Merge pull request #99 from MolarVerse/dev

Release 1.1.0

.githooks/commit-msg

@@ -96,6 +96,24 @@ if [[ "$lowercase_message" =~ ^ci(\(.+\))?: ]]; then
   group="CI"
 fi
 
+#pylint
+if [[ "$lowercase_message" =~ ^pylint(\(.+\))?: ]]; then
+  matched=true
+  group="Pylint"
+fi
+
+if [[ "$lowercase_message" =~ ^admin(\(.+\))?: ]]; then
+  matched=true
+  group="Administrative"
+fi
+
+#random stuff that doesn't fit into any of the above categories
+#starting with a $
+if [[ "$lowercase_message" =~ ^\$ ]]; then
+  matched=true
+  group="Random"
+fi
+
 # ... (similar checks for other patterns in the list)
 
 # No match found
@@ -120,6 +138,9 @@ if ! $matched; then
   echo "  - Example:        example:, examples:"
   echo "  - Dependency:     deps:"
   echo "  - CI:             ci:"
+  echo "  - Pylint:         pylint:"
+  echo "  - Administrative: admin:"
+  echo "  - Random:         $"
   # ... (similar output for other patterns in the list)
   echo "  - --------------------------------------------\n"
 

.gitignore

@@ -6,7 +6,7 @@ build/
 _version.py
 **/*.ipynb
 
-.github/.pylint_cache
+.github/.pylint_cache/__*
 
 .coverage
 coverage.xml

PQAnalysis/io/base.py

@@ -78,6 +78,7 @@ def __init__(
         self.filename = filename
 
         self.mode = FileWritingMode(mode)
+        self.original_mode = FileWritingMode(mode)
 
     def open(self) -> None:
         """
@@ -144,13 +145,15 @@ class :py:class:`~PQAnalysis.io.formats.FileWritingMode`.
         """
         mode = FileWritingMode(mode)
 
-        if (mode == FileWritingMode.WRITE and self.filename is not None
-                and os.path.isfile(self.filename)):
+        if (
+            mode == FileWritingMode.WRITE and self.filename is not None and
+            os.path.isfile(self.filename)
+        ):
             self.logger.error(
                 (
-                f"File {self.filename} already exists. "
-                "Use mode \'a\' to append to the file or mode "
-                "\'o\' to overwrite the file."
+                    f"File {self.filename} already exists. "
+                    "Use mode \'a\' to append to the file or mode "
+                    "\'o\' to overwrite the file."
                 ),
                 exception=FileWritingModeError
             )
@@ -211,8 +214,8 @@ def __init__(self, filename: str | List[str]) -> None:
                 if not os.path.isfile(_filename):
                     self.logger.error(
                         (
-                        "At least one of the given files does not exist. "
-                        f"File {_filename} not found."
+                            "At least one of the given files does not exist. "
+                            f"File {_filename} not found."
                         ),
                         exception=PQFileNotFoundError
                     )

PQAnalysis/io/topology_file/__init__.py

@@ -2,5 +2,7 @@
 A subpackage to handle trajectory files.
 """
 
+from .exceptions import TopologyFileError
+
 from .topology_file_reader import TopologyFileReader
 from .topology_file_writer import TopologyFileWriter

PQAnalysis/io/topology_file/topology_file_reader.py

@@ -6,13 +6,14 @@
 
 import logging
 
-from beartype.typing import List
+from beartype.typing import List, Tuple
 
 from PQAnalysis.io.base import BaseReader
 from PQAnalysis.topology import Bond, BondedTopology, Angle, Dihedral
 from PQAnalysis.utils.custom_logging import setup_logger
-from PQAnalysis import __package_name__
+from PQAnalysis.utils.string import is_comment_line
 from PQAnalysis.type_checking import runtime_type_checking
+from PQAnalysis import __package_name__
 
 from .exceptions import TopologyFileError
 
@@ -83,14 +84,14 @@ def _get_definitions(self) -> dict[str, List[str]]:
         with open(self.filename, "r", encoding="utf-8") as file:
             lines = file.readlines()
 
-            # remove all #.... parts from all lines
-            lines = [line.split("#")[0] for line in lines]
-
-            # remove all empty lines
-            lines = [line for line in lines if line.strip()]
+            # remove all comment lines and empty lines
+            no_comment_lines = [
+                line for line in lines if
+                not is_comment_line(line, comment_token="#", empty_line=True)
+            ]
 
