Release Notes#

vrelease#

Features#

Breaking changes#

Bugfixes#

Documentation#

Deprecations#

Stability, Maintainability, and Testing#

v23.12.0#

Features#

Bugfixes#

v23.11.1#

Bugfixes#

v23.11.0#

Features#

  • Operations on binned variables with a data array content buffer now also work with slices of binned variables #3282.

  • Reduced per-bin overhead in many operations involving binned variables by about 20 milliseconds per 1 million bins #3282.

  • It is now possible to construct Scipp variables from Numpy arrays with up to 6 dimensions for arbitrary memory layouts and any number of dimensions for c-contiguous memory layouts. The limit used to be ndim <= 4. This also improves performance in many cases #3284.

Breaking changes#

  • All items of datasets must have the same dimensions now #3199.

  • The runtime configuration has been removed #3254.

  • The deprecated function open_hdf5 and to_hdf5 have been removed in favor of load_hdf5 and save_hdf5 #3300.

Bugfixes#

  • scipp.testing.assert_identical() now compares the alignment of coordinates #3242.

  • Fixed overflow in variances with large integers #3262.

  • Fixed reduction operations for data arrays containing vectors with masks #3276.

  • Fixed scipp.where() to work with most dtypes #3276.

  • Event-centric arithmetic now uses the correct dtype in the result #3278.

  • Fixed a serious bug where operations on, e.g., transposed binned data resulted in corrupt coord, mask, and attr values of the bin contents #3282.

  • min and max now return not-a-number if any input element is not-a-number instead of ignoring that element #3299.

Documentation#

  • Removed the “What’s new” page because it had not been updated in a while and Scipp changes less drastically now #3296.

Deprecations#

  • scipp.DataArray.attrs and all related methods and properties have been deprecated #3227.

v23.08.0#

Features#

  • Improve performance when binning or grouping into many bins #3215.

Breaking changes#

  • Built-in legacy plotting support has been removed, as per prior deprecation, in favor of Plopp #3200.

Bugfixes#

  • Update units library to fix various small issues #3203.

v23.07.0#

Features#

  • Added alignment flag to Variable #3144.

  • Handle alignment of coordinates in operations #3153.

  • sc.compat.from_pandas now has additional arguments #3169.

  • Added sc.io.load_csv #3169.

Breaking changes#

  • Coordinates are no longer converted to attributes when slicing or by transform_coords. Instead, they become unaligned #3153.

Bugfixes#

  • Fixed label based indexing for arrays with a single element in the sliced dimension #3171.

  • Fixed scipp.show in the presence of bin-edge coords that have been sliced out #3178.

  • Fixed in-place mod function for float #3179.

v23.05.0#

Features#

  • scipp.Dataset now supports assign_coords, which updates or inserts the given coordinates to the scipp.Dataset #3110.

  • scipp.DataArray now supports assign_coords/ assign_masks/ assign_attrs, which updates or inserts the given coordinates/masks/attributes to the scipp.DataArray #3110.

  • Fixed performance issues for datetime64 operations #3123.

  • The HDF5 writer and reader now supports builtin types (e.g. int, str) and numpy types (e.g. np.ndarray, np.int64) as data group items #3124.

  • scipp.DataGroup reduction- and shape operations now handle items of lower dimensionality more consistently. Operations will thus work in more situations, rather than raise exceptions #3136.

Bugfixes#

  • Fix bug in scipp.lookup() raising an exception in arithmetic operations with unrelated coords #3112.

v23.03.2#

Bugfixes#

v23.03.1#

Features#

  • Added __ifloordiv__ to Variable and DataArray #3101.

Bugfixes#

  • Fix bug that caused scipp.testing.strategies.variables to produce negative variances #3100.

  • Fix the source of segmentation faults coming from caching the NumPy module in Variable.value #3105.

Deprecations#

  • scipp.geometry.position has been moved to scipp.spatial.as_vectors, the original function is deprecated #3094.

  • scipp.geometry.rotation_matrix_from_quaternion_coeffs has been deprecated without replacement #3094.

v23.03.0#

Features#

Breaking changes#

  • Plopp is now the default plotting backend #3076.

  • open_hdf5 and to_hdf5 have been renamed to load_hdf5 and save_hdf5, respectively, #3081.

  • Removed scipp.matrix and scipp.matrices. Use functions in scipp.spatial to construct more specialized variables, #3098.

Bugfixes#

  • Fix access to value of 0-D variable with “spatial transform” dtypes using the value property. Previously this raised an exception if the dtype was affine_transform3, translation3, or rotation3 #3033.

  • Fix coords.keys() and coords.items() to compare underlying dicts (same for masks and attrs) #3064.

Documentation#

Deprecations#

Stability, Maintainability, and Testing#

  • Switched to black for Python code formatting #3070.

Contributors#

Simon Heybrock a, Neil Vaytet a, Jan-Lukas Wynen a, and Sunyoung Yoo a

v23.01.0#

Features#

  • Added new data structure scipp.DataGroup, a more flexible version of Dataset that does not enforce alignment and supports nesting.

  • Added support for arbitrary unit, degrees Celsius and other special units #2931.

