I'm trying to run a code like this in Mathematica:
(* initialize everything *)
ClearAll["Global`*"]
Remove["Global`*"]
(* all *nb are in $WorkingDirectory *)
$WorkingDirectory = "/Users/U1/Workspace/BCOASMBH/Core/Fortran/"
(* Load Assumptions and format.m *)
Get[FileNameJoin[{$WorkingDirectory, "TemplateForHamiltonian.nb"}]];
However, I keep getting the error:
Get: Cannot open Utilities`FilterOptions`.
Needs: Context Utilities`FilterOptions` was not created when Needs was evaluated.
==========================
Example Script For Writing
==========================
filename = "testing.f"
stmp = OpenWrite[filename, FormatType -> OutputForm];
Write[stmp, FortranAssign[VariableInFortran, FormulaInMathematica, \
AssignPrecision -> 16, AssignTemporary -> {t, Array}]];
Close[stmp];
I'm new to the format.m package so I'm not sure what the error stems from or what can be done about it.
Related
Issue
Following is a minimal, contrived example:
read :: FilePath -> Aff String
read f = do
log ("File: " <> f) -- (1)
readTextFile UTF8 f -- (2)
I would like to do some debug logging in (1), before a potential error on (2) occurs. Executing following code in Spago REPL works for success cases so far:
$ spago repl
> launchAff_ $ read "test/data/tree/root.txt"
File: test/data/tree/root.txt
unit
Problem: If there is an error with (2) - file is directory here - , (1) seems to be not executed at all:
$ spago repl
> launchAff_ $ read "test/data/tree"
~/purescript-book/exercises/chapter9/.psci_modules/node_modules/Effect.Aff/foreign.js:532
throw util.fromLeft(step);
^
[Error: EISDIR: illegal operation on a directory, read] {
errno: -21,
code: 'EISDIR',
syscall: 'read'
}
The original problem is more complex including several layers of recursions (see E-Book exercise 3), where I need logging to debug above error.
Questions
How can I properly log regardless upcoming errors here?
(Optional) Is there a more sophisticated, well-established debugging alternative - purescript-debugger? A decicated VS Code debug extension/functionality would be the cherry on the cake.
First of all, the symptoms you observe do not mean that the first line doesn't execute. It does always execute, you're just not seeing output from it due to how console works in the PureScript REPL. The output gets swallowed. Not the only problem with REPL, sadly.
You can verify that the first line is always executed by replacing log with throwError and observing that the error always gets thrown. Or, alternatively, you can make the first line modify a mutable cell instead of writing to the console, and then examine the cell's contents.
Finally, this only happens in REPL. If you put that launchAff_ call inside main and run the program, you will always get the console output.
Now to the actual question at hand: how to debug trace.
Logging to console is fine if you can afford it, but there is a more elegant way: Debug.trace.
This function has a hidden effect - i.e. its type says it's pure, but it really produces an effect when called. This little lie lets you use trace in a pure setting and thus debug pure code. No need for Effect! This is ok as long as used for debugging only, but don't put it in production code.
The way it works is that it takes two parameters: the first one gets printed to console and the second one is a function to be called after printing, and the result of the whole thing is whatever that function returns. For example:
calculateSomething :: Int -> Int -> Int
calculateSomething x y =
trace ("x = " <> show x) \_ ->
x + y
main :: Effect Unit
main =
log $ show $ calculateSomething 37 5
> npx spago run
'x = 37'
42
The first parameter can be anything at all, not just a string. This lets you easily print a lot of stuff:
calculateSomething :: Int -> Int -> Int
calculateSomething x y =
trace { x, y } \_ ->
x + y
> npx spago run
{ x: 37, y: 5 }
42
Or, applying this to your code:
read :: FilePath -> Aff String
read f = trace ("File: " <> f) \_ -> do
readTextFile UTF8 f
But here's a subtle detail: this tracing happens as soon as you call read, even if the resulting Aff will never be actually executed. If you need tracing to happen on effectful execution, you'll need to make the trace call part of the action, and be careful not to make it the very first action in the sequence:
read :: FilePath -> Aff String
read f = do
pure unit
trace ("File: " <> f) \_ -> pure unit
readTextFile UTF8 f
It is, of course, a bit inconvenient to do this every time you need to trace in an effectful context, so there is a special function that does it for you - it's called traceM:
read :: FilePath -> Aff String
read f = do
traceM ("File: " <> f)
readTextFile UTF8 f
If you look at its source code, you'll see that it does exactly what I did in the example above.
The sad part is that trace won't help you in REPL when an exception happens, because it's still printing to console, so it'll still get swallowed for the same reasons.
