set line length to 79 for black and isort

.flake8

@@ -1,6 +1,6 @@
 [flake8]
 --select = A,B,C,D,E,F,W,C90,FS
-max-line-length = 121
+max-line-length = 120
 # For PEP8 error codes see
 # http://pep8.readthedocs.org/en/latest/intro.html#error-codes
 ignore =

nidmresults/cli/nidm_mkda_convert.py

@@ -27,7 +27,9 @@ def main(argv=sys.argv):
         help="Path to NIDM-Results packs (.nidm.zip) separated by spaces.",
         nargs="+",
     )
-    parser.add_argument("--version", action="version", version=f"{__version__}")
+    parser.add_argument(
+        "--version", action="version", version=f"{__version__}"
+    )
 
     args = parser.parse_args(argv[1:])
 
@@ -53,7 +55,10 @@ def main(argv=sys.argv):
 
         nidmgraph = Graph(nidm_zip=nidmpack)
         con_ids = nidmgraph.serialize(
-            outfile, "mkda", overwrite=overwrite, last_used_con_id=max(con_ids.values())
+            outfile,
+            "mkda",
+            overwrite=overwrite,
+            last_used_con_id=max(con_ids.values()),
         )
 
 

nidmresults/cli/nidmreader.py

@@ -19,7 +19,9 @@
 def main(argv=sys.argv):
     parser = argparse.ArgumentParser(description="NIDM-Results reader.")
     parser.add_argument("nidm_pack", help="Path to NIDM-Results pack.")
-    parser.add_argument("--version", action="version", version=f"{__version__}")
+    parser.add_argument(
+        "--version", action="version", version=f"{__version__}"
+    )
 
     args = parser.parse_args(argv[1:])
 

nidmresults/objects/constants.py

@@ -10,7 +10,8 @@
 NIDM = Namespace("nidm", "http://purl.org/nidash/nidm#")
 NIIRI = Namespace("niiri", "http://iri.nidash.org/")
 CRYPTO = Namespace(
-    "crypto", "http://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#"
+    "crypto",
+    "http://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#",
 )
 FSL = Namespace("fsl", "http://purl.org/nidash/fsl#")
 SPM = Namespace("spm", "http://purl.org/nidash/spm#")
@@ -20,7 +21,9 @@
 DCTYPE = Namespace("dctype", "http://purl.org/dc/dcmitype/")
 NLX_OLD = Namespace("nlx_old", "http://neurolex.org/wiki/")
 DC = Namespace("dc", "http://purl.org/dc/elements/1.1/")
-NFO = Namespace("nfo", "http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#")
+NFO = Namespace(
+    "nfo", "http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#"
+)
 SCR = Namespace("scr", "http://scicrunch.org/resolver/")
 NIF = Namespace("nif", "http://uri.neuinfo.org/nif/nifstd/")
 
@@ -195,13 +198,27 @@
 NIDM_IXI549_COORDINATE_SYSTEM = NIDM["NIDM_0000050"]
 NIDM_INFERENCE = NIDM["NIDM_0000049"]
 NIDM_INDEPENDENT_ERROR = NIDM["NIDM_0000048"]
-NIDM_ICBM_MNI152_NON_LINEAR6TH_GENERATION_COORDINATE_SYSTEM = NIDM["NIDM_0000047"]
-NIDM_ICBM_MNI152_NON_LINEAR2009C_SYMMETRIC_COORDINATE_SYSTEM = NIDM["NIDM_0000046"]
-NIDM_ICBM_MNI152_NON_LINEAR2009C_ASYMMETRIC_COORDINATE_SYSTEM = NIDM["NIDM_0000045"]
-NIDM_ICBM_MNI152_NON_LINEAR2009B_SYMMETRIC_COORDINATE_SYSTEM = NIDM["NIDM_0000044"]
-NIDM_ICBM_MNI152_NON_LINEAR2009B_ASYMMETRIC_COORDINATE_SYSTEM = NIDM["NIDM_0000043"]
-NIDM_ICBM_MNI152_NON_LINEAR2009A_SYMMETRIC_COORDINATE_SYSTEM = NIDM["NIDM_0000042"]
-NIDM_ICBM_MNI152_NON_LINEAR2009A_ASYMMETRIC_COORDINATE_SYSTEM = NIDM["NIDM_0000041"]
+NIDM_ICBM_MNI152_NON_LINEAR6TH_GENERATION_COORDINATE_SYSTEM = NIDM[
+    "NIDM_0000047"
+]
+NIDM_ICBM_MNI152_NON_LINEAR2009C_SYMMETRIC_COORDINATE_SYSTEM = NIDM[
+    "NIDM_0000046"
+]
+NIDM_ICBM_MNI152_NON_LINEAR2009C_ASYMMETRIC_COORDINATE_SYSTEM = NIDM[
+    "NIDM_0000045"
+]
+NIDM_ICBM_MNI152_NON_LINEAR2009B_SYMMETRIC_COORDINATE_SYSTEM = NIDM[
+    "NIDM_0000044"
+]
+NIDM_ICBM_MNI152_NON_LINEAR2009B_ASYMMETRIC_COORDINATE_SYSTEM = NIDM[
+    "NIDM_0000043"
+]
+NIDM_ICBM_MNI152_NON_LINEAR2009A_SYMMETRIC_COORDINATE_SYSTEM = NIDM[
+    "NIDM_0000042"
+]
+NIDM_ICBM_MNI152_NON_LINEAR2009A_ASYMMETRIC_COORDINATE_SYSTEM = NIDM[
+    "NIDM_0000041"
+]
 NIDM_ICBM_MNI152_LINEAR_COORDINATE_SYSTEM = NIDM["NIDM_0000040"]
 NIDM_ICBM452_WARP5_COORDINATE_SYSTEM = NIDM["NIDM_0000039"]
 NIDM_ICBM452_AIR_COORDINATE_SYSTEM = NIDM["NIDM_0000038"]

