redo SuperSequence.save as files in directory

lib/sequences.py

@@ -5,6 +5,8 @@ from .plotdefs import Plotter
 import copy
 import pathlib
 import toml
+import shutil
+import os
 
 """
 Builds on abstractions defined in lib.structures.
@@ -15,13 +17,18 @@ def _titlecase(s: str) -> str:
         for _s in s.replace(" ", "_").split("_"))
 
 def _fresh_filename(path: pathlib.Path, overwrite: bool=False) -> pathlib.Path:
-    if overwrite:
-        return path
     _path = path
-    while _path.is_file():
-        print(f"WARNING: found existing file {_path}")
-        _path = _path.parent.joinpath(_path.stem + "_" + _path.suffix)
-        print(f"Write instead to {_path}")
+    while _path.exists():
+        print(f"WARNING: {_path} exists in filesystem")
+        if overwrite:
+            print(f":: rm -rf {_path}")
+            if _path.is_dir():
+                shutil.rmtree(str(_path))
+            else:
+                os.remove(str(_path))
+        else:
+            _path = _path.parent.joinpath(_path.stem + "_" + _path.suffix)
+            print(f"Write instead to {_path}")
     return _path
 
 def min_n(generator, default=None):
@@ -55,7 +62,7 @@ class SuperSequence:
     """
 
     def __init__(self, outdir: pathlib.Path, name: str,
-            sequences: dict[str, Sequence]=None,
+            sequences: dict[str, Sequence]=None, params: dict[str, ...]=None,
             defaults: ConnectionLayout=None):
         """
         Constructor.
@@ -70,6 +77,7 @@ class SuperSequence:
         self.outdir = outdir
         self.name = name
         self.sequences = dict() if sequences is None else sequences
+        self.params = dict() if params is None else params
         self.defaults = defaults
 
     def __getitem__(self, key: str) -> Sequence:
@@ -154,21 +162,18 @@ class SuperSequence:
     def save(self, target: pathlib.Path=None, overwrite: bool=False,
             printflag: bool=True):
         T = self.outdir.joinpath(self.name) if target is None else target
-        T = T.parent.joinpath(T.name + ".toml") if T.suffix != ".toml" else T
         if printflag: print(f"[sequencing] Saving sequence data to '{T}':")
-        sequence_file = _fresh_filename(T, overwrite)
-        if printflag: print(f"[sequencing] save sequence '{sequence_file.stem}'")
-        print(sequence_file.parent.is_dir())
-        print(sequence_file.exists())
-        if not sequence_file.parent.is_dir():
-            print(f":: mkdir -p '{sequence_file.parent}'")
-            sequence_file.parent.mkdir(parents=True, exist_ok=True)
-        print(sequence_file.parent.is_dir())
-        sequence_file = sequence_file.parent.joinpath(sequence_file.name)
-        print(sequence_file)
-        print(sequence_file.parent.is_dir())
-        with sequence_file.open('w') as outfile:
+        T = _fresh_filename(T, overwrite)
+        T_seq = T.joinpath("sequence.toml")
+        T_par = T.joinpath("parameters.toml")
+
+        if not T.is_dir():
+            print(f":: mkdir -p '{T}'")
+            T.mkdir(parents=True, exist_ok=True)
+        with T_seq.open('w') as outfile:
             toml.dump(self.to_primitives(), outfile)
+        with T_par.open('w') as outfile:
+            toml.dump(self.params, outfile)
         return self
 
     @staticmethod