Search Results: "ema"

16 October 2022

Vincent Fourmond: Tutorial: analysis of multiwavelength fast kinetics data

The purpose of this post is to demonstrate a first approach to the analysis of multiwavelength kinetic data, like those obtained using stopped-flow data. To practice, we will use data that were acquired during the stopped flow practicals of the MetBio summer school from the FrenchBIC. During the practicals, the student monitored the reaction of myoglobin (in its Fe(III) state) with azide, which yields a fast and strong change in the absorbance spectrum of the protein, which was monitored using a diode array. The data is publicly available on zenodo. Aims of this tutorial The purpose of this tutorial is to teach you to use the free softwareQSoas to run a simple, multiwavelength exponential fit on the data, and to look at the results. This is not a kinetics lecture, so that it will not go in depth about the use of the exponential fit and its meaning. Getting started: loading the file First, make sure you have a working version of QSoas, you can download them (for free) there. Then download the data files from zenodo. We will work only on the data file Azide-1.25mm_001.dat, but of course, the purpose of this tutorial is to enable you to work on all of them. The data files contain the time evolution of the absorbance for all wavelengths, in a matrix format, in which each row correpond to a time point and each column to a wavelength. Start QSoas, and launch the command: 
QSoas> load /comments='"'
Then, choose the Azide-1.25mm_001.dat data file. This should bring up a horizontal red line at the bottom of the data display, with X values between about 0 and 2.5. If you zoom on the red line with the mouse wheel, you'll realize it is data. The /comments='"' part is very important since it allows the extraction of the wavelength from the data. We will look at what it means another day. At this stage, you can look at the loaded data using the command: 
QSoas> edit
You should have a window looking like this:
The rows each correspond to a data point displayed on the window below. The first column correspond to the X values, the second the Y values, and all the other ones to extra Y columns (they are not displayed by default). What is especially interesting is the first row, which contains a nan as the X value and what is obviously the wavelength for all the Y values. To tell that QSoas should take this line as the wavelength (which will be the perpendicular coordinate, the coordinate of the other direction of the matrix), first close the edit window and run: 
QSoas> set-perp /from-row=0
Splitting and fitting Now, we have a single dataset containing a lot of Y columns. We want to fit all of them simultaneously with a (mono) exponential fit. For that, we first need to split the big matrix into a series of X,Y datasets (because fitting only works on the first Y). This is possible by running: 
QSoas> expand /style=red-to-blue /flags=kinetics
Your screen should now look like this:
You're looking at the kinetics at all wavelengths at the same time (this may take some time to display on your computer, it is after all a rather large number of data points). The /style=red-to-blue is not strictly necessary, but it gives the red to blue color gradient which makes things easier to look at (and cooler !). The /flags=kinetics is there to attach a label (a flag) to the newly created datasets so we can easily manipulate all of them at the same time. Then it's time to fit, with the following command: 
QSoas> mfit-exponential-decay flagged:kinetics
This should bring up a new window. After resizing it, you should have something that looks like this:
The bottom of the fit window is taken by the parameters, each with two checkboxes on the right to set them fixed (i.e. not determined by the fitting mechanism) and/or global (i.e. with a single value for all the datasets, here all the wavelengths). The top shows the current dataset along with the corresponding fit (in green), and, below, the residuals. You can change the dataset by clicking on the horizontal arrows or using Ctrl+PgUp or Ctrl+PgDown (keep holding it to scan fast). See the Z = 728.15 showing that QSoas has recognized that the currently displayed dataset corresponds to the wavelength 728.15. The equation fitted to the data is: $$y(x) = A_\infty + A_1 \times \exp -(x - x_0)/\tau_1$$ In this case, while the \(A_1\) and \(A_\infty\) parameters clearly depend on the wavelength, the time constant of evolution should be independent of wavelength (the process happens at a certain rate regardless of the wavelength we're analyzing), so that the \(\tau_1\) parameter should be common for all the datasets/wavelengths. Just click on the global checkbox at the right of the tau_1 parameter, make sure it is checked, and hit the Fit button... The fit should not take long (less than a minute), and then you end up with the results of the fits: all the parameters. The best way to look at the non global parameters like \(A_1\) and \(A_\infty\) is to use the Show Parameters item from the Parameters menu. Using it and clicking on A_inf too should give you a display like this one:
The A_inf parameter corresponds to the spectum at infinite time (of azide-bound heme), while the A_1 parameter corresponds to the difference spectrum between the initial (azide-free) and final (azide-bound) states. Now, the fit is finished, you can save the parameters if you want to reload them in a later fit by using the Parameters/Save menu item or export them in a form more suitable for plotting using Parameters/Export (although QSoas can also display and the parameters saved using Save). This concludes this first approach to fitting the data. What you can do is How to read the code above All the lines starting by QSoas> in the code areas above are meant to be typed into the QSoas command line (at the bottom of the window), and started by pressing enter at the end. You must remove the QSoas> bit. The other lines (when applicable) show you the response of QSoas, in the terminal just above the command-line. You may want to play with the QSoas tutorial to learn more about how to interact with QSoas. About QSoas QSoas is a powerful open source data analysis program that focuses on flexibility and powerful fitting capacities. It is released under the GNU General Public License. It is described in Fourmond, Anal. Chem., 2016, 88 (10), pp 5050 5052. Current version is 3.1. You can freely (and at no cost) download its source code or precompiled versions for MacOS and Windows there. Alternatively, you can clone from the GitHub repository.
Contact: find my email address there, or contact me on LinkedIn.

