Enabled test mode in installer

.github/workflows/build.yml

@@ -61,7 +61,6 @@ jobs:
       - name: Compile Xmipp will all dependencies in branch ${{ github.head_ref }} (if such branch exists, default is devel)
         env:
           BRANCH_NAME: ${{ github.head_ref }}
-          SEND_INSTALLATION_STATISTICS: OFF 
         run: |
-          echo "XMIPP_LINK_TO_SCIPION=OFF" > xmipp.conf
+          echo -e "XMIPP_LINK_TO_SCIPION=OFF\nSEND_INSTALLATION_STATISTICS=OFF" > xmipp.conf
           ./xmipp all -b $BRANCH_NAME --keep-output || (cat compilation.log && false)

cmake/xmipp.bashrc.in

@@ -7,6 +7,7 @@ export LD_LIBRARY_PATH=@XMIPP_HOME@/@CMAKE_INSTALL_LIBDIR@:@XMIPP_HOME@/bindings
 export PYTHONPATH=@XMIPP_HOME@/bindings/python:@XMIPP_HOME@/pylib:$PYTHONPATH
 export MATLABPATH=@XMIPP_HOME@/bindings/matlab:$MATLABPATH
 export XMIPP_SRC=@PROJECT_SOURCE_DIR@/src
+export XMIPP_TEST_DATA=@PROJECT_SOURCE_DIR@/src/xmipp/tests/data
 
 alias x='xmipp'
 alias xsj='xmipp_showj'

installer/constants/errors.py

@@ -38,6 +38,7 @@
 CMAKE_COMPILE_ERROR = 5
 CMAKE_INSTALL_ERROR = 6
 IO_ERROR = 7
+ENVIROMENT_ERROR = 8
 
 # Error messages
 __CHECK_LOG_MESSAGE = f'Check the inside file \'{LOG_FILE}\'.'
@@ -49,5 +50,7 @@
 	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.']
+	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.'],
+ENVIROMENT_ERROR: ['XMIPP_SRC is not in the enviroment. To run the tests you need to run: source dist/xmipp.bashrc', '']
+
 }

installer/constants/parser.py

@@ -101,12 +101,15 @@
 PARAM_MODELS_DIRECTORY = 'models-directory'
 PARAM_TEST_NAME = 'test-name'
 PARAM_SHOW_TESTS = 'show-tests'
+PARAM_TEST_PRO = 'allPrograms'
+PARAM_TEST_FUNC = 'allFuncs'
 PARAM_GIT_COMMAND = 'git-command'
 PARAM_LOGIN = 'login'
 PARAM_MODEL_PATH = 'model-path'
 PARAM_UPDATE = 'update'
 PARAM_OVERWRITE = 'overwrite'
 PARAM_KEEP_OUTPUT = "keep-output"
+
 PARAMS = {
 	PARAM_SHORT: {
 		LONG_VERSION: "--short",
@@ -131,6 +134,14 @@
 		SHORT_VERSION: "testName",
 		DESCRIPTION: "Run certain test. If combined with --show, greps the test name from the test list."
 	},
+	PARAM_TEST_PRO: {
+		LONG_VERSION: "--allPrograms",
+		DESCRIPTION: "If set, all test available will be run."
+	},
+	PARAM_TEST_FUNC: {
+		LONG_VERSION: "--allFuncs",
+		DESCRIPTION: "If set, all function test available will be run."
+	},
 	PARAM_SHOW_TESTS: {
 		LONG_VERSION: "--show",
 		DESCRIPTION: "Shows the tests available and how to invoke those."
@@ -173,7 +184,7 @@
 	MODE_GET_SOURCES: [PARAM_BRANCH, PARAM_KEEP_OUTPUT],
 	MODE_CLEAN_BIN: [],
 	MODE_CLEAN_ALL: [],
-	MODE_TEST: [PARAM_TEST_NAME, PARAM_SHOW_TESTS],
+	MODE_TEST: [PARAM_TEST_NAME, PARAM_SHOW_TESTS, PARAM_TEST_FUNC, PARAM_TEST_PRO],
 	MODE_GIT: [PARAM_GIT_COMMAND],
 	MODE_ADD_MODEL: [PARAM_LOGIN, PARAM_MODEL_PATH, PARAM_UPDATE]
 }
@@ -215,7 +226,10 @@
 	MODE_CLEAN_ALL: [],
 	MODE_TEST: [
 		f'./xmipp {MODE_TEST} xmipp_sample_test',
-		f'./xmipp {MODE_TEST} {PARAMS[PARAM_SHORT][LONG_VERSION]}',
+		f'./xmipp {MODE_TEST} {PARAMS[PARAM_SHOW_TESTS][LONG_VERSION]}',
+		f'./xmipp {MODE_TEST} {PARAMS[PARAM_TEST_FUNC][LONG_VERSION]}',
+		f'./xmipp {MODE_TEST} {PARAMS[PARAM_TEST_PRO][LONG_VERSION]}',
+
 	],
 	MODE_GIT: [
 		f'./xmipp {MODE_GIT} pull',

