smodels 3.0.2__tar.gz → 3.0.3__tar.gz

{smodels-3.0.2 → smodels-3.0.3}/Makefile

@@ -70,18 +70,33 @@ builddeb: buildrpm
 
 pypi: clean
 	## pypi user is walten, repository is https://upload.pypi.org/legacy/
+	python -m pip install build
 	rm -rf dist
-	python3 setup.py sdist bdist_wheel
+#	python3 setup.py sdist bdist_wheel
+	python -m build .
+	twine check --strict dist/*
 	twine upload dist/smodels-*.tar.gz
 
 testpypi: clean
 	## testpypi user is smodels, repository is https://test.pypi.org/legacy/
-	# to install from testpypi: 
+	# to install from testpypi:
+	# pip3 install --user --upgrade --index-url https://test.pypi.org/simple/ smodels
+	python -m pip install build
+	rm -rf dist
+#python3 setup.py sdist bdist_wheel
+	python -m build .
+	twine check --strict dist/*
+	twine upload -r pypitest dist/smodels-*.tar.gz
+
+testpypiold: clean
+	## testpypi user is smodels, repository is https://test.pypi.org/legacy/
+	# to install from testpypi:
 	# pip3 install --user --upgrade --index-url https://test.pypi.org/simple/ smodels
 	rm -rf dist
 	python3 setup.py sdist bdist_wheel
 	twine upload -r pypitest dist/smodels-*.tar.gz
 
+
 tarballs:
 	cd distribution && make tarballs
 

{smodels-3.0.2/smodels.egg-info → smodels-3.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: smodels
-Version: 3.0.2
+Version: 3.0.3
 Summary: A tool for interpreting simplified-model results from the LHC
 Home-page: http://smodels.github.io/
 Author: The SModelS collaboration, smodels-users@lists.oeaw.ac.at Current members: Mohammad Mahdi Altakach, Sabine Kraml, Andre Lessa, Sahana Narashima, Timothee Pascal, Camila Ramos, Humberto Reyes-Gonzalez, Theo Reymermier, Yoxara Villamizar, Wolfgang Waltenberger  Previously involved in SModelS: Gael Alguero, Federico Ambrogi, Juhi Dutta, Jan Heisig, Charanjit K. Khosa, Suchita Kulkarni, Ursula Laa, Veronika Magerl, Wolfgang Magerl, Philipp Neuhuber, Doris Proschofsky, Jory Sonneveld, Michael Traub, Matthias Wolf, Alicia Wongel
@@ -10,6 +10,8 @@ Keywords: simplified models LHC BSM theories interpretation supersymmetry UEDs
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
 Requires-Dist: docutils>=0.3
 Requires-Dist: numpy>=1.22.0
 Requires-Dist: scipy>=1.0.0
@@ -20,12 +22,26 @@ Requires-Dist: pyslha>=3.1.0
 Requires-Dist: pyhf>=0.6.1
 Requires-Dist: jsonpatch>=1.25
 Requires-Dist: jsonschema>=3.2.0
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 .. image:: https://smodels.github.io/pics/banner.png
 
 .. |PyPI version| image:: https://badge.fury.io/py/smodels.svg
    :target: https://badge.fury.io/py/smodels
 
+.. |Anaconda version| image:: https://anaconda.org/conda-forge/smodels/badges/version.svg
+   :target: https://anaconda.org/conda-forge/smodels/
+
 .. |GitHub Project| image:: https://img.shields.io/badge/GitHub--blue?style=social&logo=GitHub
    :target: https://github.com/SModelS
 
@@ -41,7 +57,7 @@ Requires-Dist: jsonschema>=3.2.0
 .. |Colab| image:: https://colab.research.google.com/assets/colab-badge.svg
    :target: https://colab.research.google.com/github/SModelS/tutorials/blob/main/index.ipynb
 
-|GitHub Project| |PyPI version| |CodeFactor| |Colab| |Docs|
+|GitHub Project| |PyPI version| |Anaconda version| |CodeFactor| |Colab| |Docs|
 
