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Merge with sportran master#1

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ppegolo merged 176 commits intoppegolo:masterppegolo/sportran:masterfrom sissaschool:mastersissaschool/sportran:masterCopy head branch name to clipboardSep 16, 2024

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Commits

Commits on Mar 23, 2020

• Fixed bug in MDSample for 1-dim 1-component trajectories

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• Frequency conversion moved to mdsample.

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• Merge branch 'uniform_freq_units' into core_redesign

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Commits on Mar 27, 2020

• Fixes to freq-psd routines. Several name changes and minor style edits.

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Commits on May 9, 2020

• Author: Noam Bernstein <[email protected]>

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Commits on May 14, 2020

• Move tools.py to md/tools/ and split them into different files

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Commits on May 16, 2020

• Drop Python 2 support

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• Remove empty useless returns

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Commits on May 18, 2020

• Fix missing imports and HeatCurrent.__repr__ bug

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• HeatCurrent: j renamed traj, THz defaults freq units

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• Defined _get_builder method

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Commits on May 19, 2020

• New MDSample.resample method, substitutes resample_currents

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• Current base class introduced, new obj definition, units moved

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• Change of variables spelling: NFREQS, DF_THZ

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Commits on May 25, 2020

• Merge pull request #29 from lorisercole/core_redesign-current

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Commits on May 26, 2020

• Setup CI workflow with GitHub Actions, remove tox

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• Apply pre-commit to all files

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Commits on May 30, 2020

• Created Plotter class that contains staticmethods to plot various graph.

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Commits on Jun 3, 2020

• Moved GUI_plot_periodogram, GUI_resample_current, GUI_plot_cepstral_spectrum

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• fixed previous commit issue + reformatting

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• Fix data file path in tests -- need to implement fixtures

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Commits on Jun 4, 2020

• Moved plotter.py and plot_style.mplstyle to new plotter folder in thermocepstrum

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• New input parameters: KAPPA_SCALE, MAIN_CURRENT_INDEX, MAIN_CURRENT_FACTOR

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Commits on Jun 6, 2020

• Started units method

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Commits on Jun 16, 2020

• Created GUIPlotter and CurrentPlotter sublcasses to organize

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Commits on Jul 1, 2020

• Merge branch 'plot_reorganization' into merge

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• pre-commit run --all-files

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• Merge remote-tracking branch 'origin/fix_26_units' into merge

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Commits on Jul 2, 2020

• selected version of yapf, updated jupyter notebook examples

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• added simple fixture for tests data path

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• Started units method

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• Added simple fixture for tests data path

  

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• Merge branch 'core_redesign' into fix_27_ci_setup

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• Merge branch 'fix_27_ci_setup' into core_redesign

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• Updated dependencies, updated notebook examples

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• added more data regressions fixtures

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• added test for cli (does nothing at the moment)

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Commits on Sep 24, 2020

• New current-specific units system

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• Merge branch 'fix_26_units' into core_redesign

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• Merge branch 'core_redesign' into develop

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Commits on Sep 26, 2020

• Fix bug with units and KAPPA_SCALE

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Commits on Sep 27, 2020

• Patch to recover CLI tests

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Commits on Sep 30, 2020

• fixed tests (maybe)

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• fixed tests??

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• test fixed ???

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• giuro di avere buone intenzioni

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• la speranza è l'ultima a morire

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• Fixed Spinboxes - added textvariables to control the values

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• Fix imports, modules loaded, logger

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• Update package requirements

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Commits on Oct 1, 2020

• Merge pull request #31 from lorisercole/fix_import_utils

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• added tests for binary output

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• added authors in README.md

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Commits on Oct 4, 2020

• Updated fileManager - fixed issue #33

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Commits on Oct 5, 2020

• Fixed issue #36

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Commits on Oct 11, 2020

• Updated fileManager UI

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Commits on Oct 14, 2020

• Fixed issue #35

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• Fix fstar_analysis

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Commits on Oct 16, 2020

• Fixed issue #34 - check P* plot

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• More fixes to issue #34

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Commits on Nov 9, 2020

• Removed GUIPlotter class and related method.

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Commits on Nov 10, 2020

• Add AttributeDict class

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• Add SportranBinaryFile

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• analysis CLI: group & sort arguments, update docs

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Commits on Nov 11, 2020

• Reorganize & clean analysis CLI - resample plot=False is now the default

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Commits on May 25, 2021

• Merge branch 'develop' of github.com:lorisercole/thermocepstrum into develop

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• Merge branch 'binary_output' into develop

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Commits on Jun 16, 2021

• updated default selection of units in the GUI

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Commits on Jul 14, 2021

• Units constants and ElectricCurrent definition (#48)

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Commits on Jul 16, 2021

• New Plotter system and CurrentPlotter implemented

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• Create plot styles and assign them to each Plotter type

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Commits on Jul 19, 2021

• Remove style load in plotter, fix function names

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Commits on Jul 26, 2021

• Added class StressCurrent to compute viscosity

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Commits on Jul 27, 2021

• Create MDSamplePlotter, cleanup old plot functions

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Commits on Jul 28, 2021

• Make optional args of ploter functions keyword-only

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Commits on Jul 29, 2021

• Fix analysis script to use CLIPlotter functions

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• Update dependencies to fix tests

