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• Your thoughts on Best Practices for Scientific Computing?

  - by John Smith

  A recent paper by Wilson et al (2014) pointed out 24 Best Practices for scientific programming. It's worth to have a look. I would like to hear opinions about these points from experienced programmers in scientific data analysis. Do you think these advices are helpful and practical? Or are they good only in an ideal world? Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, Guy RT, Haddock SHD, Huff KD, Mitchell IM, Plumbley MD, Waugh B, White EP, Wilson P (2014) Best Practices for Scientific Computing. PLoS Biol 12:e1001745. http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001745 Box 1. Summary of Best Practices Write programs for people, not computers. (a) A program should not require its readers to hold more than a handful of facts in memory at once. (b) Make names consistent, distinctive, and meaningful. (c) Make code style and formatting consistent. Let the computer do the work. (a) Make the computer repeat tasks. (b) Save recent commands in a file for re-use. (c) Use a build tool to automate workflows. Make incremental changes. (a) Work in small steps with frequent feedback and course correction. (b) Use a version control system. (c) Put everything that has been created manually in version control. Don’t repeat yourself (or others). (a) Every piece of data must have a single authoritative representation in the system. (b) Modularize code rather than copying and pasting. (c) Re-use code instead of rewriting it. Plan for mistakes. (a) Add assertions to programs to check their operation. (b) Use an off-the-shelf unit testing library. (c) Turn bugs into test cases. (d) Use a symbolic debugger. Optimize software only after it works correctly. (a) Use a profiler to identify bottlenecks. (b) Write code in the highest-level language possible. Document design and purpose, not mechanics. (a) Document interfaces and reasons, not implementations. (b) Refactor code in preference to explaining how it works. (c) Embed the documentation for a piece of software in that software. Collaborate. (a) Use pre-merge code reviews. (b) Use pair programming when bringing someone new up to speed and when tackling particularly tricky problems. (c) Use an issue tracking tool. I'm relatively new to serious programming for scientific data analysis. When I tried to write code for pilot analyses of some of my data last year, I encountered tremendous amount of bugs both in my code and data. Bugs and errors had been around me all the time, but this time it was somewhat overwhelming. I managed to crunch the numbers at last, but I thought I couldn't put up with this mess any longer. Some actions must be taken. Without a sophisticated guide like the article above, I started to adopt "defensive style" of programming since then. A book titled "The Art of Readable Code" helped me a lot. I deployed meticulous input validations or assertions for every function, renamed a lot of variables and functions for better readability, and extracted many subroutines as reusable functions. Recently, I introduced Git and SourceTree for version control. At the moment, because my co-workers are much more reluctant about these issues, the collaboration practices (8a,b,c) have not been introduced. Actually, as the authors admitted, because all of these practices take some amount of time and effort to introduce, it may be generally hard to persuade your reluctant collaborators to comply them. I think I'm asking your opinions because I still suffer from many bugs despite all my effort on many of these practices. Bug fix may be, or should be, faster than before, but I couldn't really measure the improvement. Moreover, much of my time has been invested on defence, meaning that I haven't actually done much data analysis (offence) these days. Where is the point I should stop at in terms of productivity? I've already deployed: 1a,b,c, 2a, 3a,b,c, 4b,c, 5a,d, 6a,b, 7a,7b I'm about to have a go at: 5b,c Not yet: 2b,c, 4a, 7c, 8a,b,c (I could not really see the advantage of using GNU make (2c) for my purpose. Could anyone tell me how it helps my work with MATLAB?)

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• What Functional features are worth a little OOP confusion for the benefits they bring?

  - by bonomo

  After learning functional programming in Haskell and F#, the OOP paradigm seems ass-backwards with classes, interfaces, objects. Which aspects of FP can I bring to work that my co-workers can understand? Are any FP styles worth talking to my boss about retraining my team so that we can use them? Possible aspects of FP: Immutability Partial Application and Currying First Class Functions (function pointers / Functional Objects / Strategy Pattern) Lazy Evaluation (and Monads) Pure Functions (no side effects) Expressions (vs. Statements - each line of code produces a value instead of, or in addition to causing side effects) Recursion Pattern Matching Is it a free-for-all where we can do whatever the programming language supports to the limit that language supports it? Or is there a better guideline?

