xmipp3-installer 1.0.1__py3-none-any.whl → 1.1.0__py3-none-any.whl

xmipp3_installer/repository/config_vars/config_values_adapter.py

@@ -1,107 +1,113 @@
+"""
+### Configuration Values Adapter Module.
+
+This module contains functions to convert configuration values between file format and context format.
+"""
+
 from typing import Dict, Union
 
 from xmipp3_installer.application.logger.logger import logger
 from xmipp3_installer.repository.config_vars import variables, default_values
 
 def get_context_values_from_file_values(file_values: Dict[str, str], show_warnings: bool=True) -> Dict[str, Union[str, bool]]:
-	"""
-	### Converts configuration values from file format to context format.
-	
-	Processes a dictionary of configuration values read from file, converting toggle values 
-	from string ('ON'/'OFF') to boolean representation for use in the application context.
-
-	#### Params:
-	- file_values (dict(str, str)): Dictionary of configuration values as read from file.
-	- show_warnings (bool): Optional. If True, warning messages are shown when applicable.
-
-	#### Returns:
-	- (dict(str, str | bool)): Dictionary with values converted to their context format.
-	"""
-	context_values = {}
-	for key, value in file_values.items():
-		context_values[key] = __get_context_value_from_file_value(key, value, show_warnings)
-	return context_values
+  """
+  ### Converts configuration values from file format to context format.
+  
+  Processes a dictionary of configuration values read from file, converting toggle values 
+  from string ('ON'/'OFF') to boolean representation for use in the application context.
+
+  #### Params:
+  - file_values (dict(str, str)): Dictionary of configuration values as read from file.
+  - show_warnings (bool): Optional. If True, warning messages are shown when applicable.
+
+  #### Returns:
+  - (dict(str, str | bool)): Dictionary with values converted to their context format.
+  """
+  context_values = {}
+  for key, value in file_values.items():
+    context_values[key] = __get_context_value_from_file_value(key, value, show_warnings)
+  return context_values
 
 def get_file_values_from_context_values(context_values: Dict[str, Union[str, bool]]) -> Dict[str, str]:
-	"""
-	### Converts configuration values from context format to file format.
-	
-	Processes a dictionary of configuration values from the application context, converting toggle values 
-	from boolean to string ('ON'/'OFF') representation for storage in configuration file.
-
-	#### Params:
-	- context_values (dict(str, str | bool)): Dictionary of configuration values from context.
-
-	#### Returns:
-	- (dict(str, str)): Dictionary with values converted to their file storage format.
-	"""
-	file_values = {}
-	for key, value in context_values.items():
-		file_values[key] = __get_file_value_from_context_value(key, value)
-	return file_values
+  """
+  ### Converts configuration values from context format to file format.
+  
+  Processes a dictionary of configuration values from the application context, converting toggle values 
+  from boolean to string ('ON'/'OFF') representation for storage in configuration file.
+
+  #### Params:
+  - context_values (dict(str, str | bool)): Dictionary of configuration values from context.
+
+  #### Returns:
+  - (dict(str, str)): Dictionary with values converted to their file storage format.
+  """
+  file_values = {}
+  for key, value in context_values.items():
+    file_values[key] = __get_file_value_from_context_value(key, value)
+  return file_values
 
