelog](https://github.com/XENONnT/WFSim/blob/master/HISTORY.md) - [Commits](https://github.com/XENONnT/wfsim/compare/v0.5.11...v0.5.12) --- updated-dependencies: - dependency-name: wfsim 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> * Bump dask from 2021.11.2 to 2021.12.0 in /extra_requirements (#841) Bumps [dask](https://github.com/dask/dask) from 2021.11.2 to 2021.12.0. - [Release notes](https://github.com/dask/dask/releases) - [Changelog](https://github.com/dask/dask/blob/main/docs/release-procedure.md) - [Commits](https://github.com/dask/dask/compare/2021.11.2...2021.12.0) --- updated-dependencies: - dependency-name: dask 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> * Update requirements.txt (#852) * Bump scipy from 1.7.1 to 1.7.3 in /extra_requirements (#840) Bumps [scipy](https://github.com/scipy/scipy) from 1.7.1 to 1.7.3. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.7.1...v1.7.3) --- updated-dependencies: - dependency-name: scipy 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> * Bump packaging from 20.8 to 21.3 in /extra_requirements (#845) Bumps [packaging](https://github.com/pypa/packaging) from 20.8 to 21.3. - [Release notes](https://github.com/pypa/packaging/releases) - [Changelog](https://github.com/pypa/packaging/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pypa/packaging/compare/20.8...21.3) --- updated-dependencies: - dependency-name: packaging 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> * add read the docs config (#861) * add read the docs config * Update .readthedocs.yaml * one file * Pin documentation requirements (#862) * Add cmt tests and fix bug in apply_cmt_version (#860) * Add cmt tests and fix bug in apply_cmt_version * fix bug in url * Make dog happy * Add test for offline context * Skip offline text if no db * Implement Yossi's suggestion * Small typo in comment * just some bookkeeping * add comments Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * new release * Bump version: 1.2.0 → 1.2.1 * Tests for `common.py` fix #741 (#856) * Fix common.py test * simplify * solve #741 * also load from mem * Update common.py * Add `strax.Context` documentation, fix #439 (#851) * fix #439 * fix source * Update build_context_doc.py * add bokeh to wiki test (#857) * Test for rucio-documents in the rundb (#858) * add test for rucio docs * revert change * fix comments * reduce testing time * one small test * Test for Mongo-down/uploader (#859) * add down/uploader tests * fix last line * Bump psutil from 5.8.0 to 5.9.0 in /extra_requirements (#872) Bumps [psutil](https://github.com/giampaolo/psutil) from 5.8.0 to 5.9.0. - [Release notes](https://github.com/giampaolo/psutil/releases) - [Changelog](https://github.com/giampaolo/psutil/blob/master/HISTORY.rst) - [Commits](https://github.com/giampaolo/psutil/compare/release-5.8.0...release-5.9.0) --- updated-dependencies: - dependency-name: psutil 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> * Bump scikit-learn from 1.0.1 to 1.0.2 in /extra_requirements (#869) Bumps [scikit-learn](https://github.com/scikit-learn/scikit-learn) from 1.0.1 to 1.0.2. - [Release notes](https://github.com/scikit-learn/scikit-learn/releases) - [Commits](https://github.com/scikit-learn/scikit-learn/compare/1.0.1...1.0.2) --- 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> * Bump hypothesis from 6.31.6 to 6.34.1 in /extra_requirements (#868) Bumps [hypothesis](https://github.com/HypothesisWorks/hypothesis) from 6.31.6 to 6.34.1. - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](https://github.com/HypothesisWorks/hypothesis/compare/hypothesis-python-6.31.6...hypothesis-python-6.34.1) --- 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> * Bump nbsphinx from 0.8.7 to 0.8.8 in /extra_requirements (#871) Bumps [nbsphinx](https://github.com/spatialaudio/nbsphinx) from 0.8.7 to 0.8.8. - [Release notes](https://github.com/spatialaudio/nbsphinx/releases) - [Changelog](https://github.com/spatialaudio/nbsphinx/blob/master/NEWS.rst) - [Commits](https://github.com/spatialaudio/nbsphinx/compare/0.8.7...0.8.8) --- updated-dependencies: - dependency-name: nbsphinx 