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phylogenetic-component-graph.cabal
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phylogenetic-component-graph.cabal
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cabal-version: 3.0
Category: Biology
build-type: Simple
name: phylogenetic-component-graph
version: 0.3.0
author: Ward Wheeler
maintainer: wheeler@amnh.org
license: BSD-3-Clause
license-file: doc/LICENSE
synopsis: Program and library for general phylogenetic graph search
description: Phylogenetic Componet Graph provides a library for
interacting with phylogenetic graphs. It defines a
decalartive scripting language for defining phylogenetic
searches. Said scripts can be evaluated by the provided pcg
program to perform a phylogenetic search on an input dataset.
tested-with:
GHC == 8.8.4
GHC == 8.10.4
GHC == 9.0.1
extra-source-files:
doc/AUTHORS.md
doc/CHANGELOG.md
doc/FUNDING.md
README.md
-- Specify the header files as required source files here.
-- Do not specify them in the c-sources or cxx-sources stanzas.
-- This is required for sdist and install commands to work correctly.
lib/core/ffi/external-direct-optimization/alignCharacters.h
lib/core/ffi/external-direct-optimization/alignmentMatrices.h
lib/core/ffi/external-direct-optimization/c_alignment_interface.h
lib/core/ffi/external-direct-optimization/c_code_alloc_setup.h
lib/core/ffi/external-direct-optimization/costMatrix.h
lib/core/ffi/external-direct-optimization/debug_constants.h
lib/core/ffi/external-direct-optimization/dyn_character.h
lib/core/ffi/external-direct-optimization/ukkCheckPoint.h
lib/core/ffi/external-direct-optimization/ukkCommon.h
lib/tcm-memo/ffi/memoized-tcm/costMatrix_2d.hpp
lib/tcm-memo/ffi/memoized-tcm/costMatrix_3d.hpp
lib/tcm-memo/ffi/memoized-tcm/costMatrixWrapper_2d.h
lib/tcm-memo/ffi/memoized-tcm/costMatrixWrapper_3d.h
lib/tcm-memo/ffi/memoized-tcm/costMatrixWrapper.h
lib/tcm-memo/ffi/memoized-tcm/dynamicCharacterOperations.h
-- Group of buildinfo specifications to correctly build and link to the C & C++:
-- FFI code.
common ffi-buildinfo
cc-options:
--std=c11
hs-source-dirs:
lib/core/ffi
c-sources:
lib/core/ffi/external-direct-optimization/alignCharacters.c
lib/core/ffi/external-direct-optimization/alignmentMatrices.c
lib/core/ffi/external-direct-optimization/c_alignment_interface.c
lib/core/ffi/external-direct-optimization/c_code_alloc_setup.c
lib/core/ffi/external-direct-optimization/costMatrix.c
lib/core/ffi/external-direct-optimization/dyn_character.c
lib/core/ffi/external-direct-optimization/ukkCheckPoint.c
lib/core/ffi/external-direct-optimization/ukkCommon.c
-- Here we list all directories that contain C & C++ header files that the FFI
-- tools will need to locate when preprocessing the C files. Without listing
-- the directories containing the C header files here, the FFI preprocessor
-- (hsc2hs, c2hs, etc.) will fail to locate the requisite files. Note also,
-- that the parent directory of the nessicary C & C++ header files must be
-- specified. The preprocessor will not recursively look in subdirectories for
-- header files!
include-dirs:
lib/core/ffi/external-direct-optimization
-- A litany of GHC warnings designed to alert us during the build of any common
-- pitfalls, future compatibility issues, or coding conventions.
