diff --git a/CLAUDE.md b/CLAUDE.md index 91c85a6..442fef1 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -73,7 +73,7 @@ Three cooperating roles, each configurable independently and often on different ### Configuration is the program -`pyrolab/configure.py` is the center of gravity. A single YAML file (pydantic v1 models) declares +`pyrolab/configure.py` is the center of gravity. A single YAML file (pydantic 2 models) declares `nameservers`, `daemons`, `services`, and `autolaunch` (see the `sample_config_yaml` fixture in `tests/conftest.py` and `examples/library-catalog/config.yaml`; `tests/data/*.yaml` are stale and reference a `pyrolab.daemon` module that no longer exists). A `ServiceConfiguration` names a `module` + `classname` that is @@ -88,12 +88,15 @@ refers to one called `default`). `describe_config_error()` turns a load error in Anything that writes a config must re-validate before saving; `rename_entity()` renames an entity together with every reference to it. -The models derive from `_ConfigModel` (plain pydantic `BaseModel`, `extra = "forbid"`), **not** `BaseSettings`: +The models derive from `_ConfigModel` (plain pydantic `BaseModel`, `extra="forbid"`), **not** `BaseSettings`: settings models fill unset fields from same-named environment variables (`PORT`, `HOST`, ...), which silently changed configurations. Unknown keys are errors. `update_pyro_config()` warns about any field it can't apply unless the model lists it in `NOT_PYRO_OPTIONS`. Daemon placement (`host`, `port`, `unixsocket`, `nathost`, `natport`) goes to the daemon's constructor, since Pyro5 has no global `PORT`/`UNIXSOCKET` options. -Nameservers get their names (used for storage paths) whenever a `PyroLabConfiguration` is constructed. +Nameservers get their names (used for storage paths) in `PyroLabConfiguration.model_post_init`, so on every +construction or validation path. `_ConfigModel` sets `coerce_numbers_to_str` so pydantic-1-era files with +e.g. an unquoted `version: 1.0` still load. In pydantic 2, model equality includes private attributes, so two +nameserver configs with different names are unequal; compare `model_dump()` for settings only. Every config/lockfile write goes through `utils.atomic_write_text()` (temp file + fsync + `os.replace`). @@ -198,8 +201,9 @@ excluded from import sorting (a ruff per-file ignore); import order there is loa `cameras`), not in the base `dependencies`. PyPI rejects direct git URLs, so git-sourced extras stay commented out. `[tool.uv.sources]` can point development installs at git, but PyPI users never see it, so don't rely on it to fix a broken release — the Arduino driver patches PyPI's pyfirmata 1.1.0 instead. -- Pinned to **pydantic 1.x** (`BaseSettings`, `validator`, `PrivateAttr` from `pydantic.fields`). Do not - migrate to pydantic 2 piecemeal. +- **pydantic 2** (`>=2.8`): `model_config = ConfigDict(...)`, `field_validator`/`model_validator`, + `model_dump`/`model_validate`/`model_validate_json`. No v1 API (`.dict()`, `parse_file`, `@validator`, ...); + the suite passes with pydantic's deprecation warnings turned into errors. ## Releasing diff --git a/docs/_config.yml b/docs/_config.yml index 54f4cf8..d512123 100644 --- a/docs/_config.yml +++ b/docs/_config.yml @@ -55,16 +55,11 @@ sphinx: autodoc_typehints: 'signature' autodoc_mock_imports: [ "appnope", - "deprecation", - "typer", - "colorama", - "tabulate", "serial", "thorlabs_kinesis", "pyfirmata", "sacher_tec", "pyvisa", - "pyfirmata", "cv2", "WF_SDK", ] diff --git a/docs/requirements.txt