Master to devel

.github/workflows/build.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
       matrix:
         os:
-        - 'ubuntu-latest'
+        - 'ubuntu-22.04'
 
         cuda:
         - {version: '11.8.0', method: 'network'} 

CHANGELOG.md

@@ -1,4 +1,4 @@
-   ## Release 3.24.12 - Poseidon
+## Release 3.24.12.0 - Poseidon
    ### Xmipp Programs 
    - New programs
         - tomo_average_subtomos: This method carries out a subtomogram averaging. It means, given a set of subtomogram the program will estimate the average map
@@ -33,7 +33,7 @@
    - Fix for rare axis orderings in MRC/MAP files
    - Local average label added (used to measure the intensity of the particles in the original micrographs)
 
- ## Release 3.24.06 - Oceanus
+## Release 3.24.06 - Oceanus
    ### Xmipp Programs 
    - New programs
       - xtomo tigre reconstruction: This program provides a variety of algorithms to reconstruct tomogram from a set of tilt series
@@ -72,7 +72,7 @@
    - Adding fixed extension to tomo
 
 
- ## Release 3.23.11 - Nereus
+## Release 3.23.11 - Nereus
    ### Xmipp Programs 
 
    - New programs
@@ -151,7 +151,7 @@
 
 
 
-   ## Release 3.23.03 - Kratos
+## Release 3.23.03 - Kratos
    ### Xmipp Programs 
 
   - New programs: tomo_confidence_map, tomo_extract_particlestacks, tomo_extract_subtomograms, tomo_tiltseries_dose_filter, psd_estimatator

installer/api.py

@@ -34,7 +34,7 @@
 
 # Self imports
 from .cmake import parseCmakeVersions
-from .utils import runJob, getCurrentBranch, isBranchUpToDate, runParallelJobs
+from .utils import runJob, getCurrentName, isBranchUpToDate, runParallelJobs
 from .constants import (API_URL, LOG_FILE, TAIL_LOG_NCHARS, UNKNOWN_VALUE,
 	XMIPP_VERSIONS, XMIPP, VERSION_KEY, MASTER_BRANCHNAME, VERSION_FILE, CMAKE_PYTHON,
 	CMAKE_CUDA, CMAKE_MPI, CMAKE_HDF5, CMAKE_JPEG, CMAKE_SQLITE, CMAKE_JAVA,
@@ -124,7 +124,7 @@ def __getJSON(retCode: int=0) -> Optional[Dict]:
 	jsonData = runParallelJobs([
 		(getOSReleaseName, ()),
 		(__getCPUFlags, ()),
-		(getCurrentBranch, ()),
+		(getCurrentName, ()),
 		(isBranchUpToDate, ()),
 		(__getLogTail, ())
 	])

installer/constants/main.py

@@ -73,7 +73,7 @@
 # Other variables
 TAB_SIZE = 4
 SECTION_MESSAGE_LEN = 60
-TAG_BRANCH_NAME = 'HEAD'
+TAG_BRANCH_NAME = 'v3.24.12.0-Poseidon'
 
 # File names
 CONFIG_FILE = 'xmipp.conf'

installer/constants/parser.py

@@ -99,6 +99,7 @@
 PARAM_SHORT = 'short'
 PARAM_JOBS = 'jobs'
 PARAM_BRANCH = 'branch'
+PARAM_PRODUCTION = 'production'
 PARAM_MODELS_DIRECTORY = 'models-directory'
 PARAM_TEST_NAME = 'test-name'
 PARAM_SHOW_TESTS = 'show-tests'
@@ -126,6 +127,10 @@
 		LONG_VERSION: "--branch",
 		DESCRIPTION: "Branch for the source repositories."
 	},
+	PARAM_PRODUCTION: {
+		LONG_VERSION: "--production",
+		DESCRIPTION: "Flag to identify a production compilation (avoid the download of the plugin)."
+	},
 	PARAM_MODELS_DIRECTORY: {
 		SHORT_VERSION: "-d",
 		LONG_VERSION: "--directory",
@@ -178,7 +183,7 @@
 MODE_ARGS = {
 	MODE_VERSION: [PARAM_SHORT],
 	MODE_COMPILE_AND_INSTALL: [PARAM_JOBS, PARAM_BRANCH, PARAM_KEEP_OUTPUT],
-	MODE_ALL: [PARAM_JOBS, PARAM_BRANCH, PARAM_KEEP_OUTPUT],
+	MODE_ALL: [PARAM_JOBS, PARAM_BRANCH, PARAM_KEEP_OUTPUT, PARAM_PRODUCTION],
 	MODE_CONFIG_BUILD: [PARAM_KEEP_OUTPUT],
 	MODE_CONFIG: [PARAM_OVERWRITE],
 	MODE_GET_MODELS: [PARAM_MODELS_DIRECTORY],
@@ -207,6 +212,7 @@
 		'./xmipp',
 		f'./xmipp {MODE_ALL}',
 		f'./xmipp {PARAMS[PARAM_JOBS][SHORT_VERSION]} 20',
+		f'./xmipp {PARAMS[PARAM_PRODUCTION][LONG_VERSION]}',
 		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'

