fix up github release

.gitignore

@@ -11,3 +11,4 @@ nixpkgs/inparanoid/*.zip
 nixpkgs/inparanoid/*.tar.gz
 Paths_*
 *.lock
+release-*

CHANGELOG.md

@@ -7,10 +7,17 @@ and [A successful Git branching model](https://nvie.com/posts/a-successful-git-b
 
 ## [unreleased]
 
+## [0.9.1] - 2019-12-06
+### Fixed
+- install.sh should work now
+- Upload custom release archives because git/github fails on submodules
+- Improved UTF-8 locale handling
+
 ## [0.9.0] - 2019-12-05
 ### Changed
 - Move development to `develop` branch; `master` will be for releases
 - Start using semantic versioning
 
-[unreleased]: https://github.com/jefdaj/shortcut/compare/v0.9.0...HEAD
+[unreleased]: https://github.com/jefdaj/shortcut/compare/v0.9.1...HEAD
+[0.9.1]: https://github.com/jefdaj/shortcut/releases/tag/v0.9.1
 [0.9.0]: https://github.com/jefdaj/shortcut/releases/tag/v0.9.0

README.md

@@ -16,7 +16,8 @@ Quick Start
 Run [install.sh](install.sh) to install everything on Mac or Linux:
 
 ``` .bash
-curl https://raw.githubusercontent.com/jefdaj/shortcut/master/install.sh | sh
+curl https://raw.githubusercontent.com/jefdaj/shortcut/master/install.sh | bash
+source $HOME/.nix-profile/etc/profile.d/nix.sh
 ```
 
 See [the demo site][1] for a more detailed overview, tutorial, interactive

ShortCut.cabal

@@ -2,7 +2,7 @@ name:               ShortCut
 synopsis:           Short, reproducible phylogenomic cuts
 author:             Jeffrey David Johnson
 maintainer:         [email protected]
-version:            0.9.0
+version:            0.9.1
 license:            AGPL-3
 license-file:       LICENSE
 build-type:         Simple

ShortCut.hs

@@ -37,8 +37,8 @@ main = withFileLogging "shortcut.log" $ do
   debugS' "shortcut.main" "starting"
 
   -- TODO does this work everywhere?
-  _ <- setLocale LC_ALL $ Just "en_US.UTF-8"
-  setEnv "LANG" "en_US.UTF-8" -- TODO and is this part superfluous now?
+  -- _ <- setLocale LC_ALL $ Just "en_US.UTF-8"
+  -- setEnv "LANG" "en_US.UTF-8" -- TODO and is this part superfluous now?
   -- hSetBuffering stdin  LineBuffering
   -- hSetBuffering stdout LineBuffering
 

default.nix

@@ -32,12 +32,10 @@ let
 
     buildDepends = (drv.buildDepends or []) ++ [ makeWrapper ] ++ runDepends;
 
-    # TODO set LC_ALL or similar here?
     # TODO PYTHONPATH?
     postInstall = ''
       ${drv.postInstall or ""}
       wrapProgram "$out/bin/shortcut" \
-        --set LC_ALL en_US.UTF-8 \
         --set LANG en_US.UTF-8 \
         --set LANGUAGE en_US.UTF-8 \
         --prefix PATH : "${pkgs.lib.makeBinPath runDepends}"'' +

dev-scripts/build-release-archives.sh

@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+
+# Github releases fail to include submodules, so we have to fix them manually.
+# Push the release tag, run this, then go to the "edit tag" page on Github and attach the files.
+# Usage: ./dev-scripts/build-release-archives.sh <git tag>
+
+set -E
+
+tag="$1"
+
+rm -rf release-${tag}
+mkdir release-${tag}
+pushd release-${tag}
+
+git clone http://github.com/jefdaj/shortcut
+pushd shortcut
+git checkout ${tag}
+git submodule update --init --recursive
+rm -rf .git*
+popd
+
+tar cvzf shortcut-${tag}.tar.gz shortcut
+zip -r   shortcut-${tag}.zip    shortcut
+
+echo "release files:"
+du -h shortcut-*