nidmresults/objects/constants_rdflib.py

@@ -83,8 +83,12 @@
 SPM_PARTIAL_CONJUNCTION_DEGREE = SPM["SPM_0000015"]
 SPM_SMALLEST_SUPRA_THRESHOLD_CLUSTER_SIZE_IN_VOXELS_FWE05 = SPM["SPM_0000014"]
 SPM_SMALLEST_SUPRA_THRESHOLD_CLUSTER_SIZE_IN_VOXELS_FDR05 = SPM["SPM_0000013"]
-SPM_SMALLEST_SUPRA_THRESHOLD_CLUSTER_SIZE_IN_VERTICES_FWE05 = SPM["SPM_0000012"]
-SPM_SMALLEST_SUPRA_THRESHOLD_CLUSTER_SIZE_IN_VERTICES_FDR05 = SPM["SPM_0000011"]
+SPM_SMALLEST_SUPRA_THRESHOLD_CLUSTER_SIZE_IN_VERTICES_FWE05 = SPM[
+    "SPM_0000012"
+]
+SPM_SMALLEST_SUPRA_THRESHOLD_CLUSTER_SIZE_IN_VERTICES_FDR05 = SPM[
+    "SPM_0000011"
+]
 SPM_SEARCH_VOLUME_RESELS_GEOMETRY = SPM["SPM_0000010"]
 SPM_TEMPORAL_DERIVATIVE = SPM["SPM_0000006"]
 SPM_KCONJUNCTION_INFERENCE = SPM["SPM_0000005"]
@@ -200,13 +204,27 @@
 NIDM_IXI549_COORDINATE_SYSTEM = NIDM["NIDM_0000050"]
 NIDM_INFERENCE = NIDM["NIDM_0000049"]
 NIDM_INDEPENDENT_ERROR = NIDM["NIDM_0000048"]
-NIDM_ICBM_MNI152_NON_LINEAR6TH_GENERATION_COORDINATE_SYSTEM = NIDM["NIDM_0000047"]
-NIDM_ICBM_MNI152_NON_LINEAR2009C_SYMMETRIC_COORDINATE_SYSTEM = NIDM["NIDM_0000046"]
-NIDM_ICBM_MNI152_NON_LINEAR2009C_ASYMMETRIC_COORDINATE_SYSTEM = NIDM["NIDM_0000045"]
-NIDM_ICBM_MNI152_NON_LINEAR2009B_SYMMETRIC_COORDINATE_SYSTEM = NIDM["NIDM_0000044"]
-NIDM_ICBM_MNI152_NON_LINEAR2009B_ASYMMETRIC_COORDINATE_SYSTEM = NIDM["NIDM_0000043"]
-NIDM_ICBM_MNI152_NON_LINEAR2009A_SYMMETRIC_COORDINATE_SYSTEM = NIDM["NIDM_0000042"]
-NIDM_ICBM_MNI152_NON_LINEAR2009A_ASYMMETRIC_COORDINATE_SYSTEM = NIDM["NIDM_0000041"]
+NIDM_ICBM_MNI152_NON_LINEAR6TH_GENERATION_COORDINATE_SYSTEM = NIDM[
+    "NIDM_0000047"
+]
+NIDM_ICBM_MNI152_NON_LINEAR2009C_SYMMETRIC_COORDINATE_SYSTEM = NIDM[
+    "NIDM_0000046"
+]
+NIDM_ICBM_MNI152_NON_LINEAR2009C_ASYMMETRIC_COORDINATE_SYSTEM = NIDM[
+    "NIDM_0000045"
+]
+NIDM_ICBM_MNI152_NON_LINEAR2009B_SYMMETRIC_COORDINATE_SYSTEM = NIDM[
+    "NIDM_0000044"
+]
+NIDM_ICBM_MNI152_NON_LINEAR2009B_ASYMMETRIC_COORDINATE_SYSTEM = NIDM[
+    "NIDM_0000043"
+]
+NIDM_ICBM_MNI152_NON_LINEAR2009A_SYMMETRIC_COORDINATE_SYSTEM = NIDM[
+    "NIDM_0000042"
+]
+NIDM_ICBM_MNI152_NON_LINEAR2009A_ASYMMETRIC_COORDINATE_SYSTEM = NIDM[
+    "NIDM_0000041"
+]
 NIDM_ICBM_MNI152_LINEAR_COORDINATE_SYSTEM = NIDM["NIDM_0000040"]
 NIDM_ICBM452_WARP5_COORDINATE_SYSTEM = NIDM["NIDM_0000039"]
 NIDM_ICBM452_AIR_COORDINATE_SYSTEM = NIDM["NIDM_0000038"]