 ==============
 SModelS v3

{smodels-3.0.2/smodels → smodels-3.0.3}/README.rst

@@ -3,6 +3,9 @@
 .. |PyPI version| image:: https://badge.fury.io/py/smodels.svg
    :target: https://badge.fury.io/py/smodels
 
+.. |Anaconda version| image:: https://anaconda.org/conda-forge/smodels/badges/version.svg
+   :target: https://anaconda.org/conda-forge/smodels/
+
 .. |GitHub Project| image:: https://img.shields.io/badge/GitHub--blue?style=social&logo=GitHub
    :target: https://github.com/SModelS
 
@@ -18,7 +21,7 @@
 .. |Colab| image:: https://colab.research.google.com/assets/colab-badge.svg
    :target: https://colab.research.google.com/github/SModelS/tutorials/blob/main/index.ipynb
 
-|GitHub Project| |PyPI version| |CodeFactor| |Colab| |Docs|
+|GitHub Project| |PyPI version| |Anaconda version| |CodeFactor| |Colab| |Docs|
 
 ==============
 SModelS v3

smodels-3.0.3/pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"

{smodels-3.0.2 → smodels-3.0.3}/setup.py

@@ -128,6 +128,7 @@ setup(
                            'runSModelS.py=smodels.tools.runSModelS:main',
                            'smodelsTools.py=smodels.tools.smodelsTools:main' ]
     },
+    python_requires='>=3.8',
     install_requires=requirements(),
     data_files=dataFiles() ,
     description=("A tool for interpreting simplified-model results from the "
@@ -142,12 +143,14 @@ setup(
               'smodels.decomposition',
               'smodels.matching',
               'smodels.tools',
+              'smodels.tools.printers',
               'smodels.base',
               'smodels.statistics',
               'smodels.experiment'],
     include_package_data = True,
-    test_suite='test',
+    test_suite='unittests',
     long_description=read('smodels/README.rst'),
+    long_description_content_type="text/x-rst",
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Topic :: Scientific/Engineering :: Physics",

{smodels-3.0.2 → smodels-3.0.3/smodels}/README.rst

@@ -3,6 +3,9 @@
 .. |PyPI version| image:: https://badge.fury.io/py/smodels.svg
    :target: https://badge.fury.io/py/smodels
 
+.. |Anaconda version| image:: https://anaconda.org/conda-forge/smodels/badges/version.svg
+   :target: https://anaconda.org/conda-forge/smodels/
+
 .. |GitHub Project| image:: https://img.shields.io/badge/GitHub--blue?style=social&logo=GitHub
    :target: https://github.com/SModelS
 
@@ -18,7 +21,7 @@
 .. |Colab| image:: https://colab.research.google.com/assets/colab-badge.svg
    :target: https://colab.research.google.com/github/SModelS/tutorials/blob/main/index.ipynb
 
-|GitHub Project| |PyPI version| |CodeFactor| |Colab| |Docs|
+|GitHub Project| |PyPI version| |Anaconda version| |CodeFactor| |Colab| |Docs|
 
 ==============
 SModelS v3

{smodels-3.0.2 → smodels-3.0.3}/smodels/experiment/databaseObj.py

@@ -473,7 +473,7 @@ class SubDatabase(object):
                     self.loadBinaryFile(lastm_only=False)
         except Exception as e:
             import traceback
-            logger.error ( "when loading database: {e}, {traceback.format_exc()}" )
+            logger.error ( f"when loading database: {e}, {traceback.format_exc()}" )
             sys.exit(-1)
 
     def loadTextDatabase(self):

{smodels-3.0.2 → smodels-3.0.3}/smodels/installation.py

@@ -40,7 +40,7 @@ def test_requirements():
             return False
     return True
 
