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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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