From e89fbb09de67bb2217ffe56c1d26351ea5b7a453 Mon Sep 17 00:00:00 2001
From: Marvin Poul <poul@mpie.de>
Date: Thu, 10 Nov 2022 12:32:28 +0100
Subject: [PATCH 01/42] Add a tail method to inspect output files

---
 pyiron_base/jobs/job/core.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/pyiron_base/jobs/job/core.py b/pyiron_base/jobs/job/core.py
index 09f443ad9..37e9a405e 100644
--- a/pyiron_base/jobs/job/core.py
+++ b/pyiron_base/jobs/job/core.py
@@ -971,6 +971,22 @@ def __delitem__(self, key):
         """
         del self.project_hdf5[posixpath.join(self.project_hdf5.h5_path, key)]
 
+    def tail(self, file_name, lines=100):
+        """
+        Print the last lines of the given file in the job folder.
+
+        Args:
+            file_name (str): the file to print
+            lines (int): how many lines to print
+
+        Raises:
+            FileNotFoundError: if the given file name does not exist in the job folder
+        """
+        if file_name in self.list_files():
+            print(*self[file_name][-lines:])
+        else:
+            raise FileNotFoundError(file_name)
+
     def __repr__(self):
         """
         Human readable string representation

From 86df6e8a2f54008f1b8cd76474e29f848c15171d Mon Sep 17 00:00:00 2001
From: Marvin Poul <poul@mpie.de>
Date: Thu, 10 Nov 2022 12:43:35 +0100
Subject: [PATCH 02/42] Extract file reading into method

---
 pyiron_base/jobs/job/core.py | 23 ++++++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

diff --git a/pyiron_base/jobs/job/core.py b/pyiron_base/jobs/job/core.py
index 37e9a405e..6773b10e2 100644
--- a/pyiron_base/jobs/job/core.py
+++ b/pyiron_base/jobs/job/core.py
@@ -865,6 +865,25 @@ def __del__(self):
         del self._master_id
         del self._status
 
+    def _read_file(self, file_name):
+        """
+        Return list of lines of the given file.
+
+        Transparently decompresses the file if job is compressed.
+
+        Args:
+            file_name (str): the file to print
+
+        Raises:
+            FileNotFoundError: if the given file name does not exist in the job folder
+        """
+        if file_name not in self.list_files():
+            raise FileNotFoundError(file_name)
+
+        file_name = posixpath.join(self.working_directory, "{}".format(item))
+        with open(file_name) as f:
+            return f.readlines()
+
     def __getitem__(self, item):
         """
         Get/read data from the HDF5 file, child jobs or access log files.
@@ -887,9 +906,7 @@ def __getitem__(self, item):
         """
 
         if item in self.list_files():
-            file_name = posixpath.join(self.working_directory, "{}".format(item))
-            with open(file_name) as f:
-                return f.readlines()
+            return self._read_file(item)
 
         # first try to access HDF5 directly to make the common case fast
         try:

From 460dad9dd93efb3ff33b4c66cb18262ceb829ed2 Mon Sep 17 00:00:00 2001
From: Marvin Poul <poul@mpie.de>
Date: Thu, 10 Nov 2022 12:52:18 +0100
Subject: [PATCH 03/42] Use _read_file in tail

---
 pyiron_base/jobs/job/core.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/pyiron_base/jobs/job/core.py b/pyiron_base/jobs/job/core.py
index 6773b10e2..d22e96bb3 100644
--- a/pyiron_base/jobs/job/core.py
+++ b/pyiron_base/jobs/job/core.py
@@ -999,10 +999,7 @@ def tail(self, file_name, lines=100):
         Raises:
             FileNotFoundError: if the given file name does not exist in the job folder
         """
-        if file_name in self.list_files():
-            print(*self[file_name][-lines:])
-        else:
-            raise FileNotFoundError(file_name)
+        print(*self._read_file(file_name)[-lines:])
 
     def __repr__(self):
         """

From a3fbe13d622d88b053177c995b607c660aff2a86 Mon Sep 17 00:00:00 2001
From: Marvin Poul <poul@mpie.de>
Date: Thu, 10 Nov 2022 12:56:54 +0100
Subject: [PATCH 04/42] Move list files to util

---
 pyiron_base/jobs/job/core.py |  4 +---
 pyiron_base/jobs/job/util.py | 16 ++++++++++++++++
 2 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/pyiron_base/jobs/job/core.py b/pyiron_base/jobs/job/core.py
index d22e96bb3..9f51da13b 100644
--- a/pyiron_base/jobs/job/core.py
+++ b/pyiron_base/jobs/job/core.py
@@ -595,9 +595,7 @@ def list_files(self):
         Returns:
             list: list of file names
         """
-        if os.path.isdir(self.working_directory):
-            return os.listdir(self.working_directory)
-        return []
+        return _job_list_files(self)
 
     def list_childs(self):
         """
diff --git a/pyiron_base/jobs/job/util.py b/pyiron_base/jobs/job/util.py
index d54684c33..1e05d8f59 100644
--- a/pyiron_base/jobs/job/util.py
+++ b/pyiron_base/jobs/job/util.py
@@ -308,6 +308,22 @@ def _job_is_compressed(job):
     return False
 
 
+def _job_list_files(job):
+    """
+    Returns list of files in the jobs working directory.
+
+    If the job is compressed, return a list of files in the archive.
+
+    Args:
+        job (JobCore): job object to inspect files in
+
+    Returns:
+        list of str: file names
+    """
+    if os.path.isdir(self.working_directory):
+        return os.listdir(self.working_directory)
+    return []
+
 def _job_archive(job):
     """
     Compress HDF5 file of the job object to tar-archive

From e7f308f447fb9ef2fcb05fbba06ea22f7234100b Mon Sep 17 00:00:00 2001
From: Marvin Poul <poul@mpie.de>
Date: Thu, 10 Nov 2022 12:59:45 +0100
Subject: [PATCH 05/42] Move read_file to util

---
 pyiron_base/jobs/job/core.py | 25 ++++---------------------
 pyiron_base/jobs/job/util.py | 21 +++++++++++++++++++++
 2 files changed, 25 insertions(+), 21 deletions(-)

diff --git a/pyiron_base/jobs/job/core.py b/pyiron_base/jobs/job/core.py
index 9f51da13b..0bde1893d 100644
--- a/pyiron_base/jobs/job/core.py
+++ b/pyiron_base/jobs/job/core.py
@@ -26,6 +26,8 @@
     _job_is_compressed,
     _job_compress,
     _job_decompress,
+    _job_list_files,
+    _job_read_file,
     _job_delete_files,
     _job_delete_hdf,
     _job_remove_folder,
@@ -863,25 +865,6 @@ def __del__(self):
         del self._master_id
         del self._status
 
-    def _read_file(self, file_name):
-        """
-        Return list of lines of the given file.
-
-        Transparently decompresses the file if job is compressed.
-
-        Args:
-            file_name (str): the file to print
-
-        Raises:
-            FileNotFoundError: if the given file name does not exist in the job folder
-        """
-        if file_name not in self.list_files():
-            raise FileNotFoundError(file_name)
-
-        file_name = posixpath.join(self.working_directory, "{}".format(item))
-        with open(file_name) as f:
-            return f.readlines()
-
     def __getitem__(self, item):
         """
         Get/read data from the HDF5 file, child jobs or access log files.
@@ -904,7 +887,7 @@ def __getitem__(self, item):
         """
 
         if item in self.list_files():
-            return self._read_file(item)
+            return _job_read_file(item)
 
         # first try to access HDF5 directly to make the common case fast
         try:
@@ -997,7 +980,7 @@ def tail(self, file_name, lines=100):
         Raises:
             FileNotFoundError: if the given file name does not exist in the job folder
         """
-        print(*self._read_file(file_name)[-lines:])
+        print(*_job_read_file(file_name)[-lines:])
 
     def __repr__(self):
         """
diff --git a/pyiron_base/jobs/job/util.py b/pyiron_base/jobs/job/util.py
index 1e05d8f59..157439500 100644
--- a/pyiron_base/jobs/job/util.py
+++ b/pyiron_base/jobs/job/util.py
@@ -324,6 +324,27 @@ def _job_list_files(job):
         return os.listdir(self.working_directory)
     return []
 
+
+def _read_file(self, file_name):
+    """
+    Return list of lines of the given file.
+
+    Transparently decompresses the file if job is compressed.
+
+    Args:
+        file_name (str): the file to print
+
+    Raises:
+        FileNotFoundError: if the given file name does not exist in the job folder
+    """
+    if file_name not in self.list_files():
+        raise FileNotFoundError(file_name)
+
+    file_name = posixpath.join(self.working_directory, "{}".format(item))
+    with open(file_name) as f:
+        return f.readlines()
+
+
 def _job_archive(job):
     """
     Compress HDF5 file of the job object to tar-archive

From 36d3d90da5436aa48126f9b8ad316167e68c2881 Mon Sep 17 00:00:00 2001
From: Marvin Poul <poul@mpie.de>
Date: Thu, 10 Nov 2022 13:00:03 +0100
Subject: [PATCH 06/42] Extract definition of job archive name

---
 pyiron_base/jobs/job/util.py | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/pyiron_base/jobs/job/util.py b/pyiron_base/jobs/job/util.py
index 157439500..b73efa9a1 100644
--- a/pyiron_base/jobs/job/util.py
+++ b/pyiron_base/jobs/job/util.py
@@ -241,6 +241,11 @@ def _kill_child(job):
                     job_process.kill()
 
 
+def _job_compressed_name(job):
+    """Return the canonical file name of a compressed job."""
+    return os.path.join(job.working_directory, job.job_name + ".tar.bz2"),
+
+
 def _job_compress(job, files_to_compress=None):
     """
     Compress the output files of a job object.
@@ -255,10 +260,7 @@ def _job_compress(job, files_to_compress=None):
         cwd = os.getcwd()
         try:
             os.chdir(job.working_directory)
-            with tarfile.open(
-                os.path.join(job.working_directory, job.job_name + ".tar.bz2"),
-                "w:bz2",
-            ) as tar:
+            with tarfile.open(_job_compressed_name(job), "w:bz2") as tar:
                 for name in files_to_compress:
                     if "tar" not in name and not stat.S_ISFIFO(os.stat(name).st_mode):
                         tar.add(name)
@@ -272,7 +274,7 @@ def _job_compress(job, files_to_compress=None):
         finally:
             os.chdir(cwd)
     else:
-        print("The files are already compressed!")
+        job.logger.info("The files are already compressed!")
 
 
 def _job_decompress(job):
@@ -283,8 +285,7 @@ def _job_decompress(job):
         job (JobCore): job object to decompress
     """
     try:
-        tar_file_name = os.path.join(job.working_directory, job.job_name + ".tar.bz2")
-        with tarfile.open(tar_file_name, "r:bz2") as tar:
+        with tarfile.open(_job_compressed_name(job), "r:bz2") as tar:
             tar.extractall(job.working_directory)
         os.remove(tar_file_name)
     except IOError:
@@ -301,7 +302,7 @@ def _job_is_compressed(job):
     Returns:
         bool: [True/False]
     """
-    compressed_name = job.job_name + ".tar.bz2"
+    compressed_name = os.path.basename(_job_compressed_name(job))
     for name in job.list_files():
         if compressed_name in name:
             return True

From 9a00f532dec657668dc54e5fdad4eb32007e90ae Mon Sep 17 00:00:00 2001
From: Marvin Poul <poul@mpie.de>
Date: Thu, 10 Nov 2022 13:11:15 +0100
Subject: [PATCH 07/42] Add transparent compression support

---
 pyiron_base/jobs/job/util.py | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/pyiron_base/jobs/job/util.py b/pyiron_base/jobs/job/util.py
index b73efa9a1..fcd35678f 100644
--- a/pyiron_base/jobs/job/util.py
+++ b/pyiron_base/jobs/job/util.py
@@ -322,11 +322,15 @@ def _job_list_files(job):
         list of str: file names
     """
     if os.path.isdir(self.working_directory):
-        return os.listdir(self.working_directory)
+        if _job_is_compressed(job):
+            with tarfile.open(_job_compressed_name, "r") as tar:
+                return [member.name for i in tar.getmembers() if member.isfile()]
+        else:
+            return os.listdir(self.working_directory)
     return []
 
 
-def _read_file(self, file_name):
+def _job_read_file(self, file_name):
     """
     Return list of lines of the given file.
 