-def resolve_dependencies( as_user = True ):
+def resolve_dependencies( as_user = True, verbose = True ):
     """ method that is meant to resolve the SModelS dependencies,
     via pip install --user. Warns you if pip cannot be found.
     :params as_user: if False, try system-wide install.
@@ -54,8 +54,10 @@ def resolve_dependencies( as_user = True ):
     try:
         import pip
     except (ModuleNotFoundError,ImportError) as e:
-        print ( "error: pip not found. cannot install requirements. Maybe try easy_install pip" )
-        sys.exit()
+        if verbose:
+            print ( "warning: pip not found. cannot install requirements. Maybe try easy_install pip" )
+        return
+        # sys.exit()
     cmd = [ sys.executable, '-m', 'pip', 'install', '--upgrade', '-r', req ]
     if as_user:
         o = subprocess.getoutput ( " ".join ( [ sys.executable, '-m', 'pip', 'install', '--user', '--dry-run', 'pyslha' ] ) )
@@ -184,7 +186,7 @@ def banner():
 def fixpermissions():
     """ make sure that all filepermissions are such that
         we can compile the wrappers for pythia and nllfast. """
-    from smodels.tools.smodelsLogging import logger
+    from smodels.base.smodelsLogging import logger
     import glob
     Dir = "%ssmodels/lib/" % installDirectory()
     try:
@@ -208,7 +210,7 @@ def databasePath ( label ):
     :returns: URL, e.g. https://smodels.github.io/database/official
     """
     if not label in __dblabels__:
-        from smodels.tools.smodelsLogging import logger
+        from smodels.base.smodelsLogging import logger
         logger.warning ( "cannot identify label %s" % label )
         return label
     if label == None:

{smodels-3.0.2 → smodels-3.0.3}/smodels/statistics/speyTools.py

@@ -2,7 +2,7 @@
 
 """
 .. module:: speyTools
-   :synopsis: a module that contains tools and convenience methods 
+   :synopsis: a module that contains tools and convenience methods
               that we use in connection with spey.
 
 .. moduleauthor:: Wolfgang Waltenberger <wolfgang.waltenberger@gmail.com>
@@ -28,7 +28,7 @@ class SpeyComputer:
     __slots__ = [ "speyModels", "dataset", "backendType", "nsig",
                   "model_index" ]
 
-    def __init__ ( self, dataset, backendType : str, nsig : Union[float,list], 
+    def __init__ ( self, dataset, backendType : str, nsig : Union[float,list],
                    deltas_rel : Union[None,float] = None ):
         """ initialise with dataset.
         :param dataset: a smodels (combined)dataset, or a onnx file (for now, will change)
@@ -50,8 +50,8 @@ class SpeyComputer:
         """ retrieve the statistical model """
         assert self.backendType in [ "1bin", "SL", "ML", "pyhf" ], f"unknown backend type {self.backendType}"
         if hasattr ( self.dataset.globalInfo, "onnxFile" ):
-            # an onnxfile is defined, we use it!  
-            return self.getNNModel ( nsig ) 
+            # an onnxfile is defined, we use it!
+            return self.getNNModel ( nsig )
         if self.backendType == "pyhf":
             return self.getStatModelsPyhf ( nsig )
         if self.dataset.getType() == "efficiencyMap":
@@ -62,11 +62,12 @@ class SpeyComputer:
     def create ( cls, dataset : DataSet, xsection : XSection,
                  predictions, deltas_rel : float ):
         """ generic entry point for theoryPrediction. given the
-            data, create the appropriate SpeyComputer 
+            data, create the appropriate SpeyComputer
+
         :param dataset: the dataset to create the stats model for
         :param xsection: the cross section, needed just as a scale factor
         :param predictions: the individual predictions, in case of multiple SRs
-        for e.g. upper limits on them
+            for e.g. upper limits on them
         """
         dataType = dataset.getType()
         if dataType == "upperLimit":
@@ -120,10 +121,10 @@ class SpeyComputer:
         :deltas_rel: Relative uncertainty for the signal
 
         :returns: a SpeyComputer
-        """        
-        computer = SpeyComputer(dataset=dataset, backendType="1bin", 
+        """
+        computer = SpeyComputer(dataset=dataset, backendType="1bin",
                                 nsig=nsig, deltas_rel=deltas_rel)
-        
+
         return computer
 
