Merge pull request #3321 from nipy/ci/contrib

 CI: Add specs and style checks

Author: effigies

.git-blame-ignore-revs

@@ -0,0 +1,18 @@
+# Commits with messages like "STY: black" or "run black"
+f64bf338f630a9ee5cbe7a3ec98c68292897e720
+83358d7f17aac07cb90d0330f11ea2322e2974d8
+faef7d0f93013a700c882f709e98fb3cd36ebb03
+d50c1858564c0b3073fb23c54886a0454cb66afa
+417b8897a116fcded5000e21e2b6ccbe29452a52
+aaf677a87f64c485f3e305799e4a5dc73b69e5fb
+f763008442d88d8ce00ec266698268389415f8d6
+b1eccafd4edc8503b02d715f5b5f6f783520fdf9
+70db90349598cc7f26a4a513779529fba7d0a797
+6c1d91d71f6f0db0e985bd2adc34206442b0653d
+97bdbd5f48ab242de5288ba4715192a27619a803
+78fa360f5b785224349b8b85b07e510d2233bb63
+7f85f43a34de8bff8e634232c939b17cee8e8fc5
+9c50b5daa797def5672dd057155b0e2c658853e2
+47194993ae14aceeec436cfb3769def667196668
+75653feadc6667d5313d83e9c62a5d5819771a9c
+497b44d680eee0892fa59c6aaaae22a17d70a536

.github/workflows/contrib.yml

@@ -0,0 +1,76 @@
+name: Contribution checks
+
+# This checks validate contributions meet baseline checks
+#
+# * specs - Ensure make
+
+on:
+  push:
+    branches:
+      - master
+      - maint/*
+  pull_request:
+    branches:
+      - master
+      - maint/*
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  stable:
+    # Check each OS, all supported Python, minimum versions and latest releases
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ['ubuntu-18.04']
+        python-version: [3.8]
+        nipype-extras: ['dev']
+        check: ['specs', 'style']
+    env:
+      DEPENDS: ""
+      CHECK_TYPE: ${{ matrix.check }}
+      NIPYPE_EXTRAS: ${{ matrix.nipype-extras }}
+      EXTRA_PIP_FLAGS: ""
+      INSTALL_DEB_DEPENDENCIES: false
+      INSTALL_TYPE: pip
+      CI_SKIP_TEST: 1
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Create virtual environment
+        run: tools/ci/create_venv.sh
+      - name: Build archive
+        run: |
+          source tools/ci/build_archive.sh
+          echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
+      - name: Install Debian dependencies
+        run: tools/ci/install_deb_dependencies.sh
+        if: ${{ matrix.os == 'ubuntu-18.04' }}
+      - name: Install dependencies
+        run: tools/ci/install_dependencies.sh
+      - name: Install Nipype
+        run: tools/ci/install.sh
+      - name: Run tests
+        run: tools/ci/check.sh
+        if: ${{ matrix.check != 'skiptests' }}
+      - uses: codecov/codecov-action@v1
+        with:
+          file: coverage.xml
+        if: ${{ always() }}
+      - name: Upload pytest test results
+        uses: actions/upload-artifact@v2
+        with:
+          name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
+          path: test-results.xml
+        if: ${{ always() && matrix.check == 'test' }}

.pre-commit-config.yaml

@@ -2,13 +2,13 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.0.0
+    rev: v3.4.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black
-    rev: 19.3b0
+    rev: 20.8b1
     hooks:
     -   id: black

nipype/algorithms/metrics.py

@@ -63,8 +63,7 @@ class DistanceOutputSpec(TraitedSpec):
 
 
 class Distance(BaseInterface):
-    """Calculates distance between two volumes.
-    """
+    """Calculates distance between two volumes."""
 
     input_spec = DistanceInputSpec
     output_spec = DistanceOutputSpec
@@ -542,7 +541,7 @@ class ErrorMapOutputSpec(TraitedSpec):
 
 
 class ErrorMap(BaseInterface):
-    """ Calculates the error (distance) map between two input volumes.
+    """Calculates the error (distance) map between two input volumes.
 
     Example
     -------

nipype/algorithms/misc.py

@@ -141,8 +141,7 @@ class SimpleThresholdOutputSpec(TraitedSpec):
 
 
 class SimpleThreshold(BaseInterface):
-    """Applies a threshold to input volumes
-    """
+    """Applies a threshold to input volumes"""
 
     input_spec = SimpleThresholdInputSpec
     output_spec = SimpleThresholdOutputSpec
@@ -240,8 +239,7 @@ class CreateNiftiOutputSpec(TraitedSpec):
 
 
 class CreateNifti(BaseInterface):
-    """Creates a nifti volume
-    """
+    """Creates a nifti volume"""
 
     input_spec = CreateNiftiInputSpec
     output_spec = CreateNiftiOutputSpec

nipype/algorithms/modelgen.py

@@ -40,13 +40,13 @@ def spm_hrf(RT, P=None, fMRI_T=16):
       % p    - parameters of the response function (two gamma
       % functions)
       % defaults  (seconds)
-      %	p(0) - delay of response (relative to onset)	   6
-      %	p(1) - delay of undershoot (relative to onset)    16
-      %	p(2) - dispersion of response			   1
-      %	p(3) - dispersion of undershoot			   1
-      %	p(4) - ratio of response to undershoot		   6
-      %	p(5) - onset (seconds)				   0
-      %	p(6) - length of kernel (seconds)		  32
+      % p(0) - delay of response (relative to onset)       6
+      % p(1) - delay of undershoot (relative to onset)    16
+      % p(2) - dispersion of response                      1
+      % p(3) - dispersion of undershoot                    1
+      % p(4) - ratio of response to undershoot             6
+      % p(5) - onset (seconds)                             0
+      % p(6) - length of kernel (seconds)                 32
       %
       % hrf  - hemodynamic response function
       % p    - parameters of the response function
@@ -135,7 +135,7 @@ def scale_timings(timelist, input_units, output_units, time_repetition):
 
