Search Results: "nwp"

14 December 2020

Vincent Fourmond: Version 3.0 of QSoas is out

After almost two years of development, version 3.0 of QSoas is finally out ! It brings in a number of new features. An expert mode for fitting Undoubtedly the most important feature in the new version is a complete upgrade of the fit system, which now features an expert mode, turned on by using the /expert=true option with the fit commands. The expert mode features a command prompt that looks like the normal command prompt, in which it is possible: The latter feature is very important when running fits with many parameters. In that case, there are a number of local minima, and it is necessary to try a number of different starting parameters to really find the best parameters. The new parameter space exploration feature makes it much easier than before, with an interface that allows easily finding the best parameters tried so far and reuse them.
A new documentation system Another very important update is the inclusion of a new, offline, documentation system. The documentation features browsing via table of contents, a command index and text search. It also features the possibility to copy commands from the help to the command prompt, or even run them directly. To top it all, it comes with a series of startup tips that might teach you a thing or two about QSoas (try hitting Show random to learn new tricks !).
Many other features For the full list of changes, please see the changelog. Apart from the changes described above, these are my favorites:
To get the new version, you can just download the source code from the downloads page, where you can also purchase precompiled versions for Windows and MacOS. You can also clone the source from the GitHub repository. About QSoasQSoas 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 3.0. You can download its source code there (or clone from the GitHub repository) and compile it yourself, or buy precompiled versions for MacOS and Windows there.

22 June 2014

Simon Josefsson: OpenPGP Key Transition Statement

I have created a new OpenPGP key 54265e8c and will be transitioning away from my old key. If you have signed my old key, I would appreciate signatures on my new key as well. I have created a transition statement that can be downloaded from https://josefsson.org/key-transition-2014-06-22.txt. Below is the signed statement.
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
OpenPGP Key Transition Statement for Simon Josefsson
I have created a new OpenPGP key and will be transitioning away from
my old key.  The old key has not been compromised and will continue to
be valid for some time, but I prefer all future correspondence to be
encrypted to the new key, and will be making signatures with the new
key going forward.
I would like this new key to be re-integrated into the web of trust.
This message is signed by both keys to certify the transition.  My new
and old keys are signed by each other.  If you have signed my old key,
I would appreciate signatures on my new key as well, provided that
your signing policy permits that without re-authenticating me.
The old key, which I am transitioning away from, is:
pub   1280R/B565716F 2002-05-05
      Key fingerprint = 0424 D4EE 81A0 E3D1 19C6  F835 EDA2 1E94 B565 716F
The new key, to which I am transitioning, is:
pub   3744R/54265E8C 2014-06-22
      Key fingerprint = 9AA9 BDB1 1BB1 B99A 2128  5A33 0664 A769 5426 5E8C
The entire key may be downloaded from: https://josefsson.org/54265e8c.txt
To fetch the full new key from a public key server using GnuPG, run:
  gpg --keyserver keys.gnupg.net --recv-key 54265e8c
If you already know my old key, you can now verify that the new key is
signed by the old one:
  gpg --check-sigs 54265e8c
If you are satisfied that you've got the right key, and the User IDs
match what you expect, I would appreciate it if you would sign my key:
  gpg --sign-key 54265e8c
You can upload your signatures to a public keyserver directly:
  gpg --keyserver keys.gnupg.net --send-key 54265e8c
Or email simon@josefsson.org (possibly encrypted) the output from:
  gpg --armor --export 54265e8c
If you'd like any further verification or have any questions about the
transition please contact me directly.
To verify the integrity of this statement:
  wget -q -O- https://josefsson.org/key-transition-2014-06-22.txt gpg --verify
/Simon
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.12 (GNU/Linux)
iLwEAQEKAAYFAlOnV+AACgkQ7aIelLVlcW89XgUAljJgYfReyR9/bU+Om6UHUttt
CAOgSRqdcQSQ2hT69vzuhb/bc8CslIQcBtGqTgxDFsxEFhbm5zKn+tSzy5MHNHqt
MsqHcZjlYuYVhMXDhka+cfyhtd9zIxjVE5vk8v+GqEGoh8DGYq0vPy3VfvcSz5Z3
MSUpSj8gN00jlU1z4nad3maEq0ApvsLr8EsLZmtxF5TNFvzJ8mmwY+gHBGHjVYkB
8AQBAQoABgUCU6dX4AAKCRAGZKdpVCZejD1eDp46XGL2puMp0le2OF75WIUW8xqf
TMiZeB99ruk3P/jvuLnGPP2J5o7SIKE50FkMEss0yvxi6jBlHk+cJeKWGXVjBpxU
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TjlAbvbxpQsls/JPbbporK2gbAtMlzJPD8zC8z/dT+t0qjlce8fADugblVW3bACC
Kl53X4XpojzNd/U19tSXkIBdNY/GVJqci+iruiJ1WGARF9ocnIXVuNXsfyt7UGq4
UiM/AeDVzI76v1QnE8WpsmSXzi2zXe3VahUPhOU2nPDoL53ggiVsTY3TwilvQLfX
Av/74PIaEtCi1g23YeojQlpdYzcWfnE+tUyTSNwPIBzyzHvFAHNg1Pg0KKUALsD9
P7EjrMuz63z2276EBKX8++9GnQQNCNfdHSuX4WGrBx2YgmOOqRdllMKz6pVMZdJO
V+gXbCMx0D5G7v50oB58Mb5NOgIoOnh3IQhJ7LkLwmcdG39yCdpU+92XbAW73elV
kmM8i0wsj5kDUU2ys32Gj2HnsVpbnh3Fvm9fjFJRbbQL/FxNAjzNcHe4cF3g8hTb
YVJJlzhmHGvd7HvXysJJaa0=
=ZaqY
-----END PGP SIGNATURE-----
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18 May 2014