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• Software development magazines [closed]

  - by Sebastian

  Ive spent the last hour or so browsing the web for professional development magazines. I am mostly interested in the java platform, agile methods, "programming in general" (tutorials on languages or whatever, "hot new stuff" etc) and software craftmanship. My best finding yet was pragpub and maybe MSDN magazine. I am willing to pay and have a Zinio account if anyone knows a magazine about programming that is distributed by them. Ive already browsed a couple of related threads here on stackexchange. ACM and IEEE does not seem relevant, as Im not interested in research articles. Maybe conferences like OOPSLA as somebody mentioned in another thread. PS. I prefer if they are in pdf or readable on kindle or a tablet. DS. BR Sebastian

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• Should a new programmer nowadays start with C/C++ or OOP language? [closed]

  - by deviDave

  I've been a programmer for 15+ years. In my time, we all started with C or C++ and then moved to C# or Java. At that time it was a usual practice. Now, my brother wants to follow my steps and I am not sure what advice to give him. So, I am asking the community for an opinion. Should nowadays new programmer with zero programming knowledge start with functional languages (C, C++, etc.) or he should start directly with OOP languages (Java, C#, etc.)? The reply should be considered in the context of my brother's future assignments. He will mainly work on Java mobile applications as well as ASP.NET web apps. He will have to touch with desktop apps, low level programming, drivers, etc. This is the reason I am not sure if he should ever need to learn functional languages.

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• Scheme vs Haskell for an Introduction to Functional Programming?

  - by haziz

  I am comfortable with programming in C and C#, and will explore C++ in the future. I may be interested in exploring functional programming as a different programming paradigm. I am doing this for fun, my job does not involve computer programming, and am somewhat inspired by the use of functional programming, taught fairly early, in computer science courses in college. Lambda calculus is certainly beyond my mathematical abilities, but I think I can handle functional programming. Which of Haskell or Scheme would serve as a good intro to functional programming? I use emacs as my text editor and would like to be able to configure it more easily in the future which would entail learning Emacs Lisp. My understanding, however, is that Emacs Lisp is fairly different from Scheme and is also more procedural as opposed to functional. I would likely be using "The Little Schemer" book, which I have already bought, if I pursue Scheme (seems to me a little weird from my limited leafing through it). Or would use the "Learn You a Haskell for Great Good" if I pursue Haskell. I would also watch the Intro to Haskell videos by Dr Erik Meijer on Channel 9. Any suggestions, feedback or input appreciated. Thanks. P.S. BTW I also have access to F# since I have Visual Studio 2010 which I use for C# development, but I don't think that should be my main criteria for selecting a language.

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• Dynamic Code for type casting Generic Types 'generically' in C#

