Flag peaks2maps for removal in 0.0.13/0.1.0

.github/release.yml

@@ -9,6 +9,9 @@ changelog:
     - title: 🎉 Exciting New Features
       labels:
         - enhancement
+    - title: 👎 Deprecations
+      labels:
+        - deprecation
     - title: 🐛 Bug Fixes
       labels:
         - bug

README.md

@@ -26,11 +26,7 @@ pip install nimare
 
 ### Local installation (development version)
 ```
-pip install git+https://github.com/neurostuff/NiMARE.git#egg=nimare[peaks2maps-cpu]
-```
-If you have [TensorFlow configured to take advantage of your local GPU](https://www.tensorflow.org/install/) use
-```
-pip install git+https://github.com/neurostuff/NiMARE.git#egg=nimare[peaks2maps-gpu]
+pip install git+https://github.com/neurostuff/NiMARE.git
 ```
 
 ## Contributing

examples/02_meta-analyses/09_peaks2maps.py

@@ -7,6 +7,9 @@
 ================================
 Generate MA maps with peaks2maps
 ================================
+
+.. warning::
+    peaks2maps has been deprecated within NiMARE and will be removed in version 0.0.13.
 """
 ###############################################################################
 # Start with the necessary imports

nimare/cli.py

@@ -148,7 +148,9 @@ def _get_parser():
             "unthresholded maps from peak coordinates. The reconstructed "
             "maps are evaluated for statistical significance using a "
             "permutation-based approach with Family Wise Error multiple "
-            "comparison correction."
+            "comparison correction. "
+            "WARNING: "
+            "The peaks2maps workflow is deprecated and will be removed in NiMARE version 0.0.13."
         ),
     )
     peaks2maps_parser.set_defaults(func=peaks2maps_workflow)

nimare/extract/extract.py

@@ -522,6 +522,9 @@ def download_abstracts(dataset, email):
 def download_peaks2maps_model(data_dir=None, overwrite=False):
     """Download the trained Peaks2Maps model from OHBM 2018.
 
+    .. deprecated:: 0.0.11
+        `download_peaks2maps_model` will be removed in NiMARE 0.0.13.
+
     .. versionadded:: 0.0.2
 
     Parameters

nimare/meta/kernel.py

@@ -8,6 +8,7 @@
 
 import logging
 import os
+import warnings
 from hashlib import md5
 
 import nibabel as nib
@@ -438,6 +439,9 @@ class MKDAKernel(KDAKernel):
 class Peaks2MapsKernel(KernelTransformer):
     """Generate peaks2maps modeled activation images from coordinates.
 
+    .. deprecated:: 0.0.11
+        `Peaks2MapsKernel` will be removed in NiMARE 0.0.13.
+
     Parameters
     ----------
     model_dir : :obj:`str`, optional
@@ -450,13 +454,14 @@ class Peaks2MapsKernel(KernelTransformer):
     """
 
     def __init__(self, model_dir="auto"):
+        warnings.warn(
+            "Peaks2MapsKernel is deprecated, and will be removed in NiMARE version 0.0.13.",
+            DeprecationWarning,
+        )
+
         # Use private attribute to hide value from get_params.
         # get_params will find model_dir=None, which is *very important* when a path is provided.
         self._model_dir = model_dir
-        LGR.warning(
-            "The Peaks2Maps kernel transformer is not intended for serious research. "
-            "We strongly recommend against using it for any meaningful analyses."
-        )
 
     def _transform(self, mask, coordinates):
         transformed = []

nimare/meta/utils.py

@@ -19,6 +19,9 @@
 def model_fn(features, labels, mode, params):
     """Run model function used internally by peaks2maps.
 
+    .. deprecated:: 0.0.11
+        `model_fn` will be removed in NiMARE 0.0.13.
+
     .. versionadded:: 0.0.4
 
     """
@@ -163,6 +166,9 @@ def pad_and_conv(input, out_channels, conv_args):
 def _get_resize_arg(target_shape):
     """Get resizing arguments, as used by peaks2maps.
 
+    .. deprecated:: 0.0.11
+        `_get_resize_arg` will be removed in NiMARE 0.0.13.
+
     .. versionadded:: 0.0.1
 
     """
@@ -208,6 +214,9 @@ def compute_p2m_ma(
 ):
     """Generate modeled activation (MA) maps using deep ConvNet model peaks2maps.
 
+    .. deprecated:: 0.0.11
+        `compute_p2m_ma` will be removed in NiMARE 0.0.13.
+
     Parameters
     ----------
     contrasts_coordinates : list of lists that are len == 3

nimare/workflows/peaks2maps.py

@@ -16,7 +16,12 @@
 
 
 def peaks2maps_workflow(sleuth_file, output_dir=None, prefix=None, n_iters=10000):
-    """Run the peaks2maps workflow."""
+    """Run the peaks2maps workflow.
+
+    .. deprecated:: 0.0.11
+        `peaks2maps_workflow` will be removed in NiMARE 0.0.13.
+
+    """
     LGR.info("Loading coordinates...")
     dset = convert_sleuth_to_dataset(sleuth_file)