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> * Bump peaklets version (#873) * Bump peaklets version * Update peaklet_processing.py Co-authored-by: Joran Angevaare <jorana@nikhef.nl> * new version * Bump version: 1.2.1 → 1.2.2 * Bump numpy (#876) * Update requirements.txt * Update requirements.txt * Update requirements.txt * update test * typo * sort by alpha. * fix end * Update requirements-tests.txt * make new release for req. update * Bump version: 1.2.2 → 1.2.3 * fix action * Another WFSim `<->` CMT patch (#865) * just another hack for WFSim<3CMT * alternative suggestion * reveert * revert please * keep wfsim hack working as expected Co-authored-by: Yossi Mosbacher <joe.mosbacher> * introduce development branch * Tests for WFSim contexts (#855) * test for wfsim contexts * fix typo * how are you even supposed to pass these arguments?! * maybe this is the right syntax? Super convoluted.. * skip no db test * fix some leftovers * get ready for new release * Bump version: 1.2.3 → 1.2.4 * test with py3.10 (#878) * test with py3.10 * bump tf * Update pytest.yml * pin keras * fix test for wfsim * differently * Update pytest.yml * clean instructins * remove scaffolding * another try * simplify pandas * fix typo * skip HV * fix dtype * remove fixme error * bump numba (#880) * Tests for scada interface (#877) * Add additional tests * Add additional tests * Add additional tests * Update scada.py * add some more Co-authored-by: Joran R. Angevaare <jorana@nikhef.nl> * bumpversion * Bump version: 1.2.4 → 1.2.5 * Fix online monitor test (#882) * Update test_mongo_interactions.py * i love codefactor? * bumpversion * Bump version: 1.2.5 → 1.2.6 * fix typo * Delete update context collection (#883) * Delete update context collection * Delete create-utilix-config.sh * update zenodo * update github actions (#884) * URLConfig documentation (#863) * document urlconfigs * comment on URL argument order * change order Co-authored-by: Yossi Mosbacher <joe.mosbacher> Co-authored-by: Joran Angevaare <jorana@nikhef.nl> Co-authored-by: ahiguera-mx <ahiguera-mx@fried.rice.edu> Co-authored-by: Aaron Higuera <64651045+ahiguera-mx@users.noreply.github.com> Co-authored-by: Giovanni Volta <38431109+GiovanniVolta@users.noreply.github.com> Co-authored-by: GiovanniVolta <gvolta@dali-login1.rcc.local> Co-authored-by: Daniel Wenz <43881800+WenzDaniel@users.noreply.github.com> Co-authored-by: Tuan Khai Bui <82461188+tuankhaibui@users.noreply.github.com> Co-authored-by: Keita Mizukoshi <mzks@stu.kobe-u.ac.jp> Co-authored-by: Evan Shockley <eshockley@physics.ucsd.edu> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: tianyu zhu <tz2263@columbia.edu> Co-authored-by: Daniel Wenz <dwenz@students.uni-mainz.de> Co-authored-by: Shingo Kazama <kazama@isee.nagoya-u.ac.jp> Co-authored-by: Shengchao Li <li4006@purdue.edu> Co-authored-by: Shengchao Li <scli@dali-login2.rcc.local> Co-authored-by: Kexin Liu <lkx21@mails.tsinghua.edu.cn> Co-authored-by: Kexin Liu <kexinliu@dali-login1.rcc.local> Co-authored-by: Jianyu Long <38538701+Jianyu010@users.noreply.github.com> Co-authored-by: Jingqiang Ye <jyy2139@columbia.edu> Co-authored-by: Daniel Wenz <dwenz@kabelmail.de> Co-authored-by: Luisa Hoetzsch <hoetzsch@mpi-hd.mpg.de> Co-authored-by: Luisa Hoetzsch <hoetzsch@dali-login1.rcc.local> Co-authored-by: Luisa Hoetzsch <luisa.hoetzsch@mpi-hd.mpg.de> Co-authored-by: Diego Ramírez García <diego.ramirez@physik.uni-freiburg.de> Co-authored-by: Johanna Jakob <56300925+jjakob03@users.noreply.github.com> Co-authored-by: Ricardo Peres <rperes@physik.uzh.ch> Co-authored-by: Lutz Althüser <account@l-althueser.de> Co-authored-by: Yossi Mosbacher <joe.mosbacher@gmail.com> Co-authored-by: Dacheng Xu <xdc17@mails.tsinghua.edu.cn> Co-authored-by: Dacheng Xu <xudctron@gmail.com> Co-authored-by: Knut Dundas Morå <kdm2160@columbia.edu> Co-authored-by: Yue Ma <3124558229@qq.com> Co-authored-by: Shenyang Shi <ss6109@columbia.edu>
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Many tests are failing over in base_environment since we actually test there in the analysis environment (particularly containing rucio). I think this try except block should fix.