Replace relative imports with absolute ones (#206)

* Replace relative imports with absolute ones.

* Run isort.

* Remove comments between imports.

aslprep/__about__.py

@@ -1,7 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Base module variables."""
-from ._version import get_versions
+from aslprep._version import get_versions
 
 __version__ = get_versions()["version"]
 del get_versions

aslprep/__init__.py

@@ -2,7 +2,7 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Top-module metadata."""
 
-from .__about__ import __copyright__, __credits__, __packagename__, __version__
+from aslprep.__about__ import __copyright__, __credits__, __packagename__, __version__
 
 __all__ = [
     "__copyright__",

aslprep/__main__.py

@@ -1,9 +1,9 @@
-from .cli.run import main
+from aslprep.cli.run import main
 
 if __name__ == "__main__":
     import sys
 
-    from . import __name__ as module
+    from aslprep import __name__ as module
 
     # `python -m <module>` typically displays the command as __main__.py
     if "__main__.py" in sys.argv[0]:

aslprep/cli/parser.py

@@ -3,7 +3,7 @@
 """Parser."""
 import sys
 
-from .. import config
+from aslprep import config
 
 
 def _build_parser():
@@ -14,8 +14,8 @@ def _build_parser():
 
     from packaging.version import Version
 
-    from ..niworkflows.utils.spaces import OutputReferencesAction, Reference
-    from .version import check_latest, is_flagged
+    from aslprep.cli.version import check_latest, is_flagged
+    from aslprep.niworkflows.utils.spaces import OutputReferencesAction, Reference
 
     def _path_exists(path, parser):
         """Ensure a given path exists."""
@@ -47,7 +47,7 @@ def _drop_sub(value):
         return value[4:] if value.startswith("sub-") else value
 
     def _filter_pybids_none_any(dct):
-        from ..pybids import layout
+        from aslprep.pybids import layout
 
         return {k: layout.Query.ANY if v == "*" else v for k, v in dct.items()}
 
@@ -481,7 +481,7 @@ def parse_args(args=None, namespace=None):
     """Parse args and run further checks on the command line."""
     import logging
 
-    from ..niworkflows.utils.spaces import Reference, SpatialReferences
+    from aslprep.niworkflows.utils.spaces import Reference, SpatialReferences
 
     parser = _build_parser()
     opts = parser.parse_args(args, namespace)
@@ -545,7 +545,7 @@ def parse_args(args=None, namespace=None):
 
     # Wipe out existing work_dir
     if opts.clean_workdir and work_dir.exists():
-        from ..niworkflows.utils.misc import clean_directory
+        from aslprep.niworkflows.utils.misc import clean_directory
 
         build_log.info(f"Clearing previous aslprep working directory: {work_dir}")
         if not clean_directory(work_dir):
@@ -569,7 +569,7 @@ def parse_args(args=None, namespace=None):
 
     # Validate inputs
     if not opts.skip_bids_validation:
-        from ..utils.bids import validate_input_dir
+        from aslprep.utils.bids import validate_input_dir
 
         build_log.info(
             "Making sure the input data is BIDS compliant (warnings can be ignored in most "

aslprep/cli/run.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """ASL preprocessing workflow."""
-from .. import config
+from aslprep import config
 
 
 def main():
@@ -12,16 +12,16 @@ def main():
     from os import EX_SOFTWARE
     from pathlib import Path
 
-    from ..utils.bids import write_derivative_description
-    from .parser import parse_args
+    from aslprep.cli.parser import parse_args
+    from aslprep.utils.bids import write_derivative_description
 
     parse_args()
 
     sentry_sdk = None
     if not config.execution.notrack:
         import sentry_sdk
 
-        from ..utils.sentry import sentry_setup
+        from aslprep.utils.sentry import sentry_setup
 
         sentry_setup()
 
@@ -35,7 +35,7 @@ def main():
     # Because Python on Linux does not ever free virtual memory (VM), running the
     # workflow construction jailed within a process preempts excessive VM buildup.
     with Manager() as mgr:
-        from .workflow import build_workflow
+        from aslprep.cli.workflow import build_workflow
 
         retval = mgr.dict()
         p = Process(target=build_workflow, args=(str(config_file), retval))
@@ -62,7 +62,7 @@ def main():
 