nidmresults/objects/contrast.py

@@ -151,7 +151,9 @@ def __init__(
         self.name = contrast_name
         if filename is None:
             filename = "Contrast" + self.num + ".nii.gz"
-        self.file = NIDMFile(self.id, contrast_file, filename, sha=sha, fmt=fmt)
+        self.file = NIDMFile(
+            self.id, contrast_file, filename, sha=sha, fmt=fmt
+        )
         self.coord_space = coord_space
         self.type = NIDM_CONTRAST_MAP
         self.prov_type = PROV["Entity"]
@@ -218,7 +220,10 @@ def get_query(klass, oid=None):
     def export(self, nidm_version, export_dir):
         """Create prov graph."""
         # Contrast Map entity
-        atts = ((PROV["type"], NIDM_CONTRAST_MAP), (NIDM_CONTRAST_NAME, self.name))
+        atts = (
+            (PROV["type"], NIDM_CONTRAST_MAP),
+            (NIDM_CONTRAST_NAME, self.name),
+        )
 
         if not self.isderfrommap:
             atts = atts + ((NIDM_IN_COORDINATE_SPACE, self.coord_space.id),)
@@ -299,9 +304,13 @@ def export(self, nidm_version, export_dir):
             sigma_sq_img = nib.load(self.sigma_sq_file)
             sigma_sq = sigma_sq_img.get_data()
 
-            expl_mean_sq = nib.Nifti1Image(fstat * sigma_sq, fstat_img.get_qform())
+            expl_mean_sq = nib.Nifti1Image(
+                fstat * sigma_sq, fstat_img.get_qform()
+            )
 
-            self.filename = "ContrastExplainedMeanSquareMap" + self.num + ".nii.gz"
+            self.filename = (
+                "ContrastExplainedMeanSquareMap" + self.num + ".nii.gz"
+            )
             self.expl_mean_sq_file = os.path.join(export_dir, self.filename)
             nib.save(expl_mean_sq, self.expl_mean_sq_file)
 
@@ -452,15 +461,21 @@ def export(self, nidm_version, export_dir):
 
 
 class ContrastVariance(NIDMObject):
-    def __init__(self, coord_space, var_file, filename, fmt=None, sha=None, oid=None):
+    def __init__(
+        self, coord_space, var_file, filename, fmt=None, sha=None, oid=None
+    ):
         super().__init__(oid=oid)
         self.coord_space = coord_space
         self.type = NIDM_CONTRAST_VARIANCE_MAP
         self.filename = filename
         self.fmt = fmt
         self.sha = sha
         self.file = NIDMFile(
-            self.id, var_file, filename=self.filename, fmt=self.fmt, sha=self.sha
+            self.id,
+            var_file,
+            filename=self.filename,
+            fmt=self.fmt,
+            sha=self.sha,
         )
         self.prov_type = PROV["Entity"]
 
@@ -510,7 +525,9 @@ def __init__(
             elif self.stat_type.startswith("http"):
                 self.stat = Identifier(self.stat_type)
             else:
-                raise Exception("Unrecognised statistic: " + str(self.stat_type))
+                raise Exception(
+                    "Unrecognised statistic: " + str(self.stat_type)
+                )
 
         if derfrom_id is not None:
             self.derfrom = StatisticMap(
@@ -530,7 +547,9 @@ def __init__(
 
         # FIXME use new 'preferred mathematical notation from stato'
         if self.num is not None:
-            filename = self.stat_type.upper() + "Statistic" + self.num + ".nii.gz"
+            filename = (
+                self.stat_type.upper() + "Statistic" + self.num + ".nii.gz"
+            )
         self.file = NIDMFile(self.id, location, filename, sha=sha)
         self.coord_space = coord_space
 
