Feature FullAutoS0A

.github/workflows/tests.yml

@@ -10,6 +10,31 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  lint:
+    name: lint (black + flake8)
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install lint tools
+        # Pin Black to the version the pre-commit hook / local devs run so CI
+        # and pre-commit agree. flake8 reads [tool.flake8] via Flake8-pyproject.
+        run: |
+          python -m pip install --upgrade pip
+          pip install "black==25.9.0" flake8 Flake8-pyproject
+
+      - name: black --check
+        run: black --check .
+
+      - name: flake8
+        run: flake8 .
+
   unittest:
     name: unittest on Windows (Python ${{ matrix.python-version }})
     runs-on: windows-latest

.gitignore

@@ -10,6 +10,8 @@ PycroFlow.egg-info/*
 *.egg-info/
 build/
 dist/
+# Generated by setuptools-scm at build/install time (version from git tag).
+PycroFlow/_version.py
 
 # Test artifacts
 .pytest_cache/
@@ -19,6 +21,7 @@ htmlcov/
 # Local test data (fixtures live under PycroFlow/tests/fixtures/)
 PycroFlow/TestData/*
 
-# Claude Code (project instructions + local settings; kept out of version control)
-CLAUDE.md
+# Claude Code: CLAUDE.md (shared project instructions) IS committed; keep
+# local settings and personal notes out of version control.
 .claude/
+CLAUDE.local.md

.pre-commit-config.yaml

@@ -0,0 +1,44 @@
+# Applies to every hook below. Keep the vendored upstream PyHamiltonPSD
+# snapshot pristine, and leave the regression snapshot fixtures byte-exact
+# (they are written without a trailing newline by the snapshot regenerator and
+# compared via json.loads, so the end-of-file-fixer must not touch them).
+exclude: >
+  (?x)^(
+      PycroFlow/pyHamilton/pyHamiltonPSD_packagefiles/
+      |PycroFlow/tests/fixtures/snapshots/
+  )
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+  # Use the maintained black mirror, pinned to the version the team runs
+  # locally so pre-commit and a manual `black` agree (keep in sync via
+  # `pre-commit autoupdate`). black reads line-length from [tool.black].
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 25.9.0
+    hooks:
+      - id: black
+  # flake8 reads its config from pyproject.toml [tool.flake8] via the
+  # Flake8-pyproject plugin (no separate .flake8 file). The exclude below
+  # mirrors [tool.flake8].extend-exclude; it is repeated here because
+  # pre-commit passes an explicit file list that flake8's own directory-walk
+  # excludes do not filter (the generated _version.py, the pyHamilton driver's
+  # star-import idiom, and the throwaway snippets/scripts/example scripts).
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.1.1
+    hooks:
+      - id: flake8
+        additional_dependencies: [Flake8-pyproject]
+        exclude: >
+          (?x)^(
+              PycroFlow/_version\.py
+              |PycroFlow/pyHamilton/
+              |snippets/
+              |scripts/
+              |example_experiment/
+          )

CHANGELOG.md

@@ -0,0 +1,43 @@
+# Changelog
+
+All notable changes to this project are documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Changed
+
+- Versioning now derives from the git tag via `setuptools-scm` (writes
+  `PycroFlow/_version.py`); the manual `version` string in `pyproject.toml`
+  is gone. `PycroFlow.__version__` reads the generated module with a fallback.
+- Consolidated lint config into `pyproject.toml`: added `[tool.black]`
+  (line-length 79, `target-version = ["py310"]`) and `[tool.flake8]`
+  (`extend-ignore = E203,E501,W503` — Black owns line length), replacing the
+  standalone `.flake8`.
+
+### Added
+
+- Per-subsystem selection: an `enabled` flag on the fluid / img / illu
+  sections of an experiment design lets a subsystem be deselected. The
+  builder omits deselected subsystems from the compiled Run Sequence, prunes
+  cross-subsystem `wait for signal` entries that targeted a dropped
+  subsystem, and raises if nothing is selected; the orchestrator only wires
+  hardware for subsystems present in the protocol.
+- Shared `.pre-commit-config.yaml` (pre-commit-hooks + Black + flake8 via
+  Flake8-pyproject), matching the rest of the DNA-PAINT stack.
+- `black --check` and `flake8` lint job in CI.
+- This changelog.
+
+### Removed
+
+- Legacy `setup.py` shim (`pyproject.toml` is the canonical build config).
+- Empty `CHANGELOG.txt` (superseded by this `CHANGELOG.md`).
+
+## [0.1.0]
+
+Initial tagged release. PycroFlow coordinates microscopy image acquisition,
+Hamilton fluid handling, and monet illumination control for automated
+DNA-PAINT experiments (Exchange-PAINT, MERPAINT, Z-PAINT, SPH-RESI), with a
+CLI (`pycroflow`) and a PyQt6 GUI (`pycroflow-gui`) over a shared service layer.