     # Generate boilerplate
     with Manager() as mgr:
-        from .workflow import build_boilerplate
+        from aslprep.cli.workflow import build_boilerplate
 
         p = Process(target=build_boilerplate, args=(str(config_file), aslprep_wf))
         p.start()
@@ -92,7 +92,7 @@ def main():
         aslprep_wf.run(**config.nipype.get_plugin())
     except Exception as e:
         if not config.execution.notrack:
-            from ..utils.sentry import process_crashfile
+            from aslprep.utils.sentry import process_crashfile
 
             crashfolders = [
                 config.execution.output_dir
@@ -137,7 +137,7 @@ def main():
     finally:
         from pkg_resources import resource_filename as pkgrf
 
-        from ..niworkflows.reports import generate_reports
+        from aslprep.niworkflows.reports import generate_reports
 
         # Generate reports phase
         failed_reports = generate_reports(

aslprep/cli/version.py

@@ -7,7 +7,7 @@
 
 import requests
 
-from .. import __version__
+from aslprep import __version__
 
 RELEASE_EXPIRY_DAYS = 14
 DATE_FMT = "%Y%m%d"

aslprep/cli/workflow.py

@@ -12,12 +12,15 @@
 
 def build_workflow(config_file, retval):
     """Create the Nipype Workflow that supports the whole execution graph."""
-    from .. import config
-    from ..niworkflows.reports import generate_reports
-    from ..niworkflows.utils.bids import check_pipeline_version, collect_participants
-    from ..niworkflows.utils.misc import check_valid_fs_license
-    from ..utils.misc import check_deps
-    from ..workflows.base import init_aslprep_wf
+    from aslprep import config
+    from aslprep.niworkflows.reports import generate_reports
+    from aslprep.niworkflows.utils.bids import (
+        check_pipeline_version,
+        collect_participants,
+    )
+    from aslprep.niworkflows.utils.misc import check_valid_fs_license
+    from aslprep.utils.misc import check_deps
+    from aslprep.workflows.base import init_aslprep_wf
 
     config.load(config_file)
     build_log = config.loggers.workflow
@@ -108,7 +111,7 @@ def build_workflow(config_file, retval):
 
 def build_boilerplate(config_file, workflow):
     """Write boilerplate in an isolated process."""
-    from .. import config
+    from aslprep import config
 
     config.load(config_file)
     logs_path = config.execution.output_dir / "aslprep" / "logs"

aslprep/config.py

@@ -42,7 +42,7 @@
     config.to_filename(config_file)
     # Call build_workflow(config_file, retval) in a subprocess
     with Manager() as mgr:
-        from .workflow import build_workflow
+        from aslprep.cli import build_workflow
         retval = mgr.dict()
         p = Process(target=build_workflow, args=(str(config_file), retval))
         p.start()
@@ -87,7 +87,7 @@
     from nipype import logging as nlogging
     from templateflow import __version__ as _tf_ver
 
-    from . import __version__
+    from aslprep import __version__
 
 if not hasattr(sys, "_is_pytest_session"):
     sys._is_pytest_session = False  # Trick to avoid sklearn's FutureWarnings
@@ -99,12 +99,12 @@
         os.getenv("aslprep_DEV", "0").lower() in ("1", "on", "true", "y", "yes"),
     )
 ):
-    from ._warnings import logging
+    from aslprep._warnings import logging
 
     os.environ["PYTHONWARNINGS"] = "ignore"
 elif os.getenv("aslprep_WARNINGS", "0").lower() in ("1", "on", "true", "y", "yes"):
     # allow disabling warnings on development versions
-    from ._warnings import logging
+    from aslprep._warnings import logging
 else:
     import logging
 
@@ -191,7 +191,7 @@ def load(cls, settings, init=True):
     @classmethod
     def get(cls):
         """Return defined settings."""
-        from .niworkflows.utils.spaces import Reference, SpatialReferences
+        from aslprep.niworkflows.utils.spaces import Reference, SpatialReferences
 
         out = {}
         for k, v in cls.__dict__.items():
@@ -600,7 +600,7 @@ def to_filename(filename):
 
 def init_spaces(checkpoint=True):
     """Initialize the :attr:`~workflow.spaces` setting."""
-    from .niworkflows.utils.spaces import Reference, SpatialReferences
+    from aslprep.niworkflows.utils.spaces import Reference, SpatialReferences
 
     spaces = execution.output_spaces or SpatialReferences()
     if not isinstance(spaces, SpatialReferences):

