Fix discovery of output files when out-of-dir

StagyyPar.legacy_output() and .h5_output() now return absolute paths.

These methods would previously return relative paths, which were not
always made absolute at the call-site. This meant output files were not
correctly discovered when running stagpy from a different location than
the root of the run directory.

Author: amorison

stagpy/parfile.py

@@ -23,6 +23,7 @@ class StagyyPar:
     """A Fortran namelist file written for StagYY."""
 
     nml: Namelist
+    root: Path
 
     @staticmethod
     def _from_file(parfile: Path) -> StagyyPar:
@@ -35,7 +36,7 @@ def _from_file(parfile: Path) -> StagyyPar:
                     content[option] = value.strip()
                 except AttributeError:
                     pass
-        return StagyyPar(nml=par)
+        return StagyyPar(nml=par, root=parfile.parent)
 
     def _update(self, par_new: StagyyPar) -> None:
         for section, content in par_new.nml.items():
@@ -54,15 +55,14 @@ def from_main_par(parfile: Path) -> StagyyPar:
         - `par_file` itself;
         - `parameters.dat` if it can be found in the StagYY output directories.
         """
-        root = parfile.parent
         par_main = StagyyPar._from_file(parfile)
         if "default_parameters_parfile" in par_main.nml:
             dfltfile = par_main.get(
                 "default_parameters_parfile",
                 "par_name_defaultparameters",
                 "par_defaults",
             )
-            par_dflt = StagyyPar._from_file(root / dfltfile)
+            par_dflt = StagyyPar._from_file(par_main.root / dfltfile)
             par_dflt._update(par_main)
             par_main = par_dflt
 
@@ -80,8 +80,8 @@ def get(self, section: str, option: str, default: T) -> T:
 
     def legacy_output(self, suffix: str) -> Path:
         stem = self.get("ioin", "output_file_stem", "test")
-        return Path(stem + suffix)
+        return self.root / (stem + suffix)
 
     def h5_output(self, filename: str) -> Path:
         h5folder = self.get("ioin", "hdf5_output_folder", "+hdf5")
-        return Path(h5folder) / filename
+        return self.root / h5folder / filename

stagpy/stagyydata.py

@@ -447,7 +447,7 @@ def __len__(self) -> int:
                 length = isnap
                 self._all_isteps_known = True
             if length < 0:
-                out_stem = re.escape(Path(self.sdat.par.legacy_output("_")).name[:-1])
+                out_stem = re.escape(self.sdat.par.legacy_output("_").name[:-1])
                 rgx = re.compile(f"^{out_stem}_([a-zA-Z]+)([0-9]{{5}})$")
                 fstems = set(fstem for fstem in phyvars.FIELD_FILES)
                 for fname in self.sdat._files:
@@ -745,8 +745,7 @@ def rtimes(self) -> Optional[DataFrame]:
     @cached_property
     def _files(self) -> set[Path]:
         """Set of found binary files output by StagYY."""
-        out_stem = self.par.legacy_output("_")
-        out_dir = self.path / out_stem.parent
+        out_dir = self.par.legacy_output("_").parent
         if out_dir.is_dir():
             return set(out_dir.iterdir())
         return set()
@@ -791,10 +790,9 @@ def filename(
             fname += f"{timestep:05d}"
         fname += suffix
         if not force_legacy and self.hdf5:
-            fpath = self.hdf5 / fname
+            fpath = self.par.h5_output(fname)
         else:
             fpath = self.par.legacy_output(f"_{fname}")
-            fpath = self.path / fpath
         return fpath
 
     def _binfiles_set(self, isnap: int) -> set[Path]: