In order to distribute a function I've written that depends on other functions I've written that have their own dependencies and so on without distributing every m-file I have ever written, I need to figure out what the full list of dependencies is for a given m-file. Is there a built-in/freely downloadable way to do this?
Specifically I am interested in solutions for MATLAB 7.4.0 (R2007a), but if there is a different way to do it in older versions, by all means please add them here.
For newer releases of Matlab (eg 2007 or 2008) you could use the built in functions:
mlint
dependency report and
coverage report
Another option is to use Matlab's profiler. The command is profile, it can also be used to track dependencies. To use profile, you could do
>> profile on % turn profiling on
>> foo; % entry point to your matlab function or script
>> profile off % turn profiling off
>> profview % view the report
If profiler is not available, then perhaps the following two functions are (for pre-MATLAB 2015a):
depfun
depdir
For example,
>> deps = depfun('foo');
gives a structure, deps, that contains all the dependencies of foo.m.
From answers 2, and 3, newer versions of MATLAB (post 2015a) use matlab.codetools.requiredFilesAndProducts instead.
See answers
EDIT:
Caveats thanks to #Mike Katz comments
Remember that the Profiler will only
show you files that were actually used
in those runs, so if you don't go
through every branch, you may have
additional dependencies. The
dependency report is a good tool, but
only resolves static dependencies on
the path and just for the files in a
single directory.
Depfun is more reliable but gives you
every possible thing it can think of,
and still misses LOAD's and EVAL's.
For MATLAB 2015a and later you should preferably look at matlab.codetools.requiredFilesAndProducts
or doc matlab.codetools.requiredFilesAndProducts
because depfun is marked to be removed in a future release.
Related
I have a couple questions about adding options/switches (with and without parameters) to procedures/commands. I see that tcllib has cmdline and Ashok Nadkarni's book on Tcl recommends the parse_args package and states that using Tcl to handle the arguments is much slower than this package using C. The Nov. 2016 paper on parse_args states that Tcl script methods are or can be 50 times slower.
Are Tcl methods really signicantly slower? Is there some minimum threshold number of options to be reached before using a package?
Is there any reason to use parse_args (not in tcllib) over cmdline (in tcllib)?
Can both be easily included in a starkit?
Is this included in 8.7a now? (I'd like to use 8.7a but I'm using Manjaro Linux and am afraid that adding it outside the package manager will cause issues that I won't know how to resolve or even just "undo").
Thank you for considering my questions.
Are Tcl methods really signicantly slower? Is there some minimum threshold number of options to be reached before using a package?
Potentially. Procedures have overhead to do with managing the stack frame and so on, and code implemented in C can avoid a number of overheads due to the way values are managed in current Tcl implementations. The difference is much more profound for numeric code than for string-based code, as the cost of boxing and unboxing numeric values is quite significant (strings are always boxed in all languages).
As for which is the one to use, it really depends on the details as you are trading off flexibility for speed. I've never known it be a problem for command line parsing.
(If you ask me, fifty options isn't really that many, except that it's quite a lot to pass on an actual command line. It might be easier to design a configuration file format — perhaps a simple Tcl script! — and then to just pass the name of that in as the actual argument.)
Is there any reason to use parse_args (not in tcllib) over cmdline (in tcllib)?
Performance? Details of how you describe things to the parser?
Can both be easily included in a starkit?
As long as any C code is built with Tcl stubs enabled (typically not much more than define USE_TCL_STUBS and link against the stub library) then it can go in a starkit as a loadable library. Using the stubbed build means that the compiled code doesn't assume exactly which version of the Tcl library is present or what its path is; those are assumptions that are usually wrong with a starkit.
Tcl-implemented packages can always go in a starkit. Hybrid packages need a little care for their C parts, but are otherwise pretty easy.
Many packages either always build in stubbed mode or have a build configuration option to do so.
Is this included in 8.7a now? (I'd like to use 8.7a but I'm using Manjaro Linux and am afraid that adding it outside the package manager will cause issues that I won't know how to resolve or even just "undo").
We think we're about a month from the feature freeze for 8.7, and builds seem stable in automated testing so the beta phase will probably be fairly short. The list of what's in can be found here (filter for 8.7 and Final). However, bear in mind that we tend to feel that if code can be done in an extension then there's usually no desperate need for it to be in Tcl itself.
I would like to identify all functions needed to run a specific function in octave. I need this to deploy an application written in Octave.
While Matlab offers some tools to analyse a function on its dependencies, I could not find something similar for Octave.
Trying inmem as recommended in matlab does not produce the expected result:
> inmem
warning: the 'inmem' function is not yet implemented in Octave
Is there any other solution to this problem available?
First, let me point out that from your description, the matlab tool you're after is not inmem, but deprpt.
Secondly, while octave does not have a built-in tool for this, there is a number of ways to do so yourself. I have not tried these personally, so, ymmv.