aslprep/interfaces/__init__.py

@@ -1,12 +1,19 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-
-# Load modules for compatibility
-from ..niworkflows.interfaces import bids, cifti, freesurfer, images, itk, surf, utils
-from ..niworkflows.interfaces.plotting import CBFSummary, CBFtsSummary
-from .confounds import ASLSummary, GatherConfounds
-from .multiecho import T2SMap
-from .reports import AboutSummary, FunctionalSummary, SubjectSummary
+"""Nipype interfaces for aslprep."""
+from aslprep.interfaces.confounds import ASLSummary, GatherConfounds
+from aslprep.interfaces.multiecho import T2SMap
+from aslprep.interfaces.reports import AboutSummary, FunctionalSummary, SubjectSummary
+from aslprep.niworkflows.interfaces import (
+    bids,
+    cifti,
+    freesurfer,
+    images,
+    itk,
+    surf,
+    utils,
+)
+from aslprep.niworkflows.interfaces.plotting import CBFSummary, CBFtsSummary
 
 
 class DerivativesDataSink(bids.DerivativesDataSink):

aslprep/interfaces/confounds.py

@@ -201,7 +201,7 @@ class ASLSummary(SimpleInterface):
     output_spec = ASLSummaryOutputSpec
 
     def _run_interface(self, runtime):
-        from ..niworkflows.viz.plots import ASLPlot
+        from aslprep.niworkflows.viz.plots import ASLPlot
 
         self._results["out_file"] = fname_presuffix(
             self.inputs.in_func, suffix="_aslplot.svg", use_ext=False, newpath=runtime.cwd

aslprep/interfaces/reports.py

@@ -18,7 +18,7 @@
     traits,
 )
 
-from ..smriprep.interfaces.freesurfer import ReconAll
+from aslprep.smriprep.interfaces.freesurfer import ReconAll
 
 SUBJECT_TEMPLATE = """\
 \t<ul class="elem-desc">

aslprep/utils/__init__.py

@@ -0,0 +1 @@
+"""Utility functions for aslprep."""

aslprep/utils/bids.py

@@ -8,7 +8,7 @@
 
 
 def write_derivative_description(bids_dir, deriv_dir):
-    from ..__about__ import DOWNLOAD_URL, __url__, __version__
+    from aslprep.__about__ import DOWNLOAD_URL, __url__, __version__
 
     bids_dir = Path(bids_dir)
     deriv_dir = Path(deriv_dir)

aslprep/utils/sentry.py

@@ -6,8 +6,8 @@
 
 import sentry_sdk
 
-from .. import config
-from ..niworkflows.utils.misc import read_crashfile
+from aslprep import config
+from aslprep.niworkflows.utils.misc import read_crashfile
 
 CHUNK_SIZE = 16384
 # Group common events with pre specified fingerprints

aslprep/workflows/asl/__init__.py

@@ -17,8 +17,8 @@
 
 """
 
-from .base import init_asl_preproc_wf
-from .cbf import (
+from aslprep.workflows.asl.base import init_asl_preproc_wf
+from aslprep.workflows.asl.cbf import (
     init_cbf_compt_wf,
     init_cbfgeqc_compt_wf,
     init_cbfplot_wf,
@@ -27,23 +27,23 @@
     init_gecbf_compt_wf,
     init_gecbfplot_wf,
 )
-from .confounds import init_asl_confs_wf
-from .ge_utils import (
+from aslprep.workflows.asl.confounds import init_asl_confs_wf
+from aslprep.workflows.asl.ge_utils import (
     init_asl_geref_wf,
     init_asl_gereg_wf,
     init_asl_gestd_trans_wf,
     init_asl_t1_getrans_wf,
 )
-from .gecbf import init_asl_gepreproc_wf
-from .hmc import init_asl_hmc_wf
-from .registration import init_asl_reg_wf, init_asl_t1_trans_wf
-from .resampling import (
+from aslprep.workflows.asl.gecbf import init_asl_gepreproc_wf
+from aslprep.workflows.asl.hmc import init_asl_hmc_wf
+from aslprep.workflows.asl.registration import init_asl_reg_wf, init_asl_t1_trans_wf
+from aslprep.workflows.asl.resampling import (
     init_asl_preproc_trans_wf,
     init_asl_std_trans_wf,
     init_asl_surf_wf,
 )
-from .stc import init_asl_stc_wf
-from .t2s import init_asl_t2s_wf
+from aslprep.workflows.asl.stc import init_asl_stc_wf
+from aslprep.workflows.asl.t2s import init_asl_t2s_wf
 
 __all__ = [
     "init_asl_confs_wf",