 def __get_context_value_from_file_value(key: str, value: str, show_warnings: bool) -> Union[str, bool]:
-	"""
-	### Converts a single configuration value from file format to context format.
-
-	#### Params:
-	- key (str): Configuration variable key.
-	- value (str): Value as read from file.
-	- show_warnings (bool): Optional. If True, warning messages are shown when applicable.
-
-	#### Returns:
-	- (str | bool): Value converted to its context format.
-	"""
-	if key in variables.CONFIG_VARIABLES[variables.TOGGLES]:
-		return __get_boolean_value_from_string(key, value, show_warnings)
-	return value
-
-def __get_file_value_from_context_value(key: str, value: str) -> Union[str, bool]:
-	"""
-	### Converts a single configuration value from context format to file format.
-
-	#### Params:
-	- key (str): Configuration variable key.
-	- value (str | bool): Value from context.
-
-	#### Returns:
-	- (str): Value converted to its file storage format.
-	"""
-	if key in variables.CONFIG_VARIABLES[variables.TOGGLES]:
-		return __get_string_value_from_boolean(value)
-	return value
+  """
+  ### Converts a single configuration value from file format to context format.
+
+  #### Params:
+  - key (str): Configuration variable key.
+  - value (str): Value as read from file.
+  - show_warnings (bool): Optional. If True, warning messages are shown when applicable.
+
+  #### Returns:
+  - (str | bool): Value converted to its context format.
+  """
+  if key in variables.CONFIG_VARIABLES[variables.TOGGLES]:
+    return __get_boolean_value_from_string(key, value, show_warnings)
+  return value
+
+def __get_file_value_from_context_value(key: str, value: Union[str, bool]) -> Union[str, bool]:
+  """
+  ### Converts a single configuration value from context format to file format.
+
+  #### Params:
+  - key (str): Configuration variable key.
+  - value (str | bool): Value from context.
+
+  #### Returns:
+  - (str): Value converted to its file storage format.
+  """
+  if key in variables.CONFIG_VARIABLES[variables.TOGGLES]:
+    return __get_string_value_from_boolean(bool(value))
+  return value
 
 def __get_boolean_value_from_string(key: str, value: str, show_warning: bool) -> bool:
-	"""
-	### Converts a toggle value from string ('ON'/'OFF') to boolean.
-
-	#### Params:
-	- key (str): Configuration variable key.
-	- value (str): String value to convert ('ON' or 'OFF').
-	- show_warnings (bool): Optional. If True, warning message is shown when applicable.
-
-	#### Returns:
-	- (bool): Boolean representation of the toggle value.
-	"""
-	if value != default_values.ON and value != default_values.OFF:
-		default_value = default_values.CONFIG_DEFAULT_VALUES[key]
-		if show_warning:
-			logger(logger.yellow(
-				f"WARNING: config variable '{key}' has unrecognized value '{value}'. "
-				f"Toggle values must be either '{default_values.ON}' or '{default_values.OFF}'. "
-				f"Default value '{default_value}' will be used instead."
-			))
-		value = default_value
-	return value == default_values.ON
+  """
+  ### Converts a toggle value from string ('ON'/'OFF') to boolean.
+
+  #### Params:
+  - key (str): Configuration variable key.
+  - value (str): String value to convert ('ON' or 'OFF').
+  - show_warnings (bool): Optional. If True, warning message is shown when applicable.
+
+  #### Returns:
+  - (bool): Boolean representation of the toggle value.
+  """
+  if value not in {default_values.ON, default_values.OFF}:
+    default_value = default_values.CONFIG_DEFAULT_VALUES[key]
+    if show_warning:
+      logger(logger.yellow(
+        f"WARNING: config variable '{key}' has unrecognized value '{value}'. "
+        f"Toggle values must be either '{default_values.ON}' or '{default_values.OFF}'. "
+        f"Default value '{default_value}' will be used instead."
+      ))
+    value = default_value
+  return value == default_values.ON
 
 def __get_string_value_from_boolean(value: bool) -> str:
-	"""
-	### Converts a toggle value from boolean to string ('ON'/'OFF').
+  """
+  ### Converts a toggle value from boolean to string ('ON'/'OFF').
 
-	#### Params:
-	- value (bool): Boolean value to convert.
+  #### Params:
+  - value (bool): Boolean value to convert.
 
