Backport fix from PR #554

pixi.toml

@@ -18,7 +18,6 @@ parmed = "*"
 pyarrow = "*"
 py3dmol = "*"
 pydot = "*"
-pygtail = "*"
 pyyaml = "*"
 rdkit = "*"
 

recipes/biosimspace/recipe.yaml

@@ -37,7 +37,6 @@ requirements:
     - pyarrow
     - py3dmol
     - pydot
-    - pygtail
     - python
     - pyyaml
     - rdkit

src/BioSimSpace/Process/_amber.py

@@ -26,11 +26,6 @@
 
 __all__ = ["Amber"]
 
-from .._Utils import _try_import
-
-_pygtail = _try_import("pygtail")
-
-
 from . import _process
 
 
@@ -2712,7 +2707,7 @@ def stdout(self, n=10):
         self._is_header = False
 
         # Append any new lines to the stdout list.
-        for line in _pygtail.Pygtail(self._stdout_file):
+        for line in self._tail(self._stdout_file):
             self._stdout.append(line.rstrip())
             line = line.strip()
 

src/BioSimSpace/Process/_gromacs.py

@@ -26,11 +26,6 @@
 
 __all__ = ["Gromacs"]
 
-from .._Utils import _try_import
-
-_pygtail = _try_import("pygtail")
-
-
 from . import _process
 
 
@@ -2104,7 +2099,7 @@ def stdout(self, n=10):
             raise ValueError("The number of lines must be positive!")
 
         # Append any new lines to the stdout list.
-        for line in _pygtail.Pygtail(self._stdout_file):
+        for line in self._tail(self._stdout_file):
             self._stdout.append(line.rstrip())
 
         # Get the current number of lines.

src/BioSimSpace/Process/_namd.py

@@ -26,11 +26,6 @@
 
 __all__ = ["Namd"]
 
-from .._Utils import _try_import
-
-_pygtail = _try_import("pygtail")
-
-
 from . import _process
 
 
@@ -2127,7 +2122,7 @@ def stdout(self, n=10):
             raise ValueError("The number of lines must be positive!")
 
         # Append any new lines to the stdout list.
-        for line in _pygtail.Pygtail(self._stdout_file):
+        for line in self._tail(self._stdout_file):
             self._stdout.append(line.rstrip())
 
             # Split the record using whitespace.

src/BioSimSpace/Process/_openmm.py

@@ -26,11 +26,6 @@
 
 __all__ = ["OpenMM"]
 
-from .._Utils import _try_import
-
-_pygtail = _try_import("pygtail")
-
-
 from . import _process
 
 
@@ -1988,7 +1983,7 @@ def stdout(self, n=10):
             raise ValueError("The number of lines must be positive!")
 
         # Append any new lines to the stdout list.
-        for line in _pygtail.Pygtail(self._stdout_file):
+        for line in self._tail(self._stdout_file):
             self._stdout.append(line.rstrip())
 
         # Get the current number of lines.
@@ -2295,7 +2290,7 @@ def _update_stdout_dict(self):
         lines = []
 
         # Append any new lines.
-        for line in _pygtail.Pygtail(self._log_file):
+        for line in self._tail(self._log_file):
             lines.append(line)
 
         # Append any new records to the stdout dictionary.

src/BioSimSpace/Process/_plumed.py

@@ -26,12 +26,8 @@
 
 __all__ = ["Plumed"]
 
-from .._Utils import _try_import
-
-_pygtail = _try_import("pygtail")
-
-
 from .. import Types as _Types
+from .._Utils import Tail as _Tail
 
 
 class Plumed:
@@ -104,6 +100,8 @@ def __init__(self, work_dir):
         # Set the location of the HILLS and COLVAR files.
         self._hills_file = _os.path.join(str(self._work_dir), "HILLS")
         self._colvar_file = _os.path.join(str(self._work_dir), "COLVAR")
+        self._hills_tail = _Tail(self._hills_file)
+        self._colvar_tail = _Tail(self._colvar_file)
 
         # The number of collective variables and total number of components.
         self._num_colvar = 0
@@ -247,15 +245,9 @@ def _createMetadynamicsConfig(self, system, protocol, property_map={}):
         self._config = []
         self._aux_files = []
 
-        # Always remove pygtail offset files.
-        try:
-            _os.remove(_os.path.join(str(self._work_dir), "COLVAR.offset"))
-        except:
-            pass
-        try:
-            _os.remove(_os.path.join(str(self._work_dir), "HILLS.offset"))
-        except:
-            pass
+        # Reset the incremental file readers.
+        self._colvar_tail = _Tail(self._colvar_file)
+        self._hills_tail = _Tail(self._hills_file)
 