Benjamin Mako Hill: Installing GNU/Linux on a 2014 Lenovo Thinkpad X1 Carbon

I recently bought a new Lenovo X1 Carbon. It is the new second-generation, type 20A7 laptop, based on Intel s Haswell microarchiteture with the adaptive keyboard. It is the version released in 2014. I also ordered the Thinkpad OneLink Dock which I have returned for the OneLink Pro Dock which I have not yet received. The system is still very new, challenging, and different, but seems to support GNU/Linux reasonably well if you are willing to run a bleeding edge version and/or patch your kernel and if you are not afraid to spend an afternoon or two tweaking things. What follows are my installation notes for Debian testing (jessie) when I installed it in early May 2014. My general impressions about the laptop as a GNU/Linux system and overall are at the end of this write-up.
System Description The X1 Carbon I ordered included the 512GB SSD, the 14.0 inch WQHD (2560 1440) 260 nit touchscreen, and the maximum 8GB of memory. I believe the rest is not particularly negotiable but includes a 720p HD Camera, a 45.2Wh battery, and an Intel Dual Band Wireless 7260AC with Bluetooth 4.0. For those that are curious Here is the output of lspci on the system:
00:00.0 Host bridge: Intel Corporation Haswell-ULT DRAM Controller (rev 0b)
00:02.0 VGA compatible controller: Intel Corporation Haswell-ULT Integrated Graphics Controller (rev 0b)
00:03.0 Audio device: Intel Corporation Haswell-ULT HD Audio Controller (rev 0b)
00:14.0 USB controller: Intel Corporation Lynx Point-LP USB xHCI HC (rev 04)
00:16.0 Communication controller: Intel Corporation Lynx Point-LP HECI #0 (rev 04)
00:16.3 Serial controller: Intel Corporation Lynx Point-LP HECI KT (rev 04)
00:19.0 Ethernet controller: Intel Corporation Ethernet Connection I218-LM (rev 04)
00:1b.0 Audio device: Intel Corporation Lynx Point-LP HD Audio Controller (rev 04)
00:1c.0 PCI bridge: Intel Corporation Lynx Point-LP PCI Express Root Port 6 (rev e4)
00:1c.1 PCI bridge: Intel Corporation Lynx Point-LP PCI Express Root Port 3 (rev e4)
00:1d.0 USB controller: Intel Corporation Lynx Point-LP USB EHCI #1 (rev 04)
00:1f.0 ISA bridge: Intel Corporation Lynx Point-LP LPC Controller (rev 04)
00:1f.2 SATA controller: Intel Corporation Lynx Point-LP SATA Controller 1 [AHCI mode] (rev 04)
00:1f.3 SMBus: Intel Corporation Lynx Point-LP SMBus Controller (rev 04)
BIOS/Firmware The BIOS firmware is non-free and proprietary as it the case with all ThinkPads and nearly all laptops. According to this thread there is a bug in the default BIOS that means that suspend to RAM is broken in GNU/Linux. You can get updated BIOS at the Lenovo s ThinkPad X1 Carbon (Type 20A7, 20A8) Drivers and software page by looking in the the BIOS section. Honestly, the easiest approach is probably to download the Windows BIOS Update utility (documentation is here) which you can use to run the BIOS update from within Windows before you install GNU/Linux. If that s not an option (e.g., if you ve already installed GNU/Linux) the best method is to download the bootable CD ISO from the same page. Of course, since the X1 Carbon has no optical media, you have to find another way to boot the CD image. I struggled to get the ISO to boot from USB using the usually reliable dd method. This message suggest that the issue had to do with the El Torito wrapper:
I had to dump the eltorito image from the ISO they provide, after that I was able to dd the resulting image to a flash drive and the bios update went well, no cdrom needed.
