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Using multi-line commenting in Perl to inactivate blocks of code during testing

26th December 2019

Recently, I needed to inactivate blocks of code in a Perl script while doing some testing. This is something that I often do in other computing languages so I sought the same in Perl. To do that, I need to use the POD methodology. This meant enclosing the code as follows.

=start

<< Code to be inactivated by inclusion in a comment >>

=cut

The =start line could use any word after the equality sign but it seems that =cut is needed to close the multi-line comment. If this was actual programming documentation, then the comment block should include some meaningful text for use with perldoc but that was not a concern here since the commenting statements would be removed afterwards anyway and it is good practice not to leave commented code in a production script or program to avoid any later confusion.

In my case, this facility allowed me to isolate the code that I needed to alter and test before putting everything back as needed. It also saved time since I did not need to individually comment out every executable line because multiple lines could be inactivated at a time.

Getting custom Python imports to work in Visual Studio Code

18th February 2022

While I continue to use Spyder as my preferred Python code editor, I also tried out Visual Studio Code. Handily, this Integrated Development Environment also has facilities for working with R and Julia code as well as MarkDown text editing and adding the required extensions is enough for these applications; it helps that there is an unofficial Grammarly extension for content creation.

My Python code development makes use of the Pylance extension and it works a little differently from Spyder when it comes to including files using import statements. Spyder will look into the folder where the base script is located but the default behaviour of Pylance is that it looks in the root path of your workspace. This meant that any code that ran successfully in Spyder failed in Visual Studio Code.

The way around this was to add the required location using the python.analysis.extraPaths setting for the workspace. That meant opening Settings by navigating to File > Preferences > Settings in the menu system and entering python.analysis.extraPaths into the search box. That took me to the section that I needed and I then clicked on Add Item before entering the required path and clicking on the OK button. That was enough to fix the problem and all worked as it should after that.

What to do when a GPG signature becomes invalid for a package repository on Linux Mint

12th September 2024

During a package update on my main Linux system, I encountered the following kind of error message:

An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: https://cli.github.com/packages stable InRelease: The following signatures were invalid: EXPKEYSIG <GPG Key> GitHub CLI

The message indicated a problem with the GPG signature verification for the GitHub CLI repository. The cause was that the signature for the repository was invalid, preventing the package manager from updating the repository’s index files. The first step then was to remove the invalid GPG key using the following command:

sudo apt-key del <GPG Key>

With the invalid GPG key removed, the next step is to add the new GPG key for the GitHub CLI repository by issuing the following command:

curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | sudo tee /usr/share/keyrings/githubcli-archive-keyring.gpg > /dev/null

Once I had the new GPG key, I was able to use my usual system update process without any problem. The error message was gone, and updates and upgrades proceeded as intended.

SAS Data Step Hash Objects and Memory

3rd June 2008

Using hash objects in SAS data step code offers some great advantages from the speed point of view; having a set of data in memory rather than on disk makes things much faster. However, that means that you need to keep more of an eye on the amount of memory that’s being used. The first thing is to work out how much memory is available and it’s not necessarily the total amount installed on the system or, for that matter, the amount of memory per processor on a multi-processor system. What you really need is the number, in bytes, that is stored in the XMRLMEM system option and here’s a piece of code that’ll do just that:

data _null_; mem=getoption('xmrlmem'); put mem; run;

The XMRLMEM is itself an option that you can only declare in the system call that starts SAS up in the first place and there are advantages to keeping it under control, particularly on large multi-user servers. However, if your hash objects start to exceed what is available, here’s the sort of thing that you can expect to see:

ERROR: Hash object added 49136 items when memory failure occurred. FATAL: Insufficient memory to execute data step program. Aborted during the EXECUTION phase. NOTE: The SAS System stopped processing this step because of insufficient memory. NOTE: SAS set option OBS=0 and will continue to check statements. This may cause NOTE: No observations in data set.

Those messages are a cue for you to learn to keep those hash objects and to only ever make them as large as your memory settings will allow. Another thing to note is that hash objects are best retained for rather fixed data volumes instead of ones that could outgrow their limits. There’s a certain amount of common sense in operation here but it may be that promoters of hash objects don’t mention their limitations as much as they should. If you want to find out more, SAS have a useful paper on their website and the their Knowledge Base has more on the error messages that you can get.

Selecting SAS code in the Program Editor on UNIX

5th June 2007

Here’s a possible bugbear with programming using the SAS Display Manager in UNIX, selecting sections of code and running them. In the installations that I have encountered, the mouse selection is not retained so the code selection cannot be run. There is a fix for this and it is not the most obvious. Going to the Preferences dialogue box (Tools > Options > Preferences… from the menu bar) and selecting the Editing tab brings up the screen below:

SAS Editing Preferences on UNIX

Ensuring that "Automatically store selection" is switched off, as shown above, will allow one to select and submit sections of code from a SAS program like what is normal practice with Windows SAS. It isn’t an obvious solution but it does the trick for me.

