Replace relative imports with absolute ones (#674)

nimare/annotate/cogat.py

@@ -5,11 +5,11 @@
 import numpy as np
 import pandas as pd
 
-from .. import references
-from ..due import due
-from ..extract import download_cognitive_atlas
-from ..utils import _uk_to_us
-from . import utils
+from nimare import references
+from nimare.annotate import utils
+from nimare.due import due
+from nimare.extract import download_cognitive_atlas
+from nimare.utils import _uk_to_us
 
 LGR = logging.getLogger(__name__)
 

nimare/annotate/gclda.py

@@ -8,10 +8,10 @@
 from nilearn._utils import load_niimg
 from scipy.stats import multivariate_normal
 
-from .. import references
-from ..base import NiMAREBase
-from ..due import due
-from ..utils import get_template
+from nimare import references
+from nimare.base import NiMAREBase
+from nimare.due import due
+from nimare.utils import get_template
 
 LGR = logging.getLogger(__name__)
 

nimare/annotate/text.py

@@ -5,7 +5,7 @@
 import pandas as pd
 from sklearn.feature_extraction.text import CountVectorizer, TfidfVectorizer
 
-from ..utils import get_resource_path
+from nimare.utils import get_resource_path
 
 LGR = logging.getLogger(__name__)
 

nimare/base.py

@@ -13,8 +13,8 @@
 from nilearn._utils.niimg_conversions import _check_same_fov
 from nilearn.image import concat_imgs, resample_to_img
 
-from .results import MetaResult
-from .utils import get_masker, mm2vox
+from nimare.results import MetaResult
+from nimare.utils import get_masker, mm2vox
 
 LGR = logging.getLogger(__name__)
 

nimare/correct.py

@@ -6,8 +6,8 @@
 import numpy as np
 import statsmodels.stats.multitest as mc
 
-from .results import MetaResult
-from .transforms import p_to_z
+from nimare.results import MetaResult
+from nimare.transforms import p_to_z
 
 LGR = logging.getLogger(__name__)
 

nimare/dataset.py

@@ -9,8 +9,8 @@
 import pandas as pd
 from nilearn._utils import load_niimg
 
-from .base import NiMAREBase
-from .utils import (
+from nimare.base import NiMAREBase
+from nimare.utils import (
     _dict_to_coordinates,
     _dict_to_df,
     _listify,

nimare/decode/continuous.py

@@ -8,14 +8,14 @@
 from nilearn.masking import apply_mask
 from tqdm.auto import tqdm
 
-from .. import references
-from ..base import Decoder
-from ..due import due
-from ..meta.cbma.base import CBMAEstimator
-from ..meta.cbma.mkda import MKDAChi2
-from ..stats import pearson
-from ..utils import _check_type, _safe_transform
-from .utils import weight_priors
+from nimare import references
+from nimare.base import Decoder
+from nimare.decode.utils import weight_priors
+from nimare.due import due
+from nimare.meta.cbma.base import CBMAEstimator
+from nimare.meta.cbma.mkda import MKDAChi2
+from nimare.stats import pearson
+from nimare.utils import _check_type, _safe_transform
 
 LGR = logging.getLogger(__name__)
 

nimare/decode/discrete.py

@@ -6,14 +6,14 @@
 from scipy.stats import binom
 from statsmodels.sandbox.stats.multicomp import multipletests
 
-from .. import references
-from ..base import Decoder
-from ..due import due
-from ..meta.kernel import KernelTransformer, MKDAKernel
-from ..stats import one_way, pearson, two_way
-from ..transforms import p_to_z
-from ..utils import _check_type, get_masker
-from .utils import weight_priors
+from nimare import references
+from nimare.base import Decoder
+from nimare.decode.utils import weight_priors
+from nimare.due import due
+from nimare.meta.kernel import KernelTransformer, MKDAKernel
+from nimare.stats import one_way, pearson, two_way
+from nimare.transforms import p_to_z
+from nimare.utils import _check_type, get_masker
 
 
 @due.dcite(references.GCLDA_DECODING, description="Citation for GCLDA decoding.")

nimare/decode/encode.py

@@ -3,9 +3,9 @@
 from nilearn.masking import unmask
 from sklearn.feature_extraction.text import CountVectorizer
 
-from .. import references
-from ..due import due
-from .utils import weight_priors
+from nimare import references
+from nimare.decode.utils import weight_priors
+from nimare.due import due
 
 
 @due.dcite(references.GCLDA_DECODING, description="Citation for GCLDA encoding.")