But even when it doesn't get swallowed, the output is a bit garbled, because trace actually outputs in color (to help you make it out among other output), and PureScript REPL has a complicated relationship with color:
> calculateSomething 37 5
←[32m'x = 37'←[39m
42
In addition to Fyodor Soikin's great answer, I found a variant using VS Code debug view.
1.) Make sure to build with sourcemaps:
spago build --purs-args "-g sourcemaps"
2.) Add debug configuration to VS Code launch.json:
{
"version": "0.2.0",
"configurations": [
{
"type": "pwa-node",
"request": "launch",
"name": "Launch Program",
"skipFiles": ["<node_internals>/**"],
"runtimeArgs": ["-e", "require('./output/Main/index.js').main()"],
"smartStep": true // skips files without (valid) source map
}
]
}
Replace "./output/Main/index.js" / .main() with the compiled .js file / function to be debugged.
3.) Set break points and step through the .purs file via sourcemap support.
I noticed that the base package use errorWithoutStackTrace to implement lots of functions. Is there some performance different between the following two definition?
head :: [a] -> a
head (x:_) = x
head [] = errorWithoutStackTrace ("Prelude.head: empty list")
head :: [a] -> a
head (x:_) = x
head [] = withFrozenCallStack $ error ("Prelude.head: empty list")
error means something bad happened so for most, if not all purposes, it does not matter how fast it is, because it indicates a program that's not working.
That said, a quick glance at the code is enough to reasonably guess that error does strictly more work than errorWithoutStackTrace (and that is compounded by the addition of withFrozenCallStack to the error variant of your code). Confirming that with benchmarks is left as an exercise to the reader.
Here's the definition of error and errorWithoutStackTrace:
https://hackage.haskell.org/package/base-4.12.0.0/docs/src/GHC.Err.html#error
error s = raise# (errorCallWithCallStackException s ?callStack)
errorWithoutStackTrace s = raise# (errorCallException s)
Now those two internal functions are defined as follows:
errorCallException :: String -> SomeException
errorCallException s = toException (ErrorCall s)
errorCallWithCallStackException :: String -> CallStack -> SomeException
errorCallWithCallStackException s stk = unsafeDupablePerformIO $ do
...
return $ toException (ErrorCallWithLocation s stack)
Note that both essentially do toException (something s), but errorCallWithCallStackException also has a whole lot more code to handle the stack (in "...").
I have a small text file in markdown :
---
title: postWithReference
author: auf
date: 2010-07-29
keywords: homepage
abstract: |
What are the objects of
ontologists .
bibliography: "/home/frank/Workspace8/SSG/site/resources/BibTexLatex.bib"
csl: "/home/frank/Workspace8/SSG/site/resources/chicago-fullnote-bibliography-bb.csl"
---
An example post. With a reference to [#Frank2010a] and more[#navratil08].
## References
and process it in Haskell with processCites' which has a single argument, namely the Pandoc data resulting from readMarkdown. The bibliography and the csl style should be taken from the input file.
The process does not produce errors, but the result of processCites is the same text as the input; references are not treated at all. For the same input the references are resolved with the standalone pandoc (this excludes errors in the bibliography and the csl style)
pandoc -f markdown -t html --filter=pandoc-citeproc -o p1.html postWithReference.md
The issue is therefore in the API. The code I have is:
markdownToHTML4 :: Text -> PandocIO Value
markdownToHTML4 t = do
pandoc <- readMarkdown markdownOptions t
let meta2 = flattenMeta (getMeta pandoc)
-- test if biblio is present and apply
let bib = Just $ ( meta2) ^? key "bibliography" . _String
pandoc2 <- case bib of
Nothing -> return pandoc
_ -> do
res <- liftIO $ processCites' pandoc -- :: Pandoc -> IO Pandoc
when (res == pandoc) $
liftIO $ putStrLn "*** markdownToHTML3 result without references ***"
return res
htmltex <- writeHtml5String html5Options pandoc2
let withContent = ( meta2) & _Object . at "contentHtml" ?~ String ( htmltex)
return withContent
getMeta :: Pandoc -> Meta
getMeta (Pandoc m _) = m
What do I misunderstand? are there any reader options necessary for citeproc? The bibliography is a BibLatex file.
I found in hakyll code a comment, which I cannot understand in light of the code there - perhaps somebody knows what the intention is.
-- We need to know the citation keys, add then *before* actually parsing the
-- actual page. If we don't do this, pandoc won't even consider them
-- citations!