common ghc-flags
ghc-options:
-- -debug
-- -rtsopts
-- -g
-- Optimization flags
-O2
-fexcess-precision
-fexpose-all-unfoldings
-flate-specialise
-foptimal-applicative-do
-fspecialize-aggressively
-fstatic-argument-transformation
-- Usability flags
-fdiagnostics-color=always
-fhide-source-paths
-j
-- Sanity check warnings
-Wall
-Wcompat
-Wdodgy-foreign-imports
-Wduplicate-exports
-Wempty-enumerations
-Widentities
-Wincomplete-patterns
-Wincomplete-record-updates
-Wincomplete-uni-patterns
-Wmissed-specialisations
-Wmissing-deriving-strategies
-Wmissing-fields
-Wmissing-home-modules
-Wmissing-monadfail-instances
-Wmissing-signatures
-Wnoncanonical-monad-instances
-Wnoncanonical-monoid-instances
-Woverflowed-literals
-Woverlapping-patterns
-Wredundant-constraints
-Wsemigroup
-Wtabs
-Wunrecognised-warning-flags
-Wunused-binds
-Wunused-do-bind
-Wunused-foralls
-Wunused-imports
-Wunused-matches
-Wwrong-do-bind
if impl(ghc >= 8.10)
ghc-options:
-Wderiving-defaults
-Wunused-packages
-- Global deviations from Haskell98
common language-specs
-- Always use MonadFail(fail), not Monad(fail)
other-extensions:
MonadFailDesugaring
DerivingStrategies
library alphabet
import:
ghc-flags,
language-specs
visibility:
public
default-language:
Haskell2010
hs-source-dirs:
lib/alphabet/src
build-depends:
serialize,
utility,
base >= 4.11 && < 5.0,
bimap >= 0.3 && < 1.0,
binary >= 0.8 && < 1.0,
containers >= 0.6.2 && < 1.0,
deepseq >= 1.4 && < 2.0,
keys >= 3.12 && < 4.0,
mtl >= 2.2.2 && < 3.0,
QuickCheck >= 2.14 && < 3.0,
semigroupoids >= 5.3 && < 5.4,
text-short >= 0.1.3 && < 1.0,
text-show >= 3.8.1 && < 4.0,
transformers >= 0.5.6 && < 1.0,
-- Apparently this is needed to compile with profiling, which is really stupid.
-- It should only be in the modules which use TemplateHaskell, not all modules.
-- I consider this a temporary hack to get things to compile with profiling.
other-extensions: TemplateHaskell
exposed-modules:
Data.Alphabet
Data.Alphabet.IUPAC
Data.Alphabet.Special
other-modules:
Data.Alphabet.Internal
-- Library for performing parsimony analysis.
-- Provides various metrics for scoring static characters and
-- performing string alignment on dynamic characters.
library analysis
import:
ffi-buildinfo,
ghc-flags,
language-specs
visibility:
private
default-language:
Haskell2010
hs-source-dirs:
lib/core/analysis/src
build-depends:
data-structures,
exportable,
tcm,
tcm-memo,
utility,
base >= 4.11 && < 5.0,
clustering >= 0.4 && < 0.5,
containers >= 0.6.2 && < 1.0,
data-default >= 0.5.2 && < 0.8,
dlist >= 0.8 && < 1.0,
keys >= 3.12 && < 4.0,
lens >= 4.18 && < 6.0,
matrices >= 0.5 && < 1.0,
monad-loops >= 0.4 && < 1.0,
mono-traversable >= 1.0 && < 2.0,
mtl >= 2.2.2 && < 3.0,
parallel >= 3.2 && < 4.0,
primitive >= 0.7.1 && < 1.0,
unordered-containers >= 0.2.10 && < 1.0,
vector >= 0.12.0.3 && < 0.13,
vector-builder >= 0.3.7 && < 0.4,
vector-instances >= 3.4 && < 3.5,
exposed-modules:
Analysis.Clustering
Analysis.Clustering.Hierarchical
Analysis.Distance
Analysis.Parsimony.Additive
Analysis.Parsimony.Dynamic.DirectOptimization
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise
Analysis.Parsimony.Fitch
Analysis.Parsimony.Sankoff
Analysis.Scoring
Analysis.TotalEdgeCost
other-modules:
Analysis.Parsimony.Additive.Internal
Analysis.Parsimony.Dynamic.DirectOptimization.Internal
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.Internal
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.Ukkonen.Internal
Analysis.Parsimony.Fitch.Internal
Analysis.Parsimony.Sankoff.Internal
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.FFI
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.NeedlemanWunsch
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.Ukkonen
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.Ukkonen.Ribbon
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.UnboxedFullMatrix
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.UnboxedSwapping
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.UnboxedUkkonenFullSpace
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise.UnboxedUkkonenSwapping
library character-name
import:
ghc-flags,
language-specs
visibility:
private
default-language:
Haskell2010
hs-source-dirs:
lib/character-name/src
build-depends:
file-source,
base >= 4.11 && < 5.0,
binary >= 0.8 && < 1.0,
containers >= 0.6.2 && < 1.0,
deepseq >= 1.4 && < 2.0,
keys >= 3.12 && < 4.0,
mtl >= 2.2.2 && < 3.0,
mono-traversable >= 1.0 && < 2.0,
text-short >= 0.1.3 && < 1.0,
text-show >= 3.8.1 && < 4.0,
text-show-instances >= 3.8 && < 4.0,
exposed-modules:
Data.CharacterName
-- Data-types for defining and interacting with phylogenetic components.
