Coverage for src\pytribeam\command_line.py: 32%

1""" 

2Command Line Entry Points Module 

3================================ 

4 

5This module provides command line entry points for various functions and utilities. 

6It serves as the interface between the command line and the underlying functionality 

7of the application. 

8""" 

9 

10from typing import Final 

11import argparse 

12from pathlib import Path 

13 

14# import pkg_resources # part of setup tools 

15from importlib.metadata import version 

16import pytribeam.constants as cs 

17import pytribeam.GUI.runner as runner 

18import pytribeam.workflow as workflow 

19 

20CLI_DOCS: Final[ 

21 str 

22] = """ 

23-------- 

24pytribeam 

25-------- 

26 

27pytribeam 

28 (this command) 

29 

30pytribeam_info 

31 Prints the module version and ThermoFisher Scientific Autoscript and Laser 

32 API version requirements. 

33 

34pytribeam_gui 

35 Launches GUI for creating configuration .yml files and to control 

36 experimental collection. 

37 

38pytribeam_exp <path_to_file>.yml 

39 Runs 3D data collection workflow based off of input .yml file. 

40 

41 Example: 

42 path/to/experiment/directory> pytribeam_exp path/to/config/file.yml 

43 

44""" 

45 

46 

47def pytribeam(): 

48 """ 

49 Prints the command line documentation to the command window. 

50 

51 This function prints the contents of the global variable `CLI_DOCS` to the 

52 command window. It is assumed that `CLI_DOCS` contains the necessary 

53 documentation in string format. 

54 

55 Parameters 

56 ---------- 

57 None 

58 

59 Returns 

60 ------- 

61 None 

62 """ 

63 print(CLI_DOCS) 

64 

65 

66def module_info() -> None: 

67 """ 

68 Prints the module version and the yml_schema_version. 

69 

70 This function retrieves the version of the module and the YAML schema version 

71 from the `Constants` class in the `cs` module (constants.py). It prints these 

72 versions to the command window and returns the module version. 

73 

74 Parameters 

75 ---------- 

76 None 

77 

78 Returns 

79 ------- 

80 None 

81 """ 

82 

83 # ver = pkg_resources.require("recon3d")[0].version 

84 module_name = cs.Constants().module_short_name 

85 ver = version(module_name) 

86 autoscript_version = cs.Constants().autoscript_version 

87 laser_api_version = cs.Constants().laser_api_version 

88 yml_schema_version = cs.Constants().yml_schema_version 

89 print(f"{module_name} module version: v{ver}") 

90 print(f" Maximum supported .yml schema version: v{yml_schema_version}") 

91 print( 

92 f" Maximum supported Thermo Fisher Autoscript version: v{autoscript_version}" 

93 ) 

94 print(f" Maximum supported Laser API version: v{laser_api_version}") 

95 return None 

96 

97 

98def launch_gui(): 

99 # work_in_progress() 

100 app = runner.MainApplication() 

101 app.mainloop() 

102 

103 

104def run_experiment(): 

105 """run experiment from command line""" 

106 

107 def _positive_integer(prompt): 

108 """Helper function to get valid integer input""" 

109 while True: 

110 try: 

111 # Ask for input 

112 value = int(input(prompt)) 

113 if value > 0: 

114 return value # Return the valid integer 

115 else: 

116 print("Invalid input. Please enter an integer greater than 0.") 

117 except ValueError: 

118 print("Invalid input. Please enter a valid integer.") 

119 

120 # Create the parser 

121 parser = argparse.ArgumentParser(description="Process a file.") 

122 

123 # Add the file path argument 

124 parser.add_argument("file_path", type=str, help="Path to the file to process") 

125 

126 # Parse the arguments 

127 args = parser.parse_args() 

128 

129 start_slice = _positive_integer("Starting slice: ") 

130 start_step = _positive_integer("Starting step: ") 

131 

132 # Call the main function with the provided file path 

133 workflow.run_experiment_cli( 

134 start_slice=start_slice, start_step=start_step, yml_path=Path(args.file_path) 

135 ) 

136 

137 

138def work_in_progress(): 

139 """ 

140 Prints the 'Work in Progress (WIP)' warning message. 

141 

142 This function prints a warning message indicating that the function is a 

143 work in progress and has not yet been implemented. 

144 

145 Parameters 

146 ---------- 

147 None 

148 

149 Returns 

150 ------- 

151 None 

152 """ 

153 print("Warning: Work in progress (WIP), function not yet implemented.")