refactor: replace os.path with pathlib

autofit/aggregator/aggregator.py

@@ -15,7 +15,6 @@
 import os
 import zipfile
 from collections import defaultdict
-from os import path
 from pathlib import Path
 from shutil import rmtree
 from typing import List, Union, Iterator, Optional
@@ -84,8 +83,8 @@ def unzip_directory(directory: str):
         for filename in filenames:
             if filename.endswith(".zip"):
                 try:
-                    with zipfile.ZipFile(path.join(root, filename), "r") as f:
-                        f.extractall(path.join(root, filename[:-4]))
+                    with zipfile.ZipFile(Path(root) / filename, "r") as f:
+                        f.extractall(Path(root) / filename[:-4])
                 except zipfile.BadZipFile:
                     raise zipfile.BadZipFile(
                         f"File is not a zip file: \n " f"{root} \n" f"{filename}"
@@ -213,7 +212,7 @@ def remove_unzipped(self):
         Removes the unzipped output directory for each phase.
         """
         for phase in self.search_outputs:
-            split_path = path.split(phase.directory)[0]
+            split_path = Path(phase.directory).parent
 
             rmtree(split_path, ignore_errors=True)
 

autofit/aggregator/search_output.py

@@ -3,7 +3,6 @@
 import logging
 import pickle
 from abc import ABC
-from os import path
 from pathlib import Path
 from typing import Generator, Tuple, Optional, List, cast, Type
 
@@ -372,7 +371,7 @@ def header(self) -> str:
         """
         phase = self.phase or ""
         dataset_name = self.dataset_name or ""
-        return path.join(phase, dataset_name)
+        return str(Path(phase) / dataset_name) if dataset_name else phase
 
     @property
     def search(self):

autofit/database/__init__.py

@@ -1,4 +1,5 @@
 import os
+from pathlib import Path
 
 from .sqlalchemy_ import sa
 
@@ -66,7 +67,7 @@ def open_database(
             exist_ok=True
         )
 
-        exists = os.path.exists(filename)
+        exists = Path(filename).exists()
 
         string = f'sqlite:///{filename}'
         kwargs = dict(

autofit/mapper/model_mapper.py

@@ -1,8 +1,8 @@
-import os
+from pathlib import Path
 
 from autofit.mapper.prior_model.collection import Collection
 
-path = os.path.dirname(os.path.realpath(__file__))
+path = Path(__file__).resolve().parent
 
 
 class ModelMapper(Collection):

autofit/non_linear/grid/grid_search/__init__.py

@@ -1,7 +1,7 @@
 import copy
 import logging
 import os
-from os import path
+from pathlib import Path
 from typing import List, Tuple, Union, Type, Optional, Dict
 
 from autoconf.dictable import to_dict
@@ -312,11 +312,7 @@ def job_for_analysis_grid_priors_and_values(
                 )
             )
 
-        name_path = path.join(
-            self.paths.name,
-            self.paths.identifier,
-            "_".join(labels),
-        )
+        name_path = str(Path(self.paths.name) / self.paths.identifier / "_".join(labels))
 
         search_instance = self.search_instance(name_path=name_path)
         search_instance.paths.model = model

autofit/non_linear/paths/abstract.py

@@ -5,7 +5,6 @@
 import zipfile
 from abc import ABC, abstractmethod
 from configparser import NoSectionError
-from os import path
 from pathlib import Path
 from typing import Optional
 
@@ -224,7 +223,7 @@ def image_path(self) -> Path:
         The path to the image folder.
         """
 
-        if not os.path.exists(self.output_path / f"image{self.image_path_suffix}"):
+        if not (self.output_path / f"image{self.image_path_suffix}").exists():
             os.makedirs(self.output_path / f"image{self.image_path_suffix}")
 
         return self.output_path / f"image{self.image_path_suffix}"
@@ -257,7 +256,7 @@ def output_path(self) -> Path:
         if self.is_identifier_in_paths:
             strings.append(self.identifier)
 
-        return Path(path.join("", *strings))
+        return Path(*strings) if strings else Path("")
 
     @property
     def _files_path(self) -> Path:
@@ -296,7 +295,7 @@ def restore(self):
         Copy files from the ``.zip`` file to the samples folder.
         """
 