@@ -342,8 +346,12 @@ def _read_file(self, file_name):
         raise FileNotFoundError(file_name)
 
     file_name = posixpath.join(self.working_directory, "{}".format(item))
-    with open(file_name) as f:
-        return f.readlines()
+    if _job_is_compressed(job):
+        with tarfile.open(_job_compressed_name(job)) as f:
+            return f.extractfile(item).readlines()
+    else:
+        with open(file_name) as f:
+            return f.readlines()
 
 
 def _job_archive(job):

From a5965d067d791792f3153b925e129c7589a9ba20 Mon Sep 17 00:00:00 2001
From: Marvin Poul <poul@mpie.de>
Date: Tue, 22 Nov 2022 09:07:33 +0100
Subject: [PATCH 08/42] Fix typos and inadvertant recursion in
 _job_is_compressed/_job_list_files

---
 pyiron_base/jobs/job/util.py | 19 ++++++++-----------
 1 file changed, 8 insertions(+), 11 deletions(-)

diff --git a/pyiron_base/jobs/job/util.py b/pyiron_base/jobs/job/util.py
index fcd35678f..5505ff065 100644
--- a/pyiron_base/jobs/job/util.py
+++ b/pyiron_base/jobs/job/util.py
@@ -243,7 +243,7 @@ def _kill_child(job):
 
 def _job_compressed_name(job):
     """Return the canonical file name of a compressed job."""
-    return os.path.join(job.working_directory, job.job_name + ".tar.bz2"),
+    return os.path.join(job.working_directory, job.job_name + ".tar.bz2")
 
 
 def _job_compress(job, files_to_compress=None):
@@ -303,10 +303,7 @@ def _job_is_compressed(job):
         bool: [True/False]
     """
     compressed_name = os.path.basename(_job_compressed_name(job))
-    for name in job.list_files():
-        if compressed_name in name:
-            return True
-    return False
+    return compressed_name in os.listdir(job.working_directory)
 
 
 def _job_list_files(job):
@@ -321,16 +318,16 @@ def _job_list_files(job):
     Returns:
         list of str: file names
     """
-    if os.path.isdir(self.working_directory):
+    if os.path.isdir(job.working_directory):
         if _job_is_compressed(job):
-            with tarfile.open(_job_compressed_name, "r") as tar:
+            with tarfile.open(_job_compressed_name(job), "r") as tar:
                 return [member.name for i in tar.getmembers() if member.isfile()]
         else:
-            return os.listdir(self.working_directory)
+            return os.listdir(job.working_directory)
     return []
 
 
-def _job_read_file(self, file_name):
+def _job_read_file(job, file_name):
     """
     Return list of lines of the given file.
 
@@ -342,10 +339,10 @@ def _job_read_file(self, file_name):
     Raises:
         FileNotFoundError: if the given file name does not exist in the job folder
     """
-    if file_name not in self.list_files():
+    if file_name not in job.list_files():
         raise FileNotFoundError(file_name)
 
-    file_name = posixpath.join(self.working_directory, "{}".format(item))
+    file_name = posixpath.join(job.working_directory, "{}".format(item))
     if _job_is_compressed(job):
         with tarfile.open(_job_compressed_name(job)) as f:
             return f.extractfile(item).readlines()

From ecde14289353b47a059486eb6b2d58c0b9c343a0 Mon Sep 17 00:00:00 2001
From: Marvin Poul <poul@mpie.de>
Date: Tue, 22 Nov 2022 13:15:58 +0100
Subject: [PATCH 09/42] Fix slopiness

---
 pyiron_base/jobs/job/core.py | 4 ++--
 pyiron_base/jobs/job/util.py | 5 +++--
 tests/job/test_genericJob.py | 4 ++--
 3 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/pyiron_base/jobs/job/core.py b/pyiron_base/jobs/job/core.py
index 0bde1893d..376f89fc2 100644
--- a/pyiron_base/jobs/job/core.py
+++ b/pyiron_base/jobs/job/core.py
@@ -887,7 +887,7 @@ def __getitem__(self, item):
         """
 
         if item in self.list_files():
-            return _job_read_file(item)
+            return _job_read_file(job, item)
 
         # first try to access HDF5 directly to make the common case fast
         try:
@@ -980,7 +980,7 @@ def tail(self, file_name, lines=100):
         Raises:
             FileNotFoundError: if the given file name does not exist in the job folder
         """
-        print(*_job_read_file(file_name)[-lines:])
+        print(*_job_read_file(job, file_name)[-lines:])
 
     def __repr__(self):
         """
diff --git a/pyiron_base/jobs/job/util.py b/pyiron_base/jobs/job/util.py
index 5505ff065..5ec34170b 100644
--- a/pyiron_base/jobs/job/util.py
+++ b/pyiron_base/jobs/job/util.py
@@ -284,8 +284,9 @@ def _job_decompress(job):
     Args:
         job (JobCore): job object to decompress
     """
+    tar_file_name = _job_compressed_name(job)
     try:
-        with tarfile.open(_job_compressed_name(job), "r:bz2") as tar:
+        with tarfile.open(tar_file_name, "r:bz2") as tar:
             tar.extractall(job.working_directory)
         os.remove(tar_file_name)
     except IOError:
@@ -321,7 +322,7 @@ def _job_list_files(job):
     if os.path.isdir(job.working_directory):
         if _job_is_compressed(job):
             with tarfile.open(_job_compressed_name(job), "r") as tar:
-                return [member.name for i in tar.getmembers() if member.isfile()]
+                return [member.name for member in tar.getmembers() if member.isfile()]
         else:
             return os.listdir(job.working_directory)
     return []
diff --git a/tests/job/test_genericJob.py b/tests/job/test_genericJob.py
index cd6a60901..1fee07dd2 100644
--- a/tests/job/test_genericJob.py
+++ b/tests/job/test_genericJob.py
@@ -427,7 +427,7 @@ def test_error(self):
 
     def test_compress(self):
         job = self.project.load(self.project.get_job_ids()[0])
-        wd_files = job.list_files()
+        wd_files = os.listdir(job.working_directory)
         self.assertEqual(len(wd_files), 1, "Only one zipped file should be present in the working directory")
         self.assertEqual(wd_files[0], f"{job.name}.tar.bz2", "Inconsistent name for the zipped file")
 
@@ -441,7 +441,7 @@ def test_restart(self):
             job = self.project.load(self.project.get_job_ids()[0])
             job_restart = job.restart()
             job_restart.run()
-            wd_files = job_restart.list_files()
+            wd_files = os.listdir(job_restart.working_directory)
             self.assertEqual(len(wd_files), 1, "Only one zipped file should be present in the working directory")
             self.assertEqual(wd_files[0], f"{job_restart.name}.tar.bz2", "Inconsistent name for the zipped file")
             job_restart.decompress()

From 138e525040a8e9b436c84c64d4d50150d56c0eeb Mon Sep 17 00:00:00 2001
From: Marvin Poul <poul@mpie.de>
Date: Tue, 22 Nov 2022 15:11:29 +0100
Subject: [PATCH 10/42] Add test and even more bugfixes

---
 pyiron_base/jobs/job/core.py |  2 +-
 pyiron_base/jobs/job/util.py |  6 +++---
 tests/job/test_genericJob.py | 23 +++++++++++++++++++++++
 3 files changed, 27 insertions(+), 4 deletions(-)

diff --git a/pyiron_base/jobs/job/core.py b/pyiron_base/jobs/job/core.py
index 376f89fc2..9c6914f66 100644
--- a/pyiron_base/jobs/job/core.py
+++ b/pyiron_base/jobs/job/core.py
@@ -980,7 +980,7 @@ def tail(self, file_name, lines=100):
         Raises:
             FileNotFoundError: if the given file name does not exist in the job folder
         """
-        print(*_job_read_file(job, file_name)[-lines:])
+        print(*_job_read_file(self, file_name)[-lines:], sep="")
 
     def __repr__(self):
         """
diff --git a/pyiron_base/jobs/job/util.py b/pyiron_base/jobs/job/util.py
index 5ec34170b..39fa690f4 100644
--- a/pyiron_base/jobs/job/util.py
+++ b/pyiron_base/jobs/job/util.py
@@ -343,11 +343,11 @@ def _job_read_file(job, file_name):
     if file_name not in job.list_files():
         raise FileNotFoundError(file_name)
 
-    file_name = posixpath.join(job.working_directory, "{}".format(item))
     if _job_is_compressed(job):
-        with tarfile.open(_job_compressed_name(job)) as f:
-            return f.extractfile(item).readlines()
+        with tarfile.open(_job_compressed_name(job), encoding="utf8") as f:
+            return [line.decode("utf8") for line in f.extractfile(file_name).readlines()]
     else:
+        file_name = posixpath.join(job.working_directory, file_name)
         with open(file_name) as f:
             return f.readlines()
 
diff --git a/tests/job/test_genericJob.py b/tests/job/test_genericJob.py
index 1fee07dd2..7147edbb7 100644
--- a/tests/job/test_genericJob.py
+++ b/tests/job/test_genericJob.py
@@ -2,8 +2,10 @@
 # Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
+import contextlib
 import unittest
 import os
+import io
 from pyiron_base.storage.parameters import GenericParameters
 from pyiron_base.jobs.job.generic import GenericJob
 from pyiron_base._tests import TestWithFilledProject, ToyJob
@@ -489,5 +491,26 @@ def test_return_codes(self):
             pass
         self.assertTrue(j.status.aborted, "Job did not abort even though return code is 2!")
 
+    def test_tail(self):
+        """job.tail should print the last lines of a file to stdout"""
+        job = self.project.load(self.project.get_job_ids()[0])
+        job.decompress()
+        content = ["Content", "More", "Lines"]
+        with open(os.path.join(job.working_directory, "test_file"), "w") as f:
+            f.write("\n".join(content))
+
+        for i in range(len(content)):
+            with contextlib.redirect_stdout(io.StringIO()) as f:
+                job.tail("test_file", lines=i+1)
+            self.assertEqual(f.getvalue(), "\n".join(content[-i-1:]) + "\n",
+                             "tail read incorrect lines from output file when job uncompressed!")
+
+        job.compress()
+        for i in range(len(content)):
+            with contextlib.redirect_stdout(io.StringIO()) as f:
+                job.tail("test_file", lines=i+1)
+            self.assertEqual(f.getvalue(), "\n".join(content[-i-1:]) + "\n",
+                             "tail read incorrect lines from output file when job compressed!")
+
 if __name__ == "__main__":
     unittest.main()

From 16d04f8ef2c4b4348a05274458305ea05bc69b29 Mon Sep 17 00:00:00 2001
From: pyiron-runner <pyiron@mpie.de>
Date: Tue, 22 Nov 2022 14:12:37 +0000
Subject: [PATCH 11/42] Format black

---
 pyiron_base/jobs/job/util.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pyiron_base/jobs/job/util.py b/pyiron_base/jobs/job/util.py
index 39fa690f4..0fad9c444 100644
--- a/pyiron_base/jobs/job/util.py
+++ b/pyiron_base/jobs/job/util.py
@@ -345,7 +345,9 @@ def _job_read_file(job, file_name):
 
     if _job_is_compressed(job):
         with tarfile.open(_job_compressed_name(job), encoding="utf8") as f:
-            return [line.decode("utf8") for line in f.extractfile(file_name).readlines()]
+            return [
+                line.decode("utf8") for line in f.extractfile(file_name).readlines()
+            ]
     else:
         file_name = posixpath.join(job.working_directory, file_name)
         with open(file_name) as f:

From e3a2bb5e1c0d5b51a322b2de32c0e92b6d9e3e41 Mon Sep 17 00:00:00 2001
From: Marvin Poul <poul@mpie.de>
Date: Sun, 4 Dec 2022 06:27:51 +0100
Subject: [PATCH 12/42] Add efficient reverse reading with the monty package

---
 .ci_support/environment.yml  |  1 +
 pyiron_base/jobs/job/core.py |  2 +-
 pyiron_base/jobs/job/util.py | 27 +++++++++++++++++++++++----
 setup.py                     |  1 +
 4 files changed, 26 insertions(+), 5 deletions(-)

diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml
index 3472e2925..20f900760 100644
--- a/.ci_support/environment.yml
+++ b/.ci_support/environment.yml
@@ -20,3 +20,4 @@ dependencies:
 - sqlalchemy =1.4.42
 - tqdm =4.64.1
 - traitlets =5.5.0
+- monty =v2022.9.9
diff --git a/pyiron_base/jobs/job/core.py b/pyiron_base/jobs/job/core.py
index 9c6914f66..c5b3afc99 100644
--- a/pyiron_base/jobs/job/core.py
+++ b/pyiron_base/jobs/job/core.py
@@ -980,7 +980,7 @@ def tail(self, file_name, lines=100):
         Raises:
             FileNotFoundError: if the given file name does not exist in the job folder
         """
-        print(*_job_read_file(self, file_name)[-lines:], sep="")
+        print(*_job_read_file(self, file_name, tail=lines), sep="")
 
     def __repr__(self):
         """
diff --git a/pyiron_base/jobs/job/util.py b/pyiron_base/jobs/job/util.py
index 0fad9c444..660a0fddb 100644
--- a/pyiron_base/jobs/job/util.py
+++ b/pyiron_base/jobs/job/util.py
@@ -4,6 +4,7 @@
 """
 Helper functions for the JobCore and GenericJob objects
 """
+from itertools import islice
 import os
 import posixpath
 import psutil
@@ -12,6 +13,7 @@
 import shutil
 from typing import Union, Dict
 from pyiron_base.utils.instance import static_isinstance
+import monty.io
 
 __author__ = "Jan Janssen"
 __copyright__ = (
@@ -328,14 +330,18 @@ def _job_list_files(job):
     return []
 
 
-def _job_read_file(job, file_name):
+def _job_read_file(job, file_name, tail=None):
     """
     Return list of lines of the given file.
 
     Transparently decompresses the file if job is compressed.
 
+    If `tail` is given and job is decompressed, only read the last lines
+    instead of traversing the full file.
+
     Args:
         file_name (str): the file to print
+        tail (int, optional): only return the last lines
 
     Raises:
         FileNotFoundError: if the given file name does not exist in the job folder
@@ -345,13 +351,26 @@ def _job_read_file(job, file_name):
 
     if _job_is_compressed(job):
         with tarfile.open(_job_compressed_name(job), encoding="utf8") as f:
-            return [
+            lines = [
                 line.decode("utf8") for line in f.extractfile(file_name).readlines()
             ]
+            if tail is None:
+                return lines
+            else:
+                return lines[-tail:]
     else:
         file_name = posixpath.join(job.working_directory, file_name)
-        with open(file_name) as f:
-            return f.readlines()
+        if tail is None:
+            with open(file_name) as f:
+                return f.readlines()
+        else:
+            lines = list(reversed([l + "\n" for l in islice(monty.io.reverse_readfile(file_name), tail)]))
+            # compatibility with the other methods
+            # monty strips all newlines, where as reading the other ways does
+            # not.  So if a file does not end with a newline (as most text
+            # files) adding it to every line like above adds an additional one.
+            lines[-1] = lines[-1].rstrip("\n")
+            return lines
 
 
 def _job_archive(job):
diff --git a/setup.py b/setup.py
index 1a79138d5..2c9016350 100644
--- a/setup.py
+++ b/setup.py
@@ -44,6 +44,7 @@
         'tables==3.7.0',
         'tqdm==4.64.1',
         'traitlets==5.5.0',
+        'monty==2022.9.9'
     ],
     cmdclass=versioneer.get_cmdclass(),
 

From 26e0336abcf086938a7702862b8699ecdc93fe3c Mon Sep 17 00:00:00 2001
From: Marvin Poul <poul@mpie.de>
Date: Sun, 4 Dec 2022 17:59:14 +0100
Subject: [PATCH 13/42] Use system specific linesep

---
 tests/job/test_genericJob.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/job/test_genericJob.py b/tests/job/test_genericJob.py
index 82fa84444..e25944dde 100644
--- a/tests/job/test_genericJob.py
+++ b/tests/job/test_genericJob.py
@@ -493,19 +493,19 @@ def test_tail(self):
         job.decompress()
         content = ["Content", "More", "Lines"]
         with open(os.path.join(job.working_directory, "test_file"), "w") as f:
-            f.write("\n".join(content))
+            f.write(os.linesep.join(content))
 
         for i in range(len(content)):
             with contextlib.redirect_stdout(io.StringIO()) as f:
                 job.tail("test_file", lines=i+1)
-            self.assertEqual(f.getvalue(), "\n".join(content[-i-1:]) + "\n",
+            self.assertEqual(f.getvalue(), os.linesep.join(content[-i-1:]) + os.linesep,
                              "tail read incorrect lines from output file when job uncompressed!")
 
         job.compress()
         for i in range(len(content)):
             with contextlib.redirect_stdout(io.StringIO()) as f:
                 job.tail("test_file", lines=i+1)
-            self.assertEqual(f.getvalue(), "\n".join(content[-i-1:]) + "\n",
+            self.assertEqual(f.getvalue(), os.linesep.join(content[-i-1:]) + os.linesep,
                              "tail read incorrect lines from output file when job compressed!")
 
 if __name__ == "__main__":

From 4e4f44d43a1a7c7fb8fddd4a13a8d323492699b6 Mon Sep 17 00:00:00 2001
From: Marvin Poul <poul@mpie.de>
Date: Sun, 4 Dec 2022 18:14:11 +0100
Subject: [PATCH 14/42] More line separator replacements

---
 pyiron_base/jobs/job/util.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyiron_base/jobs/job/util.py b/pyiron_base/jobs/job/util.py
index 2d84b459b..16863f82b 100644
--- a/pyiron_base/jobs/job/util.py
+++ b/pyiron_base/jobs/job/util.py
@@ -362,12 +362,12 @@ def _job_read_file(job, file_name, tail=None):
             with open(file_name) as f:
                 return f.readlines()
         else:
-            lines = list(reversed([l + "\n" for l in islice(monty.io.reverse_readfile(file_name), tail)]))
+            lines = list(reversed([l + os.linesep for l in islice(monty.io.reverse_readfile(file_name), tail)]))
             # compatibility with the other methods
             # monty strips all newlines, where as reading the other ways does
             # not.  So if a file does not end with a newline (as most text
             # files) adding it to every line like above adds an additional one.
-            lines[-1] = lines[-1].rstrip("\n")
+            lines[-1] = lines[-1].rstrip(os.linesep)
             return lines
 
 

From 9392e499e684a22085edaf7a81b5f1b8ff95242f Mon Sep 17 00:00:00 2001
From: Marvin Poul <poul@mpie.de>
Date: Sun, 4 Dec 2022 18:15:29 +0100
Subject: [PATCH 15/42] Fix typo

---
 pyiron_base/jobs/job/core.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyiron_base/jobs/job/core.py b/pyiron_base/jobs/job/core.py
index d52afa058..b37cee077 100644
--- a/pyiron_base/jobs/job/core.py
+++ b/pyiron_base/jobs/job/core.py
@@ -914,7 +914,7 @@ def __getitem__(self, item):
         """
 
         if item in self.list_files():
-            return _job_read_file(job, item)
+            return _job_read_file(self, item)
 
         # first try to access HDF5 directly to make the common case fast
         try:

From 7d2089eb400853714ed89eb2cba5379347664db5 Mon Sep 17 00:00:00 2001
From: pyiron-runner <pyiron@mpie.de>
Date: Wed, 7 Dec 2022 11:45:19 +0000
Subject: [PATCH 16/42] Format black

---
 pyiron_base/jobs/job/util.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/pyiron_base/jobs/job/util.py b/pyiron_base/jobs/job/util.py
index 16863f82b..c14c280b8 100644
--- a/pyiron_base/jobs/job/util.py
+++ b/pyiron_base/jobs/job/util.py
@@ -362,7 +362,14 @@ def _job_read_file(job, file_name, tail=None):
             with open(file_name) as f:
                 return f.readlines()
         else:
-            lines = list(reversed([l + os.linesep for l in islice(monty.io.reverse_readfile(file_name), tail)]))
+            lines = list(
+                reversed(
+                    [
+                        l + os.linesep
+                        for l in islice(monty.io.reverse_readfile(file_name), tail)
+                    ]
+                )
+            )
             # compatibility with the other methods
             # monty strips all newlines, where as reading the other ways does
             # not.  So if a file does not end with a newline (as most text

From 8ecbfd13f0f4014a9c5202321ca4f1debbee072a Mon Sep 17 00:00:00 2001
From: Marvin Poul <poul@mpie.de>
Date: Fri, 6 Jan 2023 08:30:00 +0100
Subject: [PATCH 17/42] Enable newline translation in windows tests

Also use a sub test for every line test
---
 tests/job/test_genericJob.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/tests/job/test_genericJob.py b/tests/job/test_genericJob.py
index e25944dde..c6b6b3f92 100644
--- a/tests/job/test_genericJob.py
+++ b/tests/job/test_genericJob.py
@@ -496,10 +496,11 @@ def test_tail(self):
             f.write(os.linesep.join(content))
 
         for i in range(len(content)):
-            with contextlib.redirect_stdout(io.StringIO()) as f:
-                job.tail("test_file", lines=i+1)
-            self.assertEqual(f.getvalue(), os.linesep.join(content[-i-1:]) + os.linesep,
-                             "tail read incorrect lines from output file when job uncompressed!")
+            with self.subTest(i=i):
+                with contextlib.redirect_stdout(io.StringIO(newline=os.linesep)) as f:
+                    job.tail("test_file", lines=i+1)
+                self.assertEqual(f.getvalue(), os.linesep.join(content[-i-1:]) + os.linesep,
+                                "tail read incorrect lines from output file when job uncompressed!")
 
         job.compress()
         for i in range(len(content)):

From 8db9284dd99a51d54b96360e646c752522544f79 Mon Sep 17 00:00:00 2001
From: Marvin Poul <poul@mpie.de>
Date: Fri, 6 Jan 2023 09:29:28 +0100
Subject: [PATCH 18/42] Add a simple file browser

job[] is overloaded to perform many functions at once:
1. access to files
2. access to HDF stored data
3. access to child jobs

This change adds a new attribute `.files` to `JobCore` to take over
function 1 and deprecates methods on the job itself that are connected
to this: `list_files` and `tail`.
---
 pyiron_base/jobs/job/core.py | 90 ++++++++++++++++++++++++++++++++++++
 1 file changed, 90 insertions(+)

diff --git a/pyiron_base/jobs/job/core.py b/pyiron_base/jobs/job/core.py
index b37cee077..1c5b4c491 100644
--- a/pyiron_base/jobs/job/core.py
+++ b/pyiron_base/jobs/job/core.py
@@ -10,6 +10,7 @@
 import os
 import posixpath
 import shutil
+from typing import List
 import warnings
 
 from pyiron_base.interfaces.has_groups import HasGroups
@@ -33,6 +34,7 @@
     _job_remove_folder,
 )
 from pyiron_base.state import state
+from pyiron_base.utils.deprecate import deprecate
 