 
 def bids_gen_info(
-    bids_event_files, condition_column="", amplitude_column=None, time_repetition=False,
+    bids_event_files, condition_column="", amplitude_column=None, time_repetition=False
 ):
     """
     Generate a subject_info structure from a list of BIDS .tsv event files.
@@ -471,8 +471,7 @@ def _generate_standard_design(
         return sessinfo
 
     def _generate_design(self, infolist=None):
-        """Generate design specification for a typical fmri paradigm
-        """
+        """Generate design specification for a typical fmri paradigm"""
         realignment_parameters = []
         if isdefined(self.inputs.realignment_parameters):
             for parfile in self.inputs.realignment_parameters:
@@ -517,8 +516,7 @@ def _generate_design(self, infolist=None):
         )
 
     def _run_interface(self, runtime):
-        """
-        """
+        """"""
         self._sessioninfo = None
         self._generate_design()
         return runtime
@@ -739,7 +737,7 @@ class SpecifySparseModelOutputSpec(SpecifyModelOutputSpec):
 
 
 class SpecifySparseModel(SpecifyModel):
-    """ Specify a sparse model that is compatible with SPM/FSL designers [1]_.
+    """Specify a sparse model that is compatible with SPM/FSL designers [1]_.
 
     Examples
     --------
@@ -770,8 +768,7 @@ class SpecifySparseModel(SpecifyModel):
     output_spec = SpecifySparseModelOutputSpec
 
     def _gen_regress(self, i_onsets, i_durations, i_amplitudes, nscans):
-        """Generates a regressor for a sparse/clustered-sparse acquisition
-        """
+        """Generates a regressor for a sparse/clustered-sparse acquisition"""
         bplot = False
         if isdefined(self.inputs.save_plot) and self.inputs.save_plot:
             bplot = True
@@ -901,8 +898,7 @@ def _gen_regress(self, i_onsets, i_durations, i_amplitudes, nscans):
             return reg
 
     def _cond_to_regress(self, info, nscans):
-        """Converts condition information to full regressors
-        """
+        """Converts condition information to full regressors"""
         reg = []
         regnames = []
         for i, cond in enumerate(info.conditions):

nipype/algorithms/rapidart.py

@@ -686,8 +686,7 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
         save_json(statsfile, stats)
 
     def _run_interface(self, runtime):
-        """Execute this module.
-        """
+        """Execute this module."""
         funcfilelist = ensure_list(self.inputs.realigned_files)
         motparamlist = ensure_list(self.inputs.realignment_parameters)
         for i, imgf in enumerate(funcfilelist):
@@ -814,8 +813,7 @@ def _get_spm_submatrix(self, spmmat, sessidx, rows=None):
         return outmatrix
 
     def _run_interface(self, runtime):
-        """Execute this module.
-        """
+        """Execute this module."""
         import scipy.io as sio
 
         motparamlist = self.inputs.realignment_parameters

nipype/algorithms/tests/test_TSNR.py

@@ -93,8 +93,8 @@ def test_tsnr_withpoly3(self):
 
     @mock.patch("warnings.warn")
     def test_warning(self, mock_warn):
-        """ test that usage of misc.TSNR trips a warning to use
-        confounds.TSNR instead """
+        """test that usage of misc.TSNR trips a warning to use
+        confounds.TSNR instead"""
         # run
         misc.TSNR(in_file=self.in_filenames["in_file"])
 

nipype/algorithms/tests/test_modelgen.py

@@ -105,7 +105,7 @@ def test_modelgen1(tmpdir):
         np.array([6.0, 6.0]),
     )
     npt.assert_almost_equal(
-        np.array(res.outputs.session_info[0]["cond"][1]["duration"]), np.array([6.0,])
+        np.array(res.outputs.session_info[0]["cond"][1]["duration"]), np.array([6.0])
     )
     npt.assert_almost_equal(
         np.array(res.outputs.session_info[1]["cond"][1]["duration"]),
@@ -191,14 +191,14 @@ def test_modelgen_spm_concat(tmpdir):
         np.array([1.0, 1.0]),
     )
     npt.assert_almost_equal(
-        np.array(res.outputs.session_info[0]["cond"][1]["duration"]), np.array([1.0,])
+        np.array(res.outputs.session_info[0]["cond"][1]["duration"]), np.array([1.0])
     )
     npt.assert_almost_equal(
         np.array(res.outputs.session_info[1]["cond"][1]["duration"]),
         np.array([1.0, 1.0]),
     )
     npt.assert_almost_equal(
-        np.array(res.outputs.session_info[2]["cond"][1]["duration"]), np.array([1.0,])
+        np.array(res.outputs.session_info[2]["cond"][1]["duration"]), np.array([1.0])
     )
 
     # Test case for variable number of events in concatenated runs, sometimes unique.