nimare/due.py

@@ -6,7 +6,7 @@
 Note that it might be better to avoid naming it duecredit.py to avoid shadowing
 installed duecredit.
 Then use in your code as
-    from .due import due, Doi, BibTeX
+    from nimare.due import due, Doi, BibTeX
 See  https://github.com/duecredit/duecredit/blob/master/README.md for examples.
 Origin:     Originally a part of the duecredit
 Copyright:  2015-2016  DueCredit developers

nimare/extract/extract.py

@@ -18,15 +18,15 @@
 import requests
 from tqdm.auto import tqdm
 
-from ..dataset import Dataset
-from ..utils import get_resource_path
-from .utils import (
+from nimare.dataset import Dataset
+from nimare.extract.utils import (
     _download_zipped_file,
     _expand_df,
     _get_concept_reltype,
     _get_dataset_dir,
     _longify,
 )
+from nimare.utils import get_resource_path
 
 LGR = logging.getLogger(__name__)
 

nimare/extract/utils.py

@@ -10,7 +10,7 @@
 import requests
 from fuzzywuzzy import fuzz
 
-from ..utils import _uk_to_us
+from nimare.utils import _uk_to_us
 
 LGR = logging.getLogger(__name__)
 

nimare/generate.py

@@ -3,11 +3,11 @@
 
 import numpy as np
 
-from .dataset import Dataset
-from .io import convert_neurovault_to_dataset
-from .meta.utils import compute_ale_ma, get_ale_kernel
-from .transforms import ImageTransformer
-from .utils import get_template, mm2vox, vox2mm
+from nimare.dataset import Dataset
+from nimare.io import convert_neurovault_to_dataset
+from nimare.meta.utils import compute_ale_ma, get_ale_kernel
+from nimare.transforms import ImageTransformer
+from nimare.utils import get_template, mm2vox, vox2mm
 
 # defaults for creating a neurovault dataset
 NEUROVAULT_IDS = (8836, 8838, 8893, 8895, 8892, 8891, 8962, 8894, 8956, 8854, 9000)

nimare/io.py

@@ -12,8 +12,8 @@
 import requests
 from scipy import sparse
 
-from .dataset import Dataset
-from .extract.utils import _get_dataset_dir
+from nimare.dataset import Dataset
+from nimare.extract.utils import _get_dataset_dir
 
 LGR = logging.getLogger(__name__)
 

nimare/meta/cbma/ale.py

@@ -6,13 +6,13 @@
 from joblib import Parallel, delayed
 from tqdm.auto import tqdm
 
-from ... import references
-from ...due import due
-from ...stats import null_to_p, nullhist_to_p
-from ...transforms import p_to_z
-from ...utils import tqdm_joblib, use_memmap
-from ..kernel import ALEKernel
-from .base import CBMAEstimator, PairwiseCBMAEstimator
+from nimare import references
+from nimare.due import due
+from nimare.meta.cbma.base import CBMAEstimator, PairwiseCBMAEstimator
+from nimare.meta.kernel import ALEKernel
+from nimare.stats import null_to_p, nullhist_to_p
+from nimare.transforms import p_to_z
+from nimare.utils import tqdm_joblib, use_memmap
 
 LGR = logging.getLogger(__name__)
 

nimare/meta/cbma/base.py

@@ -8,20 +8,20 @@
 from scipy import ndimage
 from tqdm.auto import tqdm
 
-from ...base import MetaEstimator
-from ...results import MetaResult
-from ...stats import null_to_p, nullhist_to_p
-from ...transforms import p_to_z
-from ...utils import (
+from nimare.base import MetaEstimator
+from nimare.meta.kernel import KernelTransformer
+from nimare.meta.utils import _calculate_cluster_measures, _get_last_bin
+from nimare.results import MetaResult
+from nimare.stats import null_to_p, nullhist_to_p
+from nimare.transforms import p_to_z
+from nimare.utils import (
     _add_metadata_to_dataframe,
     _check_type,
     _safe_transform,
     tqdm_joblib,
     use_memmap,
     vox2mm,
 )
-from ..kernel import KernelTransformer
-from ..utils import _calculate_cluster_measures, _get_last_bin
 
 LGR = logging.getLogger(__name__)
 

nimare/meta/cbma/mkda.py

@@ -9,14 +9,14 @@
 from statsmodels.sandbox.stats.multicomp import multipletests
 from tqdm.auto import tqdm
 