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• Remove support for Python 3.5

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Commits on Sep 22, 2021

• Merge branch 'develop' into plotter_fix

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Commits on Sep 23, 2021

• bug fix in QE_PW units

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• previous commit made electric qepw units wrong

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Commits on Sep 29, 2021

• preliminary implementation to have all implemented currents and unit into the command line

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Commits on Sep 30, 2021

• pre-commit and tests fixed

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• pre-commit fix (hopefully)

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Commits on Oct 6, 2021

• fixing plots of the gui is started

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• fixed GUI

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• GUI fixed, added arbitrary units into the GUI

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Commits on Oct 8, 2021

• started documentation with sphinx

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Commits on Oct 27, 2021

• working sphinx doc, with basic structure

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Commits on Oct 28, 2021

• added templates for autosummary that now is producing something useful

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• updated documentation generation

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Commits on Nov 4, 2021

• added nbsphinx

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• added test that runs the notebook

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• ooops... forgot to put an absolute path

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• tests should now run

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• added files for readthedocs

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• second test

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• funzionerà?

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Commits on Nov 5, 2021

• forgot two symlinks

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Commits on Nov 17, 2021

• Rebranding

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• Delete .DS_Store

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Commits on Nov 18, 2021

• Updated import names (tc to st)

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Commits on Nov 19, 2021

• pre-commit stuff

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• forgot a THERMOCEPSTRUM

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Commits on Dec 9, 2021

• small adjustments

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• small doc update

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Commits on Dec 10, 2021

• small fix

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Commits on Dec 15, 2021

• Merge pull request #52 from lorisercole/rebranding

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Commits on Dec 16, 2021

• added pyproject.toml

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Commits on Dec 20, 2021

• Update Readme

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Commits on Dec 21, 2021

• Fix file headers

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• Fix examples and review text

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• Small doc edits and __all__ variables

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• Update README

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• Setup GitHub action for automatic push to PyPi

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• Add physical data of NaCl example

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Commits on Jan 5, 2022

• Move MDSample.compute_kappa_multi to Current._compute_psd_multi

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• Fixed tests

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Commits on Jan 7, 2022

• Implement check over ndf_chi distribution for multi-componentcase

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• Move initialization of cospectrum to Current

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• Simplify Current builder, by defining _builder property

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Commits on Jan 11, 2022

• Fix small bug in analysis.py

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• Rename N_COMPONENTS to N_EQUIV_COMPONENTS

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Commits on Jan 12, 2022

• Fix pre-commit hooks

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Commits on Jan 20, 2022

• Manual selection of P*

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• Rename CosFilter to CepstralFilter

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• Manual cepstral cutoff, meaning of aic_Kmin, variable name changes

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• Fix plotter functions

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• Rename dct to cepf

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• Fix GUI: P* selection

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• Update cepstral log output

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• Move deprecated blockanalysis modules

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• renamed MANY_COMPONENTS to MANY_EQUIV_COMPONENTS

  

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• Merge and fix some plots

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Commits on Jan 26, 2022

• Use kappa_units=True as default in plot functions

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Commits on Jan 28, 2022

• added little test for fixed number ok K

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Commits on Feb 23, 2022

• fixed 57

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Commits on Mar 2, 2022

• Improve several GUI labels

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• Update GitHub publish workflow

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• Release SporTran v1.0.0rc1

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Commits on Mar 3, 2022

• Merge pull request #58 from sissaschool/release/1.0.0

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Commits on Mar 8, 2022

• Update pre-commit config

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Commits on Jun 20, 2022

• Move fstar_analysis to current/tools

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• Define Current abstract class, and GenericCurrent

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• Get rid of dlpoly units

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Commits on Jun 25, 2022

• Move example data into examples/data subfolders

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• Improve read_lammps_log

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• Add LAMMPS Silica input/output files

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• Fix tests, add script to regenerate data

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Commits on Jun 27, 2022

• Rename examples, add silica cmdline example

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• Fix TableFile bug

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• read_lammps_log docs and variable change

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• Reorganize i_o folder

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• Add input formats example

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• Fix notebooks test

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Commits on Jun 28, 2022

• add test for new notebook, updated symlinks

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• little update of the documentation

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• update of the units documentation.

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• added small description of folder with lammps example; added jupyter notebook with inputs format example also in docs

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• Fix small typos in documentation

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• Fix label in GUI header selection

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Commits on Jun 29, 2022

• restored some units that were wrongly removed

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• Update metadata, dependencies, and package data

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• Add Python 3.9, 3.10 support & tests

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• Bump SporTran version to 1.0.0rc2

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Commits on Jul 5, 2022

• Add codeowners file

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Commits on Dec 7, 2022

• fixes #66 (#67)

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• fixes #66 (#67)

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• Merge branch 'master' into develop

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Commits on Mar 7, 2023

• fixed python version requirement *

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• Fixes issue with argparse in 3.11

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• Merge pull request #69 from sissaschool/fix-68

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Commits on Apr 13, 2023

• Added support to read data in byte format for ReadLampsLog and

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• Formatting

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Commits on Apr 14, 2023

• Merge pull request #71 from sissaschool/develop

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• Fix release workflow & bump version

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