I will like to compile files in the following steps using SCons:
.c -> .asm(assembly file) -> .o
I tried to define different builders for this.
I managed to do something like: .asm -> .o and .c -> .o
I don't know how to make SCons aware of the .asm files generated from .c files and then to use the object builder.
Is there any possibility to use current SCons implementation for this ?
EDIT: This is what I tried :
-> To define two builders: Builder 1 (c_to_asm) is intended to do .c -> .asm step
Builder 2 (asm_to_o) is intended to do .asm -> .o . After these two builders are executed for all the files defined in my SConscript I expect the Program builder to create the final executable.
SCons.Tool.createProgBuilder(env)
c_to_asm = SCons.Builder.Builder(action = {},
emitter = {},
prefix = '',
suffix = '.asm',
src_builder = '',
source_scanner = '',
single_source = 1)
c_to_asm_action = SCons.Action.Action('c to asm command line', 'Executing .c to .asm builder')
c_to_asm.add_action('.c', c_to_asm_action)
asm_to_o = SCons.Builder.Builder(action = {},
emitter = {},
prefix = '',
suffix = '.o',
src_builder = ['CTOASM'],
source_scanner = '',
single_source = 1)
asm_to_o_action = SCons.Action.Action('asm to o command line', 'Executing .asm to .o builder...')
asm_to_o.add_action('.asm', asm_to_o_action)
env['BUILDERS']['CTOASM'] = c_to_asm
env['BUILDERS']['Object'] = asm_to_o
I see the execution string for each builder but no command is executed.
I don't know how to establish in which order these builders execute actions and how to trigger this builders.
Your approach is a little complicated. From the top of my head I'd try something like this (untested, but hopefully gives you a direction to continue with):
import SCons.Action
import SCons.Builder
# Automatically inits "nasm" Tool, if it is in the $PATH
env = Environment()
c_to_asm_action = SCons.Action.Action('c to asm command line', 'Executing .c to .asm builder')
c_to_asm = SCons.Builder.Builder(action = c_to_asm_action,
suffix = '.asm',
single_source = 1)
env['BUILDERS']['CTOASM'] = c_to_asm
# Creates first.asm and second.asm
env.CTOASM(['first.c', 'second.c'])
# Compiles final program, finds the newly created ASM files via Glob
env.Program('foo', Glob('*.asm') + list_of_your_other_sources_and_libs)
Related
I need to rename multiple sequences in multiple fasta files and I found this script in order to do so for a single ID:
original_file = "./original.fasta"
corrected_file = "./corrected.fasta"
with open(original_file) as original, open(corrected_file, 'w') as corrected:
records = SeqIO.parse(original_file, 'fasta')
for record in records:
print record.id
if record.id == 'foo':
record.id = 'bar'
record.description = 'bar' # <- Add this line
print record.id
SeqIO.write(record, corrected, 'fasta')
Each fasta file corresponds to a single organism, but it is not specified in the IDs. I have the original fasta files (because these have been translated) with the same filenames but different directories and include in their IDs the name of each organism.
I wanted to figure out how to loop through all these fasta files and rename each ID in each file with the corresponding organism name.
ok my effort, got to use my own input folders/files since they where not specified in question
/old folder contains files :
MW628877.1.fasta :
>MW628877.1 Streptococcus agalactiae strain RYG82 DNA gyrase subunit A (gyrA) gene, complete cds
ATGCAAGATAAAAATTTAGTAGATGTTAATCTAACTAGTGAAATGAAAACGAGTTTTATCGATTACGCCA
TGAGTGTCATTGTTGCTCGTGCACTTCCAGATGTTAGAGATGGTTTAAAACCTGTTCATCGTCGTATTTT
>KY347969.1 Neisseria gonorrhoeae strain 1448 DNA gyrase subunit A (gyrA) gene, partial cds
CGGCGCGTACCGTACGCGATGCACGAGCTGAAAAATAACTGGAATGCCGCCTACAAAAAATCGGCGCGCA
TCGTCGGCGACGTCATCGGTAAATACCACCCCCACGGCGATTTCGCAGTTTACGGCACCATCGTCCGTAT
MG995190.1.fasta :
>MG995190.1 Mycobacterium tuberculosis strain UKR100 GyrA (gyrA) gene, complete cds
ATGACAGACACGACGTTGCCGCCTGACGACTCGCTCGACCGGATCGAACCGGTTGACATCCAGCAGGAGA
TGCAGCGCAGCTACATCGACTATGCGATGAGCGTGATCGTCGGCCGCGCGCTGCCGGAGGTGCGCGACGG
and an /empty folder.
