Keep working

.readthedocs.yml

@@ -5,7 +5,7 @@ build:
   apt_packages:
     - graphviz
   tools:
-    python: "3.10"
+    python: "3.11"
 
 sphinx:
   configuration: docs/conf.py

pyproject.toml

@@ -13,10 +13,9 @@ authors = [{name = "The NiPreps Developers", email = "[email protected]"}]
 classifiers = [
   "Development Status :: 2 - Pre-Alpha",
   "Programming Language :: Python",
-  "Programming Language :: Python :: 3.8",
-  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
 ]
 dependencies = [
   "fmriprep",

src/fmripost_aroma/data/tests/config.toml

@@ -9,7 +9,7 @@ templateflow_version = "0.4.2"
 version = "20.0.1"
 
 [execution]
-bids_dir = "ds000005/"
+bids_dir = "/data"
 bids_description_hash = "5d42e27751bbc884eca87cb4e62b9a0cca0cd86f8e578747fe89b77e6c5b21e5"
 boilerplate_only = false
 fs_license_file = "/opt/freesurfer/license.txt"

src/fmripost_aroma/tests/conftest.py

@@ -0,0 +1,84 @@
+"""Fixtures for the CircleCI tests."""
+
+import base64
+import os
+
+import pytest
+
+
+def pytest_addoption(parser):
+    """Collect pytest parameters for running tests."""
+    parser.addoption(
+        "--working_dir",
+        action="store",
+        default=(
+            "/usr/local/miniconda/lib/python3.11/site-packages/fmripost_aroma/fmripost_aroma/"
+            "tests/data/test_data/run_pytests/work"
+        ),
+    )
+    parser.addoption(
+        "--data_dir",
+        action="store",
+        default=(
+            "/usr/local/miniconda/lib/python3.11/site-packages/fmripost_aroma/fmripost_aroma/"
+            "tests/data/test_data"
+        ),
+    )
+    parser.addoption(
+        "--output_dir",
+        action="store",
+        default=(
+            "/usr/local/miniconda/lib/python3.11/site-packages/fmripost_aroma/fmripost_aroma/"
+            "tests/data/test_data/run_pytests/out"
+        ),
+    )
+
+
+# Set up the commandline options as fixtures
+@pytest.fixture(scope="session")
+def data_dir(request):
+    """Grab data directory."""
+    return request.config.getoption("--data_dir")
+
+
+@pytest.fixture(scope="session")
+def working_dir(request):
+    """Grab working directory."""
+    workdir = request.config.getoption("--working_dir")
+    os.makedirs(workdir, exist_ok=True)
+    return workdir
+
+
+@pytest.fixture(scope="session")
+def output_dir(request):
+    """Grab output directory."""
+    outdir = request.config.getoption("--output_dir")
+    os.makedirs(outdir, exist_ok=True)
+    return outdir
+
+
+@pytest.fixture(scope="session", autouse=True)
+def fslicense(working_dir):
+    """Set the FreeSurfer license as an environment variable."""
+    FS_LICENSE = os.path.join(working_dir, "license.txt")
+    os.environ["FS_LICENSE"] = FS_LICENSE
+    LICENSE_CODE = (
+        "bWF0dGhldy5jaWVzbGFrQHBzeWNoLnVjc2IuZWR1CjIwNzA2CipDZmVWZEg1VVQ4clkKRlNCWVouVWtlVElDdwo="
+    )
+    with open(FS_LICENSE, "w") as f:
+        f.write(base64.b64decode(LICENSE_CODE).decode())
+
+
+@pytest.fixture(scope="session")
+def base_config():
+    from fmripost_aroma.tests.tests import mock_config
+
+    return mock_config
+
+
+@pytest.fixture(scope="session")
+def base_parser():
+    from argparse import ArgumentParser
+
+    parser = ArgumentParser(description="Test parser")
+    return parser

src/fmripost_aroma/tests/run_local_tests.py

@@ -0,0 +1,96 @@
+#!/usr/bin/env python3
+"""Run tests locally by calling Docker."""
+import argparse
+import os
+import subprocess
+
+
+def _get_parser():
+    """Parse command line inputs for tests.
+
+    Returns
+    -------
+    parser.parse_args() : argparse dict
+    """
+    parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument(
+        "-k",
+        dest="test_regex",
+        metavar="PATTERN",
+        type=str,
+        help="Test pattern.",
+        required=False,
+        default=None,
+    )
+    parser.add_argument(
+        "-m",
+        dest="test_mark",
+        metavar="LABEL",
+        type=str,
+        help="Test mark label.",
+        required=False,
+        default=None,
+    )
+    return parser
+
+
+def run_command(command, env=None):
+    """Run a given shell command with certain environment variables set.
+
+    Keep this out of the real xcp_d code so that devs don't need to install ASLPrep to run tests.
+    """
+    merged_env = os.environ
+    if env:
+        merged_env.update(env)
+
+    process = subprocess.Popen(
+        command,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.STDOUT,
+        shell=True,
+        env=merged_env,
+    )
+    while True:
+        line = process.stdout.readline()
+        line = str(line, "utf-8")[:-1]
+        print(line)
+        if line == "" and process.poll() is not None:
+            break
+
+    if process.returncode != 0:
+        raise RuntimeError(
+            f"Non zero return code: {process.returncode}\n" f"{command}\n\n{process.stdout.read()}"
+        )
+
+
+def run_tests(test_regex, test_mark):
+    """Run the tests."""
+    local_patch = os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
+    mounted_code = "/usr/local/miniconda/lib/python3.11/site-packages/fmripost_aroma"
+    run_str = "docker run --rm -ti "
+    run_str += f"-v {local_patch}:{mounted_code} "
+    run_str += "--entrypoint pytest "
+    run_str += "nipreps/fmripost_aroma:unstable "
+    run_str += (
+        f"{mounted_code}/fmripost_aroma "
+        f"--data_dir={mounted_code}/fmripost_aroma/tests/test_data "
+        f"--output_dir={mounted_code}/fmripost_aroma/tests/pytests/out "
+        f"--working_dir={mounted_code}/fmripost_aroma/tests/pytests/work "
+    )
+    if test_regex:
+        run_str += f"-k {test_regex} "
+    elif test_mark:
+        run_str += f"-rP -o log_cli=true -m {test_mark} "
+
+    run_command(run_str)
+
+
+def _main(argv=None):
+    """Run the tests."""
+    options = _get_parser().parse_args(argv)
+    kwargs = vars(options)
+    run_tests(**kwargs)
+
+
+if __name__ == "__main__":
+    _main()