  - by Rick Strahl

  C# is a strongly typed language and while that's a fundamental feature of the language there are more and more situations where dynamic types make a lot of sense. I've written quite a bit about how I use dynamic for creating new type extensions: Dynamic Types and DynamicObject References in C# Creating a dynamic, extensible C# Expando Object Creating a dynamic DataReader for dynamic Property Access Today I want to point out an example of a much simpler usage for dynamic that I use occasionally to get around potential static typing issues in C# code especially those concerning generic types. TypeCasting Generics Generic types have been around since .NET 2.0 I've run into a number of situations in the past - especially with generic types that don't implement specific interfaces that can be cast to - where I've been unable to properly cast an object when it's passed to a method or assigned to a property. Granted often this can be a sign of bad design, but in at least some situations the code that needs to be integrated is not under my control so I have to make due with what's available or the parent object is too complex or intermingled to be easily refactored to a new usage scenario. Here's an example that I ran into in my own RazorHosting library - so I have really no excuse, but I also don't see another clean way around it in this case. A Generic Example Imagine I've implemented a generic type like this: public class RazorEngine<TBaseTemplateType> where TBaseTemplateType : RazorTemplateBase, new() You can now happily instantiate new generic versions of this type with custom template bases or even a non-generic version which is implemented like this: public class RazorEngine : RazorEngine<RazorTemplateBase> { public RazorEngine() : base() { } } To instantiate one: var engine = new RazorEngine<MyCustomRazorTemplate>(); Now imagine that the template class receives a reference to the engine when it's instantiated. This code is fired as part of the Engine pipeline when it gets ready to execute the template. It instantiates the template and assigns itself to the template: var template = new TBaseTemplateType() { Engine = this } The problem here is that possibly many variations of RazorEngine<T> can be passed. I can have RazorTemplateBase, RazorFolderHostTemplateBase, CustomRazorTemplateBase etc. as generic parameters and the Engine property has to reflect that somehow. So, how would I cast that? My first inclination was to use an interface on the engine class and then cast to the interface.  Generally that works, but unfortunately here the engine class is generic and has a few members that require the template type in the member signatures. So while I certainly can implement an interface: public interface IRazorEngine<TBaseTemplateType> it doesn't really help for passing this generically templated object to the template class - I still can't cast it if multiple differently typed versions of the generic type could be passed. I have the exact same issue in that I can't specify a 'generic' generic parameter, since there's no underlying base type that's common. In light of this I decided on using object and the following syntax for the property (and the same would be true for a method parameter): public class RazorTemplateBase :MarshalByRefObject,IDisposable { public object Engine {get;set; } } Now because the Engine property is a non-typed object, when I need to do something with this value, I still have no way to cast it explicitly. What I really would need is: public RazorEngine<> Engine { get; set; } but that's not possible. Dynamic to the Rescue Luckily with the dynamic type this sort of thing can be mitigated fairly easily. For example here's a method that uses the Engine property and uses the well known class interface by simply casting the plain object reference to dynamic and then firing away on the properties and methods of the base template class that are common to all templates:/// <summary> /// Allows rendering a dynamic template from a string template /// passing in a model. This is like rendering a partial /// but providing the input as a /// </summary> public virtual string RenderTemplate(string template,object model) { if (template == null) return string.Empty; // if there's no template markup if(!template.Contains("@")) return template; // use dynamic to get around generic type casting dynamic engine = Engine; string result = engine.RenderTemplate(template, model); if (result == null) throw new ApplicationException("RenderTemplate failed: " + engine.ErrorMessage); return result; } Prior to .NET 4.0  I would have had to use Reflection for this sort of thing which would have a been a heck of a lot more verbose, but dynamic makes this so much easier and cleaner and in this case at least the overhead is negliable since it's a single dynamic operation on an otherwise very complex operation call. Dynamic as  a Bailout Sometimes this sort of thing often reeks of a design flaw, and I agree that in hindsight this could have been designed differently. But as is often the case this particular scenario wasn't planned for originally and removing the generic signatures from the base type would break a ton of other code in the framework. Given the existing fairly complex engine design, refactoring an interface to remove generic types just to make this particular code work would have been overkill. Instead dynamic provides a nice and simple and relatively clean solution. Now if there were many other places where this occurs I would probably consider reworking the code to make this cleaner but given this isolated instance and relatively low profile operation use of dynamic seems a valid choice for me. This solution really works anywhere where you might end up with an inheritance structure that doesn't have a common base or interface that is sufficient. In the example above I know what I'm getting but there's no common base type that I can cast to. All that said, it's a good idea to think about use of dynamic before you rush in. In many situations there are alternatives that can still work with static typing. Dynamic definitely has some overhead compared to direct static access of objects, so if possible we should definitely stick to static typing. In the example above the application already uses dynamics extensively for dynamic page page templating and passing models around so introducing dynamics here has very little additional overhead. The operation itself also fires of a fairly resource heavy operation where the overhead of a couple of dynamic member accesses are not a performance issue. So, what's your experience with dynamic as a bailout mechanism? © Rick Strahl, West Wind Technologies, 2005-2012Posted in CSharp   Tweet !function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0];if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src="//platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs"); (function() { var po = document.createElement('script'); po.type = 'text/javascript'; po.async = true; po.src = 'https://apis.google.com/js/plusone.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(po, s); })();

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• Microsoft .NET Web Programming: Web Sites versus Web Applications

