eggzilla · eggzilla · Feb 11, 2019 · Feb 11, 2019 · Feb 12, 2019 · Jun 29, 2019
diff --git a/.travis.yml b/.travis.yml
@@ -1,40 +1,34 @@
-# NB: don't set `language: haskell` here
-
-# explicitly request legacy non-sudo based build environment
 sudo: required
 
-# The following enables several GHC versions to be tested; often it's enough to test only against the last release in a major GHC version. Feel free to omit lines listings versions you don't need/want testing for.
-env:
- - CABALVER=1.24 GHCVER=8.0.2
- - CABALVER=2.0 GHCVER=8.2.2
-
-# Note: the distinction between `before_install` and `install` is not important.
-before_install:
- - travis_retry sudo add-apt-repository -y ppa:hvr/ghc
- - travis_retry sudo apt-get update
- - travis_retry sudo apt-get install libcairo2 libpango1.0-0 libpangomm-1.4-dev
- - travis_retry sudo apt-get install happy-1.19.4 alex-3.1.3
- - export PATH=/opt/alex/3.1.3/bin:/opt/happy/1.19.4/bin:$PATH
- - travis_retry sudo apt-get install cabal-install-$CABALVER ghc-$GHCVER # see note about happy/alex
- - export PATH=/opt/ghc/$GHCVER/bin:/opt/cabal/$CABALVER/bin:$PATH
+language: c
+
+services:
+  - docker
 
-install:
- - cabal --version
- - echo "$(ghc --version) [$(ghc --print-project-git-commit-id 2> /dev/null || echo '?')]"
- - travis_retry cabal update
- - cabal install --only-dependencies --enable-tests --enable-benchmarks
+before_script:
+  - docker build --tag devel -f Dockerfile.dev .
 
-# Here starts the actual work to be performed for the package under test; any command which exits with a non-zero exit code causes the build to fail.
 script:
- - if [ -f configure.ac ]; then autoreconf -i; fi
- - cabal configure --enable-tests --enable-benchmarks -v2  # -v2 provides useful information for debugging
- - cabal build   # this builds all libraries and executables (including tests/benchmarks)
- - cabal test
- - cabal check
- - cabal sdist   # tests that a source-distribution can be generated
+  - docker create --name develcontainer devel
+  - mkdir cmv
+  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/cmv-1.1.0/x/CMCV/build/CMCV/CMCV CMCV
+  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/cmv-1.1.0/x/CMV/build/CMV/CMV CMV
+  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/cmv-1.1.0/x/HMMCV/build/HMMCV/HMMCV HMMCV
+  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/cmv-1.1.0/x/HMMV/build/HMMV/HMMV HMMV
+  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/cmv-1.1.0/x/CMCWStoCMCV/build/CMCWStoCMCV/CMCWStoCMCV CMCWStoCMCV
+  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/cmv-1.1.0/x/CMCtoHMMC/build/CMCtoHMMC/CMCtoHMMC CMCtoHMMC
+  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/cmv-1.1.0/x/CMCtoHMMC/build/CMCtoHMMC/CMCtoHMMC CMCtoHMMC
+  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/cmv-1.1.0/x/HMMCtoCMC/build/HMMCtoCMC/HMMCtoCMC HMMCtoCMC
+  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/cmv-1.1.0/x/StockholmV/build/StockholmV/StockholmV StockholmV
+  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/cmv-1.1.0/x/CMVJson/build/CMVJson/CMVJson CMVJson
+  - cp LICENSE cmv
+  - tar -cvzf cmv.tar.gz cmv
+
 