  • scipp.Dataset now supports drop_coords, which returns scipp.Dataset without the given coordinate by names #2940.

  • scipp.DataArray now supports drop_coords/ drop_masks/ drop_attrs, which returns scipp.DataArray without the given coordinates/masks/attributes names by names #2940.

  • Added clear, copy and popitem to the .coords, .masks, and .attrs accessors #3014.

Breaking changes#

  • The HDF5 format changed to accommodate more units, old files can still be loaded but new ones cannot be loaded with an old version of Scipp #2931.

  • Implicit and explicit broadcasting of operands with variances in operations was disabled. This introduces correlations that Scipp cannot handle and would therefore silently underestimate uncertainties. Instead a scipp.VariancesError is raised now #2895.

  • The .value and .variance properties now return numpy scalars for numeric types. This will not affect the majority of use cases but may break some edge cases, in particular isinstance checks. #2962

Bugfixes#

  • Fix a bug in scipp.hist() and scipp.bin(), leading to assignment of records with very large coord values outside the bin boundaries to a bin #2923.

  • Fix a bug in open end slicing of bins, in case the given right/left end is smaller/bigger than the min/max value of the slicing target, it uses the given end instead of min/max for the open end #2933.

  • Fix issue with events close to upper or lower bin bounds getting dropped by scipp.lookup() with edges that form a “linspace” #2942.

  • Fix minor issue with events close to bin bounds getting assigned to the wrong bin by scipp.lookup() with edges that form a “linspace” #2942.

  • Fix two memory usage and performance issue that affected certain cases of scipp.hist() #2977.

  • Fix bounds check in integer-array indexing, which previously silently skipped out-of-range indices #2986.

Documentation#

Deprecations#

Stability, Maintainability, and Testing#

  • Added type check of masks during binary operations of scipp.DataArray to provide easier error messages.

Contributors#

Simon Heybrock a, Neil Vaytet a, Jan-Lukas Wynen a, and Sunyoung Yoo a

v22.11.0 (November 2022)#

Features#

  • Added scipp.elemwise_func() for defining custom transformations of input variables based on a Python function compiled via numba.cfunc #2886.

Breaking changes#

  • The SciPy wrappers integrate, interpolate, ndimage, optimize, and signal were moved into the scipp.scipy submodule #2881.

Deprecations#

  • Scipp is migrating to use Plopp instead of a built-in plotting solution. The latter is now deprecated. Scipp v23.03.0 (March 2023) and all later versions will use Plopp by default. The built-in plotting solution is deprecated and will be removed (at the earliest) in Scipp v23.08.0 (August 2023) without further warning.

Contributors#

Simon Heybrock a, Neil Vaytet a, and Jan-Lukas Wynen a

v0.17.0 (October 2022)#

Features#

  • scipp.Bins now supports __getitem__, providing a shorthand for extracting events based on a coord value or value interval. This is equivalent functionality to label-based indexing for dense data but considers the coordinates of the underlying bin content #2831.

  • Much faster obj.bins.concat operations in presence of many bins #2825.

  • When mapping between many input and output bins: Avoid huge memory use and slow performance in use of scipp.bin() and scipp.group() when only entire bins are combined (rather than splitting bins based on bin content coordinates). This avoids a number of cases where Python kernel used to crash since Scipp ran out of memory #2827.

  • scipp.sum() now also accepts a sequence of dimension labels #2827.

  • Added aliases for units to customize string formatting and support user defined units #2855.

  • Add pip (PyPI) packages for Python 3.11.

Breaking changes#

  • Changed how units are stored in HDF5 files. Old files can still be loaded but new files cannot be loaded by an old scipp #2836.

  • Removed support for custom units as implemented by LLNL/Units. They were only usable because of an oversight #2843.

Bugfixes#

  • Fix an issue in the setup of automatic bin edges when giving a bin count to scipp.bin(), scipp.hist(), and scipp.rebin(). This lead to a minuscule shift in the resulting edges, which is irrelevant in most cases, but results in events at the lower bin bound to be placed in a correct but lower bin than expected #2838.

  • Fix runtime configuration not loading a file int he working directory #2848.

  • Fix bug in py:func:scipp.compat.from_pandas with non-string names #2851.

Documentation#

Deprecations#

Stability, Maintainability, and Testing#

Contributors#

Simon Heybrock a, Gregory Tucker a, Neil Vaytet a, and Jan-Lukas Wynen a

v0.16.4 (September 2022)#

Bugfixes#

  • Fix missing support for comparison for spatial dtypes such as affine_transform3 #2821.

  • Fix scipp.spatial.rotations() to support creation of quaternion arrays with more than 1 dimension #2822.

v0.16.2 (August 2022)#

Bugfixes#

  • Fix for pythreejs-2.4.0.

  • Fix ipython display for ipywidgets>=8

v0.16.0 (August 2022)#

Features#

Breaking changes#

  • The plots are no longer interactive by default, standard Matplotlib rules now apply (the inline static backend is the default). Use %matplotlib widget for interactive plots #2671.

  • The copy method of groupby has been removed. Use advanced indexing instead #2676.

Bugfixes#

  • Binary arithmetic operations such as x + x of x * x, i.e., with both operands the same, now handle correlations correctly and result in the correct variances in the output #2709.