             # check if last line is END else raise error
-            if lines[-1].strip().lower() != "end":
+            if no_comment_lines[-1].strip().lower() != "end":
                 self.logger.error(
                     "Something went wrong. Each block should end with 'END'",
                     exception=TopologyFileError,
@@ -101,9 +102,12 @@ def _get_definitions(self) -> dict[str, List[str]]:
             block = []
             for line in lines:
                 if line.strip().lower() == "end":
+                    block.append(line)
                     blocks.append(block)
                     block = []
-                else:
+                elif not is_comment_line(
+                    line, comment_token="#", empty_line=True
+                ):
                     block.append(line)
 
             # make a dictionary for each block with the key
@@ -201,7 +205,10 @@ def _parse_bonds(self, block: List[str]) -> List[Bond]:
             If the number of columns in the block is not 3 or 4.
         """
         bonds = []
-        for line in block:
+        for line in block[:-1]:  # [-1] to avoid the "END" line of the block
+
+            line, comment = self._get_data_line_comment(line)
+
             if len(line.split()) == 4:
                 index, target_index, bond_type, _ = line.split()
                 is_linker = True
@@ -220,6 +227,7 @@ def _parse_bonds(self, block: List[str]) -> List[Bond]:
                     index2=int(target_index),
                     bond_type=int(bond_type),
                     is_linker=is_linker,
+                    comment=comment
                 )
             )
 
@@ -251,7 +259,10 @@ def _parse_angles(self, block: List[str]) -> List[Angle]:
             If the number of columns in the block is not 4 or 5.
         """
         angles = []
-        for line in block:
+        for line in block[:-1]:  # [-1] to avoid the "END" line of the block
+
+            line, comment = self._get_data_line_comment(line)
+
             if len(line.split()) == 5:
                 index1, index2, index3, angle_type, _ = line.split()
                 is_linker = True
@@ -271,6 +282,7 @@ def _parse_angles(self, block: List[str]) -> List[Angle]:
                     index3=int(index3),
                     angle_type=int(angle_type),
                     is_linker=is_linker,
+                    comment=comment
                 )
             )
 
@@ -302,7 +314,10 @@ def _parse_dihedrals(self, block: List[str]) -> List[Dihedral]:
             If the number of columns in the block is not 5 or 6.
         """
         dihedrals = []
-        for line in block:
+        for line in block[:-1]:  # [-1] to avoid the "END" line of the block
+
+            line, comment = self._get_data_line_comment(line)
+
             if len(line.split()) == 6:
                 index1, index2, index3, index4, dihedral_type, _ = line.split()
                 is_linker = True
@@ -323,6 +338,7 @@ def _parse_dihedrals(self, block: List[str]) -> List[Dihedral]:
                     index4=int(index4),
                     dihedral_type=int(dihedral_type),
                     is_linker=is_linker,
+                    comment=comment
                 )
             )
 
@@ -354,7 +370,10 @@ def _parse_impropers(self, block: List[str]) -> List[Dihedral]:
             If the number of columns in the block is not 5 or 6.
         """
         dihedrals = []
-        for line in block:
+        for line in block[:-1]:  # [-1] to avoid the "END" line of the block
+
+            line, comment = self._get_data_line_comment(line)
+
             if len(line.split()) == 6:
                 index1, index2, index3, index4, dihedral_type, _ = line.split()
                 is_linker = True
@@ -376,6 +395,7 @@ def _parse_impropers(self, block: List[str]) -> List[Dihedral]:
                     dihedral_type=int(dihedral_type),
                     is_linker=is_linker,
                     is_improper=True,
+                    comment=comment
                 )
             )
 
@@ -407,7 +427,10 @@ def _parse_shake(self, block: List[str]) -> List[Bond]:
             If the number of columns in the block is not 3 or 4.
         """
         shake_bonds = []
-        for line in block:
+        for line in block[:-1]:  # [-1] to avoid the "END" line of the block
+
+            line, comment = self._get_data_line_comment(line)
+
             if len(line.split()) == 4:
                 index, target_index, distance, _ = line.split()
                 is_linker = True
@@ -422,7 +445,33 @@ def _parse_shake(self, block: List[str]) -> List[Bond]:
                     equilibrium_distance=float(distance),
                     is_linker=is_linker,
                     is_shake=True,
+                    comment=comment
                 )
             )
 
         return shake_bonds
+
+    @staticmethod
+    def _get_data_line_comment(line: str) -> Tuple[str, str | None]:
+        """
+        Get the data and the comment from a line.
+
+        Parameters
+        ----------
+        line : str
+            A line from the topology file.
+
+        Returns
+        -------
+        tuple[str, str]
+            A tuple with the data and the comment.
+        """
+        splitted_line = line.split("#")
+        data = splitted_line[0].strip()
+
+        if len(splitted_line) > 1:
+            comment = "#".join(splitted_line[1:]).strip()
+        else:
+            comment = None
+
+        return data, comment