  - by SAMIR BHOGAYTA

  In .NET 2.0, Microsoft introduced the Web Site. This was the default way to create a web Project in Visual Studio 2005. In Visual Studio 2008, the Web Application has been restored as the default web Project in Visual Studio/.NET 3.x The Web Site is a file/folder based Project structure. It is designed such that pages are not compiled until they are requested ("on demand"). The advantages to the Web Site are: 1) It is designed to accommodate non-.NET Applications 2) Deployment is as simple as copying files to the target server 3) Any portion of the Web Site can be updated without requiring recompilation of the entire Site. The Web Application is a .dll-based Project structure. ASP.NET pages and supporting files are compiled into assemblies that are then deployed to the target server. Advantages of the Web Application are: 1) Precompiled files do not expose code to an attacker 2) Precompiled files run faster because they are binary data (the Microsoft Intermediate Language, or MSIL) executed by the CLR (Common Language Runtime) 3) References, assemblies, and other project dependencies are built in to the compiled site and automatically managed. They do not need to be manually deployed and/or registered in the Global Assembly Cache: deployment does this for you If you are planning on using automated build and deployment, such as the Team Foundation Server Team Build engine, you will need to have your code in the form of a Web Application. If you have a Web Site, it will not properly compile as a Web Application would. However, all is not lost: it is possible to work around the issue by adding a Web Deployment Project to your Solution and then: a) configuring the Web Deployment Project to precompile your code; and b) configuring your Team Build definition to use the Web Deployment Project as its source for compilation. https://msevents.microsoft.com/cui/WebCastEventDetails.aspx?culture=en-US&EventID=1032380764&CountryCode=US

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• programming practices starting

  - by Tamim Ad Dari

  I have taken my major as computer science and Engineering and I am really confused at this moment. My first course was about learning C and C++ and I learned the basics of those. Now I am really confused what to do next. Some says I should practice algorithms and do contests in ACM-ICPC for now. Others tell me to start software development. But As I started digging its really a vast topic and there are many aspects of these, like web design, web-development, iOS-development, android... etc many things. And I am really confused about what should I do just now. Any advice for me to start with?

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• How do you research while pair programming?

  - by traffichazard

  I've recently started at a new job and pairing has helped me become effective there very quickly. I am, however, having a hard time when we must do brief joint research during our workflow, covering API features, code examples, or command options. My team lead urges us to do all research on our pairing station, rather than our individual laptops, and to synchronize our research by verbally negotiating the steps between different web resources. I research, read, and absorb information differently from my pairing partner, and I feel much more productive when I can follow a thread of research to the next web page exactly when I want to, rather than trying to keep exact pace and place with what my partner's reading. We're both smart and fast, but we can't help moving in different ways and instantaneous velocities when we're figuring stuff out. It seems so much easier to poke around individually for a minute until one of us says "I've got it," then get back together and code. When you pair program, how do you handle short research tasks? What works best for you, and how to you keep in sync with your partner?

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• Dangerous programming

  - by benhowdle89

  Ok, i'm talking pure software/web, i'm not on about code to power Life Support machines or NASA rockets. In terms of software/web development what is the most dangerous single piece of code someone could put into a program (say if they had a grudge against a client/employee) In PHP, the first thing that comes to mind is some sort of file deletion: function EmptyDir($dir) { $handle=opendir($dir); while (($file = readdir($handle))!==false) { echo "$file <br>"; @unlink($dir.'/'.$file); } closedir($handle); } EmptyDir('images'); Or a PHP script that takes a user's sensitive input and posts it to Google sitemap or something? I hope this doesnt get closed off as subjective as there surely must be a ranking order of dangerous code. So i'm asking for the No.1 spot :) DISCLAIMER: I have no grudges against anyone, just curious for the answer!

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• Defensive Programming Techniques.

  - by Pemdas

  I was attempting to identify an element of software engineering that I think is overlooked, not emphasized or not taught in typical undergraduate course work for CS or SE. What I came up is the concept of defensive programing. I would like to hear the communities options on defensive program and/or specific techniques that you use on a regular basis. Also, I would to know if there are any language specific techniques.

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• Is the C programming language still used?

  - by Pankaj Upadhyay

  I am a C# programmer, and most of my development is for websites along with a few Windows application. As far as C goes, I haven't used it in a long time, as there was no need to. It came to me as a surprise when one of my friends said that she needs to learn C for testing jobs, while I was helping her learn C#. I figured that someone would only learn C for testing only if there is development done in C. In my knowledge, all the development related to COM and hardware design are also done in C++. Therefore, learning C doesn't make sense if you need to use C++. I also don't believe in historic significance, so why waste time and money in learning C? Is C is still used in any kind of new software development or anything else?