I updated to version 1.13 of the BIOS which fixes the suspend/resume bug. By the time you read this, there may be newer versions that fix other things so check the Lenovo website.
Installing Debian I installed Debian testing using the March 19, 2014 Alpha 1 release of the Debian Installer for Jessie (currently testing). I installed in graphical mode. With the WQHD screen, everything was extremely tiny but it worked flawlessly. I downloaded the amd64 net install image from the normal place and installed the rest of the system using the built-in Ethernet port which required no firmware or extra drivers. I did the normal dd if=FILENAME.iso of=/dev/sdX method of getting the installer onto the a USB stick to boot. I turned off restricted boot in BIOS first. In general, the latest version of the Debian installation guide is always a good source of guidance on installing Debian. I used the Debian installer wizard to partition and selected Use entire disk and partition it for LVM and encrypted data which kept the UEFI partitions around. The system installed with no errors or issues and booted up normally afterward. The grub menu is hilariously narrow on the WQHD screen. If you want to use the built-in wireless and/or Bluetooth, you will need to install the non-free iwlwifi firmware package. It is very lame that we still have to do this to use hardware we have purchased.
What Works and Doesn t The following stuff works the first time I booted into the GNOME 3 desktop and logged in:
  • The WQHD 2560 1440 screen
  • The touchscreen
  • Both the TrackPoint and the touchpad
  • Built-in e1000e Ethernet using the dongle
  • The keyboard plus the adaptive row of F1-F12 keys.
  • External monitor using the full HDMI or mini-DisplayPort connectors
  • Audio (both speakers and microphone)
  • The camera/webcam
The following stuff works if you install non-free firmware:
  • Internal Wireless
  • Bluetooth 4.0
The following stuff works with qualifications:
  • Suspend to RAM Works once you have updated the firmware.
  • The adaptive keyboard The F1-F12 keys work but the button that theoretically lets you switch to different sets of function buttons (e.g., volume, brightness) does nothing.
  • Disabling the touchpad There is a BIOS option to disable the touchpad. It works in Windows and does nothing at all in GNU/Linux.
I have not tried:
  • The fingerprint reader
Disabling the touchpad As a long-term ThinkPad user, I love the TrackPoint pointing stick. If you plan on using this, the built-in touchpad is incredibly aggravating because it is very easy to brush against it while using the TrackPoint. In BIOS, there is an option to disable the touchpad. Although this works in Windows, it does absolutely nothing in GNU/Linux. Part of the issue is that, unlike the older X1 Carbon and other ThinkPads, there are no TrackPoint buttons. Instead of buttons, there are regions at the top of the touchpad which are configured, in software, to act like buttons. If you want to be able to click, the touchpad can never be truly turned off. This is not problem unique to the Haswell X1 Carbon and a number of people have been struggling with this issue on other Lenovo laptops. Essentially, what you need to do is configure your touchpad so that the buttons are where you want them and so that it ignores any input for the purposes of cursor movement. There are a few ways of doing this but this answer from an askubuntu.com question has the solution I ended up using:

Open file /usr/share/X11/xorg.conf.d/50-synaptics.conf for edit.

