🔖 [Version 0.4.0: Goodbye Singularity Hub](https://github.com/FCP-IND…

…I/cpac/releases/tag/v0.4.0) (#24)

.github/workflows/test_cpac.yml

@@ -8,7 +8,6 @@ on:
     paths-ignore:
     - README.rst
   pull_request:
-  pull_request_target:
 
 jobs:
   test_cpac:
@@ -33,9 +32,11 @@ jobs:
       with:
         go-version: ${{ matrix.go }}
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python }}
+    - name: Install --upgrade pip setuptools wheel
+      run: python -m pip install --upgrade pip setuptools wheel
     - name: Set up Singularity
       if: ${{ matrix.platform == 'singularity' }}
       uses: eWaterCycle/setup-singularity@v5

CHANGELOG.rst

@@ -1,6 +1,11 @@
 =========
 Changelog
 =========
+`Version 0.4.0: Goodbye Singularity Hub <https://github.com/FCP-INDI/cpac/releases/tag/v0.4.0>`_
+================================================================================================
+* 👽 Drop call to now-deprecated Singularity Hub
+* 🐛 Resolves issue where minimal configs would cause wrapper to crash
+
 `Version 0.3.2: Pull / Upgrade <https://github.com/FCP-INDI/cpac/releases/tag/v0.3.2>`_
 ========================================================================================
 * ➖ Remove dependecy on Nipype

README.rst

@@ -29,8 +29,7 @@ Usage
 .. code-block:: shell
 
     cpac --help
-    usage: cpac [-h] [--version] [-o [OPT [OPT ...]]]
-                [-B [CUSTOM_BINDING [CUSTOM_BINDING ...]]]
+    usage: cpac [-h] [--version] [-o OPT] [-B CUSTOM_BINDING]
                 [--platform {docker,singularity}] [--image IMAGE] [--tag TAG]
                 [--working_dir PATH] [-v] [-vv]
                 {run,group,utils,pull,upgrade,crash} ...
@@ -64,13 +63,13 @@ Usage
     optional arguments:
       -h, --help            show this help message and exit
       --version             show program's version number and exit
-      -o [OPT [OPT ...]], --container_option [OPT [OPT ...]]
+      -o OPT, --container_option OPT
                             parameters and flags to pass through to Docker or Singularity
                             
                             This flag can take multiple arguments so cannot be
                             the final argument before the command argument (i.e.,
                             run or any other command that does not start with - or --)
-      -B [CUSTOM_BINDING [CUSTOM_BINDING ...]], --custom_binding [CUSTOM_BINDING [CUSTOM_BINDING ...]]
+      -B CUSTOM_BINDING, --custom_binding CUSTOM_BINDING
                             directories to bind with a different path in
                             the container than the real path of the directory.
                             One or more pairs in the format:

setup.cfg

@@ -23,7 +23,7 @@ classifiers =
     Operating System :: OS Independent
     Programming Language :: Python :: 3
     Topic :: Scientific/Engineering :: Bio-Informatics
-version = 0.3.2.post1
+version = 0.4.0
 
 [options]
 zip_safe = False

src/cpac/backends/platform.py

@@ -9,6 +9,7 @@
 from contextlib import redirect_stderr
 from io import StringIO
 from tabulate import tabulate
+from warnings import warn
 
 from cpac.helpers import cpac_read_crash, get_extra_arg_value
 from cpac.utils import Locals_to_bind, PermissionMode
@@ -83,6 +84,7 @@ def _bind_volume(self, local, remote, mode):
             self.volumes[local] = [b]
 
