Merge pull request #118 from JulioAPeraza/drop-py367

Drop support for Python 3.6 and 3.7

.github/workflows/testing.yml

@@ -6,10 +6,10 @@ on:
       - "master"
   pull_request:
     branches:
-      - '*'
+      - "*"
   schedule:
     # Run tests every Sunday at 12am
-    - cron: '0 0 * * 0'
+    - cron: "0 0 * * 0"
 
 concurrency:
   group: environment-${{ github.ref }}
@@ -28,46 +28,39 @@ jobs:
       - id: result_step
         uses: mstachniuk/ci-skip@master
         with:
-          commit-filter: '[skip ci];[ci skip];[skip github]'
-          commit-filter-separator: ';'
+          commit-filter: "[skip ci];[ci skip];[skip github]"
+          commit-filter-separator: ";"
 
   run_tests:
     needs: check_skip
     if: ${{ needs.check_skip.outputs.skip == 'false' }}
     runs-on: ${{ matrix.os }}
     strategy:
-        fail-fast: false
-        matrix:
-            os: ["ubuntu-latest", "macos-latest"]
-            python-version: ["3.6", "3.7", "3.8", "3.9"]
-            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"
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest"]
+        python-version: ["3.8", "3.9"]
+
     name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
     defaults:
       run:
         shell: bash
     steps:
       - uses: actions/checkout@v2
-      - name: 'Set up python'
+      - name: "Set up python"
         uses: actions/setup-python@v2
         with:
-            python-version: ${{ matrix.python-version }}
-      - name: 'Display Python version'
+          python-version: ${{ matrix.python-version }}
+      - name: "Display Python version"
         shell: bash {0}
         run: python -c "import sys; print(sys.version)"
-      - name: 'Install PyMARE'
+      - name: "Install PyMARE"
         shell: bash {0}
         run: pip install -e .[tests,stan]
-      - name: 'Run tests'
+      - name: "Run tests"
         shell: bash {0}
         run: python -m pytest --pyargs pymare --cov=pymare
-      - name: 'Upload coverage to CodeCov'
+      - name: "Upload coverage to CodeCov"
         uses: codecov/codecov-action@v1
         if: success()
 

.readthedocs.yml

@@ -5,15 +5,18 @@
 # Required
 version: 2
 
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.9"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
 
 python:
-  version: 3.7
   install:
     - method: pip
       path: .
       extra_requirements:
         - doc
-  system_packages: true

pymare/__init__.py

@@ -1,4 +1,5 @@
 """PyMARE: Python Meta-Analysis & Regression Engine."""
+
 import sys
 import warnings
 

pymare/datasets/__init__.py

@@ -1,4 +1,5 @@
 """Open meta-analytic datasets."""
+
 from .metadat import michael2013
 
 __all__ = [

pymare/datasets/metadat.py

@@ -1,4 +1,5 @@
 """Datasets from metadat."""
+
 import json
 import os.path as op
 

pymare/effectsize/__init__.py

@@ -1,4 +1,5 @@
 """Tools for converting between effect-size measures."""
+
 from .base import (
     OneSampleEffectSizeConverter,
     TwoSampleEffectSizeConverter,

pymare/effectsize/base.py

@@ -68,7 +68,7 @@ def solve_system(system, known_vars=None):
 
     # solver will return a dict if there's only one non-dummy expression
     if isinstance(solutions, dict):
-        solutions = [list(solutions.values())]
+        solutions = [[solutions[s] for s in symbols]]
 
     # Prepare the dummy list and data args in a fixed order
     dummy_list = list(dummies)

pymare/effectsize/expressions.py

@@ -1,4 +1,5 @@
 """Statistical expressions."""
+
 import json
 from collections import defaultdict
 from itertools import chain

pymare/estimators/__init__.py

@@ -1,4 +1,5 @@
 """Estimators for meta-analyses and meta-regressions."""
+
 from .combination import FisherCombinationTest, StoufferCombinationTest
 from .estimators import (
     DerSimonianLaird,

pymare/estimators/combination.py

@@ -1,4 +1,5 @@
 """Estimators for combination (p/z) tests."""
+
 import warnings
 from abc import abstractmethod
 

pymare/results.py

@@ -1,4 +1,5 @@
 """Tools for representing and manipulating meta-regression results."""
+
 import itertools
 from functools import lru_cache
 from inspect import getfullargspec

pymare/tests/conftest.py

@@ -1,4 +1,5 @@
 """Data for tests."""
+
 import numpy as np
 import pytest
 

pymare/tests/test_combination_tests.py

@@ -1,4 +1,5 @@
 """Tests for pymare.estimators.combination."""
+
 import numpy as np
 import pytest
 import scipy.stats as ss

pymare/tests/test_core.py

@@ -1,4 +1,5 @@
 """Tests for pymare.core."""
+
 import numpy as np
 import pandas as pd
 import pytest

pymare/tests/test_datasets.py

@@ -1,4 +1,5 @@
 """Tests for the pymare.datasets module."""
+
 import pandas as pd
 
 from pymare import datasets

pymare/tests/test_effectsize_base.py

@@ -1,4 +1,5 @@
 """Tests for pymare.effectsize.base."""
+
 import numpy as np
 import pandas as pd
 import pytest

pymare/tests/test_effectsize_expressions.py

@@ -1,4 +1,5 @@
 """Tests for pymare.effectsize.expressions."""
+
 import pytest
 from sympy import Symbol
 from sympy.core.sympify import SympifyError

pymare/tests/test_estimators.py

@@ -1,4 +1,5 @@
 """Tests for pymare.estimators.estimators."""
+
 import numpy as np
 import pytest
 

pymare/tests/test_results.py

@@ -1,4 +1,5 @@
 """Tests for pymare.results."""
+
 import numpy as np
 import pytest
 

pymare/tests/test_stan_estimators.py

@@ -1,4 +1,5 @@
 """Tests for estimators that use stan."""
+
 import pytest
 
 from pymare.estimators import StanMetaRegression

pymare/tests/test_stats.py

@@ -1,4 +1,5 @@
 """Tests for pymare.stats."""
+
 from pymare import stats
 
 

pymare/tests/test_utils.py

@@ -1,4 +1,5 @@
 """Tests for pymare.utils."""
+
 import os.path as op
 
 import numpy as np

pymare/utils.py

@@ -1,4 +1,5 @@
 """Miscellaneous utility functions."""
+
 import os.path as op
 
 import numpy as np

setup.cfg

@@ -28,14 +28,12 @@ classifiers =
     Intended Audience :: Science/Research
     License :: OSI Approved :: MIT License
     Operating System :: OS Independent
-    Programming Language :: Python :: 3.6
-    Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Topic :: Scientific/Engineering
 
 [options]
-python_requires = >= 3.6
+python_requires = >= 3.8
 install_requires =
     numpy>=1.8.0
     pandas
@@ -57,7 +55,7 @@ doc =
     sphinx>=3.5
     sphinx-argparse
     sphinx-copybutton
-    sphinx_gallery==0.10.1
+    sphinx_gallery
     sphinx_rtd_theme
     sphinxcontrib-bibtex
 tests =