  • Made __sizeof__ and related functions more accurate #2705.

  • 1-D entries with identical dimensions but different coordinate units are no longer plotted on the same axes #2728.

  • Fixed size estimates for slices of binned variables #2719.

  • Coords and other dict-like types now raise exceptions when modifying during iteration instead of causing a segfault #2719.

  • Data arrays with missing coords can now be plotted using the experimental plotting #2748.

  • Fix a bug in the argument detection when using setitem in combination with value-based slicing #2750.

  • Fixed broken profile plot on 3-D data #2746.

  • Fixed broken boolean-indexing and sort operations on arrays that contain binned data #2759.

  • transform_coords now works with datasets with only coordinates but no data #2755.

  • Fixed a bug when using scipp.hist() on a Dataset that contains binned data #2764.

  • Fixed the rename methods to also rename bin coords and attrs of binned data #2774.

  • Fixed the rename_dims methods which failed to check for conflicting bin-edge coords of length 2 failing outside the object’s dimensions #2775.

Performance#

  • Advanced indexing is now much faster.

  • Sorting is now much faster.

Contributors#

Simon Heybrock a, Neil Vaytet a, and Jan-Lukas Wynen a

v0.15.0 (July 2022)#

Features#

  • Added conversion from Scipp objects to Xarray objects (previously only converting from Xarray to Scipp was available) #2624.

  • Added option for a more compact string format of variables #2625.

  • Overhauled and streamlined usability of functions related to binning, grouping, and histogramming with additional features such as automatic bin edges and histogramming ignoring NaN values. See scipp.bin(), scipp.group(), scipp.hist(), scipp.nanhist(), and scipp.rebin() #2633.

  • Added support for histogramming and binning variables, in addition to existing support for data arrays #2678.

  • Added keyword argument syntax to scipp.transform_coords() for more concise user experience in simple single-step transformations #2670.

  • Generalized scipp.lookup() to also support non-histogram functions for value lookup, with supported modes “previous” and “nearest”. Also adding support for custom fill values #2681.

  • Added possibility to pass keyword arguments to rename_dims, matching the signature of rename #2689.

  • Python’s builtin conversion to “bool” using __bool__ is now supported for 0-D boolean variables. This makes the results of comparison usable with assert or if #2695.

Breaking changes#

  • scipp.optimize.curve_fit() now raises ValueError if the input variance contains a 0 #2620.

  • Replaced the widget-based scipp.table() viewer with a simpler pure-HTML table #2613.

  • scipp.flatten() now drops mismatching bin edge coordinates instead of raising a BinEdgeError #2652.

  • The targets argument of scipp.transform_coords() is not position-only #2670.

  • scipp.lookup() now uses NaN as fill value for floating-point valued functions (for points out of bounds or masked points).

    Integral-valued functions are unchanged (using 0 as before). See also new argument for custom fill values #2681.

Bugfixes#

  • Fix bug where coordinates in were dropped by scipp.transform_coords() with keep_*=False even through they were specified as targets #2642.

  • Fix segmentation fault in scipp.bin() when binning in 2 or more dimensions with certain coordinate values #2644.

  • Fix issue with events close to upper or lower bin bounds getting dropped by scipp.bin() and scipp.histogram() when binning with edges that form a “linspace” #2644.

  • Fix minor issue with events close to bin bounds getting assigned to the wrong bin by scipp.bin() and scipp.histogram() when binning with edges that form a “linspace” #2644.

  • Fix issues with copying binned structured data or fields of binned structured data #2650.

  • Fix various missing dimension and/or shape checks when slicing with a condition variable #2657.

  • Fix serious bug in scipp.bin() that was introduced in scipp-0.12.0. This corrupts data when binning into more than 65536 at a time #2680.

  • Fix issue in scipp.lookup(), which led to ignored masks in case of integral function values with non-linspace coordinates #2681.

  • Fix reduction operations of 0-D binned data, which previously returned the input unchanged #2685.

Documentation#

  • Remove two ancient tutorials.

Deprecations#

Stability, Maintainability, and Testing#

Contributors#

Simon Heybrock a, Gregory Tucker a, Neil Vaytet a, and Jan-Lukas Wynen a

v0.14.0 (May 2022)#

Features#

  • Added argument max_rows to scipp.table() #2526.

  • Added support for converting scalars to builtin objects via int() and float() #2529.

  • Reduced time of initial import of Scipp by delaying imports of optional dependencies #2535.

  • Added an update method to Coords, Attrs, Masks, and Dataset #2558.

  • Support dtype=vector3 in scipp.isinf() and scipp.isfinite() #2593.

  • Added support for passing any dict-like objects or iterables of tuples as coords, attrs, and masks arguments to initializers of scipp.DataArray and scipp.Dataset #2603.

  • Added support for passing any dict-like objects or iterables of tuples as the data argument to the initializer of scipp.Dataset #2603.

  • Added support for DataArray and Dataset in more reduction operations (e.g. scipp.max()) #2600.

  • Added support for masks in reductions of binned data #2608.

  • Added more reduction operations to the .bins property (e.g. scipp.Bins.max()) #2608.

