Code

Plasma restructure#304

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wkerzendorf merged 178 commits intomastertardis-sn/tardis:masterfrom plasma/restructuretardis-sn/tardis:plasma/restructureCopy head branch name to clipboardAug 11, 2015

+12,193-10,805

Commits

Commits on Jun 26, 2015

• adding a new plasma structure

  wkerzendorf

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  851c3a8

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• first attempt to do the networkx plasma

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  f9fb773

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• first tests with the new plasma system

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• still in the phase of adding networkx to plasma

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• added getattr stuff

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• added inpout and getattr

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• added update skeleton

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• added test with atomic data dependency

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• working tests

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• further improvements to the new plasma class.

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• generating plasma overview latex graph

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• added documentation, doesn't quite work yet

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• begin of restructuring atomic api

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• added the atomic data stuff

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• adding Saha ionization to the new plasma

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• transferred most of the plasma functions into the new structure

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• restructuring the documentation system

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• further restructuring to autodetect the inputs from the calculate call signature

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• figuring out ionization calculation

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• calculating lte up to level populations

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• working simple lte plasma - off to write some tests

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• finished tests for general_properties

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• continue to write the tests

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• added test_partition_function script

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• massive change of structure

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• restructure to properties complete

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• fixed the pep8

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• fixed most of the documentation

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• added a stump for BetaSobolev

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• removed transition probabilities module for now

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• Added networkx to conda-requirements

  

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• Added atomic properties tests for plasma.

  

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• Added atomic plasma property tests

  

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• Added atomic plasma property tests

  

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• Added atomic plasma property tests

  

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• Added atomic plasma property tests

  

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• Added atomic plasma property tests

  

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• Added atomic plasma property tests

  

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• Added atomic plasma property tests

  

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• Added tests for plasma ion population properties related to LTE mode

  

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• Added tests for plasma ion population properties related to LTE mode

  

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• Added tests for plasma level population properties.

  

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• Added LTE property collection.

  

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• Added LTE property collection.

  

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• Added LTE property collection.

  

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  8b53491

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• Added LTE property collection.

  

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• Updated tests for plasma partition function properties.

  

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• Finished plasma property tests for now.

  

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• Finished plasma property tests for now.

  

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• Finished plasma property tests for now.

  

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• Work in progress: Replacing plasma_array with LegacyPlasma.

  

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• Tardis now working with new plasma structure (LTE only).

  

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• Attempt to fix Travis error.

  

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• Added LTE to possible radiative rates types in the config.

  

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• Few tweaks.

  

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• Few tweaks.

  

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• Fixing LegacyPlasma montecarlo issue.

  

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• Added montecarlo capabilities.

  

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• Changed electron density property so that it is calculated from the Saha equation rather than by summing over ions.

  

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• Code now converging on correct solution for scatter, downbranch, macroatom with LTE. Some small issues to be addressed.

  

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• Skipping spectrum test.

  

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• Naming convention, fixed spectrum test, new tests.

  

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• Naming convention, fixed spectrum test, new tests.

  

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• Added dilute-lte and nebular ionisation to the new plasma.

  

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• Added dilute-lte and nebular ionisation to the new plasma.

  

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• Added electron temperature property.

  

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• Added electron temperature property.

  

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• Added delta treatment (some minor issues to be resolved).

  

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• Made input of delta_treatment adjustable using config. file.

  

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• Changed how departure_coefficient and chi_0_species are set.

  

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• Made ZetaData a BaseAtomicPlasmaProperty to allow filtering.

  

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• Added warnings for missing ions and fix for missing zetas.

  

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• Made ion_populations BaseAtomicPlasmaProperty.

  

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• Updated module tests.

  

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• Added raise error for missing zeta data.

  

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• finished rebase

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Commits on Jun 29, 2015

• Initial steps.

  

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• testing

  

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• updated the plasma with the new outputs

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• WIP for restructuring the plasma to work with multiple outputs

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Commits on Jul 1, 2015

• in the process of making the multiple outputs into the code

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• seems to work now

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• removed a print statement for debugging

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• Fixes.

  

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• Merge pull request #17 from aoifeboyle/plasma/multiple_outputs

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• Merge pull request #343 from wkerzendorf/plasma/multi_output

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• Added electron_density output to IonNumberDensity property.

  

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• Added electron_density output to IonNumberDensity property.

  

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Commits on Jul 7, 2015

• Changes to tests.

  

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• Merge pull request #344 from aoifeboyle/plasma/multiple_outputs

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• New NLTE system.

  

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• New NLTE system.

  

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• New NLTE system.

  

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Commits on Jul 8, 2015

• Inserted fix for lines/nlte_lines indexing discrepancy.

  

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• Added classical nebular NLTE.

  

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• Re-added collision matrix.

  

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• Fix.

  

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• Fix.

  

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Commits on Jul 9, 2015

• Small fix and tidying up of atomic properties.

