From d80952aa5361d511553195999bb6a119bda5393c Mon Sep 17 00:00:00 2001 From: henrikjacobsenfys Date: Thu, 17 Sep 2026 14:55:40 +0200 Subject: [PATCH 1/3] Fix parameter units being silently changed to SI units --- CONTRIBUTING.md | 3 +- pixi.lock | 6422 +++++++++-------- .../fitting/minimizers/minimizer_bumps.py | 85 +- src/easyscience/fitting/sampler.py | 382 +- src/easyscience/variable/descriptor_array.py | 171 +- src/easyscience/variable/descriptor_number.py | 261 +- src/easyscience/variable/parameter.py | 125 +- src/easyscience/variable/units.py | 147 + .../test_integration_comprehensive.py | 2 + tests/unit/variable/test_descriptor_array.py | 22 +- tests/unit/variable/test_descriptor_number.py | 18 +- tests/unit/variable/test_parameter.py | 2 +- tests/unit/variable/test_units.py | 252 + 13 files changed, 4367 insertions(+), 3525 deletions(-) create mode 100644 src/easyscience/variable/units.py create mode 100644 tests/unit/variable/test_units.py diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 64104f8c..ca8a1bc1 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -42,7 +42,8 @@ Please make sure you follow the EasyScience organization-wide If you are not planning to contribute code, you may want to: - 🐞 Report a bug — see [Reporting Issues](#11-reporting-issues) -- 🛡 Report a security issue — see [Security Issues](#12-security-issues) +- 🛡 Report a security issue — see + [Security Issues](#12-security-issues) - 💬 Ask a question or start a discussion at [Project Discussions](https://github.com/easyscience/core/discussions) diff --git a/pixi.lock b/pixi.lock index eb033db0..96a470ca 100644 --- a/pixi.lock +++ b/pixi.lock @@ -27,51 +27,51 @@ environments: packages: p1: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-25.1.0-py314h5bd0f2a_2.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.8-hb03c661_0.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-2.1.0-py314h4a8dc5f_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-26.1.0-py314h89acca1_1.conda + - 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name: asteval - version: 1.0.9 - sha256: 60513ea5d608d27bdb0cf3785dc993a6c3adeaee45f1bded0953a09e904e461f - requires_dist: - - build ; extra == 'dev' - - twine ; extra == 'dev' - - sphinx ; extra == 'doc' - - pytest ; extra == 'test' - - pytest-cov ; extra == 'test' - - coverage ; extra == 'test' - - asteval[dev,doc,test] ; extra == 'all' - requires_python: '>=3.10' diff --git a/src/easyscience/fitting/minimizers/minimizer_bumps.py b/src/easyscience/fitting/minimizers/minimizer_bumps.py index 315d856c..500edce6 100644 --- a/src/easyscience/fitting/minimizers/minimizer_bumps.py +++ b/src/easyscience/fitting/minimizers/minimizer_bumps.py @@ -417,42 +417,45 @@ def mcmc_sample( weights : np.ndarray Flattened weight array. samples : int, default=10000 - Number of raw samples to draw across all chains, before thinning. - A guaranteed minimum, not an exact count: DREAM advances in - blocks of 10 generations (one generation = one draw per chain) - and stops at the first block boundary at or past ``samples``. + Number of raw samples to draw across all chains, before + thinning. A guaranteed minimum, not an exact count: DREAM + advances in blocks of 10 generations (one generation = one + draw per chain) and stops at the first block boundary at or + past ``samples``. burn : int, default=2000 Burn-in generations to discard. BUMPS counts ``burn`` in - generations while ``samples`` counts raw draws, so ``burn=500`` - discards ``500 * n_chains`` raw samples. + generations while ``samples`` counts raw draws, so + ``burn=500`` discards ``500 * n_chains`` raw samples. thin : int, default=10 - Thinning interval — only every ``thin``-th generation is stored. + Thinning interval — only every ``thin``-th generation is + stored. population : int | None, default=None - BUMPS DREAM population count per parameter (number of parallel - chains): BUMPS creates ``ceil(population * n_parameters)`` chains. + BUMPS DREAM population count per parameter (number of + parallel chains): BUMPS creates ``ceil(population * + n_parameters)`` chains. resume_state : MCMCDraw | None, default=None A BUMPS ``MCMCDraw`` state object from a previous - ``mcmc_sample()`` call (e.g. ``PosteriorResults.sampler_state``). - When provided, DREAM **continues** the saved chain instead of - starting cold. The population, parameter count, and parameter - names must match the current model — a ``ValueError`` is raised - otherwise. - - ``samples`` must be the **total** number of raw samples, not an - increment: to extend an existing chain of ``N`` raw samples by - ``M``, pass ``samples=N + M`` (DREAM keeps only the last - ``samples`` draws in its buffer). The `Sampler.extend` helper - computes this for you. - - ``burn`` is forced to 0 on resume: a previously-converged chain is - never re-burned. - - The ``population`` and ``initializer`` parameters - have **no effect** when ``resume_state`` is provided — they - are determined by the saved state. - - Resuming against *different* data is undefined behaviour (the - chain's likelihood changes underneath it). + ``mcmc_sample()`` call (e.g. + ``PosteriorResults.sampler_state``). When provided, DREAM + **continues** the saved chain instead of starting cold. The + population, parameter count, and parameter names must match + the current model — a ``ValueError`` is raised otherwise. + + ``samples`` must be the **total** number of raw samples, not + an increment: to extend an existing chain of ``N`` raw + samples by ``M``, pass ``samples=N + M`` (DREAM keeps only + the last ``samples`` draws in its buffer). The + ``Sampler.extend`` helper computes this for you. + + ``burn`` is forced to 0 on resume: a previously-converged + chain is never re-burned. + + The ``population`` and ``initializer`` parameters have **no + effect** when ``resume_state`` is provided — they are + determined by the saved state. + + Resuming against *different* data is undefined behaviour + (the chain's likelihood changes underneath it). sampler_kwargs : dict | None, default=None Additional keyword arguments forwarded to ``bumps.fitters.fit``. @@ -475,9 +478,9 @@ def mcmc_sample( ------ ValueError If the input shapes or weights are invalid, if - ``progress_callback`` is not callable, or if ``resume_state`` - is incompatible with the current model (parameter count, - names/order, or population mismatch). + ``progress_callback`` is not callable, or if + ``resume_state`` is incompatible with the current model + (parameter count, names/order, or population mismatch). FitError If DREAM sampling was aborted by the user (via ``abort_test``). @@ -608,28 +611,32 @@ def _validate_resume_state( population: int | None, burn: int, ) -> tuple[int, int]: - """Check that ``resume_state`` is compatible with ``problem`` and + """ + Check that ``resume_state`` is compatible with ``problem`` and resolve the population and burn values to use when resuming. Parameters ---------- problem : FitProblem - The freshly built BUMPS ``FitProblem`` for the current model. + The freshly built BUMPS ``FitProblem`` for the current + model. resume_state : MCMCDraw The saved chain state to resume from. population : int | None The caller-supplied population scale factor, or ``None``. burn : int - The caller-supplied burn-in, ignored (with a warning) on resume. + The caller-supplied burn-in, ignored (with a warning) on + resume. Returns ------- tuple[int, int] ``(population, burn)`` to pass to DREAM. The population is returned as a **negative** number, which BUMPS' - ``initpop.generate`` reads as an absolute chain count, exactly - reproducing the saved state's population. ``burn`` is always 0: - a previously converged chain is never re-burned. + ``initpop.generate`` reads as an absolute chain count, + exactly reproducing the saved state's population. ``burn`` + is always 0: a previously converged chain is never + re-burned. Raises ------ diff --git a/src/easyscience/fitting/sampler.py b/src/easyscience/fitting/sampler.py index d3915115..3917a5bc 100644 --- a/src/easyscience/fitting/sampler.py +++ b/src/easyscience/fitting/sampler.py @@ -1,6 +1,8 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -"""Bayesian MCMC sampling — the ``Sampler`` class and persistence helpers.""" +""" +Bayesian MCMC sampling — the ``Sampler`` class and persistence helpers. +""" from __future__ import annotations @@ -38,7 +40,9 @@ def _data_fingerprint( y_list: list, w_list: list, ) -> str | None: - """Return a SHA-256 hex digest of concatenated (x|y|weights), or None.""" + """ + Return a SHA-256 hex digest of concatenated (x|y|weights), or None. + """ try: h = hashlib.sha256() for arr in list(x_list) + list(y_list) + list(w_list): @@ -53,7 +57,8 @@ def _validate_dataset_arrays( data: np.ndarray | list | tuple, allow_none_entries: bool = False, ) -> None: - """Check that ``data`` (an array or list of arrays) holds numeric, + """ + Check that ``data`` (an array or list of arrays) holds numeric, at-least-1-D, non-empty arrays. Structural checks (array vs list, matching dataset counts) are in @@ -101,12 +106,13 @@ def _validate_dataset_arrays( def _copy_data(data): - """Copy