Merge pull request #53 from fphammerle/dependabot/pip/pylint-2.11.1

https://github.com/fphammerle/freesurfer-volume-reader/pull/53

Pipfile.lock

@@ -128,11 +128,11 @@
         },
         "astroid": {
             "hashes": [
-                "sha256:3b680ce0419b8a771aba6190139a3998d14b413852506d99aff8dc2bf65ee67c",
-                "sha256:dc1e8b28427d6bbef6b8842b18765ab58f558c42bb80540bd7648c98412af25e"
+                "sha256:dcc06f6165f415220013801642bd6c9808a02967070919c4b746c6864c205471",
+                "sha256:fe81f80c0b35264acb5653302ffbd935d394f1775c5e4487df745bf9c2442708"
             ],
             "markers": "python_version ~= '3.6'",
-            "version": "==2.7.3"
+            "version": "==2.8.0"
         },
         "attrs": {
             "hashes": [
@@ -212,7 +212,7 @@
                 "sha256:f0b278ce10936db1a37e6954e15a3730bea96a0997c26d7fee88e6c396c2086d",
                 "sha256:f11642dddbb0253cc8853254301b51390ba0081750a8ac03f20ea8103f0c56b6"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'",
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4.0'",
             "version": "==5.5"
         },
         "importlib-metadata": {
@@ -235,7 +235,7 @@
                 "sha256:9c2ea1e62d871267b78307fe511c0838ba0da28698c5732d54e2790bf3ba9899",
                 "sha256:e17d6e2b81095c9db0a03a8025a957f334d6ea30b26f9ec70805411e5c7c81f2"
             ],
-            "markers": "python_version < '4' and python_full_version >= '3.6.1'",
+            "markers": "python_version < '4.0' and python_full_version >= '3.6.1'",
             "version": "==5.9.3"
         },
         "lazy-object-proxy": {
@@ -350,11 +350,11 @@
         },
         "pylint": {
             "hashes": [
-                "sha256:6758cce3ddbab60c52b57dcc07f0c5d779e5daf0cf50f6faacbef1d3ea62d2a1",
-                "sha256:e178e96b6ba171f8ef51fbce9ca30931e6acbea4a155074d80cc081596c9e852"
+                "sha256:0f358e221c45cbd4dad2a1e4b883e75d28acdcccd29d40c76eb72b307269b126",
+                "sha256:2c9843fff1a88ca0ad98a256806c82c5a8f86086e7ccbdb93297d86c3f90c436"
             ],
             "index": "pypi",
-            "version": "==2.10.2"
+            "version": "==2.11.1"
         },
         "pylint-import-requirements": {
             "hashes": [
@@ -491,6 +491,7 @@
                 "sha256:d8226d10bc02a29bcc81df19a26e56a9647f8b0a6d4a83924139f4a8b01f17b7",
                 "sha256:f1d25edafde516b146ecd0613dabcc61409817af4766fbbcfb8d1ad4ec441a34"
             ],
+            "markers": "python_version < '3.10'",
             "version": "==3.10.0.2"
         },
         "wrapt": {

examples/compare_ashs_freesurfer_hipposf.ipynb

@@ -1280,7 +1280,7 @@
     "                     y='volume_mm^3',\n",
     "                     hue='segmentation_mode')\n",
     "ax.set_xticklabels(ax.get_xticklabels(), rotation=60)\n",
-    "ax.set_title('Hippocampal Subfield Volumes of Subject {}'.format(SUBJECT));"
+    "ax.set_title(f'Hippocampal Subfield Volumes of Subject {SUBJECT}');"
    ]
   }
  ],