  • Reduce effect of rounding errors when converting units #2607.

Breaking changes#

Bugfixes#

  • Fix scipp.isclose() and scipp.allclose() to support arguments without a unit #2528.

  • scipp.to_unit() avoids a rounding problem when converting datetimes. This previously led to errors, e.g., of about 300 nanoseconds when converting a current (2020s) datetime64 from seconds to nanoseconds #2533.

  • Fix handling of keyword arguments in scipp.optimize.curve_fit(). They were previously checked for conflicts but otherwise ignored #2545.

  • Fix a segmentation fault in scipp.bin() when grouping by a variable with 0 elements #2590.

  • Fix scipp.nanmean() for dtype=vector3. Previously this did not ignore NaN elements as it should. scipp.isnan() is affected by the same fix. Previously it always returned False for dtype=vector3 #2593.

Documentation#

  • Added new tutorial: RHESSI Solar Flares 2536.

  • Added new tutorial: From tabular data to binned data 2580.

  • Added documentation of our docstring format 2546.

  • Configured docs builds to enable plots generated by docstrings and added a custom extension to automate usage of the matplotlib plot directive 2609.

Contributors#

Simon Heybrock a, Neil Vaytet a, and Jan-Lukas Wynen a

v0.13.1 (April 2022)#

Bugfixes#

v0.13.0 (March 2022)#

Features#

  • Added is_edges method to coords, attrs, masks, and meta properties of DataArray and Dataset #2469.

  • Added support for arithmetic of scipp.DataArray and scipp.Dataset with builtin int and float #2473.

  • Added advanced indexing support: integer array indexing #2502.

  • Added advanced indexing support: boolean variable indexing #2477.

  • Added or exposed to Python more functions for boolean logic #2480, #2489.

  • broadcast now supports scipp.DataArray, and the sizes argument #2488.

  • The output of squeeze() is no longer read-only 2494.

  • Added support for spatial dtypes to scipp.to_unit() and scipp.isclose() #2498.

Breaking changes#

  • Changed format of Scipp native HDF5 files to allow for UTF-8 characters in coord names; migration script: tools/migration/scipp-0.13-hdf5-files.py #2463.

Bugfixes#

  • Fix permissions error for configuration file where users do not have write access to their config dir #2482.

  • Fix plotting of data with multi-dimension bin-edge coordinate in the presence of a mask that does not depend on the bin-edge dimension #2505.

  • Fix incorrect axis labels in plots with datetime tick labels #2507.

  • Fix segfault when calling scipp.GroupByDataArray.copy() or scipp.GroupByDataset.copy() with out of bounds index #2511.

Contributors#

Simon Heybrock a, Neil Vaytet a, and Jan-Lukas Wynen a

v0.12.1 (February 2022)#

Bugfixes#

  • Fix a plotting bug when 2d data has masks and a coord with no unit #2470.

Contributors#

Simon Heybrock a, Neil Vaytet a, and Jan-Lukas Wynen a

v0.12.0 (February 2022)#

Features#

Breaking changes#

  • The configuration option config['plot']['padding'] is now called config['plot']['bounding_box'], no action is required if it was never modified #2389.

  • scipp.rebin() now applies masks that depend on the rebinning dimension to avoid “growing” effect on masks which previously resulted in masking more than intended #2383.

  • The unit attribute now distinguishes None from dimensionless #2395 and #2417.

    • For number-like dtypes the default is dimensionless (unchanged) whereas all other dtypes such as strings default to None (new).

    • bool (used for masks) is not considered number-like and the default unit is None.

    • Comparison operator results now use None as unit of their output.

    • When integers without unit are used as indices, the new scipp.index() can be used to create a scalar variable without unit.

  • scipp.spatial.rotations_from_rotvecs() has been changed to taking a variable input rather than separate values/dims/units.

  • scipp.NotFoundError error has been replaced with KeyError in Python #2416.

  • Some functions now raise scipp.DimensionError instead of scipp.NotFoundError #2416.

Bugfixes#

  • Fix scipp.full(), which previously converted or attempted to convert all values to float64 unless the dtype was specified explicitly #2395.

  • Fix scipp.transform_coords() for sliced binned data, used to raise an exception #2406.

  • Fix 1d plots y-axis limits when toggling log-scale with buttons and fix 2d plot colorbar when Inf values #2426.

  • Fix bug leading to datasets dims/shape modification after failed item insertion #2437.

  • Fix a plotting bug when 2d data has y coord associated with dimension x #2446.

  • Fix plotting with custom tick labels of dtype=datetime64 which previously raised an exception #2449.

Contributors#

Simon Heybrock a, Neil Vaytet a, Tom Willemsen b, c, and Jan-Lukas Wynen a

v0.11.0 (January 2022)#

Features#

  • Added new datatypes for representing spatial transformations: affine_transform3, rotation3, and translation3. Each of these can be combined and applied to the existing vector datatype.

  • Added support for slicing without specifying a dimension (only for 1-D objects) #2321.

  • Added scipp.interpolate.interp1d() as convenience wrapper of the scipy functions of the same name #2324.