 __author__ = "Jan Janssen"
 __copyright__ = (
@@ -136,6 +138,11 @@ def __init__(self, project, job_name):
     def content(self):
         return self._hdf5_content
 
+    @property
+    def files(self):
+        return FileBrowser(self)
+    files.__doc__ = FileBrowser.__doc__
+
     @property
     def job_name(self):
         """
@@ -612,6 +619,7 @@ def get_job_id(self, job_specifier=None):
             else:
                 return None
 
+    @deprecate("use job.files.list()")
     def list_files(self):
         """
         List files inside the working directory
@@ -914,6 +922,10 @@ def __getitem__(self, item):
         """
 
         if item in self.list_files():
+            warnings.warn(
+                    "Using __getitem__ on a job to access files in deprecated: use job.files instead!",
+                    category=DeprecationWarning
+            )
             return _job_read_file(self, item)
 
         # first try to access HDF5 directly to make the common case fast
@@ -996,6 +1008,7 @@ def __delitem__(self, key):
         """
         del self.project_hdf5[posixpath.join(self.project_hdf5.h5_path, key)]
 
+    @deprecate("use job.files.tail() instead!")
     def tail(self, file_name, lines=100):
         """
         Print the last lines of the given file in the job folder.
@@ -1126,3 +1139,80 @@ def __dir__(self):
 
     def __repr__(self):
         return self._project_hdf5.__repr__()
+
+
+class FileBrowser:
+    """
+    Allows to browse the files in a job directory.
+
+    By default this object prints itself as a listing of the job directory and
+    the files inside.
+
+    >>> job.files
+    /path/to/my/job:
+    \tpyiron.log
+    \terror.out
+
+    Access to the names of files is provided with :meth:`.list`
+
+    >>> job.files.list()
+    ['pyiron.log', 'error.out', 'INCAR']
+
+    Access to the contents of files is provided by indexing into this object,
+    which returns a list of lines in the file
+
+    >>> job.files['error.out']
+    ["Oh no\n", "Something went wrong!\n"]
+
+    The :meth:`.tail` method prints the last lines of a file to stdout
+
+    >>> job.files.tail('error.out', lines=1)
+    Something went wrong!
+
+    For files that have valid python variable names can also be accessed by
+    attribute notation
+
+    >>> job.files.INCAR
+    ["SYSTEM=pyiron\n", "ENCUT=270\n", ...]
+    """
+
+    __slots__ = ("_job",)
+
+    def __init__(self, job):
+        self._job = job
+
+    def list(self) -> List[str]:
+        """
+        List all files in the working directory of the job.
+        """
+        return _job_list_files(job)
+
+    def _ipython_display_(self):
+        path = job.working_directory + ":"
+        files = ["\t" + f for f in _job_list_files(job)]
+        print(os.linesep.join([path, *files]))
+
+    def tail(self, file: str, lines: int = 100):
+        """
+        Print the last lines of a file.
+
+        Args:
+            file (str): filename
+            lines (int): number of lines to print
+
+        Raises:
+            FileNotFoundError: if the given file does not exist
+        """
+        print(*_job_read_file(self, file_name, tail=lines), sep="")
+
+    def __getitem__(self, item):
+        if item not _job_list_files(self._job):
+            raise KeyError(item)
+
+        return _job_read_file(self._job, item)
+
+    def __getattr__(self, item):
+        try:
+            return self[name]
+        except KeyError:
+            raise AttributeError(name) from None

From e1ef8c1e536b7271ecb60bad9cacd35c4769f7a3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Sun, 4 Feb 2024 10:34:31 +0100
Subject: [PATCH 19/42] Add output files class

---
 pyiron_base/jobs/flex/executablecontainer.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/pyiron_base/jobs/flex/executablecontainer.py b/pyiron_base/jobs/flex/executablecontainer.py
index 9de66f12d..9f488458a 100644
--- a/pyiron_base/jobs/flex/executablecontainer.py
+++ b/pyiron_base/jobs/flex/executablecontainer.py
@@ -1,3 +1,4 @@
+import os
 import cloudpickle
 import numpy as np
 from pyiron_base.jobs.job.template import TemplateJob
@@ -43,6 +44,7 @@ def __init__(self, project, job_name):
         super().__init__(project, job_name)
         self._write_input_funct = None
         self._collect_output_funct = None
+        self.output_files = OutputFiles(working_directory=self.working_directory)
 
     def set_job_type(
         self,
@@ -107,3 +109,21 @@ def from_hdf(self, hdf=None, group_name=None):
             self._collect_output_funct = cloudpickle.loads(
                 self.project_hdf5["collect_output_function"]
             )
+
+
+class OutputFiles:
+    def __init__(self, working_directory):
+        self._working_directory = working_directory
+
+    def __dir__(self):
+        return list(self._get_file_convert_dict().keys())
+
+    def _get_file_convert_dict(self):
+        return {f.replace(".", "_"): f for f in os.listdir(self.working_directory)}
+
+    def __getattr__(self, attr):
+        convert_dict = self._get_file_convert_dict()
+        if attr in convert_dict.keys():
+            return os.path.join(self._working_directory, convert_dict[attr])
+        else:
+            raise AttributeError()

From 020c977726b6e4e669920e534c910111903ca26f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Sun, 4 Feb 2024 11:09:35 +0100
Subject: [PATCH 20/42] Fix working directory bug

---
 pyiron_base/jobs/flex/executablecontainer.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyiron_base/jobs/flex/executablecontainer.py b/pyiron_base/jobs/flex/executablecontainer.py
index 9f488458a..6103a6f40 100644
--- a/pyiron_base/jobs/flex/executablecontainer.py
+++ b/pyiron_base/jobs/flex/executablecontainer.py
@@ -119,7 +119,7 @@ def __dir__(self):
         return list(self._get_file_convert_dict().keys())
 
     def _get_file_convert_dict(self):
-        return {f.replace(".", "_"): f for f in os.listdir(self.working_directory)}
+        return {f.replace(".", "_"): f for f in os.listdir(self._working_directory)}
 
     def __getattr__(self, attr):
         convert_dict = self._get_file_convert_dict()

From fc8ad6a3617f89773141446313f460e80317221e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Mon, 5 Feb 2024 20:39:26 +0100
Subject: [PATCH 21/42] Move OutputFiles to GenericJob

---
 pyiron_base/jobs/flex/executablecontainer.py  | 20 -------------------
 pyiron_base/jobs/job/extension/outputfiles.py | 19 ++++++++++++++++++
 pyiron_base/jobs/job/generic.py               |  2 ++
 tests/flex/test_executablecontainer.py        | 18 +++++++++++++++++
 4 files changed, 39 insertions(+), 20 deletions(-)
 create mode 100644 pyiron_base/jobs/job/extension/outputfiles.py

diff --git a/pyiron_base/jobs/flex/executablecontainer.py b/pyiron_base/jobs/flex/executablecontainer.py
index 6103a6f40..9de66f12d 100644
--- a/pyiron_base/jobs/flex/executablecontainer.py
+++ b/pyiron_base/jobs/flex/executablecontainer.py
@@ -1,4 +1,3 @@
-import os
 import cloudpickle
 import numpy as np
 from pyiron_base.jobs.job.template import TemplateJob
@@ -44,7 +43,6 @@ def __init__(self, project, job_name):
         super().__init__(project, job_name)
         self._write_input_funct = None
         self._collect_output_funct = None
-        self.output_files = OutputFiles(working_directory=self.working_directory)
 
     def set_job_type(
         self,
@@ -109,21 +107,3 @@ def from_hdf(self, hdf=None, group_name=None):
             self._collect_output_funct = cloudpickle.loads(
                 self.project_hdf5["collect_output_function"]
             )
-
-
-class OutputFiles:
-    def __init__(self, working_directory):
-        self._working_directory = working_directory
-
-    def __dir__(self):
-        return list(self._get_file_convert_dict().keys())
-
-    def _get_file_convert_dict(self):
-        return {f.replace(".", "_"): f for f in os.listdir(self._working_directory)}
-
-    def __getattr__(self, attr):
-        convert_dict = self._get_file_convert_dict()
-        if attr in convert_dict.keys():
-            return os.path.join(self._working_directory, convert_dict[attr])
-        else:
-            raise AttributeError()
diff --git a/pyiron_base/jobs/job/extension/outputfiles.py b/pyiron_base/jobs/job/extension/outputfiles.py
new file mode 100644
index 000000000..c9c6ba623
--- /dev/null
+++ b/pyiron_base/jobs/job/extension/outputfiles.py
@@ -0,0 +1,19 @@
+import os
+
+
+class OutputFiles:
+    def __init__(self, working_directory):
+        self._working_directory = working_directory
+
+    def __dir__(self):
+        return list(self._get_file_convert_dict().keys())
+
+    def _get_file_convert_dict(self):
+        return {f.replace(".", "_"): f for f in os.listdir(self._working_directory)}
+
+    def __getattr__(self, attr):
+        convert_dict = self._get_file_convert_dict()
+        if attr in convert_dict.keys():
+            return os.path.join(self._working_directory, convert_dict[attr])
+        else:
+            raise AttributeError()
diff --git a/pyiron_base/jobs/job/generic.py b/pyiron_base/jobs/job/generic.py
index e26cf1de5..2d2f1d0dd 100644
--- a/pyiron_base/jobs/job/generic.py
+++ b/pyiron_base/jobs/job/generic.py
@@ -49,6 +49,7 @@
 from pyiron_base.jobs.job.extension.server.generic import Server
 from pyiron_base.database.filetable import FileTable
 from pyiron_base.interfaces.has_dict import HasDict
+from pyiron_base.jobs.job.extension.outputfiles import OutputFiles
 
 __author__ = "Joerg Neugebauer, Jan Janssen"
 __copyright__ = (
@@ -163,6 +164,7 @@ def __init__(self, project, job_name):
         self._write_work_dir_warnings = True
         self.interactive_cache = None
         self.error = GenericError(job=self)
+        self.output_files = OutputFiles(working_directory=self.working_directory)
 
     @property
     def version(self):
diff --git a/tests/flex/test_executablecontainer.py b/tests/flex/test_executablecontainer.py
index 2563e0f64..69fad9c6b 100644
--- a/tests/flex/test_executablecontainer.py
+++ b/tests/flex/test_executablecontainer.py
@@ -81,6 +81,24 @@ def test_create_job_factory_with_projecthdfio(self):
         self.assertEqual(job_reload.input["energy"], energy_value)
         self.assertEqual(job_reload.output["energy"], energy_value)
 
+    def test_job_output_files(self):
+        create_catjob = create_job_factory(
+            write_input_funct=write_input,
+            collect_output_funct=collect_output,
+            default_input_dict={"energy": 1.0},
+            executable_str="cat input_file > output_file",
+        )
+        job = create_catjob(
+            project=ProjectHDFio(project=self.project, file_name="any.h5", h5_path=None, mode=None),
+            job_name="job_output_files"
+        )
+        job.run()
+        self.assertEqual(dir(job.output_files), ['error_out', 'input_file', 'output_file'])
+        self.assertEqual(
+            job.output_files.error_out,
+            os.path.abspath(os.path.join(__file__, "..", "test_executablecontainer", "job_output_files_hdf5", "job_output_files", "error.out"))
+        )
+
     def test_create_job_factory_typeerror(self):
         create_catjob = create_job_factory(
             write_input_funct=write_input,

From c137a6d384211ccfc4e40a6ba5354b95150b6e02 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Mon, 5 Feb 2024 21:08:05 +0100
Subject: [PATCH 22/42] rename output files to just files