Another way to look through WordPress code

10th August 2008

At times in the past, I have complained about there not being sufficient documentation of the actual code used in WordPress itself. True, there is the venerable Codex but that can be incomplete and any extra help is always useful. Peter Westwood (a.k.a westi) has generated documentation from the code itself and put it up on the web for all to peruse. While we are on the subject of information on the more advanced aspects of WordPress, blogs by Mark Jaquith and Andrew Ozz are also worth a look. As the cliché goes, every little helps…

Some SAS Macro code for detecting the presence or absence of a variable in a dataset

4th December 2013

Recently, I needed to put in place some code to detect the presence or absence of a variable in a dataset and I chose SAS Macro programming as the way to do what I wanted. The logic was based on a SAS sample that achieved the same result in a data step and some code that I had for detecting the presence or absence of a dataset. Mixing the two together gave me something like the following:

%macro testvar(ds=,var=);

%let dsid=%sysfunc(open(&ds,in)); %let varexist=%sysfunc(varnum(&dsid,&var)); %if &dsid > 0 %then %let rc=%sysfunc(close(&dsid));

%if &varexist gt 0 %then %put Info: Variable &var is in the &ds dataset; %else %put Info: Variable &var is not in the &ds dataset;

%mend testvar;

%testvar(ds=dataset,var=var);

What this does is open up a dataset and look for the variable number in the dataset. In datasets, variables are numbered from left to right with 1 for the first one, 2 for the second and so on. If the variable is not in the dataset, the result is 0 so you know that it is not there. All of this is what the VARNUM SCL function within the SYSFUNC macro function does. In the example, this resolves to %sysfunc(varnum(&dsid,var)) with no quotes around the variable name like you would do in data step programming. Once you have the variable number or 0, then you can put in place some conditional logic that makes use of the information like what you see in the above simple example. Of course, that would be expanded to something more useful in real life but I hope it helps to show you the possibilities here.

HennessyBlog theme update

12th February 2007

Over the weekend, I have been updating the theme on my other blog, HennessyBlog. It has been a task that projected me onto a learning curve with the WordPress 2.1 codebase. I have collected what I encountered so I know that it’s out there on the web for you (and I) to use and peruse. It took some digging to get to know some of what you find below. Any function used to power WordPress takes some finding so I need to find one place on the web where the code for WordPress is fully documented. The sites presenting tutorials on how to use WordPress are more often than not geared towards the non-techie rather than code cutters like myself. Then again, they might be waiting for someone to do it for them…

The changes made are as follows:

Tweaks to the interface

These are subtle with the addition of navigation controls to the sidebar and the change in location of the post metadata being the most obvious enhancements. “Decoration” with solid and dashed lines (using CSS border attributes rather than the deprecated hr tagset) and standards compliance links.

Standards compliance

Adding standards compliance links does mean that you’d better check that all is in order; it was then that I discovered that there was work to be done. There is an issue with the WordPress wpautop function (it lives in the formatting.php file) in that it sometimes doesn’t add closing tags. Finding out that it was this function that is implicated took a trip to the WordPress.org website; a good rummage in the wp-includes folder does a lot but it can’t achieve everything.

Like a lot of things in the WordPress code, the wpautop function isn’t half buried. The the_content function (see template-functions-post.php) used to output blog entries calls get_content function (also in template-functions-post.php) to extract the data from mySQL. The add_filter function (in plugin.php) associates the wpautop function and others with get_the_content function and the p tags get added to the output.

To return to the non-ideal behaviour that caused me to start out on the above quest, an example is where you have an img tag enclosed by div tags. The required substitution involves the use of regular expressions that work most of the time but get confused here. So adding a hack to the wpautop function was needed to change the code so that the p end tag got inserted. I’ll be keeping an eye out for any more scenarios like this that slip through the net and for any side effects. Otherwise, compliance is just making sure that all those img tags have their alt attributes completed.

Tweaks to navigation code

Most of my time has been spent on tweaking of the PHP code supporting the navigation. Different functions were being called in different places and I wanted to harmonise things. To do this, I created new functions in the functions.php for my theme and needed to resolve a number of issues along the way. Not least among these were regular expressions used for subsetting with the preg_match match that weren’t to my eyes Perl-compliant, as would be implied by the choice of function. I have since found that PCRE’s in PHP use a more pragmatic syntax but there remained issues with the expressions that were being used. They seemed to behave OK in their native environment but fell out of favour within the environs of my theme. Being acquainted with Perl, I went for a more familiar expression style and the issue has been resolved.