/new folder contains files :
MW628877.1.fasta :
>MW628877.1
MQDKNLVDVNLTSEMKTSFIDYAMSVIVARALPDVRDGLKPVHRRI
>KY347969.1
RRVPYAMHELKNNWNAAYKKSARIVGDVIGKYHPHGDFAVYGTIVR
MG995190.1.fasta :
>MG995190.1
MTDTTLPPDDSLDRIEPVDIQQEMQRSYIDYAMSVIVGRALPEVRD
my code is :
from Bio import SeqIO
from os import scandir
old = './old'
new = './new'
old_ids_dict = {}
for filename in scandir(old):
if filename.is_file():
print(filename)
for seq_record in SeqIO.parse(filename, "fasta"):
old_ids_dict[seq_record.id] = ' '.join(seq_record.description.split(' ')[1:3])
print('_____________________')
print('old ids ---> ',old_ids_dict)
print('_____________________')
for filename in scandir(new):
if filename.is_file():
sequences = []
for seq_record in SeqIO.parse(filename, "fasta"):
if seq_record.id in old_ids_dict.keys():
print('### ', seq_record.id,' ', old_ids_dict[seq_record.id])
seq_record.id += '.'+old_ids_dict[seq_record.id]
seq_record.description = ''
print('-->', seq_record.id)
print(seq_record)
sequences.append(seq_record)
SeqIO.write(sequences, filename, 'fasta')
check how it works, it actually overwrites both files in new folder,
as pointed out by #Vovin in his comment it needs to be adapted per your files template from-to.
I am sure there is more than a way to do this, probably better and more pythonic than may way, I am learning too. Let us know
I'm trying to add to the output executable filename of a autotool project the version number.
With libs is very simple: you can add -version-info option to Makefile.am
How can I do the same thing with bin_PROGRAMS
So far I tried:
HELLO_VERSION_CURRENT = 1
HELLO_VERSION_REVISION = 2
HELLO_VERSION_AGE = 1
bin_PROGRAMS = hello_${HELLO_VERSION_CURRENT}_${HELLO_VERSION_REVISION}_${HELLO_VERSION_AGE}
hello_SOURCES = hello.c
In this way it doesn't compile because of SOURCES must be: hello_1_2_1_SOURCES, but I don't know how to tell to automake that.
Another way could be to run a post-build script: how can I add post-build action to Makefile.am?
How about using some preset autoconf output variables in your Makefile.am:
bin_PROGRAMS = hello_#PACKAGE_VERSION#
hello_#PACKAGE_VERSION#_SOURCES = hello.c
The preceding works for me on Darwin with autoconf v2.69 and automake v1.15.
Using the PACKAGE_VERSION from within your source code is even easier: #include "config.h", that's where all the autoconf output variables are #defined. E.g.:
/* config.h. Generated from config.h.in by configure. */
/* config.h.in. Generated from configure.ac by autoheader. */
...
#define PACKAGE_VERSION "1.2.3-rc-whatever"
Reference:
https://www.gnu.org/software/autoconf/manual/autoconf#Output-Variable-Index
You can do it like this:
HELLO_VERSION_CURRENT = 1
HELLO_VERSION_REVISION = 2
HELLO_VERSION_AGE = 1
bin_PROGRAMS = hello_$(HELLO_VERSION_CURRENT)_$(HELLO_VERSION_REVISION)_$(HELLO_VERSION_AGE)
hello_$(HELLO_VERSION_CURRENT)_$(HELLO_VERSION_REVISION)_$(HELLO_VERSION_AGE)_SOURCES = hello.c
Although, in that case, I'd suggest making shorter variable names...