14 October 2022

Shirish Agarwal: Dowry, Racism, Railways

Dowry Few days back, had posted about the movie Raksha Bandhan and whatever I felt about it. Sadly, just couple of days back, somebody shared this link. Part of me was shocked and part of me was not. Couple of acquaintances of mine in the past had said the same thing for their daughters. And in such situations you are generally left speechless because you don t know what the right thing to do is. If he has shared it with you being an outsider, how many times he must have told the same to their wife and daughters? And from what little I have gathered in life, many people have justified it on similar lines. And while the protests were there, sadly the book was not removed. Now if nurses are reading such literature, how their thought process might be forming, you can tell :(. And these are the ones whom we call for when we are sick and tired :(. And I have not taken into account how the girls/women themselves might be feeling. There are similar things in another country but probably not the same, nor the same motivations though although feeling helplessness in both would be a common thing. But such statements are not alone. Another gentleman in slightly different context shared this as well
The above is a statement shared in a book recommended for CTET (Central Teacher s Eligibility Test that became mandatory to be taken as the RTE (Right To Education) Act came in.). The statement says People from cold places are white, beautiful, well-built, healthy and wise. And people from hot places are black, irritable and of violent nature. Now while I can agree with one part of the statement that people residing in colder regions are more fair than others but there are loads of other factors that determine fairness or skin color/skin pigmentation. After a bit of search came to know that this and similar articulation have been made in an idea/work called Environmental Determinism . Now if you look at that page, you would realize this was what colonialism is and was all about. The idea that the white man had god-given right to rule over others. Similarly, if you are fair, you can lord over others. Seems simplistic, but yet it has a powerful hold on many people in India. Forget the common man, this thinking is and was applicable to some of our better-known Freedom fighters. Pune s own Bal Gangadhar Tilak The Artic Home to the Vedas. It sort of talks about Aryans and how they invaded India and became settled here. I haven t read or have access to the book so have to rely on third-party sources. The reason I m sharing all this is that the right-wing has been doing this myth-making for sometime now and unless and until you put a light on it, it will continue to perpetuate . For those who have read this blog, do know that India is and has been in casteism from ever. They even took the fair comment and applied it to all Brahmins. According to them, all Brahmins are fair and hence have god-given right to lord over others. What is called the Eton boy s network serves the same in this casteism. The only solution is those idea under limelight and investigate. To take the above, how does one prove that all fair people are wise and peaceful while all people black and brown are violent. If that is so, how does one count for Mahatma Gandhi, Martin Luther King Junior, Nelson Mandela, Michael Jackson the list is probably endless. And not to forget that when Mahatma Gandhiji did his nonviolent movements either in India or in South Africa, both black and brown people in millions took part. Similar examples of Martin Luther King Jr. I know and read of so many non-violent civl movements that took place in the U.S. For e.g. Rosa Parks and the Montgomery Bus Boycott. So just based on these examples, one can conclude that at least the part about the fair having exclusive rights to being fair and noble is not correct. Now as far as violence goes, while every race, every community has had done violence in the past or been a victim of the same. So no one is and can be blameless, although in light of the above statement, the question can argumentated as to who were the Vikings? Both popular imagination and serious history shares stories about Vikings. The Vikings were somewhat nomadic in nature even though they had permanent settlements but even then they went on raids, raped women, captured both men and women and sold them at slaves. So they are what pirates came to be, but not the kind Hollywood romanticizes about. Europe in itself has been a tale in conflict since time immemorial. It is only after the formation of EU that most of these countries stopped fighting each other From a historical point perspective, it is too new. So even the part of fair being non-violent dies in face of this evidence. I could go on but this is enough on that topic.