installer/test.py

@@ -0,0 +1,85 @@
+# ***************************************************************************
+# * Authors:		Alberto Garcia ([email protected])
+# *
+# *
+# * This program is free software; you can redistribute it and/or modify
+# * it under the terms of the GNU General Public License as published by
+# * the Free Software Foundation; either version 2 of the License, or
+# * (at your option) any later version.
+# *
+# * This program is distributed in the hope that it will be useful,
+# * but WITHOUT ANY WARRANTY; without even the implied warranty of
+# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# * GNU General Public License for more details.
+# *
+# * You should have received a copy of the GNU General Public License
+# * along with this program; if not, write to the Free Software
+# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+# * 02111-1307 USA
+# *
+# * All comments concerning this program package may be sent to the
+# * e-mail address '[email protected]'
+# ***************************************************************************/
+"""
+This module contains the necessary functions to run and manage the test.
+"""
+
+# General imports
+from os import environ, path
+
+# Self imports
+from .constants import XMIPP, SCIPION_TESTS_URLS, CONFIG_FILE, XMIPP_USE_CUDA, XMIPP_LINK_TO_SCIPION, ENVIROMENT_ERROR
+from .logger import blue, red, logger
+from .utils import runJob, runStreamingJob
+from .config import readConfig
+from .main import handleRetCode
+
+####################### COMMAND FUNCTIONS #######################
+
+
+def runTests(testNames):
+	"""
+	### This function fetches the sources needed for Xmipp to compile.
+
+	#### Params:
+	- branch (str): Optional. Branch to clone the sources from.
+	"""
+	xmippSrc = environ.get('XMIPP_SRC', None)
+	if xmippSrc and path.isdir(xmippSrc):
+		environ['PYTHONPATH'] = ':'.join([
+            path.join(environ['XMIPP_SRC'], XMIPP),
+            environ.get('PYTHONPATH', '')])
+		testsPath = path.join(environ['XMIPP_SRC'], XMIPP, 'tests')
+		dataSetPath = path.join(testsPath, 'data')
+
+	else:
+		handleRetCode(ENVIROMENT_ERROR, predefinedErrorCode=ENVIROMENT_ERROR, sendAPI=False)
+
+	# downloading/updating the dataset
+	dataset = 'xmipp_programs'
+	if path.isdir(dataSetPath):
+		logger(blue("Updating the test files"))
+		task = "update"
+		showO = False
+	else:
+		logger(blue("Downloading the test files"))
+		task = "download"
+		showO = True
+	args = "%s %s %s" % ("tests/data", SCIPION_TESTS_URLS, dataset)
+	runJob("bin/xmipp_sync_data %s %s" % (task, args), cwd='src/xmipp', showOutput=showO)
+
+	configDict = readConfig(CONFIG_FILE) if path.exists(CONFIG_FILE) else {}
+	CUDA = configDict.get(XMIPP_USE_CUDA)
+	noCudaStr = '--noCuda' if CUDA == 'OFF' else ''
+
+	logger(" Tests to do: %s" % ', '.join(testNames))
+
+	# if configDict.get(XMIPP_LINK_TO_SCIPION) == 'ON':
+	# 	pythonExe = 'scipion3 python'
+	# else:
+	# 	pythonExe = 'python3'
+
+	pythonExe = 'python3' #TODO should be scipion3?
+	testScripts = path.dirname(environ['XMIPP_TEST_DATA'])
+	runStreamingJob(cmd="%s test.py %s %s" % (pythonExe, testNames, noCudaStr), cwd=testScripts, showOutput=True, showError=True)
+