At the end I add the following to my Makefile.am
all:
cp ./.libs/hello ./.libs/hello_${HELLO_VERSION_CURRENT}_${HELLO_VERSION_REVISION}_${HELLO_VERSION_AGE}
EDIT
I found a new solution
HELLO_VERSION_CURRENT = 1
HELLO_VERSION_REVISION = 2
HELLO_VERSION_AGE = 1
bin_PROGRAMS = hello_$(HELLO_VERSION_CURRENT)_$(HELLO_VERSION_REVISION)_$(HELLO_VERSION_AGE)
hello___HELLO_VERSION_CURRENT____HELLO_VERSION_REVISION____HELLO_VERSION_AGE__SOURCES = hello.c
hello___HELLO_VERSION_CURRENT____HELLO_VERSION_REVISION____HELLO_VERSION_AGE__CFLAGS =
hello___HELLO_VERSION_CURRENT____HELLO_VERSION_REVISION____HELLO_VERSION_AGE__LDFLAGS =
AM_CFLAGS = #hello___HELLO_VERSION_CURRENT____HELLO_VERSION_REVISION____HELLO_VERSION_AGE__CFLAGS#
AM_LDFLAGS = #hello___HELLO_VERSION_CURRENT____HELLO_VERSION_REVISION____HELLO_VERSION_AGE__LDFLAGS#
CLEANFILES = *~
How can I get Python to loop through a directory and find a specific string in each file located within that directory, then output a summary of what it found?
I want to search the long files for the following string:
FIRMWARE_VERSION = "2.15"
Only, the firmware version can be different in each file. So I want the log file to report back with whatever version it finds.
import glob
import os
print("The following list contains the firmware version of each server.\n")
os.chdir( "LOGS\\" )
for file in glob.glob('*.log'):
with open(file) as f:
contents = f.read()
if 'FIRMWARE_VERSION = "' in contents:
print (file + " = ???)
I was thinking I could use something like the following to return the extra characters but it's not working.
file[:+5]
I want the output to look something like this:
server1.web.com = FIRMWARE_VERSION = "2.16"
server2.web.com = FIRMWARE_VERSION = "3.01"
server3.web.com = FIRMWARE_VERSION = "1.26"
server4.web.com = FIRMWARE_VERSION = "4.1"
server5.web.com = FIRMWARE_VERSION = "3.50"
Any suggestions on how I can do this?
You can use regex for grub the text :
import re
for file in glob.glob('*.log'):
with open(file) as f:
contents = f.read()
if 'FIRMWARE_VERSION = "' in contents:
print (file + '='+ re.search(r'FIRMWARE_VERSION ="([\d.]+)"',contents).group(1))
In this case re.search will do the job! with searching the file content based on the following pattern :
r'FIRMWARE_VERSION ="([\d.]+)"'
that find a float number between two double quote!also you can use the following that match anything right after FIRMWARE_VERSIONbetween two double quote.
r'FIRMWARE_VERSION =(".*")'
In Waf how can I create multiple custom tasks, that can run parallel (with --jobs=JOBS)?
Sources = ["C:\\src1.c", "C:\\Mod1\src2.c", ... 30pcs] # one per call
Incl_Paths = ["Mod1". "Mod1"] # list all of them in all call
INCL_ST = "-I%s" # how to format an include path in an argument
Ext_out = "_loc" # output file extension
The goal:
C:\\LOC.exe -IMod1 -IMod2 C:\\src1.c > build\\src1.c_loc //or better src1_loc
C:\\LOC.exe -IMod1 -IMod2 C:\\Mod1\src2.c > build\\src2.c_loc //or better src2_loc
...
I couldn't get it work
def build(bld):
for i in Sources:
bld.new_task_gen(
source = i,
rule='C:\\LOC.exe ${INCL_ST:Incl_Paths} ${SRC} > ' + i + Ext_out,
)
Also I couldn't extract the exe
# find_program(self, filename, path_list=[], var=None, environ=None, exts=''):
cfg.find_program("C:\\LOC.exe", var='LOC')
To change from:
rule='C:\\LOC.exe ...'