Railways and Industrial Action around the World. While I have shared about Railways so many times on this blog, it continues to fascinate me that how people don t understand the first things about Railways. For e.g. Railways is a natural monopoly. What that means is and you can look at all and any type of privatization around the world, you will see it is a monopoly. Unlike the road or Skies, Railways is and would always be limited by infrastructure and the ability to have new infrastructure. Unlike in road or Skies (even they have their limits) you cannot run train services on a whim. At any particular point in time, only a single train could and should occupy a stretch of Railway network. You could have more trains on one line, but then the likelihood of front or rear-end collisions becomes a real possibility. You also need all sorts of good and reliable communications, redundant infrastructure so if one thing fails then you have something in place. The reason being a single train can carry anywhere from 2000 to 5000 passengers or more. While this is true of Indian Railways, Railways around the world would probably have some sort of similar numbers.It is in this light that I share the below videos.
To be more precise, see the fuller video
Now to give context to the recording above, Mike Lynch is the general secretary at RMT. For those who came in late, both UK and the U.S. have been threatened by railway strikes. And the reason for the strikes or threat of strikes is similar. Now from the company perspective, all they care is to invest less and make the most profits that can be given to equity shareholders. At the same time, they have freezed the salaries of railway workers for the last 3 years. While the politicians who were asking the questions, apparently gave themselves raise twice this year. They are asking them to negotiate at 8% while inflation in the UK has been 12.3% and projected to go higher. And it is not only the money. Since the 1980s when UK privatized the Railways, they stopped investing in the infrastructure. And that meant that the UK Railway infrastructure over period of time started getting behind and is even behind say Indian Railways which used to provide most bang for the buck. And Indian Railways is far from ideal. Ironically, most of the operators on UK are nationalized Railways of France, Germany etc. but after the hard Brexit, they too are mulling to cut their operations short, they have too There is also the EU Entry/Exit system that would come next year. Why am I sharing about what is happening in UK Rail, because the Indian Government wants to follow the same thing, and fooling the public into saying we would do it better. What inevitably will happen is that ticket prices go up, people no longer use the service, the number of services go down and eventually they are cancelled. This has happened both in Indian Railways as well as Airlines. In fact, GOI just recently announced a credit scheme just a few days back to help Airlines stay afloat. I was chatting with a friend who had come down to Pune from Chennai and the round-trip cost him INR 15k/- on that single trip alone. We reminisced how a few years ago, 8 years to be precise, we could buy an Air ticket for 2.5k/- just a few days before the trip and did it. I remember doing/experiencing at least a dozen odd trips via air in the years before 2014. My friend used to come to Pune, almost every weekend because he could afford it, now he can t do that. And these are people who are in the above 5-10% of the population. And this is not just in UK, but also in the United States. There is one big difference though, the U.S. is mainly a freight carrier while the UK Railway Operations are mostly passenger based. What was and is interesting that Scotland had to nationalize their services as they realized the Operators cannot or will not function when they were most needed. Most of the public even in the UK seem to want a nationalized rail service, at least their polls say so. So, it would definitely be interesting to see what happens in the UK next year. In the end, I know I promised to share about books, but the above incidents have just been too fascinating to not just share the news but also share what I think about them. Free markets function good where there is competition, for example what is and has been happening in China for EV s but not where you have natural monopolies. In all Railway privatization, you have to handover the area to one person, then they have no motivation. If you have multiple operators, then there would always be haggling as to who will run the train and at what time. In either scenario, it doesn t work and raises prices while not delivering anything better I do take examples from UK because lot of things are India are still the legacy of the British. The whole civil department that was created in 1953 is/was a copy of the British civil department at that time and it is to this day. P.S. Just came to know that the UK Chancellor Kwasi Kwarteng was just sacked as UK Chancellor. I do commend Truss for facing the press even though she might be dumped a week later unlike our PM who hasn t faced a single press conference in the last 8 odd years.