---
 pyiron_base/jobs/job/core.py                                | 5 +++++
 pyiron_base/jobs/job/extension/{outputfiles.py => files.py} | 2 +-
 pyiron_base/jobs/job/generic.py                             | 2 --
 3 files changed, 6 insertions(+), 3 deletions(-)
 rename pyiron_base/jobs/job/extension/{outputfiles.py => files.py} (96%)

diff --git a/pyiron_base/jobs/job/core.py b/pyiron_base/jobs/job/core.py
index aec146eb0..f5245b7fe 100644
--- a/pyiron_base/jobs/job/core.py
+++ b/pyiron_base/jobs/job/core.py
@@ -31,6 +31,7 @@
     _job_remove_folder,
 )
 from pyiron_base.state import state
+from pyiron_base.jobs.job.extension.files import Files
 
 __author__ = "Jan Janssen"
 __copyright__ = (
@@ -352,6 +353,10 @@ def path(self):
         """
         return self.project_hdf5.path
 
+    @property
+    def files(self):
+        return Files(working_directory=self.working_directory)
+
     def check_if_job_exists(self, job_name=None, project=None):
         """
         Check if a job already exists in an specific project.
diff --git a/pyiron_base/jobs/job/extension/outputfiles.py b/pyiron_base/jobs/job/extension/files.py
similarity index 96%
rename from pyiron_base/jobs/job/extension/outputfiles.py
rename to pyiron_base/jobs/job/extension/files.py
index c9c6ba623..f54f29d49 100644
--- a/pyiron_base/jobs/job/extension/outputfiles.py
+++ b/pyiron_base/jobs/job/extension/files.py
@@ -1,7 +1,7 @@
 import os
 
 
-class OutputFiles:
+class Files:
     def __init__(self, working_directory):
         self._working_directory = working_directory
 
diff --git a/pyiron_base/jobs/job/generic.py b/pyiron_base/jobs/job/generic.py
index 2d2f1d0dd..e26cf1de5 100644
--- a/pyiron_base/jobs/job/generic.py
+++ b/pyiron_base/jobs/job/generic.py
@@ -49,7 +49,6 @@
 from pyiron_base.jobs.job.extension.server.generic import Server
 from pyiron_base.database.filetable import FileTable
 from pyiron_base.interfaces.has_dict import HasDict
-from pyiron_base.jobs.job.extension.outputfiles import OutputFiles
 
 __author__ = "Joerg Neugebauer, Jan Janssen"
 __copyright__ = (
@@ -164,7 +163,6 @@ def __init__(self, project, job_name):
         self._write_work_dir_warnings = True
         self.interactive_cache = None
         self.error = GenericError(job=self)
-        self.output_files = OutputFiles(working_directory=self.working_directory)
 
     @property
     def version(self):

From 3146b33c0b4d34bfbbb5cb7907f43268d895094c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Mon, 5 Feb 2024 21:12:07 +0100
Subject: [PATCH 23/42] fix tests

---
 tests/flex/test_executablecontainer.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/flex/test_executablecontainer.py b/tests/flex/test_executablecontainer.py
index 69fad9c6b..f8c6a0eed 100644
--- a/tests/flex/test_executablecontainer.py
+++ b/tests/flex/test_executablecontainer.py
@@ -81,7 +81,7 @@ def test_create_job_factory_with_projecthdfio(self):
         self.assertEqual(job_reload.input["energy"], energy_value)
         self.assertEqual(job_reload.output["energy"], energy_value)
 
-    def test_job_output_files(self):
+    def test_job_files(self):
         create_catjob = create_job_factory(
             write_input_funct=write_input,
             collect_output_funct=collect_output,
@@ -93,9 +93,9 @@ def test_job_output_files(self):
             job_name="job_output_files"
         )
         job.run()
-        self.assertEqual(dir(job.output_files), ['error_out', 'input_file', 'output_file'])
+        self.assertEqual(dir(job.files), ['error_out', 'input_file', 'output_file'])
         self.assertEqual(
-            job.output_files.error_out,
+            job.files.error_out,
             os.path.abspath(os.path.join(__file__, "..", "test_executablecontainer", "job_output_files_hdf5", "job_output_files", "error.out"))
         )
 

From 254dc3cd7ac699f63d13ce959b4dc24845d6d064 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Mon, 5 Feb 2024 21:40:28 +0100
Subject: [PATCH 24/42] fix tests for windows

---
 tests/flex/test_executablecontainer.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/tests/flex/test_executablecontainer.py b/tests/flex/test_executablecontainer.py
index f8c6a0eed..227a07c82 100644
--- a/tests/flex/test_executablecontainer.py
+++ b/tests/flex/test_executablecontainer.py
@@ -94,10 +94,11 @@ def test_job_files(self):
         )
         job.run()
         self.assertEqual(dir(job.files), ['error_out', 'input_file', 'output_file'])
-        self.assertEqual(
-            job.files.error_out,
-            os.path.abspath(os.path.join(__file__, "..", "test_executablecontainer", "job_output_files_hdf5", "job_output_files", "error.out"))
-        )
+        output_file_path = os.path.abspath(os.path.join(__file__, "..", "test_executablecontainer", "job_output_files_hdf5", "job_output_files", "error.out"))
+        if os.name != "nt":
+            self.assertEqual(job.files.error_out, output_file_path)
+        else:
+            self.assertEqual(job.files.error_out.replace("/", "\\"), output_file_path)
 
     def test_create_job_factory_typeerror(self):
         create_catjob = create_job_factory(

From 086565c7b30dd6ecc7b6e5928221141bec70c9d5 Mon Sep 17 00:00:00 2001
From: Jan Janssen <janssen@mpie.de>
Date: Tue, 6 Feb 2024 16:11:04 +0100
Subject: [PATCH 25/42] update monty

---
 .ci_support/environment-docs.yml | 1 +
 .ci_support/environment-old.yml  | 1 +
 .ci_support/environment.yml      | 2 +-
 pyproject.toml                   | 1 +
 4 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.ci_support/environment-docs.yml b/.ci_support/environment-docs.yml
index 0a361dd9e..48d2d51ad 100644
--- a/.ci_support/environment-docs.yml
+++ b/.ci_support/environment-docs.yml
@@ -11,6 +11,7 @@ dependencies:
 - h5io_browser =0.0.7
 - h5py =3.10.0
 - jinja2 =3.1.3
+- monty =2024.2.2
 - numpy =1.26.3
 - pandas =2.2.0
 - pint =0.23
diff --git a/.ci_support/environment-old.yml b/.ci_support/environment-old.yml
index 3aca67905..e924430e0 100644
--- a/.ci_support/environment-old.yml
+++ b/.ci_support/environment-old.yml
@@ -6,6 +6,7 @@ dependencies:
 - h5io_browser =0.0.6
 - h5py =3.6.0
 - jinja2 =2.11.3
+- monty =2024.2.2
 - numpy =1.23.5
 - pandas =2.0.0
 - pint =0.18
diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml
index 2699e9afe..6a69922f3 100644
--- a/.ci_support/environment.yml
+++ b/.ci_support/environment.yml
@@ -8,7 +8,7 @@ dependencies:
 - h5io_browser =0.0.7
 - h5py =3.10.0
 - jinja2 =3.1.3
-- monty =2022.9.9
+- monty =2024.2.2
 - numpy =1.26.3
 - pandas =2.2.0
 - pint =0.23
diff --git a/pyproject.toml b/pyproject.toml
index 1dacb159e..46161ddc2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -30,6 +30,7 @@ dependencies = [
     "h5py==3.10.0",
     "jinja2==3.1.3",
     "numpy==1.26.3",
+    "monty==2024.2.2",
     "pandas==2.2.0",
     "pint==0.23",
     "psutil==5.9.8",

From c010b5cdbd89afcdf0d77aaf7fc8732a89108239 Mon Sep 17 00:00:00 2001
From: Jan Janssen <janssen@mpie.de>
Date: Tue, 6 Feb 2024 16:11:10 +0100
Subject: [PATCH 26/42] fix

---
 pyiron_base/jobs/job/core.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyiron_base/jobs/job/core.py b/pyiron_base/jobs/job/core.py
index 3f2ea55a8..6d4c35191 100644
--- a/pyiron_base/jobs/job/core.py
+++ b/pyiron_base/jobs/job/core.py
@@ -1190,7 +1190,7 @@ def tail(self, file: str, lines: int = 100):
         print(*_job_read_file(self, file_name, tail=lines), sep="")
 
     def __getitem__(self, item):
-        if item not _job_list_files(self._job):
+        if item not in _job_list_files(self._job):
             raise KeyError(item)
 
         return _job_read_file(self._job, item)

From b597a57ba09108a0cac65404d94397887cb7eb3e Mon Sep 17 00:00:00 2001
From: Jan Janssen <janssen@mpie.de>
Date: Tue, 6 Feb 2024 16:27:45 +0100
Subject: [PATCH 27/42] more fixes

---
 pyiron_base/jobs/job/core.py            | 78 +--------------------
 pyiron_base/jobs/job/extension/files.py | 90 +++++++++++++++++++++----
 2 files changed, 79 insertions(+), 89 deletions(-)

diff --git a/pyiron_base/jobs/job/core.py b/pyiron_base/jobs/job/core.py
index 6d4c35191..4719b097d 100644
--- a/pyiron_base/jobs/job/core.py
+++ b/pyiron_base/jobs/job/core.py
@@ -35,6 +35,7 @@
 )
 from pyiron_base.state import state
 from pyiron_base.utils.deprecate import deprecate
+from pyiron_base.jobs.job.extension.files import FileBrowser
 
 __author__ = "Jan Janssen"
 __copyright__ = (
@@ -1123,80 +1124,3 @@ def __dir__(self):
 
     def __repr__(self):
         return self._project_hdf5.__repr__()
-
-
-class FileBrowser:
-    """
-    Allows to browse the files in a job directory.
-
-    By default this object prints itself as a listing of the job directory and
-    the files inside.
-
-    >>> job.files
-    /path/to/my/job:
-    \tpyiron.log
-    \terror.out
-
-    Access to the names of files is provided with :meth:`.list`
-
-    >>> job.files.list()
-    ['pyiron.log', 'error.out', 'INCAR']
-
-    Access to the contents of files is provided by indexing into this object,
-    which returns a list of lines in the file
-
-    >>> job.files['error.out']
-    ["Oh no\n", "Something went wrong!\n"]
-
-    The :meth:`.tail` method prints the last lines of a file to stdout
-
-    >>> job.files.tail('error.out', lines=1)
-    Something went wrong!
-
-    For files that have valid python variable names can also be accessed by
-    attribute notation
-
-    >>> job.files.INCAR
-    ["SYSTEM=pyiron\n", "ENCUT=270\n", ...]
-    """
-
-    __slots__ = ("_job",)
-
-    def __init__(self, job):
-        self._job = job
-
-    def list(self) -> List[str]:
-        """
-        List all files in the working directory of the job.
-        """
-        return _job_list_files(job)
-
-    def _ipython_display_(self):
-        path = job.working_directory + ":"
-        files = ["\t" + f for f in _job_list_files(job)]
-        print(os.linesep.join([path, *files]))
-
-    def tail(self, file: str, lines: int = 100):
-        """
-        Print the last lines of a file.
-
-        Args:
-            file (str): filename
-            lines (int): number of lines to print
-
-        Raises:
-            FileNotFoundError: if the given file does not exist
-        """
-        print(*_job_read_file(self, file_name, tail=lines), sep="")
-
-    def __getitem__(self, item):
-        if item not in _job_list_files(self._job):
-            raise KeyError(item)
-
-        return _job_read_file(self._job, item)
-
-    def __getattr__(self, item):
-        try:
-            return self[name]
-        except KeyError:
-            raise AttributeError(name) from None
diff --git a/pyiron_base/jobs/job/extension/files.py b/pyiron_base/jobs/job/extension/files.py
index f54f29d49..04bcb8085 100644
--- a/pyiron_base/jobs/job/extension/files.py
+++ b/pyiron_base/jobs/job/extension/files.py
@@ -1,19 +1,85 @@
 import os
+from pyiron_base.jobs.job.util import (
+    _job_list_files,
+    _job_read_file,
+)
 
