xmipp3-installer 1.0.1__tar.gz → 1.1.0__tar.gz

xmipp3_installer-1.1.0/PKG-INFO

@@ -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-1.0.1 → xmipp3_installer-1.1.0}/README.md

@@ -1,8 +1,27 @@
 # xmipp3-installer
-Python package that handles the installation of xmipp3
+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
-The automatic tests for this package can be run using `./scripts/run-tests.sh` in bash, or `.\scripts\run-tests.ps1` in PowerShell.
+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
 {

xmipp3_installer-1.1.0/pyproject.toml

@@ -0,0 +1,50 @@
+[project]
+name = "xmipp3_installer"
+version = "1.1.0"
+authors = [
+  { name = "Martín Salinas", email = "ssalinasmartin@gmail.com" },
+]
+description = "Package to handle the installation of Xmipp3"
+keywords = ["xmipp3", "installer"]
+classifiers = [
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
+  "Operating System :: POSIX :: Linux"
+]
+readme = "README.md"
+license = { text = "GPL-3.0-only" }
+
+requires-python = ">=3.8"
+dependencies = [
+  "typing-extensions>=4.12",
+  "distro>=1.9.0"
+]
+
+[build-system]
+requires = ["setuptools>=75.1", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project.optional-dependencies]
+test = [
+  "pytest==8.*",
+  "pytest-cov==5.*; python_version < '3.9'",
+  "pytest-cov==6.*; python_version >= '3.9'",
+  "pytest-subprocess==1.*",
+  "pytest-localserver==0.*",
+  "ruff==0.*",
+  "cmake==4.*",
+  "ninja==1.*"
+]
+
+[project.urls]
+Homepage = "https://github.com/I2PC/xmipp3-installer"
+Issues = "https://github.com/I2PC/xmipp3-installer/issues"
+
+[project.scripts]
+xmipp3_installer = "xmipp3_installer.__main__:main"

{xmipp3_installer-1.0.1 → xmipp3_installer-1.1.0}/src/xmipp3_installer/__main__.py

@@ -3,4 +3,4 @@
 from xmipp3_installer.application.cli.cli import main
 
 if __name__ == "__main__":
-    main()
+  main()

xmipp3_installer-1.1.0/src/xmipp3_installer/api_client/api_client.py

@@ -0,0 +1,51 @@
+"""### Contains an API client that registers the installation attempts."""
+
+import http.client
+import json
+from typing import Dict
+from urllib.parse import urlparse, ParseResult
+
+from xmipp3_installer.installer import urls
+from xmipp3_installer.application.logger.logger import logger
+
+def send_installation_attempt(installation_info: Dict):
+  """
+  ### Sends a POST request to Xmipp's metrics's API.
+  
+  #### Params:
+  - installation_info (dict): Dictionary containing all the installation information.
+  """
+  if installation_info is None:
+    return
+  params = json.dumps(installation_info)
+  headers = {"Content-type": "application/json"}
+  parsed_url = urlparse(urls.API_URL)
+  conn = None
+  try:
+    conn = __get_https_connection(parsed_url, 6)
+    conn.request("POST", parsed_url.path, body=params, headers=headers)
+    conn.getresponse()
+  except TimeoutError:
+    logger(
+      logger.yellow("There was a timeout while sending installation data."),
+      show_in_terminal=False
+    )
+  finally:
+    if conn is not None:
+      conn.close()
+
+
+def __get_https_connection(parsed_url: ParseResult, timeout_seconds: int) -> http.client.HTTPSConnection:
+  """
+  ### Establishes the connection needed to send the API call.
+  
+  Separated to enable integration & E2E tests.
+
+  #### Params:
+  - parsed_url (ParseResult): Object containing all elements of the url.
+  - timeout_seconds (int): Number of seconds to wait until a timeout.
+
+  #### Returns:
+  - (HTTPSConnection): Established connection.
+  """
+  return http.client.HTTPSConnection(parsed_url.hostname or "localhost", parsed_url.port, timeout=timeout_seconds)

xmipp3_installer-1.1.0/src/xmipp3_installer/api_client/assembler/installation_info_assembler.py