an array (or list of arrays) and mark the copies read-only. + """ + Copy an array (or list of arrays) and mark the copies read-only. - The ``Sampler`` binds its data at construction; copying decouples the - bound data from the caller's arrays, and the read-only flag stops - in-place mutation of the copies, so the chain and the ``save()`` - fingerprint always describe the data actually sampled. + The ``Sampler`` binds its data at construction; copying decouples + the bound data from the caller's arrays, and the read-only flag + stops in-place mutation of the copies, so the chain and the + ``save()`` fingerprint always describe the data actually sampled. """ if data is None: return None @@ -118,10 +124,13 @@ def _copy_data(data): def _validate_chain_path(path: str | os.PathLike, skip: int = 0) -> str: - """Validate the persistence arguments shared by the save/load functions. + """ + Validate the persistence arguments shared by the save/load + functions. - Returns ``path`` coerced to ``str``. Raises ``TypeError`` if ``path`` is - not path-like and ``ValueError`` if ``skip`` is not a non-negative int. + Returns ``path`` coerced to ``str``. Raises ``TypeError`` if + ``path`` is not path-like and ``ValueError`` if ``skip`` is not a + non-negative int. """ if not isinstance(path, (str, os.PathLike)): raise TypeError(f'path must be a str or os.PathLike, got {type(path).__name__}.') @@ -131,14 +140,15 @@ def _validate_chain_path(path: str | os.PathLike, skip: int = 0) -> str: def _load_bumps_state(path: str, skip: int = 0) -> MCMCDraw: - """Read a BUMPS chain from disk, working around a BUMPS bug. + """ + Read a BUMPS chain from disk, working around a BUMPS bug. ``bumps.dream.state.load_state`` reads the saved buffers with - ``numpy.loadtxt``, which collapses a single-row file to a 1-D array. A - short chain stores a single CR-weight update row, so ``load_state``'s - subsequent ``stats[:, 0]`` indexing raises ``IndexError: too many indices - for array``. We coerce each buffer read back to 2-D before ``load_state`` - consumes it. + ``numpy.loadtxt``, which collapses a single-row file to a 1-D array. + A short chain stores a single CR-weight update row, so + ``load_state``'s subsequent ``stats[:, 0]`` indexing raises + ``IndexError: too many indices for array``. We coerce each buffer + read back to 2-D before ``load_state`` consumes it. Parameters ---------- @@ -170,28 +180,30 @@ def _loadtxt_2d(file, report: int = 0) -> np.ndarray: def load_chain(path: str | os.PathLike, skip: int = 0) -> tuple[MCMCDraw, list[str] | None, dict]: - """Reload a DREAM chain state saved by ``Sampler.save``. + """ + Reload a DREAM chain state saved by ``Sampler.save``. - This is the standalone reader: unlike ``Sampler.load_state`` it needs no - fitter, model or data, so a saved chain can be inspected or post-processed - on a machine that does not have the model. Parameter names are restored - from the sidecar when available (schema versions 1 and 2), falling back to - the state's labels with the minimizer prefix stripped. + This is the standalone reader: unlike ``Sampler.load_state`` it + needs no fitter, model or data, so a saved chain can be inspected or + post-processed on a machine that does not have the model. Parameter + names are restored from the sidecar when available (schema versions + 1 and 2), falling back to the state's labels with the minimizer + prefix stripped. Parameters ---------- path : str | os.PathLike File path prefix used when saving. skip : int, default=0 - Discard the first ``skip`` saved generations on load, forwarded to - ``bumps.dream.state.load_state``. + Discard the first ``skip`` saved generations on load, forwarded + to ``bumps.dream.state.load_state``. Returns ------- tuple[MCMCDraw, list[str] | None, dict] - The reloaded BUMPS chain state, the parameter names (or ``None`` if - neither sidecar nor labels yielded them), and the raw sidecar dict - (empty if absent/unreadable). + The reloaded BUMPS chain state, the parameter names (or ``None`` + if neither sidecar nor labels yielded them), and the raw sidecar + dict (empty if absent/unreadable). Raises ------ @@ -229,15 +241,18 @@ def load_chain(path: str | os.PathLike, skip: int = 0) -> tuple[MCMCDraw, list[s @dataclass class SamplingResults: - """Structured result of an MCMC sampling run (analogous to ``FitResults``). + """ + Structured result of an MCMC sampling run (analogous to + ``FitResults``). Attributes ---------- draws : np.ndarray - Posterior samples, shape ``(n_samples, n_params)``. For results from - ``Sampler.sample()``/``Sampler.extend()`` this is a *trimmed, - outlier-filtered* view of the chain, not the raw buffer, so it holds - fewer rows than ``samples / thin`` — see the notes on ``Sampler``. + Posterior samples, shape ``(n_samples, n_params)``. For results + from ``Sampler.sample()``/``Sampler.extend()`` this is a + *trimmed, outlier-filtered* view of the chain, not the raw + buffer, so it holds fewer rows than ``samples / thin`` — see the + notes on ``Sampler``. param_names : list[str] Parameter names (one per column of ``draws``). logp : np.ndarray @@ -252,8 +267,10 @@ class SamplingResults: state: MCMCDraw def to_legacy_dict(self) -> dict: - """Return the legacy dict shape produced by the deprecated - ``mcmc_sample()`` APIs.""" + """ + Return the legacy dict shape produced by the deprecated + ``mcmc_sample()`` APIs. + """ return { 'draws': self.draws, 'param_names': self.param_names, @@ -263,58 +280,64 @@ def to_legacy_dict(self) -> dict: class Sampler: - """Bayesian MCMC sampler for one dataset, backed by a Fitter's BUMPS minimizer. - - One ``Sampler`` instance represents one chain over one ``(x, y, weights)`` - dataset. The data is bound at construction; ``sample()`` and ``extend()`` - take no data arguments, so a chain can never be extended against different - data (undefined behaviour in BUMPS). The bound data is a defensive, - read-only copy of the caller's arrays, exposed via the ``x``, ``y`` and - ``weights`` properties — mutating the originals after construction has no - effect on the sampler, and there are deliberately no setters: to sample - different data, create a new ``Sampler``. - - Construct directly with a configured ``Fitter`` (or ``MultiFitter``) whose - minimizer has been switched to ``AvailableMinimizers.Bumps``. **Running a - fit first is not required** — the ``Fitter`` supplies the model and the - minimizer, not a fit result, and sampling from the initial parameter values - works fine. - - It is often worth fitting first anyway. DREAM seeds its whole starting - population inside a tiny ball around the parameters' *current* values - (BUMPS' default ``init='eps'``), so sampling from fitted values starts the - chain in the right region and shortens the burn-in needed to reach the - typical set. From a poor initial guess, expect to burn for longer. - - The sampler is BUMPS/DREAM-specific for now: the BUMPS check in ``_run()`` - is the seam where another backend would plug in. + """ + Bayesian MCMC sampler for one dataset, backed by a Fitter's BUMPS + minimizer. + + One ``Sampler`` instance represents one chain over one ``(x, y, + weights)`` dataset. The data is bound at construction; ``sample()`` + and ``extend()`` take no data arguments, so a chain can never be + extended against different data (undefined behaviour in BUMPS). The + bound data is a defensive, read-only copy of the caller's arrays, + exposed via the ``x``, ``y`` and ``weights`` properties — mutating + the originals after construction has no effect on the sampler, and + there are deliberately no setters: to sample different data, create + a new ``Sampler``. + + Construct directly with a configured ``Fitter`` (or ``MultiFitter``) + whose minimizer has been switched to ``AvailableMinimizers.Bumps``. + **Running a fit first is not required** — the ``Fitter`` supplies + the model and the minimizer, not a fit result, and sampling from the + initial parameter values works fine. + + It is often worth fitting first anyway. DREAM seeds its whole + starting population inside a tiny ball around the parameters' + *current* values (BUMPS' default ``init='eps'``), so sampling from + fitted values starts the chain in the right region and shortens the + burn-in needed to reach the typical set. From a poor initial guess, + expect to burn for longer. + + The sampler is BUMPS/DREAM-specific for now: the BUMPS check in + ``_run()`` is the seam where another backend would plug in. Parameters ---------- - fitter : Fitter - A configured ``Fitter`` (or ``MultiFitter``) whose minimizer has been - switched to ``AvailableMinimizers.Bumps``. + fitter : 'Fitter' + A configured ``Fitter`` (or ``MultiFitter``) whose minimizer has + been switched to ``AvailableMinimizers.Bumps``. x : np.ndarray | list[np.ndarray] - Independent variable array (or list of arrays for ``MultiFitter``). + Independent variable array (or list of arrays for + ``MultiFitter``). y : np.ndarray | list[np.ndarray] - Dependent variable array (or list of arrays for ``MultiFitter``). + Dependent variable array (or list of arrays for + ``MultiFitter``). weights : np.ndarray | list[np.ndarray | None] | None, default=None Weight array (or list of arrays for ``MultiFitter``). vectorized : bool, default=False When ``True``, each x array may be multi-dimensional (e.g. an ``(N, M, 2)`` grid for a 2D model) and is left as-is. sampler_kwargs : dict | None, default=None - Per-instance default keyword arguments forwarded to the BUMPS DREAM - sampler on every run, merged with (and overridden by) per-call - ``sampler_kwargs``. + Per-instance default keyword arguments forwarded to the BUMPS + DREAM sampler on every run, merged with (and overridden by) + per-call ``sampler_kwargs``. Raises ------ TypeError - If ``fitter`` is not Fitter-shaped (no ``minimizer``/``fit_function``), - if any dataset in ``x``/``y``/``weights`` is not a numeric array - (e.g. a string), or ``vectorized``/``sampler_kwargs`` have the wrong - type. + If ``fitter`` is not Fitter-shaped (no + ``minimizer``/``fit_function``), if any dataset in + ``x``/``y``/``weights`` is not a numeric array (e.g. a string), + or ``vectorized``/``sampler_kwargs`` have the wrong type. ValueError If ``x``, ``y`` and ``weights`` do not hold matching structures (all arrays, or lists of the same length), or any dataset is a @@ -322,42 +345,44 @@ class Sampler: Notes ----- - **The retained draws are a trimmed view, not the whole chain.