  

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• Small fix and tidying up of atomic properties.

  

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Commits on Jul 10, 2015

• Attempt at fix.

  

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• Updated spectrum test.

  

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Commits on Jul 11, 2015

• WIP: Fixed graphs to work with new outputs system, organised tests and properties files, added some latex labels, etc.

  

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Commits on Jul 12, 2015

• Delete test_simple_plasma.py

  

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Commits on Jul 13, 2015

• Changed graph tex file so that the image is generated as a standalone on a correctly sized page automatically.

  

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• Merge branch 'plasma/testing/properties' of github.com:aoifeboyle/tardis into plasma/testing/properties

  

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• Changed graph tex file so that the image is generated as a standalone on a correctly sized page automatically.

  

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• Changed graph tex file so that the image is generated as a standalone on a correctly sized page automatically.

  

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• Organisation of property files, improved graph.

  

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Commits on Jul 15, 2015

• Tardis can now output a plasma formula sheet in .tex format, containing all the formulae used for plasma properties in a particular simulation.

  

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Commits on Jul 16, 2015

• Removed latex file generation for now.

  

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Commits on Jul 29, 2015

• Small fix and tidying up of atomic properties.

  

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• Small fix and tidying up of atomic properties.

  

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• Attempt at fix.

  

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• Updated spectrum test.

  

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• WIP: Fixed graphs to work with new outputs system, organised tests and properties files, added some latex labels, etc.

  

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• Delete test_simple_plasma.py

  

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• Changed graph tex file so that the image is generated as a standalone on a correctly sized page automatically.

  

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• Changed graph tex file so that the image is generated as a standalone on a correctly sized page automatically.

  

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• Changed graph tex file so that the image is generated as a standalone on a correctly sized page automatically.

  

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• Organisation of property files, improved graph.

  

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• Tardis can now output a plasma formula sheet in .tex format, containing all the formulae used for plasma properties in a particular simulation.

  

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• Added more latex formulae. Needed for adding graphs to documentation.

  

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• Rebasing

  

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• Fix.

  

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• Removed unnecessary property - level_population_fraction.

  

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Commits on Jul 30, 2015

• Names.

  

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• WIP: Will fail tests. Change to NLTE structure.

  

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• Changing NLTE.

  

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Commits on Jul 31, 2015

• Combined NLTE options into single property.

  

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• Preventing nlte config contradiction.

  

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Commits on Aug 1, 2015

• Small fix.

  

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• Merge pull request #347 from aoifeboyle/plasma/nlte

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• Merging.

  

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• Few small corrections after rebase with NLTE.

  

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Commits on Aug 3, 2015

• Splitting up atomic properties - WIP.

  

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• Attempt at solution.

  

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• Merge pull request #352 from aoifeboyle/t_electron_issue

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Commits on Aug 4, 2015

• Fixing atomic issues and issues after rebase.

  

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• Merging error.

  

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• Split Lines property into separate outputs.

  

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Commits on Aug 5, 2015

• Hid certain properties in graph.

  

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• Merge pull request #350 from aoifeboyle/plasma/testing/properties

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Commits on Aug 6, 2015

• Merge remote-tracking branch 'upstream/master' into plasma/rebase_master

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• Added formulae to graph.

  

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• Adjusted stimulated emission factor for NLTE.

  

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• Added formulae to graph.

  

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• Adjusted stimulated emission factor for NLTE.

  

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• Merge pull request #362 from aoifeboyle/plasma/nlte

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Commits on Aug 7, 2015

• Added some more formulae.

  

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Commits on Aug 9, 2015

• LTE Plasma Test

  

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• LTE Plasma Test

  

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• Deleted unnecessary files.

  

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Commits on Aug 10, 2015

• Added setup to plasma.

  

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• Added setup to plasma.

  

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• Added setup to plasma.

  

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• Added setup to plasma.

  

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• Added setup to plasma.

  

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• Added setup to plasma.

  

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• Merge pull request #361 from aoifeboyle/plasma/graph

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• Added setup to plasma.

  

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• Added setup to plasma.

  

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Commits on Aug 11, 2015

• LTE Plamsa test change.

  

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• Added NLTE test.

  

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• Added NLTE plasma temperature test.

  

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• Fixed t_electron/t_electrons issue.

  

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• Attempt to fix dataframe multiplication error.

  

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• Attempt to fix dataframe multiplication error.

  

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• Attempt to fix dataframe multiplication error.

  

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• Merge pull request #365 from aoifeboyle/plasma/testing

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• Merge remote-tracking branch 'upstream/master' into plasma/restructure_rebase

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• Import LegacyPlasma

  

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• Removed plasma_array

  

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• Merge pull request #368 from aoifeboyle/plasma/rebase

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• Removed import plasma_array

  

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• Merge pull request #369 from aoifeboyle/plasma/rebase

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• Removed some tests temporarily.

  

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• Merge pull request #370 from aoifeboyle/plasma/rebase

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