-- Exposes core data-types for constructing, mutating, and scoring phylogenetic
-- components. Phylogenetic forests, the primitive component type, are defined
-- here along with the interface for interacting with phylogenetic forests.
-- Character sequences and matricies, character and graph metadata, and scoring
-- methods are defined as well.
library core
import:
language-specs
visibility:
public
default-language:
Haskell2010
build-depends:
analysis,
data-structures,
tcm
reexported-modules:
Analysis.Clustering,
Analysis.Distance,
Analysis.Parsimony.Additive,
Analysis.Parsimony.Dynamic.DirectOptimization,
Analysis.Parsimony.Dynamic.DirectOptimization.Pairwise,
Analysis.Parsimony.Fitch,
Analysis.Parsimony.Sankoff,
Analysis.Scoring,
Analysis.TotalEdgeCost,
Bio.Character,
Bio.Character.Decoration.Additive,
Bio.Character.Decoration.Continuous,
Bio.Character.Decoration.Discrete,
Bio.Character.Decoration.Discrete.Class,
Bio.Character.Decoration.Dynamic,
Bio.Character.Decoration.Fitch,
Bio.Character.Decoration.Metric,
Bio.Character.Decoration.NonMetric,
Bio.Character.Encodable,
Bio.Character.Encodable.Continuous,
Bio.Metadata,
Bio.Metadata.Continuous,
Bio.Metadata.Discrete,
Bio.Metadata.DiscreteWithTCM,
Bio.Metadata.Dynamic,
Bio.Metadata.Metric,
Bio.Sequence,
Bio.Sequence.Block,
Bio.Sequence.Character,
Bio.Sequence.Metadata,
Bio.Graph,
Bio.Graph.Component,
Bio.Graph.Constructions,
Bio.Graph.LeafSet,
Bio.Graph.Node,
Bio.Graph.Node.Context,
Bio.Graph.PhylogeneticDAG,
Bio.Graph.PhylogeneticDAG.Substitute,
Bio.Graph.ReferenceDAG,
Bio.Graph.ReferenceDAG.Internal,
Bio.Graph.ReferenceDAG.Network,
Bio.Graph.ReferenceDAG.Traversal,
Bio.Graph.ReferenceDAG.Utility,
Bio.Graph.Solution,
Data.EdgeLength,
Data.MetricRepresentation,
Data.NodeLabel,
Data.TCM,
Data.TCM.Dense,
Data.TopologyRepresentation,
Test.Custom.NucleotideSequence,
-- Normalizing disparate input sources
-- Library for taking data from disperate input sources and converting the data
-- to a normalized form. Normalization does *not* check that the disparate data
-- sources are consistent. That check is performed by the data-unification
-- library.
