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.gitignore

@@ -51,4 +51,4 @@ MANIFEST
 
 # Singularity Images
 **/*.simg
-**/*.sif
+**/*.sif

README.rst

@@ -42,38 +42,38 @@ Usage
                 [--tag TAG] [--working_dir PATH] [-v] [-vv]
                 {run,utils,version,group,gradients,tsconcat,pull,upgrade,enter,bash,shell,parse-resources,parse_resources,crash}
                 ...
-    
-    cpac: a Python package that simplifies using C-PAC <http://fcp-indi.github.io> containerized images. 
-    
+
+    cpac: a Python package that simplifies using C-PAC <http://fcp-indi.github.io> containerized images.
+
     This commandline interface package is designed to minimize repetition.
     As such, nearly all arguments are optional.
-    
-    When launching a container, this package will try to bind any paths mentioned in 
+
+    When launching a container, this package will try to bind any paths mentioned in
      • the command
      • the data configuration
-    
+
     An example minimal run command:
     	cpac run /path/to/data /path/for/outputs
-    
+
     An example run command with optional arguments:
     	cpac -B /path/to/data/configs:/configs \
     		--image fcpindi/c-pac --tag latest \
     		run /path/to/data /path/for/outputs \
     		--data_config_file /configs/data_config.yml \
     		--save_working_dir
-    
+
     Each command can take "--help" to provide additonal usage information, e.g.,
-    
+
     	cpac run --help
-    
+
     Known issues:
     - Some Docker containers unexpectedly persist after cpac finishes. To clear them, run
         1. `docker ps` to list the containers
       For each C-PAC conatainer that persists, run
         2. `docker attach <container_name>`
         3. `exit`
     - https://github.com/FCP-INDI/cpac/issues
-    
+
     positional arguments:
       {run,utils,version,group,gradients,tsconcat,pull,upgrade,enter,bash,shell,parse-resources,parse_resources,crash}
         run                 Run C-PAC. See
@@ -87,7 +87,7 @@ Usage
                             "cpac [--platform {docker,apptainer,singularity}] [--image IMAGE] [--tag TAG] group --help"
                             for more information.
         gradients           Run ba_timeseries_gradients. See
-                            "cpac [--platform "{docker,singularity}] gradients --help" 
+                            "cpac [--platform "{docker,singularity}] gradients --help"
                             for more information.
         tsconcat            Run ba-tsconcat (<0.2.0,>=0.1.2)
         pull (upgrade)      Upgrade your local C-PAC version to the latest version
@@ -98,21 +98,21 @@ Usage
                             Enter a new C-PAC container via BASH.
         parse-resources (parse_resources)
                             .
-                            
+
                             When provided with a `callback.log` file, this utility can sort through
                             the memory `runtime` usage, `estimate`, and associated `efficiency`, to
                             identify the `n` tasks with the `highest` or `lowest` of each of these
                             categories.
                             "parse-resources" is intended to be run outside a C-PAC container.
                             See "cpac parse-resources --help" for more information.
         crash               Convert a crash pickle to plain text (C-PAC < 1.8.0).
-    
+
     options:
       -h, --help            show this help message and exit
       --version             show program's version number and exit
       -o OPT, --container_option OPT, --container_options 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 --)
@@ -123,7 +123,7 @@ Usage
                             	real_path:container_path
                             (eg, /home/C-PAC/run5/outputs:/outputs).
                             Use absolute paths for both paths.
-                            
+
                             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 --)
@@ -134,7 +134,7 @@ Usage
       --image IMAGE         path to Apptainer/Singularity image file OR name of Docker image (eg, "fcpindi/c-pac").
                             Will attempt to pull from Singularity Hub or Docker Hub if not provided.
                             If image is specified but platform is not, platform is
-                            assumed to be Apptainer/Singularity if image is a path or 
+                            assumed to be Apptainer/Singularity if image is a path or
                             Docker if image is an image name.
       --tag TAG             tag of the Docker image to use (eg, "latest" or "nightly").
       --working_dir PATH    working directory

src/cpac/__init__.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 """Init file for cpac."""
+
 from importlib.metadata import distribution, PackageNotFoundError
 
 DIST_NAME = __name__

src/cpac/backends/apptainer/__init__.py

@@ -1,4 +1,5 @@
 """Backend for Apptainer images."""
+
 from .apptainer import Apptainer
 
 __all__ = ["Apptainer"]

src/cpac/backends/apptainer/apptainer.py

@@ -1,4 +1,5 @@
 """Backend for Apptainer images."""
+
 from spython import main as spython_main
 from spython.main.base import command
 

src/cpac/backends/apptainer/spython.py

@@ -2,6 +2,7 @@
 # Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
 # with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
 """Modifications to ``spython`` run Apptainer instead of Singularity."""
+
 from spython.main import get_client as get_spython_client
 
 

src/cpac/helpers/__init__.py

@@ -1,4 +1,5 @@
 """Hepler functions for cpac Python package."""
+
 from itertools import chain
 import re
 

src/cpac/helpers/cpac_parse_resources.py

@@ -7,6 +7,7 @@
 categories.
 `cpac_parse_resources` is intended to be run outside a C-PAC container.
 """
+
 from argparse import ArgumentParser
 import configparser
 import json

src/cpac/utils/checks.py

@@ -1,4 +1,5 @@
 """Functions to check things like the in-container C-PAC version."""
+
 from packaging.version import Version
 from semver import VersionInfo
 

tests/.pylintrc

@@ -1,2 +1,2 @@
 [MAIN]
-ignore-imports=y
+ignore-imports=y

tests/conftest.py

@@ -5,6 +5,7 @@
 Read more about conftest.py under:
 https://pytest.org/latest/plugins.html
 """
+
 import logging
 
 import pytest  # pylint: disable=import-error

tests/test_cpac.py

@@ -1,4 +1,5 @@
 """Tests for top-level cpac cli."""
+
 from contextlib import redirect_stderr, redirect_stdout
 from io import BytesIO, StringIO, TextIOWrapper
 import sys

tests/test_cpac_gradients.py

@@ -1,4 +1,5 @@
 """Unit tests for the command-line interface module of ``ba-timeseries-gradients``."""
+
 from argparse import Namespace
 import logging
 from pathlib import Path

tests/test_cpac_run.py

@@ -1,4 +1,5 @@
 """Test actually running C-PAC with cpac."""
+
 from datetime import date, timedelta
 import os
 from pathlib import Path

tests/test_wrapped.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """Test bare-wrapped commands."""
+
 from subprocess import call
 
 from pytest import mark, skip