** BUMPS' - DREAM sampler defaults to ``trim=True``: once sampling finishes it runs a - convergence-based burn-point detector over the chain and returns only the - portion after that point. ``state.draw()`` additionally drops chains - flagged as outliers. So ``results.draws`` is usually *smaller* than the - chain, and its length is not deterministic — the detector re-runs from - scratch on every ``sample()`` and ``extend()`` call and may place the burn - point differently each time. Read the count off the array; do not predict - it. - - Nor is the chain itself exactly ``samples / thin`` rows: ``samples`` is a - guaranteed minimum, not an exact count. DREAM advances in blocks of 10 - generations (one generation = one draw per chain) and only checks its - stopping condition between blocks, so the raw chain length is ``samples`` - rounded up to a multiple of ``10 * n_chains``. - - The trimming is only a *view* — nothing is dropped from the buffer. To - read the full untrimmed chain:: + **The retained draws are a trimmed view, not the whole chain.** + BUMPS' DREAM sampler defaults to ``trim=True``: once sampling + finishes it runs a convergence-based burn-point detector over the + chain and returns only the portion after that point. + ``state.draw()`` additionally drops chains flagged as outliers. So + ``results.draws`` is usually *smaller* than the chain, and its + length is not deterministic — the detector re-runs from scratch on + every ``sample()`` and ``extend()`` call and may place the burn + point differently each time. Read the count off the array; do not + predict it. + + Nor is the chain itself exactly ``samples / thin`` rows: ``samples`` + is a guaranteed minimum, not an exact count. DREAM advances in + blocks of 10 generations (one generation = one draw per chain) and + only checks its stopping condition between blocks, so the raw chain + length is ``samples`` rounded up to a multiple of ``10 * n_chains``. + + The trimming is only a *view* — nothing is dropped from the buffer. + To read the full untrimmed chain:: results = sampler.sample(samples=10000, burn=500, thin=2) full = results.state.draw(portion=1.0, outliers=True) full.points # (n_chain_rows, n_params) full.logp - To switch the automatic trimming off entirely, pass BUMPS' own ``trim`` - option straight through ``sampler_kwargs``; ``results.draws`` then holds - the whole chain:: + To switch the automatic trimming off entirely, pass BUMPS' own + ``trim`` option straight through ``sampler_kwargs``; + ``results.draws`` then holds the whole chain:: sampler = Sampler( fitter, x, y, weights=w, sampler_kwargs={'trim': False} ) - Note also that trimming does not survive a ``save()``/``load_state()`` - round-trip: BUMPS does not persist the trim point, so a reloaded chain - comes back untrimmed and ``load_state()`` reports *more* draws than the - ``sample()`` call that created it. The chain itself is identical. + Note also that trimming does not survive a + ``save()``/``load_state()`` round-trip: BUMPS does not persist the + trim point, so a reloaded chain comes back untrimmed and + ``load_state()`` reports *more* draws than the ``sample()`` call + that created it. The chain itself is identical. """ def __init__( @@ -435,7 +460,9 @@ def weights(self) -> np.ndarray | list[np.ndarray | None] | None: @property def state(self) -> MCMCDraw | None: - """Raw BUMPS MCMCDraw state (None before first sample/load_state).""" + """ + Raw BUMPS MCMCDraw state (None before first sample/load_state). + """ return self._state @property @@ -459,7 +486,9 @@ def logp(self) -> np.ndarray | None: return self._results.logp if self._results is not None else None def _fingerprint(self) -> str | None: - """SHA-256 fingerprint of the bound (x, y, weights) data, or None.""" + """ + SHA-256 fingerprint of the bound (x, y, weights) data, or None. + """ x_list = list(self._x) if isinstance(self._x, (list, tuple)) else [self._x] y_list = list(self._y) if isinstance(self._y, (list, tuple)) else [self._y] if self._weights is None: @@ -481,7 +510,8 @@ def _run( progress_callback: Callable[[dict], bool | None] | None, abort_test: Callable[[], bool] | None, ) -> SamplingResults: - """Shared sampling engine for ``sample()`` and ``extend()``. + """ + Shared sampling engine for ``sample()`` and ``extend()``. Argument validation for ``samples``/``burn``/``thin`` lives in ``Bumps.mcmc_sample`` (single source of truth). @@ -545,37 +575,43 @@ def sample( progress_callback: Callable[[dict], bool | None] | None = None, abort_test: Callable[[], bool] | None = None, ) -> SamplingResults: - """Run fresh Bayesian MCMC sampling on the bound data. + """ + Run fresh Bayesian MCMC sampling on the bound data. - Calling ``sample()`` on a sampler that already holds a chain starts a - **fresh** chain — the previous state and results are replaced. Use - ``extend()`` to continue an existing chain. + Calling ``sample()`` on a sampler that already holds a chain + starts a **fresh** chain — the previous state and results are + replaced. Use ``extend()`` to continue an existing chain. Parameters ---------- samples : int, default=10000 - Number of raw samples to draw across all chains, before thinning. - This is a guaranteed minimum, not an exact count: DREAM advances - in blocks of 10 generations (one generation = one draw per chain) - and stops at the first block boundary at or past ``samples``. + Number of raw samples to draw across all chains, before + thinning. This is a guaranteed minimum, not an exact count: + DREAM advances in blocks of 10 generations (one generation = + one draw per chain) and stops at the first block boundary at + or past ``samples``. burn : int, default=2000 - Burn-in generations to discard before collecting samples. Note - BUMPS counts ``burn`` in generations while ``samples`` counts raw - draws, so ``burn=500`` discards ``500 * n_chains`` raw samples. + Burn-in generations to discard before collecting samples. + Note BUMPS counts ``burn`` in generations while ``samples`` + counts raw draws, so ``burn=500`` discards ``500 * + n_chains`` raw samples. thin : int, default=10 - Thinning interval — only every ``thin``-th generation is kept, - which reduces autocorrelation between consecutive draws. + Thinning interval — only every ``thin``-th generation is + kept, which reduces autocorrelation between consecutive + draws. population : int | None, default=None - DREAM population **scale factor** (not an absolute chain count): - BUMPS creates ``ceil(population * n_parameters)`` parallel chains. + DREAM population **scale factor** (not an absolute chain + count): BUMPS creates ``ceil(population * n_parameters)`` + parallel chains. sampler_kwargs : dict | None, default=None Additional keyword arguments forwarded to the BUMPS DREAM sampler (merged over the instance defaults). progress_callback : Callable[[dict], bool | None] | None, default=None - Optional callback invoked at each DREAM generation. The payload - dict includes ``iteration`` and ``sampling: True``. + Optional callback invoked at each DREAM generation. The + payload dict includes ``iteration`` and ``sampling: True``. abort_test : Callable[[], bool] | None, default=None - Optional callable that returns ``True`` to abort sampling early. + Optional callable that returns ``True`` to abort sampling + early. Returns ------- @@ -584,14 +620,16 @@ def sample( Notes ----- - ``results.draws`` is a trimmed, outlier-filtered view of the chain, - so it is usually smaller than the chain and its length is not - predictable from ``samples``/``thin``. See the ``Sampler`` class notes - for how to read the full chain or switch trimming off. + ``results.draws`` is a trimmed, outlier-filtered view of the + chain, so it is usually smaller than the chain and its length is + not predictable from ``samples``/``thin``. See the ``Sampler`` + class notes for how to read the full chain or switch trimming + off. Exceptions propagate from the sampling engine: ``ValueError`` if - ``samples``, ``burn``, or ``thin`` are invalid, and ``RuntimeError`` - if the active minimizer is not a BUMPS instance. + ``samples``, ``burn``, or ``thin`` are invalid, and + ``RuntimeError`` if the active minimizer is not a BUMPS + instance. """ if self._state is not None: global_object.log.getLogger('fitting').warning( @@ -618,38 +656,43 @@ def extend( progress_callback: Callable[[dict], bool | None] | None = None, abort_test: Callable[[], bool] | None = None, ) -> SamplingResults: - """Continue the existing chain with additional samples. + """ + Continue the existing chain with additional samples. DREAM stores draws in a fixed-size ring buffer sized to its - ``samples`` parameter; this method does the ring-buffer arithmetic - for you (``samples = stored_generations * population + - additional_samples``) so no existing draws are dropped from the - buffer, regardless of the thinning interval. Runs with ``burn=0`` — - re-burning a converged chain is usually a mistake, and BUMPS forces - it to 0 on resume in any case. The DREAM population is recovered from - the saved state and cannot be changed on extend. + ``samples`` parameter; this method does the ring-buffer + arithmetic for you (``samples = stored_generations * population + + additional_samples``) so no existing draws are dropped from + the buffer, regardless of the thinning interval. Runs with + ``burn=0`` — re-burning a converged chain is usually a mistake, + and BUMPS forces it to 0 on resume in any case. The DREAM + population is recovered from the saved state and cannot be + changed on extend. Parameters ---------- additional_samples : int, default=5000 - Number of additional DREAM samples to draw, in the same units - as ``samples`` in ``sample()``. This grows the ring buffer by - exactly ``additional_samples``; how many of the new draws become - *visible* in ``results.draws`` depends on the thinning interval - and on BUMPS' automatic trimming (see Notes). + Number of additional DREAM samples to draw, in the same + units as ``samples`` in ``sample()``. This grows the ring + buffer by exactly ``additional_samples``; how many of the + new draws become *visible* in ``results.draws`` depends on + the thinning interval and on BUMPS' automatic trimming (see + Notes). thin : int, default=10 Thinning interval for the retained draws. total_samples : int | None, default=None - Advanced: total retained samples requested from the ring buffer, - **overriding** the ``additional_samples`` arithmetic. With - ``total_samples=N``, only the last N draws are retained. + Advanced: total retained samples requested from the ring + buffer, **overriding** the ``additional_samples`` + arithmetic. With ``total_samples=N``, only the last N draws + are retained. sampler_kwargs : dict | None, default=None Additional keyword arguments forwarded to the BUMPS DREAM sampler (merged over the instance defaults). progress_callback : Callable[[dict], bool | None] | None, default=None Optional callback invoked at each DREAM generation. abort_test : Callable[[], bool] | None, default=None - Optional callable that returns ``True`` to abort sampling early. + Optional callable that returns ``True`` to abort sampling + early. Returns ------- @@ -665,16 +708,17 @@ def extend( Notes ----- ``results.draws`` will **not** grow by exactly - ``additional_samples / thin``. Two things get in the way, neither of - them a re-applied burn-in: BUMPS re-runs its burn-point detector over - the whole extended chain and re-trims the returned view (so the - visible count can even shrink), and DREAM advances in blocks of 10 - generations, so the raw growth is ``additional_samples`` rounded up - to a multiple of ``10 * n_chains`` (i.e. at least - ``additional_samples / thin`` retained rows). To see the chain - itself, compare ``results.state.draw(portion=1.0, outliers=True)`` - before and after, or run with ``sampler_kwargs={'trim': False}``. See - the ``Sampler`` class notes. + ``additional_samples / thin``. Two things get in the way, + neither of them a re-applied burn-in: BUMPS re-runs its + burn-point detector over the whole extended chain and re-trims + the returned view (so the visible count can even shrink), and + DREAM advances in blocks of 10 generations, so the raw growth is + ``additional_samples`` rounded up to a multiple of ``10 * + n_chains`` (i.e. at least ``additional_samples / thin`` retained + rows). To see the chain itself, compare + ``results.state.draw(portion=1.0, outliers=True)`` before and + after, or run with ``sampler_kwargs={'trim': False}``. See the + ``Sampler`` class notes. """ if self._state is None: raise RuntimeError('No chain to extend. Call sample() or load_state() first.') @@ -698,14 +742,15 @@ def extend( ) def save(self, path: str | os.PathLike) -> None: - """Persist the chain state and metadata to disk. + """ + Persist the chain state and metadata to disk. Writes the BUMPS native files (``-chain.mc.gz``, ``-point.mc.gz`` and ``-stats.mc.gz``) plus a ``.params.json`` sidecar with the parameter names, the - easyscience version, and a fingerprint of the bound data (verified - with a warning on ``load_state()``). Use ``load_chain`` to read the - files back without a fitter. + easyscience version, and a fingerprint of the bound data + (verified with a warning on ``load_state()``). Use + ``load_chain`` to read the files back without a fitter. Parameters ---------- @@ -746,13 +791,14 @@ def save(self, path: str | os.PathLike) -> None: json.dump(sidecar, f, indent=2) def load_state(self, path: str | os.PathLike, skip: int = 0) -> SamplingResults: - """Load a previously saved chain into this sampler. + """ + Load a previously saved chain into this sampler. - The sampler must be constructed with the same fitter and data used to - create the chain — ``extend()`` then continues the saved chain. If the - sidecar carries a data fingerprint and it does not match this - sampler's bound data, a warning is logged (extending a chain against - different data is undefined behaviour). + The sampler must be constructed with the same fitter and data + used to create the chain — ``extend()`` then continues the saved + chain. If the sidecar carries a data fingerprint and it does not + match this sampler's bound data, a warning is logged (extending + a chain against different data is undefined behaviour). Populates ``state`` and ``results`` (draws, log-posterior and parameter names) from the saved chain, so summaries and @@ -763,8 +809,8 @@ def load_state(self, path: str | os.PathLike, skip: int = 0) -> SamplingResults: path : str | os.PathLike File path prefix used in ``save()``. skip : int, default=0 - Discard the first ``skip`` saved generations on load. Useful for - trimming additional burn-in without re-sampling. + Discard the first ``skip`` saved generations on load. Useful + for trimming additional burn-in without re-sampling. Returns ------- @@ -780,11 +826,11 @@ def load_state(self, path: str | os.PathLike, skip: int = 0) -> SamplingResults: Notes ----- - BUMPS does not persist its automatic trim point, so a reloaded chain - comes back **untrimmed**: this method reports more draws than the - ``sample()`` call that wrote the file, even though the chain is - identical. Use ``skip`` to discard leading generations explicitly. - See the ``Sampler`` class notes. + BUMPS does not persist its automatic trim point, so a reloaded + chain comes back **untrimmed**: this method reports more draws + than the ``sample()`` call that wrote the file, even though the + chain is identical. Use ``skip`` to discard leading generations + explicitly. See the ``Sampler`` class notes. """ # noqa: DOC502 -- raised in _validate_chain_path via load_chain state, param_names, sidecar = load_chain(path, skip=skip) diff --git a/src/easyscience/variable/descriptor_array.py b/src/easyscience/variable/descriptor_array.py index 35f1c022..34a55393 100644 --- a/src/easyscience/variable/descriptor_array.py +++ b/src/easyscience/variable/descriptor_array.py @@ -23,6 +23,9 @@ from .descriptor_base import DescriptorBase from .descriptor_number import DescriptorNumber +from .units import has_numeric_factor +from .units import normalisation_target +from .units import si_base_unit class DescriptorArray(DescriptorBase): @@ -97,6 +100,7 @@ def __init__( except Exception as message: raise UnitError(message) # TODO: handle 1xn and nx1 arrays + self._remember_unit(unit) super().