I am trying to redefine the \nomencl_command in LyX, in order to be able to use the glossaries package in stead of the obsolete nomencl.
LyX allows you to specify the Nomenclature command, which by default is set to:
makeindex -s nomencl.ist
For glossaries the command is thus changed to:
makeglossaries
However, the LyX implementation of nomencl uses the more recent .nlo as an input file, and the .nls as an output file. Whereas glossaries uses the 'older' .glo and .gls Unfortunately, the extensions cannot be specified.
I found that the preferences file only says:
\nomencl_command "makeglossaries"
but the log output says:
makeglossaries "[filename].nlo" -o [filename].nls
So my question is where is \nomencl_command defined further?
The relevant code is in src/LaTeX.cpp.
Note below that some diagnostic information is written to the latex debug flag. You can see this info on the terminal if you run LyX with lyx -dbg latex.
The following are excerpts from the file src/LaTeX.cpp from the soon-to-be-released (a matter of days) LyX 2.1.
FileName const nlofile(changeExtension(file.absFileName(), ".nlo"));
// If all nomencl entries are removed, nomencl writes an empty nlo file.
// DepTable::hasChanged() returns false in this case, since it does not
// distinguish empty files from non-existing files. This is why we need
// the extra checks here (to trigger a rerun). Cf. discussions in #8905.
// FIXME: Sort out the real problem in DepTable.
if (head.haschanged(nlofile) || (nlofile.exists() && nlofile.isFileEmpty()))
rerun |= runMakeIndexNomencl(file, ".nlo", ".nls");
FileName const glofile(changeExtension(file.absFileName(), ".glo"));
if (head.haschanged(glofile))
rerun |= runMakeIndexNomencl(file, ".glo", ".gls");
and
bool LaTeX::runMakeIndexNomencl(FileName const & file,
string const & nlo, string const & nls)
{
LYXERR(Debug::LATEX, "Running MakeIndex for nomencl.");
message(_("Running MakeIndex for nomencl."));
string tmp = lyxrc.nomencl_command + ' ';
// onlyFileName() is needed for cygwin
tmp += quoteName(onlyFileName(changeExtension(file.absFileName(), nlo)));
tmp += " -o "
+ onlyFileName(changeExtension(file.toFilesystemEncoding(), nls));
Systemcall one;
one.startscript(Systemcall::Wait, tmp, path);
return true;
}
and
// nomencl file
FileName const nls(changeExtension(file.absFileName(), ".nls"));
nls.removeFile();
// nomencl file (old version of the package)
FileName const gls(changeExtension(file.absFileName(), ".gls"));
gls.removeFile();
Related
i'm new to nf-core/nextflow and needless to say the documentation does not reflect what might be actually implemented. But i'm defining the basic pipeline below:
nextflow.enable.dsl=2
process RUNBLAST{
input:
val thr
path query
path db
path output
output:
path output
script:
"""
blastn -query ${query} -db ${db} -out ${output} -num_threads ${thr}
"""
}
workflow{
//println "I want to BLAST $params.query to $params.dbDir/$params.dbName using $params.threads CPUs and output it to $params.outdir"
RUNBLAST(params.threads,params.query,params.dbDir, params.output)
}
Then i'm executing the pipeline with
nextflow run main.nf --query test2.fa --dbDir blast/blastDB
Then i get the following error:
N E X T F L O W ~ version 22.10.6
Launching `main.nf` [dreamy_hugle] DSL2 - revision: c388cf8f31
Error executing process > 'RUNBLAST'
Error executing process > 'RUNBLAST'
Caused by:
Not a valid path value: 'test2.fa'
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
I know test2.fa exists in the current directory:
(nfcore) MN:nf-core-basicblast jraygozagaray$ ls
CHANGELOG.md conf other.nf
CITATIONS.md docs pyproject.toml
CODE_OF_CONDUCT.md lib subworkflows
LICENSE main.nf test.fa
README.md modules test2.fa
assets modules.json work
bin nextflow.config workflows
blast nextflow_schema.json
I also tried with "file" instead of path but that is deprecated and raises other kind of errors.
It'll be helpful to know how to fix this to get myself started with the pipeline building process.
Shouldn't nextflow copy the file to the execution path?
Thanks
You get the above error because params.query is not actually a path value. It's probably just a simple String or GString. The solution is to instead supply a file object, for example:
workflow {
query = file(params.query)
BLAST( query, ... )
}
Note that a value channel is implicitly created by a process when it is invoked with a simple value, like the above file object. If you need to be able to BLAST multiple query files, you'll instead need a queue channel, which can be created using the fromPath factory method, for example:
params.query = "${baseDir}/data/*.fa"
params.db = "${baseDir}/blastdb/nt"
params.outdir = './results'
db_name = file(params.db).name
db_path = file(params.db).parent
process BLAST {
publishDir(
path: "{params.outdir}/blast",
mode: 'copy',
)
input:
tuple val(query_id), path(query)
path db
output:
tuple val(query_id), path("${query_id}.out")
"""
blastn \\
-num_threads ${task.cpus} \\
-query "${query}" \\
-db "${db}/${db_name}" \\
-out "${query_id}.out"
"""
}
workflow{
Channel
.fromPath( params.query )
.map { file -> tuple(file.baseName, file) }
.set { query_ch }
BLAST( query_ch, db_path )
}
Note that the usual way to specify the number of threads/cpus is using cpus directive, which can be configured using a process selector in your nextflow.config. For example:
process {
withName: BLAST {
cpus = 4
}
}
This question has been posted before in the qt community: https://forum.qt.io/topic/106930/how-to-run-lupdate-with-a-qmake-config
I use such a construct in my project files:
LANGUAGES = de
TRANSLATION_NAME = authorization
include(../../gen_translations.pri)
where gen_translations.pri looks like so:
# parameters: var, prepend, append
defineReplace(prependAll) {
for(a,$$1):result += $$2$${a}$$3
return($$result)
}
TRANSLATIONS = $$prependAll(LANGUAGES, $$PWD/libs/$$TRANSLATION_NAME/translations/lib$${TRANSLATION_NAME}_, .ts)
TRANSLATIONS_FILES =
qtPrepareTool(LRELEASE, lrelease)
for(tsfile, TRANSLATIONS) {
qmfile = $$shadowed($$tsfile)
qmfile ~= s,.ts$,.qm,
qmdir = $$dirname(qmfile)
!exists($$qmdir) {
mkpath($$qmdir)|error("Aborting.")
}
command = $$LRELEASE -removeidentical $$tsfile -qm $$qmfile
system($$command)|error("Failed to run: $$command")
TRANSLATIONS_FILES += $$qmfile
}
for(qmentry, $$list($$TRANSLATIONS_FILES)) {
qmpath = $$OUT_PWD/../translations
qmpathname = $$replace(qmpath,/,)
qmpathname = $$replace(qmpathname,\.,)
qmpathname = $$replace(qmpathname,:,)
qmpathname = $$replace(qmpathname," ",)
qmentity = qmfiles_$${qmpathname}
eval($${qmentity}.files += $$qmentry)
eval($${qmentity}.path = $$qmpath)
INSTALLS *= $${qmentity}
}
It generates the *.qm files for me and moves them to a defined location with make install.
I do not want qmake to execute that whole stuff for each build on my developing machine. Therefore I want to make it conditional by wrapping it for qmake:
translate{
LANGUAGES = de
TRANSLATION_NAME = authorization
include(../../gen_translations.pri)
}
That way I can decide when I want to get *.qm files and when not.
But then I am unable to run lupdate on the project file beforehand because it is blocked by that conditional.
I am sure, that someone has a better idea to accomplish the task.
Thanks in advance.
I'm sharing here my recipe for the vmpk project. I've borrowed it from the Arora project (I think). It is much simpler than yours, and I let qmake to decide if it is necessary regenerate any .qm files when the output has been erased or the input .ts has changed, like any other compiler does.
updateqm.pri
# update translations
isEmpty(QMAKE_LRELEASE) {
win32:QMAKE_LRELEASE = $$[QT_INSTALL_BINS]\\lrelease.exe
else:QMAKE_LRELEASE = $$[QT_INSTALL_BINS]/lrelease
!exists($$QMAKE_LRELEASE) { QMAKE_LRELEASE = lrelease }
}
updateqm.input = TRANSLATIONS
updateqm.output = $$OUT_PWD/${QMAKE_FILE_BASE}.qm
updateqm.commands = $$QMAKE_LRELEASE ${QMAKE_FILE_IN} -qm $$OUT_PWD/${QMAKE_FILE_BASE}.qm
updateqm.CONFIG += no_link target_predeps
QMAKE_EXTRA_COMPILERS += updateqm
project.pro:
TRANSLATIONS += \
translations/project_en.ts \
translations/project_cs.ts \
translations/project_de.ts \
translations/project_es.ts \
translations/project_fr.ts \
translations/project_ru.ts
include(updateqm.pri)
With this project file you can do, as always:
lupdate project.pro
Anyway, Qt5 has a builtin CONFIG+=lrelease option that makes "updateqm.pri" deprecated.
When I call the embedded python from my c++ app, the application crashes. Something in _PyCodec_Lookup is not working. Debugging seems to indicate the error comes from this line in file codecs.c:
PyInterpreterState *interp = _PyInterpreterState_GET_UNSAFE();
if (interp->codec_search_path == NULL && _PyCodecRegistry_Init())
goto onError;
interp->codec_search_path is NULL and _PyCodecRegistry_Init() returns -1.
This problems is already known; Solutions like removing python27, or setting environment variables PYTHONPATH or PYTHONHOME to either "" or the src path do not work.
I link to cpython version 3.8.0a3 which I've compiled with the included scripts inside the PCBUILD folder, using the same compiler as my applications (MSVC 15 2017).
The OS is windows 8.1 64 bit.
My application links to the produced binary python38.dll / python38.lib successfully but then crashes at runtime, and I have no idea what might cause the trouble - people suggest the environment is polluted, but it must not depend on the system's environment. How would I confidently ship the app to other people's computers? Did I maybe miss some compile flags or defines?
