Qcodes

==========================

Breaking Changes:
-----------------

- The deprecated method `DataSetProtocol.cache.to_pandas` has been removed. Use the to_pandas_dataframe or to_pandas_dataframe_dict methods as an alternative. (5626)
- The following long deprecated functions and methods and functionalities have been removed.
Here ordered by top level module for clarity.

* ``qcodes.dataset``

* ``flatten_1D_data_for_plot``

* ``get_shaped_data_by_runid``

* ``get_guids_from_run_spec``

* ``dataset.get_data_as_pandas_dataframe``

* ``dataset.export_path``

* ``_conditional_parameter_set``

* ``_make_nested_setpoints``

* ``_select_active_actions_delays``

* ``_create_measurements``

* ``_extract_paramters_by_type_and_group``

* ``_build_data_query``

* ``get_data``

* ``get_interdeps_from_result_table_name``

* ``get_values``

* ``get_setpoints``

* ``get_guids_from_run_spec``

* ``data_sets``

* ``modify_values``

* ``modify_many_values``

* ``qcodes.instrument_drivers.devices`` / ``codes.parameters``

* ``VoltageDivider``

* ``qcodes.station``

* Support for driver kwarg in yaml config

* Support for limits as a string.

* ``qcodes.utils``

* ``get_qcodes_version`` (5651)
- The following deprecated instrument drivers have been removed:

* ``QDevil.QDac`` Use driver from qcodes_contrib_drivers instead.

* ``Agilent_34400A`` Use Keysight 344xxA drivers or Agilent34401A, Agilent34410A, Agilent34411A instead.

* ``E8267`` use ``AgilentE8267C`` instead.

* ``Agilent_E8527D`` use AgilentE8257D instead.

The following deprecated instrument driver methods have been removed:

* ``KeysightInfiniium`` ``DSOTimeAxisParam.prepare_curvedata``

* ``KeysightB1517A.measure_config`` replaced by ``v_measure_range_config`` and ``i_measure_range_config``

* ``RohdeSchwarz ZNB`` ``RohdeSchwarzZNBChannel.update_traces`` use ``update_lin_traces``


``qcodes.utils.deprecate`` decorator has been soft deprecated. In the future qcodes will use the ``deprecated`` decorator from
the ``typing_extensions`` package (to be part of the std library warnings module from Python 3.13). We recommend anyone else to
do the same. (5655)


Improved:
---------

- `load_by_run_spec` and `load_by_id` may now optionally load the dataset as a DataSetInMem from an exported netcdf file. This avoids reading
from the database potentially resulting in better performance. This option is off by default at the moment but can be turned on by setting
`qcodes.config.dataset.load_from_exported_file` to True. (:pr:`5320`)
- When loading a QCoDeS dataset from a netcdf file using load_from_netcdf and converted to a Xarray dataset using
``to_xarray_dataset`` or ``cache.to_xarray_dataset`` we avoid converting the data to QCoDeS format and back to Xarray format.
This should save time and avoid any potential corner cases when roundtripping the data. (:pr:`5627`)
- Fixed an issue where datasets with categorical setpoints could fail to correctly export to Pandas dataframes or Xarray dataset. (5641)


Improved Drivers:
-----------------

- Lakeshore 335: Add parameter mapping for thermocouple input when using 3060-H option (5652)

==========================

Improved:
---------

- qcodes.Monitor now runs as a daemon thread, resolving issues with closing python or ipython with a running qcodes.Monitor. (5565)
- The use of multi index when exporting to xarray (and netcdf files) has been made smarter
such that any dataset with a known shape (such as those measured by doNd etc) will
never be automatically exported using multi index even in the case of incomplete datasets (i.e. due to an interrupted measurement).
Furthermore `to_xarray_dataset` and `to_xarray_dataarray_dict` have gained a key word argument `use_multi_index` to allow the user
to control the use of multi indexes. (5589)
- The feature of exporting large DataSets to netcdf by writing individual small files and combining them, introduced in QCoDeS 0.41.0 has been made configurable
and turned off by default due to a number of corner cases where the export did not work correctly. The
feature can be enabled when required by setting the config variable `qcodes.config.dataset.export_chunked_export_of_large_files_enabled`
to True and the threshold controlled using `qcodes.config.dataset.export_chunked_threshold` (5618)


Improved Drivers:
-----------------

- Keithley 2450s by default don't block when setting their output level, differing in behavior from the keithley 2400.
I added a manual boolian parameter 'block_during_ramp' which forces a check that the ramp command has been completed when True. (5547)
- Previously, the keithley 2450 driver had an initial value for the output. This is particularly dangerous when reinitializing/recovering from a kernal crash.
Initializing the instrument should leave all parameters unchanged. This PR removes the initial value for the output. (5572)


Under the hood:
---------------

- Fix typo: instrument_drivers.mock_instruments.DummyInstrument::get_idn() now returns dict containing key "serial" instead of "seral" (5579)

Improved:
---------

- Avoid warning from OpenTelemetry when exporting datasets to netcdf. (5529)

