def test_find_files(): path = os.path.join(os.getcwd(),'tests','tests_file_io') expect = [os.path.join(os.getcwd(),'tests','tests_file_io', 'test_find_files.py')] assert(find_files(substring='test_find_files', path=path) == expect) # find recursive assert(find_files(substring='test_find_files.py', path=os.getcwd(), recursive=True) == expect) # find files and check extension assert(find_files(substring='test_find_files.py', path=path, check_ext='.py') == expect) assert(find_files(substring='test_find_files.py', path=path, check_ext='.txt') == [])
def get_index_in_folder(input_filepath, input_basename, folder): """Loop through all .dat files in a folder, calling `get_index_from_filename` on each file""" path = os.path.join(input_filepath, folder) files = find_files(input_basename, path=path, check_ext='.dat') idxs = [] for f in files: idxs.append(get_index_from_filename(f)) return idxs
def test_find_files(): path = os.path.join(os.getcwd(), 'tests', 'tests_file_io') expect = [ os.path.join(os.getcwd(), 'tests', 'tests_file_io', 'test_find_files.py') ] assert (find_files(substring='test_find_files', path=path) == expect) # find recursive assert (find_files(substring='test_find_files.py', path=os.getcwd(), recursive=True) == expect) # find files and check extension assert (find_files(substring='test_find_files.py', path=path, check_ext='.py') == expect) assert (find_files(substring='test_find_files.py', path=path, check_ext='.txt') == [])
def get_results_from_training(path): files = find_files('training', path=path, recursive=True, check_ext='.log') if len(files) == 0: return None header = [ 'network', 'n_nodes', 'extra_dense', 'upper_cutoff', 'lower_cutoff', 'smoothing', 'basename', 'best_val_loss', 'best_val_acc', 'best_epoch', 'holdout_acc', 'holdout_loss' ] missing_holdout = None result_dict = {el: list() for el in header} for logpath in tqdm(files): #do analysis try: df_log = pd.read_csv(logpath) except IOError: tqdm.write("Can't read: " + logpath) continue idx = find_best_epoch(df_log) best_val_loss, best_val_acc = df_log.loc[idx, ['val_loss', 'val_acc']] log_filename = os.path.basename(logpath) basename, _ = os.path.splitext(log_filename) params = basename.split('__')[:-1] basename = '__'.join(params) params.append(basename) params.append(best_val_loss) params.append(best_val_acc) params.append(idx) try: # Get holdout performance holdout_acc, holdout_loss = get_holdout_performance(logpath) params.append(holdout_acc) params.append(holdout_loss) except: if missing_holdout is None: tqdm.write("At least one trace missing holdout performance") missing_holdout = True continue for head, par in zip(header, params): result_dict[head].append(par) return result_dict
def test_ignore_substring(): path = os.path.join(os.getcwd(), 'tests', 'tests_file_io') assert (find_files(substring='test_find_files', path=path, ignore_substring='test_find') == [])
out = subprocess.call(['sphinx-apidoc', '-o', rst_path, '/Users/sebastian/github/mlxtend/mlxtend', '-e', '-f', '--full', '--follow-links', '--maxdepth', '8']) # Convert reStructuredText to markdown files = [(os.path.join(rst_path, f), os.path.join(mkd_path, os.path.splitext(f)[0] + '.md')) for f in os.listdir(rst_path) if f.endswith('.rst')] for f in files: out = subprocess.call(['pandoc', f[0], '--from=rst', '--to=markdown', '-o', f[1]]) # Get submodules files = [f for f in os.listdir(mkd_path) if f.endswith('.md') and len(f.split('.'))>2] for f in files: print("- ['api/%s', '%s']" % (f, os.path.splitext(f)[0])) ''' py_files = find_files(substring='', path=mlxtend_path, check_ext='.py', recursive=True) py_files = [p for p in py_files if not '__init__.py' in p] print(py_files) for f in py_files: with open(f, 'r') as fd: file_contents = fd.read() module = ast.parse(file_contents) function_definitions = [ node for node in module.body if isinstance(node, ast.FunctionDef) ] class_definitions = [ node for node in module.body if isinstance(node, ast.ClassDef) ]
def test_ignore_substring(): path = os.path.join(os.getcwd(),'tests','tests_file_io') assert(find_files(substring='test_find_files', path=path, ignore_substring='test_find') == [])
os.remove out = subprocess.call(['sphinx-apidoc', '-o', rst_path, '/Users/sebastian/github/mlxtend/mlxtend', '-e', '-f', '--full', '--follow-links', '--maxdepth', '8']) # Convert reStructuredText to markdown files = [(os.path.join(rst_path, f), os.path.join(mkd_path, os.path.splitext(f)[0] + '.md')) for f in os.listdir(rst_path) if f.endswith('.rst')] for f in files: out = subprocess.call(['pandoc', f[0], '--from=rst', '--to=markdown', '-o', f[1]]) # Get submodules files = [f for f in os.listdir(mkd_path) if f.endswith('.md') and len(f.split('.'))>2] for f in files: print("- ['api/%s', '%s']" % (f, os.path.splitext(f)[0])) ''' py_files = find_files(substring='', path=mlxtend_path, check_ext='.py', recursive=True) py_files = [p for p in py_files if not '__init__.py' in p] print(py_files) for f in py_files: with open(f, 'r') as fd: file_contents = fd.read() module = ast.parse(file_contents) function_definitions = [node for node in module.body if isinstance(node, ast.FunctionDef)] class_definitions = [node for node in module.body if isinstance(node, ast.ClassDef)] for fu in function_definitions: print(ast.get_docstring(fu)) for cl in class_definitions: print(ast.get_docstring(cl))
if not args.input: print('Please provide an input directory via the -i flag. \n') args.help() quit() if not args.output: print('Please provide an input directory via the -o flag. \n') args.help() quit() if not os.path.isdir(args.output): os.mkdir(args.output) mol2_files = find_files(substring='', path=args.input, recursive=args.recursive, check_ext='.mol2', ignore_invisible=True) pbar = pyprind.ProgBar(len(mol2_files)) for path in mol2_files: mol2_name = os.path.basename(path) if args.recursive: case_dir = os.path.split(os.path.split(path)[0])[1] new_dir = os.path.join(args.output, case_dir) else: