v0.9.8

On the road to v1.0! This now includes a testpackage framework to run the old and extended analysator testpackage in CI. Assorted fixes and refactorizations. Lazyloading to speed up startup and modularization to skirt around needing to import matplotlib fully if only using VlsvReader.

Science features:

• Pressure-strain interaction terms
• dense VDF extraction helper functions
• cut3d function AMR grid support

What's Changed

• Image compare by @lassejsc in #356
• Pin sphinx python version so it passes the build by @alhom in #362
• Wrapping matplotlib colormap version checks to use plot.get_cmap by @lassejsc in #360
• Image comparison workflow for generated plots by @lassejsc in #357
• workflow generate_reference_plots.yml by @lassejsc in #366
• Get generate_reference_plots from master by @alhom in #368
• Log exit code after job completion in script by @lassejsc in #369
• Made compare to use the latest verification set by @lassejsc in #370
• Fixes to create_env.py by @lassejsc in #372
• Pressure strain interaction by @plauri in #355
• Fixing the plot_ionosphere default colorbar position, 6h tick and autohide axis ticks by @lassejsc in #363
• Added warning for fluxrope variable in colormap3dslice by @lassejsc in #373
• Hotfix to Numpy 2.x breaking test_variable probing by @alhom in #379
• Lazyloading submodules and moving matplotlib loading inside plot submodule by @lassejsc in #361
• Removing dependency on cbfmtsci in calculuations variable.py by @lassejsc in #380
• Fixes to plot_vdfdiff by @lassejsc in #382
• Added 'limitedsize' flag to boost slow plot_colormap3dslice operations by @plauri in #374
• Horizontal colorbar support for all relevant plot functions with colorbar by @lassejsc in #359
• Added type check for center variable in plot_vdf_profiles by @lassejsc in #381
• Prune duplicate plot outputfile handling by @lassejsc in #371
• read_velocity_distribution_dense added to simply extract dense numpy … by @alhom in #383
• Typo in variable fixed by @lassejsc in #385
• Warns and errors by @alhom in #272
• Fixing the new output file handling to testpackage works as intended. by @lassejsc in #386
• Consolidating testpackage into a single script by @lassejsc in #378
• Renaming workflows by @lassejsc in #391
• Testpackage workflows dispatch by @alhom in #392
• Image compare reduce log spam by @lassejsc in #395
• Fixed if no path is found in the outputfile name the code would make … by @lassejsc in #393
• Fix figsize again by @lassejsc in #398
• fix the linter complaining by @lassejsc in #396
• Added constraint to gen.._verfset script by @lassejsc in #399
• Fixed run_compare not taking pass correctly by @lassejsc in #401
• Added missing latex export to path in verification set generation. by @lassejsc in #402
• Clean up compare by @lassejsc in #394
• Testpackage warnings by @lassejsc in #400
• Testpackage lock and print by @lassejsc in #403
• Fix bug with how get_scaled_units is called by @JonasSuni in #404
• Indexing changes to testpackage by @lassejsc in #405
• Image comparison for testpackage outputs -> CI by @alhom in #389
• image comparison for verification set generation by @lassejsc in #408
• Fixing the workflow for testing old versions of python by @lassejsc in #410
• Image compare for verification set generation and oldest python workflow fix by @lassejsc in #409
• cut3d: Use ids3d to adjust the cell lengths before sampling the box. by @alhom in #411
• Add setthreshold to dense VDF reader function, same as plot_vdf by @alhom in #412
• Function to plot contours along straight cell edges by @lassejsc in #364
• Testpackage image compare tweaks by @lassejsc in #413
• Got rid of get_job_error in favor of getting the error via exit $? and sacct by @lassejsc in #416

Full Changelog: v0.9.7...v0.9.8

v0.9.7

This was envisioned as a bit of a consolidating minor version release before some source reorganization and new features. However, this release is a bit larger, adding a top-level package infrastructure, a prototype VTK backend and quite a bit of minor fixes.