-        if path.exists(self._zip_path):
+        if Path(self._zip_path).exists():
             shutil.rmtree(self.output_path, ignore_errors=True)
 
             try:

autofit/non_linear/paths/directory.py

@@ -4,7 +4,6 @@
 import json
 import numpy as np
 import os
-from os import path
 from pathlib import Path
 from typing import Optional, Union, cast, Type
 import logging
@@ -175,14 +174,14 @@ def is_object(self, name: str) -> bool:
         """
         Is there a file pickles/{name}.pickle?
         """
-        return os.path.exists(self._path_for_pickle(name))
+        return self._path_for_pickle(name).exists()
 
     @property
     def is_complete(self) -> bool:
         """
         Has the search been completed?
         """
-        return path.exists(self._has_completed_path)
+        return self._has_completed_path.exists()
 
     def save_search_internal(self, obj):
         """
@@ -214,7 +213,7 @@ def load_search_internal(self):
             import emcee
 
             backend_filename = self.search_internal_path / "search_internal.hdf"
-            if os.path.isfile(backend_filename):
+            if backend_filename.is_file():
                 return emcee.backends.HDFBackend(filename=str(backend_filename))
         except ImportError:
             pass
@@ -400,7 +399,7 @@ def is_grid_search(self) -> bool:
         """
         Is this a grid search which comprises a number of child searches?
         """
-        return os.path.exists(self._grid_search_path)
+        return self._grid_search_path.exists()
 
     def create_child(
         self,
@@ -533,7 +532,7 @@ def _make_path(self) -> str:
         The path terminates with the identifier, unless the identifier has already
         been added to the path.
         """
-        path_ = Path(path.join(conf.instance.output_path, self.path_prefix, self.name))
+        path_ = Path(conf.instance.output_path) / self.path_prefix / self.name
         if self.is_identifier_in_paths:
             path_ = path_ / self.identifier
         return path_

autofit/non_linear/search/mcmc/blackjax/nuts/search.py

@@ -1,6 +1,7 @@
 import logging
 import os
 import pickle
+from pathlib import Path
 from typing import Optional
 
 import numpy as np
@@ -349,7 +350,7 @@ def backend_filename(self):
     @property
     def backend(self) -> dict:
         """Load the pickled search-internal dict written by ``_fit``."""
-        if not os.path.isfile(self.backend_filename):
+        if not Path(self.backend_filename).is_file():
             raise FileNotFoundError(
                 f"search_internal.pickle does not exist at "
                 f"{self.paths.search_internal_path}"

autofit/non_linear/search/mcmc/emcee/search.py

@@ -1,5 +1,6 @@
 import logging
 import os
+from pathlib import Path
 from typing import Dict, Optional
 
 import numpy as np
@@ -371,7 +372,7 @@ def backend(self) -> "emcee.backends.HDFBackend":
         """
         import emcee
 
-        if os.path.isfile(self.backend_filename):
+        if Path(self.backend_filename).is_file():
             return emcee.backends.HDFBackend(filename=str(self.backend_filename))
         else:
             raise FileNotFoundError(

autofit/non_linear/search/nest/dynesty/search/abstract.py

@@ -1,6 +1,7 @@
 import logging
 import os
 from abc import ABC
+from pathlib import Path
 from typing import Dict, Optional, Tuple, Union
 
 import numpy as np
@@ -185,7 +186,7 @@ def _fit(
         )
 
         if not isinstance(self.paths, NullPaths):
-            checkpoint_exists = os.path.exists(self.checkpoint_file)
+            checkpoint_exists = Path(self.checkpoint_file).exists()
         else:
             checkpoint_exists = False
 

autofit/non_linear/search/nest/nautilus/search.py

@@ -2,6 +2,7 @@
 import logging
 import os
 import sys
+from pathlib import Path
 from typing import Dict, Optional, Tuple
 
 from autofit.database.sqlalchemy_ import sa
@@ -169,7 +170,7 @@ def _fit(self, model: AbstractPriorModel, analysis):
         """
 
         if not isinstance(self.paths, NullPaths):
-            checkpoint_exists = os.path.exists(self.checkpoint_file)
+            checkpoint_exists = Path(self.checkpoint_file).exists()
         else:
             checkpoint_exists = False
 

autofit/tools/util.py

@@ -46,8 +46,8 @@ def zip_directory(source_directory, output=None):
         for root, dirs, files in os.walk(source_directory):
             for file in files:
                 f.write(
-                    os.path.join(root, file),
-                    os.path.join(root[len(str(source_directory)) :], file),
+                    Path(root) / file,
+                    Path(root[len(str(source_directory)):]) / file,
                 )
 
