xmipp3-installer 1.0.0__py3-none-any.whl → 1.1.0__py3-none-any.whl

xmipp3_installer/application/cli/parsers/format.py

@@ -7,29 +7,29 @@ from xmipp3_installer.application.cli.arguments import params
 TAB_SIZE = 4
 
 def get_formatting_tabs(text: str) -> str:
-	"""
-	### Returns the given text, formatted to expand tabs into a fixed tab size.
+  """
+  ### Returns the given text, formatted to expand tabs into a fixed tab size.
 
-	### Params:
-	- text (str): The text to be formatted.
+  ### Params:
+  - text (str): The text to be formatted.
 
-	### Returns:
-	- (str): Formatted text.
-	"""
-	return text.expandtabs(TAB_SIZE)
+  ### Returns:
+  - (str): Formatted text.
+  """
+  return text.expandtabs(TAB_SIZE)
 
 def get_param_names(param_key: str) -> List[str]:
-	"""
-	### Returns the list of possible names a given param has.
-
-	#### Params:
-	- param_key (str): Key to find the param.
-
-	#### Returns:
-	- (list[str]): Names of the given param.
-	"""
-	names = [
-		params.PARAMS[param_key].get(params.SHORT_VERSION, ''),
-		params.PARAMS[param_key].get(params.LONG_VERSION, '')
-	]
-	return [name for name in names if name]
+  """
+  ### Returns the list of possible names a given param has.
+
+  #### Params:
+  - param_key (str): Key to find the param.
+
+  #### Returns:
+  - (list[str]): Names of the given param.
+  """
+  names = [
+    params.PARAMS[param_key].get(params.SHORT_VERSION, ''),
+    params.PARAMS[param_key].get(params.LONG_VERSION, '')
+  ]
+  return [name for name in names if name]

xmipp3_installer/application/cli/parsers/general_help_formatter.py

@@ -6,87 +6,105 @@ from xmipp3_installer.application.cli.parsers.base_help_formatter import BaseHel
 from xmipp3_installer.application.logger.logger import logger
 
