How to use argv method in tox

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parse.py

Source:parse.py

1"""2This module contains code to parse the input arguments to the command line:3- easysvm.py4- datagen.py5"""6#############################################################################################7#                                                                                           #8#    This program is free software; you can redistribute it and/or modify                   #9#    it under the terms of the GNU General Public License as published by                   #10#    the Free Software Foundation; either version 3 of the License, or                      #11#    (at your option) any later version.                                                    #12#                                                                                           #13#    This program is distributed in the hope that it will be useful,                        #14#    but WITHOUT ANY WARRANTY; without even the implied warranty of                         #15#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the                           # 16#    GNU General Public License for more details.                                           #17#                                                                                           #18#    You should have received a copy of the GNU General Public License                      # 19#    along with this program; if not, see http://www.gnu.org/licenses                       #20#    or write to the Free Software Foundation, Inc., 51 Franklin Street,                    #21#    Fifth Floor, Boston, MA 02110-1301  USA                                                #22#                                                                                           #23#############################################################################################24import datafuncs25import sys26################################################################################27# basic types28def parse_range(str):29    list=str.split("-")30    if len(list)==1:31        return (int(list[0]), int(list[0]))32    if len(list)==2:33        return (int(list[0]), int(list[1]))34    sys.stderr.write("Cannot parse range '%s'\n" %str) 35    sys.exit(-1)36def parse_float_list(str):37    list=str.split(",")38    float_list=[] ;39    for elem in list:40        float_list.append(float(elem))41    return float_list42def parse_int_list(str):43    list=str.split(",")44    int_list=[] ;45    for elem in list:46        int_list.append(int(elem))47    return int_list48################################################################################49# input files50def parse_input_file_train(kernelname, argv):51    """Parse the input and output file names"""52    if len(argv)<2 or (argv[0]=="fasta" and len(argv)<3) or (argv[0]!='fasta' and argv[0]!='arff'):53        sys.stderr.write("data usage: arff <train.arff>\n        or: fasta <train_pos.fa> <train_neg.fa>\n") 54        sys.exit(-1)55    if argv[0] == 'fasta':56        datafilenamepos = argv[1]57        datafilenameneg = argv[2]58        (examples, labels) = datafuncs.fastaread(datafilenamepos, datafilenameneg)59        argv_rest=argv[3:]60    elif argv[0] == 'arff':61        datafilename = argv[1]62        (examples, labels) = datafuncs.arffread(kernelname, datafilename)63        argv_rest=argv[2:]64    else:65        print 'Error in parse_input_file'66    return (examples,labels,argv_rest)67def parse_input_file_train_test(kernelname, argv):68    """Parse the input and output file names"""69    if len(argv)<3 or (argv[0]=="fasta" and len(argv)<4) or (argv[0]!='fasta' and argv[0]!='arff'):70        sys.stderr.write("data usage: arff <train.arff> <test.arff>\n        or: fasta <train_pos.fa> <train_neg.fa> <test.fa>\n") 71        sys.exit(-1)72 73    if argv[0] == 'fasta':74        datafilenamepos = argv[1]75        datafilenameneg = argv[2]76        datafilenametest = argv[3]77        (trainex, trainlab) = datafuncs.fastaread(datafilenamepos, datafilenameneg)78        (testex, testlab) = datafuncs.fastaread(datafilenametest)79        argv_rest=argv[4:]80    elif argv[0] == 'arff':81        datafilename = argv[1]82        datafilenametest = argv[2]83        (trainex, trainlab) = datafuncs.arffread(kernelname, datafilename)84        (testex, testlab) = datafuncs.arffread(kernelname, datafilenametest)85        argv_rest=argv[3:]86    else:87        