Make torch optional (#836)

* Make `torch` optional

* Update test_meta_cbmr.py

* try import torch for cbmr models as well

* Update test_meta_cbmr.py

* Update test_meta_cbmr.py

* Skip model function

* Update test_meta_cbmr.py

* Update test_meta_cbmr.py

Author: JulioAPeraza

.github/workflows/testing.yml

@@ -51,7 +51,7 @@ jobs:
             python-version: ${{ matrix.python-version }}
       - name: 'Install NiMARE'
         shell: bash {0}
-        run: pip install -e .[tests]
+        run: pip install -e .[tests,cbmr]
       - name: 'Run tests'
         shell: bash {0}
         run: make unittest
@@ -83,7 +83,7 @@ jobs:
             python-version: 3.8
       - name: 'Install NiMARE'
         shell: bash {0}
-        run: pip install -e .[minimum,tests]
+        run: pip install -e .[minimum,tests,cbmr]
       - name: 'Run tests'
         shell: bash {0}
         run: make unittest
@@ -115,7 +115,7 @@ jobs:
             python-version: ${{ matrix.python-version }}
       - name: 'Install NiMARE'
         shell: bash {0}
-        run: pip install -e .[tests]
+        run: pip install -e .[tests,cbmr]
       - name: 'Run tests'
         shell: bash {0}
         run: make test_performance_estimators
@@ -147,7 +147,7 @@ jobs:
             python-version: ${{ matrix.python-version }}
       - name: 'Install NiMARE'
         shell: bash {0}
-        run: pip install -e .[tests]
+        run: pip install -e .[tests,cbmr]
       - name: 'Run tests'
         shell: bash {0}
         run: make test_performance_correctors
@@ -179,7 +179,7 @@ jobs:
             python-version: ${{ matrix.python-version }}
       - name: 'Install NiMARE'
         shell: bash {0}
-        run: pip install -e .[tests]
+        run: pip install -e .[tests,cbmr]
       - name: 'Run tests'
         shell: bash {0}
         run: make test_performance_smoke
@@ -190,9 +190,41 @@ jobs:
           path: coverage.xml
         if: success()
 
+  test_cbmr_importerror:
+    name: CBMR ImportError tests
+    needs: check_skip
+    if: ${{ needs.check_skip.outputs.skip == 'false' }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-latest"]
+            python-version: ["3.8"]
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - uses: actions/checkout@v2
+      - name: 'Set up python'
+        uses: actions/setup-python@v2
+        with:
+            python-version: ${{ matrix.python-version }}
+      - name: 'Install NiMARE'
+        shell: bash {0}
+        run: pip install -e .[tests]
+      - name: 'Run tests'
+        shell: bash {0}
+        run: make test_cbmr_importerror
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v2
+        with:
+          name: cbmr_importerror
+          path: coverage.xml
+        if: success()
+
   upload_to_codecov:
     name: Upload coverage
-    needs: [run_unit_tests,run_unit_tests_with_minimum_dependencies,test_performance_estimators,test_performance_correctors,test_performance_smoke]
+    needs: [run_unit_tests,run_unit_tests_with_minimum_dependencies,test_performance_estimators,test_performance_correctors,test_performance_smoke,test_cbmr_importerror]
     runs-on: "ubuntu-latest"
     steps:
       - name: Checkout

.readthedocs.yaml

@@ -20,3 +20,4 @@ python:
       path: .
       extra_requirements:
         - doc
+        - cbmr

Makefile

@@ -9,12 +9,13 @@ help:
 	@echo "  test_performance_estimators	to run performance tests on meta estimators"
 	@echo "  test_performance_correctors	to run performance tests on correctors"
 	@echo "  test_performance_smoke			to run performance smoke tests"
+	@echo "  test_cbmr_importerror			to run cbmr importerror tests"
 
 lint:
 	@flake8 nimare
 
 unittest:
-	@py.test -m "not performance_estimators and not performance_correctors and not performance_smoke" --cov-append --cov-report=xml --cov=nimare nimare
+	@py.test -m "not performance_estimators and not performance_correctors and not performance_smoke and not cbmr_importerror" --cov-append --cov-report=xml --cov=nimare nimare
 
 test_performance_estimators:
 	@py.test -m "performance_estimators" --cov-append --cov-report=xml --cov=nimare nimare
@@ -24,3 +25,6 @@ test_performance_correctors:
 
 test_performance_smoke:
 	@py.test -m "performance_smoke" --cov-append --cov-report=xml --cov=nimare nimare
+
+test_cbmr_importerror:
+	@py.test -m "cbmr_importerror" --cov-append --cov-report=xml --cov=nimare nimare

nimare/meta/cbmr.py

@@ -1,4 +1,5 @@
 """Coordinate Based Meta Regression Methods."""
+
 import logging
 import re
 from functools import wraps
@@ -7,7 +8,13 @@
 import numpy as np
 import pandas as pd
 import scipy
-import torch
+
+try:
+    import torch
+except ImportError as e:
+    raise ImportError(
+        "Torch is required to use `CBMR` classes. Install with `pip install 'nimare[cbmr]'`."
+    ) from e
 
 from nimare import _version
 from nimare.diagnostics import FocusFilter
@@ -22,6 +29,8 @@
 class CBMREstimator(Estimator):
     """Coordinate-based meta-regression with a spatial model.
 
+    .. versionadded:: 0.1.0
+
     Parameters
     ----------
     group_categories : :obj:`~str` or obj:`~list` or obj:`~None`, optional
@@ -408,6 +417,8 @@ def _fit(self, dataset):
 class CBMRInference(object):
     """Statistical inference on outcomes of CBMR.
 
+    .. versionadded:: 0.1.0
+
     (intensity estimation and study-level moderator regressors)
 
     Parameters

nimare/meta/models.py

@@ -4,7 +4,13 @@
 
 import numpy as np
 import pandas as pd
-import torch
+
+try:
+    import torch
+except ImportError as e:
+    raise ImportError(
+        "Torch is required to use `CBMR` models. Install with `pip install 'nimare[cbmr]'`."
+    ) from e
 
 LGR = logging.getLogger(__name__)
 

nimare/tests/test_meta_cbmr.py

@@ -1,13 +1,21 @@
 """Tests for CBMR meta-analytic methods."""
 import logging
+import warnings
 
 import pytest
-import torch
+
+try:
+    import torch
+except ImportError:
+    warnings.warn("Torch not installed. CBMR tests will be skipped.")
+    TORCH_INSTALLED = False
+else:
+    TORCH_INSTALLED = True
+    from nimare.meta import models
+    from nimare.meta.cbmr import CBMREstimator, CBMRInference
 
 import nimare
 from nimare.correct import FDRCorrector, FWECorrector
-from nimare.meta import models
-from nimare.meta.cbmr import CBMREstimator, CBMRInference
 from nimare.transforms import StandardizeField
 
 # numba has a lot of debug messages that are not useful for testing
@@ -16,17 +24,24 @@
 logging.getLogger("indexed_gzip").setLevel(logging.WARNING)
 
 
-@pytest.fixture(
-    scope="session",
-    params=[
-        pytest.param(models.PoissonEstimator, id="Poisson"),
-        pytest.param(models.NegativeBinomialEstimator, id="NegativeBinomial"),
-        pytest.param(models.ClusteredNegativeBinomialEstimator, id="ClusteredNegativeBinomial"),
-    ],
-)
-def model(request):
-    """CBMR models."""
-    return request.param
+if TORCH_INSTALLED:
+
+    @pytest.fixture(
+        scope="session",
+        params=[
+            pytest.param(models.PoissonEstimator, id="Poisson"),
+            pytest.param(models.NegativeBinomialEstimator, id="NegativeBinomial"),
+            pytest.param(
+                models.ClusteredNegativeBinomialEstimator, id="ClusteredNegativeBinomial"
+            ),
+        ],
+    )
+    def model(request):
+        """CBMR models."""
+        return request.param
+
+else:
+    model = None
 
 
 @pytest.fixture(scope="session")
@@ -243,3 +258,37 @@ def test_StandardizeField(testdata_cbmr_simulated):
     assert dset.annotations["standardized_sample_sizes"].std() == pytest.approx(1.0, abs=1e-3)
     assert dset.annotations["standardized_avg_age"].mean() == pytest.approx(0.0, abs=1e-3)
     assert dset.annotations["standardized_avg_age"].std() == pytest.approx(1.0, abs=1e-3)
+
+
+@pytest.mark.cbmr_importerror
+def test_cbmr_importerror():
+    """Test that ImportErrors are raised when torch is not installed."""
+    with pytest.raises(ImportError):
+        from nimare.meta.cbmr import CBMREstimator
+
+        CBMREstimator()
+
+    with pytest.raises(ImportError):
+        from nimare.meta.cbmr import CBMRInference
+
+        CBMRInference()
+
+    with pytest.raises(ImportError):
+        from nimare.meta.models import GeneralLinearModelEstimator
+
+        GeneralLinearModelEstimator()
+
+    with pytest.raises(ImportError):
+        from nimare.meta.models import PoissonEstimator
+
+        PoissonEstimator()
+
+    with pytest.raises(ImportError):
+        from nimare.meta.models import NegativeBinomialEstimator
+
+        NegativeBinomialEstimator()
+
+    with pytest.raises(ImportError):
+        from nimare.meta.models import ClusteredNegativeBinomialEstimator
+
+        ClusteredNegativeBinomialEstimator()

pyproject.toml

@@ -28,6 +28,7 @@ markers = [
     "performance_smoke: mark smoke tests that measure performance",
     "performance_estimators: mark tests that measure estimator performance",
     "performance_correctors: mark tests that measure corrector performance",
+    "cbmr_importerror: mark tests that should fail due to missing torch dependencies",
 ]
 
 [tool.isort]

setup.cfg

@@ -58,14 +58,15 @@ install_requires =
     seaborn  # nimare.reports
     sparse>=0.13.0  # for kernel transformers
     statsmodels!=0.13.2  # this version doesn't install properly
-    torch>=2.0 # for cbmr models
     tqdm  # progress bars throughout package
 packages = find:
 include_package_data = False
 
 [options.extras_require]
 gzip = 
     indexed_gzip>=1.4.0  # working with gzipped niftis
+cbmr = 
+    torch>=2.0 # for cbmr models
 doc =
     m2r
     matplotlib