Find Section InputClass which the following line is Identifier Default clickpad buttons .

Edit option for SoftButtonAreas to values 64% 0 1 42% 36% 64% 1 42%, this is size of the right and middle button.

Enable option AreaBottomEdge and change value to 1, this will disable touchpad movement.

If everything done right, your class should looks like:

Section "InputClass"
     Identifier "Default clickpad buttons"
     MatchDriver "synaptics"
     Option "SoftButtonAreas" "64% 0 1 42% 36% 64% 1 42%"
     Option "AreaBottomEdge" "1"
EndSection
Essentially, the first Option line will create a middle button that is 32% of the width and 42% of the height, and a right button that is 32% of the width and 42% of the height. The synaptics manpage (man synpatics) will give you more detail on the general way this works. Of course, something does feel very wrong about editing a file in /usr/share.
Fixing the Adaptive Keyboard The most wild feature of the laptop is the adaptive keyboard strip. The strip is a back-lit LCD that looks almost like E Ink screen and acts as a touchscreen keyboard. The default mode gives you the F1-F12 keys. If you press the keys (since they aren t buttons, you just put your finger on top of them) they act like normal F-keys. You can Ctrl-Alt-F1, etc., to switch to virtual terminals out of the box. There are four modes: Function (i.e., normal F-keys), Home, Web, and Chat. The last three overlap quite a bit (e.g., they all have brightness and volume). You can play with an example on the Lenovo homepage. In Windows, switching programs will apparently change these keys so that an appropriate set of buttons is shown for the application you are using. You can also change these keys manually with a big Fn button at the far left of the adaptive keyboard strip. As I write this this, released kernels do not support the adaptive keyboard Fn button which means you cannot use anything other than the F-keys out of the box. I believe it also means that resuming from suspend to RAM breaks these keys. That said, Shuduo Sang from Canonical has released several versions of a patch to to the thinkpad_acpi kernel module which adds support for the Home mode. The other modes (web and chat) do not seem to be supported. The latest version of the patch is on on the Linux Kernel Mailing List and the relevant commits are:
330947b save and restore adaptive keyboard mode for suspend and,resume
3a9d20b support Thinkpad X1 Carbon 2nd generation's adaptive keyboard
Although this is not supported in Debian testing at the time of writing, a bug was filed in Debian and quickly fixed by Ben Hutchings in Debian kernel version 3.14.2-1 which is currently in sid/unstable. As a result, if you install the latest version kernel from Debian unstable (3.14.2-1 or later), the adaptive keyboard just works. If you aren t using Debian and if kernel you are using does not have support, you might be patching your kernel.
General Impressions As I have described in my interview with The Setup, I have been a user of ThinkPad X-series laptops for many years. This is my sixth X-series ThinkPad. Overall, I quite like the hardware! Once things mature a little bit, I think that this will be a great laptop for running GNU/Linux. That said, I ordered the laptop without realizing that the X1 Carbon had gone through a major revision! The keyboard was quite a suprise. I think that changing a system so radically without changing the model name/number is a very bad move on Lenovo s part. There are two remaining issues with the system I m still struggling with: (1) the keyboard layout is freaky and weird, and (2) the super high resolution screen breaks many things. The quality of the keyboard itself is great and worthy of the ThinkPad name. That said, there are two ways in which it is strange. The first is the adaptive keyboard strip. Overall, it works surprisingly well and I think it is a clever idea. My sense is that the strip is more annoying in Windows because it changes out from under you all the time. In GNU/Linux, only manual changing of modes is supported. This, in my opinion, is a feature. I do miss the real feedback you get from pressing keys but for F-keys and volume-keys that I don t use often this isn t too important. On the downside, I have realized several times that I had been holding down a button for several seconds and not noticed. The more annoying issue with the keyboard is the way that the other keys have moved around. Getting rid of the CapsLock is wonderful! How has this taken so long? Replacing it with a split Home and End keys is nuts. I ve remapped the Home and End to put Control back where it should be. My right Control to now Home but I still don t have an End key. The split Backspace and Delete is not a problem for me. The tilde/apostrophe is in a very bad place. There is no Insert, Print Screen/SysRq, Scroll Lock, Pause/Break or NumLock. They are all just gone. Surprisingly, I haven t missed any of them. The second issue is the 2560 1440 resolution on the 14 inch screen. I use a 27 inch external monitor with the same native resolution laptop but, by my arithmetic, the pixel density on the laptop is 210 DPI instead 109 DPI on the external monitor. The result is the scaling problem and it s a huge pain that seems mostly unsolved on any operating system. Fonts and widgets that look good on the laptop look huge on my external monitor. Stuff that looks good on my external monitor looks minuscule on the laptop. I routinely move windows between my laptop screen and my large monitor. Until I find a display system that can handle this kind of scaling effectively, this requires changing font size and zooming all the time. At the moment, I m shrinking and expanding my font size using the built in hot keys in Emacs, Gnome Terminal, and Firefox/Iceweasel. I love the high resolution screen but the current situation is crazy-making. Finally, this setup will not get you into the Church of Emacs and it s not about to find its way onto the FSF s list of endorsed hardware. For one, I paid the Windows tax. Beyond that, there is the non-free BIOS and the need for non-free firmware to use the wireless and Bluetooth. This is standard for ThinkPads but it isn t getting any easier to swallow. There are alternatives in the form of Gluglug s X60 laptops running CoreBoot, Lemote Yeelong laptops, Bunnie Huang s Novena and others that are better in these regards. I am very excited for these projects but, for a number of reasons, these just weren t an option for the laptop I use for my research computing.