To:
rule='${LOC} ...'
Something like this should work with waf 1.7:
from waflib.Task import Task
from waflib.TaskGen import extension
Ext_out = "_loc" # output file extension
def configure(conf):
# loc.exe must be in the system path for this to work
conf.find_program(
'loc',
var = "LOC",
)
conf.env.Incl_Paths = ["Mod1", "Mod1"]
conf.env.INCL_ST = "-I%s"
#extension('.c')
def process_loc(self, node):
out_node = node.change_ext(Ext_out)
tsk = self.create_task('loc')
tsk.set_inputs(node)
tsk.set_outputs(out_node)
class loc_task(Task):
ext_in = ['.c']
ext_out = ['_loc']
run_str = "${LOC} ${INCL_ST:Incl_Paths} ${SRC} > ${TGT}"
def build(bld):
bld(source = ["src1.c", "src2.c"])
Well it works for me on linux faking loc ...
The waf command waf build shows compiler errors (if there are any) while waf debug or waf release does not and always fails, utilizing the following wscript file (or maybe the wscript file has some other shortcomings I am currently not aware of):
APPNAME = 'waftest'
VERSION = '0.0.1'
def configure(ctx):
ctx.load('compiler_c')
ctx.define('VERSION', VERSION)
ctx.define('GETTEXT_PACKAGE', APPNAME)
ctx.check_cfg(atleast_pkgconfig_version='0.1.1')
ctx.check_cfg(package='glib-2.0', uselib_store='GLIB', args=['--cflags', '--libs'], mandatory=True)
ctx.check_cfg(package='gobject-2.0', uselib_store='GOBJECT', args=['--cflags', '--libs'], mandatory=True)
ctx.check_cfg(package='gtk+-3.0', uselib_store='GTK3', args=['--cflags', '--libs'], mandatory=True)
ctx.check_cfg(package='libxml-2.0', uselib_store='XML', args=['--cflags', '--libs'], mandatory=True)
ctx.check_large_file(mandatory=False)
ctx.check_endianness(mandatory=False)
ctx.check_inline(mandatory=False)
ctx.setenv('debug')
ctx.env.CFLAGS = ['-g', '-Wall']
ctx.define('DEBUG',1)
ctx.setenv('release')
ctx.env.CFLAGS = ['-O2', '-Wall']
ctx.define('RELEASE',1)
def pre(ctx):
print ('Building [[[' + ctx.variant + ']]] ...')
def post(ctx):
print ('Building is complete.')
def build(ctx):
ctx.add_pre_fun(pre)
ctx.add_post_fun(post)
# if not ctx.variant:
# ctx.fatal('Do "waf debug" or "waf release"')
exe = ctx.program(
features = ['c', 'cprogram'],
target = APPNAME+'.bin',
source = ctx.path.ant_glob(['src/*.c']),
includes = ['src/'],
export_includes = ['src/'],
uselib = 'GOBJECT GLIB GTK3 XML'
)
# for item in exe.includes:
# print(item)
from waflib.Build import BuildContext
class release(BuildContext):
cmd = 'release'
variant = 'release'
class debug(BuildContext):
cmd = 'debug'
variant = 'debug'
Error resulting from waf debug :
Build failed
-> task in 'waftest.bin' failed (exit status -1):
{task 46697488: c qqq.c -> qqq.c.1.o}
[useless filepaths]
I had a look at the waf demos, read the wafbook at section 6.2.2 but those did not supply me with valuable information in order to fix this issue.
What's wrong, and how do I fix it?
You need to do at least the following:
def configure(ctx):
...
ctx.setenv('debug')
ctx.load('compiler_c')
...
Since the cfg.setenv function resets whole previous environment. If you want to save previous environment, you can do cfg.setenv('debug', env=cfg.env.derive()).
Also, you don't need to explicitly specify the features = ['c', 'cprogram'], since, it's redundant, when you call bld.program(...).
P.S. Don't forget to reconfigure after modifying wscript file.