msw-core 0.2.0__tar.gz

msw_core-0.2.0/.forgejo/workflows/ci.yml

@@ -0,0 +1,41 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+    tags-ignore: ["v*"]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    if: "!startsWith(github.event.head_commit.message, 'bump:')"
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: astral-sh/setup-uv@v7
+        with:
+          python-version: "3.12"
+
+      - name: Run pre-commit (ruff + commitizen + gitleaks)
+        run: uvx pre-commit run --all-files --show-diff-on-failure
+
+  ci:
+    name: CI
+    runs-on: ubuntu-latest
+    needs: [lint]
+    if: always()
+    steps:
+      - name: Check required jobs
+        run: |
+          if [[ "${{ needs.lint.result }}" != "success" && "${{ needs.lint.result }}" != "skipped" ]]; then
+            echo "lint failed" && exit 1
+          fi
+          echo "All required checks passed."

msw_core-0.2.0/.githooks/fix_commit_msg.py

@@ -0,0 +1,52 @@
+#!/usr/bin/env python3
+"""Auto-fix mechanical commit message formatting issues before linting."""
+
+import sys
+from pathlib import Path
+
+
+def fix(path: Path) -> None:
+    text = path.read_text()
+    lines = text.splitlines(keepends=True)
+
+    fixed = []
+    for i, line in enumerate(lines):
+        if line.startswith("#"):
+            fixed.append(line)
+            continue
+
+        # Strip trailing whitespace on every line
+        line = line.rstrip() + "\n"
+
+        # Strip leading whitespace from subject line (first content line)
+        if i == 0 or all(ln.startswith("#") for ln in lines[:i]):
+            line = line.lstrip()
+
+        # Convert hard tabs to four spaces
+        line = line.replace("\t", "    ")
+
+        fixed.append(line)
+
+    # Ensure blank line between subject and body if body is present
+    first = next((i for i, ln in enumerate(fixed) if not ln.startswith("#")), None)
+    if first is not None and first + 1 < len(fixed):
+        next_content = next(
+            (
+                i
+                for i, ln in enumerate(fixed[first + 1 :], first + 1)
+                if not ln.startswith("#")
+            ),
+            None,
+        )
+        if (
+            next_content is not None
+            and next_content == first + 1
+            and fixed[first + 1].strip()
+        ):
+            fixed.insert(first + 1, "\n")
+
+    path.write_text("".join(fixed))
+
+
+if __name__ == "__main__":
+    fix(Path(sys.argv[1]))

msw_core-0.2.0/.github/workflows/ci.yml

@@ -0,0 +1,41 @@
+name: CI
+
+on:
+  push:
+    branches: ["**"]
+    tags-ignore: ["v*"]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    if: "!startsWith(github.event.head_commit.message, 'bump:')"
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - uses: astral-sh/setup-uv@v7
+        with:
+          python-version: "3.12"
+
+      - name: Run pre-commit (ruff + commitizen + gitleaks)
+        run: uvx pre-commit run --all-files --show-diff-on-failure
+
+  ci:
+    name: CI
+    runs-on: ubuntu-latest
+    needs: [lint]
+    if: always()
+    steps:
+      - name: Check required jobs
+        run: |
+          if [[ "${{ needs.lint.result }}" != "success" && "${{ needs.lint.result }}" != "skipped" ]]; then
+            echo "lint failed" && exit 1
+          fi
+          echo "All required checks passed."

msw_core-0.2.0/.github/workflows/release.yml

@@ -0,0 +1,73 @@
+name: Release
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+    inputs:
+      publish_only:
+        description: 'Skip version bump and publish the current VERSION tag'
+        type: boolean
+        default: false
+
+permissions:
+  contents: write
+  id-token: write
+
+jobs:
+  release:
+    name: Bump, build, publish
+    runs-on: ubuntu-latest
+    if: "!startsWith(github.event.head_commit.message, 'bump:')"
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Configure git identity
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+
+      - uses: astral-sh/setup-uv@v7
+        with:
+          python-version: "3.11"
+
+      - name: Bump version
+        id: bump
+        if: inputs.publish_only != true
+        run: |
+          uvx --from commitizen cz bump --yes || EXIT=$?
+          if [ "${EXIT:-0}" -eq 21 ]; then
+            echo "No bumpable commits since last tag — skipping."
+            echo "skipped=true" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+          [ "${EXIT:-0}" -eq 0 ] || exit $EXIT
+          VERSION=$(cat VERSION)
+          git push origin HEAD:main
+          git push origin "v${VERSION}"
+          echo "version=${VERSION}" >> "$GITHUB_OUTPUT"
+
+      - name: Read version (publish-only mode)
+        id: read_version
+        if: inputs.publish_only == true
+        run: |
+          VERSION=$(cat VERSION)
+          echo "version=${VERSION}" >> "$GITHUB_OUTPUT"
+
+      - name: Build
+        if: steps.bump.outputs.skipped != 'true'
+        run: uv build
+
+      - name: Create GitHub release
+        if: steps.bump.outputs.skipped != 'true' && inputs.publish_only != true
+        uses: softprops/action-gh-release@v3
+        with:
+          tag_name: "v${{ steps.bump.outputs.version || steps.read_version.outputs.version }}"
+          files: dist/*
+          generate_release_notes: false
+
+      - name: Publish to PyPI
+        if: steps.bump.outputs.skipped != 'true'
+        run: uv publish --trusted-publishing automatic

msw_core-0.2.0/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*.pyo
+*.pyd
+*.so
+*.egg
+*.egg-info/
+dist/
+build/
+eggs/
+parts/
+var/
+sdist/
+develop-eggs/
+.installed.cfg
+lib/
+lib64/
+wheels/
+
+# Virtual environments
+.venv/
+venv/
+env/
+ENV/
+.python-version
+
+# uv
+uv.lock
+
+# Distribution / packaging
+MANIFEST
+
+# Testing
+.pytest_cache/
+.coverage
+.coverage.*
+coverage.xml
+htmlcov/
+*.cover
+.hypothesis/
+
+# Type checking
+.mypy_cache/
+.dmypy.json
+dmypy.json
+.pytype/
+.pyre/
+
+# Build artifacts (hatch-vcs generated)
+src/*/_version.py
+
+# Jupyter
+.ipynb_checkpoints
+*.ipynb
+
+# IDEs
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Secrets / local config
+.env
+.env.*
+!.env.example
+site/

msw_core-0.2.0/.pre-commit-config.yaml

@@ -0,0 +1,49 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-merge-conflict
+      - id: mixed-line-ending
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.14
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v2.1.0
+    hooks:
+      - id: mypy
+        additional_dependencies: []
+
+  # commit-msg stage: fix first, then validate
+  - repo: local
+    hooks:
+      - id: fix-commit-msg
+        name: Auto-fix commit message formatting
+        language: system
+        entry: python3 .githooks/fix_commit_msg.py
+        stages: [commit-msg]
+
+  - repo: https://github.com/commitizen-tools/commitizen
+    rev: v4.16.2
+    hooks:
+      - id: commitizen
+        stages: [commit-msg]
+
+  - repo: https://github.com/jorisroovers/gitlint
+    rev: v0.19.1
+    hooks:
+      - id: gitlint
+        stages: [commit-msg]
+
+  - repo: https://github.com/gitleaks/gitleaks
+    rev: v8.30.0
+    hooks:
+      - id: gitleaks

msw_core-0.2.0/PKG-INFO

@@ -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/README.md

@@ -0,0 +1,11 @@
+# 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/VERSION

@@ -0,0 +1 @@
+0.2.0

msw_core-0.2.0/pyproject.toml

@@ -0,0 +1,112 @@
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[project]
+name = "msw-core"
+dynamic = ["version"]
+description = "Murine Shift Work acquisition stack: CLI, hardware, hooks, and logic."
+readme = { file = "README.md", content-type = "text/markdown" }
+license = { file = "LICENSE" }
+authors = [
+    { name = "Lars B. Rollik", email = "lars@rollik.me" },
+]
+requires-python = ">=3.12"
+dependencies = [
+    "msw-io>=1.0.2",
+    "msw-plugin-api>=0.1.0",
+    "ttl-barcoder>=0.4.1",
+    "pydantic>=2.0",
+    "rich",
+    "pyyaml",
+    "numpy",
+    "scipy",
+    "pandas",
+    "matplotlib",
+    "seaborn",
+    "pyserial",
+    "pybpod-api",
+    "one-axis-stage",
+    "sounddevice",
+]
+
+[project.urls]
+Homepage = "https://github.com/MurineShiftWork/msw-core"
+"Issue Tracker" = "https://github.com/MurineShiftWork/msw-core/issues"
+
+[project.scripts]
+murineshiftwork = "murineshiftwork.cli:run_cli"
+msw = "murineshiftwork.cli:run_cli"
+
+[project.optional-dependencies]
+dev = [
+    "commitizen",
+    "pytest>=8",
+    "pytest-cov",
+    "pre-commit",
+    "mypy",
+    "types-PyYAML",
+]
+docs = [
+    "mkdocs-material",
+    "mkdocstrings[python]",
+]
+
+[tool.hatch.version]
+source = "vcs"
+fallback-version = "0.1.0"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "src/murineshiftwork/_version.py"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/murineshiftwork"]
+
+# ---------------------------------------------------------------------------
+# Pytest
+# ---------------------------------------------------------------------------
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "--cov=src/murineshiftwork --durations=0"
+
+# ---------------------------------------------------------------------------
+# Ruff
+# ---------------------------------------------------------------------------
+
+[tool.ruff]
+line-length = 88
+indent-width = 4
+src = ["src"]
+
+[tool.ruff.lint]
+select = ["E", "W", "F", "I", "B", "N", "UP", "SIM", "PTH"]
+ignore = ["E501", "B017", "N817"]
+fixable = ["ALL"]
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+line-ending = "auto"
+docstring-code-format = true
+
+# ---------------------------------------------------------------------------
+# Mypy
+# ---------------------------------------------------------------------------
+
+[tool.mypy]
+python_version = "3.12"
+warn_return_any = false
+ignore_missing_imports = true
+
+# ---------------------------------------------------------------------------
+# Commitizen
+# ---------------------------------------------------------------------------
+
+[tool.commitizen]
+name = "cz_conventional_commits"
+version_provider = "commitizen"
+version = "0.2.0"
+tag_format = "v$version"
+update_changelog_on_bump = false
+version_files = ["VERSION"]

msw_core-0.2.0/src/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

msw_core-0.2.0/src/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()

msw_core-0.2.0/src/murineshiftwork/cli/__main__.py

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

msw_core-0.2.0/src/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()