__init__( name=name, @@ -107,12 +111,22 @@ def __init__( parent=parent, ) - # Call convert_unit during initialization to ensure that the unit has no numbers in it, and to ensure unit consistency. - if self.unit is not None: - self.convert_unit(self._base_unit()) + # Make sure no magnitude is left hiding inside the unit, e.g. that a unit of + # 'm/mm' becomes a dimensionless value scaled by 1000. This must not be recorded + # on the undo stack: it is part of building the object. + target_unit = normalisation_target( + self._array.unit, has_spelling=self._input_unit is not None + ) + if target_unit is not None: + self.convert_unit(target_unit, record_undo=False) + # The normalised unit is scipp's choice, not the user's, so there is no + # spelling to remember for it. + self._remember_unit(None) @classmethod - def from_scipp(cls, name: str, full_value: Variable, **kwargs: Any) -> DescriptorArray: + def from_scipp( + cls, name: str, full_value: Variable, sources: tuple = (), **kwargs: Any + ) -> DescriptorArray: """ Create a DescriptorArray from a scipp array. @@ -122,6 +136,10 @@ def from_scipp(cls, name: str, full_value: Variable, **kwargs: Any) -> Descripto Name of the descriptor. full_value : Variable Value of the descriptor as a scipp variable. + sources : tuple, default=() + Operands of the operation which produced ``full_value``, if + any. Used to display the result with the unit spelling its + operands were given. **kwargs : Any Additional parameters for the descriptor. @@ -140,7 +158,7 @@ def from_scipp(cls, name: str, full_value: Variable, **kwargs: Any) -> Descripto return cls( name=name, value=full_value.values, - unit=full_value.unit, + unit=cls._spelling_from_sources(full_value.unit, sources), variance=full_value.variances, dimensions=full_value.dims, **kwargs, @@ -266,11 +284,20 @@ def unit(self) -> str: """ Get the unit. + The unit is reported with the spelling it was given, rather than + with scipp's preferred name for it, so that an array created + with 'angstrom' does not report 'Å'. The remembered spelling is + only used while it still describes the array we hold; if the + array has since been converted or normalised, scipp's own name + is reported instead. + Returns ------- str Unit as a string. """ + if self._input_unit_parsed is not None and self._input_unit_parsed == self._array.unit: + return self._input_unit return str(self._array.unit) @unit.setter @@ -387,7 +414,7 @@ def error(self, error: Union[list, np.ndarray]) -> None: else: self._array.variances = None - def convert_unit(self, unit_str: str) -> None: + def convert_unit(self, unit_str: str, record_undo: bool = True) -> None: """ Convert the value from one unit system to another. @@ -395,6 +422,10 @@ def convert_unit(self, unit_str: str) -> None: ---------- unit_str : str New unit in string form. + record_undo : bool, default=True + Whether to push the conversion onto the undo stack. False + while constructing the object, where there is nothing to + undo back to. Raises ------ @@ -408,7 +439,7 @@ def convert_unit(self, unit_str: str) -> None: new_unit = sc.Unit(unit_str) # Save the current state for undo/redo - old_array = self._array + old_state = (self._array, self._input_unit, self._input_unit_parsed) # Perform the unit conversion try: @@ -416,19 +447,86 @@ def convert_unit(self, unit_str: str) -> None: except Exception as e: raise UnitError(f'Failed to convert unit: {e}') from e - # Define the setter function for the undo stack - def set_array(obj, scalar): - obj._array = scalar + self._array = new_array + self._remember_unit(unit_str) - # Push to undo stack - self._global_object.stack.push( - PropertyStack( - self, set_array, old_array, new_array, text=f'Convert unit to {unit_str}' + # Define the setter function for the undo stack + def set_unit_state(obj, state): + obj._array, obj._input_unit, obj._input_unit_parsed = state + + if record_undo: + self._global_object.stack.push( + PropertyStack( + self, + set_unit_state, + old_state, + (self._array, self._input_unit, self._input_unit_parsed), + text=f'Convert unit to {unit_str}', + ) ) - ) - # Update the array - self._array = new_array + @staticmethod + def _spelling_from_sources(unit: sc.Unit, sources: tuple) -> Union[str, sc.Unit]: + """ + Return an operand's spelling for ``unit``, if one of them has + the same unit. + + An operation such as an addition, or a multiplication by a plain + number, leaves the unit untouched, and the result should be + displayed the way its operands were rather than falling back to + scipp's name for it. Only an exactly equal unit is used, so a + result can never be relabelled as something it is not. + + Parameters + ---------- + unit : sc.Unit + Unit of the result. + sources : tuple + Operands of the operation. Anything which is not a + descriptor, such as a plain number, is ignored. + + Returns + ------- + Union[str, sc.Unit] + The operand's spelling, or ``unit`` unchanged if no operand + offers one. + """ + for source in sources: + parsed_unit = getattr(source, '_input_unit_parsed', None) + if parsed_unit is not None and parsed_unit == unit: + return source._input_unit + return unit + + def _remember_unit(self, unit: Union[str, sc.Unit, None]) -> None: + """ + Remember the spelling a unit was given with, for display + purposes. + + Nothing is remembered for a unit which did not arrive as a + string, or for a dimensionless one: reporting 'one' or '' + instead of 'dimensionless' would break the comparisons against + 'dimensionless' made throughout this class. + + Parameters + ---------- + unit : Union[str, sc.Unit, None] + Unit as it was supplied. + """ + self._input_unit = None + self._input_unit_parsed = None + if not isinstance(unit, str) or not unit.strip(): + return + if has_numeric_factor(unit.strip()): + # A spelling such as '10dm^2' is no better than what scipp would print. + return + try: + parsed_unit = sc.Unit(unit.strip()) + except Exception: + return + if parsed_unit == sc.units.dimensionless: + return + self._input_unit = unit.strip() + self._input_unit_parsed = parsed_unit def __copy__(self) -> DescriptorArray: """Return a copy of the current DescriptorArray.""" @@ -481,7 +579,7 @@ def as_dict(self, skip: Optional[List[str]] = None) -> Dict[str, Any]: """ raw_dict = super().as_dict(skip=skip) raw_dict['value'] = self._array.values - raw_dict['unit'] = str(self._array.unit) + raw_dict['unit'] = self.unit raw_dict['variance'] = self._array.variances raw_dict['dimensions'] = self._array.dims return raw_dict @@ -591,7 +689,9 @@ def _apply_operation( else: return NotImplemented - descriptor_array = DescriptorArray.from_scipp(name=self.name, full_value=new_full_value) + descriptor_array = DescriptorArray.from_scipp( + name=self.name, full_value=new_full_value, sources=(self, other) + ) descriptor_array.name = descriptor_array.unique_name return descriptor_array @@ -887,7 +987,9 @@ def __pow__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorA raise message from None if np.any(np.isnan(new_value.values)): raise ValueError('The result of the exponentiation is not a number') - descriptor_number = DescriptorArray.from_scipp(name=self.name, full_value=new_value) + descriptor_number = DescriptorArray.from_scipp( + name=self.name, full_value=new_value, sources=(self, other) + ) descriptor_number.name = descriptor_number.unique_name return descriptor_number @@ -903,7 +1005,9 @@ def __rpow__(self, other: numbers.Number): def __neg__(self) -> DescriptorArray: """Negate all values in the DescriptorArray.""" new_value = -self.full_value - descriptor_array = DescriptorArray.from_scipp(name=self.name, full_value=new_value) + descriptor_array = DescriptorArray.from_scipp( + name=self.name, full_value=new_value, sources=(self,) + ) descriptor_array.name = descriptor_array.unique_name return descriptor_array @@ -916,7 +1020,9 @@ def __abs__(self) -> DescriptorArray: DescriptorArray. """ new_value = abs(self.full_value) - descriptor_array = DescriptorArray.from_scipp(name=self.name, full_value=new_value) + descriptor_array = DescriptorArray.from_scipp( + name=self.name, full_value=new_value, sources=(self,) + ) descriptor_array.name = descriptor_array.unique_name return descriptor_array @@ -927,7 +1033,7 @@ def __getitem__(self, a) -> DescriptorArray: Defer slicing to scipp. """ descriptor = DescriptorArray.from_scipp( - name=self.name, full_value=self.full_value.__getitem__(a) + name=self.name, full_value=self.full_value.