-	#### Returns:
-	- (str): String representation of the toggle value ('ON' or 'OFF').
-	"""
-	return default_values.ON if value else default_values.OFF
+  #### Returns:
+  - (str): String representation of the toggle value ('ON' or 'OFF').
+  """
+  return default_values.ON if value else default_values.OFF

xmipp3_installer/repository/config_vars/default_values.py

@@ -9,28 +9,28 @@ __TUNE_FLAG = '-mtune=native'
 ON = 'ON'
 OFF = 'OFF'
 CONFIG_DEFAULT_VALUES = {
-	variables.SEND_INSTALLATION_STATISTICS: ON,
-	variables.CMAKE: None,
-	variables.CUDA: ON,
-	variables.MPI: ON,
-	variables.CC: None,
-	variables.CXX: None,
-	variables.CMAKE_INSTALL_PREFIX: paths.INSTALL_PATH,
-	variables.CC_FLAGS: __TUNE_FLAG,
-	variables.CXX_FLAGS: __TUNE_FLAG,
-	variables.CUDA_COMPILER: None,
-	variables.PREFIX_PATH: conda_handler.get_conda_prefix_path(),
-	variables.MPI_HOME: None,
-	variables.PYTHON_HOME: None,
-	variables.FFTW_HOME: None,
-	variables.TIFF_HOME: None,
-	variables.HDF5_HOME: None,
-	variables.JPEG_HOME: None,
-	variables.SQLITE_HOME: None,
-	variables.CUDA_CXX: None,
-	variables.MATLAB: ON,
-	variables.LINK_SCIPION: ON,
-	variables.BUILD_TESTING: ON,
- 	variables.SKIP_RPATH: ON,
-	variables.BUILD_TYPE: "Release"
+  variables.SEND_INSTALLATION_STATISTICS: ON,
+  variables.CMAKE: None,
+  variables.CUDA: ON,
+  variables.MPI: ON,
+  variables.CC: None,
+  variables.CXX: None,
+  variables.CMAKE_INSTALL_PREFIX: paths.INSTALL_PATH,
+  variables.CC_FLAGS: __TUNE_FLAG,
+  variables.CXX_FLAGS: __TUNE_FLAG,
+  variables.CUDA_COMPILER: None,
+  variables.PREFIX_PATH: conda_handler.get_conda_prefix_path(),
+  variables.MPI_HOME: None,
+  variables.PYTHON_HOME: None,
+  variables.FFTW_HOME: None,
+  variables.TIFF_HOME: None,
+  variables.HDF5_HOME: None,
+  variables.JPEG_HOME: None,
+  variables.SQLITE_HOME: None,
+  variables.CUDA_CXX: None,
+  variables.MATLAB: ON,
+  variables.LINK_SCIPION: ON,
+  variables.BUILD_TESTING: OFF,
+  variables.SKIP_RPATH: ON,
+  variables.BUILD_TYPE: "Release"
 }

xmipp3_installer/repository/config_vars/variables.py

@@ -33,15 +33,15 @@ TOGGLES = 'toggles'
 LOCATIONS = 'locations'
 COMPILATION_FLAGS = 'flags'
 CONFIG_VARIABLES = {
-	TOGGLES: [
-		SEND_INSTALLATION_STATISTICS, CUDA, MPI, MATLAB, LINK_SCIPION, BUILD_TESTING, SKIP_RPATH
-	],
-	LOCATIONS: [
-		CMAKE, CC, CXX, CMAKE_INSTALL_PREFIX, PREFIX_PATH, MPI_HOME,
-		CUDA_COMPILER, PYTHON_HOME, FFTW_HOME, TIFF_HOME, 
-	 	HDF5_HOME, JPEG_HOME, SQLITE_HOME, CUDA_CXX
-	],
-	COMPILATION_FLAGS: [CC_FLAGS, CXX_FLAGS, BUILD_TYPE]
+  TOGGLES: [
+    SEND_INSTALLATION_STATISTICS, CUDA, MPI, MATLAB, LINK_SCIPION, BUILD_TESTING, SKIP_RPATH
+  ],
+  LOCATIONS: [
+    CMAKE, CC, CXX, CMAKE_INSTALL_PREFIX, PREFIX_PATH, MPI_HOME,
+    CUDA_COMPILER, PYTHON_HOME, FFTW_HOME, TIFF_HOME, 
+     HDF5_HOME, JPEG_HOME, SQLITE_HOME, CUDA_CXX
+  ],
+  COMPILATION_FLAGS: [CC_FLAGS, CXX_FLAGS, BUILD_TYPE]
 }
 