What's Changed

• Bool method to test whether a cell id has a vdf or not by @kstppd in #292
• New versions of magnetopause scripts and a small fix for plot_colormap3dslice by @jreimi in #291
• Enforce Sphinx docstring error and warning fixes by @alhom in #295
• added doc link to readme by @Gekbako in #297
• Guard against double-registration of colormaps in Matplotlib. by @alhom in #298
• Add weekly import test to catch fresh dependency issues (or GitHub Ac… by @alhom in #299
• Filter MPL-included colormaps with a version check by @alhom in #300
• pylab imports replaced with matplotlib.pyplot, as strongly recommended by @alhom in #302
• Pylab deprecation by @alhom in #303
• Vtk interface by @alhom in #296
• Add import guard for vtk module by @alhom in #304
• Population-specific beta_star reducers (non-pop beta_star reducers ar… by @alhom in #305
• Remove unnecessary htg parameter from addArrayFromVlsv by @alhom in #306
• Packagination by @alhom in #301
• Simple matplotlib plotter taking a list of cellids by @ykempf in #307
• Added v5 reducers for the Hall field + keyword for field line colour in plot_colormap by @lturc in #308
• Reducer aliases by @alhom in #284
• Testpackage redux by @alhom in #310
• Added separate plot helpers for the 3 components of current density by @lturc in #311
• Pops init on demand by @alhom in #282
• Updating analysator to a python package structure and renaming to analysator by @alhom in #309
• Ubuntu_20.04 runner is being deprecated. Coverage for Turso system in… by @alhom in #312
• Remove matplotlib dependency from vlsvfile by @alhom in #313
• Explicit reshape to fix numpy broadcast ambiguity by @alhom in #314
• Pointwise time evolution by @alhom in #319
• Allow ionosphere plots without a valid time value. by @ursg in #320
• typos in obliqueshock.py corrected: the polynome input has VuHT inste… by @mattia-l in #318
• Try using ensurepip instead of pip instal upgrade, see UH#768 by @alhom in #322
• obliqueshock.py and obliqueshock_nif.py revised by adding docstring-s… by @mattia-l in #324
• Plot_vdf pathological binning fix by @alhom in #327
• Add mlt check on vg and ig grid, field line oc values by @taoshi-117 in #321
• Roll dev fwd by @alhom in #328
• Plot vdf v fallthrough by @alhom in #329
• Fixed error with plot_colormap3Dslice by @hoilijoki in #331
• Reader interp problem by @alhom in #332
• Hotfix for missing variable read trying to close undeclared fptr by @alhom in #333
• Jonas cutthrough timeseries script by @JonasSuni in #224
• Added the PLASMA-PEPSC workshop analysator tutorial by Markus to Sphinx by @alhom in #330
• Add option to flip x-axis to plot_colormap and plot_colormap3dslice by @JonasSuni in #317
• plot_colormap3dslice overlays fSaved, fluxrope and AMR levels by @ykempf in #204
• Flux ropes paper scripts by @ykempf in #339
• Blockspercell reads, Vbulk reads more comprehensive in plot_vdf and d… by @alhom in #345
• Vlsv time interpolation class by @alhom in #346
• Swap to uv-driven install for Turso by @alhom in #348
• Hotfix for some function call signatures by @alhom in #349

New Contributors

• @Gekbako made their first contribution in #297
• @mattia-l made their first contribution in #318
• @taoshi-117 made their first contribution in #321
• @hoilijoki made their first contribution in #331

