Merge pull request #345 from ISISNeutronMuon/improved-labels

Improved labels, corrected text output

MDANSE/Src/MDANSE/Framework/Configurators/AseInputFileConfigurator.py

@@ -102,4 +102,4 @@ def get_information(self):
         except KeyError:
             print(f"No VALUE in {self._name}")
 
-        return "Input file: %r" % self["value"]
+        return "Input file: %r\n" % self["value"]

MDANSE/Src/MDANSE/Framework/Configurators/AtomMappingConfigurator.py

@@ -79,4 +79,4 @@ def get_information(self) -> str:
         if "value" not in self:
             return "Not configured yet\n"
 
-        return str(self["value"])
+        return str(self["value"]) + "\n"

MDANSE/Src/MDANSE/Framework/Configurators/AtomSelectionConfigurator.py

@@ -126,7 +126,7 @@ def get_information(self):
         info.append("Number of selected atoms:%d" % self["selection_length"])
         info.append("Selected elements:%s" % self["unique_names"])
 
-        return "\n".join(info)
+        return "\n".join(info) + "\n"
 
     def get_selector(self) -> Selector:
         traj_config = self._configurable[self._dependencies["trajectory"]]

MDANSE/Src/MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py

@@ -137,6 +137,6 @@ def get_information(self):
             return "Not configured yet"
 
         if self["value"] is None:
-            return "No atoms selected for transmutation"
+            return "No atoms selected for transmutation\n"
 
         return "Number of transmutated atoms:%d\n" % self._nTransmutatedAtoms

MDANSE/Src/MDANSE/Framework/Configurators/AtomsListConfigurator.py

@@ -114,4 +114,4 @@ def get_information(self):
             "Number of selected %d-tuplets:%d" % (self._nAtoms, self["n_values"])
         )
 
-        return "\n".join(info)
+        return "\n".join(info) + "\n"

MDANSE/Src/MDANSE/Framework/Configurators/AxisSelectionConfigurator.py

@@ -78,4 +78,4 @@ def get_information(self):
         :rtype: str
         """
 
-        return "Axis vector:%s" % self["value"]
+        return "Axis vector:%s\n" % self["value"]

MDANSE/Src/MDANSE/Framework/Configurators/BasisSelectionConfigurator.py

@@ -81,4 +81,4 @@ def get_information(self):
         :rtype: str
         """
 
-        return "Basis vector:%s" % self["value"]
+        return "Basis vector:%s\n" % self["value"]

MDANSE/Src/MDANSE/Framework/Configurators/BooleanConfigurator.py

@@ -71,4 +71,4 @@ def get_information(self):
         :rtype: str
         """
 
-        return "Value: %r" % self["value"]
+        return "Value: %r\n" % self["value"]

MDANSE/Src/MDANSE/Framework/Configurators/FloatConfigurator.py

@@ -124,4 +124,4 @@ def get_information(self):
         :rtype: str
         """
 
-        return "Value: %r" % self["value"]
+        return "Value: %r\n" % self["value"]

MDANSE/Src/MDANSE/Framework/Configurators/HDFInputFileConfigurator.py

@@ -103,4 +103,4 @@ def get_information(self):
             for v in variables:
                 info.append("\t-{}".format(v))
 
-        return "\n".join(info)
+        return "\n".join(info) + "\n"

MDANSE/Src/MDANSE/Framework/Configurators/InputDirectoryConfigurator.py

@@ -52,4 +52,4 @@ def get_information(self):
         :rtype: str
         """
 
-        return "Input directory: %r" % self["value"]
+        return "Input directory: %r\n" % self["value"]

MDANSE/Src/MDANSE/Framework/Configurators/InputFileConfigurator.py

@@ -82,4 +82,4 @@ def get_information(self):
         :rtype: str
         """
 
-        return "Input file: %r" % self["value"]
+        return "Input file: %r\n" % self["value"]

MDANSE/Src/MDANSE/Framework/Configurators/InstrumentResolutionConfigurator.py

@@ -112,4 +112,4 @@ def get_information(self):
 
         info = "\n".join(info)
 
-        return info
+        return info + "\n"

MDANSE/Src/MDANSE/Framework/Configurators/IntegerConfigurator.py

@@ -133,4 +133,4 @@ def get_information(self):
         :rtype: str
         """
 
-        return "Value: %r" % self["value"]
+        return "Value: %r\n" % self["value"]