install.sh

@@ -1,9 +1,9 @@
 #/usr/bin/env bash
 
 case "$(uname)" in
-  Linux ); export NIX_PATH=nixpkgs=channel:nixpkgs-19.03;;
-  Darwin); export NIX_PATH=nixpkgs=channel:nixpkgs-19.03-darwin;;
-  *); (echo "Sorry, unsupported OS: $(uname). Manual install?"; exit 1)
+  Linux ) export CHANNEL=nixos-19.09 ;;
+  Darwin) export CHANNEL=nixpkgs-19.09-darwin ;;
+  *) (echo "Sorry, unsupported OS: $(uname). Manual install?"; exit 1) ;;
 esac
 
 echo "Installing the Nix package manager..."
@@ -12,12 +12,15 @@ if [[ $? != 0 ]]; then
   curl https://nixos.org/nix/install | sh
   source $HOME/.nix-profile/etc/profile.d/nix.sh
 fi
+# the options thing works around: https://github.com/NixOS/nix/issues/2733
+nix-channel --add https://nixos.org/channels/${CHANNEL}
+nix-channel --options substituters "" --update
 
 # TODO name the cache shortcut?
 echo "Setting Nix to use the ShortCut package cache..."
 nix-env -iA cachix -f https://cachix.org/api/v1/install
 [[ "$(uname)" == Darwin ]] && sudo cachix use jefdaj || cachix use jefdaj
 
 echo "Installing ShortCut from GitHub..."
-branch='master'
-nix-env -i -f https://github.com/jefdaj/shortcut/archive/${branch}.tar.gz
+archive='https://github.com/jefdaj/shortcut/files/3934119/shortcut-v0.9.1.tar.gz'
+nix-env -i -f $archive

modules.nix

@@ -2,12 +2,11 @@ with import ./nixpkgs;
 let
   mkModule = src: extraRunDeps: extraWraps:
     let name = "Shortcut-" + baseNameOf src;
-        runDeps = [ coreutils ] ++ extraRunDeps;
+        runDeps = [ bash coreutils ] ++ extraRunDeps;
     in stdenv.mkDerivation {
       inherit src name extraRunDeps extraWraps;
       buildInputs = [ makeWrapper ] ++ extraRunDeps;
       builder = writeScript "builder.sh" ''
-        #!/usr/bin/env bash
         source ${stdenv}/setup
         mkdir -p $out/bin
         for script in $src/*; do

shell.nix

@@ -4,6 +4,7 @@ let
   shortcut = import ./default.nix;
   devDepends = [
     stack
+    zip
     # pypi2nix
   ];
 
@@ -15,7 +16,6 @@ in haskell.lib.overrideCabal shortcut (drv: {
   # TODO is the find command going? that could maybe make the difference
   shellHook = ''
     ${drv.shellHook or ""}
-    export LC_ALL=en_US.UTF-8
     export LANG=en_US.UTF-8
     export LANGUAGE=en_US.UTF-8
     # export TASTY_HIDE_SUCCESSES=True

shortcut.nix

@@ -11,23 +11,11 @@
 }:
 mkDerivation {
   pname = "ShortCut";
-  version = "0.8.4.11";
+  version = "0.9.1";
   src = ./.;
   isLibrary = true;
   isExecutable = true;
   enableSeparateDataOutput = true;
-  libraryHaskellDepends = [
-    ansi-terminal base bytestring concurrent-extra configurator
-    containers cryptohash data-default-class directory dlist docopt
-    download filelock filepath Glob haskeline hspec logging MissingH
-    mtl parsec path path-io posix-escape pretty process progress-meter
-    QuickCheck random random-shuffle raw-strings-qq regex-compat
-    regex-posix retry safe-exceptions scientific setlocale shake
-    silently split strict tasty tasty-golden tasty-hspec tasty-hunit
-    tasty-quickcheck temporary terminal-size text time transformers
-    unbounded-delays unix utility-ht
-  ];
-  libraryPkgconfigDepends = [ zlib ];
   executableHaskellDepends = [
     ansi-terminal base bytestring concurrent-extra configurator
     containers cryptohash data-default-class directory dlist docopt

singularity.sh

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 
 # TODO why is setting it here different from inside singularity?
-export LC_ALL="en_US.UTF-8"
+export LC_ALL="en_US.utf8"
 
 condo=/clusterfs/rosalind/users
 scratch=/global/scratch