 
@@ -94,12 +94,12 @@ def numpy_array_to_json(
     numpy_array_to_json(array_2d=array_2d, file_path='/path/to/file/filename.json', overwrite=True)
     """
 
-    file_dir = os.path.split(file_path)[0]
+    file_dir = Path(file_path).parent
 
-    if not os.path.exists(file_dir):
+    if not file_dir.exists():
         os.makedirs(file_dir)
 
-    if overwrite and os.path.exists(file_path):
+    if overwrite and Path(file_path).exists():
         os.remove(file_path)
 
     with open(file_path, "w+") as f:

docs/conf.py

@@ -9,13 +9,13 @@
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
+# documentation root, use Path(...).resolve() to make it absolute, like shown here.
 #
 
-import os
 import sys
+from pathlib import Path
 
-sys.path.insert(0, os.path.abspath("."))
+sys.path.insert(0, str(Path(".").resolve()))
 
 import autofit
 

test_autofit/aggregator/conftest.py

@@ -1,4 +1,3 @@
-from os import path
 from pathlib import Path
 
 import pytest
@@ -28,7 +27,7 @@ def make_directory():
 
 @pytest.fixture(name="aggregator_directory")
 def make_aggregator_directory(directory):
-    directory = path.dirname(path.realpath(__file__))
+    directory = Path(__file__).resolve().parent
 
     return directory.parent / "tools" / "files" / "aggregator"
 

test_autofit/conftest.py

@@ -2,7 +2,6 @@
 import os
 import shutil
 import sys
-from os import path
 from pathlib import Path
 from unittest.mock import MagicMock
 
@@ -79,7 +78,7 @@ def __init__(self):
         self.paths = []
 
     def __call__(self, path, *args, **kwargs):
-        self.paths.append(path)
+        self.paths.append(str(path))
 
 
 @pytest.fixture(name="plot_patch")
@@ -105,14 +104,14 @@ def remove_logs():
     for d, _, files in os.walk(directory):
         for file in files:
             if file.endswith(".log"):
-                os.remove(path.join(d, file))
+                os.remove(Path(d) / file)
 
 
 @pytest.fixture(autouse=True)
 def set_config_path():
     conf.instance.push(
-        new_path=path.join(directory, "config"),
-        output_path=path.join(directory, "output"),
+        new_path=str(directory / "config"),
+        output_path=str(directory / "output"),
     )
 
 

test_autofit/database/paths/test_paths.py

@@ -1,5 +1,4 @@
 import logging
-import os
 from pathlib import Path
 
 import pytest
@@ -29,9 +28,7 @@ def query_fit(session, paths):
 )
 def test_create():
     m.open_database("test.sqlite")
-    assert os.path.exists(
-        output_path
-    )
+    assert Path(output_path).exists()
 
 
 @output_path_for_test(
@@ -53,9 +50,7 @@ def test_create_postgres():
         )
     except Exception as e:
         logging.exception(e)
-    assert not os.path.exists(
-        output_path
-    )
+    assert not Path(output_path).exists()
 
 
 def test_incomplete(paths):

test_autofit/database/paths/test_switch.py

@@ -69,6 +69,4 @@ def test_is_database_paths(search):
 #         Analysis()
 #     )
 #
-#     assert not os.path.exists(
-#         output_path
-#     )
+#     assert not Path(output_path).exists()

test_autofit/non_linear/paths/test_paths.py

@@ -1,4 +1,3 @@
-import os
 import pickle
 from pathlib import Path
 
@@ -61,7 +60,7 @@ def test_identifier_file(model):
     paths.search = af.DynestyStatic()
     paths.save_all({}, {})
 
-    assert os.path.exists(output_path / paths.identifier / ".identifier")
+    assert (output_path / paths.identifier / ".identifier").exists()
 
 
 def test_serialize(model):