     @classmethod
@@ -136,14 +137,14 @@ class SpeyComputer:
 
         :returns: a StatsComputer
         """
-        
-        computer = SpeyComputer(dataset=dataset,  
-                                backendType="SL", 
+
+        computer = SpeyComputer(dataset=dataset,
+                                backendType="SL",
                                  nsig=nsig, deltas_rel=deltas_rel)
         return computer
 
     def getNNModel ( self, nsig ):
-        """ here is the code for how we create a spey speyModel that uses an NN 
+        """ here is the code for how we create a spey speyModel that uses an NN
             as its backend """
         #For the moment, the ml-likelihood backned has to be dowanloaded and installed manually. In the future, the backend could be directly embedded and installed in SmodelS.
 #        import sys
@@ -153,13 +154,13 @@ class SpeyComputer:
 #        sys.path.append(MLlikePath)
         import spey
         stat_wrapper = spey.get_backend('ml.likelihoods')
-        
+
         #The current ML-likelihood backend takes a local path. This has to be
         #updated, I think the idea is that the backend takes 'dataset' as input,
 #        where 'dataset' is a loaded onnx model. Thus, the onnx has to be loaded
 #        by SmodelS beforehand. It seems to be the more consistent wrt the other
 #        backends.
-        
+
         #network_path='/Users/humberto/Documents/work/learn_pyhf_smodels/ML_LHClikelihoods/ML_models/ATLAS-SUSY-2018-04/ensemble_model.onnx'
         onnxBlob=self.dataset.globalInfo.onnx
         # self.speyModel = stat_wrapper(nsig,onnxBlob) # this is how i want it long run
@@ -182,13 +183,15 @@ class SpeyComputer:
         """
         Create a statistical model from multibin data.
 
-        :param nsig: number of signal events. For simplified likelihood backend this input can
-        contain `np.array` or `List[float]` which contains signal yields per region.
-        For `pyhf` backend this input expected to be a JSON-patch i.e. `List[Dict]`,
-        see `pyhf` documentation for details on JSON-patch format.
+        :param nsig: number of signal events. For simplified likelihood backend
+            this input can contain `np.array` or `List[float]` which contains
+            signal yields per region.
+            For `pyhf` backend this input expected to be a JSON-patch
+            i.e. `List[Dict]`, see `pyhf` documentation for details on
+            JSON-patch format.
         :param delta_sys: systematic uncertainty on signal. Currently unused.
-        :param allow_negative_signal: if True, the expected upper limit on mu, 
-        used to find the best statistical model, can be negative.
+        :param allow_negative_signal: if True, the expected upper limit on mu,
+            used to find the best statistical model, can be negative.
 
         :returns: spey StatisticalModel object.
 
@@ -264,14 +267,14 @@ class SpeyComputer:
             analysis = dataset.globalInfo.id
 
             speyModel = stat_wrapper( analysis = analysis,
-                            signal_patch = signal_patch, 
+                            signal_patch = signal_patch,
                             background_only_model = inputJson )
             models.append ( speyModel )
         self.speyModels = models
         self.model_index = self.getBestCombinationIndex( data )
         return models
 
-    def getStatModelSingleBin(self, nsig: Union[float, np.ndarray], 
+    def getStatModelSingleBin(self, nsig: Union[float, np.ndarray],
             delta_sys : Union[None,float] = None,
             allow_negative_signal : bool = False
     ):
@@ -316,7 +319,8 @@ class SpeyComputer:
     def get_five_values ( self, expected : Union [ bool, Text ],
                       return_nll : bool = False,
                       check_for_maxima : bool = False )-> Dict:
-        """ return the Five Values: l(bsm), l(sm), muhat, l(muhat), sigma(mu_hat) 
+        """ return the Five Values: l(bsm), l(sm), muhat, l(muhat), sigma(mu_hat)
+
         :param check_for_maxima: if true, then check lmax against l(sm) and l(bsm)
              correct, if necessary
         """
@@ -356,11 +360,12 @@ class SpeyComputer:
 