==========================

Breaking Changes:
-----------------

- Tests are no longer shipped as part of the qcodes package. The `qcodes.tests`
namespace still exists but will be deprecated in QCoDeS 0.43.0.
`qcodes.test` is deprecated and will be removed in a future release.
To run the tests against an installed version clone git repo to matching tag and
run `pytest tests` from the root of the repo. (5452)


Improved:
---------

- Fixed a bug in the Agilent 8257D where on and off would call a non existing parameter. The methods have been updated to call ``output_enabled``. (5496)
- QCoDeS in memory datasets exported to netcdf with MultiIndexes are now
correctly decompressed when reloaded with load_by_id and friends. (5517)
- Lakeshore 335 Output: Add parameter mapping for input=None (5520)
- The size calculation used to estimate when a dataset should be exported in chuncks has been improved.
This will prevent "small" dataset with many rows from being exported in chuncks when not required. (5523)


New:
----

- Mark python 3.12 as supported and fix deprecation warnings with python 3.12 (5408)
- Mock instruments have been moved from `qcodes.tests.instrument_mocks` to `qcodes.instrument_drivers.mock_instruments` and `DriverTestCase` from
`qcodes.tests.driver_test_case` to `qcodes.extensions`. This is in preparation for no longer shipping `qcodes.tests` as part of the
public api. The previous locations remain functional but will be deprecated after one release. (5486)

==========================

Improved:
---------

- Corrected a bug where non integer step sizes were incorrectly rejected
from parameters without integer validators. (:pr:`5446`)

==========================

Breaking Changes:
-----------------

- The deprecated modules
`qcodes.data`, `qcodes.loop`, `qcodes.actions`, `qcodes.plots`,
`qcodes.measure`, `qcodes.extensions.slack`, `qcodes.utils.magic`, `qcodes.utils.qt_helpers`
`qcodes.utils.slack` has been removed.
The modules can be found in `qcodes_loop <https://github.com/qcodes/qcodes_loop>`_ (#5367)
- Update QCoDeS to work with the upcoming release of numpy 2.0.
The unused attributes `qcodes.utils.types.numpy_non_concrete_floats_instantiable` and
`qcodes.utils.types.numpy_non_concrete_complex_instantiable` have been removed from QCoDeS. (5399)
- The extra install targets qcodes[slack] and qcodes[qtplot] have been removed.
All dependencies on slack and pyqtgraph have moved to qcodes_loop. (5425)


New:
----

- QCoDeS now exports data that isn't measured on a grid to a XArray using `MultiIndex`.
Support for exporting these datasets to NetCDF has also been implemented.
See `this notebook <../examples/DataSet/Working-With-Pandas-and-XArray.ipynb>`__ for additional details. (5334)
- Add a register_name keyword to the ParameterBase constructor. If supplied, this value
will be used to register parameters in datasets instead of the default full_name.
Note that the MultiParameter and ArrayParameter classes do not currently support use
of the register_name. (5381)
- Large datasets are now exported to NetCDF4 using Dask delayed writer.
This avoids allocating a large amount of memory to process the whole dataset at the same time.
Size threshold at the moment is set to approximately 1 GB. (5391)
- The QCoDeS Parameters have now gained the ability to use multiple validators.
See `here <../examples/Parameters/Parameters.ipynb>`__ for examples of how to use this. (5426)

