Finalizing refactoring of 'replicate results'

Author: recursion-ninja

README.md

@@ -0,0 +1 @@
+doc/README.md

README.md

@@ -380,6 +380,7 @@ timeFilePoint taxaNumPadder strLenPadder counter tcmPath fp = do
             , "--output"
             , "/dev/null"
             ]
+    putStrLn commandStr
 
     p <- makeCleanProcess counter [] commandStr
 

app/generate-timings/Main.hs

@@ -1,5 +1,12 @@
 # Revision history for commutative-multi-string-alignment
 
+## 1.1.1 -- 2022-03-01
+
+* Refactoring replicate results script
+* Droppping `stack` build support
+
+
+
 ## 1.1.0 -- 2022-02-23
 
 * Added support for GHC `9.0.*` and `9.2.*`

bin/measure-scaling-performance.sh

@@ -0,0 +1,40 @@
+ Efficient Implied Alignment
+=============================
+
+[![DOI:10.1186/s12859-020-03595-2](https://zenodo.org/badge/DOI/10.1186/s12859-020-03595-2.svg)](https://doi.org/10.1186/s12859-020-03595-2)
+
+This repository hosts the program `implied-align` implementing the algorithm described in the paper *Efficient Implied Alignment* and a script to replicate the results of the paper.
+
+### Installation of `implied-align`
+
+You can build and install `implied-align` from source using the Haskell build system `ghcup` via the supplied `makefile` from the source directory of this project:
+
+```
+$ make install
+```
+
+After the `make install` command has completed, the `implied-align` binary will be placed in this project's `bin` directory.
+
+### Running `implied-align`
+
+The `implied-align` program takes a number of command line arguments to specify inputs and outputs. For more information run the following command:
+
+```
+$ implied-align --help
+```
+
+### Replicating results of the paper
+
+For convience of replicating the results of the paper, a "replicate-results" script has been provided. All that is need to replicate the paper's results is to run the following command:
+
+```
+$ make replicate
+```
+
+This will create a `replicate-results` directory, with sub directories `csv`, `data`, `img`, `taxa`, and `tree`. 
+ 
+ - The `taxa` directory holds temporary files used in pruning the data-sets. 
+ - The `data` & `tree` directories hold the pruned input files for the data-sets.
+ - The `csv` directory holds the timing information measured during the replication of the results.
+ - The `img` directory holds the generted images from the results.
+ 

runtime-linear-model.R renamed to bin/runtime-linear-model.R

@@ -3,7 +3,7 @@ category:       Algorithms
 build-type:     Simple
 
 name:           efficient-implied-alignment
-version:        1.1.0
+version:        1.1.1
 
 author:         Alex Washburn
 maintainer:     github@recursion.ninja
@@ -31,8 +31,8 @@ tested-with:
     GHC == 9.2.1
 
 extra-source-files:
-    ChangeLog.md
-    README.md
+    doc/CHANGELOG.md
+    doc/README.md
 
 source-repository head
   type: git