  • Added scipp.integrate.trapezoid() and scipp.integrate.simpson() as convenience wrappers of the scipy functions of the same name #2324.

  • Added unit property to obj.bins for getting and setting unit of bin elements #2330.

  • Added scipp.optimize.curve_fit() as convenience wrappers of the scipy function of the same name #2350.

  • Added scipp.signal.butter() and scipp.signal.sosfiltfilt() as wrappers of the scipy functions of the same name #2356.

  • Added scipp.Variable.to() and scipp.DataArray.to() as a convenience function for simultaneously converting dtype and units.

  • Added scipp.datetime(), scipp.datetimes(), and scipp.epoch() to conveniently construct variables containing datetimes #2360.

  • Added camera option for 3-D scatter plots to control camera position and the point the camera is looking at #2361.

  • Allow more interoperability between scipp.DType and other ways of encoding dtypes #2373.

Breaking changes#

  • Minor change in behavior of dimension renaming in transform_coords, new behavior documented in Coordinate transformations. Most use cases are unaffected. #2319.

  • sc.spatial.transform.as_rotvec has been moved to scipp.spatial.rotation_as_rotvec()

  • sc.spatial.transform.from_rotvec has been moved to scipp.spatial.rotations_from_rotvecs(), and now returns a rotation data type rather than a matrix. For consistency with other transformation creation functions, rotations_from_rotvecs now takes values, dims, and unit separately.

  • The matrix dtype matrix_3_float64 has been renamed to linear_transform3, and should now be constructed with scipp.spatial.linear_transform().

  • The vector dtype vector_3_float64 has been renamed to vector3.

  • Scipp’s logger is no longer preconfigured, this has to be done by the user #2372.

  • Data types are now attributes of the scipp.DType class and the scipp.dtype module has been removed #2373.

Bugfixes#

  • Fix coordinate and attribute comparisons to treat NaN (not-a-number) values as equal, which previously prevented most operations with data arrays or datasets that contained NaN values in their coordinates or attributes #2331.

  • Fix incorrect result from sc.bin when rebinning an inner dimension to a multi-dimensional coordinate #2355.

Deprecations#

Contributors#

Simon Heybrock a, Neil Vaytet a, Tom Willemsen b, c, and Jan-Lukas Wynen a

v0.10.0 (December 2021)#

Features#

  • Add support for auto-completions for slices and metadata access in Jupyter #2304.

  • Start publishing pip packages to PyPI in addition to conda packages.

Bugfixes#

  • Fix kernel crash or poor performance when using bin or da.bins.concat along an inner dimension in the presence of a long outer dimension #2278.

  • Improved the rendering of cut slices in 3d plots where some strange artifacts could appear depending on the order in which the pixels were being drawn #2287.

Deprecations#

  • The deprecated events property has been removed.

Stability, Maintainability, and Testing#

  • Improve a number of error messages #2286 and #2301, by Jan-Lukas Wynen.

Contributors#

Simon Heybrock a, Neil Vaytet a, Tom Willemsen b, c, and Jan-Lukas Wynen a

v0.9.0 (November 2021)#

Features#

  • Added erf and erfc functions #2195.

  • Reduction operations such as sum, nansum, and cumsum of single precision (float32) data now use double precision (float64) internally to reduce rounding errors #2218.

  • Added bins_like for broadcasting dense variables to binned variables, e.g., for converting bin coordinates into event coordinates #2225.

  • groupby now also supports grouping by attributes instead of just by coordinates #2227.

  • Added concat to replace concatenate. In contrast to the now deprecated concatenate, concat supports concatenation of lists of objects instead of just two objects #2232.

  • Added dim property to Variable and DataArray #2251.

  • Added preconfigured logging support including a widget for output to notebooks #2255, #2267.

  • Added reduce for setting up reductions across a list of inputs #2267.

  • Added toggle buttons for hiding/showing the 3d axes and outline box in 3d plots #2265.

Breaking changes#

  • Name changes of arguments of transform_coords #2267.

  • Graphs in transform_coords must now name all outputs of functions or else the outputs are discarded #2267.

Bugfixes#

  • Fix bugs in rebin if data and/or edges had strides other than 1 along rebinned dimension, typically only occurring with multi-dimensional (ragged) coordinates #2211.

  • Fix exception that was thrown when importing empty datasets from HDF5 files using open_hdf5 #2216.

  • Fix exception in astype when called with binned data that does not require conversion #2222.

  • Fix bug in concatenate that could lead to masks being shared with input rather than being copied #2232.

  • Fix exception in bin when binning in a new dimension but with an existing bin coord #2237.

  • Fix exception when plotting data with masks in presence of multi-dimensional coords #2269.

Deprecations#

  • concatenate and groupby(..).concatenate are deprecated. Use concat and groupby(..).concat instead.

Stability, Maintainability, and Testing#

  • More thorough unit testing for low-level code underlying most operations on dense as well as binned data #1900, by Jan-Lukas Wynen.

  • Switch to Jupyter Book theme for documentation, avoiding a number of issues with the RTD theme #2233, by Neil Vaytet.

  • Added benchmark suite to allow for identification of performance regressions, by Samuel Jones.

  • Added code coverage tooling to allow for identification of dark spots in our test coverage, by Simon Heybrock.