library data-normalization
import:
ghc-flags,
language-specs
visibility:
public
default-language:
Haskell2010
hs-source-dirs:
lib/data-normalization/src
build-depends:
alphabet,
core,
file-parsers,
utility,
base >= 4.11 && < 5.0,
containers >= 0.6.2 && < 1.0,
deepseq >= 1.4 && < 2.0,
graphviz >= 2999.20 && < 3000,
hashable >= 1.3 && < 2.0,
keys >= 3.12 && < 4.0,
semigroupoids >= 5.3 && < 5.4,
text-short >= 0.1.3 && < 1.0,
vector >= 0.12.0.3 && < 0.13,
vector-instances >= 3.4 && < 3.5,
exposed-modules:
Data.Normalization.Character
Data.Normalization.Metadata
Data.Normalization.Topology
other-modules:
Data.Normalization.Character.Class
Data.Normalization.Character.Internal
Data.Normalization.Metadata.Class
Data.Normalization.Metadata.Internal
library data-structures
import:
ghc-flags,
language-specs
visibility:
private
default-language:
Haskell2010
hs-source-dirs:
lib/core/data-structures/src
build-depends:
alphabet,
character-name,
evaluation,
exportable,
file-source,
serialize,
tcm,
tcm-memo,
utility,
base >= 4.11 && < 5.0,
bimap >= 0.3 && < 1.0,
binary >= 0.8 && < 1.0,
binary-instances >= 1 && < 2.0,
bv-little >= 1.0.1 && < 2.0,
bv-little:instances >= 1.0.1 && < 2.0,
-- concurrent-hashtable >= 0.1.8 && < 2.0,
containers >= 0.6.2 && < 1.0,
data-default >= 0.5.2 && < 0.8,
deepseq >= 1.4 && < 2.0,
dlist >= 0.8 && < 1.0,
graphviz >= 2999.20 && < 3000,
hashable >= 1.3 && < 2.0,
hashtables >= 1.2 && < 2.0,
keys >= 3.12 && < 4.0,
lens >= 4.18 && < 6.0,
monad-loops >= 0.4 && < 1.0,
mono-traversable >= 1.0 && < 2.0,
mtl >= 2.2.2 && < 3.0,
parallel >= 3.2 && < 4.0,
pretty-tree >= 0.1 && < 0.2,
QuickCheck >= 2.14 && < 3.0,
semigroupoids >= 5.3 && < 5.4,
smallcheck >= 1.1.5 && < 2.0,
text >= 1.2.4 && < 2.0,
text-short >= 0.1.3 && < 1.0,
text-show >= 3.8.1 && < 4.0,
text-show-instances >= 3.8 && < 4.0,
unordered-containers >= 0.2.10 && < 1.0,
vector >= 0.12.0.3 && < 0.13,
vector-builder >= 0.3.7 && < 0.4,
vector-binary-instances >= 0.2.1.1 && < 0.3,
vector-instances >= 3.4 && < 3.5,
xml >= 1.3.14 && < 1.4,
exposed-modules:
Bio.Character
Bio.Character.Decoration.Additive
Bio.Character.Decoration.Continuous
Bio.Character.Decoration.Discrete
Bio.Character.Decoration.Discrete.Class
Bio.Character.Decoration.Dynamic
Bio.Character.Decoration.Fitch
Bio.Character.Decoration.Metric
Bio.Character.Decoration.NonMetric
Bio.Character.Encodable
Bio.Character.Encodable.Continuous
Bio.Metadata
Bio.Metadata.Continuous
Bio.Metadata.Discrete
Bio.Metadata.DiscreteWithTCM
Bio.Metadata.Dynamic
Bio.Metadata.Metric
Bio.Metadata.Overlap
Bio.Sequence
Bio.Sequence.Block
Bio.Sequence.Character
Bio.Sequence.Metadata
Bio.Graph
Bio.Graph.Component
Bio.Graph.Constructions
Bio.Graph.LeafSet
Bio.Graph.Node
Bio.Graph.Node.Context
Bio.Graph.PhylogeneticDAG
Bio.Graph.PhylogeneticDAG.Substitute
Bio.Graph.ReferenceDAG
Bio.Graph.ReferenceDAG.Internal
Bio.Graph.ReferenceDAG.Network
Bio.Graph.ReferenceDAG.Traversal
Bio.Graph.ReferenceDAG.Utility
Bio.Graph.Solution
Data.EdgeLength
Data.Hashable.Memoize
Data.NodeLabel
Data.TopologyRepresentation
Test.Custom.NucleotideSequence
other-modules:
