Drop support for Python 3.6 and 3.7 (#780)

* Drop Python 3.6 and 3.7. Support Python 3.11

* Drop 3.11

* regex=True for pandas 2.0.0

.github/workflows/testing.yml

@@ -38,15 +38,7 @@ jobs:
         fail-fast: false
         matrix:
             os: ["ubuntu-latest", "macos-latest"]
-            python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
-            include:
-              # ubuntu-20.04 is used only to test python 3.6
-              - os: "ubuntu-20.04"
-                python-version: "3.6"
-            exclude:
-              # ubuntu-latest does not support python 3.6
-              - os: "ubuntu-latest"
-                python-version: "3.6"
+            python-version: ["3.8", "3.9", "3.10"]
 
     defaults:
       run:

docs/installation.rst

@@ -15,9 +15,13 @@ If you want to use the most up-to-date version, you can install from the ``main`
 
     pip install git+https://github.com/neurostuff/NiMARE.git
 
-NiMARE requires Python >=3.6 and a number of packages.
+NiMARE requires Python ``>=3.8`` and a number of packages.
 For a complete list, please see ``nimare/setup.cfg``.
 
+.. note::
+    We only support Python versions that are part of the Python release cycle (i.e., 3.8, 3.9, and
+    3.10). For more information, see `Python Supported Versions`_.
+
 What Next?
 ----------
 

docs/links.rst

@@ -68,6 +68,8 @@
 
 .. _PyMARE: https://pymare.readthedocs.io/en/latest/
 
+.. _Python Supported Versions: https://devguide.python.org/versions/#supported-versions
+
 .. _scikit-learn: https://scikit-learn.org/stable/developers/index.html
 
 .. _Scribe: https://brainmap.org/scribe/

nimare/__init__.py

@@ -1,6 +1,5 @@
 """NiMARE: Neuroimaging Meta-Analysis Research Environment."""
 import logging
-import sys
 import warnings
 
 from ._version import get_versions
@@ -41,34 +40,3 @@
     ]
 
 del get_versions
-
-
-def _py367_deprecation_warning():
-    """Deprecation warnings message.
-
-    Notes
-    -----
-    Adapted from Nilearn.
-    """
-    py36_warning = (
-        "Python 3.6 and 3.7 support is deprecated and will be removed in release 0.1.0 of NiMARE. "
-        "Consider switching to Python 3.8, 3.9 or 3.10."
-    )
-    warnings.filterwarnings("once", message=py36_warning)
-    warnings.warn(message=py36_warning, category=FutureWarning, stacklevel=3)
-
-
-def _python_deprecation_warnings():
-    """Raise deprecation warnings.
-
-    Notes
-    -----
-    Adapted from Nilearn.
-    """
-    if sys.version_info.major == 3 and (
-        sys.version_info.minor == 6 or sys.version_info.minor == 7
-    ):
-        _py367_deprecation_warning()
-
-
-_python_deprecation_warnings()

nimare/annotate/cogat.py

@@ -161,7 +161,7 @@ def extract_cogat(text_df, id_df=None, text_column="abstract"):
         term_id = id_df["id"].loc[term_idx]
         pattern = regex_dict[term]
         counts_df[term_id] += text_df[text_column].str.count(pattern).astype(int)
-        text_df[text_column] = text_df[text_column].str.replace(pattern, term_id)
+        text_df[text_column] = text_df[text_column].str.replace(pattern, term_id, regex=True)
 
     return counts_df, text_df