https://www.youtube.com/watch?v=oTP6ogBqU7of The difference in Indian and UK politics seems to be that the English are now asking questions while here in India, most people are still sleeping without a care in the world. Another thing to note Minidebconf Palakkad is gonna happen 12-13th November 2022. I am probably not gonna go but would request everyone who wants to do something in free software to attend it. I am not sure whether I would be of any use like this and also when I get back, it would be an empty house. But for people young and old, who want to do anything with free/open source software it is a chance not to be missed. Registration of the same closes on 1st of November 2022. All the best, break a leg Just read this, beautifully done.

Simon Josefsson: On language bindings & Relaunching Guile-GnuTLS

The Guile bindings for GnuTLS has been part of GnuTLS since spring 2007 when Ludovic Court s contributed it after some initial discussion. I have been looking into getting back to do GnuTLS coding, and during a recent GnuTLS meeting one topic was Guile bindings. It seemed like a fairly self-contained project to pick up on. It is interesting to re-read the old thread when this work was included: some of the concerns brought up there now have track record to be evaluated on. My opinion that the cost of introducing a new project per language binding today is smaller than the cost of maintaining language bindings as part of the core project. I believe the cost/benefit ratio has changed during the past 15 years: introducing a new project used to come with a significant cost but this is no longer the case, as tooling and processes for packaging have improved. I have had similar experience with Java, C# and Emacs Lisp bindings for GNU Libidn as well, where maintaining them centralized slow down the pace of updates. Andreas Metzler pointed to a similar conclusion reached by Russ Allbery. There are many ways to separate a project into two projects; just copying the files into a new git repository would have been the simplest and was my original plan. However Ludo mentioned git-filter-branch in an email, and the idea of keeping all git history for some of the relevant files seemed worth pursuing to me. I quickly found git-filter-repo which appears to be the recommend approach, and experimenting with it I found a way to filter out the GnuTLS repo into a small git repository that Guile-GnuTLS could be based on. The commands I used were the following, if you want to reproduce things. 
$ git clone https://gitlab.com/gnutls/gnutls.git guile-gnutls
$ cd guile-gnutls/
$ git checkout f5dcbdb46df52458e3756193c2a23bf558a3ecfd
$ git-filter-repo --path guile/ --path m4/guile.m4 --path doc/gnutls-guile.texi --path doc/extract-guile-c-doc.scm --path doc/cha-copying.texi --path doc/fdl-1.3.texi
I debated with myself back and forth whether to include some files that would be named the same in the new repository but would share little to no similar lines, for example configure.ac, Makefile.am not to mention README and NEWS. Initially I thought it would be nice to preserve the history for all lines that went into the new project, but this is a subjective judgement call. What brought me over to a more minimal approach was that the contributor history and attribution would be quite strange for the new repository: Should Guile-GnuTLS attribute the work of the thousands of commits to configure.ac which had nothing to do with Guile? Should the people who wrote that be mentioned as contributor of Guile-GnuTLS? I think not. The next step was to get a reasonable GitLab CI/CD pipeline up, to make sure the project builds on some free GNU/Linux distributions like Trisquel and PureOS as well as the usual non-free distributions like Debian and Fedora to have coverage of dpkg and rpm based distributions. I included builds on Alpine and ArchLinux as well, because they tend to trigger other portability issues. I wish there were GNU Guix docker images available for easy testing on that platform as well. The GitLab CI/CD rules for a project like this are fairly simple. To get things out of the door, I tagged the result as v3.7.9 and published a GitLab release page for Guile-GnuTLS that includes OpenPGP-signed source tarballs manually uploaded built on my laptop. The URLs for these tarballs are not very pleasant to work with, and discovering new releases automatically appears unreliable, but I don t know of a better approach. To finish this project, I have proposed a GnuTLS merge request to remove all Guile-related parts from the GnuTLS core. Doing some GnuTLS-related work again felt nice, it was quite some time ago so thank you for giving me this opportunity. Thoughts or comments? Happy hacking!

