add mode to cli

PQAnalysis/analysis/thermal_expansion/api.py

@@ -8,6 +8,7 @@
 from PQAnalysis.io import BoxFileReader
 from PQAnalysis.traj import MDEngineFormat
 from PQAnalysis.type_checking import runtime_type_checking
+from PQAnalysis.io.formats import FileWritingMode
 
 from .thermal_expansion import ThermalExpansion
 from .thermal_expansion_input_file_reader import ThermalExpansionInputFileReader
@@ -16,7 +17,10 @@
 
 
 @runtime_type_checking
-def thermal_expansion(input_file: str, md_format: MDEngineFormat | str = MDEngineFormat.PQ):
+def thermal_expansion(
+        input_file: str,
+        md_format: MDEngineFormat | str = MDEngineFormat.PQ,
+        mode: FileWritingMode | str = "w"):
     """
     Calculates the thermal expansion coefficient using a given input file.
 
@@ -38,6 +42,13 @@ def thermal_expansion(input_file: str, md_format: MDEngineFormat | str = MDEngin
         the format of the input trajectory. Default is "PQ".
         For more information on the supported formats please visit
         :py:class:`~PQAnalysis.traj.formats.MDEngineFormat`.    
+    mode : FileWritingMode | str, optional
+        The writing mode. Default is "w".
+        The writing mode can be either a string or a FileWritingMode enum value.
+        Possible values are:
+        - "w" or FileWritingMode.WRITE: write mode (default, no overwrite)
+        - "a" or FileWritingMode.APPEND: append mode
+        - "o" or FileWritingMode.OVERWRITE: overwrite mode
     """
     md_format = MDEngineFormat(md_format)
 
@@ -69,10 +80,12 @@ def thermal_expansion(input_file: str, md_format: MDEngineFormat | str = MDEngin
     )
 
     data_writer = ThermalExpansionDataWriter(
-        filename=input_reader.out_file_key
+        filename=input_reader.out_file_key,
+        mode=mode
     )
 
-    log_writer = ThermalExpansionLogWriter(filename=input_reader.log_file)
+    log_writer = ThermalExpansionLogWriter(
+        filename=input_reader.log_file, mode=mode)
 
     log_writer.write_before_run(_thermal_expansion)
 

PQAnalysis/analysis/thermal_expansion/thermal_expansion_input_file_reader.py

@@ -84,7 +84,7 @@ def read(self):
     * - Key
         - Value
     * - {Reader.unit_key}
-        - The unit of the box dimensions. Default is Å.
+        - The unit of the box dimensions.
     * - {Reader.log_file_key}
         - The log file to write the log information to.
 Note
@@ -93,7 +93,7 @@ def read(self):
 They are optional in the input file, but they might be required for
 the analysis. This means that if an optional keyword is specified
 other keywords might be required.
-
+- :code:`{Reader.unit_key}` is optional for the analysis.
 - :code:`{Reader.log_file_key}` is optional for the analysis.
 (for more information see
 :py:class:`~PQAnalysis.io.input_file_reader.pq_analysis.thermal_expansion.thermal_expansion.ThermalExpansion`).

PQAnalysis/analysis/thermal_expansion/thermal_expansion_output_file_writer.py

@@ -9,6 +9,7 @@
 from PQAnalysis.io import BaseWriter
 from PQAnalysis.utils import __header__
 from PQAnalysis.type_checking import runtime_type_checking
+from PQAnalysis.io.formats import FileWritingMode
 
 from .thermal_expansion import ThermalExpansion
 
@@ -22,15 +23,25 @@ class ThermalExpansionDataWriter(BaseWriter):
     """
 
     @runtime_type_checking
-    def __init__(self, filename: str) -> None:
+    def __init__(
+            self,
+            filename: str,
+            mode: str | FileWritingMode = "w") -> None:
         """
         Parameters
         ----------
         filename : str
             the filename to write to
+        mode : str | FileWritingMode, optional
+            The writing mode. Default is "w".
+            The writing mode can be either a string or a FileWritingMode enum value.
+            Possible values are:
+            - "w" or FileWritingMode.WRITE: write mode (default, no overwrite)
+            - "a" or FileWritingMode.APPEND: append mode
+            - "o" or FileWritingMode.OVERWRITE: overwrite mode
         """
         self.filename = filename
-        super().__init__(filename)
+        super().__init__(filename, mode=mode)
 
     @runtime_type_checking
     def write(
@@ -59,14 +70,15 @@ def write(
         thermal_expansion_data_mega = thermal_expansion_data * 1e6
         super().open()
         angstrom = '\u212B'.encode('utf-8')
-        self.file.write(
+        print(
             f"T / K"
             f"a_avg in {angstrom}      a_std in {angstrom}"
             f"b_avg in {angstrom}      b_std in {angstrom}"
             f"c_avg in {angstrom}      c_std in {angstrom}"
             f"volume in {angstrom}³       volume_std in {angstrom}³"
             f"thermal_expansion_a in (M/K)       thermal_expansion_b in (M/K)"
-            f"thermal_expansion_c in (M/K)      volumetric expansion in (M/K)\n"
+            f"thermal_expansion_c in (M/K)      volumetric expansion in (M/K)",
+            file=self.file
         )
         for i, temperature_point in enumerate(temperature_points):
             print(
@@ -91,15 +103,25 @@ class ThermalExpansionLogWriter(BaseWriter):
     """
 
     @runtime_type_checking
-    def __init__(self, filename: str) -> None:
+    def __init__(
+            self,
+            filename: str,
+            mode: str | FileWritingMode = "w") -> None:
         """
         Parameters
         ----------
         filename : str
             the filename to write to
+        mode : str | FileWritingMode, optional
+            The writing mode. Default is "w".
+            The writing mode can be either a string or a FileWritingMode enum value.
+            Possible values are:
+            - "w" or FileWritingMode.WRITE: write mode (default, no overwrite)
+            - "a" or FileWritingMode.APPEND: append mode
+            - "o" or FileWritingMode.OVERWRITE: overwrite mode
         """
         self.filename = filename
-        super().__init__(filename)
+        super().__init__(filename, mode=mode)
 
     @runtime_type_checking
     def write_before_run(self, thermal_expansion: ThermalExpansion) -> None:

PQAnalysis/cli/thermal_expansion.py

@@ -64,6 +64,7 @@ def add_arguments(cls, parser: _ArgumentParser) -> None:
         """
         parser.parse_input_file()
         parser.parse_engine()
+        parser.parse_mode()
 
     @classmethod
     def run(cls, args):
@@ -75,7 +76,7 @@ def run(cls, args):
         args : argparse.Namespace
             The arguments parsed by the parser.
         """
-        thermal_expansion(args.input_file, args.engine)
+        thermal_expansion(args.input_file, args.engine, args.mode)
 
 
 def main():