Full Changelog: v0.9.6...v0.9.7

What's Changed

• Bool method to test whether a cell id has a vdf or not by @kstppd in #292
• New versions of magnetopause scripts and a small fix for plot_colormap3dslice by @jreimi in #291
• Enforce Sphinx docstring error and warning fixes by @alhom in #295
• added doc link to readme by @Gekbako in #297
• Guard against double-registration of colormaps in Matplotlib. by @alhom in #298
• Add weekly import test to catch fresh dependency issues (or GitHub Ac… by @alhom in #299
• Filter MPL-included colormaps with a version check by @alhom in #300
• pylab imports replaced with matplotlib.pyplot, as strongly recommended by @alhom in #302
• Pylab deprecation by @alhom in #303
• Vtk interface by @alhom in #296
• Add import guard for vtk module by @alhom in #304
• Population-specific beta_star reducers (non-pop beta_star reducers ar… by @alhom in #305
• Remove unnecessary htg parameter from addArrayFromVlsv by @alhom in #306
• Packagination by @alhom in #301
• Simple matplotlib plotter taking a list of cellids by @ykempf in #307
• Added v5 reducers for the Hall field + keyword for field line colour in plot_colormap by @lturc in #308
• Reducer aliases by @alhom in #284
• Testpackage redux by @alhom in #310
• Added separate plot helpers for the 3 components of current density by @lturc in #311
• Pops init on demand by @alhom in #282
• Updating analysator to a python package structure and renaming to analysator by @alhom in #309
• Ubuntu_20.04 runner is being deprecated. Coverage for Turso system in… by @alhom in #312
• Remove matplotlib dependency from vlsvfile by @alhom in #313
• Explicit reshape to fix numpy broadcast ambiguity by @alhom in #314
• Pointwise time evolution by @alhom in #319
• Allow ionosphere plots without a valid time value. by @ursg in #320
• typos in obliqueshock.py corrected: the polynome input has VuHT inste… by @mattia-l in #318
• Try using ensurepip instead of pip instal upgrade, see UH#768 by @alhom in #322
• obliqueshock.py and obliqueshock_nif.py revised by adding docstring-s… by @mattia-l in #324
• Plot_vdf pathological binning fix by @alhom in #327
• Add mlt check on vg and ig grid, field line oc values by @taoshi-117 in #321
• Roll dev fwd by @alhom in #328
• Plot vdf v fallthrough by @alhom in #329
• Fixed error with plot_colormap3Dslice by @hoilijoki in #331
• Reader interp problem by @alhom in #332
• Hotfix for missing variable read trying to close undeclared fptr by @alhom in #333
• Jonas cutthrough timeseries script by @JonasSuni in #224
• Added the PLASMA-PEPSC workshop analysator tutorial by Markus to Sphinx by @alhom in #330
• Add option to flip x-axis to plot_colormap and plot_colormap3dslice by @JonasSun...

v0.9.6

A long-overdue release-freshening. Highlight features:

• Ionosphere mesh handling and plotting
• VlsvWriter features and updates for producing sidecar files
• 3D interpolation and streamline tracing
• fixes for FsGrid decomposition issues
• recursive datareducer listing
• Sphinx autodoc manual at fmihpc.github
• CITATION.cff file