__getitem__(a), sources=(self,) ) descriptor.name = descriptor.unique_name return descriptor @@ -1027,7 +1133,7 @@ def trace( ) constructor = DescriptorArray.from_scipp - descriptor = constructor(name=self.name, full_value=trace) + descriptor = constructor(name=self.name, full_value=trace, sources=(self,)) descriptor.name = descriptor.unique_name return descriptor @@ -1057,7 +1163,7 @@ def sum( else: constructor = DescriptorArray.from_scipp - descriptor = constructor(name=self.name, full_value=new_full_value) + descriptor = constructor(name=self.name, full_value=new_full_value, sources=(self,)) descriptor.name = descriptor.unique_name return descriptor @@ -1084,18 +1190,3 @@ def sum( # # other = sc.array(dims=self._array.dims, values=other) # new_full_value = operation(self._array, other) # Let scipp handle operation for uncertainty propagation - - def _base_unit(self) -> str: - """ - Returns the base unit of the current array. - - For example, if the unit is ``100m``, returns ``m``. - """ - string = str(self._array.unit) - for i, letter in enumerate(string): - if letter == 'e': - if string[i : i + 2] not in ['e+', 'e-']: - return string[i:] - elif letter not in ['0', '1', '2', '3', '4', '5', '6', '7', '8', '9', '.', '+', '-']: - return string[i:] - return '' diff --git a/src/easyscience/variable/descriptor_number.py b/src/easyscience/variable/descriptor_number.py index 5bcbcb0d..465cd59b 100644 --- a/src/easyscience/variable/descriptor_number.py +++ b/src/easyscience/variable/descriptor_number.py @@ -21,6 +21,9 @@ from easyscience.global_object.undo_redo import property_stack from .descriptor_base import DescriptorBase +from .units import has_numeric_factor +from .units import normalisation_target +from .units import si_base_unit # Why is this a decorator? Because otherwise we would need a flag on the convert_unit method to avoid @@ -48,6 +51,24 @@ def wrapper(self, *args, **kwargs): return wrapper +def _set_unit_state(obj: Any, state: tuple) -> None: + """ + Restore a unit state on the undo stack. + + A module level function rather than a closure, so that the call + dispatches to the ``_restore_unit_state`` of whichever subclass owns + the object. + + Parameters + ---------- + obj : Any + Object to restore the state on. + state : tuple + State captured by ``_unit_state``. + """ + obj._restore_unit_state(state) + + class DescriptorNumber(DescriptorBase): """ A ``Descriptor`` for Number values with units. @@ -101,6 +122,7 @@ def __init__( self._scalar = sc.scalar(float(value), unit=unit, variance=variance) except Exception as message: raise UnitError(message) + self._remember_unit(unit) super().__init__( name=name, unique_name=unique_name, @@ -109,13 +131,23 @@ def __init__( display_name=display_name, parent=parent, ) - - # Call convert_unit during initialization to ensure that the unit has no numbers in it, and to ensure unit consistency. - if self.unit is not None: - self._convert_unit(self._base_unit()) + # Make sure no magnitude is left hiding inside the unit. This has to happen after + # super().__init__, so that subclasses which convert more than the scalar (such + # as Parameter, with its bounds) are fully constructed. It should not be recorded + # on the undo stack as it is part of building the object. + target_unit = normalisation_target( + self._scalar.unit, has_spelling=self._input_unit is not None + ) + if target_unit is not None: + self._convert_unit(target_unit, record_undo=False) + # The normalised unit is scipp's choice, not the user's, so there is no + # spelling to remember for it. + self._remember_unit(None) @classmethod - def from_scipp(cls, name: str, full_value: Variable, **kwargs: Any) -> DescriptorNumber: + def from_scipp( + cls, name: str, full_value: Variable, sources: tuple = (), **kwargs: Any + ) -> DescriptorNumber: """ Create a DescriptorNumber from a scipp constant. @@ -125,6 +157,10 @@ def from_scipp(cls, name: str, full_value: Variable, **kwargs: Any) -> Descripto Name of the descriptor. full_value : Variable Value of the descriptor as a scipp scalar. + sources : tuple, default=() + Operands of the operation which produced ``full_value``, if + any. Used to display the result with the unit spelling its + operands were given. **kwargs : Any Additional parameters for the descriptor. @@ -145,7 +181,7 @@ def from_scipp(cls, name: str, full_value: Variable, **kwargs: Any) -> Descripto return cls( name=name, value=full_value.value, - unit=full_value.unit, + unit=cls._spelling_from_sources(full_value.unit, sources), variance=full_value.variance, **kwargs, ) @@ -258,11 +294,19 @@ def unit(self) -> str: """ Get the unit. + The unit is reported with the spelling it was given, rather than + with scipp's preferred name for it. The remembered spelling is + only used while it still describes the scalar we hold; if the + scalar has since been converted or normalised, scipp's own name + is reported instead. + Returns ------- str Unit as a string. """ + if self._input_unit_parsed is not None and self._input_unit_parsed == self._scalar.unit: + return self._input_unit return str(self._scalar.unit) @unit.setter @@ -358,7 +402,7 @@ def error(self, value: float) -> None: # When we convert units internally, we dont want to notify observers as this can cause infinite recursion. # Therefore the convert_unit method is split into two methods, a private internal method and a public method. - def _convert_unit(self, unit_str: str) -> None: + def _convert_unit(self, unit_str: str, record_undo: bool = True) -> None: """ Convert the value from one unit system to another. @@ -366,6 +410,10 @@ def _convert_unit(self, unit_str: str) -> None: ---------- unit_str : str New unit in string form. + record_undo : bool, default=True + Whether to push the conversion onto the undo stack. False + while constructing the object, where there is nothing to + undo back to. Raises ------ @@ -379,27 +427,136 @@ def _convert_unit(self, unit_str: str) -> None: new_unit = sc.Unit(unit_str) # Save the current state for undo/redo - old_scalar = self._scalar + old_state = self._unit_state() # Perform the unit conversion try: - new_scalar = self._scalar.to(unit=new_unit) + self._apply_unit_conversion(new_unit) + except Exception: + self._restore_unit_state(old_state) + raise + self._remember_unit(unit_str) + + if record_undo: + self._global_object.stack.push( + PropertyStack( + self, + _set_unit_state, + old_state, + self._unit_state(), + text=f'Convert unit to {unit_str}', + ) + ) + + def _apply_unit_conversion(self, new_unit: sc.Unit) -> None: + """ + Convert everything that carries this object's unit to + ``new_unit``. + + Subclasses that hold more than the scalar in the unit, such as + ``Parameter`` with its bounds, extend this so that the whole + conversion is a single undoable step. + + Parameters + ---------- + new_unit : sc.Unit + Unit to convert to. + + Raises + ------ + UnitError + If the unit conversion fails. + """ + try: + self._scalar = self._scalar.to(unit=new_unit) except Exception as e: raise UnitError(f'Failed to convert unit: {e}') from e - # Define the setter function for the undo stack - def set_scalar(obj, scalar): - obj._scalar = scalar + @staticmethod + def _spelling_from_sources(unit: sc.Unit, sources: tuple) -> Union[str, sc.Unit]: + """ + Return an operand's spelling for ``unit``, if one of them has + the same unit. - # Push to undo stack - self._global_object.stack.push( - PropertyStack( - self, set_scalar, old_scalar, new_scalar, text=f'Convert unit to {unit_str}' - ) - ) + An operation such as an addition, or a multiplication by a plain + number, leaves the unit untouched, and the result should be + displayed the way its operands were rather than falling back to + scipp's name for it. Only an exactly equal unit is used, so a + result can never be relabelled as something it is not. + + Parameters + ---------- + unit : sc.Unit + Unit of the result. + sources : tuple + Operands of the operation. Anything which is not a + descriptor, such as a plain number, is ignored. + + Returns + ------- + Union[str, sc.Unit] + The operand's spelling, or ``unit`` unchanged if no operand + offers one. + """ + for source in sources: + parsed_unit = getattr(source, '_input_unit_parsed', None) + if parsed_unit is not None and parsed_unit == unit: + return source._input_unit + return unit + + def _unit_state(self) -> tuple: + """ + Capture everything a unit conversion changes, so that it can be + undone as one. + + Returns + ------- + tuple + Opaque state, to be passed back to ``_restore_unit_state``. + """ + return (self._scalar, self._input_unit, self._input_unit_parsed) + + def _restore_unit_state(self, state: tuple) -> None: + """ + Restore state captured by ``_unit_state``. - # Update the scalar - self._scalar = new_scalar + Parameters + ---------- + state : tuple + State to restore. + """ + self._scalar, self._input_unit, self._input_unit_parsed = state + + def _remember_unit(self, unit: str | sc.Unit | None) -> None: + """ + Remember the spelling a unit was given with, for display + purposes. + + Nothing is remembered for a unit which did not arrive as a + string, or for a dimensionless one: reporting 'one' or '' + instead of 'dimensionless' would break the comparisons against + 'dimensionless' made throughout this class. + + Parameters + ---------- + unit : str | sc.Unit | None + Unit as it was supplied. + """ + self._input_unit = None + self._input_unit_parsed = None + if not isinstance(unit, str) or not unit.strip(): + return + if has_numeric_factor(unit.strip()): + # A spelling such as '10dm^2' is no better than what scipp would print. + return + try: + parsed_unit = sc.Unit(unit.strip()) + except Exception: + return + if parsed_unit == sc.units.dimensionless: + return + self._input_unit = unit.strip() + self._input_unit_parsed = parsed_unit # When the user calls convert_unit, we want to notify observers of the change to propagate the change. @notify_observers @@ -434,7 +591,7 @@ def __repr__(self) -> str: string += f'{self._scalar.value:.4f}' if self.variance: string += f' \u00b1 {self.error:.4f}' - obj_unit = self._scalar.unit + obj_unit = self.unit if obj_unit == 'dimensionless': obj_unit = '' else: @@ -447,7 +604,7 @@ def __repr__(self) -> str: def as_dict(self, skip: Optional[List[str]] = None) -> Dict[str, Any]: raw_dict = super().as_dict(skip=skip) raw_dict['value'] = self._scalar.value - raw_dict['unit'] = str(self._scalar.unit) + raw_dict['unit'] = self.unit raw_dict['variance'] = self._scalar.variance if hasattr(self, '_DescriptorNumber__serializer_id'): raw_dict['__serializer_id'] = self.