Contributors#

Owen Arnold b, c, Simon Heybrock a, Samuel Jones b, Neil Vaytet a, Tom Willemsen b, c, and Jan-Lukas Wynen a

v0.8.3 (September 2021)#

Bugfixes#

  • Fix serious correctness bug in groupby.sum and groupby.mean #2200.

v0.8.0 (September 2021)#

Features#

  • Added sizes argument to zeros, ones, and empty variable creation functions #1951.

  • Slicing syntax now supports ellipsis, e.g., da.data[...] = var #1961.

  • Added bound method equivalents to many free functions which take a single Variable or DataArray #1969.

  • Variables can now be constructed directly from multi dimensional lists and tuples #1977.

  • Plotting 1-D event data is now supported #2018.

  • Add transform_coords for (multi-step) transformations based on existing coords, with support of event coords #2058.

  • Add from_pandas and from_xarray for conversion of pandas dataframes, xarray data arrays and dataset to Scipp objects #2054.

  • Added full and full_like variable creation functions #2069.

  • islinspace can now take multi-dimensional variables as long as you pass the dimension to be checked #2094.

  • Added a power function and support for the ** operator #2083.

  • Binned data now has a mean method as well as sum, which returns the mean of each element within a bin.

  • Add scipp.constants module for physical constants #2101.

  • Add scipp.spatial.transform module providing from_rotvec and as_rotvec #2102.

  • Add cross function to complementing existing dot function #2109.

  • The fields property of structured variables (vector and matrix dtypes) can now be iterated and provides dict-like access #2116.

  • Add where function.

  • Unary operations such as sin are now available for datasets as well #2112.

  • Add rounding functions floor, ceil, and round that performs similarly to NumPy equivalents #2147.

Breaking changes#

  • Changed names of arithmetic functions to match NumPy’s names: plus → scipp.add(), minus → scipp.subtract(), times → scipp.multiply() #1999.

  • Changed Variable init method, all arguments are keyword-only, special overloads which default-initialize data were removed #1994.

  • The axes keyword arg of plot has been removed. Use labels to define labels and transpose to transpose instead #2018.

  • The redraw method of plots does not support replacing data variables of data arrays any more, but only updates of data values #2018.

  • Made most arguments of DataArray and Dataset constructors keyword-only #2008.

  • Made arguments of many functions keyword-only, e.g. constructors of DataArray and Dataset, bin, and atan2 #1983, #2008, #2012.

  • astype and to_unit now copy the input by default even when no transformation is required, use the new copy argument to avoid #2016.

  • rename_dims does not rename dimension-coords any more, only dims will be renamed #2058.

  • rename_dims does not modify the input anymore but returns a new object with renamed dims #2058.

  • issorted and islinspace return a variable of type boolean instead of a boolean #2094.

  • Multi-dimensional coordinates are no longer associated with their inner dimension, which affects the behavior when slicing: Such coords will no longer be turned into attributes during a slice operation on the inner dimension #2098.

  • buckets.map(histogram, da.data, 'time') has been replaced by lookup(histogram, 'time')[da.bins.coords['time']] #2112.

  • rebin and histogram now support any unit. plot() guesses which resampling mode to use and provides a button to toggle this #2180.

Bugfixes#

  • Various fixes in plot, see #2018 for details.

  • Operations with Python floats to long interpret the float as 32-bit float #2101.

  • Multi-dimensional bin-edge coordinates may now be edges for a non-inner dimension #2098.

Deprecations#

  • The events property is deprecated and is scheduled for removal with v0.9.

Contributors#

Owen Arnold b, c, Simon Heybrock a, Samuel Jones b, Greg Tucker a, Neil Vaytet a, Tom Willemsen b, c, and Jan-Lukas Wynen a

v0.7.2 (September 2021)#

Bugfixes#

  • Fix serious correctness bug in groupby.sum and groupby.mean #2200.

v0.7.0 (June 2021)#

Features#

  • Licence changed from GPLv3 to BSD-3-Clause.

  • Can now control the position and visibility of the legend in 1d plots with plot(da, legend={"show": True, "loc": 4}) #1790.

  • Added zeros_like, ones_like and empty_like functions #1864.

  • sort is now considerably faster for data with more rows #1872.

  • Added numpy-like linspace, logspace, geomspace, and arange variable creation functions #1871.

  • to_unit now supports binned data #1841.

  • broadcast now returns a view instead of copying #1861.

  • fold now returns a view instead of copying #1861.

  • fold now works for binned data #1861.

  • flatten now returns a view of the input buffer if the input data is contiguous #1861.

  • Add redraw method to plot which enables an easy update on a figure when the underlying data has been modified #1907.

  • Several improvements for work with (3-D position) vectors and (3-D rotation) matrices #1905:

    • Add creation functions vector, vectors, matrix, matrices.

    • Direct creation and initialization of 2-D (or higher) arrays of matrices and vectors is now possible from NumPy arrays.

    • Fix extremely slow initialization of array of vectors or matrices from NumPy arrays.

    • The values property now returns a NumPy array with ndim+1 (vectors) or ndim+2` (matrices) axes, with the inner 1 (vectors) or 2 (matrices) axes corresponding o the vector or matrix axes.