 class GeneralHelpFormatter(BaseHelpFormatter):
-	"""
-	### Overrides the default help formatter to display a custom help message.
-	"""
-	def format_help(self):
-		"""
-		### Prints the help message of the argument parser.
-		"""
-		help_message = "Run Xmipp's installer script\n\nUsage: xmipp [options]\n"
-		for section in list(modes.MODES.keys()):
-			help_message += self.__get_section_message(section)
-		help_message += f"\n{self.__get_epilog()}"
-		help_message += self.__get_note()
-		return format.get_formatting_tabs(help_message)
-	
-	def __get_mode_args_str(self, mode: str) -> str:
-		"""
-		### This method returns the args text for a given mode.
-
-		### Params:
-		- mode (str): Mode to get args text for.
-
-		### Returns:
-		- (str): Args text for given mode.
-		"""
-		arg_list = modes.MODE_ARGS[mode]
-		param_names = []
-		for param in arg_list:
-			param_name = self._get_param_first_name(param)
-			if param_name:
-				param_names.append(f'[{param_name}]')
-		return ' '.join(param_names)
-
-	def __get_mode_args_and_help_str(self, previous_text: str, mode: str) -> str:
-		"""
-		### This method returns the args and help text for a given mode.
-
-		### Params:
-		- previous_text (str): Text inserted before the one to be returned.
-		- mode (str): Mode to get help text for.
-
-		### Returns:
-		- (str): Args and help text for given mode.
-		"""
-		return self._text_with_limits(
-			previous_text + self.__get_mode_args_str(mode),
-			self._get_mode_help(mode)
-		)
-
-	def __get_epilog(self) -> str:
-		"""
-		### Returns the epilogue.
-
-		#### Returns:
-		- (str): Epilogue.
-		"""
-		epilogue = "Example 1: ./xmipp\n"
-		epilogue += "Example 2: ./xmipp compileAndInstall -j 4\n"
-		return epilogue
-	
-	def __get_note(self) -> str:
-		"""
-		### Returns the additional note message.
-
-		#### Returns:
-		- (str): Note message.
-		"""
-		note_message = "Note: You can also view a specific help message for each mode with \"./xmipp [mode] -h\".\n"
-		note_message += f"Example: ./xmipp {modes.MODE_ALL} -h\n"
-		return logger.yellow(note_message)
-
-	def __get_section_message(self, section: str) -> str:
-		"""
-		### Returns the given section's message.
-
-		#### Params:
-		- section (str): Section name.
-
-		#### Return:
-		- (str): Section's message.
-		"""
-		section_message = self._get_help_separator() + f"\t# {section} #\n\n"
-		for mode in list(modes.MODES[section].keys()):
-			section_message += self.__get_mode_args_and_help_str(f"\t{mode} ", mode)
-		return section_message
+  """### Overrides the default help formatter to display a custom help message."""
+
+  def format_help(self):
+    """### Prints the help message of the argument parser."""
+    help_message = "Run Xmipp's installer script\n\nUsage: xmipp [options]\n"
+    for section in modes.MODES.keys():
+      help_message += self.__get_section_message(section)
+    help_message += f"\n{self.__get_epilog()}"
+    help_message += self.__get_note()
+    return format.get_formatting_tabs(help_message)
+  
+  def __get_mode_arg_group_str(self, args: str) -> str:
+    """
+    ### This method returns the args text for a given arg group.
+
+    ### Params:
+    - args (str): Args to format into a message string.
+
+    ### Returns:
+    - (str): Args text for given mode.
+    """
+    param_names = []
+    for param in args:
+      param_name = self._get_param_first_name(param)
+      if param_name:
+        param_names.append(f'[{param_name}]')
+    return ' '.join(param_names)
+
+  def __get_mode_args_str(self, mode: str) -> str:
+    """
+    ### This method returns the args text for a given mode.
+
+    ### Params:
+    - mode (str): Mode to get args text for.
+
+    ### Returns:
+    - (str): Args text for given mode.
+    """
+    args = modes.MODE_ARGS[mode]
+    if not self._has_mutually_exclusive_groups(args):
+      return self.__get_mode_arg_group_str(args)
+    
+    group_strs = [
+      self.__get_mode_arg_group_str(arg_group) for arg_group in args
+    ]
+    exclusive_group_str = " | ".join(group_strs)
+    return f"({exclusive_group_str})"
+
+  def __get_mode_args_and_help_str(self, previous_text: str, mode: str) -> str:
+    """
+    ### This method returns the args and help text for a given mode.
+
+    ### Params:
+    - previous_text (str): Text inserted before the one to be returned.
+    - mode (str): Mode to get help text for.
+
+    ### Returns:
+    - (str): Args and help text for given mode.
+    """
+    return self._text_with_limits(
+      previous_text + self.__get_mode_args_str(mode),
+      self._get_mode_help(mode)
+    )
+
+  @staticmethod
+  def __get_epilog() -> str:
+    """
+    ### Returns the epilogue.
+
+    #### Returns:
+    - (str): Epilogue.
+    """
+    epilogue = "Example 1: ./xmipp\n"
+    epilogue += "Example 2: ./xmipp compileAndInstall -j 4\n"
+    return epilogue
+  
+  @staticmethod
+  def __get_note() -> str:
+    """
+    ### Returns the additional note message.
+
+    #### Returns:
+    - (str): Note message.
+    """
+    note_message = "Note: You can also view a specific help message for each mode with \"./xmipp [mode] -h\".\n"
+    note_message += f"Example: ./xmipp {modes.MODE_ALL} -h\n"
+    return logger.yellow(note_message)
+
+  def __get_section_message(self, section: str) -> str:
+    """
+    ### Returns the given section's message.
+
+    #### Params:
+    - section (str): Section name.
+
+    #### Return:
+    - (str): Section's message.
+    """
+    section_message = self._get_help_separator() + f"\t# {section} #\n\n"
+    for mode in modes.MODES[section].keys():
+      section_message += self.__get_mode_args_and_help_str(f"\t{mode} ", mode)
+    return section_message

xmipp3_installer/application/cli/parsers/mode_help_formatter.py

@@ -1,6 +1,6 @@
 """### Help formatter specific for non-generic usage modes."""
 
-from typing import List
+from typing import List, Union, cast
 
 from xmipp3_installer.application.cli import arguments
 from xmipp3_installer.application.cli.arguments import modes, params
@@ -9,107 +9,146 @@ from xmipp3_installer.application.cli.parsers.base_help_formatter import BaseHel
 from xmipp3_installer.application.logger.logger import logger
 
