Do not convert edge labels that are already Strings #115
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GeorgeR227
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Apr 28, 2023
commit 34ea660 Author: AlgebraicJulia Bot <129184742+algebraicjuliabot@users.noreply.github.com> Date: Mon Apr 24 10:39:01 2023 -0400 Set version to 0.2.0 commit f80c513 Author: Micah Halter <micah@mehalter.com> Date: Fri Apr 21 09:49:04 2023 -0400 Remove architecture specific integer types commit 3b3ab55 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Mon Apr 10 14:55:55 2023 -0400 Remove NamedDecapode constructor and compiler commit d2d5cfb Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Mon Apr 10 14:44:44 2023 -0400 Use @decapode macro commit 28d6eb5 Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 27 10:36:20 2023 -0400 Move to organization level github actions commit b3c2476 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Mon Mar 20 14:38:08 2023 -0400 Remove Decapodes_v0.1 files commit a40d7a1 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Tue Apr 18 14:46:50 2023 -0400 Do not convert edge labels that are already Strings (#115) commit 9fc12f8 Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 20 12:08:24 2023 -0400 fix missing compat entries commit 7533c9f Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 20 10:48:23 2023 -0400 add more contributors commit 71a015f Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 20 10:39:05 2023 -0400 fix github action versionf for julia-actions commit 1790e48 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Tue Mar 7 15:28:59 2023 -0500 Import compile from Catlab.Programs (#104) commit e7ffee9 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Wed Feb 22 00:53:43 2023 -0500 Fix old tests and add compatibility specs (#103) * Explicitly give initial primal orientations * Fix MvNormal deprecation * Set some compatibilities commit 69d63b5 Author: GeorgeR227 <78235421+GeorgeR227@users.noreply.github.com> Date: Tue Feb 21 17:46:08 2023 -0500 Gr/parsing overhaul (#95) * Basic literal support * Added Lit data term * Fix composed op2s and add test * Replaced Var for term in \circ decomp * Quick patch for arbitrary multiplication support. * Fixed Tvar's unable to parse on rhs * Added inferred spaces for variables * Do not infer literals as states * Check types are in recognized set * Fixed strange TVar behavior * Fix cache invalidation error and add tests * Add new parsing features tests * Updated visualization for support new parsing. Also cleaned up the parsing code. * Support Literals in simulations * Do not namespace Literals, and do not vcat Nothing * Move CombinatorialSpaces using * Remove erroneous for loop --------- Co-authored-by: Luke Morris <lukelukemorrismorris@gmail.com> Co-authored-by: Luke Morris <70283489+lukem12345@users.noreply.github.com> commit ead3181 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Sat Feb 18 13:07:37 2023 -0500 Add Brusselator Example * Add Brusselator, type, and function resolve * Generate and run first phase of simulation * Change alpha and add gif * Perform second stage of simulation * Showcase using F as a time-varying parameter * Keep compatibility with old CombinatorialSpaces * Demonstrate brusselator on sphere * Clean and change gif frames * Add GLMakie back commit 4027d3e Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Fri Feb 3 16:47:44 2023 -0500 Check if name attribute is nothing (#96)
lukem12345
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May 2, 2023
* Contract operators * Generate functions with composed ops * Start chains from results of summations * Define unpacked operators * Added DEC matrix precomputation Greatly reduces memory usage from calling DEC functions and seems to work well with contract operators * Rough implementation of prealloc wedge product. * Improved decapodes wedge_product * Added support for more DEC operators * Run Brusselator on Icosphere6 * Rearranged memory testing files * Quick fix for Brusselator mem test Do not run Brusselator on an earth-sized mesh! * Prevented duplicate ops from being defined in compile_env Strange error occuring in Simulations Test * Fixed Multiscalearrays and Simulation tests * Add scaffolding for recursive node deletion * Remove pasted line * Use stack for recursive var deletion * Testing for memory optimizations * Updated testing brusselator * Remove unnecessary broadcast assignment * Run Brusselator on GPU * Cast to CPU for plotting * Use views in GPU * Fix parent check in sums and add tests * Cleaned up testing Brusselator * Squashed commit of the following: commit 9fc12f8 Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 20 12:08:24 2023 -0400 fix missing compat entries commit 7533c9f Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 20 10:48:23 2023 -0400 add more contributors commit 71a015f Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 20 10:39:05 2023 -0400 fix github action versionf for julia-actions commit 1790e48 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Tue Mar 7 15:28:59 2023 -0500 Import compile from Catlab.Programs (#104) commit e7ffee9 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Wed Feb 22 00:53:43 2023 -0500 Fix old tests and add compatibility specs (#103) * Explicitly give initial primal orientations * Fix MvNormal deprecation * Set some compatibilities commit 69d63b5 Author: GeorgeR227 <78235421+GeorgeR227@users.noreply.github.com> Date: Tue Feb 21 17:46:08 2023 -0500 Gr/parsing overhaul (#95) * Basic literal support * Added Lit data term * Fix composed op2s and add test * Replaced Var for term in \circ decomp * Quick patch for arbitrary multiplication support. * Fixed Tvar's unable to parse on rhs * Added inferred spaces for variables * Do not infer literals as states * Check types are in recognized set * Fixed strange TVar behavior * Fix cache