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Build Scripts with Perfect Dependencies [article]

Sarah Spall and Neil Mitchell and Sam Tobin-Hochstadt
2020 arXiv   pre-print
Build scripts for most build systems describe the actions to run, and the dependencies between those actions---but often build scripts get those dependencies wrong.  ...  Most build scripts have both too few dependencies (leading to incorrect build outputs) and too many dependencies (leading to excessive rebuilds and reduced parallelism).  ...  Build scripts (Mokhov et al. 2018 ) describe commands to run and dependencies to respect.  ... 
arXiv:2007.12737v1 fatcat:lndgdlf75jdjnbsfwrjp2oe66e

Design recovery and maintenance of build systems

Bram Adams, Herman Tromp, Kris de Schutter, Wolfgang de Meuter
2007 Conference on Software Maintenance, Proceedings of the  
The build system forms an indispensable part of any software project. It needs to evolve in parallel with the source code in order to build, test and install the software.  ...  At its heart the framework makes the build's dependency graph available in a tangible way.  ...  AO is a perfect fit for these kinds of refactorings.  ... 
doi:10.1109/icsm.2007.4362624 dblp:conf/icsm/AdamsTSM07 fatcat:kdlcvqghejg5llsyxb4mpkuyve

Forward Build Systems, Formally [article]

Sarah Spall, Neil Mitchell, Sam Tobin-Hochstadt
2022 arXiv   pre-print
In this paper, we address the correctness of forward build systems, which automatically determine the dependency structure of the build, rather than having it specified by the programmer.  ...  Of course, realistic build systems avoid repeated work, stop early when possible, and run commands in parallel, and we prove that these optimizations, as embodied in the recent forward build system Rattle  ...  by executing with script.  ... 
arXiv:2202.05328v1 fatcat:s5a56brrurdutmvmoi3mvj4ity

LEMPAS: A make-do lemmatizer for the Swedish PAROLE-corpus

Silvie Cinková, Jan Pomikálek
2006 Prague Bulletin of Mathematical Linguistics  
., 2004) on Swedish, since many of the desirable features of the Sketch Engine, such as building word sketches, are only available for lemmatized corpora.  ...  The lemmatization is tag-dependent. We used a simple regular expressions syntax to build the basic lemmatization rules.  ...  LEMPAS comprises a sed script and a complementary Perl script. The sed script gathered related inflection forms, while the Perl script corrected the pre-lemmas to comply with headwords.  ... 
dblp:journals/pbml/CinkovaP06 fatcat:4qhenta7efawrnyrsz67kgr7iu

MicrosatDesign is a pipeline for transforming sequencer trace files into DNA markers

Vasanth Singan, John K. Colbourne
2005 CGB Technical Report  
MicrosatDesign version 2.0 is freely available as a script that works on any UNIX based platforms where Perl v5.8  ...  Our prgram integrates a suite of computational programs to automatically build a microsatellite primer database from the raw output of large sequencing projects.  ...  By design, MicrosatDesign calls EMBOSS etandem to identify perfect dinucleotide repeats with a minimum repeat count of 5, and to identify perfect tri-and tetra-nucleotide repeats with minimum repeat counts  ... 
doi:10.2506/cgbtr-200501 fatcat:xyw3b2jivvg2rpqqa5j7y35dzi

Detecting microsatellites in genome data: variance in definitions and bioinformatic approaches cause systematic bias

Angelika Merkel, Neil J Gemmell
2008 Evolutionary Bioinformatics  
These differences arise because varying definitions of microsatellites, spanning repeat size, array length and array composition, are used in different search paradigms, with minimum array length being  ...  and Schlötterer (2003) C-script, -motif search for consecutive sequence stretches Perfect repeats (incl.  ...  Perfect repeats Pattern size: 1, 2, 3, 4, 5, 6bp Minimum length: 10bp Lim et al. (2004) C++ script, -base-by-base search using adjacent sliding windows for alignment Perfect repeats Pattern  ... 
pmid:19204802 pmcid:PMC2614199 fatcat:lk5p3rz3ozbkpfqxwti6ku37ny

Portage: Bringing Hackers' Wisdom to Science [article]

Guilherme Amadio, Benda Xu
2016 arXiv   pre-print
Providing users of HPC systems with a wide variety of up to date software packages is a challenging task.  ...  USE flags affect which dependencies are required to build a package, which allows, for example, a headless server to be installed with a lighter system footprint, by stripping all options for building  ...  It must also be able to distinguish between build time, run time, and post build dependencies, and be able to force package rebuilds when configuration options of dependencies change, without rebuilding  ... 
arXiv:1610.02742v1 fatcat:z32wdu3vund4nmsdyl3nwqvueq

Page 101 of American Chiropractic Association. The ACA Journal of Chiropractic Vol. 31, Issue 4 [page]

1994 American Chiropractic Association. The ACA Journal of Chiropractic  
35mm SLIDEISOUND PROGRAM IS PERFECT FOR GROUP USE PREVENTING BACK INJURY Based on Original Script by M.D. Jacobs, D.C. and F.  ...  ^MERICA IS^GING Build good relations with older citizens and expand your practice How to add years to LIFE. A ^ ■f I How to add LIFE to years.  ... 

Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology

Stephen J. Goodswen, Paul J. Kennedy, John T. Ellis
2014 Bioinformatics  
To build proteome: Change directory to ~/vacceed/start and type… perl startup build <pathogen> e.g. perl startup build tg Description of arguments: 'build' instructs the script to build the proteome of  ...  The programs to install depend on which of the following two main tasks you intend to perform: 1) build a proteome for the target pathogen and/or 2) run the vaccine candidate discovery pipeline.  ... 
doi:10.1093/bioinformatics/btu300 pmid:24790156 pmcid:PMC4207429 fatcat:hr6r5apn7ngh3ikegsu5yqshmm

The Java Build Framework: Large Scale Compilation [article]

Pedro Martins and Rohan Achar and Cristina V. Lopes
2018 arXiv   pre-print
Two elements are at the core: a very large repository of JAR files, and techniques of resolution of compilation faults and dependencies.  ...  We present the Java Build Framework, a method and tool capable of automatically compiling a large percentage of Java projects available in open source repositories like GitHub.  ...  After this round, the projects that build are stored with the same information as described before, now with build scripts that contain encoding and dependency information that is specific to the actual  ... 
arXiv:1804.04621v1 fatcat:tguajllrc5ecjbnjrgvu6psjti

ParaMonte: A high-performance serial/parallel Monte Carlo simulation library for C, C++, Fortran

Amir Shahmoradi, Fatemeh Bagheri
2021 Zenodo  
The ParaMonte library has been developed with the design goal of unifying the automation, accessibility, high-performance, scalability, and reproducibility of Monte Carlo simulations.  ...  implementation of the library includes ParaDRAM, a Parallel Delayed-Rejection Adaptive Metropolis Markov Chain Monte Carlo sampler, accessible from a wide range of programming languages including C, C++, Fortran, with  ...  These prebuilt libraries automatically ship with the language-specific example codes and build scripts that fully automate the process of building and running the examples.  ... 
doi:10.5281/zenodo.4739757 fatcat:qcf4fjmdkrgxvnipzuvkz7rdci

Computational Design of Parametric Scripts for Digital Fabrication of Curved Structures

Sergio Araya Goldberg
2006 International Journal of Architectural Computing  
This paper explores strategies for building toolchains to design, develop and fabricate architectural designs.  ...  I describe this through a series of experiments, using parametric design environments and scripted functions, implementing certain techniques to fabricate these designs using rapid prototyping machines  ...  New computational tools however, called parametric design environments, allow programming these dependencies, with variables called parameters, between one point and another, and build the rules to trace  ... 
doi:10.1260/147807706778658801 fatcat:e4yt6hlqvbekbemfepelbz6zxy

A Hybrid Approach to English to Malayalam Machine Translation

Nithya B, Shibily Joseph
2013 International Journal of Computer Applications  
This hybrid approach extends the baseline statistical machine translator with a translation memory.  ...  GIZA++ implements IBM-4 alignment model with a dependency of word classes and also implement an alignment model based on Hidden Markov model.  ...  The evaluation was done by running multi-bleu.perl script with the reference files and MT output.  ... 
doi:10.5120/14031-1816 fatcat:w4aqnqv25fcsdjzv552f4bb6du

Parametric Urbanism and Environment Optimization: Toward a Quality Environmental Urban Morphology

Yingyi Zhang, Chang Liu
2021 International Journal of Environmental Research and Public Health  
This paper critically assesses environmental optimization with a focus on parametric urbanism.  ...  Parametric thinking has found wide acceptance in both the building industry and environmental sciences.  ...  However, it does not necessarily result in perfect environmental optimization strategies.  ... 
doi:10.3390/ijerph18073558 pmid:33808119 fatcat:ubqeiy2sozevlobdr326m25wny

ParaMonte: A high-performance serial/parallel Monte Carlo simulation library for C, C++, Fortran

Amir Shahmoradi, Fatemeh Bagheri
2021 Journal of Open Source Software  
The ParaMonte library has been developed with the design goal of unifying the automation, accessibility, high-performance, scalability, and reproducibility of Monte Carlo simulations.  ...  implementation of the library includes ParaDRAM, a Parallel Delayed-Rejection Adaptive Metropolis Markov Chain Monte Carlo sampler, accessible from a wide range of programming languages including C, C++, Fortran, with  ...  These prebuilt libraries automatically ship with the language-specific example codes and build scripts that fully automate the process of building and running the examples.  ... 
doi:10.21105/joss.02741 fatcat:fvmemcxqhjhv5b6nikpsbxndm4
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