What's Changed

• Remove Julia scripts from Python-based package by @henry2004y in #142
• Bidirectional streamlines, imshow backend for plot_colormap, unique cid helper function by @alhom in #144
• Threeslice by @maximegrandin in #143
• SCM7 by @alhom in #145
• various fixes: colormaps, neighbour indexing, version checks etc by @markusbattarbee in #148
• Fixed bug when op(erator)=0 which resulted in 'pass' instead of … by @maximegrandin in #149
• Adaptation of read_interpolated_variable() to the AMR by @maximegrandin in #140
• Added precipitation integral flux and mean energy DROs by @maximegrandin in #146
• Add gridspec example by @markusbattarbee in #152
• Replaced Python 3.6 string interpolation syntax with Python 2-support… by @alhom in #153
• corrected task indexing in vlsvreader for fsgrids by @markusbattarbee in #159
• Support for printing vlasiator version and config info from VLSV files by @kstppd in #163
• Fixed flux function normalization for fg data, changed config and ver… by @markusbattarbee in #165
• Allow reading vlsv files without a spatialCell or populations. by @ursg in #167
• Fix to construction of some colormaps. by @ykempf in #168
• Up for discussion: Cut_throughs with curves, spectrum calculations, static streamlines vol centering by @alhom in #147
• Added support for blocks with WID=8 by @markusbattarbee in #169
• Extendedmanual matplotlib colormaps inclusion to work the same way as… by @alhom in #170
• Support for ionosphere meshes and plot_ionosphere implementation. by @ursg in #151
• One-line change to plot_threeslice.py, data type issue (list vs. nump… by @kostahoraites in #173
• Fs Grid data interpolation by @kstppd in #164
• No mathrm pascals as non latex units, another fallthrough for variable scaler by @alhom in #175
• Pitch angle update II by @markusbattarbee in #176
• Scaleunits wrapper for old-style compatibility with ionosp. plotting by @alhom in #179
• Imshow plot3dslice by @alhom in #181
• Read vg_b_vol if fg_b is not available for fluxfunction plotting. by @ykempf in #183
• Vlsv postprocessor2 by @alhom in #182
• Readconfig by @kostahoraites in #185
• Fix handling when missing fsgrid metadata. by @ykempf in #186
• vlsvReader improvements by @alhom in #184
• FHA-style jacobian reducer, incl. vg_J. by @alhom in #188
• Refinement support by @lkotipal in #189
• Add the Brenner beta_star by @alhom in #190
• Use numpy dtypes of array instead of checking the first element. by @alhom in #191
• plot_isosurfaces for 3D AMR data by @plauri in #192
• Interpolation optimizations - vectorized versions of get_cellid, read_interpolated_variable by @alhom in #195
• Attribute reading interface and a helper function by @alhom in #197
• VlsvReader.check_variable does not check for datareducers -> plot_iso… by @alhom in #199
• Updated fieldtracer.py by @kostahoraites in #196
• Beta star reducer with old style variable names. by @jreimi in #203
• Fixing np.int deprecation by @alhom in #201
• Write none checks by @alhom in #200
• Neutral (current) sheet plotter by @plauri in #194
• Varname slashes by @alhom in #202
• Went too deep with the varname fixes, reverting a bit. by @alhom in #205
• Workaroundwhen no rhomap exists by @markusbattarbee in #206
• Vlsvreader fixes by @markusbattarbee in #178
• Add hall E reducer, update helper functions to calculate Hall term via charge density instead of mass density by @markusbattarbee in #177
• Fix for minor tick marks in newer matplotlibs by @markusbattarbee in #209
• Write none checks by @alhom in #214
• Prevent misleading return of data from vlsvreader when using ill-formed requests by @markusbattarbee in #213
• Fsgrid decomposition stabilization by @alhom in #211
• Interp irregulars fix by @alhom in #198
• vlsvWriter write function wrapped with a warning, towards forcing wri… by @alhom in #210
• Suppress confusing printouts by @alhom in #217
• RBFInterpolator guarding by @alhom in #216
• Update SCM colormaps to version 8. by @alhom in #218
• Converted deprecated scipy.meshgrid calls to np.meshgrid by @alhom in #230
• added nearest_vdf keyword to vlsvReader's get_cellid() by @kostahoraites in #226
• Close figures after save by @JonasSuni in #240
• Deprecated escape by @alhom in #239
• Enable deprecationwarnings by @alhom in #238
• Interpolation for fg_e field tracing by @kostahoraites in #234
• None/empty string confusion fixes, plus one extra function removed! by @alhom in #232
• Update plot_ionosphere.py by @ArnaudLalague in #233
• Isosurfaces by @plauri in #229
• Scale colorbar tick width and length with thick parameter in plot_col… by @ykempf in #228
• Fix plot vdf centering by @markusbattarbee in #221
• ULF waves filter by @FasilGibdaw in #215
• Projects folder + small patch to plot_VDF by Markus + Diffusion scripts by @MaximeII in #225
• Initial fixes to plot on LUMI / python 3.10.10 and matplotlib 3.9. by @ykempf in #236
• Hotfix for import funnies by @alhom in #242
• LooseVersion removals, latex strings to raw strings by @alhom in #243
• Neighbourhood updates by @alhom in #220
• Added check to catch masked constants in read_interpolated_variable by @JonasSuni in #247
• read_interpolated_fsgrid_variable() bug fix by @kostahoraites in #246
• Added automatic inference for shading in plot_ionosphere, as done in … by @alhom in #251
• several scripts by @kostahoraites in #223
• Fix cmap api change in plot_vdf too. by @ykempf in #253
• Don't have a fixed 100kb sizelimit for the xml footer anymore. by @ursg in #33
• Pickleable fptr by @alhom in #256
• Fix a 6yo typo by @alhom in #257
• A script for calculating non-Maxwellianity by @vetarvus in #255
• Couple of helper functions for handling VDF data: get_velocity_block_… by @alhom in #258
• Add plot_vdfdiff to plot_vdf.py by @ursg in #227
• Bad import fixed, raw strings added to remove deprecationwarnigns by @alhom in #261
• vlsvreader destructor guard for nonexisting fptr by @alhom in #263
• Added rudimentary CI workflow for analysator ...