print 'Error in parse_input_file'88    return (trainex,trainlab,testex,argv_rest)89################################################################################90# prediction file91def parse_prediction_file(fname):92    outputs=[]93    splitassignments=[]94    f = open(fname)95    str=f.read()96    lines = str.split('\n') 97    num=0 98    for line in lines:99        if len(line)>0 and line[0] != '#':100            elems=line.split('\t') 101            assert(len(elems)>1)102            assert(int(elems[0]) == num) 103            num+=1 104            if len(elems)==2:105                outputs.append(float(elems[1]))106            else:107                assert(len(elems)==3)108                outputs.append(float(elems[1]))109                splitassignments.append(float(elems[2]))110    f.close() 111    if len(splitassignments)==0:112        splitassignments = None113    return (outputs, splitassignments)114################################################################################115# kernel parameters116def parse_kernel_param(argv, allow_modelsel_params):117    """Parse the arguments for a particular kernel"""118    if len(argv)<1:119        sys.stderr.write("kernel usage: <kernelname> [<parameters>]\n")120        sys.exit(-1)121    kernelname = argv[0] 122    kparam = {}123    kparam["name"]=kernelname124    kparam["modelsel_name"]=None125    kparam["modelsel_params"]=None126    127    if kernelname == 'gauss':128        if len(argv)<2:129            sys.stderr.write("kernel usage: gauss <width>\n")130            sys.exit(-1)131        if allow_modelsel_params:132            kparam['width'] = None133            kparam["modelsel_name"]="width"134            kparam["modelsel_params"]=parse_float_list(argv[1])135        else:136            kparam['width'] = float(argv[1])137        argv_rest=argv[2:]138    elif kernelname == 'linear':139	kparam['scale']=1140        # no parameters141        argv_rest=argv[1:]142    elif kernelname == 'poly':143        if len(argv)<4:144            sys.stderr.write("kernel usage: poly <degree> <true|false> <true|false>\n")145            sys.exit(-1)146        if allow_modelsel_params:147            kparam['degree'] = None148            kparam["modelsel_name"]="degree"149            kparam["modelsel_params"]=parse_int_list(argv[1])150        else:151            kparam['degree'] = int(argv[1])152        kparam['inhomogene'] = (argv[2] == 'true')153        kparam['normal'] = (argv[3] == 'true')154        argv_rest=argv[4:]155    elif kernelname == 'wd':156        if len(argv)<3:157            sys.stderr.write("kernel usage: wd <degree> <shift>\n")158            sys.exit(-1)159        if allow_modelsel_params:160            kparam['degree'] = None161            kparam["modelsel_name"]="degree"162            kparam["modelsel_params"]=parse_int_list(argv[1])163        else:164            kparam['degree'] = int(argv[1])165        if allow_modelsel_params and len(kparam["modelsel_params"])==1:166            kparam['degree'] = kparam["modelsel_params"][0]167            kparam['shift'] = None168            kparam["modelsel_name"] = "shift"169            kparam["modelsel_params"]=parse_int_list(argv[2])170        else:171            kparam['shift'] = int(argv[2])172        argv_rest=argv[3:]173    elif kernelname == 'spec':174        if len(argv)<2:175            sys.stderr.write("kernel usage: spec <degree>\n")176            sys.exit(-1)177        if allow_modelsel_params:178            kparam['degree'] = None179            kparam["modelsel_name"]="degree"180            kparam["modelsel_params"]=parse_int_list(argv[1])181        else:182            kparam['degree'] = int(argv[1])183        argv_rest=argv[2:]184    elif kernelname == 'localalign':185        # no parameters186        argv_rest=argv[1:]187    elif kernelname == 'localimprove':188        if len(argv)<4:189            sys.stderr.write("kernel usage: localimprove <length> <indegree> <outdegree>\n")190            sys.exit(-1)191        kparam['length'] = int(argv[1])192        if allow_modelsel_params:193            kparam['width'] = None194            kparam["modelsel_name"]="indeg"195            kparam["modelsel_params"]=parse_int_list(argv[2])196        else:197            kparam['indeg'] = int(argv[2])198        kparam['outdeg'] = int(argv[3])199        argv_rest=argv[4:]200    else:201        sys.stderr.write( 'Unknown kernel name %s in parse_kernel_param\n' % kernelname )202        sys.exit(-1)...