-from ... import references
-from ...due import due
-from ...stats import null_to_p, one_way, two_way
-from ...transforms import p_to_z
-from ...utils import tqdm_joblib, use_memmap, vox2mm
-from ..kernel import KDAKernel, MKDAKernel
-from ..utils import _calculate_cluster_measures
-from .base import CBMAEstimator, PairwiseCBMAEstimator
+from nimare import references
+from nimare.due import due
+from nimare.meta.cbma.base import CBMAEstimator, PairwiseCBMAEstimator
+from nimare.meta.kernel import KDAKernel, MKDAKernel
+from nimare.meta.utils import _calculate_cluster_measures
+from nimare.stats import null_to_p, one_way, two_way
+from nimare.transforms import p_to_z
+from nimare.utils import tqdm_joblib, use_memmap, vox2mm
 
 LGR = logging.getLogger(__name__)
 

nimare/meta/ibma.py

@@ -8,9 +8,9 @@
 from nilearn.input_data import NiftiMasker
 from nilearn.mass_univariate import permuted_ols
 
-from ..base import MetaEstimator
-from ..transforms import p_to_z, t_to_z
-from ..utils import _boolean_unmask
+from nimare.base import MetaEstimator
+from nimare.transforms import p_to_z, t_to_z
+from nimare.utils import _boolean_unmask
 
 LGR = logging.getLogger(__name__)
 

nimare/meta/kernel.py

@@ -16,17 +16,22 @@
 import pandas as pd
 from nilearn import image
 
-from .. import references
-from ..base import Transformer
-from ..due import due
-from ..utils import (
+from nimare import references
+from nimare.base import Transformer
+from nimare.due import due
+from nimare.meta.utils import (
+    compute_ale_ma,
+    compute_kda_ma,
+    compute_p2m_ma,
+    get_ale_kernel,
+)
+from nimare.utils import (
     _add_metadata_to_dataframe,
     _safe_transform,
     mm2vox,
     use_memmap,
     vox2mm,
 )
-from .utils import compute_ale_ma, compute_kda_ma, compute_p2m_ma, get_ale_kernel
 
 LGR = logging.getLogger(__name__)
 

nimare/meta/utils.py

@@ -7,10 +7,10 @@
 import numpy.linalg as npl
 from scipy import ndimage
 
-from .. import references
-from ..due import due
-from ..extract import download_peaks2maps_model
-from ..utils import _determine_chunk_size
+from nimare import references
+from nimare.due import due
+from nimare.extract import download_peaks2maps_model
+from nimare.utils import _determine_chunk_size
 
 os.environ["TF_CPP_MIN_LOG_LEVEL"] = "2"
 LGR = logging.getLogger(__name__)

nimare/references.py

@@ -1,5 +1,5 @@
 """References to be imported and injected at relevant places throughout the library."""
-from .due import BibTeX, Doi
+from nimare.due import BibTeX, Doi
 
 TEXT2BRAIN = Doi("https://doi.org/10.1007/978-3-030-00931-1_67")
 

nimare/results.py

@@ -5,7 +5,7 @@
 
 from nibabel.funcs import squeeze_image
 
-from .utils import get_masker
+from nimare.utils import get_masker
 
 LGR = logging.getLogger(__name__)
 

nimare/stats.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 
-from . import utils
+from nimare import utils
 
 LGR = logging.getLogger(__name__)
 

nimare/tests/conftest.py

@@ -9,8 +9,7 @@
 
 import nimare
 from nimare.tests.utils import get_test_data_path
-
-from ..utils import get_resource_path
+from nimare.utils import get_resource_path
 
 # Only enable the following once in a while for a check for SettingWithCopyWarnings
 # pd.options.mode.chained_assignment = "raise"

nimare/tests/test_estimator_performance.py

@@ -5,12 +5,12 @@
 import numpy as np
 import pytest
 
-from ..correct import FDRCorrector, FWECorrector
-from ..generate import create_coordinate_dataset
-from ..meta import ale, kernel, mkda
-from ..results import MetaResult
-from ..utils import mm2vox
-from .utils import _check_p_values, _create_signal_mask, _transform_res
+from nimare.correct import FDRCorrector, FWECorrector
+from nimare.generate import create_coordinate_dataset
+from nimare.meta import ale, kernel, mkda
+from nimare.results import MetaResult
+from nimare.tests.utils import _check_p_values, _create_signal_mask, _transform_res
+from nimare.utils import mm2vox
 
 # set significance levels used for testing.
 ALPHA = 0.05

nimare/tests/test_generate.py

@@ -4,8 +4,8 @@
 import pytest
 from numpy.random import RandomState
 
-from ..dataset import Dataset
-from ..generate import (
+from nimare.dataset import Dataset
+from nimare.generate import (
     _array_like,
     _create_foci,
     _create_source,