@@ -549,7 +568,9 @@ def __init__(
         self.fmt = fmt
 
         # Effect degrees of freedom for T-test is always 1
-        if (effdof is None) and (self.stat in [STATO_TSTATISTIC, STATO_ZSTATISTIC]):
+        if (effdof is None) and (
+            self.stat in [STATO_TSTATISTIC, STATO_ZSTATISTIC]
+        ):
             effdof = 1.0
 
         self.effdof = effdof
@@ -608,10 +629,15 @@ def get_query(klass, oid=None):
 
     def export(self, nidm_version, export_dir):
         """Create prov graph."""
-        attributes = [(PROV["type"], NIDM_STATISTIC_MAP), (DCT["format"], self.fmt)]
+        attributes = [
+            (PROV["type"], NIDM_STATISTIC_MAP),
+            (DCT["format"], self.fmt),
+        ]
 
         if not self.isderfrommap:
-            attributes.insert(0, (NIDM_IN_COORDINATE_SPACE, self.coord_space.id))
+            attributes.insert(
+                0, (NIDM_IN_COORDINATE_SPACE, self.coord_space.id)
+            )
             attributes.insert(0, (PROV["label"], self.label))
 
         if not self.stat_type == "Z":
@@ -681,4 +707,6 @@ def get_query(klass, oid=None):
 
     def export(self, nidm_version, export_dir):
         """Create prov graph."""
-        self.add_attributes(((PROV["type"], self.type), (PROV["label"], self.label)))
+        self.add_attributes(
+            ((PROV["type"], self.type), (PROV["label"], self.label))
+        )

nidmresults/objects/generic.py

@@ -222,7 +222,9 @@ def is_mni(self):
             return False
 
     def is_talairach(self):
-        if str(self.coordinate_system) in [NIDM_TALAIRACH_COORDINATE_SYSTEM.uri]:
+        if str(self.coordinate_system) in [
+            NIDM_TALAIRACH_COORDINATE_SYSTEM.uri
+        ]:
             return True
         else:
             return False
@@ -270,9 +272,13 @@ def export(self, nidm_version, export_dir):
         self.add_attributes(
             {
                 PROV["type"]: self.type,
-                NIDM_DIMENSIONS_IN_VOXELS: json.dumps(self.dimensions.tolist()),
+                NIDM_DIMENSIONS_IN_VOXELS: json.dumps(
+                    self.dimensions.tolist()
+                ),
                 NIDM_NUMBER_OF_DIMENSIONS: self.number_of_dimensions,
-                NIDM_VOXEL_TO_WORLD_MAPPING: json.dumps(self.voxel_to_world.tolist()),
+                NIDM_VOXEL_TO_WORLD_MAPPING: json.dumps(
+                    self.voxel_to_world.tolist()
+                ),
                 NIDM_IN_WORLD_COORDINATE_SYSTEM: self.coordinate_system,
                 NIDM_VOXEL_UNITS: json.dumps(self.units),
                 NIDM_VOXEL_SIZE: json.dumps(self.voxel_size.tolist()),
@@ -285,7 +291,13 @@ class NIDMFile(NIDMObject):
     """Object representing a File (to be used as attribute of another class)."""
 
     def __init__(
-        self, rdf_id, location, filename=None, sha=None, fmt=None, temporary=False
+        self,
+        rdf_id,
+        location,
+        filename=None,
+        sha=None,
+        fmt=None,
+        temporary=False,
     ):
         super().__init__()
         self.prov_type = PROV["Entity"]
@@ -371,7 +383,9 @@ def export(self, nidm_version, export_dir, prepend_path):
             if self.fmt is None:
                 self.fmt = "image/nifti"
 
-            self.add_attributes([(CRYPTO["sha512"], self.sha), (DCT["format"], self.fmt)])
+            self.add_attributes(
+                [(CRYPTO["sha512"], self.sha), (DCT["format"], self.fmt)]
+            )
 
 
 class Image(NIDMObject):
@@ -423,7 +437,9 @@ def export(self, nidm_version, export_dir):
 class NeuroimagingSoftware(NIDMObject):
     """Class representing a NeuroimagingSoftware Agent."""
 
-    def __init__(self, software_type, version, label=None, feat_version=None, oid=None):
+    def __init__(
+        self, software_type, version, label=None, feat_version=None, oid=None
+    ):
         super().__init__(oid=oid)
         self.version = version
 
@@ -606,4 +622,6 @@ def get_query(klass, oid=None):
 
     def export(self, nidm_version, export_dir):
         """Create prov entities and activities."""
-        self.add_attributes([(PROV["label"], self.label), (PROV["type"], self.type)])
+        self.add_attributes(
+            [(PROV["label"], self.label), (PROV["type"], self.type)]
+        )