parse.js

Source:parse.js

1var parse = require('../');2var test = require('tape');3test('parse args', function (t) {4    t.deepEqual(5        parse([ '--no-moo' ]),6        { moo : false, _ : [] },7        'no'8    );9    t.deepEqual(10        parse([ '-v', 'a', '-v', 'b', '-v', 'c' ]),11        { v : ['a','b','c'], _ : [] },12        'multi'13    );14    t.end();15});16 17test('comprehensive', function (t) {18    t.deepEqual(19        parse([20            '--name=meowmers', 'bare', '-cats', 'woo',21            '-h', 'awesome', '--multi=quux',22            '--key', 'value',23            '-b', '--bool', '--no-meep', '--multi=baz',24            '--', '--not-a-flag', 'eek'25        ]),26        {27            c : true,28            a : true,29            t : true,30            s : 'woo',31            h : 'awesome',32            b : true,33            bool : true,34            key : 'value',35            multi : [ 'quux', 'baz' ],36            meep : false,37            name : 'meowmers',38            _ : [ 'bare', '--not-a-flag', 'eek' ]39        }40    );41    t.end();42});43test('nums', function (t) {44    var argv = parse([45        '-x', '1234',46        '-y', '5.67',47        '-z', '1e7',48        '-w', '10f',49        '--hex', '0xdeadbeef',50        '789'51    ]);52    t.deepEqual(argv, {53        x : 1234,54        y : 5.67,55        z : 1e7,56        w : '10f',57        hex : 0xdeadbeef,58        _ : [ 789 ]59    });60    t.deepEqual(typeof argv.x, 'number');61    t.deepEqual(typeof argv.y, 'number');62    t.deepEqual(typeof argv.z, 'number');63    t.deepEqual(typeof argv.w, 'string');64    t.deepEqual(typeof argv.hex, 'number');65    t.deepEqual(typeof argv._[0], 'number');66    t.end();67});68test('flag boolean', function (t) {69    var argv = parse([ '-t', 'moo' ], { boolean: 't' });70    t.deepEqual(argv, { t : true, _ : [ 'moo' ] });71    t.deepEqual(typeof argv.t, 'boolean');72    t.end();73});74test('flag boolean value', function (t) {75    var argv = parse(['--verbose', 'false', 'moo', '-t', 'true'], {76        boolean: [ 't', 'verbose' ],77        default: { verbose: true }78    });79    80    t.deepEqual(argv, {81        verbose: false,82        t: true,83        _: ['moo']84    });85    86    t.deepEqual(typeof argv.verbose, 'boolean');87    t.deepEqual(typeof argv.t, 'boolean');88    t.end();89});90test('flag boolean default false', function (t) {91    var argv = parse(['moo'], {92        boolean: ['t', 'verbose'],93        default: { verbose: false, t: false }94    });95    96    t.deepEqual(argv, {97        verbose: false,98        t: false,99        _: ['moo']100    });101    102    t.deepEqual(typeof argv.verbose, 'boolean');103    t.deepEqual(typeof argv.t, 'boolean');104    t.end();105});106test('boolean groups', function (t) {107    var argv = parse([ '-x', '-z', 'one', 'two', 'three' ], {108        boolean: ['x','y','z']109    });110    111    t.deepEqual(argv, {112        x : true,113        y : false,114        z : true,115        _ : [ 'one', 'two', 'three' ]116    });117    118    t.deepEqual(typeof argv.x, 'boolean');119    t.deepEqual(typeof argv.y, 'boolean');120    t.deepEqual(typeof argv.z, 'boolean');121    t.end();122});123test('newlines in params' , function (t) {124    var args = parse([ '-s', "X\nX" ])125    t.deepEqual(args, { _ : [], s : "X\nX" });126    127    // reproduce in bash:128    // VALUE="new129    // line"130    // node program.js --s="$VALUE"131    args = parse([ "--s=X\nX" ])132    t.deepEqual(args, { _ : [], s : "X\nX" });133    t.end();134});135test('strings' , function (t) {136    var s = parse([ '-s', '0001234' ], { string: 's' }).s;137    t.equal(s, '0001234');138    t.equal(typeof s, 'string');139    140    var x = parse([ '-x', '56' ], { string: 'x' }).x;141    t.equal(x, '56');142    t.equal(typeof x, 'string');143    t.end();144});145test('stringArgs', function (t) {146    var s = parse([ '  ', '  ' ], { string: '_' })._;147    t.same(s.length, 