 # Do not pass this variables to CMake, only for installer logic

xmipp3_installer/repository/invalid_config_line.py

@@ -3,8 +3,25 @@
 from xmipp3_installer.application.logger.logger import logger
 
 class InvalidConfigLineError(RuntimeError):
+  """
+  ### Custom exception for invalid configuration lines.
+  
+  Raised when a line in the configuration file does not follow the expected format.
+  """
+  
   @staticmethod
   def generate_error_message(config_file, line_number, line):
+    """
+    ### Generates an error message for an invalid configuration line.
+    
+    #### Params:
+    - config_file (str): The name of the configuration file.
+    - line_number (int): The line number where the error occurred.
+    - line (str): The content of the invalid line.
+    
+    #### Returns:
+    - (str): The generated error message.
+    """
     return '\n'.join([
       logger.yellow(f"WARNING: There was an error parsing {config_file} file: "),
       logger.red(f'Unable to parse line {line_number}: {line}'),

xmipp3_installer/shared/file_operations.py

@@ -1,18 +1,20 @@
+"""# Module containing file-related functions."""
+
 import os
 import shutil
 from typing import List
 
 def delete_paths(paths: List[str]):
-	"""
-	### Deletes all the given paths (files or directories).
+  """
+  ### Deletes all the given paths (files or directories).
 
-	#### Params:
-	- path (list(str)): List of paths to delete.
-	"""
-	for path in paths:
-		if not os.path.exists(path):
-			continue
-		if os.path.isdir(path):
-			shutil.rmtree(path, ignore_errors=True)
-		else:
-			os.remove(path)
+  #### Params:
+  - path (list(str)): List of paths to delete.
+  """
+  for path in paths:
+    if not os.path.exists(path):
+      continue
+    if os.path.isdir(path):
+      shutil.rmtree(path, ignore_errors=True)
+    else:
+      os.remove(path)

xmipp3_installer/shared/singleton.py

@@ -3,23 +3,22 @@
 from typing_extensions import Self
 
 class Singleton:
-	"""
-	### Generic singleton class.
-	"""
-	__instance = None
+  """### Generic singleton class."""
 
-	def __new__(cls, *args, **kwrgs) -> Self:
-		"""
-		### Singleton instancer.
+  __instance = None
 
-		#### Params:
-		- cls (self): Current class.
-		- *args (any): Positional params.
-		- **kwargs (any): Argument params.
+  def __new__(cls, *args, **kwrgs) -> Self:
+    """
+    ### Singleton instancer.
 
-		#### Returns:
-		- (self): Instance of current class.
-		"""
-		if not cls.__instance:
-			cls.__instance = super().__new__(cls)
-		return cls.__instance
+    #### Params:
+    - cls (self): Current class.
+    - *args (any): Positional params.
+    - **kwargs (any): Argument params.
+
+    #### Returns:
+    - (self): Instance of current class.
+    """
+    if not cls.__instance:
+      cls.__instance = super().__new__(cls)
+    return cls.__instance

