v0.47.2 - PeerJ submission (number two)

The initial submission was flagged because I was missing code for the
comparison between morloc and other workflow approaches. When I
submitted the paper, I had no such code and meant the diagram to be more
conceptual. However, the editor's request was quite reasonable. So I
reimplemented the case study with bash, python, snakemake and nextflow.
This is all in a different repo. This release is needed for the
lighter-weight containers I want to share with my reviewers and readers.

 * made the build static
 * fixed the dockerfile
 * exported the vim-syntax file out to its own repo
 * added a --version option
 * upgraded to LTS 22.18

container/ubuntu/base/Dockerfile

@@ -0,0 +1,82 @@
+###############################################################################
+# Stage 1: Build the morloc compiler 
+FROM alpine:3.19 as morloc-build
+
+RUN apk update \
+  && apk add --no-cache git \
+  && apk add --no-cache gmp-dev \
+  && apk add --no-cache build-base \
+  && apk add --no-cache ncurses \
+  && apk add --no-cache curl
+
+# Build morloc
+RUN curl -SL https://get.haskellstack.org/ | sh
+
+RUN git clone https://github.com/morloc-project/morloc
+
+# Build morloc
+RUN cd morloc && stack install
+
+
+###############################################################################
+# Stage 2: Copy just the compiler binary
+FROM ubuntu:22.04 AS morloc-base
+COPY --from=morloc-build /root/.local/bin/morloc /bin/morloc
+
+WORKDIR $HOME
+
+RUN apt-get update
+
+# Set the timezone, this avoids hanging later on
+RUN DEBIAN_FRONTEND=noninteractive TZ=Antarctica/Troll apt-get -y install tzdata
+
+RUN apt-get install -y r-base python3.10 python3-pip libgsl-dev git
+
+# Set up Python environment
+RUN pip3.10 install pymorlocinternals
+
+# Set up C++ environment
+RUN mkdir -p $HOME/.morloc/include \
+  && git clone https://github.com/morloclib/mlccpptypes $HOME/.morloc/include/mlccpptypes
+
+# Set up R environment
+RUN Rscript -e 'install.packages("remotes", repos  = "https://cloud.r-project.org")'
+RUN Rscript -e 'remotes::install_github("morloc-project/rmorlocinternals", dependencies=TRUE)'
+
+# Setup the morloc home
+RUN mkdir -p $HOME/.morloc/lib
+RUN mkdir -p $HOME/.morloc/tmp
+RUN echo "home : $HOME/.morloc" > ~/.morloc/config && \
+    echo "library : $HOME/.morloc/lib" >> $HOME/.morloc/config && \
+    echo "tmpdir : $HOME/.morloc/tmp" >> $HOME/.morloc/config && \
+    echo "lang_python3 : python3" >> $HOME/.morloc/config
+
+# Install the morloc modules that are required for the morloc tests to pass
+RUN morloc install prelude
+RUN morloc install types
+RUN morloc install conventions
+RUN morloc install base
+RUN morloc install rbase
+RUN morloc install pybase
+RUN morloc install cppbase
+RUN morloc install math
+
+RUN apt-get install -y vim
+
+# Copy over custom vimrc
+COPY assets/vimrc /root/.vimrc
+COPY assets/README /root/README
+
+# Set up vim highlighting for morloc
+RUN git clone https://github.com/morloc-project/vimmorloc \
+  && mkdir -p ~/.vim/syntax/ \
+  && mkdir -p ~/.vim/ftdetect/ \
+  && cp vimmorloc/loc.vim ~/.vim/syntax/ \
+  && echo 'au BufRead,BufNewFile *.loc set filetype=loc' > ~/.vim/ftdetect/loc.vim \
+  && rm -rf vimmorloc
+
+RUN git clone https://github.com/morloc-project/morloc \
+  && mv morloc/test-suite/golden-tests ~/tests
+
+# Cleanup to reduce image size
+RUN apt-get clean && rm -rf /var/lib/apt/lists/*

container/ubuntu/base/Makefile

@@ -0,0 +1,7 @@
+# Build the required docker image
+build:
+	docker build -t morloc-base .
+
+# Open a shell
+shell:
+	docker run -w "/root" -it morloc-base /bin/bash

container/ubuntu/base/assets/README

@@ -0,0 +1,5 @@
+This container has a full morloc installation and language support for R, Python3, and C++.
+
+The ~/tests folder contains a set of tests from the morloc test suite. These may
+serve as simplistic examples of morloc scripts. Though they are designed for
+testing the language not pedagogy.

container/ubuntu/base/assets/vimrc

@@ -0,0 +1,16 @@
+" Jump to the last position when reopening a file
+au BufReadPost * if line("'\"") > 1 && line("'\"") <= line("$") | exe "normal! g'\"" | endif
+
+" Load indentation rules and plugins according to the detected filetype.
+filetype plugin indent on
+syntax on
+set showcmd             " Show (partial) command in status line.
+set showmatch           " Show matching brackets.
+set ignorecase          " Do case insensitive matching
+set smartcase           " Do smart case matching
+set incsearch           " Incremental search
+set autowrite           " Automatically save before commands like :next and :make
+set hidden              " Hide buffers when they are abandoned
+
+" An OK colorscheme
+colorscheme torte

executable/UI.hs

@@ -8,12 +8,16 @@ module UI (
 ) where
 
 import Options.Applicative
+import qualified Options.Applicative.Extra as OAE
+
+version :: String
+version = "v0.47.2"   -- FIXME: HARDCODED VERSION NUMBER!!!
 
