diff --git a/ChangeLog.md b/ChangeLog.md index 909fc1c..e13090a 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -2,6 +2,11 @@ ## [Unreleased] +## [0.1.3.2] - 2020-04-15 +### Changed +- Resolver version up. +- Moving from `less-wrong` to `biocad`. + ## [0.1.3.1] - 2020-04-02 ### Fixed - Reading of insertion code for residues in MAE. diff --git a/package.yaml b/package.yaml index e98534f..1bbda2f 100644 --- a/package.yaml +++ b/package.yaml @@ -1,11 +1,11 @@ name: cobot-io -version: 0.1.3.1 -github: "less-wrong/cobot-io" +version: 0.1.3.2 +github: "biocad/cobot-io" license: BSD3 category: Bio author: "Pavel Yakovlev, Bogdan Neterebskii, Alexander Sadovnikov" maintainer: "pavel@yakovlev.me" -copyright: "2018-2019, Less Wrong Bio" +copyright: "2020, Biocad" synopsis: Biological data file formats and IO extra-source-files: @@ -17,7 +17,7 @@ extra-source-files: # To avoid duplicated efforts in documentation and dealing with the # complications of embedding Haddock markup inside cabal files, it is # common to point users to the README.md file. -description: Please see the README on GitHub at +description: Please see the README on GitHub at dependencies: - base >= 4.7 && < 5 diff --git a/src/Bio/ABI/Decode.hs b/src/Bio/ABI/Decode.hs index 049faae..efa77e6 100644 --- a/src/Bio/ABI/Decode.hs +++ b/src/Bio/ABI/Decode.hs @@ -9,8 +9,7 @@ import Data.ByteString as BS (ByteString) import Data.ByteString.Lazy as BSL (ByteString, fromStrict) import Data.ByteString.Lazy.Char8 as BSL8 (unpack) import Data.Char (ord) -import Data.List (elem, find) -import Data.Maybe (maybe) +import Data.List (find) import Data.Text (Text) import Hyrax.Abif (Abif (..), Directory (..)) import Hyrax.Abif.Read (getAbif) diff --git a/src/Bio/MMTF.hs b/src/Bio/MMTF.hs index 8f4766a..362498f 100644 --- a/src/Bio/MMTF.hs +++ b/src/Bio/MMTF.hs @@ -16,9 +16,8 @@ import Control.Monad.IO.Class (MonadIO) import Data.Bifunctor (Bifunctor (..)) import Data.ByteString.Lazy (ByteString) import Data.Int (Int32) -import Data.List (mapAccumL, zip3, zip4) +import Data.List (mapAccumL, zip4) import Data.MessagePack (unpack) -import Data.Monoid ((<>)) import Data.String (IsString (..)) import Data.Text (Text) import Data.Vector (Vector, empty, toList, (!)) diff --git a/src/Bio/MMTF/Decode/MessagePack.hs b/src/Bio/MMTF/Decode/MessagePack.hs index 6a46a56..22b99ce 100644 --- a/src/Bio/MMTF/Decode/MessagePack.hs +++ b/src/Bio/MMTF/Decode/MessagePack.hs @@ -2,13 +2,12 @@ module Bio.MMTF.Decode.MessagePack where -import Data.ByteString.Lazy (ByteString, fromStrict) -import Data.Map.Strict (Map, fromList) -import qualified Data.Map.Strict as M (lookup) +import Data.ByteString.Lazy (ByteString, fromStrict) +import Data.Map.Strict (Map, fromList) +import qualified Data.Map.Strict as M (lookup) import Data.MessagePack -import Data.Monoid ((<>)) -import Data.Text (Text) -import qualified Data.Text as T (unpack) +import Data.Text (Text) +import qualified Data.Text as T (unpack) #if !MIN_VERSION_base(4,13,0) -- Data.MessagePack includes MonadFail constraints only for GHC-8.8+, so we can't use diff --git a/src/Bio/PDB/Parser.hs b/src/Bio/PDB/Parser.hs index 942cb1b..304399e 100644 --- a/src/Bio/PDB/Parser.hs +++ b/src/Bio/PDB/Parser.hs @@ -16,7 +16,6 @@ import Data.Attoparsec.Text (Parser, choice, count, endOfInput, import qualified Data.List as L (groupBy) import Data.Map.Strict (Map, fromListWithKey) import Data.Maybe (catMaybes) -import Data.Monoid ((<>)) import Data.Text as T (Text, concat, pack, stripEnd) import qualified Data.Vector as V (Vector, concat, fromList, singleton) import GHC.Generics () diff --git a/src/Bio/Sequence/Class.hs b/src/Bio/Sequence/Class.hs index f183125..9191389 100644 --- a/src/Bio/Sequence/Class.hs +++ b/src/Bio/Sequence/Class.hs @@ -45,7 +45,6 @@ module Bio.Sequence.Class import Bio.Sequence.Utilities (Range, checkRange, unsafeEither) import Control.Lens import Control.Monad.Except (MonadError, throwError) -import Data.Bifunctor (bimap) import Data.Kind (Constraint) import qualified Data.List as L (length, null) import Data.Text (Text) diff --git a/src/Bio/Sequence/Functions/Sequence.hs b/src/Bio/Sequence/Functions/Sequence.hs index 9839e95..bf92614 100644 --- a/src/Bio/Sequence/Functions/Sequence.hs +++ b/src/Bio/Sequence/Functions/Sequence.hs @@ -18,7 +18,6 @@ import Bio.Sequence.Class (ContainsNoMarking, IsSequence (..), import Bio.Sequence.Utilities (Range, checkRange, unsafeEither) import Control.Lens import Control.Monad.Except (MonadError, throwError) -import Data.Bifunctor (bimap) import qualified Data.Foldable as F (length, null, toList) import qualified Data.List as L (drop, take) import Data.Maybe (fromMaybe) diff --git a/src/Bio/Uniprot/Parser.hs b/src/Bio/Uniprot/Parser.hs index f0cee40..345d12a 100644 --- a/src/Bio/Uniprot/Parser.hs +++ b/src/Bio/Uniprot/Parser.hs @@ -16,7 +16,6 @@ import Data.Attoparsec.Text import Data.Bifunctor (second) import Data.Char (isSpace) import Data.Functor (($>)) -import Data.Monoid ((<>)) import Data.Text (Text, append, isPrefixOf, null, pack, splitOn, unpack) diff --git a/stack.yaml b/stack.yaml index 1aa4378..cd491eb 100644 --- a/stack.yaml +++ b/stack.yaml @@ -1,64 +1,12 @@ -# This file was automatically generated by 'stack init' -# -# Some commonly used options have been documented as comments in this file. -# For advanced use and comprehensive documentation of the format, please see: -# https://docs.haskellstack.org/en/stable/yaml_configuration/ +resolver: lts-15.5 -# Resolver to choose a 'specific' stackage snapshot or a compiler version. -# A snapshot resolver dictates the compiler version and the set of packages -# to be used for project dependencies. For example: -# -# resolver: lts-3.5 -# resolver: nightly-2015-09-21 -# resolver: ghc-7.10.2 -# -# The location of a snapshot can be provided as a file or url. Stack assumes -# a snapshot provided as a file might change, whereas a url resource does not. -# -# resolver: ./custom-snapshot.yaml -# resolver: https://example.com/snapshots/2018-01-01.yaml -resolver: lts-14.11 - -# User packages to be built. -# Various formats can be used as shown in the example below. -# -# packages: -# - some-directory -# - https://example.com/foo/bar/baz-0.0.2.tar.gz -# - location: -# git: https://github.com/commercialhaskell/stack.git -# commit: e7b331f14bcffb8367cd58fbfc8b40ec7642100a -# - location: https://github.com/commercialhaskell/stack/commit/e7b331f14bcffb8367cd58fbfc8b40ec7642100a -# subdirs: -# - auto-update -# - wai packages: - . -# Dependency packages to be pulled from upstream that are not in the resolver -# using the same syntax as the packages field. -# (e.g., acme-missiles-0.3) -# extra-deps: - -# Override default flag values for local packages and extra-deps -# flags: {} -# Extra package databases containing global packages -# extra-package-dbs: [] +extra-deps: +- data-msgpack-0.0.13 +- data-msgpack-types-0.0.3 +- hyraxAbif-0.2.3.21 -# Control whether we use the GHC we find on the path -# system-ghc: true -# -# Require a specific version of stack, using version ranges -# require-stack-version: -any # Default -# require-stack-version: ">=1.9" -# -# Override the architecture used by stack, especially useful on Windows -# arch: i386 -# arch: x86_64 -# -# Extra directories used by stack for building -# extra-include-dirs: [/path/to/dir] -# extra-lib-dirs: [/path/to/dir] -# -# Allow a newer minor version of GHC than the snapshot specifies -# compiler-check: newer-minor +ghc-options: + $locals: -Wall -fdiagnostics-color=always