@@ -0,0 +1,176 @@
+"""### Contains functions to assemble the data dictionary required by the API client."""
+
+import getpass
+import hashlib
+import platform
+import re
+import os
+from typing import Optional, List, Dict
+
+import distro
+
+from xmipp3_installer.installer import constants, orquestrator
+from xmipp3_installer.installer.constants import paths
+from xmipp3_installer.installer.handlers import shell_handler, git_handler, versions_manager
+from xmipp3_installer.installer.handlers.cmake import cmake_constants, cmake_handler
+
+def get_installation_info(version_manager: versions_manager.VersionsManager, ret_code: int=0) -> Dict:
+  """
+  ### Creates a dictionary with the necessary data for the API POST message.
+  
+  #### Params:
+  - version_manager (VersionsManager): Object containing all the version-related info.
+  - ret_code (int): Optional. Return code for the API request.
+  
+  #### Return:
+  - (dict): Dictionary with the required info.
+  """
+  library_versions = cmake_handler.get_library_versions_from_cmake_file(
+    paths.LIBRARY_VERSIONS_FILE
+  )
+  environment_info = orquestrator.run_parallel_jobs(
+    [
+      __get_cpu_flags,
+      git_handler.get_current_branch,
+      git_handler.is_branch_up_to_date,
+      __is_installed_by_scipion,
+      __get_log_tail
+    ],
+    [(), (), (), (), ()]
+  )
+
+  return {
+    "user": {
+      "userId": __get_user_id()
+    },
+    "version": {
+      "os": get_os_release_name(),
+      "cpuFlags": environment_info[0],
+      "cuda": library_versions.get(cmake_constants.CMAKE_CUDA),
+      "cmake": library_versions.get(cmake_constants.CMAKE_CMAKE),
+      "gcc": library_versions.get(cmake_constants.CMAKE_GCC),
+      "gpp": library_versions.get(cmake_constants.CMAKE_GPP),
+      "mpi": library_versions.get(cmake_constants.CMAKE_MPI),
+      "python": library_versions.get(cmake_constants.CMAKE_PYTHON),
+      "sqlite": library_versions.get(cmake_constants.CMAKE_SQLITE),
+      "java": library_versions.get(cmake_constants.CMAKE_JAVA),
+      "hdf5": library_versions.get(cmake_constants.CMAKE_HDF5),
+      "jpeg": library_versions.get(cmake_constants.CMAKE_JPEG)
+    },
+    "xmipp": {
+      "branch": __get_installation_branch_name(
+        environment_info[1], version_manager
+      ),
+      "updated": environment_info[2],
+      "installedByScipion": environment_info[3]
+    },
+    "returnCode": ret_code,
+    "logTail": environment_info[4] if ret_code else None # Only needed if something went wrong
+  }
+
+def get_os_release_name() -> str:
+  """
+  ### Returns the name of the current system OS release.
+
+  #### Returns:
+  - (str): OS release name.
+  """
+  platform_system = platform.system()
+  if platform_system == "Linux":
+    return f"{distro.name()} {distro.version()}"
+  return f"{platform_system} {platform.release()}"
+
+def __get_installation_branch_name(branch_name: str, version_manager: versions_manager.VersionsManager) -> str:
+  """
+  ### Returns the branch or release name of Xmipp.