Bio.Character.Decoration.Additive.Class
Bio.Character.Decoration.Additive.Internal
Bio.Character.Decoration.Continuous.Class
Bio.Character.Decoration.Continuous.Internal
Bio.Character.Decoration.Dynamic.Class
Bio.Character.Decoration.Dynamic.Internal
Bio.Character.Decoration.Fitch.Class
Bio.Character.Decoration.Fitch.Internal
Bio.Character.Decoration.Metric.Class
Bio.Character.Decoration.Metric.Internal
Bio.Character.Decoration.NonMetric.Class
Bio.Character.Decoration.NonMetric.Internal
Bio.Character.Decoration.Shared
Bio.Character.Encodable.Continuous.Class
Bio.Character.Encodable.Continuous.Internal
Bio.Character.Encodable.Dynamic
Bio.Character.Encodable.Dynamic.AmbiguityGroup
Bio.Character.Encodable.Dynamic.Class
Bio.Character.Encodable.Dynamic.Element
Bio.Character.Encodable.Dynamic.Internal
Bio.Character.Encodable.Internal
Bio.Character.Encodable.Static
Bio.Character.Encodable.Static.Class
Bio.Character.Encodable.Static.Internal
Bio.Character.Encodable.Stream
Bio.Metadata.General
Bio.Metadata.General.Class
Bio.Metadata.General.Internal
Bio.Metadata.Discrete.Class
Bio.Metadata.Discrete.Internal
Bio.Metadata.DiscreteWithTCM.Class
Bio.Metadata.DiscreteWithTCM.Internal
Bio.Metadata.Dynamic.Class
Bio.Metadata.Dynamic.Internal
Bio.Metadata.Metric.Class
Bio.Metadata.Metric.Internal
Bio.Graph.BinaryRenderingTree
Bio.Graph.Forest
Bio.Graph.Node.Internal
Bio.Graph.PhylogeneticDAG.Internal
Bio.Graph.PhylogeneticDAG.NetworkEdgeQuantification
Bio.Graph.PhylogeneticDAG.DynamicCharacterRerooting
Bio.Graph.PhylogeneticDAG.Postorder
Bio.Graph.PhylogeneticDAG.Preorder
Bio.Graph.PhylogeneticDAG.Reification
Bio.Sequence.Block.Builder
Bio.Sequence.Block.Character
Bio.Sequence.Block.Internal
Bio.Sequence.Block.Metadata
Bio.Sequence.Internal
Data.EdgeSet
-- Checking consistentcy and unifiying data from disprate input sources.
-- Library for taking data from disperate input sources and unified the data into
-- a consistent form.
library data-unification
import:
ghc-flags,
language-specs
visibility:
public
default-language:
Haskell2010
hs-source-dirs:
lib/data-unification/src
build-depends:
character-name,
core,
data-normalization,
file-source,
serialize,
utility,
base >= 4.11 && < 5.0,
containers >= 0.6.2 && < 1.0,
data-default >= 0.5.2 && < 0.8,
deepseq >= 1.4 && < 2.0,
keys >= 3.12 && < 4.0,
lens >= 4.18 && < 6.0,
mtl >= 2.2.2 && < 3.0,
parallel >= 3.2 && < 4.0,
semigroupoids >= 5.3 && < 5.4,
text >= 1.2.4 && < 2.0,
text-short >= 0.1.3 && < 1.0,
text-show >= 3.8.1 && < 4.0,
text-show-instances >= 3.8 && < 4.0,
transformers >= 0.5.6 && < 1.0,
validation >= 1.1 && < 2.0,
exposed-modules:
Data.Unification
other-modules:
Data.Unification.Error
Data.Unification.InputData
-- Monad transformer for managing the stateful evaluation of PCG scripts.
-- This monad transformer provides a concrete, efficient implementation for many
-- useful monad typeclasses required to manage the effects of the evaluating PCG
-- scripts. PCG script evaluation is inherently stateful, requiring management of
-- random seeds, logs, IO, global state variables, and error short-ciruiting.