installer/constants/versions.py

@@ -28,9 +28,9 @@
 from .main import XMIPP, XMIPP_CORE, XMIPP_VIZ, XMIPP_PLUGIN
 
 # Xmipp's current versions
-__LATEST_RELEASE_NUMBER = '3.XX.YY.0'
-__LATEST_RELEASE_NAME = 'v3.XX.YY-TBD'
-RELEASE_DATE = 'dd/mm/yyyy'
+LATEST_RELEASE_NUMBER = '3.24.12.0'
+LATEST_RELEASE_NAME = 'v3.24.12.0-Poseidon'
+RELEASE_DATE = '23/12/2024'
 #####################################
 DEVEL_BRANCHNAME = 'devel'					
 MASTER_BRANCHNAME = 'master'				
@@ -39,20 +39,20 @@
 VERNAME_KEY = 'vername'							
 XMIPP_VERSIONS = {									
 	XMIPP: {													
-		VERSION_KEY: __LATEST_RELEASE_NUMBER,				
-		VERNAME_KEY: __LATEST_RELEASE_NAME  
+		VERSION_KEY: LATEST_RELEASE_NUMBER,
+		VERNAME_KEY: LATEST_RELEASE_NAME
 	},																
 	XMIPP_CORE: {											
-		VERSION_KEY: __LATEST_RELEASE_NUMBER,				
-		VERNAME_KEY: __LATEST_RELEASE_NAME  
+		VERSION_KEY: LATEST_RELEASE_NUMBER,
+		VERNAME_KEY: LATEST_RELEASE_NAME
 	},																
 	XMIPP_VIZ: {											
-		VERSION_KEY: __LATEST_RELEASE_NUMBER,				
-		VERNAME_KEY: __LATEST_RELEASE_NAME  
+		VERSION_KEY: LATEST_RELEASE_NUMBER,
+		VERNAME_KEY: LATEST_RELEASE_NAME
 	},																
 	XMIPP_PLUGIN: {										
-		VERSION_KEY: __LATEST_RELEASE_NUMBER,				
-		VERNAME_KEY: __LATEST_RELEASE_NAME  
+		VERSION_KEY: LATEST_RELEASE_NUMBER,
+		VERNAME_KEY: LATEST_RELEASE_NAME
 	}																	
 }																		
 #####################################

installer/main.py

@@ -30,18 +30,18 @@
 from typing import Tuple, Optional
 
 # Module imports
-from .utils import runJob, getCurrentBranch, isProductionMode
+from .utils import runJob, getCurrentBranch, isProductionMode, getCurrentName
 from .logger import logger, yellow, green, bold
 from .constants import (REPOSITORIES, XMIPP_SOURCES, SOURCES_PATH, MASTER_BRANCHNAME,
 	SOURCE_CLONE_ERROR, TAG_BRANCH_NAME, INTERRUPTED_ERROR, VERSION_FILE, RELEASE_DATE,
 	XMIPP_VERSIONS, XMIPP, VERSION_KEY, SECTION_MESSAGE_LEN, VERNAME_KEY, MODE_GET_SOURCES,
-	MODE_CONFIG_BUILD, CONFIG_FILE)
+	MODE_CONFIG_BUILD, CONFIG_FILE, XMIPP_PLUGIN)
 from .api import sendApiPOST, getOSReleaseName
 from .cmake import parseCmakeVersions
 from .config import getConfigDate
 
 ####################### COMMAND FUNCTIONS #######################
-def getSources(branch: str=None):
+def getSources(branch: str=None, production: bool=False):
 	"""
 	### This function fetches the sources needed for Xmipp to compile.
 
@@ -51,10 +51,13 @@ def getSources(branch: str=None):
 	# Clone or download internal sources
 	logger(getSectionMessage("Getting Xmipp sources"), forceConsoleOutput=True)
 	for source in XMIPP_SOURCES:
-		logger(f"Cloning {source}...", forceConsoleOutput=True)
-		retCode, output = __cloneSourceRepo(REPOSITORIES[source][0], path=SOURCES_PATH, branch=branch)
-		message = output if retCode else ''
-		handleRetCode(retCode, predefinedErrorCode=SOURCE_CLONE_ERROR, message=message, sendAPI=False)
+		if source == XMIPP_PLUGIN and production:
+			pass
+		else:
+			logger(f"Cloning {source}...", forceConsoleOutput=True)
+			retCode, output = __cloneSourceRepo(REPOSITORIES[source][0], path=SOURCES_PATH, branch=branch)
+			message = output if retCode else ''
+			handleRetCode(retCode, predefinedErrorCode=SOURCE_CLONE_ERROR, message=message, sendAPI=False)
 
 def exitXmipp(retCode: int=0):
 	"""
@@ -98,7 +101,7 @@ def getSuccessMessage() -> str:
 	- (str): Success message.
 	"""
 	# Getting release name
-	branchName = getCurrentBranch()
+	branchName = getCurrentName()
 	releaseName = branchName
 	if branchName is None or branchName == MASTER_BRANCHNAME:
 		releaseName = XMIPP_VERSIONS[XMIPP][VERSION_KEY]

installer/utils.py

@@ -35,6 +35,7 @@
 
 # Installer imports
 from .constants import XMIPP, VERNAME_KEY, XMIPP_VERSIONS, INTERRUPTED_ERROR
+from .constants.versions import LATEST_RELEASE_NAME
 from .logger import blue, red, logger
 