MDANSE/Src/MDANSE/Framework/Configurators/McStasOptionsConfigurator.py

@@ -83,4 +83,4 @@ def get_information(self):
         :rtype: str
         """
 
-        return "McStas command line options: %s" % self["value"]
+        return "McStas command line options: %s\n" % self["value"]

MDANSE/Src/MDANSE/Framework/Configurators/McStasParametersConfigurator.py

@@ -114,4 +114,4 @@ def get_information(self):
         :rtype: str
         """
 
-        return "McStas command line parameters:%s" % self["value"]
+        return "McStas command line parameters:%s\n" % self["value"]

MDANSE/Src/MDANSE/Framework/Configurators/MultipleChoicesConfigurator.py

@@ -102,4 +102,4 @@ def nChoices(self):
         return self._nChoices
 
     def get_information(self):
-        return "Selected items: %r" % self["choices"]
+        return "Selected items: %r\n" % self["choices"]

MDANSE/Src/MDANSE/Framework/Configurators/OutputDirectoryConfigurator.py

@@ -71,4 +71,4 @@ def get_information(self):
         :rtype: str
         """
 
-        return "Output directory: %r" % self["value"]
+        return "Output directory: %r\n" % self["value"]

MDANSE/Src/MDANSE/Framework/Configurators/OutputFilesConfigurator.py

@@ -32,7 +32,7 @@ class OutputFilesConfigurator(IConfigurator):
     Once configured, this configurator will provide a list of files built by joining the given output directory, the
     basename and the extensions corresponding to the input file formats.
 
-    For analysis, MDANSE currently supports only the HDF and ASCII formats. To define a new output file format
+    For analysis, MDANSE currently supports only the HDF and Text formats. To define a new output file format
     for an analysis, you must inherit from MDANSE.Framework.Formats.IFormat.IFormat interface.
     """
 

MDANSE/Src/MDANSE/Framework/Configurators/OutputTrajectoryConfigurator.py

@@ -113,7 +113,7 @@ def get_information(self):
         :rtype: str
         """
 
-        info = "Output file: %s" % self["file"]
+        info = "Output file: %s\n" % self["file"]
 
         return info
 

MDANSE/Src/MDANSE/Framework/Configurators/PartialChargeConfigurator.py

@@ -85,6 +85,6 @@ def get_information(self):
         :rtype: str
         """
 
-        info = "Sum of partial charges = %8.3f" % sum(self["charges"].values())
+        info = "Sum of partial charges = %8.3f\n" % sum(self["charges"].values())
 
         return info

MDANSE/Src/MDANSE/Framework/Configurators/PythonObjectConfigurator.py

@@ -58,4 +58,4 @@ def get_information(self):
         :rtype: str
         """
 
-        return "Python object: %r" % self["value"]
+        return "Python object: %r\n" % self["value"]

MDANSE/Src/MDANSE/Framework/Configurators/RangeConfigurator.py

@@ -211,8 +211,8 @@ def get_information(self):
         info = "%d values from %s to %s" % (self["number"], self["first"], self["last"])
 
         if self._includeLast:
-            info += "last value included"
+            info += " last value included"
         else:
-            info += "last value excluded"
+            info += " last value excluded"
 
-        return info
+        return info + "\n"

MDANSE/Src/MDANSE/Framework/Configurators/RunningModeConfigurator.py

@@ -27,21 +27,21 @@ class RunningModeConfigurator(IConfigurator):
     """
     This configurator allows to choose the mode used to run the calculation.
 
-    MDANSE currently support monoprocessor or multiprocessor (SMP) running modes. In the laster case, you have to
+    MDANSE currently support single-core or multicore (SMP) running modes. In the laster case, you have to
     specify the number of slots used for running the analysis.
     """
 
-    availablesModes = ["monoprocessor", "threadpool", "multiprocessor"]
+    availablesModes = ["single-core", "threadpool", "multicore"]
 
-    _default = ("monoprocessor", 1)
+    _default = ("single-core", 1)
 
     def configure(self, value):
         """
         Configure the running mode.
      