1) Run your function while using the profiler, then inspect the functions used during the running process. As suggested in the octave archives: https://lists.gnu.org/archive/html/help-octave/2015-10/msg00135.html
2) There are some external tools on github that attempt just this, e.g. :
https://git.osuv.de/m/about
https://github.com/KaeroDot/mDepGen
3) If I had to attack this myself, I would approach the problem as follows:
Parse and tokenise the m-file in question. (possibly also use binary checks like isvarname to further filter useless tokens before moving to the next step.)
For each token x, wrap a "help(x)" call to a try / catch block
Inspect the error, this will be one of:
"Invalid input" (i.e. token was not a function)
"Not found" (i.e. not a valid identifier etc)
"Not documented" (function exists but has no help string)
No error, in which case you stumbled upon a valid function call within the file
To further check if these are builtin functions or part of a loaded package, you could further parse the first line of the "help" output, which typically tells you where this function came from.
If the context for this is that you're trying to check if a matlab script will work on octave, one complication will be that typically packages that will be required on octave are not present in matlab code. Then again, if this is your goal, you should probably be using deprpt from matlab directly instead.
Good luck.
PS. I might add that the above is for creating a general tool etc. In terms of identifying dependencies in your own code, good software engineering practices go a long way towards providing maintenable code and easily resolving dependency problems for your users. E.g: -- clearly identifying required packages (which, unlike matlab, octave does anyway by requiring such packages to be visibly loaded in code) -- similarly, for custom dependencies, consider wrapping and providing these as packages / namespaces, rather than scattered files -- if packaging dependencies isn't possible, you can create tests / checks in your file that throw errors if necessary files are missing, or at least mention such dependencies in comments in the file itself, etc.
According to Octave Compatibility FAQ here,
Q. inmem
A. who -functions
You can use who -function. (Note: I have not tried yet.)
I think this is more of a Tcl configuration question rather than a Tcl coding question...
I inherited a whole series of Tcl scripts that are used within a simulation tool that my company built in-house. In my scripts, I'm finding numerous instances where there are function calls to functions that don't seem to be declared anywhere. How can I trace the path to these phantom functions?
For example, rather than use source, someone build a custom include function that they named INCLUDE. Tclsh obviously balks when I try to run it there, but with my simulation software, it runs fine.
I've tried grep-ing through the entire simulation software for INCLUDE, but I'm not having any luck. Are there any other obvious locations outside the simulation software where a Tcl function might be defined?
The possibilities:
Within your software. (you have checked for this).
Within some other package included by the software.
Check and see if the environment variable TCLLIBPATH is set.
Also check and see if the simulation software sets TCLLIBPATH.
This will be a list of directories to search for Tcl packages, and you
will need to search the packages that are located outside of the
main source tree.
Another possibility is that the locations are specified in the pkgIndex.tcl file.
Check any pkgIndex.tcl files and look for locations outside the main source tree.
Within an unknown command handler. This could be in
your software or within some other package. You should be able to find
some code that processes the INCLUDE statement.
Within a binary package. These are shared libraries that are loaded
by Tcl. If this is the case, there should be some C code used to
build the shared library that can be searched.
Since you say there are numerous instances of unknown functions, my first
guess is that you have
not found all the directories where packages are loaded from. But an
''unknown'' command handler is also a possibility.
Edit:
One more possibility I forgot. Check and see if your software sets the auto_path variable. Check any directories added to the auto_path for
other packages.
This isn't a great answer for you, but I suspect it is the best you're going to get...
The procedure could be defined in a great many places. Your best bet for finding it is to use a tool like findstr (on Windows) or grep -R (on POSIX platforms) to search across all the relevant source files. But that still might not help! It might not be a procedure but instead a general command, which could be implemented in C and not as a procedure, or it could be defined in a packaged application archive (which are usually awkward to look inside). There are also other types of script-implemented command too, which could make things awkward. Generally searching and investigating is your best bet, but it might not work.
Tcl doesn't really differentiate strongly between different types of command except in some introspection operations. If you're lucky, you could find that info body tells you the definition of the procedure (and info args and info default tell you about the arguments) but that won't help with other command types at all. Tcl 8.7 will include a command (info cmdtype) that would help a lot with narrowing down what to do next, but that's no use to you now and it definitely doesn't exist in older versions.
Essentially I want to rewrite a binary file to perform additional tasks regarding its actual tasks.
Regarding binary rewriting the process seems to be following:
Create a Control Flow Graph from an existing binary
Create a Code Snippet with the desired changes in an appropriate format
Create a binary file from the modified CFG
I came across a couple of tools, which either won't compile on my ubuntu 12.04, are not available for download or I can not find a decent tutorial / howto on how to hot patch / rewrite a binary. Those tools are:
ParseAPI, Code-Surfer/x86, EEL, LEEL, Jakstab, DynInst, Diablo + Lancet
To be more precise I want to analyze a given binary for its most frequently used functions and change it in such a way that before executing these functions, a given set of instructions are performed.