src/xmipp/tests/test.py

@@ -37,14 +37,6 @@
 import shutil
 from traceback import format_exception
 
-VAHID = "vahid"
-RM = 'rmarabini'
-COSS = 'coss'
-JMRT = 'delarosatrevin'
-JOTON = 'joton'
-DISCONTINUED = 'nobody'
-JMOTA = 'javimota'
-EFG = 'estrellafg'
 
 
 class Command(object):
@@ -75,7 +67,7 @@ class ProgramTest(unittest.TestCase):
     _timeout = 300
 
     # _labels = [WEEKLY]
-               
+
     @classmethod
     def setTestDir(cls, newTestDir):
         cls._testDir = newTestDir
@@ -93,12 +85,12 @@ def _parseArgs(self, args):
         args = args.replace("%o", self.outputDir)
         args = args.replace("%p", self.program)
         #args = args.replace("%d", self.fnDir)
-        return args     
+        return args
 
     def _runCommands(self, cmdList, cmdType):
         """ Run several commands.
         Params:
-            cmdList: the list of commands to execute. 
+            cmdList: the list of commands to execute.
             cmdType: either 'preruns' or 'postruns'
         """
         pipe = '>'
@@ -113,7 +105,7 @@ def _runCommands(self, cmdList, cmdType):
                 pipe = ">>"
                 sys.stdout.flush()
 
-    def runCase(self, args, mpi=0, changeDir=False, 
+    def runCase(self, args, mpi=0, changeDir=False,
                 preruns=None, postruns=None, validate=None,
                 outputs=None, random=False, errorthreshold=0.001):
         # Retrieve the correct case number from the test name id
@@ -222,18 +214,15 @@ def __init__(self):
         unittest.TestResult.__init__(self)
         self.startTimeAll = time.time()
 
-    def openXmlReport(self, classname, filename):
-        # self.xml = open(filename, 'w')
-        # self.xml.write('<testsuite name="%s">\n' % classname)
-        pass
-
     def doReport(self):
         secs = time.time() - self.startTimeAll
         sys.stderr.write("%s run %d tests (%0.3f secs)\n" %
                          (green("[==========]"), self.numberTests, secs))
+        sys.stderr.flush()
         if self.testFailed:
             sys.stderr.write(red("[  FAILED  ]") + " %d tests\n" % self.testFailed)
-        sys.stderr.write(green("[  PASSED  ]") + " %d tests" % (self.numberTests - self.testFailed))
+        sys.stderr.write(green("[  PASSED  ]") + " %d tests\n" % (self.numberTests - self.testFailed))
+        sys.stderr.flush()
         sys.stdout.flush()
         return -1 if self.testFailed else 0
 
@@ -246,6 +235,9 @@ def toc(self):
     def startTest(self, test):
         self.tic()
         self.numberTests += 1
+        sys.stderr.write(
+	        "%s %s\n" % (green('[ RUN      ]'), self.getTestName(test)))
+        sys.stderr.flush()
 
     def getTestName(self, test):
         parts = str(test).split()
@@ -257,19 +249,20 @@ def getTestName(self, test):
     def addSuccess(self, test):
         secs = self.toc()
         sys.stderr.write("%s %s (%0.3f secs)\n\n" % (green('[ RUN   OK ]'), self.getTestName(test), secs))
+        sys.stderr.flush()
 
     def reportError(self, test, err):
         sys.stderr.write("\n%s" % ("".join(format_exception(*err))))
-        sys.stderr.write("%s %s\n\n" % (red('[  FAILED  ]'),
-                                      self.getTestName(test)))
+        sys.stderr.write("%s %s\n\n" % (red('[  FAILED  ]'), self.getTestName(test)))
+        sys.stderr.flush()
         self.testFailed += 1
 
     def addError(self, test, err):
         self.reportError(test, err)
 
     def addFailure(self, test, err):
         self.reportError(test, err)
-
+	    
 def green(text):
     return "\033[92m "+text+"\033[0m"
 