    • Vector or matrix element can now be accessed and modified directly using the new fields property of Variable. The fields property provides properties x, y, z (for variables containing vectors) or xx, xy, …, zz (for matrices) that can be read as well as set.

  • Reduction operations such as sum and mean are now also multi-threaded and thus considerably faster #1923.

Bugfixes#

  • Profile plots are no longer disabled for binned data with only a single bin in the 3rd dimension #1936.

Breaking changes#

  • Scipp’s data structures now behave mostly like normal nested Python objects, i.e., copies are shallow by default #1823.

  • filter and split removed. Identical functionality can be achieved using groupby and/or slicing.

  • reshape has been removed. Use fold and flatten instead #1861.

  • geometry.x, geometry.y, and geometry.z have been removed. Use the Variable.fields property instead #1925.

Contributors#

Owen Arnold b, c, Simon Heybrock a, Matthew D. Jones b, c, Neil Vaytet a, and Jan-Lukas Wynen a

v0.6.1 (April 2021)#

Bugfixes#

  • map and scale operations as well as histogram for binned data now also work with datetime64 #1834.

  • bin now works on previously binned data with 2-D edges, even if the outer dimensions(s) are not rebinned #1836.

  • bin and histogram now work with int32-valued coordinates and support binning with int64- or int32-valued bin edges.

v0.6.0 (March 2021)#

Features#

  • Add sizes properties, an ordered dict to lookup the size of a specific dimension #1636.

  • Add access to data, coords, attrs, and masks of bins via the bins property, e.g., obj.bins.coords['x'] #1752.

  • Add more functions for data arrays that were previously available only for variables #1638 #1660.

  • Add named versions of operators such as logical_and #1660.

  • Add to_unit to converter variables, e.g., between m and mm #1756.

  • Add modulo operations #1660.

  • Add scaling operations for Variables of type vector_3_float64.

  • sum and mean implemented for Variables of type vector_3_float64.

  • Add fold and flatten which allow to reshape dimensions of a Variable or DataArray #1676.

  • It is now possible to reshape a Variable also with sc.reshape(var, sizes={'x': 2, 'y': 3}), in addition to sc.reshape(var, dims=['x', 'y'], shape=(2, 3)).

  • Add ones and empty creation functions, similar to what is known from NumPy #1732.

  • scipp.neutron has been removed and is replaced by scippneutron

  • scipp.neutron (now scippneutron)

    • Support unit conversion to energy transfer, for inelastic TOF experiments #1635.

    • Support loading/converting Mantid WorkspaceGroup, this will produce a dict of data arrays #1654.

    • Fixes to support loading/converting McStasNexus files #1659.

  • isclose added (is_approx removed). Fuzzy data comparison isclose is an analogue to NumPy’s isclose

  • stddevs added #1762.

  • Support for datetime

    • sc.dtype.datetime64 with copy-less casting between NumPy and Scipp where possible. #1639

    • Binning with datetime edges #1739

Breaking changes#

  • The plot module has been renamed to plotting, and plotting is now achieved via sc.plot(data). Wrapper functions superplot, image, and scatter3d have been dropped #1696.

  • Properties dim, begin, end, and data of the bins property of and object are now accessible as a dict via obj.bins.constituents.

  • scipp.neutron has been removed and is replaced by scippneutron

  • scipp.neutron (now scippneutron)

  • is_equal renamed identical

  • is_linspace renamed islinspace

  • is_sorted renamed issorted

  • is_approx superseded by isclose. is_approx removed.

  • Removed support for facility-specific convert_with_calibration and load_calibration

Contributors#

Matthew Andrew, Owen Arnold, Simon Heybrock, Matthew D. Jones, Andrew McCluskey, Neil Vaytet, and Jan-Lukas Wynen

v0.5.0 (January 2021)#

Features#

  • New profile plotting functionality where one of the slider dimensions can be displayed as a profile in a subplot (1-D and 2-D projections only).

  • Sliders have a thickness slider associated with them and can be used to show slices of arbitrary thickness.

  • Can hide/show individual masks on plots.

  • Can toggle log scale of axes and colorbar with buttons in figure toolbar.

  • Add binned data support, replacing “event list” dtypes as well as “realign” support.

  • Plotting of event data (binned data) with dynamic resampling with “infinite zoom” functionality.

  • Value-based slicing support.

  • Possibility to plot Scipp objects using my_data_array.plot() in addition to the classical plot() free function.

  • Support for saving and loading Scipp data structures to HDF5.

  • More functions such as nanmean for better handling of special values such as INF and NaN.

  • TBB (multi-threading) support for MacOS.

  • scipp.neutron

    • Improved instrument view, e.g., with buttons to align camera with an axis.

    • Experiment logs (previously using Mantid’s Run) are now represented as native Scipp objects, e.g., as scalar attributes holding a data array representing a time-series such as a temperature log.

    • Support conversion of mantid.MaskWorkspace.

Breaking changes#

  • Dataset does not have a masks property any more. Use ds['item'].masks instead.

  • Dataset does not support attributes any more.