9 October 2022

Jonathan Dowland: Focus writing with (despite) LaTeX

LaTeX the age-old typesetting system makes me angry. Not because it's bad. To clarify, not because there's something better. But because there should be. When writing a document using LaTeX, if you are prone to procrastination it can be very difficult to focus on the task at hand, because there are so many yaks to shave. Here's a few points of advice. In a nutshell, I think it's wise to move much document reviewing work back into the editor rather than the rendered document, at least in the early stages of a section. And to do that, you need the document to be as legible as possible in the editor. The important stuff is the text you write, not the TeX macros you've sprinkled around to format it. A few tips I benefit from in terms of source formatting: Of course, you need to review the rendered document too! I like to bounce that to a tablet with a pen/stylus/pencil and review it in a different environment to where I write. I then end up with a long list of scrawled notes, and a third distinct activity, back at the writing desk, is to systematically go through them and apply some GTD-style thinking to them: can I fix it in a few seconds? Do it straight away. Delegate it? Unlikely Defer it? transfer the review note into another system of record (such as LaTeX \\todo ). And finally

7 October 2022

Reproducible Builds: Reproducible Builds in September 2022

Welcome to the September 2022 report from the Reproducible Builds project! In our reports we try to outline the most important things that we have been up to over the past month. As a quick recap, whilst anyone may inspect the source code of free software for malicious flaws, almost all software is distributed to end users as pre-compiled binaries. If you are interested in contributing to the project, please visit our Contribute page on our website.
David A. Wheeler reported to us that the US National Security Agency (NSA), Cybersecurity and Infrastructure Security Agency (CISA) and the Office of the Director of National Intelligence (ODNI) have released a document called Securing the Software Supply Chain: Recommended Practices Guide for Developers (PDF). As David remarked in his post to our mailing list, it expressly recommends having reproducible builds as part of advanced recommended mitigations . The publication of this document has been accompanied by a press release.
Holger Levsen was made aware of a small Microsoft project called oss-reproducible. Part of, OSSGadget, a larger collection of tools for analyzing open source packages , the purpose of oss-reproducible is to:
analyze open source packages for reproducibility. We start with an existing package (for example, the NPM left-pad package, version 1.3.0), and we try to answer the question, Do the package contents authentically reflect the purported source code?
More details can be found in the README.md file within the code repository.
David A. Wheeler also pointed out that there are some potential upcoming changes to the OpenSSF Best Practices badge for open source software in relation to reproducibility. Whilst the badge programme has three certification levels ( passing , silver and gold ), the gold level includes the criterion that The project MUST have a reproducible build . David reported that some projects have argued that this reproducibility criterion should be slightly relaxed as outlined in an issue on the best-practices-badge GitHub project. Essentially, though, the claim is that the reproducibility requirement doesn t make sense for projects that do not release built software, and that timestamp differences by themselves don t necessarily indicate malicious changes. Numerous pragmatic problems around excluding timestamps were raised in the discussion of the issue.
Sonatype, a pioneer of software supply chain management , issued a press release month to report that they had found:
[ ] a massive year-over-year increase in cyberattacks aimed at open source project ecosystems. According to early data from Sonatype s 8th annual State of the Software Supply Chain Report, which will be released in full this October, Sonatype has recorded an average 700% jump in repository attacks over the last three years.
More information is available in the press release.
A number of changes were made to the Reproducible Builds website and documentation this month, including Chris Lamb adding a redirect from /projects/ to /who/ in order to keep old or archived links working [ ], Jelle van der Waa added a Rust programming language example for SOURCE_DATE_EPOCH [ ][ ] and Mattia Rizzolo included Protocol Labs amongst our project-level sponsors [ ].