invalidation error and add tests * Add new parsing features tests * Updated visualization for support new parsing. Also cleaned up the parsing code. * Support Literals in simulations * Do not namespace Literals, and do not vcat Nothing * Move CombinatorialSpaces using * Remove erroneous for loop --------- Co-authored-by: Luke Morris <lukelukemorrismorris@gmail.com> Co-authored-by: Luke Morris <70283489+lukem12345@users.noreply.github.com> commit ead3181 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Sat Feb 18 13:07:37 2023 -0500 Add Brusselator Example * Add Brusselator, type, and function resolve * Generate and run first phase of simulation * Change alpha and add gif * Perform second stage of simulation * Showcase using F as a time-varying parameter * Keep compatibility with old CombinatorialSpaces * Demonstrate brusselator on sphere * Clean and change gif frames * Add GLMakie back commit 4027d3e Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Fri Feb 3 16:47:44 2023 -0500 Check if name attribute is nothing (#96) * Started work on compiler optimizations * Added optimizations for Op2 and Summations * Support using mul! for op1 DEC calls * Added optimizing compiler Still need to handle dual forms and add specific constant/parameter typing * Added support for DualForms in optimizations * Cleaned up the type inference system * Integrated optimizing compiler into Decapodes Also added AdvDiff and Brusselator simulations to test new compilation * Run optimizations on pressure-driven flow Also moved out type inference rules relating to parameters. * Squashed commit of the following: commit 34ea660 Author: AlgebraicJulia Bot <129184742+algebraicjuliabot@users.noreply.github.com> Date: Mon Apr 24 10:39:01 2023 -0400 Set version to 0.2.0 commit f80c513 Author: Micah Halter <micah@mehalter.com> Date: Fri Apr 21 09:49:04 2023 -0400 Remove architecture specific integer types commit 3b3ab55 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Mon Apr 10 14:55:55 2023 -0400 Remove NamedDecapode constructor and compiler commit d2d5cfb Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Mon Apr 10 14:44:44 2023 -0400 Use @decapode macro commit 28d6eb5 Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 27 10:36:20 2023 -0400 Move to organization level github actions commit b3c2476 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Mon Mar 20 14:38:08 2023 -0400 Remove Decapodes_v0.1 files commit a40d7a1 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Tue Apr 18 14:46:50 2023 -0400 Do not convert edge labels that are already Strings (#115) commit 9fc12f8 Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 20 12:08:24 2023 -0400 fix missing compat entries commit 7533c9f Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 20 10:48:23 2023 -0400 add more contributors commit 71a015f Author: Micah Halter <micah@mehalter.com> Date: Mon Mar 20 10:39:05 2023 -0400 fix github action versionf for julia-actions commit 1790e48 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Tue Mar 7 15:28:59 2023 -0500 Import compile from Catlab.Programs (#104) commit e7ffee9 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Wed Feb 22 00:53:43 2023 -0500 Fix old tests and add compatibility specs (#103) * Explicitly give initial primal orientations * Fix MvNormal deprecation * Set some compatibilities commit 69d63b5 Author: GeorgeR227 <78235421+GeorgeR227@users.noreply.github.com> Date: Tue Feb 21 17:46:08 2023 -0500 Gr/parsing overhaul (#95) * Basic literal support * Added Lit data term * Fix composed op2s and add test * Replaced Var for term in \circ decomp * Quick patch for arbitrary multiplication support. * Fixed Tvar's unable to parse on rhs * Added inferred spaces for variables * Do not infer literals as states * Check types are in recognized set * Fixed strange TVar behavior * Fix cache invalidation error and add tests * Add new parsing features tests * Updated visualization for support new parsing. Also cleaned up the parsing code. * Support Literals in simulations * Do not namespace Literals, and do not vcat Nothing * Move CombinatorialSpaces using * Remove erroneous for loop --------- Co-authored-by: Luke Morris <lukelukemorrismorris@gmail.com> Co-authored-by: Luke Morris <70283489+lukem12345@users.noreply.github.com> commit ead3181 Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Sat Feb 18 13:07:37 2023 -0500 Add Brusselator Example * Add Brusselator, type, and function resolve * Generate and run first phase of simulation * Change alpha and add gif * Perform second stage of simulation * Showcase using F as a time-varying parameter * Keep compatibility with old CombinatorialSpaces * Demonstrate brusselator on sphere * Clean and change gif frames * Add GLMakie back commit 4027d3e Author: Luke Morris <70283489+lukem12345@users.noreply.github.com> Date: Fri Feb 3 16:47:44 2023 -0500 Check if name attribute is nothing (#96) * Patched some errors caused by merging * Cleaned up some code Deleted unnecessary files and cleaned up default_dec_generate * Removed return As per request * Shifted type inference ahead This shift allows us to infer types for variables that were originally parameters or constants before being set to infer by the compiler. * Removing debugging packages from Project.toml --------- Co-authored-by: Luke Morris <lukelukemorrismorris@gmail.com> Co-authored-by: Luke Morris <70283489+lukem12345@users.noreply.github.com>
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Currently, the visualization code expects that edge labels are Symbols. During visualization, these Symbols are converted to Strings.
However, the types of such quantities in Decapodes read-in from JSON files are Strings.
So - without overhauling the visualization code - I implement a fix which relies on multiple dispatch to not "greedily" convert Symbols to Strings when assigning edge labels.