     def _collect_config_binding(self, config, config_key):
+        config_binding = None
         if isinstance(config, str):
             if os.path.exists(config):
                 path = os.path.dirname(config)
@@ -93,7 +95,21 @@ def _collect_config_binding(self, config, config_key):
                     f'yaml.dump(Configuration({config}).dict())"'
                 )
             config = yaml.safe_load(config)
-        return config.get('pipeline_setup', {}).get(config_key, {}).get('path')
+        pipeline_setup = config.get('pipeline_setup', {})
+        minimal = pipeline_setup.get('FROM', False)
+        if isinstance(pipeline_setup, dict):
+            config_binding = pipeline_setup.get(config_key, {}).get('path')
+        else:
+            minimal = True
+        if minimal:
+            warn(
+                'This run is using a minimal pipeline configuration. If this '
+                'configuration imports a configuration that requires paths to '
+                'be bound from your real environment to your container, you '
+                'need to bind those paths manually with the `-B` flag.',
+                UserWarning
+            )
+        return config_binding
 
     def collect_config_bindings(self, config, **kwargs):
         kwargs['output_dir'] = kwargs.get(

src/cpac/backends/singularity.py

@@ -68,19 +68,12 @@ def pull(self, force=False, **kwargs):
         else:  # pragma: no cover
             try:
                 self.image = Client.pull(
-                    "shub://FCP-INDI/C-PAC",
+                    "docker://fcpindi/c-pac:latest",
                     force=force,
                     pull_folder=pwd
                 )
             except Exception:
-                try:
-                    self.image = Client.pull(
-                        "docker://fcpindi/c-pac:latest",
-                        force=force,
-                        pull_folder=pwd
-                    )
-                except Exception:
-                    raise OSError("Could not connect to Singularity")
+                raise OSError("Could not connect to Singularity")
 
     def _try_to_stream(self, args, stream_command='run', **kwargs):
         self._bindings_as_option()

tests/test_cpac_installation.py

@@ -1,4 +1,5 @@
-from pip._internal.utils.misc import get_installed_distributions
+"""Test if cpac is installed as expected"""
+from pkg_resources import working_set
 from setuptools.config import read_configuration
 
 
@@ -22,7 +23,7 @@ def test_requirements():
                 'but not in setup.cfg'
             )
             assert package_in_list(
-                req, requirements_list(get_installed_distributions())
+                req, requirements_list(working_set)
             ), (
                 f'package {req} is in requirements.txt '
                 'but not installed'

tests/test_cpac_run.py

@@ -8,6 +8,10 @@
 from cpac.__main__ import run
 from CONSTANTS import args_before_after, set_commandline_args
 
+MINIMAL_CONFIG = os.path.join(
+    os.path.dirname(__file__), 'test_data', 'minimal.min.yml'
+)
+
 
 @pytest.mark.parametrize('helpflag', ['--help', '-h'])
 @pytest.mark.parametrize('argsep', [' ', '='])
@@ -32,7 +36,10 @@ def run_test(argv):
 
 
 @pytest.mark.parametrize('argsep', [' ', '='])
-def test_run_test_config(argsep, tmp_path, platform=None, tag=None):
+@pytest.mark.parametrize('pipeline_file', [None, MINIMAL_CONFIG])
+def test_run_test_config(
+    argsep, pipeline_file, tmp_path, platform=None, tag=None
+):
     def run_test(argv):
         with mock.patch.object(sys, 'argv', argv):
             run()
@@ -42,10 +49,14 @@ def run_test(argv):
 
     wd = tmp_path
     args = set_commandline_args(platform, tag, argsep)
+    pipeline = '' if pipeline_file is None else ' '.join([
+        ' --pipeline_file',
+        pipeline_file
+    ])
     argv = (
         'run '
         f's3://fcp-indi/data/Projects/ABIDE/RawDataBIDS/NYU {wd} '
-        'test_config --participant_ndx=2'
+        f'test_config --participant_ndx=2{pipeline}'
     )
     if len(args):
         before, after = args_before_after(argv, args)

tests/test_data/minimal.min.yml

@@ -0,0 +1,5 @@
+FROM: default
+
+pipeline_setup:
+
+  pipeline_name: test-minimal-imports