Debian There was a large amount of reproducibility work taking place within Debian this month:
  • The nfft source package was removed from the archive, and now all packages in Debian bookworm now have a corresponding .buildinfo file. This can be confirmed and tracked on the associated page on the tests.reproducible-builds.org site.
  • Vagrant Cascadian announced on our mailing list an informal online sprint to help clear the huge backlog of reproducible builds patches submitted by performing NMU (Non-Maintainer Uploads). The first such sprint took place on September 22nd with the following results:
    • Holger Levsen:
      • Mailed #1010957 in man-db asking for an update and whether to remove the patch tag for now. This was subsequently removed and the maintainer started to address the issue.
      • Uploaded gmp to DELAYED/15, fixing #1009931.
      • Emailed #1017372 in plymouth and asked for the maintainer s opinion on the patch. This resulted in the maintainer improving Vagrant s original patch (and uploading it) as well as filing an issue upstream.
      • Uploaded time to DELAYED/15, fixing #983202.
    • Vagrant Cascadian:
      • Verify and updated patch for mylvmbackup (#782318)
      • Verified/updated patches for libranlip. (#788000, #846975 & #1007137)
      • Uploaded libranlip to DELAYED/10.
      • Verified patch for cclive. (#824501)
      • Uploaded cclive to DELAYED/10.
      • Vagrant was unable to reproduce the underlying issue within #791423 (linuxtv-dvb-apps) and so the bug was marked as done .
      • Researched #794398 (in clhep).
    The plan is to repeat these sprints every two weeks, with the next taking place on Thursday October 6th at 16:00 UTC on the #debian-reproducible IRC channel.
  • Roland Clobus posted his 13th update of the status of reproducible Debian ISO images on our mailing list. During the last month, Roland ensured that the live images are now automatically fed to openQA for automated testing after they have been shown to be reproducible. Additionally Roland asked on the debian-devel mailing list about a way to determine the canonical timestamp of the Debian archive. [ ]
  • Following up on last month s work on reproducible bootstrapping, Holger Levsen filed two bugs against the debootstrap and cdebootstrap utilities. (#1019697 & #1019698)
Lastly, 44 reviews of Debian packages were added, 91 were updated and 17 were removed this month adding to our knowledge about identified issues. A number of issue types have been updated too, including the descriptions of cmake_rpath_contains_build_path [ ], nondeterministic_version_generated_by_python_param [ ] and timestamps_in_documentation_generated_by_org_mode [ ]. Furthermore, two new issue types were created: build_path_used_to_determine_version_or_package_name [ ] and captures_build_path_via_cmake_variables [ ].