v0.9.5

A long-overdue release-freshening. Highlight features:

• Ionosphere mesh handling and plotting
• VlsvWriter features and updates for producing sidecar files
• 3D interpolation and streamline tracing
• fixes for FsGrid decomposition issues
• recursive datareducer listing
• Sphinx autodoc manual at fmihpc.github

What's Changed

• Remove Julia scripts from Python-based package by @henry2004y in #142
• Bidirectional streamlines, imshow backend for plot_colormap, unique cid helper function by @alhom in #144
• Threeslice by @maximegrandin in #143
• SCM7 by @alhom in #145
• various fixes: colormaps, neighbour indexing, version checks etc by @markusbattarbee in #148
• Fixed bug when op(erator)=0 which resulted in 'pass' instead of … by @maximegrandin in #149
• Adaptation of read_interpolated_variable() to the AMR by @maximegrandin in #140
• Added precipitation integral flux and mean energy DROs by @maximegrandin in #146
• Add gridspec example by @markusbattarbee in #152
• Replaced Python 3.6 string interpolation syntax with Python 2-support… by @alhom in #153
• corrected task indexing in vlsvreader for fsgrids by @markusbattarbee in #159
• Support for printing vlasiator version and config info from VLSV files by @kstppd in #163
• Fixed flux function normalization for fg data, changed config and ver… by @markusbattarbee in #165
• Allow reading vlsv files without a spatialCell or populations. by @ursg in #167
• Fix to construction of some colormaps. by @ykempf in #168
• Up for discussion: Cut_throughs with curves, spectrum calculations, static streamlines vol centering by @alhom in #147
• Added support for blocks with WID=8 by @markusbattarbee in #169
• Extendedmanual matplotlib colormaps inclusion to work the same way as… by @alhom in #170
• Support for ionosphere meshes and plot_ionosphere implementation. by @ursg in #151
• One-line change to plot_threeslice.py, data type issue (list vs. nump… by @kostahoraites in #173
• Fs Grid data interpolation by @kstppd in #164
• No mathrm pascals as non latex units, another fallthrough for variable scaler by @alhom in #175
• Pitch angle update II by @markusbattarbee in #176
• Scaleunits wrapper for old-style compatibility with ionosp. plotting by @alhom in #179
• Imshow plot3dslice by @alhom in #181
• Read vg_b_vol if fg_b is not available for fluxfunction plotting. by @ykempf in #183
• Vlsv postprocessor2 by @alhom in #182
• Readconfig by @kostahoraites in #185
• Fix handling when missing fsgrid metadata. by @ykempf in #186
• vlsvReader improvements by @alhom in #184
• FHA-style jacobian reducer, incl. vg_J. by @alhom in #188
• Refinement support by @lkotipal in #189
• Add the Brenner beta_star by @alhom in #190
• Use numpy dtypes of array instead of checking the first element. by @alhom in #191
• plot_isosurfaces for 3D AMR data by @plauri in #192
• Interpolation optimizations - vectorized versions of get_cellid, read_interpolated_variable by @alhom in #195
• Attribute reading interface and a helper function by @alhom in #197
• VlsvReader.check_variable does not check for datareducers -> plot_iso… by @alhom in #199
• Updated fieldtracer.py by @kostahoraites in #196
