from less-wrong to cobot (#35)

* from less-wrong to cobot

* pedantic

* version up

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.

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:          "[email protected]"
-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 <https://github.com/less-wrong/cobot-io#readme>
+description:         Please see the README on GitHub at <https://github.com/biocad/cobot-io#readme>
 
 dependencies:
 - base >= 4.7 && < 5

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)

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, (!))

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

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         ()

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)

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)

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)
 

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