How to use get_homedir method in tox

Best Python code snippet using tox_python

reader_ (stephen-desktop-linux's conflicted copy 2019-08-24).py

Source:reader_ (stephen-desktop-linux's conflicted copy 2019-08-24).py

...10        self.atomlistName = atomlistName11        self.trajDir = trajDir12        self.trajExt = trajExt13        self.File_TOP = File_TOP14        self.homedir = self.get_homedir()15        self.trajlist_list = self.get_trajlist(trajlistName, self.homedir)16        self.atom_indices = self.get_atom_indices( atomlistName, self.homedir)17        #self.framelist = self.get_framelist()18    '''19    def walk_dir(self,input_traj_dir, input_traj_ext,topdown=True):20        frame_list = []21        for root, dirs, files in os.walk(input_traj_dir, topdown):22            for name in files:23                if os.path.splitext(name)[1] == input_traj_ext:24                    frame_list.append( os.path.join( root, name ))25        return frame_list26    def get_trajlist(self,trajlist_filename, trajlist_dir):27        trajlist_file = open( trajlist_filename )28        #trajlist_dir = self.get_homedir()29        trajlist_list = []30        for line in trajlist_file:31            list = trajlist_dir + '/' + line.rstrip("\n")32            list = list.strip() # remove the spaces in the end line, thanks to Yang Xi for reporting this bug, Stephen 2014120833            trajlist_list.append( list )34        trajlist_file.close()35        return trajlist_list36    def get_homedir(self):37        return os.getcwd()38    def get_atom_indices(self, indices_filename, indices_dir):39        if indices_filename != None:40            atom_indices = np.loadtxt(indices_filename, dtype=np.int32).tolist()41            return atom_indices42        else:43            return None44    def get_framefile_list(self, trajlist_list):45        framefile_list = []46        #trajlist_list = self.trajlist_list47        Ext = '.' + self.trajExt48        for trajlist in trajlist_list:49            framefile_list.extend( self.walk_dir(trajlist, Ext))50        return framefile_list51class XTCReader(TrajReader):52    def __init__(self, trajlistName, atomlistName, homedir, trajExt, File_TOP, nSubSample=None):53        self.trajlistName = trajlistName54        self.atomlistName = atomlistName55        self.trajDir = homedir56        self.trajExt = trajExt57        self.File_TOP = File_TOP58        self.homedir = homedir59        self.nSubSample = nSubSample60        #self.homedir = self.get_homedir()61        self.trajlist_list = self.get_trajlist(trajlistName, self.homedir)62        self.atom_indices = self.get_atom_indices( atomlistName, self.homedir)63        self.framefile_list = self.get_framefile_list(self.trajlist_list)64        self.trajs, self.traj_len = self.read_trajs(self.framefile_list)65    def read_trajs(self, framelist):66        trajs = []67        traj_len = []68        print("Reading trajs...")69        for frame in framelist:70            print('Reading: ', frame)71            #traj = md.load(frame, top=self.File_TOP, atom_indices=self.atom_indices)72            traj = md.load(frame, discard_overlapping_frames=True, top=self.File_TOP, #atom_indices=self.atom_indices,73                           stride=self.nSubSample)74            #traj = traj[:-1] #remove last one75            trajs.append(traj)76            traj_len.append(len(traj))77        len_trajs = len(trajs)78        whole_trajs= reduce(operator.add, (trajs[i] for i in range(len_trajs)))79        print("Done.")80        print(len_trajs, "trajs,", len(whole_trajs), "frames.")81        #print "debug output: len_trajs", len_trajs, "len_whole_trajs", len(whole_trajs)82        return whole_trajs, traj_len83    def get_phipsi(self, trajs, phi, psi):84        #phi = [6, 8, 14, 16]85        #psi = [4, 6, 8, 14]86        PHI_INDICES = []87        PSI_INDICES = []88        for i in range(len(phi)):89            PHI_INDICES.append(self.atom_indices.index(phi[i]))90            PSI_INDICES.append(self.atom_indices.index(psi[i]))91        #len_trajs = len(trajs)92        print("PSI:", PSI_INDICES)93        print("PHI:", PHI_INDICES)94        phi_angles = md.compute_dihedrals(trajs, [PHI_INDICES]) * 180.0 / np.pi95        psi_angles = md.compute_dihedrals(trajs, [PSI_INDICES]) * 180.0 / np.pi96        #phi_psi=np.column_stack((phi_angles, psi_angles))97        #return phi_psi98        return phi_angles, psi_angles99class DCDReader(TrajReader):100    def __init__(self, trajlistName, atomlistName, homedir, trajExt, File_TOP, nSubSample):101        self.trajlistName = trajlistName102        self.atomlistName = atomlistName103        self.trajDir = homedir104        self.trajExt = trajExt105        self.File_TOP = File_TOP106        self.homedir = homedir107        self.nSubSample = nSubSample108        #self.homedir = self.get_homedir()109        self.trajlist_list = self.get_trajlist(trajlistName, self.homedir)110        self.atom_indices = self.get_atom_indices( atomlistName, self.homedir)111    def read_trajs(self, framelist):112        #data = []113        trajs = []114        for frame in framelist:115            #framedata = []116            #print 'Reading: ', frame117            traj = md.load_dcd(frame, self.File_TOP, stride=self.nSubSample)118            trajs.append(traj)119        return trajs120class AmberReader(TrajReader):121    def __init__(self, trajlistName, atomlistName, homedir, trajExt, File_TOP, nSubSample):122        self.trajlistName = trajlistName123        self.atomlistName = atomlistName124        self.trajDir = homedir125        self.trajExt = trajExt126        self.File_TOP = File_TOP127        self.homedir = homedir128        self.nSubSample = nSubSample129        #self.homedir = self.get_homedir()130        self.trajlist_list = self.get_trajlist(trajlistName, self.homedir)131        self.atom_indices = self.get_atom_indices( atomlistName, self.homedir)132    def read_trajs(self, framelist):133        #data = []134        trajs = []135        for frame in framelist:136            #framedata = []137            print('Reading: ', frame)138            traj = md.load_netcdf(frame, self.File_TOP, stride=self.nSubSample)139            trajs.append(traj)140        return trajs141class VectorReader(TrajReader):142    def __init__(self, trajlistName, atomlistName=None, homedir='.', trajExt='txt', File_TOP=None, stride=None, framefile=None):143        self.trajlistName = trajlistName144        #self.atomlistName = atomlistName145        self.trajDir = homedir146        self.trajExt = trajExt147        #self.File_TOP = File_TOP148        self.homedir = homedir149        self.stride = stride150        #self.homedir = self.get_homedir()151        if framefile is not None:152            self.framefile_list = self.get_framefile(framefile)153        else:154            self.trajlist_list = self.get_trajlist(trajlistName, self.homedir)155            self.framefile_list = self.get_framefile_list(self.trajlist_list)156        #self.atom_indices = self.get_atom_indices( atomlistName, self.homedir)157        self.trajs, self.traj_len = self.read_trajs(self.framefile_list)158    def read_trajs(self, framelist):159        #data = []160        trajs = []161        traj_len = []162        for frame in framelist:163            #framedata = []164            print('Reading: ', frame)...