library evaluation
import:
ghc-flags,
language-specs
visibility:
public
default-language:
Haskell2010
hs-source-dirs:
lib/evaluation/src
build-depends:
base >= 4.11 && < 5.0,
bimap >= 0.3 && < 1.0,
containers >= 0.6.2 && < 1.0,
deepseq >= 1.4 && < 2.0,
mtl >= 2.2.2 && < 3.0,
QuickCheck >= 2.14 && < 3.0,
quickcheck-instances >= 0.3.22 && < 1.0,
semigroupoids >= 5.3 && < 5.4,
text >= 1.2.4 && < 2.0,
text-show >= 3.8.1 && < 4.0,
transformers >= 0.5.6 && < 1.0,
exposed-modules:
Control.Evaluation
Control.Monad.Logger
System.ErrorPhase
other-modules:
Control.Evaluation.Notification
Control.Evaluation.Result
Control.Evaluation.Trans
library exportable
import:
ghc-flags,
language-specs,
visibility:
private
default-language:
Haskell2010
hs-source-dirs:
lib/exportable/src
build-depends:
base >= 4.11 && < 5.0,
lens >= 4.18 && < 6.0,
mono-traversable >= 1.0 && < 2.0,
exposed-modules:
Bio.Character.Exportable
other-modules:
Bio.Character.Exportable.Class
-- Parsers for the input file types accepted by PCG
-- Defines file parsers for Fasta files with sequence splitting, Newick files with
-- support for extended newick format, Nexus files (though many block types are
-- skipped), DOT files as graph input, TNT files (though many commands are
-- skipped), and custom file formats for parsing transition cost matrices with an
-- alphabet, and the depricated vertex/edge/root set format.
library file-parsers
import:
ghc-flags,
language-specs
visibility:
public
default-language:
Haskell2010
hs-source-dirs:
lib/file-parsers/src
build-depends:
alphabet,
utility,
base >= 4.11 && < 5.0,
bimap >= 0.3 && < 1.0,
case-insensitive >= 1.2.0 && < 1.3,
containers >= 0.6.2 && < 1.0,
deepseq >= 1.4 && < 2.0,
graphviz >= 2999.20 && < 3000,
keys >= 3.12 && < 4.0,
matrix >= 0.3.6 && < 0.4,
megaparsec >= 9.0 && < 10.0,
mtl >= 2.2.2 && < 3.0,
parser-combinators >= 1.0 && < 2.0,
safe >= 0.3.17 && < 0.4,
scientific >= 0.3.6 && < 0.4,
semigroupoids >= 5.3 && < 5.4,
text >= 1.2.4 && < 2.0,
text-short >= 0.1.3 && < 1.0,
transformers >= 0.5.6 && < 1.0,
vector >= 0.12.0.3 && < 0.13,
exposed-modules:
File.Format.Dot
File.Format.Fasta
File.Format.Fastc
File.Format.Newick
File.Format.Nexus
File.Format.TNT
File.Format.TransitionCostMatrix
File.Format.VertexEdgeRoot
other-modules:
File.Format.Fasta.Converter
File.Format.Fasta.Internal
File.Format.Fasta.Parser
File.Format.Fastc.Parser
File.Format.Newick.Internal
File.Format.Newick.Parser
File.Format.Nexus.Data
File.Format.Nexus.Parser
File.Format.Nexus.Partition
File.Format.Nexus.Validate
File.Format.TNT.Command.CCode
File.Format.TNT.Command.CNames
File.Format.TNT.Command.Cost
File.Format.TNT.Command.NStates
File.Format.TNT.Command.Procedure
File.Format.TNT.Command.TRead
File.Format.TNT.Command.XRead
File.Format.TNT.Parser
File.Format.TNT.Partitioning
File.Format.TNT.Internal
File.Format.TransitionCostMatrix.Parser
File.Format.VertexEdgeRoot.Parser
Text.Megaparsec.Custom
-- Library for interacting with file paths in a type-safe manner.
-- Exposes a well-typed file path type and functionality for interacting with the
-- file system through with this type.
library file-source
import:
ghc-flags,
language-specs
visibility:
public
default-language:
Haskell2010
hs-source-dirs:
lib/file-source/src
build-depends:
serialize,
validation-transformer,
base >= 4.11 && < 5.0,
binary >= 0.8 && < 1.0,
bytestring >= 0.10.10 && < 0.11,
deepseq >= 1.4 && < 2.0,
directory >= 1.3.6 && < 2.0,
filepath >= 1.4.2 && < 2.0,
Glob >= 0.9 && < 2.0,
hashable >= 1.3 && < 2.0,
keys >= 3.12 && < 4.0,
megaparsec >= 9.0 && < 10.0,
mono-traversable >= 1.0 && < 2.0,
mono-traversable-keys >= 0.1 && < 1.0,
pipes >= 4.3.10 && < 5.0,
QuickCheck >= 2.14 && < 3.0,
semigroupoids >= 5.3 && < 5.4,
text >= 1.2.4 && < 2.0,
text-short >= 0.1.3 && < 1.0,
text-show >= 3.8.1 && < 4.0,
validation >= 1.1 && < 2.0,
vector >= 0.12.0.3 && < 0.13,
exposed-modules:
Data.FileSource
Data.FileSource.IO
Data.FileSource.InputStreamError
Data.FileSource.ParseStreamError
Data.FileSource.OutputStreamError
-- Library for phylogenetic graphs
-- Defines data type for phylogenetic graphs and various helper functions.
