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 Github

copy

Full Screen

...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)...

Full Screen

Full Screen

reader_.py

Source: reader_.py Github

copy

Full Screen

...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)...

Full Screen

Full Screen

config.py

Source: config.py Github

copy

Full Screen

...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 ...

Full Screen

Full Screen

Blogs

Check out the latest blogs from LambdaTest on this topic:

Test Managers in Agile – Creating the Right Culture for Your SQA Team

I was once asked at a testing summit, “How do you manage a QA team using scrum?” After some consideration, I realized it would make a good article, so here I am. Understand that the idea behind developing software in a scrum environment is for development teams to self-organize.

Complete Guide To Styling Forms With CSS Accent Color

The web paradigm has changed considerably over the last few years. Web 2.0, a term coined way back in 1999, was one of the pivotal moments in the history of the Internet. UGC (User Generated Content), ease of use, and interoperability for the end-users were the key pillars of Web 2.0. Consumers who were only consuming content up till now started creating different forms of content (e.g., text, audio, video, etc.).

A Complete Guide To Flutter Testing

Mobile devices and mobile applications – both are booming in the world today. The idea of having the power of a computer in your pocket is revolutionary. As per Statista, mobile accounts for more than half of the web traffic worldwide. Mobile devices (excluding tablets) contributed to 54.4 percent of global website traffic in the fourth quarter of 2021, increasing consistently over the past couple of years.

Webinar: Building Selenium Automation Framework [Voices of Community]

Even though several frameworks are available in the market for automation testing, Selenium is one of the most renowned open-source frameworks used by experts due to its numerous features and benefits.

A Comprehensive Guide On JUnit 5 Extensions

JUnit is one of the most popular unit testing frameworks in the Java ecosystem. The JUnit 5 version (also known as Jupiter) contains many exciting innovations, including support for new features in Java 8 and above. However, many developers still prefer to use the JUnit 4 framework since certain features like parallel execution with JUnit 5 are still in the experimental phase.

Automation Testing Tutorials

Learn to execute automation testing from scratch with LambdaTest Learning Hub. Right from setting up the prerequisites to run your first automation test, to following best practices and diving deeper into advanced test scenarios. LambdaTest Learning Hubs compile a list of step-by-step guides to help you be proficient with different test automation frameworks i.e. Selenium, Cypress, TestNG etc.

LambdaTest Learning Hubs:

YouTube

You could also refer to video tutorials over LambdaTest YouTube channel to get step by step demonstration from industry experts.

Run tox automation tests on LambdaTest cloud grid

Perform automation testing on 3000+ real desktop and mobile devices online.

Try LambdaTest Now !!

Get 100 minutes of automation test minutes FREE!!

Next-Gen App & Browser Testing Cloud

Was this article helpful?

Helpful

NotHelpful