-        :param value: the running mode specification. It can be *'monoprocessor'* or a 2-tuple whose first element \
-        must be *'multiprocessor'* and 2nd element the number of slots allocated for running the analysis.
-        :type value: *'monoprocessor'* or 2-tuple
+        :param value: the running mode specification. It can be *'single-core'* or a 2-tuple whose first element \
+        must be *'multicore'* and 2nd element the number of slots allocated for running the analysis.
+        :type value: *'single-core'* or 2-tuple
         """
 
         if isinstance(value, str):
@@ -53,13 +53,13 @@ def configure(self, value):
             self.error_status = f"{mode} is not a valid running mode."
             return
 
-        if mode == "monoprocessor":
+        if mode == "single-core":
             slots = 1
 
         else:
             slots = int(value[1])
 
-            if mode == "multiprocessor":
+            if mode == "multicore":
                 maxSlots = multiprocessing.cpu_count()
                 if slots > maxSlots:
                     self.error_status = "invalid number of allocated slots."
@@ -82,4 +82,4 @@ def get_information(self):
         :rtype: str
         """
 
-        return "Run in %s mode (%d slots)" % (self["mode"], self["slots"])
+        return "Run in %s mode (%d slots)\n" % (self["mode"], self["slots"])

MDANSE/Src/MDANSE/Framework/Configurators/SingleChoiceConfigurator.py

@@ -77,4 +77,4 @@ def get_information(self):
         :rtype: str
         """
 
-        return "Selected item: %r" % self["value"]
+        return "Selected item: %r\n" % self["value"]

MDANSE/Src/MDANSE/Framework/Configurators/SingleOutputFileConfigurator.py

@@ -115,7 +115,7 @@ def get_information(self):
         :rtype: str
         """
 
-        info = "Output file: %s" % self["file"]
+        info = "Output file: %s\n" % self["file"]
 
         return info
 

MDANSE/Src/MDANSE/Framework/Configurators/StringConfigurator.py

@@ -103,4 +103,4 @@ def get_information(self):
         :rtype: str
         """
 
-        return "Value: %r" % self["value"]
+        return "Value: %r\n" % self["value"]

MDANSE/Src/MDANSE/Framework/Configurators/TrajectoryVariableConfigurator.py

@@ -56,4 +56,4 @@ def get_information(self):
         :rtype: str
         """
 
-        return "Selected variable: %r" % self["value"]
+        return "Selected variable: %r\n" % self["value"]

MDANSE/Src/MDANSE/Framework/Configurators/VectorConfigurator.py

@@ -141,4 +141,4 @@ def get_information(self):
         :rtype: str
         """
 
-        return "Value: %r" % self["value"]
+        return "Value: %r\n" % self["value"]

MDANSE/Src/MDANSE/Framework/Configurators/WeightsConfigurator.py

@@ -92,4 +92,4 @@ def get_information(self):
         :rtype: str
         """
 
-        return "selected weight: %s" % self["property"]
+        return "selected weight: %s\n" % self["property"]

MDANSE/Src/MDANSE/Framework/Formats/IFormat.py

@@ -20,7 +20,7 @@ class IFormat(metaclass=SubclassFactory):
     """
     This is the base class for writing MDANSE output data. In MDANSE, the output of an analysis can be written in different file format.
 
-    Currently, MDANSE supports HDF5 and ASCII output file formats. To introduce a new file output file format, just create a new concrete
+    Currently, MDANSE supports HDF5 and Text output file formats. To introduce a new file output file format, just create a new concrete
     subclass of IFormat and overload the "write" class method as defined in IFormat base class which will actually write the output variables,
     and redefine the "type", "extension" and "extensions" class attributes.
     """

MDANSE/Src/MDANSE/Framework/Formats/ASCIIFormat.py → MDANSE/Src/MDANSE/Framework/Formats/TextFormat.py

@@ -2,8 +2,8 @@
 #
 # MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
 #
-# @file      Src/Framework/Formats/ASCIIFormat.py
-# @brief     Implements module/class/test ASCIIFormat
+# @file      Src/Framework/Formats/TextFormat.py
+# @brief     Implements module/class/test TextFormat
 #
 # @homepage  https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
 # @license   GNU General Public License v3 or higher (see LICENSE)
@@ -16,16 +16,23 @@
 import os
 import io
 import tarfile
+import codecs
+import time
 
 import numpy as np
 
 
 from MDANSE.Framework.Formats.IFormat import IFormat
 
 
-class ASCIIFormat(IFormat):
+def length_stringio(input: "io.BytesIO") -> int:
+    result = input.getbuffer().nbytes
+    return result
+
+
+class TextFormat(IFormat):
     """
-    This class handles the writing of output variables in ASCII format. Each output variable is written into separate ASCII files which are further
+    This class handles the writing of output variables in Text format. Each output variable is written into separate Text files which are further
     added to a single archive file.
     """
 
@@ -36,11 +43,11 @@ class ASCIIFormat(IFormat):
     @classmethod
     def write(cls, filename, data, header=""):
         """
-        Write a set of output variables into a set of ASCII files.
+        Write a set of output variables into a set of Text files.
 
