Merge pull request #96 from effigies/ci/test_minimum_dependencies

MAINT: Test minimum dependencies with TravisCI

Author: oesteban

.travis.yml

@@ -0,0 +1,68 @@
+# vim ft=yaml
+os: linux
+dist: xenial
+
+addons:
+  apt:
+    packages:
+      - libgomp1
+
+
+language: python
+cache: pip
+
+python:
+  - 3.6
+  - 3.7
+  - 3.8
+
+env:
+  global:
+    - CHECK_TYPE="tests"
+    - INSTALL_DEPENDS="pip setuptools"
+    - DEPENDS="-r min-requirements.txt"
+    - MRI_ROBUST_TEMPLATE=sx2n7/providers/osfstorage/5e825301d0e35400ebb481f2
+    - FS_LICENSE=/tmp/freesurfer/license.txt
+    - TEST_DATA_HOME=/tmp/data
+
+before_install:
+  - python -m pip install --upgrade pip virtualenv
+  - virtualenv --python=python /tmp/venv
+  - source /tmp/venv/bin/activate
+  - python --version
+  - python -m pip --version
+  - python -m pip install --upgrade $INSTALL_DEPENDS
+  - python -m pip --version
+
+install:
+  - if [ -n "$DEPENDS" ]; then python -m pip install $DEPENDS; fi
+  - python -m pip install .
+  - python -c "import sdcflows; print(sdcflows.__version__)"
+  - travis_retry python -m pip install "sdcflows[$CHECK_TYPE]"
+
+before_script:
+  # External dependencies
+  - travis_retry bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh);
+  - sudo apt-get update
+  - sudo apt-get install -y --no-install-recommends git-annex-standalone fsl afni ants
+  - curl https://files.osf.io/v1/resources/$MRI_ROBUST_TEMPLATE?direct > mri_robust_template
+  - sudo install mri_robust_template /usr/local/bin
+  - mkdir /tmp/freesurfer
+  - echo "b2VzdGViYW5Ac3RhbmZvcmQuZWR1CjMwNzU2CiAqQ1MzYkJ5VXMxdTVNCiBGU2kvUGJsejJxR1V3Cg==" | base64 -d > $FS_LICENSE
+  - python -m pip install datalad
+  # Data dependencies
+  - python -c "from templateflow import api as tfapi;
+               tfapi.get('MNI152NLin2009cAsym', resolution=2, desc='brain', suffix='mask');
+               tfapi.get('MNI152NLin2009cAsym', resolution=1, label='brain', suffix='probseg');
+               tfapi.get('MNI152NLin2009cAsym', resolution=2, desc='fMRIPrep', suffix='boldref');"
+  - mkdir -p $TEST_DATA_HOME
+  - datalad install -rg -J 1 -s ///openneuro/ds001600 $TEST_DATA_HOME/ds001600
+  - curl https://files.osf.io/v1/resources/9sy2a/providers/osfstorage/5d44b940bcd6d900198ed6be/?zip= --output testdata.zip
+  - unzip testdata.zip -d $TEST_DATA_HOME/testdata
+
+script:
+  - pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules sdcflows
+
+after_script:
+  - python -m pip install codecov
+  - python -m codecov --flags travis --file cov.xml -e $TRAVIS_JOB_NUMBER

min-requirements.txt

@@ -0,0 +1,8 @@
+# Auto-generated by tools/update_requirements.py
+nibabel==3.0.1
+niflow-nipype1-workflows==0.0.1
+nipype==1.5.1
+niworkflows==1.3.0
+numpy
+pybids==0.11.1
+templateflow==0.6

requirements.txt

@@ -0,0 +1,8 @@
+# Auto-generated by tools/update_requirements.py
+nibabel>=3.0.1
+niflow-nipype1-workflows~=0.0.1
+nipype<2.0,>=1.5.1
+niworkflows~=1.3.0
+numpy
+pybids>=0.11.1
+templateflow>=0.6

sdcflows/conftest.py

@@ -47,7 +47,9 @@ def outdir():
 
 @pytest.fixture
 def bids_layouts():
-    return layouts
+    if layouts:
+        return layouts
+    pytest.skip()
 
 
 @pytest.fixture

sdcflows/models/tests/test_pepolar.py

@@ -1,4 +1,5 @@
 """Test pepolar type of fieldmaps."""
+import os
 from pathlib import Path
 from json import loads
 import pytest
@@ -9,6 +10,7 @@
 from ..pepolar import Workflow, init_topup_wf
 
 
+@pytest.mark.skipif(os.getenv("TRAVIS") == "true", reason="this is TravisCI")
 @pytest.mark.parametrize(
     "epi_path",
     [

sdcflows/models/tests/test_phdiff.py

@@ -1,4 +1,5 @@
 """Test phase-difference type of fieldmaps."""
+import os
 from pathlib import Path
 from json import loads
 
@@ -9,6 +10,7 @@
 from ..fieldmap import init_fmap_wf, Workflow
 
 
+@pytest.mark.skipif(os.getenv("TRAVIS") == "true", reason="this is TravisCI")
 @pytest.mark.parametrize(
     "fmap_path",
     [

setup.cfg

@@ -6,9 +6,9 @@ classifiers =
     Intended Audience :: Science/Research
     Topic :: Scientific/Engineering :: Image Recognition
     License :: OSI Approved :: BSD License
-    Programming Language :: Python :: 3.5
     Programming Language :: Python :: 3.6
     Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
 description = Susceptibility Distortion Correction (SDC) workflows for EPI MR schemes.
 license = Apache-2.0
 long_description = file:README.rst
@@ -20,7 +20,7 @@ project_urls =
 url = https://www.nipreps.org/sdcflows
 
 [options]
-python_requires = >=3.5
+python_requires = >=3.6
 setup_requires =
     setuptools >= 42.0
     setuptools_scm >= 3.4
@@ -56,8 +56,8 @@ docs =
     %(doc)s
 tests =
     pytest
-    pytest-xdist
-    pytest-cov == 2.5.1
+    pytest-xdist >= 2.0
+    pytest-cov == 2.10.1
     coverage
 all =
     %(doc)s

tools/update_requirements.py

@@ -0,0 +1,37 @@
+#!/usr/bin/env python3
+from copy import copy
+from configparser import ConfigParser
+from pathlib import Path
+from packaging.requirements import Requirement, SpecifierSet
+
+repo_root = Path(__file__).parent.parent
+setup_cfg = repo_root / "setup.cfg"
+reqs = repo_root / "requirements.txt"
+min_reqs = repo_root / "min-requirements.txt"
+
+config = ConfigParser()
+config.read(setup_cfg)
+requirements = [Requirement(req)
+                for req in config.get("options", "install_requires").strip().splitlines()]
+
+script_name = Path(__file__).relative_to(repo_root)
+
+
+def to_min(req):
+    if req.specifier:
+        req = copy(req)
+        min_spec = [spec for spec in req.specifier if spec.operator in ('>=', '~=')][0]
+        min_spec._spec = ('==', ) + min_spec._spec[1:]
+        req.specifier = SpecifierSet(str(min_spec))
+    return req
+
+
+lines = [f"# Auto-generated by {script_name}", ""]
+
+# Write requirements
+lines[1:-1] = [str(req) for req in requirements]
+reqs.write_text("\n".join(lines))
+
+# Write minimum requirements
+lines[1:-1] = [str(to_min(req)) for req in requirements]
+min_reqs.write_text("\n".join(lines))