Updating for v1.1.1 release

Author: recursion-ninja

efficient-implied-alignment.cabal

@@ -1,4 +1,4 @@
-cabal-version:  2.2
+cabal-version:  3.0
 category:       Algorithms
 build-type:     Simple
 
@@ -7,9 +7,9 @@ version:        1.1.1
 
 author:         Alex Washburn
 maintainer:     [email protected]
-copyright:      2020 Alex Washburn
+copyright:      2019 Alex Washburn
 license:        BSD-3-Clause
-license-file:   LICENSE
+license-file:   doc/LICENSE
 
 synopsis:       Proof of concept of efficient multiple string alignment
 
@@ -21,7 +21,7 @@ description:    Using a commutative, binary string alignment operator and a
                 case /O(n*k*log(k))/ and the pre-order traversal should be
                 /O(n*k)/.
 
-homepage:       https://github.com/recursion-ninja/efficient-implied-alignment#readme
+homepage:       https://github.com/recursion-ninja/efficient-implied-alignment
 bug-reports:    https://github.com/recursion-ninja/efficient-implied-alignment/issues
 
 tested-with:
@@ -32,6 +32,7 @@ tested-with:
 
 extra-source-files:
     doc/CHANGELOG.md
+    doc/LICENSE
     doc/README.md
 
 source-repository head

makefile

@@ -8,21 +8,14 @@
 
 dir-bin         := ./bin
 dir-data        := replicate-results
-bin-aln         := implied-align
-bin-aln-path    := $(dir-bin)/$(bin-aln)
-bin-gen         := generate-timings
-bin-gen-path    := $(dir-bin)/$(bin-gen)
+programs-needed := generate-timings implied-align newick-add-delete-taxon reduce-fasta
+programs-placed := $(addprefix $(dir-bin)/,$(programs-needed))
 measure-script  := measure-scaling-performance.sh
 measure-dataset := $(dir-bin)/$(measure-script) using
-prerequisites   := $(bin-aln-path) $(bin-aln-path) ensure-python ensure-workspace
-
+prerequisites   := $(programs-placed) ensure-python ensure-workspace
 
 # All synonyms for replicating the paper's results.
-replicate: results
-
-reproduce: results
-
-results:   fungi metazoa pathological
+replicate reproduce results: fungi metazoa pathological
 
 
 # Install dependencies required to replicate results.
@@ -45,16 +38,20 @@ ensure-workspace:
 
 
 # Build binaries
-require := ensure-haskell $(wildcard app/**/*.hs) $(wildcard src/**/*.hs)
-install := ghcup run --ghc 9.2.1 --cabal 3.6.2.0 -- \
-		cabal update &&	cabal install $(bin-gen) $(bin-aln) \
-		--installdir=$(dir-bin) --install-method=copy
+project := cabal.project efficient-implied-alignment.cabal
+sources := $(wildcard app/**/*.hs) $(wildcard src/**/*.hs)
+require := ensure-haskell $(project) $(sources)
+compile := ghcup run --ghc 9.2.1 --cabal 3.6.2.0 --
+
+install: $(refresh) $(require)
+	@$(compile) cabal install \
+		$(programs-needed) --installdir=$(dir-bin) --install-method=copy
 
-$(bin-aln-path): $(require)
-	@$(install)
+refresh:
+	@$(compile) cabal update
 
-$(bin-gen-path): $(require)
-	@$(install)
+$(programs-placed):
+	@$(MAKE) --no-print-directory install
 
 
 # Generate timing data of data sets
@@ -95,7 +92,21 @@ measure:
 
 # Clean up after replicating results
 clean:
-	@rm -fr replicate-results
-	@rm -fr dist-newstyle
-	@rm -f  $(bin-aln-path)
-	@rm -f  $(bin-gen-path)
+	rm -fr replicate-results
+	rm -fr dist-newstyle
+	rm -f  $(programs-placed)
+
+.PHONY: \
+clean \
+ensure-haskell \
+ensure-python \
+ensure-workspace \
+fungi \
+install \
+measure \
+metazoa \
+pathological \
+refresh \
+replicate \
+reproduce \
+results