  • DataArray and dataset item attributes are now are now handled as “unaligned” coords. Use ds['item'].coords or array.attrs to access these.

  • API for log scale on axes and colors has changed. Use plot(da, scale={'tof': 'log'}) to set a log scale on a coordinate axis, and use plot(da, norm='log') to have a log image colorscale or a log y axis on a 1d plot.

  • vmin and vmax now represent absolute values instead of exponents when norm='log'.

  • The ipympl matplotlib backend is now required for using inside Jupyter notebooks. This has been added as a dependency. It is also the only interactive backend that works in JupyterLab.

  • Removed support for event_list dtype, use binned data instead.

  • Removed support for “realigned” data. This is replaced by the more flexible and generic support for “binned” data.

Contributors#

Matthew Andrew, Owen Arnold, Thibault Chatel, Simon Heybrock, Matthew D. Jones, Daniel Nixon, Piotr Rozyczko, Neil Vaytet, and Jan-Lukas Wynen

v0.4 (July 2020)#

Features#

  • New realign functionality.

  • Support for event-filtering.

  • Support for subtraction and addition for (realigned) event data.

  • Non-range slicing changed to preserve coords as attrs rather than dropping

  • scipp.neutron: Instrument view with advanced geometry support, showing correct pixel shapes.

  • Instrument view working on doc pages.

  • Made it simpler to add new dtype and support transform for all types.

  • Comparison functions such as less, greater_equal, …

  • all and any can work over all dimensions as well as explicitly provided dimension argument

  • It is now possible to convert between Scipp objects and Python dictionaries using to_dict and from_dict.

  • New functions collapse and slices can be use to split one or more dimensions of a DataArray to a dict of DataArrays.

  • You can now inspect the global object list of via the repr for Scipp showing Datasets, DataArrays and Variables

  • Internal cleanup and documentation additions.

Notable bug fixes#

  • Several fixes in the plotting (non-regular bins, colorbar limits, axes tick labels from unaligned coordinates, etc…)

Breaking changes#

  • Coord and attributes names for neutron data have been standardized, now using hyphens instead of underscore, except for subscripts. Affected examples: pulse-time (previously pulse_times), source-position (previously source_position), sample-position (previously sample_position), detector-info (previously detector_info).

  • scipp.neutron.load must use advanced_geometry=True option for loading detector-info and pixel shapes.

  • Normalization of event data cannot be done directly any more, must use realign.

  • Plotting variances in 2D has been removed, and the API for using matplotlib axes has been simplified slightly, since we no longer have axes for variances:

    • Before: plot(..., mpl_axes={"ax": myax0, "cax": myax1})

    • After: plot(..., ax=myax0, cax=myax1)

  • Plot with keyword argument collapse has been removed in favor of two more generic free functions that return a dict of data arrays that can then directly be passed to the plot function:

    • collapse(d, keep='x') slices all dimensions away to keep only 'x', thus always returning 1D slices.

    • slices(d, dim='x') slices along dimension 'x', returning slices with ndim-1 dimensions contaiing all dimensions other than 'x'.

Contributors#

Owen Arnold, David Fairbrother, Simon Heybrock, Daniel Nixon, Pawel Ptasznik, Piotr Rozyczko, and Neil Vaytet

v0.3 (March 2020)#

  • Many bug fixes and small additions

  • Multi-threading with TBB for many operations.

  • Performance improvements in hotspots

  • Remove Dim labels in favor of plain strings. Connected to this, the labels property for data arrays and datasets has been removed. Use coords instead.

  • Start to support out arguments (not everywhere yet)

  • scipp.neutron: Instrument view added

Contributors in this release: Owen Arnold, Simon Heybrock, Daniel Nixon, Dimitar Tasev, and Neil Vaytet

v0.2 (December 2019)#

  • Support for masks stored in DataArray and Dataset.

  • Support for groupby, implementing a split-apply-combine approach as known from pandas.

  • Enhanced support for event data:

    • Histogramming with “weighted” data.

    • Multiplication/division operators between event data and histogram.

  • Enhanced plotting support:

    • Now focussing on matplotlib.

    • Multi-dimensional plots with interactive sliders, and much more.

  • Significant performance improvements for majority of operations. Typically performance is now in the same ballpark as what the memory bandwidth on a single CPU core can support.

  • Fancy _repr_html_ for quick views of datasets in Jupyter notebooks.

  • Conda packages now also available for Windows.

  • scipp.neutron gets improved converters from Mantid, supporting neutron monitors, sample information, and run information stored as attributes.

Contributors in this release: Owen Arnold, Igor Gudich, Simon Heybrock, Daniel Nixon, Dimitar Tasev, and Neil Vaytet

v0.1 (September 2019)#

This is the first official release of scipp. It is not yet meant for production-use, but marks a big step for us in terms of usability and features. The API may change without notice in future releases.

Features:

  • All key data structures (Variable, DataArray, and Dataset).

  • Slicing.

  • Basic arithmetic operations.

  • Physical units.

  • Propagation of uncertainties.

  • Event data.

Limitations:

  • Limited performance and no parallelization.

  • Numerous “edge cases” not supported yet.

  • While tested, probably far from bug-free.

Contributing Organizations#