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added in hacks to package.yaml to get tests to run
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tclose committed Apr 22, 2024
1 parent 0fe7565 commit 31e1293
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Showing 4 changed files with 16 additions and 28 deletions.
2 changes: 1 addition & 1 deletion nipype-auto-conv/generate
Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
#!/usr/bin/env bash
conv_dir=$(dirname $0)
nipype2pydra convert $conv_dir/specs $conv_dir/.. $conv_dir/to_include.txt
nipype2pydra convert $conv_dir/specs $conv_dir/..
18 changes: 15 additions & 3 deletions nipype-auto-conv/specs/package.yaml
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Expand Up @@ -7,13 +7,25 @@ config_params: null
# Mappings between nipype packages and their pydra equivalents. Regular expressions are supported
import_translations: null
find_replace:
- [NIWORKFLOWS_LOG = logging.getLogger\(__packagename__\), ""]
- ["from .. import config, logging", ""]
- [NIWORKFLOWS_LOG, "logger"]
- ["_cifs_table = _generate_cifs_table\\(\\)", ""]
copy_packages:
- niworkflows.data
omit_objects:
omit_functions:
- nipype.utils.filemanip._generate_cifs_table
omit_modules:
- niworkflows.config
- niworkflows.logging
omit_constants:
- niworkflows.NIWORKFLOWS_LOG
- nipype.utils.filemanip._cifs_table
- nipype.config
- nipype.logging
to_include:
- niworkflows.utils.connections.pop_file
import_find_replace:
- ["\\b\\w*_cifs_table,", ""]
- [
"\\bpydra\\.tasks\\.niworkflows\\.nipype_ports\\.interfaces import afni",
"pydra.tasks.afni import auto as afni",
]
11 changes: 0 additions & 11 deletions nipype-auto-conv/to_include.txt

This file was deleted.

13 changes: 0 additions & 13 deletions pydra/tasks/niworkflows/__init__.py
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@@ -1,13 +0,0 @@
import attrs
from fileformats.generic import Directory, File
import logging
from pathlib import Path
from pydra.engine import Workflow
from pydra.engine.specs import MultiInputObj
import pydra.mark


logger = logging.getLogger(__name__)



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