Other distributions In openSUSE, Bernhard M. Wiedemann published his usual openSUSE monthly report.

diffoscope diffoscope is our in-depth and content-aware diff utility. Not only can it locate and diagnose reproducibility issues, it can provide human-readable diffs from many kinds of binary formats. This month, Chris Lamb prepared and uploaded versions 222 and 223 to Debian, as well as made the following changes:
  • The cbfstools utility is now provided in Debian via the coreboot-utils package so we can enable that functionality within Debian. [ ]
  • Looked into Mach-O support.
  • Fixed the try.diffoscope.org service by addressing a compatibility issue between glibc/seccomp that was preventing the Docker-contained diffoscope instance from spawning any external processes whatsoever [ ]. I also updated the requirements.txt file, as some of the specified packages were no longer available [ ][ ].
In addition Jelle van der Waa added support for file version 5.43 [ ] and Mattia Rizzolo updated the packaging:
  • Also include coreboot-utils in the Build-Depends and Test-Depends fields so that it is available for tests. [ ]
  • Use pep517 and pip to load the requirements. [ ]
  • Remove packages in Breaks/Replaces that have been obsoleted since the release of Debian bullseye. [ ]

Reprotest reprotest is our end-user tool to build the same source code twice in widely and deliberate different environments, and checking whether the binaries produced by the builds have any differences. This month, reprotest version 0.7.22 was uploaded to Debian unstable by Holger Levsen, which included the following changes by Philip Hands:
  • Actually ensure that the setarch(8) utility can actually execute before including an architecture to test. [ ]
  • Include all files matching *.*deb in the default artifact_pattern in order to archive all results of the build. [ ]
  • Emit an error when building the Debian package if the Debian packaging version does not patch the Python version of reprotest. [ ]
  • Remove an unneeded invocation of the head(1) utility. [ ]

Upstream patches The Reproducible Builds project detects, dissects and attempts to fix as many currently-unreproducible packages as possible. We endeavour to send all of our patches upstream where appropriate. This month, we wrote a large number of such patches, including:

Testing framework The Reproducible Builds project runs a significant testing framework at tests.reproducible-builds.org in order to check packages and other artifacts for reproducibility. This month, however, the following changes were made:
  • Holger Levsen:
    • Add a job to build reprotest from Git [ ] and use the correct Git branch when building it [ ].
  • Mattia Rizzolo:
    • Enable syncing of results from building live Debian ISO images. [ ]
    • Use scp -p in order to preserve modification times when syncing live ISO images. [ ]
    • Apply the shellcheck shell script analysis tool. [ ]
    • In a build node wrapper script, remove some debugging code which was messing up calling scp(1) correctly [ ] and consquently add support to use both scp -p and regular scp [ ].
  • Roland Clobus:
    • Track and handle the case where the Debian archive gets updated between two live image builds. [ ]
    • Remove a call to sudo(1) as it is not (or no longer) required to delete old live-build results. [ ]

Contact As ever, if you are interested in contributing to the Reproducible Builds project, please visit our Contribute page on our website. However, you can get in touch with us via:

Edward Betts: Fish shell now has underscore as a number separator (my feature request)

In November 2021 I filed a feature request for the fish shell to add underscore as a thousand separator in numbers. My feature request has been implemented and is available in fish 3.5.0, released 16 June 2022. The fish shell supports mathematical operations using the math command. 
edward@x1c9 ~> math 2_000 + 22
2022
edward@x1c9 ~>
The underscore can be used as a thousand separator, but there are other uses for a number separator. Here's a list taken from a post by Mathias Bynens about the number separator in JavaScript: 
// A decimal integer literal with its digits grouped per thousand:
1_000_000_000_000
// A decimal literal with its digits grouped per thousand:
1_000_000.220_720
// A binary integer literal with its bits grouped per octet:
0b01010110_00111000
// A binary integer literal with its bits grouped per nibble:
0b0101_0110_0011_1000
// A hexadecimal integer literal with its digits grouped by byte:
0x40_76_38_6A_73
// A BigInt literal with its digits grouped per thousand:
4_642_473_943_484_686_707n
Programming languages are gradually adding a number separator to their syntax, I think Perl was the first. Most are languages use underscore, but C++ 14 uses an apostrophe for the number separator.