reader_.py

Source:reader_.py

...10        self.atomlistName = atomlistName11        self.trajDir = trajDir12        self.trajExt = trajExt13        self.File_TOP = File_TOP14        self.homedir = self.get_homedir()15        self.trajlist_list = self.get_trajlist(trajlistName, self.homedir)16        self.atom_indices = self.get_atom_indices( atomlistName, self.homedir)17        #self.framelist = self.get_framelist()18    '''19    def walk_dir(self,input_traj_dir, input_traj_ext,topdown=True):20        frame_list = []21        for root, dirs, files in os.walk(input_traj_dir, topdown):22            for name in files:23                if os.path.splitext(name)[1] == input_traj_ext:24                    frame_list.append( os.path.join( root, name ))25        return frame_list26    def get_trajlist(self,trajlist_filename, trajlist_dir):27        trajlist_file = open( trajlist_filename )28        #trajlist_dir = self.get_homedir()29        trajlist_list = []30        for line in trajlist_file:31            list = trajlist_dir + '/' + line.rstrip("\n")32            list = list.strip() # remove the spaces in the end line, thanks to Yang Xi for reporting this bug, Stephen 2014120833            trajlist_list.append( list )34        trajlist_file.close()35        return trajlist_list36    def get_homedir(self):37        return os.getcwd()38    def get_atom_indices(self, indices_filename, indices_dir):39        if indices_filename != None:40            atom_indices = np.loadtxt(indices_filename, dtype=np.int32).tolist()41            return atom_indices42        else:43            return None44    def get_framefile_list(self, trajlist_list):45        framefile_list = []46        #trajlist_list = self.trajlist_list47        Ext = '.' + self.trajExt48        for trajlist in trajlist_list:49            framefile_list.extend(self.walk_dir(trajlist, Ext))50        return framefile_list51class XTCReader(TrajReader):52    def __init__(self, trajlistName, atomlistName, homedir, trajExt, File_TOP, nSubSample=None):53        self.trajlistName = trajlistName54        self.atomlistName = atomlistName55        self.trajDir = homedir56        self.trajExt = trajExt57        self.File_TOP = File_TOP58        self.homedir = homedir59        self.nSubSample = nSubSample60        #self.homedir = self.get_homedir()61        self.trajlist_list = self.get_trajlist(trajlistName, self.homedir)62        self.atom_indices = self.get_atom_indices( atomlistName, self.homedir)63        self.framefile_list = self.get_framefile_list(self.trajlist_list)64        self.trajs, self.traj_len = self.read_trajs(self.framefile_list)65    def read_trajs(self, framelist):66        trajs = []67        traj_len = []68        print("Reading trajs...")69        for frame in framelist:70            print('Reading: ', frame)71            #traj = md.load(frame, top=self.File_TOP, atom_indices=self.atom_indices)72            traj = md.load(frame, discard_overlapping_frames=True, top=self.File_TOP, #atom_indices=self.atom_indices,73                           stride=self.nSubSample)74            #traj = traj[:-1] #remove last one75            trajs.append(traj)76            traj_len.append(len(traj))77        len_trajs = len(trajs)78        whole_trajs= reduce(operator.add, (trajs[i] for i in range(len_trajs)))79        print("Done.")80        print(len_trajs, "trajs,", len(whole_trajs), "frames.")81        #print "debug output: len_trajs", len_trajs, "len_whole_trajs", len(whole_trajs)82        return whole_trajs, traj_len83    def get_phipsi(self, trajs, phi, psi):84        #phi = [6, 8, 14, 16]85        #psi = [4, 6, 8, 14]86        PHI_INDICES = []87        PSI_INDICES = []88        for i in range(len(phi)):89            PHI_INDICES.append(self.atom_indices.index(phi[i]))90            PSI_INDICES.append(self.atom_indices.index(psi[i]))91        #len_trajs = len(trajs)92        print("PSI:", PSI_INDICES)93        print("PHI:", PHI_INDICES)94        phi_angles = md.compute_dihedrals(trajs, [PHI_INDICES]) * 180.0 / np.pi95        psi_angles = md.compute_dihedrals(trajs, [PSI_INDICES]) * 