2);148    t.same(typeof s[0], 'string');149    t.same(s[0], '  ');150    t.same(typeof s[1], 'string');151    t.same(s[1], '  ');152    t.end();153});154test('empty strings', function(t) {155    var s = parse([ '-s' ], { string: 's' }).s;156    t.equal(s, '');157    t.equal(typeof s, 'string');158    var str = parse([ '--str' ], { string: 'str' }).str;159    t.equal(str, '');160    t.equal(typeof str, 'string');161    var letters = parse([ '-art' ], {162        string: [ 'a', 't' ]163    });164    t.equal(letters.a, '');165    t.equal(letters.r, true);166    t.equal(letters.t, '');167    t.end();168});169test('slashBreak', function (t) {170    t.same(171        parse([ '-I/foo/bar/baz' ]),172        { I : '/foo/bar/baz', _ : [] }173    );174    t.same(175        parse([ '-xyz/foo/bar/baz' ]),176        { x : true, y : true, z : '/foo/bar/baz', _ : [] }177    );178    t.end();179});180test('alias', function (t) {181    var argv = parse([ '-f', '11', '--zoom', '55' ], {182        alias: { z: 'zoom' }183    });184    t.equal(argv.zoom, 55);185    t.equal(argv.z, argv.zoom);186    t.equal(argv.f, 11);187    t.end();188});189test('multiAlias', function (t) {190    var argv = parse([ '-f', '11', '--zoom', '55' ], {191        alias: { z: [ 'zm', 'zoom' ] }192    });193    t.equal(argv.zoom, 55);194    t.equal(argv.z, argv.zoom);195    t.equal(argv.z, argv.zm);196    t.equal(argv.f, 11);197    t.end();198});199test('nested dotted objects', function (t) {200    var argv = parse([201        '--foo.bar', '3', '--foo.baz', '4',202        '--foo.quux.quibble', '5', '--foo.quux.o_O',203        '--beep.boop'204    ]);205    206    t.same(argv.foo, {207        bar : 3,208        baz : 4,209        quux : {210            quibble : 5,211            o_O : true212        }213    });214    t.same(argv.beep, { boop : true });215    t.end();216});217test('boolean and alias with chainable api', function (t) {218    var aliased = [ '-h', 'derp' ];219    var regular = [ '--herp',  'derp' ];220    var opts = {221        herp: { alias: 'h', boolean: true }222    };223    var aliasedArgv = parse(aliased, {224        boolean: 'herp',225        alias: { h: 'herp' }226    });227    var propertyArgv = parse(regular, {228        boolean: 'herp',229        alias: { h: 'herp' }230    });231    var expected = {232        herp: true,233        h: true,234        '_': [ 'derp' ]235    };236    237    t.same(aliasedArgv, expected);238    t.same(propertyArgv, expected); 239    t.end();240});241test('boolean and alias with options hash', function (t) {242    var aliased = [ '-h', 'derp' ];243    var regular = [ '--herp', 'derp' ];244    var opts = {245        alias: { 'h': 'herp' },246        boolean: 'herp'247    };248    var aliasedArgv = parse(aliased, opts);249    var propertyArgv = parse(regular, opts);250    var expected = {251        herp: true,252        h: true,253        '_': [ 'derp' ]254    };255    t.same(aliasedArgv, expected);256    t.same(propertyArgv, expected);257    t.end();258});259test('boolean and alias using explicit true', function (t) {260    var aliased = [ '-h', 'true' ];261    var regular = [ '--herp',  'true' ];262    var opts = {263        alias: { h: 'herp' },264        boolean: 'h'265    };266    var aliasedArgv = parse(aliased, opts);267    var propertyArgv = parse(regular, opts);268    var expected = {269        herp: true,270        h: true,271        '_': [ ]272    };273    t.same(aliasedArgv, expected);274    t.same(propertyArgv, expected); 275    t.end();276});277// regression, see https://github.com/substack/node-optimist/issues/71278test('boolean and --x=true', function(t) {279    var parsed = parse(['--boool', '--other=true'], {280        boolean: 'boool'281    });282    t.same(parsed.boool, true);283    t.same(parsed.other, 'true');284    parsed = parse(['--boool', '--other=false'], {285        boolean: 'boool'286    });287    288    t.same(parsed.boool, true);289    t.same(parsed.other, 'false');290    t.end();...