4 October 2022

Jonathan Dowland: rewrite rule representation

I've begun writing up my phd and, not for the first time, I'm pondering issues of how best to represent things. Specifically, rewrite rules. Here's one way of representing an example rewrite rule: 
streamFilter g . streamFilter f = streamFilter (g . f)
This is a fairly succinct representation. It's sort-of Haskell, but not quite. It's an equation. The left-hand side is a pattern: it's intended to describe not one expression but a family of expressions that match. The lower case individual letters g and f are free variables: labelled placeholders within the pattern that can be referred to on the right hand side. I haven't stipulated what defines a free variable and what is a more concrete part of the pattern. It's kind-of Haskell, and I've used the well-known operator . to represent the two stream operators (streamFilters) being connected together. (In practice, when we get to the system where rules are actually applied, the connecting operator is not going to be . at all, so this is also an approximation). One thing I don't like about . here, despite its commonness, is having to read right-to-left. I adopted the habit of using the lesser-known >>> in a lot of my work (which is defined as (>>>) = flip (.)), which reads left-to-right. And then I have the reverse problem: people aren't familiar with >>>, and, just like ., it's a stand-in anyway. Towards the beginning of my PhD, I spent some time inventing rewrite rules to operate on pairs of operators taken from a defined, known set. I began representing the rules much as in the example above. Later on, I wanted to encode them as real Haskell, in order to check them more thoroughly. The above rule, I first encoded like this 
filterFilterPre     = streamFilter g . streamFilter f
filterFilterPost    = streamFilter (g . f)
prop_filterFilter s = filterFilterPre s == filterFilterPost s
This is real code: the operators were already implemented in StrIoT, and the final expression defined a property for QuickCheck. However, it's still not quite a rewrite rule. The left-hand side, which should be a pattern, is really a concrete expression. The names f and g are masquerading as free variables but are really concretely defined in a preamble I wrote to support running QuickCheck against these things: usually simple stuff like g = odd, etc. Eventually, I had to figure out how to really implement rewrite rules in StrIoT. There were a few approaches I could take. One would be to express the rules in some abstract form like the first example (but with properly defined semantics) and write a parser for them: I really wanted to avoid doing that. As a happy accident, the solution I landed on was enabled by the semantics of algebraic-graphs, a Graph library we adopted to support representing a stream-processing topology. I wrote more about that in data-types for representing stream-processing programs. I was able to implement rewrite rules as ordinary Haskell functions. The left-hand side of the rewrite rule maps to the left-hand side (pattern) part of a function definition. The function body implements the right-hand side. The system that applies the rules attempts to apply each rewrite rule to every sub-graph of a stream-processing program. The rewrite functions therefore need to signal whether or not they're applicable at runtime. For that reason, the return type is wrapped in Maybe, and we provide a catch-all pattern for every rule which simply returns Nothing. The right-hand side implementation can be pretty thorny. On the left-hand side, the stream operator connector we've finally ended up with is Connect from algebraic-graphs. Here's filter fuse, taken from the full ruleset: 
filterFuse :: RewriteRule
filterFuse (Connect (Vertex a@(StreamVertex i (Filter sel1) (p:_) ty _ s1))
                    (Vertex b@(StreamVertex _ (Filter sel2) (q:_) _ _ s2))) =
    let c = a   operator    = Filter (sel1 * sel2)
              , parameters  = [\[  (\p q x -> p x && q x) $(p) $(q)  ]]
              , serviceTime = sumTimes s1 sel1 s2
               
    in Just (removeEdge c c . mergeVertices ( elem  [a,b]) c)
filterFuse _ = Nothing
That's perhaps the simplest rule in the set. (See e.g. hoistOp for one of the worst!) The question that remains to me, is, which representation, or representations, to use in the thesis? I'm currently planning to skip the abstract example I started with and start with the concrete Haskell encoding using QuickCheck. I'm not sure if it seems weird to have two completely separate implementations of the rules, but the simpler QuickCheck-checked rules are much closer to the "core essence" of the rules than the final implementation in StrIoT. And the derivation of the rules comes earlier in the timeline than the design work that led to the final StrIoT implementation. The middle-option is still compromised, however, by having concrete expressions pretending to be patterns. So I'm not sure.

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