Merge pull request #1319 from pyiron/depworkdir

Deprecate workdir path getter in favour of job.files

.ci_support/environment-old.yml

@@ -13,7 +13,7 @@ dependencies:
 - pandas =2.0.3
 - phonopy =2.20.0
 - pint =0.18
-- pyiron_base =0.7.3
+- pyiron_base =0.7.7
 - pylammpsmpi =0.2.7
 - pyscal =2.10.4
 - scikit-learn =1.2.1

.ci_support/environment.yml

@@ -15,7 +15,7 @@ dependencies:
 - pandas =2.2.0
 - phonopy =2.21.0
 - pint =0.23
-- pyiron_base =0.7.5
+- pyiron_base =0.7.7
 - pylammpsmpi =0.2.13
 - pyscal =2.10.18
 - scikit-learn =1.4.0

pyiron_atomistics/atomistics/job/atomistic.py

@@ -449,6 +449,7 @@ def restart(self, job_name=None, job_type=None):
         new_ham._generic_input["structure"] = "atoms"
         return new_ham
 
+    @deprecate("use job.files instead!")
     def get_workdir_file(self, filename: str) -> None:
         """
         Checks if a given file exists within the job's working directory and returns the absolute path to it.

pyiron_atomistics/lammps/base.py

@@ -771,7 +771,7 @@ def compress(self, files_to_compress=None):
         """
         if files_to_compress is None:
             files_to_compress = [
-                f for f in list(self.list_files()) if f not in ["restart.out"]
+                f for f in self.files.list() if f not in ["restart.out"]
             ]
         super(LammpsBase, self).compress(files_to_compress=files_to_compress)
 
@@ -831,9 +831,9 @@ def restart(self, job_name=None, job_type=None):
         new_ham = super(LammpsBase, self).restart(job_name=job_name, job_type=job_type)
         if new_ham.__name__ == self.__name__:
             new_ham.potential = self.potential
-            if "restart.out" in self.list_files():
+            if "restart.out" in self.files.list():
                 new_ham.read_restart_file(filename="restart.out")
-                new_ham.restart_file_list.append(self.get_workdir_file("restart.out"))
+                new_ham.restart_file_list.append(self.files.restart_out)
         return new_ham
 
     @staticmethod

pyiron_atomistics/sphinx/base.py

@@ -1742,15 +1742,15 @@ def compress(self, files_to_compress=None):
         if files_to_compress is None:
             files_to_compress = [
                 f
-                for f in list(self.list_files())
+                for f in self.files.list()
                 if (
                     f not in ["rho.sxb", "waves.sxb"]
                     and not stat.S_ISFIFO(
                         os.stat(os.path.join(self.working_directory, f)).st_mode
                     )
                 )
             ]
-        for f in list(self.list_files()):
+        for f in self.files.list():
             filename = os.path.join(self.working_directory, f)
             if (
                 f not in files_to_compress
@@ -1857,7 +1857,7 @@ def run_addon(
 
                 # --- link other files
                 linkfiles = []
-                for file in self.list_files():
+                for file in self.files.list():
                     linkfile = os.path.join(tempd, file)
                     if not os.path.isfile(linkfile):
                         os.symlink(

pyiron_atomistics/vasp/base.py

@@ -533,8 +533,7 @@ def cleanup(self, files_to_remove=("WAVECAR", "CHGCAR", "CHG", "vasprun.xml")):
         """
         Removes excess files (by default: WAVECAR, CHGCAR, CHG)
         """
-        list_files = self.list_files()
-        for file in list_files:
+        for file in self.files.list():
             if file in files_to_remove:
                 abs_file_path = os.path.join(self.working_directory, file)
                 os.remove(abs_file_path)
@@ -1631,7 +1630,7 @@ def restart_from_charge_density(
         new_ham = self.restart(job_name=job_name, job_type=job_type)
 