examples/freesurfer_hipposf.ipynb

@@ -235,7 +235,7 @@
     "\n",
     "volume_frame['segmentation_mode'] = volume_frame.apply(generate_mode_label, axis=1)\n",
     "volume_frame.sort_values(by=['subfield', 'segmentation_mode']) \\\n",
-    "    .to_csv('freesurfer_hipposf_volumes_{}.csv'.format(SUBJECT), index=False)\n",
+    "    .to_csv(f'freesurfer_hipposf_volumes_{SUBJECT}.csv', index=False)\n",
     "volume_frame['segmentation_mode'].value_counts().sort_index()"
    ]
   },
@@ -1195,7 +1195,7 @@
     "                     x='hemisphere',\n",
     "                     y='volume_mm^3',\n",
     "                     hue='segmentation_mode')\n",
-    "ax.set_title('Hippocampal Volume of Subject {}'.format(SUBJECT))\n",
+    "ax.set_title(f'Hippocampal Volume of Subject {SUBJECT}')\n",
     "ax.legend(loc='lower right');"
    ]
   },
@@ -2007,7 +2007,7 @@
     "                     y='volume_mm^3',\n",
     "                     hue='segmentation_mode')\n",
     "ax.set_xticklabels(ax.get_xticklabels(), rotation=60)\n",
-    "ax.set_title('Hippocampal Subfield Volumes of Subject {}\\nLeft Hemisphere'.format(SUBJECT));"
+    "ax.set_title(f'Hippocampal Subfield Volumes of Subject {SUBJECT}\\nLeft Hemisphere');"
    ]
   }
  ],

freesurfer_volume_reader/__main__.py

@@ -49,8 +49,8 @@ def main():
     )
     for source_type, file_class in VOLUME_FILE_FINDERS.items():
         argparser.add_argument(
-            "--{}-filename-regex".format(source_type),
-            dest="filename_regex.{}".format(source_type),
+            f"--{source_type}-filename-regex",
+            dest=f"filename_regex.{source_type}",
             metavar="REGULAR_EXPRESSION",
             type=re.compile,
             default=remove_group_names_from_regex(file_class.FILENAME_PATTERN),
@@ -65,7 +65,7 @@ def main():
         metavar="ROOT_DIR",
         nargs="*" if subjects_dir_path else "+",
         default=[subjects_dir_path],
-        help="default: $SUBJECTS_DIR ({})".format(subjects_dir_path),
+        help=f"default: $SUBJECTS_DIR ({subjects_dir_path})",
     )
     argparser.add_argument("--version", action="version", version=__version__)
     args = argparser.parse_args()

freesurfer_volume_reader/ashs.py

@@ -43,7 +43,9 @@ class IntracranialVolumeFile(freesurfer_volume_reader.VolumeFile):
         return str(self._absolute_path)
 
     def read_volume_mm3(self) -> float:
-        subject, icv = self._absolute_path.read_text().rstrip().split(" ")
+        subject, icv = (
+            self._absolute_path.read_text(encoding="ascii").rstrip().split(" ")
+        )
         assert subject == self.subject, (subject, self.subject)
         return float(icv)
 
@@ -80,7 +82,9 @@ class HippocampalSubfieldsVolumeFile(freesurfer_volume_reader.SubfieldVolumeFile
 
     def read_volumes_mm3(self) -> typing.Dict[str, float]:
         subfield_volumes = {}
-        for line in self._absolute_path.read_text().rstrip().split("\n"):
+        for line in (
+            self._absolute_path.read_text(encoding="ascii").rstrip().split("\n")
+        ):
             # > echo $ASHS_SUBJID $side $SUB $NBODY $VSUB >> $FNBODYVOL
             # https://github.com/pyushkevich/ashs/blob/515ff7c2f50928adabc4e64bded9a7e76fc750b1/bin/ashs_extractstats_qsub.sh#L94
             (

freesurfer_volume_reader/freesurfer.py

@@ -52,7 +52,9 @@ class HippocampalSubfieldsVolumeFile(freesurfer_volume_reader.SubfieldVolumeFile
 
     def read_volumes_mm3(self) -> typing.Dict[str, float]:
         subfield_volumes = {}
-        for line in self._absolute_path.read_text().rstrip().split("\n"):
+        for line in (
+            self._absolute_path.read_text(encoding="ascii").rstrip().split("\n")
+        ):
             # https://github.com/freesurfer/freesurfer/blob/release_6_0_0/HippoSF/src/segmentSubjectT1T2_autoEstimateAlveusML.m#L8
             # https://github.com/freesurfer/freesurfer/blob/release_6_0_0/HippoSF/src/segmentSubjectT1T2_autoEstimateAlveusML.m#L1946
             subfield_name, subfield_volume_mm3_str = line.split(" ")