 
-class Files:
-    def __init__(self, working_directory):
-        self._working_directory = working_directory
+class FileBrowser:
+    """
+    Allows to browse the files in a job directory.
+
+    By default this object prints itself as a listing of the job directory and
+    the files inside.
+
+    >>> job.files
+    /path/to/my/job:
+    \tpyiron.log
+    \terror.out
+
+    Access to the names of files is provided with :meth:`.list`
+
+    >>> job.files.list()
+    ['pyiron.log', 'error.out', 'INCAR']
+
+    Access to the contents of files is provided by indexing into this object,
+    which returns a list of lines in the file
+
+    >>> job.files['error.out']
+    ["Oh no\n", "Something went wrong!\n"]
+
+    The :meth:`.tail` method prints the last lines of a file to stdout
+
+    >>> job.files.tail('error.out', lines=1)
+    Something went wrong!
+
+    For files that have valid python variable names can also be accessed by
+    attribute notation
+
+    >>> job.files.INCAR
+    ["SYSTEM=pyiron\n", "ENCUT=270\n", ...]
+    """
+
+    __slots__ = ("_job",)
+
+    def __init__(self, job):
+        self._job = job
 
     def __dir__(self):
-        return list(self._get_file_convert_dict().keys())
+        return _job_list_files(job=self._job) + ["list", "tail", "__dir__", "__getitem__", "__getattr__", "_ipython_display_"]
+
+    def list(self) -> List[str]:
+        """
+        List all files in the working directory of the job.
+        """
+        return _job_list_files(job=self._job)
+
+    def _ipython_display_(self):
+        path = job.working_directory + ":"
+        files = ["\t" + f for f in _job_list_files(job=self._job)]
+        print(os.linesep.join([path, *files]))
+
+    def tail(self, file: str, lines: int = 100):
+        """
+        Print the last lines of a file.
+
+        Args:
+            file (str): filename
+            lines (int): number of lines to print
+
+        Raises:
+            FileNotFoundError: if the given file does not exist
+        """
+        print(*_job_read_file(job=self._job, file_name=file, tail=lines), sep="")
+
+    def __getitem__(self, item):
+        if item not in _job_list_files(job=self._job):
+            raise KeyError(item)
 
-    def _get_file_convert_dict(self):
-        return {f.replace(".", "_"): f for f in os.listdir(self._working_directory)}
+        return _job_read_file(job=self._job, file_name=item)
 
-    def __getattr__(self, attr):
-        convert_dict = self._get_file_convert_dict()
-        if attr in convert_dict.keys():
-            return os.path.join(self._working_directory, convert_dict[attr])
-        else:
-            raise AttributeError()
+    def __getattr__(self, item):
+        try:
+            return self[name]
+        except KeyError:
+            raise AttributeError(name) from None

From 7b6b94e6faf3f54a14e853ae3f8271e04bc26de8 Mon Sep 17 00:00:00 2001
From: pyiron-runner <pyiron@mpie.de>
Date: Tue, 6 Feb 2024 15:29:16 +0000
Subject: [PATCH 28/42] Format black

---
 pyiron_base/jobs/job/core.py            | 5 +++--
 pyiron_base/jobs/job/extension/files.py | 9 ++++++++-
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/pyiron_base/jobs/job/core.py b/pyiron_base/jobs/job/core.py
index 4719b097d..8975915b1 100644
--- a/pyiron_base/jobs/job/core.py
+++ b/pyiron_base/jobs/job/core.py
@@ -142,6 +142,7 @@ def content(self):
     @property
     def files(self):
         return FileBrowser(self)
+
     files.__doc__ = FileBrowser.__doc__
 
     @property
@@ -908,8 +909,8 @@ def __getitem__(self, item):
 
         if item in self.list_files():
             warnings.warn(
-                    "Using __getitem__ on a job to access files in deprecated: use job.files instead!",
-                    category=DeprecationWarning
+                "Using __getitem__ on a job to access files in deprecated: use job.files instead!",
+                category=DeprecationWarning,
             )
             return _job_read_file(self, item)
 
diff --git a/pyiron_base/jobs/job/extension/files.py b/pyiron_base/jobs/job/extension/files.py
index 04bcb8085..cc3a25ba0 100644
--- a/pyiron_base/jobs/job/extension/files.py
+++ b/pyiron_base/jobs/job/extension/files.py
@@ -46,7 +46,14 @@ def __init__(self, job):
         self._job = job
 
     def __dir__(self):
-        return _job_list_files(job=self._job) + ["list", "tail", "__dir__", "__getitem__", "__getattr__", "_ipython_display_"]
+        return _job_list_files(job=self._job) + [
+            "list",
+            "tail",
+            "__dir__",
+            "__getitem__",
+            "__getattr__",
+            "_ipython_display_",
+        ]
 
     def list(self) -> List[str]:
         """

From b02aa2fe2c30cad789e54a736f3c643717237316 Mon Sep 17 00:00:00 2001
From: Jan Janssen <janssen@mpie.de>
Date: Tue, 6 Feb 2024 16:29:32 +0100
Subject: [PATCH 29/42] fix typing

---
 pyiron_base/jobs/job/extension/files.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyiron_base/jobs/job/extension/files.py b/pyiron_base/jobs/job/extension/files.py
index 04bcb8085..fcbb3755c 100644
--- a/pyiron_base/jobs/job/extension/files.py
+++ b/pyiron_base/jobs/job/extension/files.py
@@ -1,4 +1,5 @@
 import os
+from typing import List
 from pyiron_base.jobs.job.util import (
     _job_list_files,
     _job_read_file,

From 2ad939185154d28ff77cb5dc842234f66960cb37 Mon Sep 17 00:00:00 2001
From: Jan Janssen <janssen@mpie.de>
Date: Tue, 6 Feb 2024 16:43:29 +0100
Subject: [PATCH 30/42] fix tests

---
 pyiron_base/jobs/job/extension/files.py |  7 +++++--
 tests/flex/test_executablecontainer.py  | 10 +++++-----
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/pyiron_base/jobs/job/extension/files.py b/pyiron_base/jobs/job/extension/files.py
index fbc8debba..7160689a1 100644
--- a/pyiron_base/jobs/job/extension/files.py
+++ b/pyiron_base/jobs/job/extension/files.py
@@ -46,8 +46,11 @@ class FileBrowser:
     def __init__(self, job):
         self._job = job
 
+    def _get_file_dict(self):
+        return {f.replace(".", "_"):f for f in _job_list_files(job=self._job)}
+
     def __dir__(self):
-        return _job_list_files(job=self._job) + [
+        return list(self._get_file_dict().keys()) + [
             "list",
             "tail",
             "__dir__",
@@ -88,6 +91,6 @@ def __getitem__(self, item):
 
     def __getattr__(self, item):
         try:
-            return self[name]
+            return self[self._get_file_dict()[item]]
         except KeyError:
             raise AttributeError(name) from None
diff --git a/tests/flex/test_executablecontainer.py b/tests/flex/test_executablecontainer.py
index 227a07c82..366bb03ab 100644
--- a/tests/flex/test_executablecontainer.py
+++ b/tests/flex/test_executablecontainer.py
@@ -93,12 +93,12 @@ def test_job_files(self):
             job_name="job_output_files"
         )
         job.run()
-        self.assertEqual(dir(job.files), ['error_out', 'input_file', 'output_file'])
+        self.assertEqual(dir(job.files), ['__dir__', '__getattr__', '__getitem__', '_ipython_display_','error_out', 'input_file', 'list', 'output_file', 'tail'])
         output_file_path = os.path.abspath(os.path.join(__file__, "..", "test_executablecontainer", "job_output_files_hdf5", "job_output_files", "error.out"))
-        if os.name != "nt":
-            self.assertEqual(job.files.error_out, output_file_path)
-        else:
-            self.assertEqual(job.files.error_out.replace("/", "\\"), output_file_path)
+        # if os.name != "nt":
+        #     self.assertEqual(job.files.error_out, output_file_path)
+        # else:
+        #     self.assertEqual(job.files.error_out.replace("/", "\\"), output_file_path)
 
     def test_create_job_factory_typeerror(self):
         create_catjob = create_job_factory(

From fe1bf2ee0d215bc5ce200f124fcab9ee824f3297 Mon Sep 17 00:00:00 2001
From: Jan Janssen <janssen@mpie.de>
Date: Tue, 6 Feb 2024 16:47:20 +0100
Subject: [PATCH 31/42] fix ipython representation

---
 pyiron_base/jobs/job/extension/files.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyiron_base/jobs/job/extension/files.py b/pyiron_base/jobs/job/extension/files.py
index 7160689a1..874ca58d8 100644
--- a/pyiron_base/jobs/job/extension/files.py
+++ b/pyiron_base/jobs/job/extension/files.py
@@ -66,7 +66,7 @@ def list(self) -> List[str]:
         return _job_list_files(job=self._job)
 
     def _ipython_display_(self):
-        path = job.working_directory + ":"
+        path = self._job.working_directory + ":"
         files = ["\t" + f for f in _job_list_files(job=self._job)]
         print(os.linesep.join([path, *files]))
 

From 5eb2054d0c1245854d43dcb9b4ecfc79545f4ade Mon Sep 17 00:00:00 2001
From: pyiron-runner <pyiron@mpie.de>
Date: Tue, 6 Feb 2024 15:47:52 +0000
Subject: [PATCH 32/42] Format black

---
 pyiron_base/jobs/job/extension/files.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyiron_base/jobs/job/extension/files.py b/pyiron_base/jobs/job/extension/files.py
index 874ca58d8..4e34177c7 100644
--- a/pyiron_base/jobs/job/extension/files.py
+++ b/pyiron_base/jobs/job/extension/files.py
@@ -47,7 +47,7 @@ def __init__(self, job):
         self._job = job
 
     def _get_file_dict(self):
-        return {f.replace(".", "_"):f for f in _job_list_files(job=self._job)}
+        return {f.replace(".", "_"): f for f in _job_list_files(job=self._job)}
 
     def __dir__(self):
         return list(self._get_file_dict().keys()) + [

From 36ca620bf2939433e3f00125928a4b46ea7bb12b Mon Sep 17 00:00:00 2001
From: Jan Janssen <janssen@mpie.de>
Date: Tue, 6 Feb 2024 17:00:47 +0100
Subject: [PATCH 33/42] try to fix tests

---
 pyiron_base/jobs/job/extension/files.py | 2 +-
 tests/job/test_genericJob.py            | 8 +++++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/pyiron_base/jobs/job/extension/files.py b/pyiron_base/jobs/job/extension/files.py
index 874ca58d8..63982e2cb 100644
--- a/pyiron_base/jobs/job/extension/files.py
+++ b/pyiron_base/jobs/job/extension/files.py
@@ -93,4 +93,4 @@ def __getattr__(self, item):
         try:
             return self[self._get_file_dict()[item]]
         except KeyError:
-            raise AttributeError(name) from None
+            raise AttributeError(item) from None
diff --git a/tests/job/test_genericJob.py b/tests/job/test_genericJob.py
index 870f18775..09d51dcd1 100644
--- a/tests/job/test_genericJob.py
+++ b/tests/job/test_genericJob.py
@@ -582,14 +582,16 @@ def test_tail(self):
             with self.subTest(i=i):
                 with contextlib.redirect_stdout(io.StringIO(newline=os.linesep)) as f:
                     job.tail("test_file", lines=i+1)
-                self.assertEqual(f.getvalue(), os.linesep.join(content[-i-1:]) + os.linesep,
-                                "tail read incorrect lines from output file when job uncompressed!")
+                reference_str = os.linesep.join(content[-i-1:]) + os.linesep
+                self.assertEqual(f.getvalue().rstrip(), reference_str.rstrip(),
+                                 "tail read incorrect lines from output file when job uncompressed!")
 
         job.compress()
         for i in range(len(content)):
             with contextlib.redirect_stdout(io.StringIO()) as f:
                 job.tail("test_file", lines=i+1)
-            self.assertEqual(f.getvalue(), os.linesep.join(content[-i-1:]) + os.linesep,
+            reference_str = os.linesep.join(content[-i-1:]) + os.linesep
+            self.assertEqual(f.getvalue().rstrip(), reference_str.rstrip(),
                              "tail read incorrect lines from output file when job compressed!")
 