PycroFlow/__init__.py

@@ -9,16 +9,24 @@
 a protocol in a startup script) does not flood the terminal. Until
 ``setup_logging`` installs the real sinks, records simply go nowhere.
 """
+
 from loguru import logger
 import os
 import sys
 
+# Version comes from the git tag via setuptools-scm, which writes the
+# resolved value into the generated ``_version.py`` at build/install time.
+# Fall back to importlib.metadata (installed dist) and finally a sentinel so
+# importing from an uninstalled source tree without a build never crashes.
 try:
-    from importlib.metadata import PackageNotFoundError, version
+    from ._version import version as __version__
+except ImportError:  # no generated file (uninstalled source tree)
+    try:
+        from importlib.metadata import PackageNotFoundError, version
 
-    __version__ = version("PycroFlow")
-except (ImportError, PackageNotFoundError):  # not installed (e.g. source tree)
-    __version__ = "0.0.0"
+        __version__ = version("PycroFlow")
+    except (ImportError, PackageNotFoundError):
+        __version__ = "0.0.0"
 
 
 # loguru auto-installs a DEBUG->stderr handler (id 0) on import. Drop it so
@@ -43,7 +51,7 @@
 
 def log_filter(record):
     """Exclude subpackage logs (pyHamilton, monet) from the main log file."""
-    subpackages = ['pyHamilton', 'monet']
+    subpackages = ["pyHamilton", "monet"]
     if any(sp in record["name"] for sp in subpackages):
         return False
     return True
@@ -59,7 +67,7 @@ def logging_configured():
     return _LOGGING_CONFIGURED
 
 
-def clean_old_logs(prefix='pycroflow.log', directory='.'):
+def clean_old_logs(prefix="pycroflow.log", directory="."):
     """Delete rotated log files matching ``prefix`` in ``directory``.
 
     Previously called ``rem_old_logfiles`` and run at import time, which
@@ -78,8 +86,12 @@ def clean_old_logs(prefix='pycroflow.log', directory='.'):
                 pass
 
 
-def setup_logging(logfile='pycroflow.log', clean_old=False,
-                  stderr_level='ERROR', hamilton_logfile='hamilton.log'):
+def setup_logging(
+    logfile="pycroflow.log",
+    clean_old=False,
+    stderr_level="ERROR",
+    hamilton_logfile="hamilton.log",
+):
     """Configure loguru sinks for PycroFlow.
 
     Three sinks are installed:

PycroFlow/configs/__init__.py

@@ -8,21 +8,21 @@
 The package data is included via ``[tool.setuptools.package-data]`` in
 ``pyproject.toml``.
 """
+
 import copy
 from pathlib import Path
 
 import yaml
 
-
 _CONFIG_DIR = Path(__file__).resolve().parent
-_SETUP_DIR = _CONFIG_DIR / 'setups'
+_SETUP_DIR = _CONFIG_DIR / "setups"
 
 
 def _resolve(path_or_name, suffix, base=None):
     """Accept either a bare name ('default') or a path; return a Path."""
     p = Path(path_or_name)
-    if p.suffix == '':
-        p = (base or _CONFIG_DIR) / f'{path_or_name}{suffix}'
+    if p.suffix == "":
+        p = (base or _CONFIG_DIR) / f"{path_or_name}{suffix}"
     return p
 
 
@@ -35,22 +35,22 @@ def _records_to_tubing(records):
     """
     result = {}
     for record in records:
-        result[(record['from'], record['to'])] = record['volume']
+        result[(record["from"], record["to"])] = record["volume"]
     return result
 
 
-def load_legacy_system(name='legacy_system'):
+def load_legacy_system(name="legacy_system"):
     """Load a legacy system config YAML and return the parsed dict.
 
     ``name`` may be either a basename (e.g. ``'legacy_system'``) found in
     :mod:`PycroFlow.configs`, or an absolute / relative path to a YAML file.
     """
-    path = _resolve(name, '.yaml')
+    path = _resolve(name, ".yaml")
     with open(path) as f:
         return yaml.safe_load(f)
 
 
-def load_legacy_tubing(name='legacy_tubing'):
+def load_legacy_tubing(name="legacy_tubing"):
     """Load a legacy tubing config and convert list-of-records to
     tuple-keyed dict, matching the original in-source dict shape.
 
@@ -62,14 +62,15 @@ def load_legacy_tubing(name='legacy_tubing'):
 
     which round-trips to ``{('R21', 'pump_a'): 365, ...}``.
     """
-    path = _resolve(name, '.yaml')
+    path = _resolve(name, ".yaml")
     with open(path) as f:
         records = yaml.safe_load(f)
     return _records_to_tubing(records)
 
 
 # --- Per-microscope setup (hardware) configs -----------------------------
 
+
 def list_setups():
     """Return the names of the available setup configs.
 
@@ -81,7 +82,7 @@ def list_setups():
     """
     if not _SETUP_DIR.is_dir():
         return []
-    return sorted(p.stem for p in _SETUP_DIR.glob('*.yaml'))
+    return sorted(p.stem for p in _SETUP_DIR.glob("*.yaml"))
 
 
 def load_setup(name):
@@ -101,11 +102,11 @@ def load_setup(name):
     dict
         The parsed setup with ``tubing`` converted to a tuple-keyed dict.
     """
-    path = _resolve(name, '.yaml', base=_SETUP_DIR)
+    path = _resolve(name, ".yaml", base=_SETUP_DIR)
     with open(path) as f:
         setup = yaml.safe_load(f)
-    if isinstance(setup.get('tubing'), list):
-        setup['tubing'] = _records_to_tubing(setup['tubing'])
+    if isinstance(setup.get("tubing"), list):
+        setup["tubing"] = _records_to_tubing(setup["tubing"])
     return setup
 
 
@@ -135,14 +136,14 @@ def assemble_hamilton_config(setup, fluid_settings):
         ``(hamilton_config, tubing_config)`` ready for
         ``LegacyArchitecture(hamilton_config, tubing_config)``.
     """
-    hamilton = copy.deepcopy(setup['hamilton'])
-    manifold = hamilton.pop('reservoir_a_manifold', [])
-    by_id = {entry['id']: entry for entry in manifold}
+    hamilton = copy.deepcopy(setup["hamilton"])
+    manifold = hamilton.pop("reservoir_a_manifold", [])
+    by_id = {entry["id"]: entry for entry in manifold}
 
-    special_names = dict(fluid_settings.get('special_names', {}))
-    cleaning = fluid_settings.get('cleaning_reservoirs', []) or []
+    special_names = dict(fluid_settings.get("special_names", {}))
+    cleaning = fluid_settings.get("cleaning_reservoirs", []) or []
 
-    used_ids = list(fluid_settings.get('reservoir_names', {}).keys())
+    used_ids = list(fluid_settings.get("reservoir_names", {}).keys())
     for res in cleaning:
         if isinstance(res, int):
             rid = res
@@ -151,7 +152,8 @@ def assemble_hamilton_config(setup, fluid_settings):
             if rid is None:
                 raise KeyError(
                     "Cleaning reservoir {!r} is neither an int id nor a "
-                    "name in special_names {}".format(res, special_names))
+                    "name in special_names {}".format(res, special_names)
+                )
         if rid not in used_ids:
             used_ids.append(rid)
 
@@ -160,14 +162,14 @@ def assemble_hamilton_config(setup, fluid_settings):
         if rid not in by_id:
             raise KeyError(
                 "Reservoir id {!r} is not wired in setup "
-                "{!r}'s reservoir_a_manifold".format(
-                    rid, setup.get('setup')))
+                "{!r}'s reservoir_a_manifold".format(rid, setup.get("setup"))
+            )
         reservoir_a.append(by_id[rid])
 
-    hamilton['reservoir_a'] = reservoir_a
-    hamilton['special_names'] = special_names
-    hamilton['cleaning_reservoirs'] = cleaning
-    return hamilton, setup.get('tubing', {})
+    hamilton["reservoir_a"] = reservoir_a
+    hamilton["special_names"] = special_names
+    hamilton["cleaning_reservoirs"] = cleaning
+    return hamilton, setup.get("tubing", {})
 
 
 def assemble_imaging_config(setup, design):
@@ -188,11 +190,11 @@ def assemble_imaging_config(setup, design):
     dict
         Config for :class:`PycroFlow.imaging.ImagingSystem`.
     """
-    cfg = copy.deepcopy(setup.get('imaging', {}))
-    cfg.setdefault('save_dir', design.get('save_dir', '.'))
-    cfg['base_name'] = design.get('base_name', 'experiment')
-    img = design.get('img', {})
-    settings = img.get('settings', {}) if isinstance(img, dict) else {}
-    if 'use_positions' in settings:
-        cfg['use_positions'] = settings['use_positions']
+    cfg = copy.deepcopy(setup.get("imaging", {}))
+    cfg.setdefault("save_dir", design.get("save_dir", "."))
+    cfg["base_name"] = design.get("base_name", "experiment")
+    img = design.get("img", {})
+    settings = img.get("settings", {}) if isinstance(img, dict) else {}
+    if "use_positions" in settings:
+        cfg["use_positions"] = settings["use_positions"]
     return cfg