180.0 / np.pi96        #phi_psi=np.column_stack((phi_angles, psi_angles))97        #return phi_psi98        return phi_angles, psi_angles99class DCDReader(TrajReader):100    def __init__(self, trajlistName, atomlistName, homedir, trajExt, File_TOP, nSubSample):101        self.trajlistName = trajlistName102        self.atomlistName = atomlistName103        self.trajDir = homedir104        self.trajExt = trajExt105        self.File_TOP = File_TOP106        self.homedir = homedir107        self.nSubSample = nSubSample108        #self.homedir = self.get_homedir()109        self.trajlist_list = self.get_trajlist(trajlistName, self.homedir)110        self.atom_indices = self.get_atom_indices( atomlistName, self.homedir)111    def read_trajs(self, framelist):112        #data = []113        trajs = []114        for frame in framelist:115            #framedata = []116            #print 'Reading: ', frame117            traj = md.load_dcd(frame, self.File_TOP, stride=self.nSubSample)118            trajs.append(traj)119        return trajs120class AmberReader(TrajReader):121    def __init__(self, trajlistName, atomlistName, homedir, trajExt, File_TOP, nSubSample):122        self.trajlistName = trajlistName123        self.atomlistName = atomlistName124        self.trajDir = homedir125        self.trajExt = trajExt126        self.File_TOP = File_TOP127        self.homedir = homedir128        self.nSubSample = nSubSample129        #self.homedir = self.get_homedir()130        self.trajlist_list = self.get_trajlist(trajlistName, self.homedir)131        self.atom_indices = self.get_atom_indices( atomlistName, self.homedir)132    def read_trajs(self, framelist):133        #data = []134        trajs = []135        for frame in framelist:136            #framedata = []137            print('Reading: ', frame)138            traj = md.load_netcdf(frame, self.File_TOP, stride=self.nSubSample)139            trajs.append(traj)140        return trajs141class VectorReader(TrajReader):142    def __init__(self, trajlistName, atomlistName=None, homedir='.', trajExt='txt', File_TOP=None, stride=None, framefile=None):143        self.trajlistName = trajlistName144        #self.atomlistName = atomlistName145        self.trajDir = homedir146        self.trajExt = trajExt147        #self.File_TOP = File_TOP148        self.homedir = homedir149        self.stride = stride150        #self.homedir = self.get_homedir()151        if framefile is not None:152            self.framefile_list = self.get_framefile(framefile)153        else:154            self.trajlist_list = self.get_trajlist(trajlistName, self.homedir)155            self.framefile_list = self.get_framefile_list(self.trajlist_list)156        #self.atom_indices = self.get_atom_indices( atomlistName, self.homedir)157        self.trajs, self.traj_len = self.read_trajs(self.framefile_list)158    def read_trajs(self, framelist):159        #data = []160        trajs = []161        traj_len = []162        for frame in framelist:163            #framedata = []164            print('Reading: ', frame)...

config.py

Source:config.py

...5from synapse_admin.utils import dirs6from synapse_admin.types.config import Config, LogedUser7def save(server_url, user_id, access_token):8    config = Config(server_url, LogedUser(user_id, access_token))9    with open(dirs.get_homedir()+"/.synapse-admin.config.json", "w") as conf_file:10        if dataclasses.is_dataclass(config):11            json.dump(dataclasses.asdict(config), conf_file)12def load():13    if not Path(dirs.get_homedir()+"/.synapse-admin.config.json").is_file():14        print("Config file not found. Please init synapse-admin by command: synapse-admin init")15        exit(1)16    17    with open(dirs.get_homedir()+"/.synapse-admin.config.json", "r") as conf_file:18        config_dict = json.load(conf_file)19        config = Config(server_url=config_dict.get("server_url"))20        if config_dict.get("loged_as"):21            config.loged_as = LogedUser(**config_dict["loged_as"])22            ...

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