-        Each output variable will be output in a separate ASCII file. All the ASCII files will be compressed into a tar file.
+        Each output variable will be output in a separate Text file. All the Text files will be compressed into a tar file.
 
-        :param filename: the path to the output archive file that will contain the ASCII files written for each output variable.
+        :param filename: the path to the output archive file that will contain the Text files written for each output variable.
         :type filename: str
         :param data: the data to be written out.
         :type data: dict of Framework.OutputVariables.IOutputVariable
@@ -49,29 +56,34 @@ def write(cls, filename, data, header=""):
         """
 
         filename = os.path.splitext(filename)[0]
-        filename = "%s_ascii.tar" % filename
+        filename = "%s_text.tar" % filename
 
         tf = tarfile.open(filename, "w")
 
+        if header:
+            real_buffer = io.BytesIO()
+            tempStr = codecs.getwriter("utf-8")(real_buffer)
+            for line in header:
+                tempStr.write(str(line))
+            tempStr.write("\n\n")
+            real_buffer.seek(0)
+            info = tarfile.TarInfo(name="jobinfo.txt")
+            info.size = length_stringio(real_buffer)
+            info.mtime = time.time()
+            tf.addfile(tarinfo=info, fileobj=real_buffer)
+
         for var in list(data.values()):
-            tempStr = io.StringIO()
+            real_buffer = io.BytesIO()
+            tempStr = codecs.getwriter("utf-8")(real_buffer)
             tempStr.write(var.info())
             tempStr.write("\n\n")
             cls.write_data(tempStr, var, data)
-            tempStr.seek(0)
+            real_buffer.seek(0)
 
             info = tarfile.TarInfo(name="%s%s" % (var.varname, cls.extensions[0]))
-            info.size = tempStr.len
-            tf.addfile(tarinfo=info, fileobj=tempStr)
-
-        if header:
-            tempStr = io.StringIO()
-            tempStr.write(header)
-            tempStr.write("\n\n")
-            tempStr.seek(0)
-            info = tarfile.TarInfo(name="jobinfo.txt")
-            info.size = tempStr.len
-            tf.addfile(tarinfo=info, fileobj=tempStr)
+            info.size = length_stringio(real_buffer)
+            info.mtime = time.time()
+            tf.addfile(tarinfo=info, fileobj=real_buffer)
 
         tf.close()
 
@@ -91,9 +103,7 @@ def write_data(cls, fileobject, data, allData):
         """
 
         if data.ndim > 2:
-            fileobject.write(
-                "Can not write ASCII output for data of dimensionality > 2"
-            )
+            fileobject.write("Can not write Text output for data of dimensionality > 2")
 
         elif data.ndim == 2:
             xData, yData = data.axis.split("|")

MDANSE/Src/MDANSE/Framework/Jobs/AngularCorrelation.py

@@ -74,7 +74,7 @@ class AngularCorrelation(IJob):
     )
     settings["output_files"] = (
         "OutputFilesConfigurator",
-        {"formats": ["MDAFormat", "ASCIIFormat"]},
+        {"formats": ["MDAFormat", "TextFormat"]},
     )
     settings["running_mode"] = ("RunningModeConfigurator", {})
 

MDANSE/Src/MDANSE/Framework/Jobs/AreaPerMolecule.py

@@ -66,7 +66,7 @@ class AreaPerMolecule(IJob):
     )
     settings["output_files"] = (
         "OutputFilesConfigurator",
-        {"formats": ["MDAFormat", "ASCIIFormat"]},
+        {"formats": ["MDAFormat", "TextFormat"]},
     )
     settings["running_mode"] = ("RunningModeConfigurator", {})
 

MDANSE/Src/MDANSE/Framework/Jobs/CoordinationNumber.py

@@ -61,7 +61,7 @@ class CoordinationNumber(DistanceHistogram):
     )
     settings["output_files"] = (
         "OutputFilesConfigurator",
-        {"formats": ["MDAFormat", "ASCIIFormat"]},
+        {"formats": ["MDAFormat", "TextFormat"]},
     )
     settings["running_mode"] = ("RunningModeConfigurator", {})