 

From 905bd1a4c48c73835e0b4276ab3e56e696de3f05 Mon Sep 17 00:00:00 2001
From: Jan Janssen <janssen@mpie.de>
Date: Tue, 6 Feb 2024 17:07:42 +0100
Subject: [PATCH 34/42] try to remove \r

---
 tests/job/test_genericJob.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/job/test_genericJob.py b/tests/job/test_genericJob.py
index 09d51dcd1..64b690bf6 100644
--- a/tests/job/test_genericJob.py
+++ b/tests/job/test_genericJob.py
@@ -583,7 +583,7 @@ def test_tail(self):
                 with contextlib.redirect_stdout(io.StringIO(newline=os.linesep)) as f:
                     job.tail("test_file", lines=i+1)
                 reference_str = os.linesep.join(content[-i-1:]) + os.linesep
-                self.assertEqual(f.getvalue().rstrip(), reference_str.rstrip(),
+                self.assertEqual(f.getvalue().replace('\r', ''), reference_str.replace('\r', ''),
                                  "tail read incorrect lines from output file when job uncompressed!")
 
         job.compress()
@@ -591,7 +591,7 @@ def test_tail(self):
             with contextlib.redirect_stdout(io.StringIO()) as f:
                 job.tail("test_file", lines=i+1)
             reference_str = os.linesep.join(content[-i-1:]) + os.linesep
-            self.assertEqual(f.getvalue().rstrip(), reference_str.rstrip(),
+            self.assertEqual(f.getvalue().replace('\r', ''), reference_str.replace('\r', ''),
                              "tail read incorrect lines from output file when job compressed!")
 
 

From 4ee136f1a050cc75af65f29e38772d4c648cb967 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Wed, 7 Feb 2024 08:25:15 +0100
Subject: [PATCH 35/42] Use working directory rather than job object

---
 pyiron_base/jobs/job/core.py            |  2 +-
 pyiron_base/jobs/job/extension/files.py | 41 ++++++++---
 pyiron_base/jobs/job/util.py            | 98 +++++++++++++++++++++----
 3 files changed, 113 insertions(+), 28 deletions(-)

diff --git a/pyiron_base/jobs/job/core.py b/pyiron_base/jobs/job/core.py
index 8975915b1..ef4a46e19 100644
--- a/pyiron_base/jobs/job/core.py
+++ b/pyiron_base/jobs/job/core.py
@@ -141,7 +141,7 @@ def content(self):
 
     @property
     def files(self):
-        return FileBrowser(self)
+        return FileBrowser(working_directory=self.working_directory)
 
     files.__doc__ = FileBrowser.__doc__
 
diff --git a/pyiron_base/jobs/job/extension/files.py b/pyiron_base/jobs/job/extension/files.py
index 50a5748e0..3a00dc30a 100644
--- a/pyiron_base/jobs/job/extension/files.py
+++ b/pyiron_base/jobs/job/extension/files.py
@@ -1,8 +1,8 @@
 import os
 from typing import List
 from pyiron_base.jobs.job.util import (
-    _job_list_files,
-    _job_read_file,
+    _working_directory_list_files,
+    _working_directory_read_file,
 )
 
 
@@ -41,13 +41,18 @@ class FileBrowser:
     ["SYSTEM=pyiron\n", "ENCUT=270\n", ...]
     """
 
-    __slots__ = ("_job",)
+    __slots__ = ("_working_directory",)
 
-    def __init__(self, job):
-        self._job = job
+    def __init__(self, working_directory):
+        self._working_directory = working_directory
 
     def _get_file_dict(self):
-        return {f.replace(".", "_"): f for f in _job_list_files(job=self._job)}
+        return {
+            f.replace(".", "_"): f
+            for f in _working_directory_list_files(
+                working_directory=self._working_directory
+            )
+        }
 
     def __dir__(self):
         return list(self._get_file_dict().keys()) + [
@@ -63,11 +68,16 @@ def list(self) -> List[str]:
         """
         List all files in the working directory of the job.
         """
-        return _job_list_files(job=self._job)
+        return _working_directory_list_files(working_directory=self._working_directory)
 
     def _ipython_display_(self):
         path = self._job.working_directory + ":"
-        files = ["\t" + f for f in _job_list_files(job=self._job)]
+        files = [
+            "\t" + f
+            for f in _working_directory_list_files(
+                working_directory=self._working_directory
+            )
+        ]
         print(os.linesep.join([path, *files]))
 
     def tail(self, file: str, lines: int = 100):
@@ -81,13 +91,22 @@ def tail(self, file: str, lines: int = 100):
         Raises:
             FileNotFoundError: if the given file does not exist
         """
-        print(*_job_read_file(job=self._job, file_name=file, tail=lines), sep="")
+        print(
+            *_working_directory_read_file(
+                working_directory=self._working_directory, file_name=file, tail=lines
+            ),
+            sep="",
+        )
 
     def __getitem__(self, item):
-        if item not in _job_list_files(job=self._job):
+        if item not in _working_directory_list_files(
+            working_directory=self._working_directory
+        ):
             raise KeyError(item)
 
-        return _job_read_file(job=self._job, file_name=item)
+        return _working_directory_read_file(
+            working_directory=self._working_directory, file_name=item
+        )
 
     def __getattr__(self, item):
         try:
diff --git a/pyiron_base/jobs/job/util.py b/pyiron_base/jobs/job/util.py
index 876ea8b63..a76e3e877 100644
--- a/pyiron_base/jobs/job/util.py
+++ b/pyiron_base/jobs/job/util.py
@@ -265,7 +265,14 @@ def _kill_child(job):
 
 def _job_compressed_name(job):
     """Return the canonical file name of a compressed job."""
-    return os.path.join(job.working_directory, job.job_name + ".tar.bz2")
+    return _get_compressed_job_name(working_directory=job.working_directory)
+
+
+def _get_compressed_job_name(working_directory):
+    """Return the canonical file name of a compressed job from the working directory."""
+    return os.path.join(
+        working_directory, os.path.basename(working_directory) + ".tar.bz2"
+    )
 
 
 def _job_compress(job, files_to_compress=None):
@@ -315,6 +322,22 @@ def _job_decompress(job):
         pass
 
 
+def _working_directory_is_compressed(working_directory):
+    """
+    Check if the working directory of a given job is already compressed or not.
+
+    Args:
+        working_directory (str): working directory of the job object
+
+    Returns:
+        bool: [True/False]
+    """
+    compressed_name = os.path.basename(
+        _get_compressed_job_name(working_directory=working_directory)
+    )
+    return compressed_name in os.listdir(working_directory)
+
+
 def _job_is_compressed(job):
     """
     Check if the job is already compressed or not.
@@ -325,52 +348,74 @@ def _job_is_compressed(job):
     Returns:
         bool: [True/False]
     """
-    compressed_name = os.path.basename(_job_compressed_name(job))
-    return compressed_name in os.listdir(job.working_directory)
+    return _working_directory_is_compressed(working_directory=job.working_directory)
 
 
-def _job_list_files(job):
+def _working_directory_list_files(working_directory):
     """
     Returns list of files in the jobs working directory.
 
-    If the job is compressed, return a list of files in the archive.
+    If the working directory is compressed, return a list of files in the archive.
 
     Args:
-        job (JobCore): job object to inspect files in
+        working_directory (str): working directory of the job object to inspect files in
 
     Returns:
         list of str: file names
     """
-    if os.path.isdir(job.working_directory):
-        if _job_is_compressed(job):
-            with tarfile.open(_job_compressed_name(job), "r") as tar:
+    if os.path.isdir(working_directory):
+        if _working_directory_is_compressed(working_directory=working_directory):
+            with tarfile.open(
+                _get_compressed_job_name(working_directory=working_directory), "r"
+            ) as tar:
                 return [member.name for member in tar.getmembers() if member.isfile()]
         else:
-            return os.listdir(job.working_directory)
+            return os.listdir(working_directory)
     return []
 
 
-def _job_read_file(job, file_name, tail=None):
+def _job_list_files(job):
+    """
+    Returns list of files in the jobs working directory.
+
+    If the job is compressed, return a list of files in the archive.
+
+    Args:
+        job (JobCore): job object to inspect files in
+
+    Returns:
+        list of str: file names
+    """
+    return _working_directory_list_files(working_directory=job.working_directory)
+
+
+def _working_directory_read_file(working_directory, file_name, tail=None):
     """
     Return list of lines of the given file.
 
-    Transparently decompresses the file if job is compressed.
+    Transparently decompresses the file if working directory is compressed.
 
     If `tail` is given and job is decompressed, only read the last lines
     instead of traversing the full file.
 
     Args:
+        working_directory (str): working directory of the job object
         file_name (str): the file to print
         tail (int, optional): only return the last lines
 
     Raises:
         FileNotFoundError: if the given file name does not exist in the job folder
     """
-    if file_name not in job.list_files():
+    if file_name not in _working_directory_list_files(
+        working_directory=working_directory
+    ):
         raise FileNotFoundError(file_name)
 
-    if _job_is_compressed(job):
-        with tarfile.open(_job_compressed_name(job), encoding="utf8") as f:
+    if _working_directory_is_compressed(working_directory=working_directory):
+        with tarfile.open(
+            _get_compressed_job_name(working_directory=working_directory),
+            encoding="utf8",
+        ) as f:
             lines = [
                 line.decode("utf8") for line in f.extractfile(file_name).readlines()
             ]
@@ -379,7 +424,7 @@ def _job_read_file(job, file_name, tail=None):
             else:
                 return lines[-tail:]
     else:
-        file_name = posixpath.join(job.working_directory, file_name)
+        file_name = posixpath.join(working_directory, file_name)
         if tail is None:
             with open(file_name) as f:
                 return f.readlines()
@@ -400,6 +445,27 @@ def _job_read_file(job, file_name, tail=None):
             return lines
 
 
+def _job_read_file(job, file_name, tail=None):
+    """
+    Return list of lines of the given file.
+
+    Transparently decompresses the file if job is compressed.
+
+    If `tail` is given and job is decompressed, only read the last lines
+    instead of traversing the full file.
+
+    Args:
+        file_name (str): the file to print
+        tail (int, optional): only return the last lines
+
+    Raises:
+        FileNotFoundError: if the given file name does not exist in the job folder
+    """
+    return _working_directory_read_file(
+        working_directory=job.working_directory, file_name=file_name, tail=tail
+    )
+
+
 def _job_archive(job):
     """
     Compress HDF5 file of the job object to tar-archive

From 5cca59ef5ccf0001bf4cf0084ced36702801d247 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Wed, 7 Feb 2024 08:51:12 +0100
Subject: [PATCH 36/42] Return files as strings

---
 pyiron_base/jobs/job/extension/files.py | 14 +++++++++++---
 tests/flex/test_executablecontainer.py  | 13 ++++++++-----
 tests/job/test_genericJob.py            | 20 ++++++++++++++++++++
 3 files changed, 39 insertions(+), 8 deletions(-)

diff --git a/pyiron_base/jobs/job/extension/files.py b/pyiron_base/jobs/job/extension/files.py
index 3a00dc30a..d916def7c 100644
--- a/pyiron_base/jobs/job/extension/files.py
+++ b/pyiron_base/jobs/job/extension/files.py
@@ -104,12 +104,20 @@ def __getitem__(self, item):
         ):
             raise KeyError(item)
 
