GenericJob: extend the compress() function

For codes like VASP we typically remove certain files before we compress the working directory and other files we leave out of the archive. This is now possible using `job.files_to_compress` and `job.files_to_remove`. Both properties return a list, so the user can append additional files.

pyiron_base/jobs/job/core.py

@@ -209,6 +209,8 @@ def __init__(self, project, job_name):
         self._import_directory = None
         self._database_property = DatabaseProperties()
         self._hdf5_content = HDF5Content(project_hdf5=self._hdf5)
+        self._files_to_remove = list()
+        self._files_to_compress = list()
 
     @property
     def content(self):
@@ -385,6 +387,14 @@ def project_hdf5(self, project):
         """
         self._hdf5 = project.copy()
 
+    @property
+    def files_to_compress(self):
+        return self._files_to_compress
+
+    @property
+    def files_to_remove(self):
+        return self._files_to_remove
+
     def relocate_hdf5(self, h5_path=None):
         """
         Relocate the hdf file. This function is needed when the child job is
@@ -1061,14 +1071,22 @@ def _list_ext_childs(self):
         childs = self.list_childs()
         return list(set(childs) - set(nodes))
 
-    def compress(self, files_to_compress=None):
+    def compress(self, files_to_compress=None, files_to_remove=None):
         """
         Compress the output files of a job object.
 
         Args:
             files_to_compress (list):
         """
-        _job_compress(job=self, files_to_compress=files_to_compress)
+        if files_to_compress is None and len(self._files_to_compress) != 0:
+            files_to_compress = self._files_to_compress
+        elif files_to_compress is None:
+            files_to_compress = self.files.list()
+        if files_to_remove is None:
+            files_to_remove = self._files_to_remove
+        else:
+            files_to_remove = []
+        _job_compress(job=self, files_to_compress=files_to_compress, files_to_remove=files_to_remove)
 
     def decompress(self):
         """

pyiron_base/jobs/job/generic.py

@@ -1069,6 +1069,10 @@ def to_dict(self):
             data_dict["import_directory"] = self._import_directory
         if self._executor_type is not None:
             data_dict["executor_type"] = self._executor_type
+        if len(self._files_to_compress) > 0:
+            data_dict["files_to_compress"] = self._files_to_compress
+        if len(self._files_to_remove) > 0:
+            data_dict["files_to_compress"] = self._files_to_remove
         return data_dict
 
     def from_dict(self, job_dict):

pyiron_base/jobs/job/util.py

@@ -275,17 +275,25 @@ def _get_compressed_job_name(working_directory):
     )
 
 
-def _job_compress(job, files_to_compress=None):
+def _job_compress(job, files_to_compress=[], files_to_remove=[]):
     """
     Compress the output files of a job object.
 
     Args:
         job (JobCore): job object to compress
         files_to_compress (list): list of files to compress
+        files_to_remove (list): list of files to remove
     """
+
+    def delete_file_or_folder(fullname):
+        if os.path.isfile(fullname):
+            os.remove(fullname)
+        elif os.path.isdir(fullname):
+            shutil.rmtree(fullname)
+
     if not _job_is_compressed(job):
-        if files_to_compress is None:
-            files_to_compress = job.files.list()
+        for name in files_to_remove:
+            delete_file_or_folder(fullname=os.path.join(job.working_directory, name))
         cwd = os.getcwd()
         try:
             os.chdir(job.working_directory)
@@ -295,11 +303,9 @@ def _job_compress(job, files_to_compress=None):
                         tar.add(name)
             for name in files_to_compress:
                 if "tar" not in name:
-                    fullname = os.path.join(job.working_directory, name)
-                    if os.path.isfile(fullname):
-                        os.remove(fullname)
-                    elif os.path.isdir(fullname):
-                        shutil.rmtree(fullname)
+                    delete_file_or_folder(
+                        fullname=os.path.join(job.working_directory, name)
+                    )
         finally:
             os.chdir(cwd)
     else: