msw-core 0.2.0__py3-none-any.whl

msw_core-0.2.0.dist-info/METADATA

@@ -0,0 +1,47 @@
+Metadata-Version: 2.4
+Name: msw-core
+Version: 0.2.0
+Summary: Murine Shift Work acquisition stack: CLI, hardware, hooks, and logic.
+Project-URL: Homepage, https://github.com/MurineShiftWork/msw-core
+Project-URL: Issue Tracker, https://github.com/MurineShiftWork/msw-core/issues
+Author-email: "Lars B. Rollik" <lars@rollik.me>
+License-File: LICENSE
+Requires-Python: >=3.12
+Requires-Dist: matplotlib
+Requires-Dist: msw-io>=1.0.2
+Requires-Dist: msw-plugin-api>=0.1.0
+Requires-Dist: numpy
+Requires-Dist: one-axis-stage
+Requires-Dist: pandas
+Requires-Dist: pybpod-api
+Requires-Dist: pydantic>=2.0
+Requires-Dist: pyserial
+Requires-Dist: pyyaml
+Requires-Dist: rich
+Requires-Dist: scipy
+Requires-Dist: seaborn
+Requires-Dist: sounddevice
+Requires-Dist: ttl-barcoder>=0.4.1
+Provides-Extra: dev
+Requires-Dist: commitizen; extra == 'dev'
+Requires-Dist: mypy; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Requires-Dist: pytest>=8; extra == 'dev'
+Requires-Dist: types-pyyaml; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: mkdocs-material; extra == 'docs'
+Requires-Dist: mkdocstrings[python]; extra == 'docs'
+Description-Content-Type: text/markdown
+
+# msw-core
+
+[![PyPI](https://img.shields.io/pypi/v/msw-core.svg)](https://pypi.org/project/msw-core)
+
+Murine Shift Work acquisition stack: CLI, hardware drivers, session hooks, and task logic.
+
+Provides the `murineshiftwork.cli`, `murineshiftwork.hardware`, `murineshiftwork.hooks`,
+and `murineshiftwork.logic` namespace sub-packages. Installs the `msw` / `murineshiftwork`
+CLI entry points.
+
+Part of the [MurineShiftWork](https://github.com/MurineShiftWork) namespace package ecosystem.

msw_core-0.2.0.dist-info/RECORD

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+msw_core-0.2.0.dist-info/WHEEL,sha256=mffPy8wBnZQn2VnJUU5jE99KsxaSfiyMHV9Yt0aLVxs,87
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+msw_core-0.2.0.dist-info/licenses/LICENSE,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+msw_core-0.2.0.dist-info/RECORD,,

msw_core-0.2.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.30.1
+Root-Is-Purelib: true
+Tag: py3-none-any

msw_core-0.2.0.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+msw = murineshiftwork.cli:run_cli
+murineshiftwork = murineshiftwork.cli:run_cli

murineshiftwork/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '0.2.0'
+__version_tuple__ = version_tuple = (0, 2, 0)
+
+__commit_id__ = commit_id = None

murineshiftwork/cli/__init__.py

@@ -0,0 +1,68 @@
+import logging
+import sys
+
+from murineshiftwork.cli.evaluate import evaluate_args
+from murineshiftwork.cli.parser import parse_args
+from murineshiftwork.hardware.bpod import patch_user_settings
+from murineshiftwork.logic.log import patch_logging_levels
+
+
+def _print_run_banner():
+    from importlib.metadata import version as _v
+
+    try:
+        ver = _v("murineshiftwork")
+    except Exception:
+        ver = "unknown"
+    print(f"msw {ver} | © Lars B. Rollik | PolyForm Internal Use 1.0.0")
+
+
+def run_cli(*args):
+    """Command line interface for Murine Shift Work."""
+    patch_logging_levels()
+    patch_user_settings()
+
+    if not args:
+        args = sys.argv[1:]
+
+    if len(args) > 0 and not isinstance(args[0], str):
+        args = args[0]
+
+    if len(args) > 0 and str(args[0]).endswith(".py"):
+        _, args = args[0], args[1:]
+
+    if len(args) <= 1:
+        args = args + ["-h"]
+
+    args_dict = parse_args(args=args)
+
+    # These subcommands bypass evaluate_args (no hardware/subject/task context needed)
+    if args_dict.get("command") in (
+        "init",
+        "setup",
+        "subject",
+        "calibration",
+        "action",
+        "tasks",
+        "post",
+    ):
+        args_dict["func"](**args_dict)
+        logging.debug("EXITING CLI.")
+        return
+
+    if args_dict.get("command") == "run":
+        _print_run_banner()
+
+    args_dict = evaluate_args(args_dict=args_dict)
+
+    if "exit_flag" in args_dict:
+        return
+
+    # Call module
+    args_dict["func"](**args_dict)
+
+    logging.debug("EXITING CLI.")
+
+
+if __name__ == "__main__":
+    run_cli()

murineshiftwork/cli/__main__.py

@@ -0,0 +1,4 @@
+from murineshiftwork.cli import run_cli
+
+if __name__ == "__main__":
+    run_cli()

murineshiftwork/cli/defaults.py

@@ -0,0 +1,44 @@
+"""Module-load-time defaults for the CLI.
+
+Factored out of evaluate.py so parser.py can import them without importing the
+full evaluate pipeline, avoiding any risk of a circular dependency.
+"""
+
+from pathlib import Path
+
+from murineshiftwork.cli.tasks import list_available_tasks
+from murineshiftwork.logic.machine_config import (
+    resolve_config_dir,
+    resolve_data_dir,
+)
+
+default_out_path = resolve_data_dir()
+default_config_dir = resolve_config_dir()
+
+CALIBRATION_FILE_PATH = Path("~/.murineshiftwork").expanduser()
+DEFAULT_CALIBRATION_FILE_LIQUID = str(
+    CALIBRATION_FILE_PATH / "calibration.liquid.default.csv"
+)
+DEFAULT_CALIBRATION_FILE_SOUND = "calibration.sound.default.csv"
+DEFAULT_CALIBRATION_FILE_STAGE = str(
+    CALIBRATION_FILE_PATH / "calibration.stage.default.yaml"
+)
+
+
+def _build_task_list() -> str:
+    all_tasks = list_available_tasks()
+    main = sorted(t for t in all_tasks if not t.startswith("_"))
+    calibration = sorted(t for t in all_tasks if t.startswith("_calibration"))
+    tests = sorted(t for t in all_tasks if t.startswith("_test"))
+    lines = []
+    for heading, group in (
+        ("Tasks", main),
+        ("Calibration", calibration),
+        ("Tests", tests),
+    ):
+        lines.append(f"  {heading}:")
+        lines.extend(f"    - {t}" for t in group)
+    return "\n".join(lines)
+
+
+available_tasks = _build_task_list()