+
+  #### Params:
+  - branch_name (str): Retrieved branch name.
+  - version_manager (VersionsManager): Object containing all the version-related info.
+
+  #### Return:
+  - (str): Release name if Xmipp is in a release branch, or the branch name otherwise.
+  """
+  if not branch_name or branch_name == constants.MASTER_BRANCHNAME:
+    return version_manager.xmipp_version_number
+  return branch_name
+
+def __get_user_id() -> str:
+  """
+  ### Returns the unique user id for this machine.
+  
+  #### Returns:
+  - (str): User id, or 'Anoymous' if there were any errors.
+  """
+  identifier = __get_mac_address()
+  if not identifier:
+    identifier = getpass.getuser()
+    if not identifier:
+      return "Anonymous"
+  
+  sha256 = hashlib.sha256()
+  sha256.update(identifier.encode())
+  return sha256.hexdigest()
+
+def __get_cpu_flags() -> List[str]:
+  """
+  ### This function obtains the list of compilation flags supported by the CPU.
+
+  #### Returns:
+  - (list(str)): List of flags supported by the CPU.  
+  """
+  flags_header = "Flags:"
+  ret_code, flags_line = shell_handler.run_shell_command(f'lscpu | grep \"{flags_header}\"')
+  if ret_code:
+    return []
+  flags_line = flags_line.replace(flags_header, "").strip()
+  return [flag for flag in flags_line.split(" ") if flag]
+
+def __get_log_tail() -> Optional[str]:
+  """
+  ### Returns the last lines of the installation log.
+  
+  #### Returns:
+  - (str | None): Installation log's last lines, or None if there were any errors.
+  """
+  ret_code, output = shell_handler.run_shell_command(
+    f"tail -n {constants.TAIL_LOG_NCHARS} {paths.LOG_FILE}"
+  )
+  return output if ret_code == 0 else None
+
+def __get_mac_address() -> Optional[str]:
+  """
+  ### Returns a physical MAC address for this machine. It prioritizes ethernet over wireless.
+  
+  #### Returns:
+  - (str | None): MAC address, or None if there were any errors.
+  """
+  ret_code, output = shell_handler.run_shell_command("ip addr")
+  return __find_mac_address_in_lines(output.split('\n')) if ret_code == 0 else None
+
+def __find_mac_address_in_lines(lines: List[str]) -> Optional[str]:
+  """
+  ### Returns a physical MAC address within the text lines provided.
+
+  #### Params:
+  - lines (list(str)): Lines of text where MAC address should be looked for.
+  
+  #### Returns:
+  - (str | None): MAC address if found, None otherwise.
+  """
+  for line_index in range(len(lines) - 1):
+    match = re.match(r"^\d+: (enp|wlp|eth|ens|eno)\w+", lines[line_index])
+    if not match:
+      continue
+    mac_match = re.search(r"link/ether ([0-9a-f:]{17})", lines[line_index + 1])
+    if mac_match:
+      return mac_match.group(1)
+
+def __is_installed_by_scipion() -> bool:
+  """
+  ### Checks if the current xmipp installation is being carried out from Scipion.
+
+  #### Returns:
+  - (bool): True if the installation is executed by Scipion, False otherwise.
+  """
+  return bool(os.getenv("SCIPION_SOFTWARE"))