 ####################### RUN FUNCTIONS #######################
@@ -215,6 +216,24 @@ def isTag(dir: str='./') -> bool:
 	currentBranch = getCurrentBranch(dir=dir)
 	return not currentBranch or currentBranch == "HEAD"
 
+
+def getCurrentName():
+	"""
+	### This function returns the current branch of the repository of the given directory or the name of the tag.
+
+	#### Params:
+	- dir (str): Optional. Directory of the repository where the check will happen. Default is current directory.
+
+	#### Returns:
+	- (str): The name of the branch or the tag.
+	"""
+	if isTag():
+		return LATEST_RELEASE_NAME
+	else:
+		return getCurrentBranch()
+
+
+
 def isBranchUpToDate(dir: str='./') -> bool:
 	"""
 	### This function returns True if the current branch is up to date, or False otherwise or if some error happened.

xmipp

@@ -34,7 +34,7 @@ from installer.constants import (MODE_ALL, MODE_COMPILE_AND_INSTALL, MODE_CONFIG
 	CMAKE_CONFIGURE_ERROR, CMAKE_COMPILE_ERROR, CMAKE_INSTALL_ERROR, PARAM_LOGIN, PARAM_SHORT,
 	PARAM_JOBS, PARAM_BRANCH, PARAM_GIT_COMMAND, PARAM_TEST_PRO, PARAM_TEST_PRO, PARAM_TEST_FUNC, PARAM_MODEL_PATH,
 	PARAM_MODELS_DIRECTORY, PARAM_KEEP_OUTPUT, PARAM_SHOW_TESTS, PARAM_TEST_NAME, PARAM_UPDATE,
-	PARAM_OVERWRITE, BUILD_PATH, INSTALL_PATH, BUILD_TYPE, SOURCES_PATH, XMIPP_SOURCES, XMIPP,
+	PARAM_OVERWRITE, BUILD_PATH, INSTALL_PATH, BUILD_TYPE, SOURCES_PATH, XMIPP_SOURCES, XMIPP, PARAM_PRODUCTION,
 	LOG_FILE, CMAKE_ERROR, MODE_GET_SOURCES, VERSION_FILE, PARAMS, LONG_VERSION, SHORT_VERSION, SEND_INSTALLATION_STATISTICS)
 from installer.utils import runStreamingJob, runJob
 from installer.parser import ModeHelpFormatter, GeneralHelpFormatter, ErrorHandlerArgumentParser, getParamNames
@@ -87,9 +87,9 @@ def modeCleanBin():
 		userInput = ''
 		logger("", forceConsoleOutput=True)
 	if userInput == confirmationText:
-		runJob(f"find {SOURCES_PATH}/* -name \"*.so\" -exec rm -rf {{}} \;", showCommand=True)
-		runJob(f"find {SOURCES_PATH}/* -name \"*.os\" -exec rm -rf {{}} \;", showCommand=True)
-		runJob(f"find {SOURCES_PATH}/* -name \"*.o\" -exec rm -rf {{}} \;", showCommand=True)
+		runJob(f"find {SOURCES_PATH}/* -name \"*.so\" -exec rm -rf {{}}", showCommand=True)
+		runJob(f"find {SOURCES_PATH}/* -name \"*.os\" -exec rm -rf {{}}", showCommand=True)
+		runJob(f"find {SOURCES_PATH}/* -name \"*.o\" -exec rm -rf {{}}", showCommand=True)
 		runJob("find . -iname \"*.pyc\" -delete", showCommand=True)
 		runJob("find . -iname \"*.dblite\" -delete", showCommand=True)
 		runJob(f"find {os.path.join(SOURCES_PATH, XMIPP, 'applications', 'programs')} --type d -empty", showCommand=True)
@@ -221,7 +221,7 @@ def modeGetSources(args: argparse.Namespace):
 	- args (Namespace): Command line arguments parsed by argparse library.
 	"""
 	# Clone sources from specified branch
-	getSources(branch=args.branch)
+	getSources(branch=args.branch, production=args.production)
 
 def modeGit(args: argparse.Namespace):
 	"""
@@ -372,6 +372,7 @@ if __name__ == "__main__":
 	allSubparser = subparsers.add_parser(MODE_ALL, formatter_class=ModeHelpFormatter)
 	allSubparser.add_argument(*getParamNames(PARAM_JOBS), type=int, default=JOBS)
 	allSubparser.add_argument(*getParamNames(PARAM_BRANCH))
+	allSubparser.add_argument(*getParamNames(PARAM_PRODUCTION), type=bool, default=False)
 	allSubparser.add_argument(*getParamNames(PARAM_KEEP_OUTPUT), action='store_true')
 
 	# Arguments for mode 'cleanAll'