     def poi_upper_limit ( self, expected : Union [ bool, Text ],
            limit_on_xsec : bool = False, model_index : Union [int,None] = None ) -> float:
-        """ simple frontend, to spey::poi_upper_limit 
+        """ simple frontend to spey::poi_upper_limit
+
         :param limit_on_xsec: if True, then return the limit on the
-                              cross section
+            cross section
         :param model_index: if None, then get upper limit for most sensitive model,
-                           if integer, get UL for that model
+            if integer, get UL for that model
         """
         if model_index == None:
             model_index = self.model_index
@@ -371,12 +376,15 @@ class SpeyComputer:
         except ValueError as e:
             logger.warning ( f"when computing upper limit for SL: {e}. Will try with other method" )
             sys.exit(-1)
+        except spey.system.exceptions.AsimovTestStatZero as e:
+            logger.debug ( f"spey returned: {e}. will interpret as ul=inf" )
+            ret = float("inf")
         ret = float(ret) # cast for the printers
         if limit_on_xsec:
             totsig = self.nsig
             if type ( self.nsig ) in [ list ]:
                 totsig = sum ( self.nsig )
-            xsec = totsig / self.dataset.globalInfo.lumi    
+            xsec = totsig / self.dataset.globalInfo.lumi
             ret = ret * xsec
         return ret
 
@@ -403,7 +411,7 @@ class SpeyComputer:
         return i_best
 
 
-    def asimov_likelihood ( self, poi_test : float, expected : Union[bool,Text], 
+    def asimov_likelihood ( self, poi_test : float, expected : Union[bool,Text],
                             return_nll : bool ) -> float:
         """ simple frontend to spey functionality """
         self.checkMinimumPoi( poi_test )
@@ -421,7 +429,7 @@ class SpeyComputer:
 
         :returns: a StatsComputer
         """
-        computer = SpeyComputer(dataset=dataset, backendType="pyhf", 
+        computer = SpeyComputer(dataset=dataset, backendType="pyhf",
                                 nsig=nsig, deltas_rel=deltas_rel)
         return computer
 
@@ -431,7 +439,7 @@ class SpeyComputer:
         if poi_test < config.minimum_poi:
             logger.error ( f'Calling likelihood for {self.dataset.globalInfo.id} (using combination of SRs) for a mu giving a negative total yield. mu = {mu} and minimum_mu = {config.minimum_poi}.' )
 
-    def likelihood ( self, poi_test : float, expected : Union[bool,Text], 
+    def likelihood ( self, poi_test : float, expected : Union[bool,Text],
                             return_nll : bool ) -> float:
         """ simple frontend to spey functionality """
         self.checkMinimumPoi ( poi_test )
@@ -449,7 +457,7 @@ class SpeyComputer:
         :returns: tuple of muhat,lmax
         """
         expected = self.translateExpectationType ( expected )
-        speyret = self.speyModels[self.model_index].maximize_likelihood ( expected = expected, 
+        speyret = self.speyModels[self.model_index].maximize_likelihood ( expected = expected,
                 allow_negative_signal = allow_negative_signal,
                 return_nll = return_nll )
         ret = { "muhat": float(speyret[0]), "lmax": float(speyret[1]) }
@@ -471,7 +479,7 @@ class SpeyComputer:
 
     def maximize_asimov_likelihood ( self, expected : Union[bool,Text],
            return_nll : bool = False ) -> Tuple[float,float]:
-        """ simple frontend to spey functionality 
+        """ simple frontend to spey functionality
         :param return_nll: if True, return negative log likelihood
         :param allow_negative_signal: allow also negative muhats
         :returns: tuple of muhat,lmax
@@ -480,7 +488,7 @@ class SpeyComputer:
         # init = self.getSpeyInitialisation ( True )
         # opt = init["optimiser"]
         # opt["test_statistics"]="qmutilde"
-        ret = self.speyModels[self.model_index].maximize_asimov_likelihood ( expected = expected, 
+        ret = self.speyModels[self.model_index].maximize_asimov_likelihood ( expected = expected,
             return_nll = return_nll ) # , **opt )
         assert ret[0]>=0., "maximum of asimov likelihood should not be below zero"
         for k,v in ret.items():
@@ -497,7 +505,7 @@ class SimpleSpeyDataSet:
     """ a very simple data class that can replace a smodels.dataset,
     for 1d SL data only. used for testing and in dataPreparation """
     class SimpleInfo:
-        def __init__ ( self, observedN : float, expectedBG : float, 
+        def __init__ ( self, observedN : float, expectedBG : float,
                        bgError : float ):
             self.observedN = observedN
             self.expectedBG = expectedBG
@@ -546,7 +554,8 @@ class SpeyAnalysesCombosComputer:
 