 opts :: ParserInfo CliCommand
-opts = info (cliParser <**> helper)
+opts = info (cliParser <**> helper <**> OAE.simpleVersioner version)
   (    fullDesc
     <> progDesc "call 'morloc make -h', 'morloc install -h', etc for details"
-    <> header "morloc v0.47.1"  -- FIXME: HARDCODED VERSION NUMBER!!!
+    <> header ("morloc " <> version)
   )
 
 

library/Morloc/Config.hs

@@ -20,10 +20,10 @@ module Morloc.Config
 import Morloc.Data.Doc
 import Morloc.Namespace
 import qualified Morloc.Language as ML
-import qualified Data.HashMap.Strict as H
 import qualified Data.Yaml.Config as YC
 import qualified Morloc.Data.Text as MT
 import qualified Morloc.System as MS
+import qualified Data.Aeson.KeyMap as K
 
 
 getDefaultConfigFilepath :: IO Path
@@ -35,10 +35,10 @@ loadDefaultMorlocConfig = do
   defaults <- defaultFields
   return $
     Config
-      (MT.unpack $ defaults H.! "home")
-      (MT.unpack $ defaults H.! "source")
-      (MT.unpack $ defaults H.! "plane")
-      (MT.unpack $ defaults H.! "tmpdir")
+      (MT.unpack . fromJust $ defaults K.!? "home")
+      (MT.unpack . fromJust $ defaults K.!? "source")
+      (MT.unpack . fromJust $ defaults K.!? "plane")
+      (MT.unpack . fromJust $ defaults K.!? "tmpdir")
       "python3" -- lang_python3
       "Rscript" -- lang_R
       "perl" -- lang_perl
@@ -86,12 +86,12 @@ buildPoolCallBase c (Just Python3Lang) i =
 buildPoolCallBase _ _ _ = Nothing -- FIXME: add error handling
 
 -- A key value map
-defaultFields :: IO (H.HashMap MT.Text MT.Text)
+defaultFields :: IO (K.KeyMap MT.Text)
 defaultFields = do
   home <- MT.pack <$> getDefaultMorlocHome
   lib <- MT.pack <$> getDefaultMorlocSource
   tmp <- MT.pack <$> getDefaultMorlocTmpDir
-  return $ H.fromList [("home", home), ("source", lib), ("plane", "morloclib"), ("tmpdir", tmp)]
+  return $ K.fromList [("home", home), ("source", lib), ("plane", "morloclib"), ("tmpdir", tmp)]
 
 -- | Get the Morloc home directory (absolute path)
 getDefaultMorlocHome :: IO Path

package.yaml

@@ -1,5 +1,5 @@
 name:             morloc
-version:          0.47.1
+version:          0.47.2
 homepage:         https://github.com/morloc-project/morloc
 synopsis:         A multi-lingual, typed, workflow language
 description:      See GitHub README <https://github.com/morloc-project/morloc#readme>
@@ -16,6 +16,9 @@ extra-source-files:
   - README.md
   - ChangeLog.md
 
+default-extensions:
+  - TypeOperators
+
 dependencies:
   - base
   - aeson
@@ -68,7 +71,16 @@ executables:
       - -threaded
       - -rtsopts
       - -with-rtsopts=-N
+      - -O2
+      # The static build requires a static `libgmp.a` file
+      # On arch, this requires libgmp-static from AUR
+      # On debian systems, libgmp-dev should cover it
+      - -static
       - -haddock
+    cc-options:
+      - -static
+    ld-options:
+      - -static
     dependencies:
       - morloc 
       - base

stack.yaml

@@ -15,7 +15,7 @@
 # resolver:
 #  name: custom-snapshot
 #  location: "./custom-snapshot.yaml"
-resolver: lts-18.28
+resolver: lts-22.18
 
 # User packages to be built.
 # Various formats can be used as shown in the example below.
@@ -37,10 +37,10 @@ resolver: lts-18.28
 # will not be run. This is useful for tweaking upstream packages.
 packages:
 - .
-# Dependency packages to be pulled from upstream that are not in the resolver
-# (e.g., acme-missiles-0.3)
-extra-deps:
- - partial-order-0.2.0.0@sha256:a0d6ddc9ebcfa965a5cbcff1d06d46a79d44ea5a0335c583c2a51bcb41334487,2275
+# # Dependency packages to be pulled from upstream that are not in the resolver
+# # (e.g., acme-missiles-0.3)
+# extra-deps:
+#  - partial-order-0.2.0.0@sha256:a0d6ddc9ebcfa965a5cbcff1d06d46a79d44ea5a0335c583c2a51bcb41334487,2275
 
 # Override default flag values for local packages and extra-deps
 # flags: {}