datagen.py

Source:datagen.py

1#!/usr/bin/env python2#############################################################################################3#                                                                                           #4#    This program is free software; you can redistribute it and/or modify                   #5#    it under the terms of the GNU General Public License as published by                   #6#    the Free Software Foundation; either version 3 of the License, or                      #7#    (at your option) any later version.                                                    #8#                                                                                           #9#    This program is distributed in the hope that it will be useful,                        #10#    but WITHOUT ANY WARRANTY; without even the implied warranty of                         #11#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the                           # 12#    GNU General Public License for more details.                                           #13#                                                                                           #14#    You should have received a copy of the GNU General Public License                      # 15#    along with this program; if not, see http://www.gnu.org/licenses                       #16#    or write to the Free Software Foundation, Inc., 51 Franklin Street,                    #17#    Fifth Floor, Boston, MA 02110-1301  USA                                                #18#                                                                                           #19#############################################################################################20import sys21import random22from numpy import array23import esvm.parse24import esvm.plots25from esvm.datafuncs import MotifDataDef, fastawrite_sequence, arffwrite_sequence, arffwrite_real26from esvm.mldata import init_datasetfile27if __name__ == '__main__':28    if len(sys.argv)<3 or (sys.argv[1]=='motif' and sys.argv[2]!='arff' and sys.argv[2]!='fasta') \29           or (sys.argv[1]=='motif' and sys.argv[2]=='fasta' and len(sys.argv)<9) \30           or (sys.argv[1]=='motif' and sys.argv[2]=='arff' and len(sys.argv)<14) \31           or (sys.argv[1]=='cloud' and len(sys.argv)<7) or (sys.argv[1]!='motif') \32           and (sys.argv[1]!='cloud'):33        sys.stderr.write( "usage: %s motif fasta MOTIF numSeq seqLenRange"+\34                          "positionRange mutationRate output.fa\n"+\35                          "or: %s motif arff MOTIFPOS numSeq-pos seqLenRange-pos "+\36                          "positionRange-pos mutationRate-pos \\\n"+\37                          "motif-neg numSeq-neg seqLenRange-neg positionRange-neg "+\38                          "mutationRange-neg output.arff\n"+\39                          "or: %s cloud numpoints dimensions fractionOfPositives "+\40                          "cloudWidth output.arff\n" % (sys.argv[0],sys.argv[0],sys.argv[0]) )41        sys.exit(-1)42    random.seed()43    if sys.argv[1] == 'motif':44        if sys.argv[2]=='fasta':45            # generate sequences in FASTA format46            p = MotifDataDef()47            p.motif = sys.argv[3]48            p.numseq = int(sys.argv[4])49            (p.seqlenmin,p.seqlenmax) = esvm.parse.parse_range(sys.argv[5])50            (p.posstart,p.posend) = esvm.parse.parse_range(sys.argv[6])51            p.mutrate = float(sys.argv[7])52            filename = sys.argv[8]53            fastawrite_sequence(filename, p)54        else:55            # generate sequences in ARFF format56            assert(sys.argv[2]=='arff')57            p = MotifDataDef()58            p.motif = sys.argv[3]59            p.numseq = int(sys.argv[4])60            (p.seqlenmin,p.seqlenmax) = esvm.parse.parse_range(sys.argv[5])61            (p.posstart,p.posend) = esvm.parse.parse_range(sys.argv[6])62            p.mutrate = float(sys.argv[7])63            64            n = MotifDataDef()65            n.motif = sys.argv[8]66            n.numseq = int(sys.argv[9])67            (n.seqlenmin,n.seqlenmax) = esvm.parse.parse_range(sys.argv[10])68            (n.posstart,n.posend) = esvm.parse.parse_range(sys.argv[11])69            n.mutrate = float(sys.argv[12])70            71            filename = sys.argv[13]72            arffwrite_sequence(filename, p, n)73        74    elif sys.argv[1] == 'cloud':75        # generate a data cloud in ARFF format76        numpoint = int(sys.argv[2])77        numfeat = int(sys.argv[3])78        fracpos = float(sys.argv[4])79        width = float(sys.argv[5])80        filename = sys.argv[6]81        arffwrite_real(filename, numpoint, numfeat, fracpos, width)82        if len(sys.argv)>=8:83            fp = init_datasetfile(filename,'vec')84            (examples,labels) = fp.readlines()85            pointcloud = []86            for ix in xrange(numpoint):87                pointcloud.append(array([labels[ix],examples[0,ix],examples[1,ix]]))88            esvm.plots.plotcloud(pointcloud,sys.argv[7],'Pointcloud')89            90	#(examples,labels,metadata)=arffwrite_real(filename, numpoint, numfeat, fracpos, width)91	#if len(sys.argv)>=8:92	#	plots.plotcloud(pointcloud,sys.argv[7],metadata)93    else:...