{xmipp3_installer-1.0.1 → xmipp3_installer-1.1.0}/src/xmipp3_installer/application/cli/arguments/__init__.py

@@ -1,8 +1,9 @@
 """### Containis all common constants needed for the argument parsing part of Xmipp's installation."""
 
+from xmipp3_installer.installer.constants import paths
+
 XMIPP_PROGRAM_NAME = "xmipp"
 
 # Other variables
 COMMON_USAGE_HELP_MESSAGE = 'Run \"./xmipp -h\" for usage help.'
-DEFAULT_BUILD_DIR = 'build'
-DEFAULT_MODELS_DIR = DEFAULT_BUILD_DIR
+DEFAULT_MODELS_DIR = paths.INSTALL_PATH

xmipp3_installer-1.1.0/src/xmipp3_installer/application/cli/arguments/modes.py

@@ -0,0 +1,147 @@
+"""### Containis all mode constants needed for the argument parsing part of Xmipp's installation."""
+
+from xmipp3_installer.application.cli import arguments
+from xmipp3_installer.application.cli.arguments.params import (
+  PARAM_SHORT, PARAM_JOBS, PARAM_BRANCH, PARAM_KEEP_OUTPUT, PARAM_OVERWRITE,
+  PARAM_MODELS_DIRECTORY, PARAM_TEST_NAMES, PARAM_SHOW_TESTS, PARAM_GIT_COMMAND,
+  PARAM_LOGIN, PARAM_MODEL_PATH, PARAM_UPDATE, PARAMS, PARAM_ALL_FUNCTIONS,
+  PARAM_ALL_PROGRAMS, SHORT_VERSION, LONG_VERSION
+)
+from xmipp3_installer.installer import urls, constants
+
+MODE = "mode"
+
+# Mode list (alphabetical order)
+MODE_ADD_MODEL = 'addModel'
+MODE_ALL = 'all'
+MODE_CLEAN_ALL = 'cleanAll'
+MODE_CLEAN_BIN = 'cleanBin'
+MODE_COMPILE_AND_INSTALL = 'compileAndInstall'
+MODE_CONFIG_BUILD = 'configBuild'
+MODE_CONFIG = 'config'
+MODE_GET_MODELS = 'getModels'
+MODE_GET_SOURCES = 'getSources'
+MODE_GIT = 'git'
+MODE_TEST = 'test'
+MODE_VERSION = 'version'
+
+# Modes with help message
+MODES = {
+  'General': {
+    MODE_VERSION: ['Returns the version information. Add \'--short\' to print only the version number.'],
+    MODE_COMPILE_AND_INSTALL: ['Compiles and installs Xmipp based on already obtained sources.'],
+    MODE_ALL: [f'Default param. Runs {MODE_CONFIG}, {MODE_CONFIG_BUILD}, and {MODE_COMPILE_AND_INSTALL}.'],
+    MODE_CONFIG_BUILD: ['Configures the project with CMake.']
+  },
+  'Config': {
+    MODE_CONFIG: ['Generates a config file template with default values.'],
+  },
+  'Downloads': {
+    MODE_GET_MODELS: [
+      f'Downloads the Deep Learning Models required by the DLTK tools at dir/models ({arguments.DEFAULT_MODELS_DIR} by default).',
+      f'Visit {urls.DLTK_DOCS_URL} for more details.'
+    ],
+    MODE_GET_SOURCES: [f'Clones Xmipp\'s source repositories {constants.XMIPP_CORE} & {constants.XMIPP_VIZ}.']
+  },
+  'Clean': {
+    MODE_CLEAN_BIN: ['Removes all compiled binaries.'],
+    MODE_CLEAN_ALL: ['Removes all compiled binaries and sources, leaves the repository as if freshly cloned (without pulling).']
+  },
+  'Test': {
+    MODE_TEST: [
+      'Runs Xmipp\'s tests.',
+      f'If used with \'{PARAMS[PARAM_TEST_NAMES][SHORT_VERSION]}\', only the tests provided will run.',
+      f'If used with \'{PARAMS[PARAM_SHOW_TESTS][LONG_VERSION]}\', a list the tests available and how to invoke them will be shown.',
+      f'If used with \'{PARAMS[PARAM_ALL_FUNCTIONS][LONG_VERSION]}\', all function tests will run.',
+      f'If used with \'{PARAMS[PARAM_ALL_PROGRAMS][LONG_VERSION]}\', all program tests will run.'
+    ]
+  },
+  'Developers': {
+    MODE_GIT: ['Runs the given git action for all source repositories.'],
+    MODE_ADD_MODEL: [
+      "Takes a DeepLearning model from the modelPath, makes a tgz of it and uploads the .tgz according to the <login>.",
+      "This mode is used to upload a model folder to the Scipion/Xmipp server.",
