amnh PCG issues - Githubissues

amnh / PCG

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search

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issues

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Make postorder and preorder functions perform a single memoized pass of the graph

#117 Boarders opened 5 years ago
0
Update AutoBench to Megaparsec v7.0

#116 recursion-ninja closed 5 years ago
2
Use custom ExitCode values to indicate different failure types

#115 recursion-ninja closed 5 years ago
7
Refactor out the "Data Unification" modules into a sub library

#114 recursion-ninja closed 5 years ago
1
Refactor out the "Data Normalization" modules into a sub library

#113 recursion-ninja closed 5 years ago
1
Refactor out Analysis module into a sub library

#112 recursion-ninja closed 5 years ago
6
Refactor out Control.Evaluation into a sub library

#111 recursion-ninja closed 5 years ago
4
Refactor out Control.Parallel.Custom into pcg-utilities sub library

#110 recursion-ninja closed 5 years ago
1
Create a "serializing/rendering" sub library

#109 recursion-ninja closed 5 years ago
1
Refactor out Data.TCM module into a sub library

#108 recursion-ninja closed 5 years ago
2
Refactor Data.Vector.NonEmpty to pcg-utilities library

#107 recursion-ninja closed 5 years ago
1
Refactor out Alphabet module into a sub library

#106 recursion-ninja closed 5 years ago
1
Add unit tests and integration tests for the candidate network edge set of a given graph

#105 recursion-ninja closed 5 years ago
5
Write an elimination function for the `EvaluationT` data type

#104 recursion-ninja closed 5 years ago
1
Use the cassava library for metadata "cross-references" implementation

#103 recursion-ninja closed 5 years ago
1
Make `mono-traversable-keys` package

#102 recursion-ninja closed 5 years ago
1
Investigate runtime regression

#101 recursion-ninja closed 6 years ago
1
Experiment with Haskell-side, hashable memoized function(s)

#100 recursion-ninja opened 6 years ago
8
Add "dense" Threeway Median Matrix (TMM) for small alphabets

#99 recursion-ninja closed 6 years ago
1
Add a specialized Threeway Median Matrix (TMM) for L1 norm

#98 recursion-ninja closed 6 years ago
4
Add a specialized Threeway Median Matrix (TMM) for discrete metric

#97 recursion-ninja closed 6 years ago
1
Request mainatinership of huffman library.

#96 recursion-ninja closed 4 years ago
1
Don't always perform a Wagner build before a network build

#95 recursion-ninja closed 6 years ago
1
Code review and remove unnecessary Python files.

#94 recursion-ninja closed 5 years ago
1
Check to ensure that each taxa has at least one, non-missing character value

#93 recursion-ninja opened 6 years ago
0
Replace Show instance of many data structures with render funtions that produce Text

#92 recursion-ninja closed 5 years ago
1
Represent Leaf Labels with Data.Text.Short

#91 Boarders closed 5 years ago
1
Missing data is not handled appropriately for additive characters

#90 recursion-ninja closed 6 years ago
1
TNT parser doesn't correctly construct intervals from additive characters

#89 recursion-ninja opened 6 years ago
0
Add benchmarking suite

#88 recursion-ninja closed 4 years ago
8
Add "heartbeat" functionality

#87 recursion-ninja opened 6 years ago
0
Reimplement topological representation

#86 recursion-ninja opened 6 years ago
6
Reimplement character sequences into a character matrix.

#85 recursion-ninja opened 6 years ago
2
Update integration tests to access values in a well typed manner

#84 recursion-ninja closed 5 years ago
3
Review TODOs in FFI codebase

#83 recursion-ninja opened 6 years ago
1
Improve Wagner build performace by adding virtual node data to edges labels

#82 recursion-ninja closed 5 years ago
1
Investigate possible space leaks with the memoized TCM

#81 recursion-ninja closed 6 years ago
6
Sankoff characters throw runtime exception when given the L1 norm metric

#80 recursion-ninja closed 6 years ago
1
Dynamic characters on large alphabets are prohibitively expensive to compute.

#79 recursion-ninja closed 6 years ago
5
The dynamic character analysis is broken for the L1-norm (additive)

#78 recursion-ninja closed 6 years ago
3
Change the postorder and preorder "signatures" to be well typed

#77 recursion-ninja closed 6 years ago
0
Add a command to remove network edges from a graph

#76 recursion-ninja opened 6 years ago
0
Add a command to take the current search state and add network edges to it

#75 recursion-ninja opened 6 years ago
0
Update the DOT file parser to accept labels

#74 recursion-ninja closed 6 years ago
0
Generating the set of candidate network edges to add includes phylogenetically inconsistent edges

#73 recursion-ninja closed 6 years ago
3
Add back parallelism after Vector is compatible with compact regions

#72 recursion-ninja closed 5 years ago
2
Add integration tests

#71 recursion-ninja closed 6 years ago
1
Correctly interpret dynamic characters marked as prealigned

#70 recursion-ninja closed 6 years ago
1
Remove gaps from unaligned, dynamic character inputs

#69 recursion-ninja closed 6 years ago
1
Data.Vector.NonEmpty.unfoldr is incorrect

#68 recursion-ninja closed 6 years ago
1

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