-# Check that the resulting source distribution can be built & installed.
-# If there are no other `.tar.gz` files in `dist`, this can be even simpler:
-# `cabal install --force-reinstalls dist/*-*.tar.gz`
- - SRC_TGZ=$(cabal info . | awk '{print $2;exit}').tar.gz &&
-   (cd dist && cabal install --force-reinstalls "$SRC_TGZ")
+deploy:
+  provider: releases
+  skip_cleanup: true
+  api_key: $GITHUB_TOKEN
+  file: "cmv.tar.gz" 
+  on:
+    tags: true
diff --git a/ChangeLog.md b/ChangeLog.md
@@ -0,0 +1,43 @@
+-*-change-log-*-
+### 1.1.0 [Florian Eggenhofer](mailto:egg@informatik.uni-freiburg.de) 12. July 2019
+
+	* Added StockholmV
+	* Added statically compiled executables via  CI
+
+### 1.0.8 [Florian Eggenhofer](mailto:egg@informatik.uni-freiburg.de) 27. January 2018
+
+	* Fixed secondary structure visualisation for missing consensus
+	secondary structure
+
+### 1.0.7 [Florian Eggenhofer](mailto:egg@informatik.uni-freiburg.de) 15. January 2018
+	* Improved placment of index labels
+	* Prepared for layout direction extension
+
+### 1.0.6 [Florian Eggenhofer](mailto:egg@informatik.uni-freiburg.de) 26. September 2017
+
+	* Fixed a missing output bug in HMMCV
+
+### 1.0.5 [Florian Eggenhofer](mailto:egg@informatik.uni-freiburg.de) 18. September 2017
+
+	* Changed used stack lts due to problems with build tool dependencies
+
+### 1.0.4 [Florian Eggenhofer](mailto:egg@informatik.uni-freiburg.de) 14. September 2017
+	* Initial compatiblity with GHC 8.2.1
+
+### 1.0.3 [Florian Eggenhofer](mailto:egg@informatik.uni-freiburg.de) 12. September 2017
+
+	* Added missing README instructions
+	* Added link to biocontainer
+	* Fixed changed dependency in travis file, updated stack file
+
+### 1.0.2 [Florian Eggenhofer](mailto:egg@informatik.uni-freiburg.de) 22. June 2017
+
+	* Added package meta files for stack and cabal-new
+
+### 1.0.1 [Florian Eggenhofer](mailto:egg@informatik.uni-freiburg.de) 16. June 2017
+
+	* Additions to documentation
+
+### 1.0.0 [Florian Eggenhofer](mailto:egg@informatik.uni-freiburg.de) 16. June 2017
+
+	* Initial release
diff --git a/Dockerfile.dev b/Dockerfile.dev
@@ -0,0 +1,8 @@
+FROM alpine:latest
+
+RUN apk update
+RUN apk add --no-cache musl musl-dev musl-utils musl-dbg ghc ghc-dev ghc-doc cabal zlib-dev zlib tar gzip wget
+
+ADD . source
+WORKDIR source
+RUN cabal new-update && cabal new-build --ghc-options="-optl-static -optl-pthread -fPIC"
diff --git a/changelog b/changelog
diff --git a/cmv.cabal b/cmv.cabal
@@ -1,12 +1,12 @@
 name:                cmv
-version:             1.0.8
+version:             1.1.0
 synopsis:            Detailed visualization of CMs, HMMs and their comparisions
 description:         cmv is a collection of tools for the visualisation of Hidden Markov Models (HMMV) and RNA-family models (CMV). Moreover it can visualise comparisons of these models (HMMCV,CMCV), and annotate linked regions in the structural alignments they were constructed from and via, 3rd party tools, in their consensus secondary structure.
 license:             GPL-3
 license-file:        LICENSE
 author:              Florian Eggenhofer
 maintainer:          egg@informatik.uni-freiburg.de
-Tested-With: GHC == 8.0.2, GHC == 8.2.2
+Tested-With: GHC == 8.4.4
 category:            Bioinformatics
 build-type:          Simple
 cabal-version:       >=1.8
@@ -20,8 +20,8 @@ source-repository head
 
 source-repository this
   type:     git
-  location: https://github.com/eggzilla/cmv/tree/1.0.8
-  tag:      1.0.8
+  location: https://github.com/eggzilla/cmv/tree/1.1.0
+  tag:      1.1.0
 
 library
   -- Modules exported by the library.
@@ -33,7 +33,7 @@ library
 
   -- Other library packages from which modules are imported.
   build-depends:       base >=4.5 && <5, parsec>=3.1.9, diagrams-lib, BiobaseInfernal, text, vector, ParsecTools, diagrams-cairo, filepath, colour, PrimitiveArray, BiobaseXNA, mtl, directory, either-unwrap, SVGFonts>=1.6.0.2, BioHMM>=1.2.0, StockholmAlignment>=1.1.2, BiobaseTypes,containers,diagrams-core
-  
+
   -- Directories containing source files.
   hs-source-dirs:      src
 
@@ -46,26 +46,26 @@ executable CMCV
 executable CMV
   Hs-Source-Dirs:      ./src/cmv/
   main-is:	       CMVisualisation.hs
-  ghc-options:         -Wall 
+  ghc-options:         -Wall
   build-depends:       base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, StockholmAlignment>=1.1.2
 
 executable CMCWStoCMCV
   Hs-Source-Dirs:      ./src/cmcv/
   main-is:	       cmcwsvtocmcv.hs
-  ghc-options:         -Wall 
+  ghc-options:         -Wall
   build-depends:       base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath
 
 executable CMCtoHMMC
   Hs-Source-Dirs:      ./src/cmcv/
   main-is:	       cmctohmmc.hs
-  ghc-options:         -Wall 
+  ghc-options:         -Wall
   build-depends:       base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0
 
 executable HMMCtoCMC
   Hs-Source-Dirs:      ./src/cmcv/
   main-is:	       hmmctocmc.hs
-  ghc-options:         -Wall 
-  build-depends:       base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0 
+  ghc-options:         -Wall
+  build-depends:       base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0
 
 executable CMVJson
   Hs-Source-Dirs:      ./src/cmv/
@@ -84,3 +84,9 @@ executable HMMV
   main-is:	       HMMVisualisation.hs
   ghc-options:         -Wall
   build-depends:       base >=4.5, cmdargs, diagrams-lib, parsec, colour, containers, bytestring, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0, StockholmAlignment>=1.1.2
+
+executable StockholmV
+  Hs-Source-Dirs:      ./src/Stockholm/
+  main-is:	       StockholmVisualisation.hs
+  ghc-options:         -Wall
+  build-depends:       base >=4.5, cmdargs, diagrams-lib, parsec, colour, containers, bytestring, text, vector, directory, cmv, either-unwrap, filepath, StockholmAlignment>=1.1.2