     def poi_upper_limit ( self, expected : Union [ bool, Text ],
            limit_on_xsec : bool = False ) -> float:
-        """ simple frontend, to spey::poi_upper_limit 
+        """ simple frontend, to spey::poi_upper_limit
+
         :param limit_on_xsec: if True, then return the limit on the
                               cross section
         """
@@ -558,7 +567,7 @@ class SpeyAnalysesCombosComputer:
             ret = ret * totxsec
         return ret
 
-    def likelihood ( self, poi_test : float, expected : Union[bool,Text], 
+    def likelihood ( self, poi_test : float, expected : Union[bool,Text],
                             return_nll : bool ) -> float:
         """ simple frontend to spey functionality """
         expected = SpeyComputer.translateExpectationType ( expected )
@@ -575,7 +584,7 @@ class SpeyAnalysesCombosComputer:
         :returns: tuple of muhat,lmax
         """
         expected = SpeyComputer.translateExpectationType ( expected )
-        speyret = self.speyModel.maximize_likelihood ( expected = expected, 
+        speyret = self.speyModel.maximize_likelihood ( expected = expected,
                 allow_negative_signal = allow_negative_signal,
                 return_nll = return_nll )
         ret = { "muhat": float(speyret[0]), "lmax": float(speyret[1]) }
@@ -588,9 +597,11 @@ class SpeyAnalysesCombosComputer:
     def get_five_values ( self, expected : Union [ bool, Text ],
                       return_nll : bool = False,
                       check_for_maxima : bool = False )-> Dict:
-        """ return the Five Values: l(bsm), l(sm), muhat, l(muhat), sigma(mu_hat) 
+        """ method returning the Five Values:
+        l(bsm), l(sm), muhat, l(muhat), sigma(mu_hat)
+
         :param check_for_maxima: if true, then check lmax against l(sm) and l(bsm)
-             correct, if necessary
+            correct, if necessary
         """
         ret = self.maximize_likelihood ( expected = expected, return_nll = return_nll  )
         lmax = ret['lmax']
@@ -636,7 +647,7 @@ class SpeyAnalysesCombosComputer:
                                             test_statistics=test_statistic )
         return float(sigma_mu)
 
-    
+
 if __name__ == "__main__":
     # nobs,bg,bgerr,lumi = 3., 4.1, 0.6533758489567854, 35.9/fb
     # nobs,bg,bgerr,lumi = 0, 1., 0.2, 35.9/fb

smodels-3.0.3/smodels/tools/printers/__init__.py

@@ -0,0 +1,5 @@
+"""
+.. module:: tools.printers.__init__
+    :synopsis: This package contains tools for handling printers
+"""
+