b/docs/requirements.txt index 72683ed..392020a 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,13 +1,6 @@ +# Read the Docs installs these, then PyroLab itself (pip install .), which +# brings PyroLab's own dependencies. Don't repeat those here: a pin that +# disagrees with pyproject.toml makes the docs build unresolvable. +# Keep in step with the "docs" dependency group in pyproject.toml. jupyter-book==1.0.3 -# sphinx==7.4.7 -# pydata-sphinx-theme==0.15.4 numpydoc==1.5.0 -numpy==2.2.3 -scipy==1.15.2 -# sphinx_design==0.6.1 -# sphinx-copybutton==0.5.2 -# sphinx-togglebutton==0.3.2 -linkify-it-py==2.0.3 -pydantic==1.10.21 -pyyaml==6.0.2 -Pyro5==5.15 \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 3df08a2..63e6f7e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -62,7 +62,7 @@ dependencies = [ "numpy", "scipy", "Pyro5", - "pydantic >= 1.9.1, < 2.0.0", + "pydantic>=2.8,<3", "pyyaml", "deprecation", "typer", diff --git a/pyrolab/cli.py b/pyrolab/cli.py index 6ccaff6..494bee6 100644 --- a/pyrolab/cli.py +++ b/pyrolab/cli.py @@ -562,7 +562,7 @@ def info(): ns_data = [] for name in config.nameservers: - ns_data.append({"name": name, **config.nameservers[name].dict()}) + ns_data.append({"name": name, **config.nameservers[name].model_dump()}) for item in ns_data: item["ns_autoclean"] = ( f"{item['ns_autoclean']} sec" if item["ns_autoclean"] else "Off" @@ -573,7 +573,7 @@ def info(): daemon_data = [] for name in config.daemons: - daemon_data.append({"name": name, **config.daemons[name].dict()}) + daemon_data.append({"name": name, **config.daemons[name].model_dump()}) for item in daemon_data: item["nameservers"] = "".join([f"- {name}\n" for name in item["nameservers"]]) if daemon_data: @@ -582,7 +582,7 @@ def info(): service_data = [] for name in config.services: - service_data.append({"name": name, **config.services[name].dict()}) + service_data.append({"name": name, **config.services[name].model_dump()}) for item in service_data: item["parameters"] = "".join( [f"{k}: {v}\n" for k, v in item["parameters"].items()] diff --git a/pyrolab/configure.py b/pyrolab/configure.py index 897abe1..ebe1176 100644 --- a/pyrolab/configure.py +++ b/pyrolab/configure.py @@ -40,8 +40,14 @@ from typing import IO, Any, ClassVar, Dict, List, Optional, Tuple, Type, Union import Pyro5 -from pydantic import BaseModel, root_validator, validator -from pydantic.fields import PrivateAttr +from pydantic import ( + BaseModel, + ConfigDict, + PrivateAttr, + ValidationError, + field_validator, + model_validator, +) from yaml import dump, load from yaml.constructor import ConstructorError from yaml.nodes import MappingNode @@ -202,7 +208,7 @@ def update_pyro_config(self, values: dict = None) -> Dict[str, Any]: debugging or informational purposes. """ if values is None: - values = self.dict() + values = self.model_dump() for key in ["host", "ns_host", "ns_bchost"]: if key in values: @@ -238,9 +244,13 @@ class _ConfigModel(BaseModel): in the environment would silently change the configuration. """ - class Config: - extra = "forbid" # a misspelled key is an error, not silently ignored - validate_all = True + model_config = ConfigDict( + extra="forbid", # a misspelled key is an error, not silently ignored + validate_default=True, + # pydantic 1 accepted e.g. an unquoted `version: 1.0` for a string + # field; keep accepting numbers where text is expected. + coerce_numbers_to_str=True, + ) class YAMLMixin: @@ -266,7 +276,7 @@ def yaml( includes them (default False). """ return