+      "Usually the model folder contains big files used to feed deep learning procedures "
+      "with pretrained data. All the models stored in the server will be downloaded "
+      "using the 'get_models' mode, during the compilation/installation time, "
+      "or with scipion3 installb deepLearningToolkit.",
+      "Param <modelsPath> must be an absolute path.",
+      "",
+      "Usage: -> ./xmipp addModel <usr@server> <modelsPath> [--update]",
+      "Steps:	0. modelName = basename(modelsPath) <- Please, check the folders name!",
+      "        1. Packing in 'xmipp_model_modelName.tgz'",
+      "        2. Check if that model already exists (use --update to override an existing model)",
+      "        3. Upload the model to the server.",
+      "        4. Update the MANIFEST file.",
+      "",
+      "The model name will be the folder name in <modelsPath>",
+      "Must have write permissions to such machine."
+    ]
+  }
+}
+
+# Arguments of each mode, sorted by group
+# Inside each mode, params are grouped by mutually exclusive groups
+# For example: MYMODE: [[PARAM1, PARAM2], [PARAM3, PARAM4]] would translate to
+# "mymode ([param1] [param2] | [param3] [param4])" in the general help message
+MODE_ARGS = {
+  MODE_VERSION: [PARAM_SHORT],
+  MODE_COMPILE_AND_INSTALL: [PARAM_JOBS, PARAM_KEEP_OUTPUT],
+  MODE_ALL: [PARAM_JOBS, PARAM_BRANCH, PARAM_KEEP_OUTPUT],
+  MODE_CONFIG_BUILD: [PARAM_KEEP_OUTPUT],
+  MODE_CONFIG: [PARAM_OVERWRITE],
+  MODE_GET_MODELS: [PARAM_MODELS_DIRECTORY],
+  MODE_GET_SOURCES: [PARAM_BRANCH, PARAM_KEEP_OUTPUT],
+  MODE_CLEAN_BIN: [],
+  MODE_CLEAN_ALL: [],
+  MODE_TEST: [[PARAM_TEST_NAMES], [PARAM_SHOW_TESTS], [PARAM_ALL_FUNCTIONS], [PARAM_ALL_PROGRAMS]],
+  MODE_GIT: [PARAM_GIT_COMMAND],
+  MODE_ADD_MODEL: [PARAM_LOGIN, PARAM_MODEL_PATH, PARAM_UPDATE]
+}
+
+# Examples for the help message of each mode
+MODE_EXAMPLES = {
+  MODE_VERSION: [
+    f'./xmipp {MODE_VERSION}',
+    f'./xmipp {MODE_VERSION} {PARAMS[PARAM_SHORT][LONG_VERSION]}',
+  ],
+  MODE_COMPILE_AND_INSTALL: [
+    f'./xmipp {MODE_COMPILE_AND_INSTALL}',
+    f'./xmipp {MODE_COMPILE_AND_INSTALL} {PARAMS[PARAM_JOBS][SHORT_VERSION]} 20',
+  ],
+  MODE_ALL: [
+    './xmipp',
+    f'./xmipp {MODE_ALL}',
+    f'./xmipp {PARAMS[PARAM_JOBS][SHORT_VERSION]} 20',
+    f'./xmipp {PARAMS[PARAM_BRANCH][SHORT_VERSION]} devel',
+    f'./xmipp {MODE_ALL} {PARAMS[PARAM_JOBS][SHORT_VERSION]} 20 '
+    f'{PARAMS[PARAM_BRANCH][SHORT_VERSION]} devel'
+  ],
+  MODE_CONFIG_BUILD: [],
+  MODE_CONFIG: [
+    f'./xmipp {MODE_CONFIG} {PARAMS[PARAM_OVERWRITE][LONG_VERSION]}'
+  ],
+  MODE_GET_MODELS: [
+    f'./xmipp {MODE_GET_MODELS}',
+    f'./xmipp {MODE_GET_MODELS} {PARAMS[PARAM_MODELS_DIRECTORY][SHORT_VERSION]} /path/to/my/model/directory'
+  ],
+  MODE_GET_SOURCES: [
+    f'./xmipp {MODE_GET_SOURCES}'
+    f'./xmipp {MODE_GET_SOURCES} {PARAMS[PARAM_BRANCH][SHORT_VERSION]} devel'
+  ],
+  MODE_CLEAN_BIN: [],
+  MODE_CLEAN_ALL: [],
+  MODE_TEST: [
+    f'./xmipp {MODE_TEST} xmipp_sample_test',
+    f'./xmipp {MODE_TEST} {PARAMS[PARAM_SHOW_TESTS][LONG_VERSION]}',
+    f'./xmipp {MODE_TEST} {PARAMS[PARAM_ALL_FUNCTIONS][LONG_VERSION]}',
+    f'./xmipp {MODE_TEST} {PARAMS[PARAM_ALL_PROGRAMS][LONG_VERSION]}'
+  ],
+  MODE_GIT: [
+    f'./xmipp {MODE_GIT} pull',
+    f'./xmipp {MODE_GIT} checkout devel'
+  ],
+  MODE_ADD_MODEL: [
+    f'./xmipp {MODE_ADD_MODEL} myuser@127.0.0.1 /home/myuser/mymodel'
+  ]
+}