I have a workaround (not an answer to the original question, I still hope that somebody can identify my error!). It is simple to call the standalone pandoc with System.readProess and pass the text and get the result back, not even reading and writing files:
processCites2x :: Maybe FilePath -> Maybe FilePath -> Text -> ErrIO Text
-- porcess the cites in the text (not with the API)
-- using systemcall because the standalone pandoc works with
-- call: pandoc -f markdown -t html --filter=pandoc-citeproc
-- with the input text on stdin and the result on stdout
-- the csl and bib file are used from text, not from what is in the arguments
processCites2x _ _ t = do
putIOwords ["processCite2" ] -- - filein\n", showT styleFn2, "\n", showT bibfn2]
let cmd = "pandoc"
let cmdargs = ["--from=markdown", "--to=html5", "--filter=pandoc-citeproc" ]
let cmdinp = t2s t
res :: String <- callIO $ System.readProcess cmd cmdargs cmdinp
return . s2t $ res
-- error are properly caught and reported in ErrIO
t2s and s2t are conversion utilities between string and text, ErrIO is ErrorT Text a IO and callIO is essentially liftIO with handling of errors.
The original problem was very simple: I had not included the option Ext_citations in the markdownOptions. When it is included, the example works (thanks to help I received from the pandoc-citeproc issue page). The referenced code is updated...
I'm trying to use erl_lint() to build a simple Erlang syntax and style checker. I've gotten far enough to load the file and parse it into Forms and to get erl_lint to partially understand it, but then erl_lint complains about undefined functions that are defined. What am I doing wrong?
erlint.erl :
-module(erlint).
-export([lint/1]).
% based on http://stackoverflow.com/a/28086396/13675
lint(File) ->
{ok, B} = file:read_file(File),
Forms = scan(erl_scan:tokens([],binary_to_list(B),1),[]),
F = fun(X) -> {ok,Y} = erl_parse:parse_form(X), Y end,
erl_lint:module([F(X) || X <- Forms],File).
scan({done,{ok,T,N},S},Res) ->
scan(erl_scan:tokens([],S,N),[T|Res]);
scan(_,Res) ->
lists:reverse(Res).
hello.erl :
-module(hello).
-export([hello_world/0]).
hello_world() -> io:fwrite("hello, world\n").
attempt to use :
1> c(erlint).
{ok,erlint}
2> erlint:lint("hello.erl").
{error,[{"hello.erl",
[{2,erl_lint,{undefined_function,{hello_world,0}}}]}],
[]}
I'm not sure this approach fits with your overall plan, but you could instead compile the input file, extract its abstract forms from the resulting beam, and pass them to erl_lint:
-module(erlint).
-export([lint/1]).
lint(File) ->
{ok,_,Bin} = compile:file(File,[debug_info,binary]),
{ok,{_,[{abstract_code,{_,AC}}]}} = beam_lib:chunks(Bin,[abstract_code]),
erl_lint:module(AC,File).
Let's change your hello.erl to include an unused variable:
-module(hello).
-export([hello_world/0]).
hello_world() ->
X = io:fwrite("hello, world\n").
We see that this version of erlint:lint/1 correctly reports it:
1> erlint:lint("hello.erl").
{ok,[{"hello.erl",[{5,erl_lint,{unused_var,'X'}}]}]}
If you need them for your overall purposes, note that you can retrieve source code forms from the abstract forms variable AC by calling erl_syntax:form_list(AC).
I am try to learn Erlang. I've installed a runtime but cannot get it working. The following code:
X = 3.
works, but none of the following statements work:
f(X)->X.
F() ->0.
F([])->[].
I get back 1: syntax error before: '->'. I tried the word_count from this tutorial. And I get the same error.
What is wrong here?
In REPL you have to use fun(...) -> ... end:
1> F = fun(X) -> X end.
#Fun<erl_eval.6.80484245>
2> F(42).
42
If you have code in file use c command:
1> c(word_count).
{ok,word_count}
2> word_count:word_count([]).
0
There is difference in sytax when writing functions in Erlang module and Erlang shell (REPL). As P_A mentioned you need to call as F = fun(X) -> X end, F("Echo").
Also note that function names are atoms so has to start with lowercase when you are writing in Erlang module. If you are serious about learning Erlang I would suggest you go through this.
You mentioned that you worked on F#. The basic difference between F# and Erlang in this case is that expression
let Lilo = [|5; 3; -3; 0; 0.5|];; Can be written directly in the file and executed. In Erlang it can only be done in Erlang shell and not inside a file.
So the expression you are trying should be inside a function inside a module with the same name as file. Consider test.erl file. Any function you export can be called from outside (shell).
-module(test).
-export([test/0]).
test() ->
Lilo = [5, 3, -3, 0, 0.5],
[X*2 || X <-Lilo].