         # Restart if existing HILLS and COLVAR files are present.
         if _os.path.isfile(self._colvar_file) and _os.path.isfile(self._hills_file):
@@ -959,11 +951,8 @@ def _createSteeringConfig(self, system, protocol, property_map={}):
         self._config = []
         self._aux_files = []
 
-        # Always remove pygtail offset files.
-        try:
-            _os.remove(_os.path.join(str(self._work_dir), "COLVAR.offset"))
-        except:
-            pass
+        # Reset the incremental file reader.
+        self._colvar_tail = _Tail(self._colvar_file)
 
         # Restart if an existing COLVAR files is present.
         if _os.path.isfile(self._colvar_file):
@@ -1610,7 +1599,7 @@ def _update_colvar_dict(self):
         # Parse the HILLS file for OpenMM.
         if self._use_hills:
             # Loop over all new lines in the file.
-            for line in _pygtail.Pygtail(self._hills_file):
+            for line in self._hills_tail:
                 # Is this a header line. If so, store the keys.
                 if line[3:9] == "FIELDS":
                     self._colvar_keys = line[10:].split()[: self._num_components + 1]
@@ -1623,7 +1612,7 @@ def _update_colvar_dict(self):
 
         else:
             # Loop over all new lines in the file.
-            for line in _pygtail.Pygtail(self._colvar_file):
+            for line in self._colvar_tail:
                 # Is this a header line. If so, store the keys.
                 if line[3:9] == "FIELDS":
                     self._colvar_keys = line[10:].split()
@@ -1643,7 +1632,7 @@ def _update_hills_dict(self):
             return
 
         # Loop over all new lines in the file.
-        for line in _pygtail.Pygtail(self._hills_file):
+        for line in self._hills_tail:
             # Is this a header line. If so, store the keys.
             if line[3:9] == "FIELDS":
                 self._hills_keys = line[10:].split()

src/BioSimSpace/Process/_process.py

@@ -27,11 +27,6 @@
 __all__ = ["Process"]
 
 
-from .._Utils import _try_import
-
-_pygtail = _try_import("pygtail")
-
-
 from .. import Units as _Units
 from .. import _is_notebook
 
@@ -332,9 +327,6 @@ def __repr__(self):
 
     def _clear_output(self):
         """Reset stdout and stderr."""
-        import glob as _glob
-        import os as _os
-
         # Create the files. This makes sure that the 'stdout' and 'stderr'
         # methods can be called when the files are empty.
         open(self._stdout_file, "a").close()
@@ -344,19 +336,31 @@ def _clear_output(self):
         self._stdout = []
         self._stderr = []
 
-        # Clean up any existing offset files.
-        offset_files = _glob.glob(_os.path.join(str(self._work_dir), "*.offset"))
+        # Reset the incremental file readers.
+        self._tails = {}
 
-        # Remove any HILLS or COLVAR files from the list. These will be dealt
-        # with by the PLUMED interface.
-        try:
-            offset_files.remove(_os.path.join(str(self._work_dir), "COLVAR.offset"))
-            offset_files.remove(_os.path.join(str(self._work_dir), "HILLS.offset"))
-        except:
-            pass
+    def _tail(self, filename):
+        """
+        Return the lines appended to a file since it was last read.
+
+        Parameters
+        ----------
+
+        filename : str
+            The path to the file.
+
+        Returns
+        -------
+
+        lines : iterable
+            An iterable over the new lines.
+        """
+        from .._Utils import Tail as _Tail
+
+        if filename not in self._tails:
+            self._tails[filename] = _Tail(filename)
 
-        for file in offset_files:
-            _os.remove(file)
+        return self._tails[filename]
 
     def _getPlumedConfig(self):
         """
@@ -1018,7 +1022,7 @@ def stdout(self, n=10):
             raise ValueError("The number of lines must be positive!")
 
         # Append any new lines to the stdout list.
-        for line in _pygtail.Pygtail(self._stdout_file):
+        for line in self._tail(self._stdout_file):
             self._stdout.append(line.rstrip())
 
         # Get the current number of lines.
@@ -1050,7 +1054,7 @@ def stderr(self, n=10):
             raise ValueError("The number of lines must be positive!")
 