• Beta star reducer with old style variable names. by @jreimi in #203
• Fixing np.int deprecation by @alhom in #201
• Write none checks by @alhom in #200
• Neutral (current) sheet plotter by @plauri in #194
• Varname slashes by @alhom in #202
• Went too deep with the varname fixes, reverting a bit. by @alhom in #205
• Workaroundwhen no rhomap exists by @markusbattarbee in #206
• Vlsvreader fixes by @markusbattarbee in #178
• Add hall E reducer, update helper functions to calculate Hall term via charge density instead of mass density by @markusbattarbee in #177
• Fix for minor tick marks in newer matplotlibs by @markusbattarbee in #209
• Write none checks by @alhom in #214
• Prevent misleading return of data from vlsvreader when using ill-formed requests by @markusbattarbee in #213
• Fsgrid decomposition stabilization by @alhom in #211
• Interp irregulars fix by @alhom in #198
• vlsvWriter write function wrapped with a warning, towards forcing wri… by @alhom in #210
• Suppress confusing printouts by @alhom in #217
• RBFInterpolator guarding by @alhom in #216
• Update SCM colormaps to version 8. by @alhom in #218
• Converted deprecated scipy.meshgrid calls to np.meshgrid by @alhom in #230
• added nearest_vdf keyword to vlsvReader's get_cellid() by @kostahoraites in #226
• Close figures after save by @JonasSuni in #240
• Deprecated escape by @alhom in #239
• Enable deprecationwarnings by @alhom in #238
• Interpolation for fg_e field tracing by @kostahoraites in #234
• None/empty string confusion fixes, plus one extra function removed! by @alhom in #232
• Update plot_ionosphere.py by @ArnaudLalague in #233
• Isosurfaces by @plauri in #229
• Scale colorbar tick width and length with thick parameter in plot_col… by @ykempf in #228
• Fix plot vdf centering by @markusbattarbee in #221
• ULF waves filter by @FasilGibdaw in #215
• Projects folder + small patch to plot_VDF by Markus + Diffusion scripts by @MaximeII in #225
• Initial fixes to plot on LUMI / python 3.10.10 and matplotlib 3.9. by @ykempf in #236
• Hotfix for import funnies by @alhom in #242
• LooseVersion removals, latex strings to raw strings by @alhom in #243
• Neighbourhood updates by @alhom in #220
• Added check to catch masked constants in read_interpolated_variable by @JonasSuni in #247
• read_interpolated_fsgrid_variable() bug fix by @kostahoraites in #246
• Added automatic inference for shading in plot_ionosphere, as done in … by @alhom in #251
• several scripts by @kostahoraites in #223
• Fix cmap api change in plot_vdf too. by @ykempf in #253
• Don't have a fixed 100kb sizelimit for the xml footer anymore. by @ursg in #33
• Pickleable fptr by @alhom in #256
• Fix a 6yo typo by @alhom in #257
• A script for calculating non-Maxwellianity by @vetarvus in #255
• Couple of helper functions for handling VDF data: get_velocity_block_… by @alhom in #258
• Add plot_vdfdiff to plot_vdf.py by @ursg in #227
• Bad import fixed, raw strings added to remove deprecationwarnigns by @alhom in #261
• vlsvreader destructor guard for nonexisting fptr by @alhom in #263
• Added rudimentary CI workflow for analysator by @alhom in https://...

v0.9

Partial support for reading and plotting 3D AMR files is included.