smodels-3.0.3/smodels/tools/printers/basicPrinter.py

@@ -0,0 +1,164 @@
+"""
+.. module:: basicPrinter
+   :synopsis: Base class for defining printer classes
+
+.. moduleauthor:: Andre Lessa <lessa.a.p@gmail.com>
+"""
+
+import sys
+import os
+from smodels.base.smodelsLogging import logger
+import numpy as np
+import time
+
+
+class BasicPrinter(object):
+    """
+    Super class to handle the basic printing methods
+    """
+
+    def __init__(self, output, filename, outputFormat = 'current'):
+        """
+        :ivar str typeofexpectedvalues: what type of expected values to print,
+              apriori or posteriori
+        """
+
+        self.name = "basic"
+        self.time = time.time()  # time stamps
+
+        self.outputList = []
+        self.filename = filename
+        self.output = output
+        self.printingOrder = []
+        self.typeofexpectedvalues = "apriori"
+        self.toPrint = []
+        self.outputFormat = outputFormat
+
+        if filename and os.path.isfile(filename):
+            logger.warning("Removing file %s" % filename)
+            os.remove(filename)
+
+    def getTypeOfExpected(self):
+        """ tiny convenience function for what expected values to print,
+            apriori (True) or posteriori """
+        expected = True
+        if self.typeofexpectedvalues == "posteriori":
+            expected = "posteriori"
+        return expected
+
+    @property
+    def filename(self):
+        return self._filename
+
+    @filename.setter
+    def filename(self, fn):
+        self._filename = fn
+        self.mkdir()
+
+    def mkdir(self):
+        """ create directory to file, if necessary """
+        if not self.filename:
+            return
+        dirname = os.path.dirname(self.filename)
+        if dirname != "" and not os.path.exists(dirname):
+            os.makedirs(dirname)
+
+    def setOptions(self, options):
+        """
+        Store the printer specific options to control the output of each printer.
+        Each option is stored as a printer attribute.
+
+        :param options: a list of (option,value) for the printer.
+        """
+
+        for opt, value in options:
+            setattr(self, opt, eval(value))
+
+    def addObj(self, obj):
+        """
+        Adds object to the Printer.
+
+        :param obj: A object to be printed. Must match one of the types defined in formatObj
+
+        :return: True if the object has been added to the output. If the object does not belong
+                to the pre-defined printing list toPrint, returns False.
+        """
+
+        for iobj, objType in enumerate(self.printingOrder):
+            if isinstance(obj, objType):
+                self.toPrint[iobj] = obj
+                return True
+        return False
+
+    def openOutFile(self, filename, mode):
+        """ creates and opens a data sink,
+            creates path if needed """
+        d = os.path.dirname(filename)
+        if not os.path.exists(d):
+            os.makedirs(d)
+            logger.info("creating directory %s" % d)
+        return open(filename, mode)
+
+    def flush(self):
+        """
+        Format the objects added to the output, print them to the screen
+        or file and remove them from the printer.
+        """
+        ret = ""
+
+        for obj in self.toPrint:
+            if obj is None:
+                continue
+            output = self._formatObj(obj)
+            if not output:
+                continue  # Skip empty output
+            ret += output
+            if self.output == 'stdout':
+                sys.stdout.write(output)
+            elif self.output == 'file':
+                if not self.filename:
+                    logger.error('Filename not defined for printer')
+                    return False
+                with self.openOutFile(self.filename, "a") as outfile:
+                    outfile.write(output)
+                    outfile.close()
+
+        self.toPrint = [None]*len(self.printingOrder)  # Reset printing objects
+        self.time = time.time()  # prepare next timestamp
+        return ret
+
+    def _formatObj(self, obj):
+        """
+        Method for formatting the output depending on the type of object
+        and output.
+
+        :param obj: A object to be printed. Must match one of the types defined in formatObj
+
+        """
+
+        typeStr = type(obj).__name__
+        try:
+            formatFunction = getattr(self, '_format'+typeStr)
+            ret = formatFunction(obj)
+            # print ( " `-", len(ret))
+            return ret
+        except AttributeError as e:
+            logger.warning('Error formating object %s: \n %s' % (typeStr, e))
+            return False
+
+    def _round(self, number, n=6):
+        """ round a number to n significant digits, if it *is* a number """
+        if type(number) not in [float, np.float64]:
+            return number
+        if not np.isfinite(number):
+            return f'float("{number}")'
+        if np.isnan(number) or not np.isfinite(number):
+            return number
+        try:
+            if abs(number) < 1e-40:
+                return number
+            return round(number, -int(np.floor(np.sign(number) * np.log10(abs(number)))) + n)
+        except Exception:
+            pass
+        return number
+        # return round ( number, n )