16 March 2014

Benjamin Mako Hill: Community Data Science Workshops in Seattle

Photo from the Boston Python Workshop   a similar workshop run in Boston that has inspired and provided a template for the CDSW.

Photo from the Boston Python Workshop a similar workshop run in Boston that has inspired and provided a template for the CDSW.

On three Saturdays in April and May, I will be helping run three day-long project-based workshops at the University of Washington in Seattle. The workshops are for anyone interested in learning how to use programming and data science tools to ask and answer questions about online communities like Wikipedia, Twitter, free and open source software, and civic media. The workshops are for people with no previous programming experience and the goal is to bring together researchers as well as participants and leaders in online communities. The workshops will all be free of charge and open to the public given availability of space. Our goal is that, after the three workshops, participants will be able to use data to produce numbers, hypothesis tests, tables, and graphical visualizations to answer questions like: If you are interested in participating, fill out our registration form here. The deadline to register is Wednesday March 26th. We will let participants know if we have room for them by Saturday March 29th. Space is limited and will depend on how many mentors we can recruit for the sessions. If you already have experience with Python, please consider helping out at the sessions as a mentor. Being a mentor will involve working with participants and talking them through the challenges they encounter in programming. No special preparation is required. If you re interested, send me an email.

13 March 2013

Paul Tagliamonte: hilariously debuggable lisp: Hy

If anyone wants to check out some new Hy stuff, check out the REPL 3.0 at hy.pault.ag Also, check out the GitHub Repo, and star it, or consider contributing to it. Hang tight, this is technical Hopefully you re a rockn Pythonista already. If not, hang on! Right, so, here s the Hython we re working with:
;;;; testing.hy
(import-from sunlight openstates)
(defn get-legislators [state]
  "Get some Legislators from a state"
  (kwapply (.legislators openstates)  "state" state ))
(defn print-legislator-count [state]
  "Print the Legislative count for a state"
  (print (len (get-legislators state))))
And a Python script to run it:
#!/usr/bin/env python
import hy
import testing
# import pdb; pdb.set_trace()
testing.print_legislator_count("ma")
Which outputs (correctly): 198. Now, let s try and debug this sucker: I added import pdb; pdb.set_trace() to the top of the Pythonic script (after the imports), to drop into a pdb shell:
> /home/tag/tmp/invoke.py(8)()
-> testing.print_legislator_count("ma")
(Pdb) 
Here s where we are:
(Pdb) l
  3     import hy
  4     import testing
  5     
  6     import pdb; pdb.set_trace()
  7     
  8  ->  testing.print_legislator_count("ma")
[EOF]
OK. Let s step into it.
(Pdb) s
--Call--
> /home/tag/tmp/testing.hy(12)print_legislator_count()
-> (defn print-legislator-count [state]
Whoh! Right! We ve just invoked Lisp. Let s step through the Lisp code:
> /home/tag/tmp/testing.hy(14)print_legislator_count()
-> (print (len (get-legislators state))))
(Pdb) 
--Call--
> /home/tag/tmp/testing.hy(7)get_legislators()
-> (defn get-legislators [state]
(Pdb) 
> /home/tag/tmp/testing.hy(9)get_legislators()->[ (SNIP) ]
-> (kwapply (.legislators openstates)  "state" state ))
(Pdb) l
  4     (import-from sunlight openstates)
  5     
  6     
  7     (defn get-legislators [state]
  8       "Get some Legislators from a state"
  9  ->    (kwapply (.legislators openstates)  "state" state ))
 10     
 11     
 12     (defn print-legislator-count [state]