@@ -287,7 +280,6 @@ def createDir(dirname, clean=False):
         shutil.rmtree(dirname)
     os.makedirs(dirname)
 
-
 def visitTests(tests, grepStr=''):
     """ Show the list of tests available """
 
@@ -309,7 +301,6 @@ def visitTests(tests, grepStr=''):
     lastModule = None
 
     grepPrint = '' if grepStr == '' else red(' (grep: %s)'%grepStr)
-
     for t in testsFlat:
         moduleName, className, testName = t.id().rsplit('.', 2)
 
@@ -330,30 +321,24 @@ def visitTests(tests, grepStr=''):
 
 
 if __name__ == "__main__":
-
     cudaTests = True
     for i, arg in enumerate(sys.argv):
         if arg == '--noCuda':
             cudaTests = False
             sys.argv.pop(i)
-
     testNames = sys.argv[1:]
-
     cudaExcludeStr = '| grep -v xmipp_test_cuda_' if not cudaTests else ''
     cTests = subprocess.check_output('compgen -ac | grep xmipp_test_ %s' % cudaExcludeStr,
                                      shell=True, executable='/bin/bash').decode('utf-8').splitlines()
-
+    
     tests = unittest.TestSuite()
     if '--show' in testNames or '--allPrograms' in testNames:
-        # tests.addTests(unittest.defaultTestLoader.discover(os.environ.get("XMIPP_TEST_DATA")+'/..',
-        #                pattern='test*.py'))#,top_level_dir=os.environ.get("XMIPP_TEST_DATA")+'/..'))
-        listDir = os.listdir(os.environ.get("XMIPP_TEST_DATA")+'/..')
-        for path in listDir:
-            if path.startswith('test_') and path.endswith('.py'):
-                tests.addTests(unittest.defaultTestLoader.loadTestsFromName('tests.' + path[:-3]))
-
+        testData = os.environ['XMIPP_TEST_DATA']
+        testScripts = os.path.dirname(testData)
+        tests.addTests(unittest.defaultTestLoader.discover(start_dir=testScripts, pattern='test*.py', top_level_dir=testScripts + '/..'))
+
         if '--show' in testNames:
-            print(blue("\n    > >  You can run any of the following tests by:\n"))
+            print(blue("\n >>  You can run any of the following tests by:\n"))
             grepStr = '' if len(testNames)<2 else testNames[1]
             visitTests(tests, grepStr)
             print("\n - From applications/function_tests (to run all use --allFuncs):")
@@ -362,7 +347,8 @@ def visitTests(tests, grepStr=''):
         elif '--allPrograms' in testNames:
             result = GTestResult()
             tests.run(result)
-            sys.exit(result.doReport())
+            result.doReport()
+            sys.exit(0)
     elif '--allFuncs' in testNames:
         xmippBinDir = os.path.join(os.environ.get("XMIPP_SRC"), 'xmipp', 'bin')
         errors = []
@@ -400,4 +386,6 @@ def visitTests(tests, grepStr=''):
 
             result = GTestResult()
             tests.run(result)
-            sys.exit(result.doReport())
+            result.doReport()
+            sys.exit(0)
+

src/xmipp/tests/test_programs.py

@@ -20,16 +20,22 @@
 # *  All comments concerning this program package may be sent to the
 # *  e-mail address '[email protected]'
 # ***************************************************************************/
-
+VAHID = "vahid"
+RM = 'rmarabini'
+COSS = 'coss'
+JMRT = 'delarosatrevin'
+JOTON = 'joton'
+DISCONTINUED = 'nobody'
+JMOTA = 'javimota'
+EFG = 'estrellafg'
 
 # import math
 import os
 
 # import pyworkflow.utils as pwutils
 # import xmipp3
 # from pyworkflow.tests import DataSet
-from tests.test import *
-
+from tests.test import ProgramTest
 
 
 class XmippProgramTest(ProgramTest):