xmipp3_installer-1.1.0/src/xmipp3_installer/application/cli/arguments/params.py

@@ -0,0 +1,86 @@
+"""### Containis all param constants needed for the argument parsing part of Xmipp's installation."""
+
+from xmipp3_installer.application.cli import arguments
+
+# Definition of all params found in the
+SHORT_VERSION = 'short'
+LONG_VERSION = 'long'
+DESCRIPTION = 'description'
+
+# Possible param list
+PARAM_SHORT = 'short'
+PARAM_JOBS = 'jobs'
+PARAM_BRANCH = 'branch'
+PARAM_MODELS_DIRECTORY = 'directory'
+PARAM_TEST_NAMES = 'testNames'
+PARAM_SHOW_TESTS = 'show'
+PARAM_ALL_FUNCTIONS = 'all_functions'
+PARAM_ALL_PROGRAMS = 'all_programs'
+PARAM_GIT_COMMAND = 'command'
+PARAM_LOGIN = 'login'
+PARAM_MODEL_PATH = 'modelPath'
+PARAM_UPDATE = 'update'
+PARAM_OVERWRITE = 'overwrite'
+PARAM_KEEP_OUTPUT = "keep_output"
+PARAMS = {
+  PARAM_SHORT: {
+    LONG_VERSION: "--short",
+    DESCRIPTION: "If set, only version number is shown."
+  },
+  PARAM_JOBS: {
+    SHORT_VERSION: "-j",
+    LONG_VERSION: "--jobs",
+    DESCRIPTION: "Number of jobs. Defaults to all available."
+  },
+  PARAM_BRANCH: {
+    SHORT_VERSION: "-b",
+    LONG_VERSION: "--branch",
+    DESCRIPTION: "Branch for the source repositories."
+  },
+  PARAM_MODELS_DIRECTORY: {
+    SHORT_VERSION: "-d",
+    LONG_VERSION: "--directory",
+    DESCRIPTION: f"Directory where models will be saved. Default is \"{arguments.DEFAULT_MODELS_DIR}\"."
+  },
+  PARAM_TEST_NAMES: {
+    SHORT_VERSION: PARAM_TEST_NAMES,
+    DESCRIPTION: "Name of the tests to run."
+  },
+  PARAM_SHOW_TESTS: {
+    LONG_VERSION: "--show",
+    DESCRIPTION: "Shows the tests available and how to invoke those."
+  },
+  PARAM_ALL_FUNCTIONS : {
+    LONG_VERSION: "--all-functions",
+    DESCRIPTION: "If set, all function tests will be run."
+  },
+  PARAM_ALL_PROGRAMS : {
+    LONG_VERSION: "--all-programs",
+    DESCRIPTION: "If set, all program tests will be run."
+  },
+  PARAM_GIT_COMMAND: {
+    SHORT_VERSION: PARAM_GIT_COMMAND,
+    DESCRIPTION: "Git command to run on all source repositories."
+  },
+  PARAM_LOGIN: {
+    SHORT_VERSION: "login",
+    DESCRIPTION: "Login (usr@server) for remote host to upload the model with. Must have write permissions to such machine."
+  },
+  PARAM_MODEL_PATH: {
+    SHORT_VERSION: PARAM_MODEL_PATH,
+    DESCRIPTION: "Path to the model to upload to remote host."
+  },
+  PARAM_UPDATE: {
+    LONG_VERSION: "--update",
+    DESCRIPTION: "Flag to update an existing model"
+  },
+  PARAM_OVERWRITE: {
+    SHORT_VERSION: "-o",
+    LONG_VERSION: "--overwrite",
+    DESCRIPTION: "If set, current config file will be overwritten with a new one."
+  },
+  PARAM_KEEP_OUTPUT: {
+    LONG_VERSION: "--keep-output",
+    DESCRIPTION: "If set, output sent through the terminal won't substitute lines, looking more like the log."
+  }
+}