 13       "Print the Legislative count for a state"
 14       (print (len (get-legislators state))))
(Pdb) 
Rockn . This worked hilariously well.
-> (kwapply (.legislators openstates)  "state" state ))
(Pdb) state
'ma'
Whoh, right there. Look at that! Python s pdb has access to Hy s bits! Neat :)
(Pdb) openstates
(Pdb) s
And. just to prove it s actually Python :)
(Pdb) s
198
--Return--
> /home/tag/tmp/testing.hy(14)print_legislator_count()->None
-> (print (len (get-legislators state))))
(Pdb) s
--Return--
> /home/tag/tmp/invoke.py(8)()->None
-> testing.print_legislator_count("ma")
Whoo! From Python to Lisp and back! Now, for fun, here s some pudb action: And, now, some bpython voodoo: Hopefully this is the start of something wicked neat! :)

4 January 2013

David Welton: The Software Millionaire Next Door

I've been reading "The Millionaire Next Door" and have so far found it to be a pleasant book with a good message: don't waste your money on silly things and appearance (fancy suits, fancy cars, expensive boats, etc...), save what you do earn consistently and constantly, invest wisely, and so on. Wikipedia has a good summary:
http://en.wikipedia.org/wiki/The_Millionaire_Next_Door
One of the things I like about it is that it focuses on "ordinary" wealthy people, those with a million or more in the bank, but not the Warren Buffets or Bill Gates types that are extreme statistical outliers. There are plenty of people in the US who have done well by themselves by slowly but surely putting together enough money to be financially independent, without, however, being in the spotlight. As the book says, these are the kind of people who maybe own a local chain of businesses doing something fairly ordinary, but doing it well enough to succeed. They may very well not live in a fancy house, nor drive an expensive car, or otherwise outwardly draw much attention to themselves. The world of software does not revolve around "dressing for success" (you noticed?), but we do tend to focus on the "big winners". Gates, Jobs, Zuckerberg, Larry & Sergey, Larry Ellison, and so on are the stars of the show. Of course, the economics of software being what they are, instances of winner-take-all markets with one big fish and a lot of also-rans are not uncommon. However, that is not the only story, and I think it'd be interesting to know more about those in our industry who have accumulated significant wealth, yet are not the guys with more money than they could possibly ever spend on things that aren't, say, country-sized chunks of real-estate. I'm guessing they'd fall into these categories: It'd be very interesting to gather some actual data on this, although I'm not in a position to do so myself - I wouldn't even really know where to start. As I age, I think the third category has begun to seem appealing in many ways - I'm simply not cut out for the Big Company life, and I'm not interested in living in Silicon Valley and going "all in" on the latest startup - I already did that, and while it was fun and I don't regret it, it's not the kind of thing I'd want to do now that I'm married and have kids. Incidentally, this more relaxed, under the radar approach is exactly what is expoused in one of my favorite books of the past few years, Start Small, Stay Small. Edit : I finished reading the book and reviewed it here: http://davids-book-reviews.blogspot.com/

18 August 2010

Martin Meredith: Mark Shuttleworth is driving me insane

With his announcement of the N-imal for Ubuntu 11.04 I m being driven slightly insane, as I now now have this song stuck in my head (and probably will do for weeks to come!)

19 March 2006

Clint Adams: This report is flawed, but it sure is fun

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