resolve-args.js

Source:resolve-args.js

1var fs = require('fs'),2    path = require('path'),3    nodeResolve = require('resolve');4var layoutDir = __dirname + '/../layouts/';5module.exports = function(argv) {6  // defaults7  argv.input = path.resolve(process.cwd(), argv.input || './input/');8  argv.output = path.resolve(process.cwd(), argv.output || './output/');9  if (!argv.layout) {10    if (argv['export']) {11      argv.layout = argv['export'];12    } else {13      argv.layout = 'github';14    }15  }16  if (argv.template) {17    throw new Error('--template is deprecated in v2.0, please point --layout to ' +18      'the layout directory with ./page.html in it.');19  }20  if (argv['asset-dir'] || argv.assetDir) {21    throw new Error('--asset-dir is deprecated in v2.0, please point --layout to ' +22      'the layout directory with ./page.html and ./assets in it.');23  }24  if (argv.command) {25    throw new Error('--command is deprecated in v2.0');26  }27  if (argv.runner) {28    throw new Error('--runner is deprecated in v2.0');29  }30  // we only accept a single layout argument, --layout31  if (argv.layout && argv.layout.charAt(0) === '/' && fs.existsSync(argv.layout)) {32    // 1) it can be an absolute path to a folder with ./page.html33    argv.layout = path.normalize(argv.layout);34  } else if (fs.existsSync(process.cwd() + '/' + argv.layout)) {35    // 2) it can be a relative path36    argv.layout = path.normalize(process.cwd() + '/' + argv.layout);37  } else if (fs.existsSync(layoutDir + argv.layout + '/')) {38    // 3c) it can be the name of a builtin layout39    argv.layout = path.normalize(layoutDir + argv.layout + '/');40  }41  if (argv['export']) {42    argv['export'] = argv.layout;43  }44  // set up partials and helpers directories45  var layoutBase = path.dirname(argv.template);46  ['partials', 'helpers'].forEach(function(name) {47    if (argv[name]) {48      argv[name] = path.resolve(process.cwd(), argv[name]);49    } else if (fs.existsSync(layoutBase + '/' + name)) {50      // if the folder exists in the layout, use it automatically51      argv[name] = layoutBase + '/' + name;52    }53  });54  // parse --highlight-<extension>55  var hl = {};56  Object.keys(argv).forEach(function(name) {57    var matched = (typeof name === 'string' ? name.match(/highlight\-(.*)/) : false);58    if (matched) {59      var ext = matched[1];60      argv[name] = findModule(argv[name], [process.cwd, __dirname]);61      hl[ext] = require(argv[name]);62    }63  });64  argv['highlight'] = hl;65  return argv;66};67function findModule(name) {68  var result = '';69  try {70    result = nodeResolve.sync(name, { basedir: process.cwd() });71  } catch(e) {72    try {73      result = nodeResolve.sync(name, { basedir: __dirname });74    } catch(e) {75      console.error('Cannot find module ' + name + ' from ' + process.cwd()  + ' or ' + __dirname);76      throw e;77    }78  }79  return result;...

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