Along the way, I broke the RSS feed. This was on my off-line test blog so no one, apart from myself, that is, would have noticed. After a bit of searching, I realised that some stray white-space from the end of a PHP file (wp-config.php being a favourite culprit), after the PHP end tag in the script file as it happens, was finding its way into the feed and causing things to fall over. Feed readers don’t take too kindly to the idea of the XML declaration not making an appearance on the first line of the file. The refusal of Firefox to refresh things as it should caused some confusion until I realised that a forced refresh of the feed display was needed -- sometimes, it takes a while for an addled brain to think of these kinds of things.

Adobe CS3 Launch

28th March 2007

Last night, I sat through part of Adobe’s CS3 launch and must admit that I came away intrigued. Products from the Macromedia stable have been very much brought under the Adobe umbrella and progressed to boot. One of these that attracts my interest in Dreamweaver and Adobe is promoting its AJAX capabilities (using the Spry library), its browser compatibility checking facility and integration with Photoshop, among other things. Dreamweaver’s CSS support also gets taken forward. In addition, Dreamweaver can now integrate with Adobe Bridge and Adobe Device Central. The latter allows you to preview how your site might look on a plethora of WAP-enabled mobile phones while the latter, unless I have been missing something, seems to have become a media manager supporting all of CS3 and not just Photoshop.

Speaking of Photoshop, this now gets such new features as smart filters, I think of these as adjustment layers for things like sharpening, monochrome conversion and much more. Raw image processing now has a non-destructive element and Photoshop Lightroom is being touted as a companion for the main Photoshop. Speaking of new additions to the Photoshop family, there is a new Extended edition for those working with digital imaging with a 3D aspect and this is targeted at scientists, engineers, medical professionals and others. It seems that data analysis and interpretation is becoming part of the Photoshop remit now as well.

Dreamweaver and Photoshop are the components of the suite in which I have most interest but I also note that Contribute now has blogging capabilities; it would be interesting to see how these work, especially given Word 2007’s support for blogging tools like WordPress and Blogger. Another member of note is Version Cue, adding version control to the mix and making CS3 more like a group of platforms than collections of applications.

Unsurprisingly, the changes are rung out for the rest of the suite with integration being a major theme and this very much encompasses Flash too. The sight of an image selection being copied straight into Dreamweaver was wondrous in its own way and rendering of Photoshop files into 3D images was also something to behold. The latter was used to demonstrate the optimisations that have been added for the Mac platform, a major selling point apparently.

I suppose that the outstanding question is this: do I buy into all of this? It’s a good question because the computer enthusiast seems to be getting something of a sidelining lately. And that seems to the impression left by Windows Vista in its giving the appearance that Microsoft is trying to be system administrator to the world. There is no doubt but CS3 is very grown up now and centred around work flows and processes. These have always been professional tools and the present level of sophistication and pricing* very much reflects this. That said, enthusiasts like me have been known to use them too, at least for learning purposes. The latter point may yet cause me to get my hands on Photoshop CS3 with its powerful tools for digital imaging but Dreamweaver is another story. It doesn’t fit what how I work now so this is an upgrade that I may give a miss, as impressive as it looks. For a learning experience, I might download a demo but that would a separate matter from updating my web presence. This time next month may tell a tale…

*Pricing remains the bugbear for the U.K. market that it always has been. At the present exchange rates, we should be getting a much better deal on Adobe products that we do. For instance, Amazon.com has the Web Premium CS3 suite from Macromedia Studio 8 priced at $493.99 while it is £513.99 on Amazon.co.uk. Using the exchange rate current as I write this, £1 buying $1.96605, the U.K. price is a whopping $1010.53 in U.S. terms. To me, this looks like price gouging and Microsoft has been slated for this too. I wonder what will be said to Adobe on this one.

Google Analytics

25th May 2007

Furthering my excursions into things related to Google, I have been giving Google Analytics a whirl for my hillwalking and photo gallery website. Aside from the fact that it is updated once a day, it could have enabled me to eject WordPress plug-ins like Popularity Contest and FireStats getting the chop. As it happens, I also have a Google Analytics plugin installed but a little editing of the blog template that I have developed would get rid of that too.

That’s enough about WordPress plug-ins; let’s return to Google Analytics. It has all the usual stuff: who’s visiting, from where are they coming, what are they using to see your site, etc. In addition, it captures if they are coming back, how long they are staying on the site and how deep they are going. Bounce rate is another term that features heavily: it is when a user only goes to one page and then leaves. With a blog, this unfortunately seems to come out as a high figure and that is ironic given that the blog was meant to promote the online photo gallery; it has very much taken on a life all of its own. There’s more to the information from Google Analytics but it’s all useful stuff and I plan to make good use of it to improve how my site works.

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