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• Procedural, Semi-Procedural and Declarative Programming in SQL

  A lot of the time, the key to making SQL databases perform well is to take a break from the keyboard and rethink the way of approaching the problem; and rethinking in terms of a set-based declarative approach. Joe takes a simple discussion abut a problem with a UDF to illustrate the point that ingrained procedural reflexes can often prevent us from seeing simpler set-based techniques.

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• What are functional-programming ways of implementing Conway's Game of Life

  - by George Mauer

  I recently implemented for fun Conway's Game of Life in Javascript (actually coffeescript but same thing). Since javascript can be used as a functional language I was trying to stay to that end of the spectrum. I was not happy with my results. I am a fairly good OO programmer and my solution smacked of same-old-same-old. So long question short: what is the (pseudocode) functional style of doing it? Here is Pseudocode for my attempt: class Node update: (board) -> get number_of_alive_neighbors from board get this_is_alive from board if this_is_alive and number_of_alive_neighbors < 2 then die if this_is_alive and number_of_alive_neighbors > 3 then die if not this_is_alive and number_of_alive_neighbors == 3 then alive class NodeLocations at: (x, y) -> return node value at x,y of: (node) -> return x,y of node class Board getNeighbors: (node) -> use node_locations to check 8 neighbors around node and return count nodes = for 1..100 new Node state = new NodeState(nodes) locations = new NodeLocations(nodes) board = new Board(locations, state) executeRound: state = clone state accumulated_changes = for n in nodes n.update(board) apply accumulated_changes to state board = new Board(locations, state)

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• Programming Geek's CV Design

  - by benhowdle89

  What is the best practice or advice for a programmer's CV? If I were a graphic designer or more of a web designer as opposed to a programmer, then I'd imagine a CV would have a bit more flourish to it. Yet as a programmer, aren't we judged on not only efficiency and results but also creativity, imagination and initiative? Should this be reflected in a CV? Or is it all about the information, no wishy washy designs in sight? Has anyone experimented with an original alternative to a PDF CV with a template from MS Word or Mac Pages?

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• Basic Defensive Database Programming Techniques

  We can all recognise good-quality database code: It doesn't break with every change in the server's configuration, or on upgrade. It isn't affected by concurrent usage, or high workload. In an extract from his forthcoming book, Alex explains just how to go about producing resilient TSQL code that works, and carries on working.

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• Functional programming readability

  - by Jimmy Hoffa

  I'm curious about this because I recall before learning any functional languages, I thought them all horribly, awfully, terribly unreadable. Now that I know Haskell and f#, I find it takes a little longer to read less code, but that little code does far more than an equivalent amount would in an imperative language, so it feels like a net gain and I'm not extremely practiced in functional. Here's my question, I constantly hear from OOP folks that functional style is terribly unreadable. I'm curious if this is the case and I'm deluding myself, or if they took the time to learn a functional language, the whole style would no longer be more unreadable than OOP? Has anybody seen any evidence or got any anecdotes where they saw this go one way or another with frequency enough to possibly say? If writing functionally really is of lower readability than I don't want to keep using it, but I really don't know if that's the case or not..

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• learn the programming language for computing functions about integers

  - by asd

  Hi I know something about Pascal, Mathematica and Matlab, but I dont have any idea about C,C++,C# languages. I want to learn one of the languages that they they are fast and exact to compute some arithmetic functions for large numbers(for example larger than $10^3000$). I asked somebody and he said he used C++ and he said I computed this sequence in less than 10 min. I want to know C, C++, C# and visual kind of theses programs and know which is better for my goal. Let $f$ be an arithmetic function and A={k1,k2,...,kn} are integers in increasing order. Now I want to start with k1 and compare f(ki) with f(k1). If f(ki)f(k1), put ki as k1. Now start with ki, and compare f(kj) with f(ki), for ji. If f(kj)f(ki), put kj as ki, and repeat this procedure. At the end we will have a sub sequence B={L1,...,Lm} of A by this property: f(L(i+1))f(L(i)), for any 1<=i<=m-1 I have written a code for this program with Mathematica, and it take some hours to compute f of ki's or the set B for large numbers. For example, let f is the divisor function of integers. Do you know how to write the code for my purpose in Mathematica or Matlab. Mathematica is preferable.