         # Append any new lines to the stdout list.
-        for line in _pygtail.Pygtail(self._stderr_file):
+        for line in self._tail(self._stderr_file):
             self._stderr.append(line.rstrip())
 
         # Get the current number of lines.
@@ -1126,7 +1130,7 @@ def getStdout(self, block="AUTO"):
             self.wait()
 
         # Append any new lines to the stdout list.
-        for line in _pygtail.Pygtail(self._stdout_file):
+        for line in self._tail(self._stdout_file):
             self._stdout.append(line.rstrip())
 
         return self._stdout.copy()
@@ -1155,7 +1159,7 @@ def getStderr(self, block="AUTO"):
             self.wait()
 
         # Append any new lines to the stdout list.
-        for line in _pygtail.Pygtail(self._stderr_file):
+        for line in self._tail(self._stderr_file):
             self._stderr.append(line.rstrip())
 
         return self._stderr.copy()

src/BioSimSpace/Process/_somd.py

@@ -26,10 +26,6 @@
 
 __all__ = ["Somd"]
 
-from .._Utils import _try_import
-
-_pygtail = _try_import("pygtail")
-
 import string as _string
 
 from . import _process
@@ -876,7 +872,7 @@ def getGradient(self, time_series=False, block="AUTO"):
             return None
 
         # Append any new lines to the gradients list.
-        for line in _pygtail.Pygtail(self._gradient_file):
+        for line in self._tail(self._gradient_file):
             # Ignore comments.
             if line[0] != "#":
                 self._gradients.append(float(line.rstrip().split()[-1]))

src/BioSimSpace/Sandpit/Exscientia/Process/_amber.py

@@ -27,11 +27,6 @@
 __all__ = ["Amber"]
 
 
-from .._Utils import _try_import
-
-_pygtail = _try_import("pygtail")
-
-
 from .._Utils import _have_imported, _try_import
 
 # alchemlyb isn't available on all variants of Python that we support, so we
@@ -2795,7 +2790,7 @@ def stdout(self, n=10):
         self._is_header = False
 
         # Append any new lines to the stdout list.
-        for line in _pygtail.Pygtail(self._stdout_file):
+        for line in self._tail(self._stdout_file):
             self._stdout.append(line.rstrip())
             line = line.strip()
 
@@ -3053,9 +3048,6 @@ def _init_stdout_dict(self):
         into the working directory, start and wait again. In this case, the result will
         be a combination of both runs. This function ensures that the results are
         regenerated from the new output file."""
-        import os
-        from pathlib import Path as _Path
-
         # Initialise dictionaries to hold stdout records for all possible
         # degrees of freedom. For regular simulations there will be one,
         # for free-energy simulations there will be three, i.e. one for
@@ -3080,9 +3072,9 @@ def _init_stdout_dict(self):
         self._finished_results = False
         self._is_header = False
 
-        # Initiate the pytails.
-        for file in _Path(self.workDir()).glob("*.out.offset"):
-            os.remove(file)
+        # Reset the incremental readers for the output files.
+        for file in [f for f in self._tails if f.endswith(".out")]:
+            del self._tails[file]
 
     def _saveMetric(
         self, filename="metric.parquet", u_nk="u_nk.parquet", dHdl="dHdl.parquet"

src/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py

@@ -27,11 +27,6 @@
 __all__ = ["Gromacs"]
 
 
-from .._Utils import _try_import
-
-_pygtail = _try_import("pygtail")
-
-
 from .._Utils import _have_imported, _try_import
 
 # alchemlyb isn't available on all variants of Python that we support, so we
@@ -2187,7 +2182,7 @@ def stdout(self, n=10):
             raise ValueError("The number of lines must be positive!")
 
         # Append any new lines to the stdout list.
-        for line in _pygtail.Pygtail(self._stdout_file):
+        for line in self._tail(self._stdout_file):
             self._stdout.append(line.rstrip())
 
         # Get the current number of lines.

src/BioSimSpace/Sandpit/Exscientia/Process/_namd.py

@@ -26,11 +26,6 @@
 
 __all__ = ["Namd"]
 
-from .._Utils import _try_import
-
-_pygtail = _try_import("pygtail")
-
-
 from . import _process
 
 
@@ -2103,7 +2098,7 @@ def stdout(self, n=10):
             raise ValueError("The number of lines must be positive!")
 
         # Append any new lines to the stdout list.
-        for line in _pygtail.Pygtail(self._stdout_file):
+        for line in self._tail(self._stdout_file):
             self._stdout.append(line.rstrip())
 
             # Split the record using whitespace.