xmipp3_installer-1.1.0.dist-info/METADATA

@@ -0,0 +1,86 @@
+Metadata-Version: 2.4
+Name: xmipp3_installer
+Version: 1.1.0
+Summary: Package to handle the installation of Xmipp3
+Author-email: Martín Salinas <ssalinasmartin@gmail.com>
+License: GPL-3.0-only
+Project-URL: Homepage, https://github.com/I2PC/xmipp3-installer
+Project-URL: Issues, https://github.com/I2PC/xmipp3-installer/issues
+Keywords: xmipp3,installer
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Operating System :: POSIX :: Linux
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: typing-extensions>=4.12
+Requires-Dist: distro>=1.9.0
+Provides-Extra: test
+Requires-Dist: pytest==8.*; extra == "test"
+Requires-Dist: pytest-cov==5.*; python_version < "3.9" and extra == "test"
+Requires-Dist: pytest-cov==6.*; python_version >= "3.9" and extra == "test"
+Requires-Dist: pytest-subprocess==1.*; extra == "test"
+Requires-Dist: pytest-localserver==0.*; extra == "test"
+Requires-Dist: ruff==0.*; extra == "test"
+Requires-Dist: cmake==4.*; extra == "test"
+Requires-Dist: ninja==1.*; extra == "test"
+Dynamic: license-file
+
+# xmipp3-installer
+Python package that handles the installation of [xmipp3](https://github.com/I2PC/xmipp).
+
+## Installation
+To install the package, simply run:
+```
+pip install xmipp3-installer
+```
+
+## Usage
+This package has a CLI built-in, with help messages that explain how to use it.
+To run such help, once the package is installed, run:
+```
+xmipp3_installer -h
+```
+
+## Testing the code
+In order to run the tests for this project, the project needs to be installed in development mode and also the test dependencies need to be installed.
+
+To do that, you need to clone this project, move inside the repository's folder, and run:
+```
+pip install -e .[test]
+```
+Once the dependencies have been installed, the automatic tests for this package can be run using `./scripts/run-tests.sh` in bash, or `.\scripts\run-tests.ps1` in PowerShell.
+If you intend to run this tests from within VSCode, you will need extension `Test Adapter Converter`, and a local `.vscode` folder with a file named `settings.json` inside with the following content:
+```json
+{
+  "python.testing.pytestArgs": [
+    ".",
+    "--capture=no"
+  ],
+  "python.testing.unittestEnabled": false,
+  "python.testing.pytestEnabled": true
+}
+```
+
+## SonarQube status
+[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=I2PC_xmipp3-installer&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=I2PC_xmipp3-installer)
+
+### Ratings
+[![Maintainability Rating](https://sonarcloud.io/api/project_badges/measure?project=I2PC_xmipp3-installer&metric=sqale_rating)](https://sonarcloud.io/summary/new_code?id=I2PC_xmipp3-installer)
+[![Reliability Rating](https://sonarcloud.io/api/project_badges/measure?project=I2PC_xmipp3-installer&metric=reliability_rating)](https://sonarcloud.io/summary/new_code?id=I2PC_xmipp3-installer)
+[![Security Rating](https://sonarcloud.io/api/project_badges/measure?project=I2PC_xmipp3-installer&metric=security_rating)](https://sonarcloud.io/summary/new_code?id=I2PC_xmipp3-installer)
+
+### Specific metrics
+[![Bugs](https://sonarcloud.io/api/project_badges/measure?project=I2PC_xmipp3-installer&metric=bugs)](https://sonarcloud.io/summary/new_code?id=I2PC_xmipp3-installer)
+[![Code Smells](https://sonarcloud.io/api/project_badges/measure?project=I2PC_xmipp3-installer&metric=code_smells)](https://sonarcloud.io/summary/new_code?id=I2PC_xmipp3-installer)
+[![Vulnerabilities](https://sonarcloud.io/api/project_badges/measure?project=I2PC_xmipp3-installer&metric=vulnerabilities)](https://sonarcloud.io/summary/new_code?id=I2PC_xmipp3-installer)
+[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=I2PC_xmipp3-installer&metric=coverage)](https://sonarcloud.io/summary/new_code?id=I2PC_xmipp3-installer)
+[![Duplicated Lines (%)](https://sonarcloud.io/api/project_badges/measure?project=I2PC_xmipp3-installer&metric=duplicated_lines_density)](https://sonarcloud.io/summary/new_code?id=I2PC_xmipp3-installer)
+[![Lines of Code](https://sonarcloud.io/api/project_badges/measure?project=I2PC_xmipp3-installer&metric=ncloc)](https://sonarcloud.io/summary/new_code?id=I2PC_xmipp3-installer)
+[![Technical Debt](https://sonarcloud.io/api/project_badges/measure?project=I2PC_xmipp3-installer&metric=sqale_index)](https://sonarcloud.io/summary/new_code?id=I2PC_xmipp3-installer)

xmipp3_installer-1.1.0.dist-info/RECORD

@@ -0,0 +1,70 @@
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{xmipp3_installer-1.0.1.dist-info → xmipp3_installer-1.1.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (76.0.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any