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• A programming language that does not allow IO. Haskell is not a pure language

  - by TheIronKnuckle

  (I asked this on Stack Overflow and it got closed as off-topic, I was a bit confused until I read the FAQ, which discouraged subjective theoratical debate style questions. The FAQ here doesn't seem to have a problem with it and it sounds like this is a more appropriate place to post. If this gets closed again, forgive me, I'm not trying to troll) Are there any 100% pure languages (as I describe in the Stack Overflow post) out there already and if so, could they feasibly be used to actually do stuff? i.e. do they have an implementation? I'm not looking for raw maths on paper/Pure lambda calculus. However Pure lambda calculus with a compiler or a runtime system attached is something I'd be interested in hearing about.

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• Yet another use of OUTER APPLY in defensive programming

  - by Alexander Kuznetsov

  When a SELECT is used to populate variables from a subquery, it fails to change them if the subquery returns nothing - and that can lead to subtle bugs. We shall use OUTER APPLY to eliminate this problem. Prerequisites All we need is the following mock function that imitates a subquery: CREATE FUNCTION dbo.BoxById ( @BoxId INT ) RETURNS TABLE AS RETURN ( SELECT CAST ( 1 AS INT ) AS [Length] , CAST ( 2 AS INT ) AS [Width] , CAST ( 3 AS INT ) AS [Height] WHERE @BoxId = 1 ) ; Let us assume that this...(read more)

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• Is using ELSE bad programming?

  - by dave.b

  I've often come across bugs that have been caused by using the ELSE construct. A prime example is something along the lines of: If (passwordCheck() == false){ displayMessage(); }else{ letThemIn(); } To me this screams security problem. I know that passwordCheck is likely to be a boolean, but I wouldn't place my applications security on it. What would happen if its a string, int etc? I usually try to avoid using ELSE, and instead opt for two completely separate IF statements to test for what I expect. Anything else then either gets ignored OR is specifically handled. Surely this is a better way to prevent bugs / security issues entering your app. How do you guys do it?

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• Book Review: Defensive Database Programming With SQL Server

  It distils a great deal of practical experience; the writing of it was a considerable task; It packs in a great deal of information. Alex's book shows how to write robust database applications, and we can all learn from it. We took the book to a critic who never minces his words, and were relieved to find that Joe Celko liked it.

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• Is there any officially recognized, specific determinants that make a language programming/scripting?

  - by Dan

  I remember when I was first learning web-based programming everyone was intent on JavaScript not being a "programming language," but rather a scripting language; I have not heard that argument in quite a while now. I hear a lot of languages, like perl for example, referred to at different times as both a scripting and programming language. I know that a scripting language is less capable than a programming language, but where exactly does the line lie? Citation would be appreciated.

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• Programming bots in games

  - by Bane

  I'm interested in how bots are usually written. Here's my situation: I plan to make an online 2D mecha game in HTML5, and the server-side will be done with node. It is intended to be multiplayer, but I also want to make bots in case there aren't enough players. How does my game logic see them, as players or as bots? Is there a standard by which I should make them? Also, any general tips and hints will be OK.

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• C programming in 2011

  - by Duncan Bayne

  Many moons ago I cut C code for a living, primarily while maintaining a POP3 server that supported a wide range of OSs (Linux, *BSD, HPUX, VMS ...). I'm planning to polish the rust off my C skills and learn a bit about language implementation by coding a simple FORTH in C. But I'm wondering how (or whether?) have things changed in the C world since 2000. When I think C, I think ... comp.lang.c ANSI C wherever possible (but C89 as C99 isn't that widely supported) gcc -Wall -ansi -pedantic in lieu of static analysis tools Emacs Ctags Autoconf + make (and see point 2 for VMS, HP-UX etc. goodness) Can anyone who's been writing in C for the past eleven years let me know what (if anything ;-) ) has changed over the years? (In other news, holy crap, I've been doing this for more than a decade).

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