These instructions comprise of loading an array of stored bytes, reading a byte at a certain position and comparing it with a pre-defined value.
I want to make sure that the binary definitely executes these instructions during every trial.
There are 2 alternative approaches I came across which basically alter standard c functions (like memcpy(), strcpy(), printf(), etc.) since I assume these functions to be part of the binary with high probability:
LD_PRELOAD: Define my own libraries and let them get loaded before the ordinary ones
Compile the binary (of sourcecode is given) with own versions of the standard functions using something like gcc -fno-builtin -o strcpy strcpy.c
Drawback of this approach is that eventhough I subsitute standard c functions they do not necessarily have to get called, hence my instruction will not get executed neither.
Do you guys have experience regarding binary rewriting or do your have clues for accomplishing this rather exotic task?
Best regards!
BAP and Dyninst would help you. You may use BAP (http://bap.ece.cmu.edu/) to get the control flow graph of a binary. It have a very easy to use utility to create control flow graph from binaries. And you may use dyninst to instrument binaries and perform your desired operations. BAP absolutely runs on ubuntu12.04. Dyninst might not compile on 12.04 (there might be some linking problems). A simple walk around is that you do instrumentation on 10.04 and run the rewritten binaries on 12.04. Both tools are free.
I am a new one to Common Lisp (using Clozure Common Lisp under Microsoft Windows), who is familiar with c and python before. So maybe the questions are stupid here, but be patient to give me some help.
1) What's is the usual way to run a common lisp script?
Now, I wrote a bat file under windows to call ccl exe(wx86cl.exe) and evaluate (progn (load "my_script_full_path") (ccl:quit)) every time when I want to "run" my script. Is this a standard way to "run" a script for common lisp?
Any other suggestion about this?
2) What's the difference between (require 'cxml) and (asdf:operate 'asdf:load-op :cxml)?
They are seems to be the same for my script, which one should I use?
3) ignore it, not a clear question
4) When I want to load some library (such as require 'cxml), it always takes time(3s or even 5s) to load cxml every time when I "run" my script, there is also much log to standard output I show below, it seems like checking something internal. Does it means I have to spent 3-5s to load cxml every time when I want to run a simple test? It seems like a little inefficient and the output is noisy. Any suggestion?
My Script
(require 'cxml) (some-code-using-cxml)
And the output
; Loading system definition from D:/_play_/lispbox-0.7/quicklisp/dists/quicklisp/software/cxml-20101107-git/cxml.asd into #<Package "ASDF0">
;;; Checking for wide character support... yes, using code points.
; Registering #<SYSTEM "cxml-xml">
......
some my script output
---EDIT TO ADD MORE----
5) I must say that I almost forget the way of dumping image to accelerate the loading speed of lisp library. So, what is the normal process for us to develop a (maybe very simple) lisp script?
Base on the answer of what I got now, I guess maybe
a) edit your script
b) test it via a REPL environment, SLIME is a really good choice, and there should be many loop between a <==> b
c) dump the image to distribute it?( I am no sure about this)
6) Furthermore, what is the common way/form for us to release/distribute the final program?
For a lisp library, we just release our source code, and let someone else can "load/require" them.
For a lisp program, we dump a image to distribute it when we confirm that all functions go well.
Am I right?
What form do we use in a real product? Do we always dump all the thing into a image at final to speed up the loading speed?
1) Yes, the normal way to run a whole programme is to use a launcher script. However, windows has much, much better scripting support these days than just the bat interpreter. Windows Scripting Host and PowerShell ship as standard.
1a) During development, it is usual to simply type things in a the REPL (Read-Eval-Print-Loop, i.e. the lisp command line), or to use something like SLIME (for emacs or xemacs) as a development environment. If you don't know what they are, look them up. You may wish to use Cygwin to install xemacs, which will give you access to a range of linux-ish tools.
2) Require is, IIRC, a part of the standard. ASDF is technically not, it is a library that operates to make libraries work more conveniently. ASDF has a bunch of features that you will eventually want if you really get into writing large Lisp programmes.
3) Question unclear, pass.
4) See 1a) - do your tests and modifications in a running instance, thus avoiding the need to load the library more than once (just as you would in Python - you found the python repl, right?). In addition, when your programme is complete, you can probably dump an image which has all of your libraries pre-loaded.
Edit: additional answers:
5) Yes
6) Once you have dumped the image, you will still need to distribute the lisp binary to load the memory image. To make this transparent to the user, you will also have to have a loader script (or binary) to run the lisp binary with the image.
You don't have to start the lisp from scratch and load everything over again each time you want to run a simple test. For more efficient development, interactively evaluate code in the listener (REPL) of a running lisp environment.
For distribution, I use Zachary Beane's Buildapp tool. Very easy to install and use.
Regarding distribution -
I wrote a routine (it's at home and unavailable at the moment) that will write out the current image as a standard executable and quit. It works for both CLISP and SBCL.
I can rummage it up if you like.