I'm sure you are, but you are doing this after Py_Initialize ?
I include the python3.8 dll but when starting up I take the executable full
path and then add that to the python path (the code below is not tested but
it's roughly what I do)
void py_add_to_path (const char *path)
{
PyObject *py_cur_path, *py_item;
char *new_path;
int wc_len, i;
wchar_t *wc_new_path;
char *item;
new_path = strdup(path);
py_cur_path = PySys_GetObject("path");
for (i = 0; i < PyList_Size(py_cur_path); i++) {
char *tmp = strappend(new_path, PATHSEP);
myfree(new_path);
new_path = tmp;
py_item = PyList_GetItem(py_cur_path, i);
if (!PyUnicode_Check(py_item)) {
continue;
}
item = py_obj_to_str(py_item);
if (!item) {
continue;
}
tmp = strappend(new_path, item);
free(new_path);
new_path = tmp;
free(item);
}
/* Convert to wide chars. */
wc_len = sizeof(wchar_t) * (strlen(new_path) + 1);
wc_new_path = (wchar_t *) malloc(wc_len, "wchar str");
mbstowcs(wc_new_path, new_path, wc_len);
PySys_SetPath(wc_new_path);
}
Seems a bit old now but looks like there is need to add the Lib folder including all the python system files to the search paths of the application.
Take a look at this Python port for UWP
It has an embedded python34app.zip that includes the codec files.
I am trying to use qmake to include all files in a directory (this project is an external subversion project with hundreds of files). I am using qmake version 3.1.
What I tried was something like:
server_files = $$files($$PWD/server)
SOURCES += server_files(*.cpp, true)
The first line does not give any error but the second line gives:
:-1: warning: Failure to find: server_files(*.cpp,
:-1: warning: Failure to find: true)
Putting a $ sign in front of the variable as SOURCES += $server_files(*.cpp, true) gives the same error.
The following example function takes a variable name as its only argument, extracts a list of values from the variable with the eval() built-in function, and compiles a list of files:
defineReplace(headersAndSources) {
variable = $$1
names = $$eval($$variable)
headers =
sources =
for(name, names) {
header = $${name}.h
exists($$header) {
headers += $$header
}
source = $${name}.cpp
exists($$source) {
sources += $$source
}
}
return($$headers $$sources)
}
Variable Processing Functions
I have a python script that needs to be called from within an Extendscript script. Is there any library function available which can do this? I tried finding a solution in the documentation and many other online resources but nothing has worked for me so far. Any help is appreciated.
ExtendScript File objects have an execute() method, as already shown by Fabian.
I did not know about .term files and would have used a .command file instead, that's a plain shell script rather than XML.
If running within InDesign, you can bypass Terminal.app and use AppleScript:
myScript = 'do shell script "diff f1 f2 > o" ';
app.doScript(myScript, ScriptLanguage.applescriptLanguage);
Take a look at this example.
It creates a .term file next to the script file and executes it.
This is a cleaned version:
main();
function main() {
var script_file = File($.fileName); // get the full path of the script
var script_folder = script_file.path; // get the path from that
var new_termfile = createTermFile("execute_something", script_folder);
new_termfile.execute(); // now execute the termfile
}
/**
* creates a .term file
* #param {String} term_file_name --> the name for the .term file
* #param {Strin} path --> the path to the script file
* #return {File} the created termfile
*/
function createTermFile(term_file_name, path) {
/*
http://docstore.mik.ua/orelly/unix3/mac/ch01_03.htm
1.3.1.1. .term files
You can launch a customized Terminal window from the command line by saving some prototypical Terminal settings to a .term file,
then using the open command to launch the .term file (see "open" in Section 1.5.4, later in this chapter).
You should save the .term file someplace where you can find it later, such as ~/bin or ~/Documents.
If you save it in ~/Library/Application Support/Terminal, the .term file will show up in Terminal's File Library menu.
To create a .term file, open a new Terminal window, and then open the Inspector (File Show Info, or -I)
and set the desired attributes, such as window size, fonts, and colors. When the Terminal's attributes
have been set, save the Terminal session (File Save, or -S) to a .term file (for example, ~/Documents/proto.term).
Now, any time you want to launch a Terminal window from the command line, you can issue the following command:
*/
var termfile = new File(path + "/" + term_file_name + ".term");
termfile.open("w");
termfile.writeln(
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
"<!DOCTYPE plist PUBLIC \"-//Apple Computer//DTD PLIST 1.0//EN\"" +
"\"http://www.apple.com/DTDs/PropertyList-1.0.dtd\">\n" +
"<plist version=\"1.0\">\n" +
"<dict>\n" +
"<key>WindowSettings</key>\n" +
"<array>\n" +
" <dict>\n" +
"<key>CustomTitle</key>\n" +
"<string>My first termfile</string>\n" +
"<key>ExecutionString</key>\n" +
"<string>python\nprint \"Hello World\"\nexit()</string>\n" +
"</dict>\n" +
"</array>\n" +
"</dict>\n" +
"</plist>\n");
termfile.close();
return termfile;
};