 class ModeHelpFormatter(BaseHelpFormatter):
-	"""
-	### Overrides the default help formatter to display a custom help message deppending on the mode selected.
-	"""
-	def format_help(self):
-		"""
-		### This method prints the help message of the argument parser.
-		"""
-		mode = self.__get_mode()
-		help_message = f"{self._get_mode_help(mode, general=False)}\n\n"
-		help_message += self.__get_args_message(mode)
-		help_message += self.__get_examples_message(mode)
-		return format.get_formatting_tabs(help_message)
-
-	def __get_mode(self):
-		"""
-		### Returns the execution mode.
-
-		#### Returns:
-		- (str): Execution mode.
-		"""
-		# Retrieved from the parent help message
-		# Message received is the format_help output of the main parser's
-		# formatter, adding the mode at the end
-		return self._prog.split(' ')[-1]
-	
-	def __get_args_message(self, mode: str) -> str:
-		"""
-		### Returns the help section containing all the parameters.
-
-		#### Params:
-		- mode (str): Usage mode selected.
-
-		#### Returns:
-		- (str): Help section containing all parameters.
-		"""
-		args = modes.MODE_ARGS[mode]
-		help_message = ''
-		options_str = ''
-		separator = ''
-		
-		if len(args) > 0:
-			arg_names = [self._get_param_first_name(arg_name) for arg_name in args]
-			if self.__args_contain_optional(arg_names):
-				help_message += logger.yellow("Note: only params starting with '-' are optional. The rest are required.\n")
-			options_str = ' [options]'
-			separator = self._get_help_separator() + '\t# Options #\n\n'
-
-		help_message += f'Usage: {arguments.XMIPP_PROGRAM_NAME} {mode}{options_str}\n{separator}'
-		help_message += self.__get_args_info(args)
-		return help_message
-
-	def __args_contain_optional(self, arg_names: List[str]) -> bool:
-		"""
-		### Returns True if the param name list contains at least one optional param.
-
-		### Params:
-		- arg_names (list[str]): List containing the param names.
-
-		### Returns:
-		- (bool): True if there is at least one optional param. False otherwise.
-		"""
-		for name in arg_names:
-			if name.startswith('-'):
-				return True
-		return False
-
-	def __get_args_info(self, args: List[str]) -> str:
-		"""
-		### Returns the info of each param.
-
-		#### Params:
-		- args (list[str]): List of parameters.
-
-		#### Returns:
-		- (str): Info of all parameters.
-		"""
-		help_message = ''
-		for arg in args:
-			help_message += self._text_with_limits(
-				'\t' + ', '.join(format.get_param_names(arg)),
-				params.PARAMS[arg][params.DESCRIPTION]
-			)
-		return help_message
-
-	def __get_examples_message(self, mode: str) -> str:
-		"""
-		### Returns the message section containig usage examples.
-
-		#### Params:
-		- mode (str): Usage mode selected.
-
-		#### Returns:
-		- (str): Message section containing usage examples.
-		"""
-		help_message = ''
-		examples = modes.MODE_EXAMPLES[mode]
-		for i in range(len(examples)):
-			number_str = '' if len(examples) == 1 else f' {i+1}'	
-			help_message += f"\nExample{number_str}: {examples[i]}"
-		
-		if len(examples) > 0:
-			help_message += '\n'
-
-		return help_message
+  """### Overrides the default help formatter to display a custom help message deppending on the mode selected."""
+
+  def format_help(self):
+    """### This method prints the help message of the argument parser."""
+    mode = self.__get_mode()
+    help_message = f"{self._get_mode_help(mode, general=False)}\n\n"
+    help_message += self.__get_args_message(mode)
+    help_message += self.__get_examples_message(mode)
+    return format.get_formatting_tabs(help_message)
+
+  def __get_mode(self):
+    """
+    ### Returns the execution mode.
+
+    #### Returns:
+    - (str): Execution mode.
+    """
+    # Retrieved from the parent help message
+    # Message received is the format_help output of the main parser's
+    # formatter, adding the mode at the end
+    return self._prog.split(' ')[-1]
+  
+  def __get_args_message(self, mode: str) -> str:
+    """
+    ### Returns the help section containing all the parameters.
+
+    #### Params:
+    - mode (str): Usage mode selected.
+
+    #### Returns:
+    - (str): Help section containing all parameters.
+    """
+    args = modes.MODE_ARGS[mode]
+    help_message = ''
+    options_str = ''
+    separator = ''
+    
+    if len(args) > 0:
+      arg_names = [
+        self._get_param_first_name(arg_name) for arg_name in self.__flatten_args(args)
+      ]
+      if self._has_mutually_exclusive_groups(args):
+        help_message += logger.yellow(
+          "Important: In this mode, there are mutually exclusive groups of params. "
+          "You can only use from one of them at a time.\n"
+          )
+      if self.__args_contain_optional(arg_names):
+        help_message += logger.yellow("Note: only params starting with '-' are optional. The rest are required.\n")
+      options_str = ' [options]'
+      separator = self._get_help_separator() + '\t# Options #\n\n'
+
+    help_message += f'Usage: {arguments.XMIPP_PROGRAM_NAME} {mode}{options_str}\n{separator}'
+    help_message += self.__get_args_info(args)
+    return help_message
+
+  @staticmethod
+  def __args_contain_optional(arg_names: List[str]) -> bool:
+    """
+    ### Returns True if the param name list contains at least one optional param.
+
+    ### Params:
+    - arg_names (list[str]): List containing the param names.
+
+    ### Returns:
+    - (bool): True if there is at least one optional param. False otherwise.
+    """
+    for name in arg_names:
+      if name.startswith('-'):
+        return True
+    return False
+
+  def __get_args_info(self, args: List[Union[str, List[str]]]) -> str:
+    """
+    ### Returns the info of each param.
+
+    #### Params:
+    - args (list[str]): List of parameters.
+
+    #### Returns:
+    - (str): Info of all parameters.
+    """
+    if not self._has_mutually_exclusive_groups(args):
+      return self.__get_args_group_info(cast(List[str], args))
+    return "\t---------------\n".join([self.__get_args_group_info(cast(List[str], group)) for group in args])
+
+  def __get_args_group_info(self, args: List[str]) -> str:
+    """
+    ### Returns the info of each param.
+
+    #### Params:
+    - args (list[str]): List of parameters.
+
+    #### Returns:
+    - (str): Info of all parameters.
+    """
+    help_message = ''
+    for arg in args:
+      help_message += self._text_with_limits(
+        '\t' + ', '.join(format.get_param_names(arg)),
+        params.PARAMS[arg][params.DESCRIPTION]
+      )
+    return help_message
+
+  @staticmethod
+  def __get_examples_message(mode: str) -> str:
+    """
+    ### Returns the message section containig usage examples.
+
+    #### Params:
+    - mode (str): Usage mode selected.
+
+    #### Returns:
+    - (str): Message section containing usage examples.
+    """
+    help_message = ''
+    examples = modes.MODE_EXAMPLES[mode]
+    for i in range(len(examples)):
+      number_str = '' if len(examples) == 1 else f' {i+1}'	
+      help_message += f"\nExample{number_str}: {examples[i]}"
+    
+    if len(examples) > 0:
+      help_message += '\n'
+
+    return help_message
+
+  def __flatten_args(self, args: List[Union[str, List[str]]]) -> List[str]:
+    """
+    ### Flattens a list of arguments.
+
+    #### Params:
+    - args (list[str | list[str]]): A list of arguments, which can include nested lists representing mutually exclusive groups.
+
+    #### Returns:
+    - (list[str]): A flattened list of arguments, where nested groups are expanded into a single list.
+    """
+    if not self._has_mutually_exclusive_groups(args):
+      return cast(List[str], args)
+
+    return [
+      arg
+      for arg_group in args
+      for arg in arg_group
+    ]

