Merge pull request #88 from oesteban/maint/config-module

ENH: Adopt config module

Author: oesteban

.circleci/config.yml

@@ -451,7 +451,7 @@ jobs:
             which dmriprep | grep sdist\\/bin
             INSTALLED_VERSION=$(dmriprep --version)
             INSTALLED_VERSION=${INSTALLED_VERSION%$'\r'}
-            INSTALLED_VERSION=${INSTALLED_VERSION#*"dmriprep v"}
+            INSTALLED_VERSION=${INSTALLED_VERSION#*"dMRIPrep v"}
             echo "VERSION: \"$THISVERSION\""
             echo "INSTALLED: \"$INSTALLED_VERSION\""
             test "$INSTALLED_VERSION" = "$THISVERSION"
@@ -470,7 +470,7 @@ jobs:
             which dmriprep | grep wheel\\/bin
             INSTALLED_VERSION=$(dmriprep --version)
             INSTALLED_VERSION=${INSTALLED_VERSION%$'\r'}
-            INSTALLED_VERSION=${INSTALLED_VERSION#*"dmriprep v"}
+            INSTALLED_VERSION=${INSTALLED_VERSION#*"dMRIPrep v"}
             echo "VERSION: \"$THISVERSION\""
             echo "INSTALLED: \"$INSTALLED_VERSION\""
             test "$INSTALLED_VERSION" = "$THISVERSION"

.dockerignore

@@ -12,6 +12,11 @@ dmriprep.egg-info/**/*
 dmriprep.egg-info
 .eggs/**/*
 .eggs
+.pytest_cache/**/*
+.pytest_cache
+.ipynb_checkpoints/**/*
+.ipynb_checkpoints
+
 
 # housekeeping tools
 .maintenance/**/*
@@ -27,6 +32,8 @@ src/
 .gitignore
 .git/**/*
 .git
+.github/**/*
+.github
 .mailmap
 
 # other
@@ -41,7 +48,6 @@ out/
 .codecov.yml
 .coveragerc
 .pep8speaks.yml
-.readthedocs.yml
 .travis.yml
 .zenodo.json
 

MANIFEST.in

@@ -5,6 +5,3 @@ include LICENSE
 # versioneer
 include versioneer.py
 include dmriprep/_version.py
-
-# data
-include dmriprep/config/reports-spec.yml

dmriprep/__init__.py

@@ -1,23 +1,14 @@
 """Top-level package for dmriprep."""
-import warnings as _warnings
 from .__about__ import (
     __version__,
     __copyright__,
     __credits__,
     __packagename__,
 )
 
-
 __all__ = [
     '__version__',
     '__copyright__',
     '__credits__',
     '__packagename__',
 ]
-
-# cmp is not used by dmriprep, so ignore nipype-generated warnings
-_warnings.filterwarnings('ignore', r'cmp not installed')
-_warnings.filterwarnings('ignore', r'This has not been fully tested. Please report any failures.')
-_warnings.filterwarnings('ignore', r"can't resolve package from __spec__ or __package__")
-_warnings.simplefilter('ignore', DeprecationWarning)
-_warnings.simplefilter('ignore', ResourceWarning)

dmriprep/cli/parser.py

@@ -0,0 +1,117 @@
+"""Test parser."""
+from packaging.version import Version
+import pytest
+from ..parser import _build_parser
+from .. import version as _version
+from ... import config
+
+MIN_ARGS = ['data/', 'out/', 'participant']
+
+
+@pytest.mark.parametrize('args,code', [
+    ([], 2),
+    (MIN_ARGS, 2),  # bids_dir does not exist
+    (MIN_ARGS + ['--fs-license-file'], 2),
+    (MIN_ARGS + ['--fs-license-file', 'fslicense.txt'], 2),
+])
+def test_parser_errors(args, code):
+    """Check behavior of the parser."""
+    with pytest.raises(SystemExit) as error:
+        _build_parser().parse_args(args)
+
+    assert error.value.code == code
+
+
+@pytest.mark.parametrize('args', [
+    MIN_ARGS,
+    MIN_ARGS + ['--fs-license-file'],
+])
+def test_parser_valid(tmp_path, args):
+    """Check valid arguments."""
+    datapath = (tmp_path / 'data').absolute()
+    datapath.mkdir(exist_ok=True)
+    args[0] = str(datapath)
+
+    if '--fs-license-file' in args:
+        _fs_file = tmp_path / 'license.txt'
+        _fs_file.write_text('')
+        args.insert(args.index('--fs-license-file') + 1,
+                    str(_fs_file.absolute()))
+
+    opts = _build_parser().parse_args(args)
+
+    assert opts.bids_dir == datapath
+
+
+@pytest.mark.parametrize('argval,gb', [
+    ('1G', 1),
+    ('1GB', 1),
+    ('1000', 1),    # Default units are MB
+    ('32000', 32),  # Default units are MB
+    ('4000', 4),    # Default units are MB
+    ('1000M', 1),
+    ('1000MB', 1),
+    ('1T', 1000),
+    ('1TB', 1000),
+    ('%dK' % 1e6, 1),
+    ('%dKB' % 1e6, 1),
+    ('%dB' % 1e9, 1),
+])
+def test_memory_arg(tmp_path, argval, gb):
+    """Check the correct parsing of the memory argument."""
+    datapath = (tmp_path / 'data').absolute()
+    datapath.mkdir(exist_ok=True)
+    _fs_file = tmp_path / 'license.txt'
+    _fs_file.write_text('')
+
+    args = MIN_ARGS + ['--fs-license-file', str(_fs_file)] \
+        + ['--mem', argval]
+    args[0] = str(datapath)
+    opts = _build_parser().parse_args(args)
+
+    assert opts.memory_gb == gb
+
+
+@pytest.mark.parametrize('current,latest', [
+    ('1.0.0', '1.3.2'),
+    ('1.3.2', '1.3.2')
+])
+def test_get_parser_update(monkeypatch, capsys, current, latest):
+    """Make sure the out-of-date banner is shown."""
+    expectation = Version(current) < Version(latest)
+
+    def _mock_check_latest(*args, **kwargs):
+        return Version(latest)
+
+    monkeypatch.setattr(config.environment, 'version', current)
+    monkeypatch.setattr(_version, 'check_latest', _mock_check_latest)
+
+    _build_parser()
+    captured = capsys.readouterr().err
+
+    msg = """\
+You are using dMRIPrep-%s, and a newer version of dMRIPrep is available: %s.
+Please check out our documentation about how and when to upgrade:
+https://dmriprep.readthedocs.io/en/latest/faq.html#upgrading""" % (current, latest)
+
+    assert (msg in captured) is expectation
+
+
+@pytest.mark.parametrize('flagged', [
+    (True, None),
+    (True, 'random reason'),
+    (False, None),
+])
+def test_get_parser_blacklist(monkeypatch, capsys, flagged):
+    """Make sure the blacklisting banner is shown."""
+    def _mock_is_bl(*args, **kwargs):
+        return flagged
+
+    monkeypatch.setattr(_version, 'is_flagged', _mock_is_bl)
+
+    _build_parser()
+    captured = capsys.readouterr().err
+
+    assert ('FLAGGED' in captured) is flagged[0]
+    if flagged[0]:
+        assert ((flagged[1] or 'reason: unknown') in captured)