Merge pull request #77 from MolarVerse/hotfix/1.0.7

Hotfix/1.0.7

.github/workflows/release.yml

@@ -73,7 +73,6 @@ jobs:
         name=$(git --no-pager tag --sort=creatordate --merged ${{ github.ref_name }} | tail -2 | head -1)
         echo "previousTag: $name"
         echo "previousTag=$name" >> $GITHUB_ENV
-        echo "::set-output name=previousTag::$name"
 
     - name: Update CHANGELOG
       id: changelog
@@ -97,7 +96,7 @@ jobs:
         gh release create
         '${{ github.ref_name }}'
         --repo '${{ github.repository }}'
-        --notes '${{ steps.changelog.outputs.changes }}''
+        --notes '${{ steps.changelog.outputs.changes }}'
 
   pypi-release-update:
     name: >-

PQAnalysis/atomic_system/atomic_system.py

@@ -194,7 +194,10 @@ def __init__(
         self._stress = stress
         self._cell = cell
 
-    @runtime_type_checking
+    #TODO: check why dynamic formatting does
+    #      not work here for "AtomicSystem"
+    #
+    # @runtime_type_checking
     def fit_atomic_system(
         self,
         system: "AtomicSystem",

PQAnalysis/io/formats.py

@@ -10,9 +10,7 @@
 from PQAnalysis import __package_name__
 
 from .exceptions import (
-    BoxFileFormatError,
-    FileWritingModeError,
-    OutputFileFormatError
+    BoxFileFormatError, FileWritingModeError, OutputFileFormatError
 )
 
 logger = logging.getLogger(__package_name__).getChild("OutputFileFormat")
@@ -87,8 +85,8 @@ def _missing_(cls, values: Any) -> Any:  # pylint: disable=arguments-differ
         if output_file_format == cls.AUTO and filename is None:
             logger.error(
                 (
-                "The file format could not be inferred from "
-                "the file extension because no filename was given."
+                    "The file format could not be inferred from "
+                    "the file extension because no filename was given."
                 ),
                 exception=OutputFileFormatError
             )
@@ -119,9 +117,7 @@ def file_extensions(cls):
         file_extensions[cls.VIRIAL.value] = [".virial", ".virials", ".vir"]
         file_extensions[cls.INFO.value] = [".info", ".information"]
         file_extensions[cls.INSTANTANEOUS_ENERGY.value] = [
-            ".instant_en",
-            ".instant_energies",
-            ".inst_energy"
+            ".instant_en", ".instant_energies", ".inst_energy"
         ]
 
         return file_extensions
@@ -142,36 +138,37 @@ def infer_format_from_extension(cls, file_path: str) -> "OutputFileFormat":
             The inferred file format.
         """
 
-        file_extension = file_path.split(".")[-1]
+        file_extension = "." + file_path.split(".")[-1]
 
-        if file_extension in cls.file_extensions()[cls.XYZ]:
+        print(file_extension)
+
+        if file_extension in cls.file_extensions()[cls.XYZ.value]:
             return cls.XYZ
 
-        if file_extension in cls.file_extensions()[cls.VEL]:
+        if file_extension in cls.file_extensions()[cls.VEL.value]:
             return cls.VEL
 
-        if file_extension in cls.file_extensions()[cls.FORCE]:
+        if file_extension in cls.file_extensions()[cls.FORCE.value]:
             return cls.FORCE
 
-        if file_extension in cls.file_extensions()[cls.CHARGE]:
+        if file_extension in cls.file_extensions()[cls.CHARGE.value]:
             return cls.CHARGE
 
-        if file_extension in cls.file_extensions()[cls.RESTART]:
+        if file_extension in cls.file_extensions()[cls.RESTART.value]:
             return cls.RESTART
 
         logger.error(
             (
-            "Could not infer the file format from the file extension of "
-            f"\"{file_path}\". Possible file formats are: "
-            f"{cls.__members__.values()}"
+                "Could not infer the file format from the file extension of "
+                f"\"{file_path}\". Possible file formats are: "
+                f"{cls.__members__.values()}"
             ),
             exception=OutputFileFormatError
         )
 
     @classmethod
     def get_file_extensions(
-        cls,
-        file_format: "OutputFileFormat | str"
+        cls, file_format: "OutputFileFormat | str"
     ) -> List[str]:
         """
         Get the file extensions of the given file format.

PQAnalysis/tools/add_molecule.py

@@ -110,9 +110,7 @@ def add_molecule(
     """
 
     _check_topology_args(
-        topology_file,
-        topology_file_to_add,
-        topology_file_output
+        topology_file, topology_file_to_add, topology_file_output
     )
 
     _add_molecule = AddMolecule(
@@ -179,8 +177,8 @@ def _check_topology_args(
         if topology_file_output is not None:
             AddMolecule.logger.warning(
                 (
-                "The output topology file is specified, but no topology "
-                "files are given to add. The output topology file will be ignored."
+                    "The output topology file is specified, but no topology "
+                    "files are given to add. The output topology file will be ignored."
                 )
             )
 
@@ -201,9 +199,9 @@ def _check_topology_args(
     if topology_file_output is None:
         AddMolecule.logger.error(
             (
-            "The output topology file must be specified if topology files are "
-            "given to add. This is a special case where None cannot be treated "
-            "as stdout as it is already used for the restart file."
+                "The output topology file must be specified if topology files are "
+                "given to add. This is a special case where None cannot be treated "
+                "as stdout as it is already used for the restart file."
             ),
             exception=PQValueError
         )
@@ -309,19 +307,21 @@ def __init__(
         self.restart_system = None
 
         self.molecule_file_type = OutputFileFormat(
-            (molecule_file_type,
-            self.molecule_file)
+            (molecule_file_type, self.molecule_file)
         )
 
-        if (self.molecule_file_type != OutputFileFormat.RESTART and
-                self.molecule_moldescriptor_file is not None):
+        if (
+            self.molecule_file_type != OutputFileFormat.RESTART and
+            self.molecule_moldescriptor_file is not None
+        ):
             self.logger.error(
                 "A moldescriptor file can only be specified for restart files.",
                 exception=PQValueError
             )
 
-        if self.molecule_file_type not in [OutputFileFormat.RESTART,
-            OutputFileFormat.XYZ]:
+        if self.molecule_file_type not in [
+            OutputFileFormat.RESTART, OutputFileFormat.XYZ
+        ]:
             self.logger.error(
                 "The molecule file type must be either RESTART or XYZ.",
                 exception=PQValueError
@@ -375,8 +375,8 @@ def extend_topology_file(
 
         self.logger.warning(
             (
-            "Extension of the topology file is only implemented for shake bonds. "
-            "The extension of general bonded topologies is not implemented yet."
+                "Extension of the topology file is only implemented for shake bonds. "
+                "The extension of general bonded topologies is not implemented yet."
             )
         )
 
@@ -386,9 +386,9 @@ def extend_topology_file(
         if self.restart_system is None or self.molecule is None:
             self.logger.error(
                 (
-                "The restart frame and the molecule must be read "
-                "before extending the topology file. Either call "
-                "the read_files method or the add_molecules method first."
+                    "The restart frame and the molecule must be read "
+                    "before extending the topology file. Either call "
+                    "the read_files method or the add_molecules method first."
                 ),
                 exception=PQValueError
             )