xmipp3_installer/application/logger/__init__.py

@@ -0,0 +1,5 @@
+"""
+### Logger Module.
+
+This module provides logging functionalities for the Xmipp installer.
+"""

xmipp3_installer/application/logger/errors.py

@@ -17,12 +17,12 @@ IO_ERROR = 7
 # Error messages
 __CHECK_LOG_MESSAGE = f'Check the inside file \'{paths.LOG_FILE}\'.'
 ERROR_CODES = {
-	INTERRUPTED_ERROR: ['Process was interrupted by the user.', ''],
-	UNKOW_ERROR: ['', ''],
-	SOURCE_CLONE_ERROR: ['Error cloning xmipp repository with git.', 'Please review the internet connection and the git package.'],
-	CMAKE_ERROR: ['There was an error with CMake.', f'Please install it by following the instructions at {CMAKE_INSTALL_DOCS_URL}'],
-	CMAKE_CONFIGURE_ERROR: ['Error configuring with CMake.', __CHECK_LOG_MESSAGE],
-	CMAKE_COMPILE_ERROR: ['Error compiling with CMake.', __CHECK_LOG_MESSAGE],
-	CMAKE_INSTALL_ERROR: ['Error installing with CMake.', __CHECK_LOG_MESSAGE],
-	IO_ERROR: ['Input/output error.', 'This error can be caused by the installer not being able to read/write/create/delete a file. Check your permissions on this directory.']
+  INTERRUPTED_ERROR: ['Process was interrupted by the user.', ''],
+  UNKOW_ERROR: ['', ''],
+  SOURCE_CLONE_ERROR: ['Error cloning xmipp repository with git.', 'Please review the internet connection and the git package.'],
+  CMAKE_ERROR: ['There was an error with CMake.', f'Please install it by following the instructions at {CMAKE_INSTALL_DOCS_URL}'],
+  CMAKE_CONFIGURE_ERROR: ['Error configuring with CMake.', __CHECK_LOG_MESSAGE],
+  CMAKE_COMPILE_ERROR: ['Error compiling with CMake.', __CHECK_LOG_MESSAGE],
+  CMAKE_INSTALL_ERROR: ['Error installing with CMake.', __CHECK_LOG_MESSAGE],
+  IO_ERROR: ['Input/output error.', 'This error can be caused by the installer not being able to read/write/create/delete a file. Check your permissions on this directory.']
 }