What's Changed
* remove deprecated scrict_concatenate flag from mypy by jenshnielsen in https://github.com/QCoDeS/Qcodes/pull/5366
* Update traitlets requirement from ~=5.9.0 to ~=5.10.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5370
* remove deprecated loop moved to qcodes loop. by jenshnielsen in https://github.com/QCoDeS/Qcodes/pull/5367
* Update matplotlib requirement from ~=3.7.0 to ~=3.8.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5371
* Update numpy requirement from ~=1.25.0 to ~=1.26.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5373
* Update typing-extensions requirement from ~=4.7.0 to ~=4.8.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5375
* Update portalocker requirement from ~=2.7.0 to ~=2.8.2 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5372
* Bump opencensus from 0.11.2 to 0.11.3 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5376
* Update zipp requirement from ~=3.16.2 to ~=3.17.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5377
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/QCoDeS/Qcodes/pull/5378
* Update hypothesis requirement from ~=6.84.0 to ~=6.86.2 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5382
* Stop using __file__ outside tests by jenshnielsen in https://github.com/QCoDeS/Qcodes/pull/4797
* Update hypothesis requirement from ~=6.86.2 to ~=6.87.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5383
* Remove deprecated compare_dictionaries by jenshnielsen in https://github.com/QCoDeS/Qcodes/pull/5385
* Bump actions/checkout from 4.0.0 to 4.1.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5384
* Instrument tests: Avoid leaking state between tests by jenshnielsen in https://github.com/QCoDeS/Qcodes/pull/5360
* Update google-api-core requirement from ~=2.11.0 to ~=2.12.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5386
* Export non gridded data to MultiIndex Xarray and compressed netcdf file by jenshnielsen in https://github.com/QCoDeS/Qcodes/pull/5334
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/QCoDeS/Qcodes/pull/5387
* Update xarray requirement from ~=2023.8.0 to ~=2023.9.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5388
* Update CONTRIBUTING.rst by DCEM in https://github.com/QCoDeS/Qcodes/pull/5389
* Update index.rst (Add instructions about fetching tags) by DCEM in https://github.com/QCoDeS/Qcodes/pull/5390
* Fix pandas type check by jenshnielsen in https://github.com/QCoDeS/Qcodes/pull/5398
* Update cffi requirement from ~=1.15.1 to ~=1.16.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5396
* Bump wcwidth from 0.2.6 to 0.2.7 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5397
* Bump cycler from 0.11.0 to 0.12.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5395
* Bump ruamel-yaml from 0.17.32 to 0.17.33 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5394
* Create Coord before passing it to xarray by jenshnielsen in https://github.com/QCoDeS/Qcodes/pull/5392
* Bump wcwidth from 0.2.7 to 0.2.8 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5400
* Update ipython requirement from ~=8.15.0 to ~=8.16.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5401
* Bump packaging from 23.1 to 23.2 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5404
* Update fonttools requirement from ~=4.42.0 to ~=4.43.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5405
* Update charset-normalizer requirement from ~=3.2.0 to ~=3.3.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5406
* Rework config fixtures by jenshnielsen in https://github.com/QCoDeS/Qcodes/pull/4906
* Update executing requirement from ~=1.2.0 to ~=2.0.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5402
* Bump stack-data from 0.6.2 to 0.6.3 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5403
* remove non local CI job by jenshnielsen in https://github.com/QCoDeS/Qcodes/pull/5407
* Update urllib3 requirement from ~=1.26.15 to ~=2.0.5 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5379
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/QCoDeS/Qcodes/pull/5409
* upgrade type stubs by jenshnielsen in https://github.com/QCoDeS/Qcodes/pull/5410
* Remove main example by jenshnielsen in https://github.com/QCoDeS/Qcodes/pull/5411
* Bump ruamel-yaml from 0.17.33 to 0.17.34 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5413
* Update babel requirement from ~=2.12.1 to ~=2.13.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5414
* Update traitlets requirement from ~=5.10.0 to ~=5.11.2 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5417
* Update nbconvert requirement from ~=7.8.0 to ~=7.9.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5415
* Bump ruamel-yaml-clib from 0.2.7 to 0.2.8 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5416
* Improve logger test by jenshnielsen in https://github.com/QCoDeS/Qcodes/pull/5419
* Use Dask delayed to export large datasets to NetCDF by jenshnielsen in https://github.com/QCoDeS/Qcodes/pull/5391
* Update quantify doc links by ereehuis in https://github.com/QCoDeS/Qcodes/pull/5421
* Bump ruamel-yaml from 0.17.34 to 0.17.35 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5424
* Update slack-sdk requirement from ~=3.22.0 to ~=3.23.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5423
* Update deepdiff requirement from ~=6.5.0 to ~=6.6.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5422
* remove slack and qtplot extra install targets by jenshnielsen in https://github.com/QCoDeS/Qcodes/pull/5425
* Add register_name to register parameters by in datasets by samantha-ho in https://github.com/QCoDeS/Qcodes/pull/5381
* Bump cycler from 0.12.0 to 0.12.1 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5428
* Update bleach requirement from ~=6.0.0 to ~=6.1.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5429
* Update qcodes to support numpy 2.0 by peendebak in https://github.com/QCoDeS/Qcodes/pull/5399
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/QCoDeS/Qcodes/pull/5430
* Update h5py requirement from ~=3.9.0 to ~=3.10.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5431
* Update jupyter-core requirement from ~=5.3.0 to ~=5.4.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5432
* Update mypy requirement from ~=1.5.0 to ~=1.6.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5433
* Allow additional validators on parameter at runtime by jenshnielsen in https://github.com/QCoDeS/Qcodes/pull/5426
* Update jupyter-client requirement from ~=8.3.0 to ~=8.4.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5434
* Update googleapis-common-protos requirement from ~=1.60.0 to ~=1.61.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5435
* Update hypothesis requirement from ~=6.87.0 to ~=6.88.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5437
* Update pillow requirement from ~=10.0.0 to ~=10.1.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5438
* Update pyqt5-sip requirement from ~=12.12.0 to ~=12.13.0 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5436
* Bump actions/checkout from 4.1.0 to 4.1.1 by dependabot in https://github.com/QCoDeS/Qcodes/pull/5439
* add changelog for 0.41.0 by jenshnielsen in https://github.com/QCoDeS/Qcodes/pull/5440

New Contributors
* DCEM made their first contribution in https://github.com/QCoDeS/Qcodes/pull/5389

**Full Changelog**: https://github.com/QCoDeS/Qcodes/compare/v0.40.0...v0.41.0