         if new_ham.__name__ == self.__name__:
-            new_ham.restart_file_list.append(self.get_workdir_file("CHGCAR"))
+            new_ham.restart_file_list.append(self.files.CHGCAR)
             new_ham.input.incar["ICHARG"] = self.get_icharg_value(
                 icharg=icharg,
                 self_consistent_calc=self_consistent_calc,
@@ -1680,8 +1679,8 @@ def restart_from_wave_and_charge(
         """
         new_ham = self.restart(job_name=job_name, job_type=job_type)
         if new_ham.__name__ == self.__name__:
-            new_ham.restart_file_list.append(self.get_workdir_file("CHGCAR"))
-            new_ham.restart_file_list.append(self.get_workdir_file("WAVECAR"))
+            new_ham.restart_file_list.append(self.files.CHGCAR)
+            new_ham.restart_file_list.append(self.files.WAVECAR)
             new_ham.input.incar["ISTART"] = istart
             new_ham.input.incar["ICHARG"] = self.get_icharg_value(
                 icharg=icharg,
@@ -1699,7 +1698,7 @@ def compress(self, files_to_compress=None):
         if files_to_compress is None:
             files_to_compress = [
                 f
-                for f in list(self.list_files())
+                for f in self.files.list()
                 if f
                 not in [
                     "CHGCAR",
@@ -1712,7 +1711,7 @@ def compress(self, files_to_compress=None):
                 ]
             ]
         # delete empty files
-        for f in list(self.list_files()):
+        for f in self.files.list():
             filename = os.path.join(self.working_directory, f)
             if (
                 f not in files_to_compress
@@ -1736,7 +1735,7 @@ def restart_from_wave_functions(self, job_name=None, job_type=None, istart=1):
         """
         new_ham = self.restart(job_name=job_name, job_type=job_type)
         if new_ham.__name__ == self.__name__:
-            new_ham.restart_file_list.append(self.get_workdir_file("WAVECAR"))
+            new_ham.restart_file_list.append(self.files.WAVECAR)
             new_ham.input.incar["ISTART"] = istart
         return new_ham
 

pyproject.toml

@@ -35,7 +35,7 @@ dependencies = [
     "pandas==2.2.0",
     "phonopy==2.21.0",
     "pint==0.23",
-    "pyiron_base==0.7.5",
+    "pyiron_base==0.7.7",
     "pylammpsmpi==0.2.13",
     "scipy==1.12.0",
     "scikit-learn==1.4.0",

tests/vasp/test_vasp.py

@@ -365,7 +365,7 @@ def test_run_complete(self):
         job_chg_den = self.job_complete.restart_from_charge_density(job_name="chg")
         self.assertEqual(job_chg_den.structure, self.job_complete.get_structure(-1))
         self.assertTrue(
-            posixpath.join(self.job_complete.working_directory, "CHGCAR")
+            os.path.join(self.job_complete.working_directory, "CHGCAR")
             in job_chg_den.restart_file_list
         )
 
@@ -380,11 +380,11 @@ def check_group_is_empty(example_job, group_name):
         )
         self.assertEqual(job_chg_wave.structure, self.job_complete.get_structure(-1))
         self.assertTrue(
-            posixpath.join(self.job_complete.working_directory, "WAVECAR")
+            os.path.join(self.job_complete.working_directory, "WAVECAR")
             in job_chg_wave.restart_file_list
         )
         self.assertTrue(
-            posixpath.join(self.job_complete.working_directory, "CHGCAR")
+            os.path.join(self.job_complete.working_directory, "CHGCAR")
             in job_chg_wave.restart_file_list
         )
         for key, val in job_chg_wave.restart_file_dict.items():
@@ -456,7 +456,7 @@ def test_kspacing(self):
         job_kspace.input.incar["KSPACING"] = 0.5
         with warnings.catch_warnings(record=True) as w:
             job_kspace.run(run_mode="manual")
-            self.assertNotIn("KPOINTS", job_kspace.list_files(), "'KPOINTS' file written even when "
+            self.assertNotIn("KPOINTS", job_kspace.files.list(), "'KPOINTS' file written even when "
                                                                  "KPACING tag is present in INCAR")
 
             self.assertTrue(len(w) <= 2)