-        return _working_directory_read_file(
-            working_directory=self._working_directory, file_name=item
-        )
+        return File(os.path.join(self._working_directory, item))
 
     def __getattr__(self, item):
         try:
             return self[self._get_file_dict()[item]]
         except KeyError:
             raise AttributeError(item) from None
+
+
+class File(str):
+    def tail(self, lines: int = 100):
+        print(
+            *_working_directory_read_file(
+                working_directory=os.path.dirname(self), file_name=os.path.basename(self), tail=lines
+            ),
+            sep="",
+        )
diff --git a/tests/flex/test_executablecontainer.py b/tests/flex/test_executablecontainer.py
index 366bb03ab..3edf7e7de 100644
--- a/tests/flex/test_executablecontainer.py
+++ b/tests/flex/test_executablecontainer.py
@@ -93,12 +93,15 @@ def test_job_files(self):
             job_name="job_output_files"
         )
         job.run()
-        self.assertEqual(dir(job.files), ['__dir__', '__getattr__', '__getitem__', '_ipython_display_','error_out', 'input_file', 'list', 'output_file', 'tail'])
+        self.assertEqual(
+            dir(job.files),
+            ['__dir__', '__getattr__', '__getitem__', '_ipython_display_', 'error_out', 'input_file', 'list', 'output_file', 'tail']
+        )
         output_file_path = os.path.abspath(os.path.join(__file__, "..", "test_executablecontainer", "job_output_files_hdf5", "job_output_files", "error.out"))
-        # if os.name != "nt":
-        #     self.assertEqual(job.files.error_out, output_file_path)
-        # else:
-        #     self.assertEqual(job.files.error_out.replace("/", "\\"), output_file_path)
+        if os.name != "nt":
+            self.assertEqual(job.files.error_out, output_file_path)
+        else:
+            self.assertEqual(job.files.error_out.replace("/", "\\"), output_file_path)
 
     def test_create_job_factory_typeerror(self):
         create_catjob = create_job_factory(
diff --git a/tests/job/test_genericJob.py b/tests/job/test_genericJob.py
index 64b690bf6..082a17400 100644
--- a/tests/job/test_genericJob.py
+++ b/tests/job/test_genericJob.py
@@ -585,6 +585,16 @@ def test_tail(self):
                 reference_str = os.linesep.join(content[-i-1:]) + os.linesep
                 self.assertEqual(f.getvalue().replace('\r', ''), reference_str.replace('\r', ''),
                                  "tail read incorrect lines from output file when job uncompressed!")
+                with contextlib.redirect_stdout(io.StringIO(newline=os.linesep)) as f:
+                    job.files.tail("test_file", lines=i+1)
+                reference_str = os.linesep.join(content[-i-1:]) + os.linesep
+                self.assertEqual(f.getvalue().replace('\r', ''), reference_str.replace('\r', ''),
+                                 "tail read incorrect lines from output file when job uncompressed!")
+                with contextlib.redirect_stdout(io.StringIO(newline=os.linesep)) as f:
+                    job.files.test_file.tail(lines=i+1)
+                reference_str = os.linesep.join(content[-i-1:]) + os.linesep
+                self.assertEqual(f.getvalue().replace('\r', ''), reference_str.replace('\r', ''),
+                                 "tail read incorrect lines from output file when job uncompressed!")
 
         job.compress()
         for i in range(len(content)):
@@ -593,6 +603,16 @@ def test_tail(self):
             reference_str = os.linesep.join(content[-i-1:]) + os.linesep
             self.assertEqual(f.getvalue().replace('\r', ''), reference_str.replace('\r', ''),
                              "tail read incorrect lines from output file when job compressed!")
+            with contextlib.redirect_stdout(io.StringIO()) as f:
+                job.files.tail("test_file", lines=i+1)
+            reference_str = os.linesep.join(content[-i-1:]) + os.linesep
+            self.assertEqual(f.getvalue().replace('\r', ''), reference_str.replace('\r', ''),
+                             "tail read incorrect lines from output file when job compressed!")
+            with contextlib.redirect_stdout(io.StringIO()) as f:
+                job.files.test_file.tail(lines=i+1)
+            reference_str = os.linesep.join(content[-i-1:]) + os.linesep
+            self.assertEqual(f.getvalue().replace('\r', ''), reference_str.replace('\r', ''),
+                             "tail read incorrect lines from output file when job compressed!")
 
 
 if __name__ == "__main__":

From 7718b987293de8643880a6098f33d78bbac725a9 Mon Sep 17 00:00:00 2001
From: pyiron-runner <pyiron@mpie.de>
Date: Wed, 7 Feb 2024 07:52:14 +0000
Subject: [PATCH 37/42] Format black

---
 pyiron_base/jobs/job/extension/files.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pyiron_base/jobs/job/extension/files.py b/pyiron_base/jobs/job/extension/files.py
index d916def7c..9bbad020f 100644
--- a/pyiron_base/jobs/job/extension/files.py
+++ b/pyiron_base/jobs/job/extension/files.py
@@ -117,7 +117,9 @@ class File(str):
     def tail(self, lines: int = 100):
         print(
             *_working_directory_read_file(
-                working_directory=os.path.dirname(self), file_name=os.path.basename(self), tail=lines
+                working_directory=os.path.dirname(self),
+                file_name=os.path.basename(self),
+                tail=lines,
             ),
             sep="",
         )

From f48201ac1856ce01e9752c0dd7a6a7ae3bbf9df2 Mon Sep 17 00:00:00 2001
From: Jan Janssen <jan-janssen@users.noreply.github.com>
Date: Wed, 7 Feb 2024 14:19:26 +0100
Subject: [PATCH 38/42] Update pyiron_base/jobs/job/core.py

Co-authored-by: Marvin Poul <poul@mpie.de>
---
 pyiron_base/jobs/job/core.py | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/pyiron_base/jobs/job/core.py b/pyiron_base/jobs/job/core.py
index ef4a46e19..b8126cae9 100644
--- a/pyiron_base/jobs/job/core.py
+++ b/pyiron_base/jobs/job/core.py
@@ -994,20 +994,6 @@ def __delitem__(self, key):
         """
         del self.project_hdf5[posixpath.join(self.project_hdf5.h5_path, key)]
 
-    @deprecate("use job.files.tail() instead!")
-    def tail(self, file_name, lines=100):
-        """
-        Print the last lines of the given file in the job folder.
-
-        Args:
-            file_name (str): the file to print
-            lines (int): how many lines to print
-
-        Raises:
-            FileNotFoundError: if the given file name does not exist in the job folder
-        """
-        print(*_job_read_file(self, file_name, tail=lines), sep="")
-
     def __repr__(self):
         """
         Human readable string representation

From 2f8cd569ee6ecd75dc3023680698bb4cb0f2c04a Mon Sep 17 00:00:00 2001
From: Jan Janssen <jan-janssen@users.noreply.github.com>
Date: Wed, 7 Feb 2024 14:19:45 +0100
Subject: [PATCH 39/42] Update pyiron_base/jobs/job/extension/files.py

Co-authored-by: Marvin Poul <poul@mpie.de>
---
 pyiron_base/jobs/job/extension/files.py | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/pyiron_base/jobs/job/extension/files.py b/pyiron_base/jobs/job/extension/files.py
index 9bbad020f..2287e21f7 100644
--- a/pyiron_base/jobs/job/extension/files.py
+++ b/pyiron_base/jobs/job/extension/files.py
@@ -55,14 +55,7 @@ def _get_file_dict(self):
         }
 
     def __dir__(self):
-        return list(self._get_file_dict().keys()) + [
-            "list",
-            "tail",
-            "__dir__",
-            "__getitem__",
-            "__getattr__",
-            "_ipython_display_",
-        ]
+        return list(self._get_file_dict().keys()) + super().__dir__()
 
     def list(self) -> List[str]:
         """

From 5ae46937df65c2734c102eae8b55c00e05924289 Mon Sep 17 00:00:00 2001
From: Jan Janssen <jan-janssen@users.noreply.github.com>
Date: Wed, 7 Feb 2024 14:20:11 +0100
Subject: [PATCH 40/42] Update pyiron_base/jobs/job/extension/files.py

Co-authored-by: Marvin Poul <poul@mpie.de>
---
 pyiron_base/jobs/job/extension/files.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyiron_base/jobs/job/extension/files.py b/pyiron_base/jobs/job/extension/files.py
index 2287e21f7..4422edb7c 100644
--- a/pyiron_base/jobs/job/extension/files.py
+++ b/pyiron_base/jobs/job/extension/files.py
@@ -37,8 +37,8 @@ class FileBrowser:
     For files that have valid python variable names can also be accessed by
     attribute notation
 
-    >>> job.files.INCAR
-    ["SYSTEM=pyiron\n", "ENCUT=270\n", ...]
+    >>> job.files.INCAR # doctest: +SKIP
+    File('INCAR')
     """
 
     __slots__ = ("_working_directory",)

From 149fa23f8756862dbd285cf812f7505e4c3c7790 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Wed, 7 Feb 2024 14:27:26 +0100
Subject: [PATCH 41/42] fix test

---
 tests/flex/test_executablecontainer.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/tests/flex/test_executablecontainer.py b/tests/flex/test_executablecontainer.py
index 3edf7e7de..95eb35138 100644
--- a/tests/flex/test_executablecontainer.py
+++ b/tests/flex/test_executablecontainer.py
@@ -93,10 +93,8 @@ def test_job_files(self):
             job_name="job_output_files"
         )
         job.run()
-        self.assertEqual(
-            dir(job.files),
-            ['__dir__', '__getattr__', '__getitem__', '_ipython_display_', 'error_out', 'input_file', 'list', 'output_file', 'tail']
-        )
+        for file in ['error_out', 'input_file', 'output_file']:
+            self.assertTrue(file in dir(job.files))
         output_file_path = os.path.abspath(os.path.join(__file__, "..", "test_executablecontainer", "job_output_files_hdf5", "job_output_files", "error.out"))
         if os.name != "nt":
             self.assertEqual(job.files.error_out, output_file_path)

From 2ff2c782941bb56bb231e6e89eac5d5d7440b3ce Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Wed, 7 Feb 2024 14:31:08 +0100
Subject: [PATCH 42/42] fix genericjob test

---
 tests/job/test_genericJob.py | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/tests/job/test_genericJob.py b/tests/job/test_genericJob.py
index 082a17400..5ef2a7339 100644
--- a/tests/job/test_genericJob.py
+++ b/tests/job/test_genericJob.py
@@ -580,11 +580,6 @@ def test_tail(self):
 
         for i in range(len(content)):
             with self.subTest(i=i):
-                with contextlib.redirect_stdout(io.StringIO(newline=os.linesep)) as f:
-                    job.tail("test_file", lines=i+1)
-                reference_str = os.linesep.join(content[-i-1:]) + os.linesep
-                self.assertEqual(f.getvalue().replace('\r', ''), reference_str.replace('\r', ''),
-                                 "tail read incorrect lines from output file when job uncompressed!")
                 with contextlib.redirect_stdout(io.StringIO(newline=os.linesep)) as f:
                     job.files.tail("test_file", lines=i+1)
                 reference_str = os.linesep.join(content[-i-1:]) + os.linesep
@@ -598,11 +593,6 @@ def test_tail(self):
 
         job.compress()
         for i in range(len(content)):
-            with contextlib.redirect_stdout(io.StringIO()) as f:
-                job.tail("test_file", lines=i+1)
-            reference_str = os.linesep.join(content[-i-1:]) + os.linesep
-            self.assertEqual(f.getvalue().replace('\r', ''), reference_str.replace('\r', ''),
-                             "tail read incorrect lines from output file when job compressed!")
             with contextlib.redirect_stdout(io.StringIO()) as f:
                 job.files.tail("test_file", lines=i+1)
             reference_str = os.linesep.join(content[-i-1:]) + os.linesep