dump( - self.dict(exclude_defaults=exclude_defaults), + self.model_dump(exclude_defaults=exclude_defaults), sort_keys=sort_keys, default_flow_style=default_flow_style, ) @@ -289,7 +299,7 @@ def from_yaml( The YAML to load. """ loaded = load(yaml, Loader=UniqueOrAutoKeyLoader) - cfg = cls.parse_obj(loaded) + cfg = cls.model_validate(loaded) return cfg @classmethod @@ -398,7 +408,8 @@ class NameServerConfiguration(_ConfigModel, PyroConfigMixin, YAMLMixin): # Passed to the nameserver directly rather than through Pyro5.config. NOT_PYRO_OPTIONS: ClassVar[frozenset] = frozenset({"broadcast", "storage"}) - @validator("storage") + @field_validator("storage") + @classmethod def valid_memory_format(cls, v: str): if v == "memory": return v @@ -453,7 +464,7 @@ def update_pyro_config(self) -> Dict[str, Any]: A dictionary of Pyro5 key-value pairs that were updated, for debugging or informational purposes. """ - values = self.dict() + values = self.model_dump() values["ns_host"] = values["host"] return super().update_pyro_config(values=values) @@ -694,10 +705,10 @@ class PyroLabConfiguration(_ConfigModel, YAMLMixin): services: Dict[str, ServiceConfiguration] = {} autolaunch: AutolaunchSettings = AutolaunchSettings() - @root_validator(skip_on_failure=True) - def references_are_defined(cls, values): - nameservers = values["nameservers"] - daemons = values["daemons"] + @model_validator(mode="after") + def references_are_defined(self) -> "PyroLabConfiguration": + nameservers = self.nameservers + daemons = self.daemons problems = [] def check(kind, names, defined, where): @@ -707,25 +718,26 @@ def check(kind, names, defined, where): f"{where} refers to {kind} '{name}', which is not defined" ) - for sname, svc in values["services"].items(): + for sname, svc in self.services.items(): where = f"service '{sname}'" if svc.daemon not in daemons: - hint = "" if "daemon" in svc.__fields_set__ else " (the default)" + hint = "" if "daemon" in svc.model_fields_set else " (the default)" problems.append( f"{where} refers to daemon '{svc.daemon}'{hint}, which is not defined" ) check("nameserver", svc.nameservers, nameservers, where) for dname, dcfg in daemons.items(): check("nameserver", dcfg.nameservers, nameservers, f"daemon '{dname}'") - check("nameserver", values["autolaunch"].nameservers, nameservers, "autolaunch") - check("daemon", values["autolaunch"].daemons, daemons, "autolaunch") + check("nameserver", self.autolaunch.nameservers, nameservers, "autolaunch") + check("daemon", self.autolaunch.daemons, daemons, "autolaunch") if problems: raise ValueError("; ".join(problems)) - return values + return self - def __init__(self, **data: Any) -> None: - super().__init__(**data) + def model_post_init(self, context: Any) -> None: + # Runs however the configuration was created (constructed, validated + # from YAML, ...), so nameservers always know their names. self.initialize_nameservers() def initialize_nameservers(self): @@ -755,14 +767,16 @@ def describe_config_error(exc: Exception) -> List[str]: Human-readable problem descriptions, e.g. ``"daemons.lab.port: value is not a valid integer"``. """ - from pydantic import ValidationError - if not isinstance(exc, ValidationError): return [str(exc)] lines = [] for err in exc.errors(): - loc = ".".join(str(part) for part in err["loc"] if part != "__root__") - for msg in err["msg"].split("; "): + loc = ".".join(str(part) for part in err["loc"]) + # A ValueError raised by one of our validators: use its own message + # rather than pydantic's "Value error, ..." wrapping of it. + original = (err.get("ctx") or {}).get("error") + message = str(original) if isinstance(original, ValueError) else err["msg"] + for msg in message.split("; "): lines.append(f"{loc}: {msg}" if loc else msg) return lines @@ -1037,7 +1051,7 @@ def rename_entity( KeyError If there is no ``kind`` named ``old``. """ - data = config.dict() + data = config.model_dump() section = data[SECTIONS[kind]] if old not in section: raise KeyError(old) @@ -1071,4 +1085,4 @@ def swap(names: List[str], where: str) -> List[str]: auto = data["autolaunch"] auto["daemons"] = swap(auto["daemons"], "autolaunch") - return PyroLabConfiguration.parse_obj(data), changes + return PyroLabConfiguration.model_validate(data), changes diff --git a/pyrolab/pyrolabd.py b/pyrolab/pyrolabd.py index d725661..b7ff0d9 100644 --- a/pyrolab/pyrolabd.py +++ b/pyrolab/pyrolabd.py @@ -56,7 +56,7 @@ def write_lockfile(info: InstanceInfo) -> None: replaces the lockfile in one step, so readers see either no lockfile or a complete one, never a partial write. """ - atomic_write_text(LOCKFILE, info.json()) + atomic_write_text(LOCKFILE, info.model_dump_json()) def read_lockfile() -> Optional[InstanceInfo]: @@ -68,7 +68,7 @@ def read_lockfile() -> Optional[InstanceInfo]: :py:func:`pyrolab.utils.pid_is_running`. """ try: - return InstanceInfo.parse_file(LOCKFILE) + return InstanceInfo.model_validate_json(LOCKFILE.read_text()) except (OSError, ValueError): # missing, unreadable, or not valid JSON return None diff --git a/tests/test_cli.py b/tests/test_cli.py index 4d49797..2a3a67d 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -53,7 +53,7 @@ def running_daemon(data_dir, monkeypatch): FakeDaemonProxy.returns = {} monkeypatch.setattr(cli, "Proxy", FakeDaemonProxy) data_dir.LOCKFILE.write_text( - InstanceInfo(pid=os.getpid(), uri="PYRO:pyrolabd@localhost:1").json() + InstanceInfo(pid=os.getpid(), uri="PYRO:pyrolabd@localhost:1").model_dump_json() ) return FakeDaemonProxy @@ -99,7 +99,7 @@ def dead_pid(): def test_stale_lockfile_means_not_running(data_dir, dead_pid): data_dir.LOCKFILE.write_text( - InstanceInfo(pid=dead_pid, uri="PYRO:pyrolabd@localhost:1").json() + InstanceInfo(pid=dead_pid, uri="PYRO:pyrolabd@localhost:1").model_dump_json() ) result = runner.invoke(cli.app, ["ps"]) assert result.exit_code == 1 @@ -394,7 +394,8 @@ def test_rename(config_with_spare_daemon, kind, section, old): entities = getattr(PyroLabConfiguration.from_file(user_config), section) assert old not in entities - assert entities["renamed"] == before + # Compare settings: in pydantic 2, equality also compares the private name. + assert entities["renamed"].model_dump() == before.model_dump() def _load(path): @@ -720,7 +721,9 @@ def poll(self): return None if self.exit_code is None: self.data_dir.LOCKFILE.write_text( - InstanceInfo(pid=os.getpid(), uri="PYRO:pyrolabd@localhost:1").json() + InstanceInfo( + pid=os.getpid(), uri="PYRO:pyrolabd@localhost:1" + ).model_dump_json() ) return None if self.error: @@ -759,7 +762,7 @@ def test_up_waits_until_daemon_responds(spawn): def test_up_replaces_stale_lockfile(spawn, data_dir, dead_pid): data_dir.LOCKFILE.write_text( - InstanceInfo(pid=dead_pid, uri="PYRO:pyrolabd@localhost:1").json() + InstanceInfo(pid=dead_pid, uri="PYRO:pyrolabd@localhost:1").model_dump_json() ) result = runner.invoke(cli.app, ["up"]) assert result.exit_code == 0, result.output @@ -768,7 +771,7 @@ def test_up_replaces_stale_lockfile(spawn, data_dir, dead_pid): def test_up_when_already_running(spawn, data_dir): data_dir.LOCKFILE.write_text( - InstanceInfo(pid=os.getpid(), uri="PYRO:pyrolabd@localhost:1").json() + InstanceInfo(pid=os.getpid(), uri="PYRO:pyrolabd@localhost:1").model_dump_json() ) result = runner.invoke(cli.app, ["up"]) assert result.exit_code == 1 @@ -778,7 +781,7 @@ def test_up_when_already_running(spawn, data_dir): def test_up_when_running_but_not_responding(spawn, data_dir, monkeypatch): data_dir.LOCKFILE.write_text( - InstanceInfo(pid=os.getpid(), uri="PYRO:pyrolabd@localhost:1").json() + InstanceInfo(pid=os.getpid(), uri="PYRO:pyrolabd@localhost:1").model_dump_json() ) monkeypatch.setattr(cli, "_daemon_responds", lambda uri: False) result = runner.invoke(cli.app, ["up"]) diff --git a/tests/test_configure.py b/tests/test_configure.py index 50dceb0..5c03ec6 100644 --- a/tests/test_configure.py +++ b/tests/test_configure.py @@ -455,7 +455,7 @@ def test_export_config(tmp_path, sample_config_file): def test_rename_entity_leaves_input_unchanged(sample_config_file): config = PyroLabConfiguration.from_file(sample_config_file) - before = config.copy(deep=True) + before = config.model_copy(deep=True) renamed, changes = rename_entity(config, "nameserver", "local", "lab") assert config == before assert "lab" in renamed.nameservers and "local" not in renamed.nameservers @@ -511,7 +511,7 @@ def test_misspelled_keys_are_rejected(yaml_text, field): with pytest.raises(ValidationError) as excinfo: PyroLabConfiguration.from_yaml(yaml_text) (line,) = describe_config_error(excinfo.value) - assert field in line and "extra fields not permitted" in line + assert field in line and "Extra inputs are not permitted" in line @pytest.mark.parametrize( @@ -576,3 +576,29 @@ def test_export_and_save_failure_keeps_existing_file( def test_update_config_missing_file_message(data_dir, tmp_path): with pytest.raises(FileNotFoundError, match="does not exist"): update_config(tmp_path / "missing.yaml") + + +############################################################################### +# pydantic 2 compatibility with configurations written for pydantic 1 +############################################################################### + + +def test_numbers_are_accepted_where_text_is_expected(): + # pydantic 1 coerced these; pydantic 2 rejects them unless told not to, + # and existing configs have e.g. an unquoted `version: 1.0`. + cfg = PyroLabConfiguration.from_yaml( + "version: 1.0\n" + "daemons: {d: {}}\n" + "services:\n" + " s: {module: m, classname: C, description: 42, daemon: d}\n" + ) + assert cfg.version == "1.0" + assert cfg.services["s"].description == "42" + + +def test_nameservers_know_their_names_however_created(sample_config_file): + loaded = PyroLabConfiguration.from_file(sample_config_file) + validated = PyroLabConfiguration.model_validate(loaded.model_dump()) + copied = loaded.model_copy(deep=True) + for cfg in (loaded, validated, copied): + assert cfg.nameservers["persistent"].name == "persistent" diff --git a/tests/test_pyrolabd.py b/tests/test_pyrolabd.py index 25881ca..4aeccd4 100644 --- a/tests/test_pyrolabd.py +++ b/tests/test_pyrolabd.py @@ -202,7 +202,7 @@ def test_ps_returns_plain_string(pld): def test_instance_info_round_trip(): ii = InstanceInfo(pid=1234, uri="PYRO:pyrolabd@localhost:5555") - assert InstanceInfo.parse_raw(ii.json()) == ii + assert InstanceInfo.model_validate_json(ii.model_dump_json()) == ii ############################################################################### diff --git a/uv.lock b/uv.lock index b8d0204..2cf60cd 100644 --- a/uv.lock +++ b/uv.lock @@ -38,6 +38,15 @@ wheels = [ { url = 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