library graph
import:
ghc-flags,
language-specs
visibility:
public
default-language:
Haskell2010
hs-source-dirs:
lib/graph/src
build-depends:
utility,
base >= 4.11 && < 5.0,
comonad >= 5.0 && < 6.0,
containers >= 0.6.2 && < 0.7,
keys >= 3.12 && < 4.0,
lens >= 4.18 && < 6.0,
mtl ^>= 2.2.2 ,
QuickCheck >= 2.14 && < 3.0,
semigroupoids >= 5.3 && < 5.4,
text-show >= 3.8.1 && < 4.0,
vector >= 0.12.0.3 && < 0.13,
vector-builder >= 0.3.7 && < 0.4,
vector-instances >= 3.4 && < 3.5,
exposed-modules:
Data.Graph
Data.Graph.Type
Data.Graph.Memo
Data.Graph.Internal
Data.Graph.Indices
Data.Graph.NodeContext
Data.Graph.Moves
Data.Graph.Hash
Data.Graph.Intermediate
Data.Graph.Build
Data.Graph.Sequence.Class
-- Defines the grammar & specific commands of the PCG language
-- In addition to the grammar definition, this library exports a parser for the
-- grammar. Each command available in PCG is defined here and a script parser is
-- exported to parse a sequence of commands which represents the computation to
-- be performed by PCG.
library language
import:
ghc-flags,
language-specs
visibility:
public
default-language:
Haskell2010
hs-source-dirs:
lib/language/src
build-depends:
file-source,
base >= 4.11 && < 5.0,
case-insensitive >= 1.2.0 && < 1.3,
containers >= 0.6.2 && < 1.0,
free >= 5.1 && < 6.0,
keys >= 3.12 && < 4.0,
megaparsec >= 9.0 && < 10.0,
parser-combinators >= 1.0 && < 2.0,
scientific >= 0.3.6 && < 0.4,
text-short >= 0.1.3 && < 1.0,
time >= 1.9.3 && < 2.0,
exposed-modules:
PCG.Syntax
PCG.Command.Build
PCG.Command.Echo
PCG.Command.Load
PCG.Command.Read
PCG.Command.Report
PCG.Command.Save
PCG.Command.Version
PCG.Syntax.Combinators
other-modules:
PCG.Syntax.Parser
PCG.Syntax.Primitive
-- A library for defining custom serialisation and rendering functionality.
-- Defines custom helper functions for serializing to data formats and related
-- to text representations.
library serialize
import:
ghc-flags,
language-specs
visibility:
private
default-language:
Haskell2010
hs-source-dirs:
lib/serialize/src
build-depends:
base >= 4.11 && < 5.0,
keys >= 3.12 && < 4.0,
text >= 1.2.4 && < 2.0,
text-show >= 3.8.1 && < 4.0,
xml >= 1.3.14 && < 1.4,
exposed-modules:
TextShow.Custom
Text.Newick.Class
Text.XML
Text.XML.Class
Text.XML.Custom
-- Library for working with TCMs and SCMs in various representations.
-- General purpose library for working with transition cost matrices (TCMs)
-- and symbol change matrices (SCMs). Specialization options are provided
-- for the discrete metric (non-additive) and the L1 norm (additive) TCMs &
-- SCMs. Exposes a memoized binding for sparsely indexed, large TCMs.
library tcm
import:
ffi-buildinfo,
ghc-flags,
language-specs,
visibility:
private
default-language:
Haskell2010
hs-source-dirs:
lib/core/tcm/src
build-depends:
exportable,
serialize,
tcm-memo,