__serializer_id @@ -470,7 +627,9 @@ def __add__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorN other._convert_unit(original_unit) else: return NotImplemented - descriptor_number = DescriptorNumber.from_scipp(name=self.name, full_value=new_value) + descriptor_number = DescriptorNumber.from_scipp( + name=self.name, full_value=new_value, sources=(self, other) + ) descriptor_number.name = descriptor_number.unique_name return descriptor_number @@ -481,7 +640,9 @@ def __radd__(self, other: numbers.Number) -> DescriptorNumber: new_value = other + self.full_value else: return NotImplemented - descriptor_number = DescriptorNumber.from_scipp(name=self.name, full_value=new_value) + descriptor_number = DescriptorNumber.from_scipp( + name=self.name, full_value=new_value, sources=(self, other) + ) descriptor_number.name = descriptor_number.unique_name return descriptor_number @@ -502,7 +663,9 @@ def __sub__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorN other._convert_unit(original_unit) else: return NotImplemented - descriptor_number = DescriptorNumber.from_scipp(name=self.name, full_value=new_value) + descriptor_number = DescriptorNumber.from_scipp( + name=self.name, full_value=new_value, sources=(self, other) + ) descriptor_number.name = descriptor_number.unique_name return descriptor_number @@ -513,7 +676,9 @@ def __rsub__(self, other: numbers.Number) -> DescriptorNumber: new_value = other - self.full_value else: return NotImplemented - descriptor = DescriptorNumber.from_scipp(name=self.name, full_value=new_value) + descriptor = DescriptorNumber.from_scipp( + name=self.name, full_value=new_value, sources=(self, other) + ) descriptor.name = descriptor.unique_name return descriptor @@ -524,8 +689,9 @@ def __mul__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorN new_value = self.full_value * other.full_value else: return NotImplemented - descriptor_number = DescriptorNumber.from_scipp(name=self.name, full_value=new_value) - descriptor_number._convert_unit(descriptor_number._base_unit()) + descriptor_number = DescriptorNumber.from_scipp( + name=self.name, full_value=new_value, sources=(self, other) + ) descriptor_number.name = descriptor_number.unique_name return descriptor_number @@ -534,7 +700,9 @@ def __rmul__(self, other: numbers.Number) -> DescriptorNumber: new_value = other * self.full_value else: return NotImplemented - descriptor_number = DescriptorNumber.from_scipp(name=self.name, full_value=new_value) + descriptor_number = DescriptorNumber.from_scipp( + name=self.name, full_value=new_value, sources=(self, other) + ) descriptor_number.name = descriptor_number.unique_name return descriptor_number @@ -549,8 +717,9 @@ def __truediv__(self, other: Union[DescriptorNumber, numbers.Number]) -> Descrip new_value = self.full_value / other.full_value else: return NotImplemented - descriptor_number = DescriptorNumber.from_scipp(name=self.name, full_value=new_value) - descriptor_number._convert_unit(descriptor_number._base_unit()) + descriptor_number = DescriptorNumber.from_scipp( + name=self.name, full_value=new_value, sources=(self, other) + ) descriptor_number.name = descriptor_number.unique_name return descriptor_number @@ -561,7 +730,9 @@ def __rtruediv__(self, other: numbers.Number) -> DescriptorNumber: new_value = other / self.full_value else: return NotImplemented - descriptor_number = DescriptorNumber.from_scipp(name=self.name, full_value=new_value) + descriptor_number = DescriptorNumber.from_scipp( + name=self.name, full_value=new_value, sources=(self, other) + ) descriptor_number.name = descriptor_number.unique_name return descriptor_number @@ -582,7 +753,9 @@ def __pow__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorN raise message from None if np.isnan(new_value.value): raise ValueError('The result of the exponentiation is not a number') - descriptor_number = DescriptorNumber.from_scipp(name=self.name, full_value=new_value) + descriptor_number = DescriptorNumber.from_scipp( + name=self.name, full_value=new_value, sources=(self, other) + ) descriptor_number.name = descriptor_number.unique_name return descriptor_number @@ -599,26 +772,16 @@ def __rpow__(self, other: numbers.Number) -> numbers.Number: def __neg__(self) -> DescriptorNumber: new_value = -self.full_value - descriptor_number = DescriptorNumber.from_scipp(name=self.name, full_value=new_value) + descriptor_number = DescriptorNumber.from_scipp( + name=self.name, full_value=new_value, sources=(self,) + ) descriptor_number.name = descriptor_number.unique_name return descriptor_number def __abs__(self) -> DescriptorNumber: new_value = abs(self.full_value) - descriptor_number = DescriptorNumber.from_scipp(name=self.name, full_value=new_value) + descriptor_number = DescriptorNumber.from_scipp( + name=self.name, full_value=new_value, sources=(self,) + ) descriptor_number.name = descriptor_number.unique_name return descriptor_number - - def _base_unit(self) -> str: - """ - Extract the base unit from the unit string by removing numeric - components and scientific notation. - """ - string = str(self._scalar.unit) - for i, letter in enumerate(string): - if letter == 'e': - if string[i : i + 2] not in ['e+', 'e-']: - return string[i:] - elif letter not in ['0', '1', '2', '3', '4', '5', '6', '7', '8', '9', '.', '+', '-']: - return string[i:] - return '' diff --git a/src/easyscience/variable/parameter.py b/src/easyscience/variable/parameter.py index 3ec654f7..f22ef351 100644 --- a/src/easyscience/variable/parameter.py +++ b/src/easyscience/variable/parameter.py @@ -231,6 +231,9 @@ def _update(self) -> None: ) # noqa: E501 self._min.unit = temporary_parameter.unit self._max.unit = temporary_parameter.unit + # The scalar's unit was relabelled directly above, so the remembered + # spelling has to follow it. + self._remember_unit(temporary_parameter.unit) if self._desired_unit is not None: self._convert_unit(self._desired_unit) @@ -662,22 +665,44 @@ def error(self, value: float) -> None: 'This is a dependent parameter, its error cannot be set directly.' ) - def _convert_unit(self, unit_str: str) -> None: + def _apply_unit_conversion(self, new_unit: sc.Unit) -> None: """ - Perform unit conversion. - - The value, max and min can change on unit change. + Convert the value and the bounds to ``new_unit``. Parameters ---------- - unit_str : str - New unit. + new_unit : sc.Unit + Unit to convert to. """ - super()._convert_unit(unit_str=unit_str) - new_unit = sc.Unit(unit_str) # unit_str is tested in super method + super()._apply_unit_conversion(new_unit) self._min = self._min.to(unit=new_unit) self._max = self._max.to(unit=new_unit) + def _unit_state(self) -> tuple: + """ + Capture the bounds along with the base class' unit state, so + that undoing a unit conversion returns the value and the bounds + together. + + Returns + ------- + tuple + Opaque state, to be passed back to ``_restore_unit_state``. + """ + return (super()._unit_state(), self._min, self._max) + + def _restore_unit_state(self, state: tuple) -> None: + """ + Restore state captured by ``_unit_state``. + + Parameters + ---------- + state : tuple + State to restore. + """ + base_state, self._min, self._max = state + super()._restore_unit_state(base_state) + @notify_observers def convert_unit(self, unit_str: str) -> None: """ @@ -1067,7 +1092,11 @@ def __add__(self, other: Union[DescriptorNumber, Parameter, numbers.Number]) -> else: return NotImplemented parameter = Parameter.from_scipp( - name=self.name, full_value=new_full_value, min=min_value, max=max_value + name=self.name, + full_value=new_full_value, + min=min_value, + max=max_value, + sources=(self, other), ) parameter.name = parameter.unique_name return parameter @@ -1096,7 +1125,11 @@ def __radd__(self, other: Union[DescriptorNumber, numbers.Number]) -> Parameter: else: return NotImplemented parameter = Parameter.from_scipp( - name=self.name, full_value=new_full_value, min=min_value, max=max_value + name=self.name, + full_value=new_full_value, + min=min_value, + max=max_value, + sources=(self, other), ) parameter.name = parameter.unique_name return parameter @@ -1129,7 +1162,11 @@ def __sub__(self, other: Union[DescriptorNumber, Parameter, numbers.Number]) -> else: return NotImplemented parameter = Parameter.from_scipp( - name=self.name, full_value=new_full_value, min=min_value, max=max_value + name=self.name, + full_value=new_full_value, + min=min_value, + max=max_value, + sources=(self, other), ) parameter.name = parameter.unique_name return parameter @@ -1158,7 +1195,11 @@ def __rsub__(self, other: Union[DescriptorNumber, numbers.Number]) -> Parameter: else: return NotImplemented parameter = Parameter.from_scipp( - name=self.name, full_value=new_full_value, min=min_value, max=max_value + name=self.name, + full_value=new_full_value, + min=min_value, + max=max_value, + sources=(self, other), ) parameter.name = parameter.unique_name return parameter @@ -1168,7 +1209,7 @@ def __mul__(self, other: Union[DescriptorNumber, Parameter, numbers.Number]) -> new_full_value = self.full_value * other if other == 0: descriptor_number = DescriptorNumber.from_scipp( - name=self.name, full_value=new_full_value + name=self.name, full_value=new_full_value, sources=(self, other) ) descriptor_number.name = descriptor_number.unique_name return descriptor_number @@ -1181,7 +1222,7 @@ def __mul__(self, other: Union[DescriptorNumber, Parameter, numbers.Number]) -> other.value == 0 and type(other) is DescriptorNumber ): # Only return DescriptorNumber if other is strictly 0, i.e. not a parameter # noqa: E501 descriptor_number = DescriptorNumber.from_scipp( - name=self.name, full_value=new_full_value + name=self.name, full_value=new_full_value, sources=(self, other) ) descriptor_number.name = descriptor_number.unique_name return descriptor_number @@ -1206,9 +1247,12 @@ def __mul__(self, other: Union[DescriptorNumber, Parameter, numbers.Number]) -> min_value = min(combinations) max_value = max(combinations) parameter = Parameter.from_scipp( - name=self.name, full_value=new_full_value, min=min_value, max=max_value + name=self.name, + full_value=new_full_value, + min=min_value, + max=max_value, + sources=(self, other), ) - parameter._convert_unit(parameter._base_unit()) parameter.name = parameter.unique_name return parameter @@ -1217,7 +1261,7 @@ def __rmul__(self, other: Union[DescriptorNumber, numbers.Number]) -> Parameter: new_full_value = other * self.full_value if other == 0: descriptor_number = DescriptorNumber.from_scipp( - name=self.name, full_value=new_full_value + name=self.name, full_value=new_full_value, sources=(self, other) ) descriptor_number.name = descriptor_number.unique_name return descriptor_number @@ -1228,7 +1272,7 @@ def __rmul__(self, other: Union[DescriptorNumber, numbers.Number]) -> Parameter: new_full_value = other.full_value * self.full_value if other.value == 0: descriptor_number = DescriptorNumber.from_scipp( - name=self.name, full_value=new_full_value + name=self.name, full_value=new_full_value, sources=(self, other) ) descriptor_number.name = descriptor_number.unique_name return descriptor_number @@ -1238,9 +1282,12 @@ def __rmul__(self, other: Union[DescriptorNumber, numbers.Number]) -> Parameter: min_value = min(combinations) max_value = max(combinations) parameter = Parameter.from_scipp( - name=self.name, full_value=new_full_value, min=min_value, max=max_value + name=self.name, + full_value=new_full_value, + min=min_value, + max=max_value, + sources=(self, other), ) - parameter._convert_unit(parameter._base_unit()) parameter.name = parameter.unique_name return parameter @@ -1288,9 +1335,12 @@ def __truediv__(self, other: Union[DescriptorNumber, Parameter, numbers.Number]) min_value = min(combinations) max_value = max(combinations) parameter = Parameter.from_scipp( - name=self.name, full_value=new_full_value, min=min_value, max=max_value + name=self.name, + full_value=new_full_value, + min=min_value, + max=max_value, + sources=(self, other), ) - parameter._convert_unit(parameter._base_unit()) parameter.name = parameter.unique_name return parameter @@ -1303,7 +1353,7 @@ def __rtruediv__(self, other: Union[DescriptorNumber, numbers.Number]) -> Parame other_value = other if other_value == 0: descriptor_number = DescriptorNumber.from_scipp( - name=self.name, full_value=new_full_value + name=self.name, full_value=new_full_value, sources=(self, other) ) descriptor_number.name = descriptor_number.unique_name return descriptor_number @@ -1314,7 +1364,7 @@ def __rtruediv__(self, other: Union[DescriptorNumber, numbers.Number]) -> Parame other_value = other.value if other_value == 0: descriptor_number = DescriptorNumber.from_scipp( - name=self.name, full_value=new_full_value + name=self.name, full_value=new_full_value, sources=(self, other) ) descriptor_number.name = descriptor_number.unique_name return descriptor_number @@ -1337,9 +1387,12 @@ def __rtruediv__(self, other: Union[DescriptorNumber, numbers.Number]) -> Parame min_value = min(combinations) max_value = max(combinations) parameter = Parameter.from_scipp( - name=self.name, full_value=new_full_value, min=min_value, max=max_value + name=self.name, + full_value=new_full_value, + min=min_value, + max=max_value, + sources=(self, other), ) - parameter._convert_unit(parameter._base_unit()) parameter.name = parameter.unique_name return parameter @@ -1366,7 +1419,7 @@ def __pow__(self, other: Union[DescriptorNumber, numbers.Number]) -> Parameter: raise ValueError('The result of the exponentiation is not a number') if exponent == 0: descriptor_number = DescriptorNumber.from_scipp( - name=self.name, full_value=new_full_value + name=self.name, full_value=new_full_value, sources=(self, other) ) descriptor_number.name = descriptor_number.unique_name return descriptor_number @@ -1392,7 +1445,11 @@ def __pow__(self, other: Union[DescriptorNumber, numbers.Number]) -> Parameter: min_value = min(combinations) max_value = max(combinations) parameter = Parameter.from_scipp( - name=self.name, full_value=new_full_value, min=min_value, max=max_value + name=self.name, + full_value=new_full_value, + min=min_value, + max=max_value, + sources=(self, other), ) parameter.name = parameter.unique_name return parameter @@ -1402,7 +1459,11 @@ def __neg__(self) -> Parameter: min_value = -self.max max_value = -self.min parameter = Parameter.from_scipp( - name=self.name, full_value=new_full_value, min=min_value, max=max_value + name=self.name, + full_value=new_full_value, + min=min_value, + max=max_value, + sources=(self,), ) parameter.name = parameter.unique_name return parameter @@ -1415,7 +1476,11 @@ def __abs__(self) -> Parameter: min_value = min(combinations) max_value = max(combinations) parameter = Parameter.from_scipp( - name=self.name, full_value=new_full_value, min=min_value, max=max_value + name=self.name, + full_value=new_full_value, + min=min_value, + max=max_value, + sources=(self,), ) parameter.name = parameter.unique_name return parameter diff --git a/src/easyscience/variable/units.py b/src/easyscience/variable/units.py new file mode 100644 index 00000000..7b2eac5d --- /dev/null +++ b/src/easyscience/variable/units.py @@ -0,0 +1,147 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + +""" +Helpers for how units are stored and displayed. + +Scipp can display a unit in two ways that surprise a user, and they need +different remedies: + +1. It prints a **numeric factor** because it has no name for a scaled unit, so + ``m/mm`` becomes ``1000`` and ``dm*m`` becomes ``0.1m^2``. The magnitude is then + hiding inside the unit. This module fixes that, by folding the factor back into + the value. +2. It prints **a different name than the one that was written**, so ``angstrom`` + becomes ``Å`` and ``nm*m/s`` becomes ``nGy*s``. That is a display concern only, and + is handled by the descriptors, which remember the spelling a unit arrived as. See + ``DescriptorNumber.unit``. + +The descriptors' ``unit`` property is therefore a *display* string; +``_scalar.unit`` / ``_array.unit`` remains the source of truth for +meaning. The two never disagree about what the unit is, only about how +it is spelled. +""" + +from __future__ import annotations + +import re +from typing import Optional +from typing import Union + +import scipp as sc + +# Scipp writes a scaled unit it cannot name as a numeric factor followed by the +# dimensions, in any of the forms '1000', '0.1m^2', '2.57e-44*J^2' and '3.9e+43/J^2'. + +# ^: start of string +# \s*: optional whitespace +# (?P[0-9]+(?:\.[0-9]+)?(?:[eE][+-]?[0-9]+)?): a number, possibly with decimal point and exponent, captured as 'number' +# \s*: optional whitespace +# (?P[*/])?: an optional separator, either '*' or '/', captured as 'separator' +# \s*: optional whitespace +# (?P.*): the rest of the string, captured as 'rest' +_NUMERIC_FACTOR = re.compile( + r'^\s*(?P[0-9]+(?:\.[0-9]+)?(?:[eE][+-]?[0-9]+)?)\s*(?P[*/])?\s*(?P.*)$' +) + + +def has_numeric_factor(unit: Union[str, sc.Unit]) -> bool: + """ + Report whether a unit carries a numeric factor in the way it is + written. + + Applied to a ``sc.Unit`` this asks how scipp displays it; applied to + a string it asks how the user wrote it, which is how a spelling such + as '10dm^2' is rejected while 'dm*m' is accepted. + + Parameters + ---------- + unit : Union[str, sc.Unit] + Unit to inspect. + + Returns + ------- + bool + True if the unit is written with a leading multiplier. + """ + match = _NUMERIC_FACTOR.match(str(unit)) + if match is None: + return False + if match.group('rest') == '' and match.group('separator') is None: + # A pure number, such as '1000'. + return True + # The leading '1' of '1/meV' is a placeholder for the numerator, not a factor. + return float(match.group('number')) != 1.0 + + +def si_base_unit(unit: sc.Unit) -> sc.Unit: + """ + Return the unit with the same dimensions as ``unit`` but no + multiplier. + + The dimensions are read from ``sc.Unit.to_dict()``, which stores the + base units and powers, which is more robust than parsing the string. + + Parameters + ---------- + unit : sc.Unit + Unit to reduce. + + Returns + ------- + sc.Unit + The corresponding SI base unit, or dimensionless if the unit has + no dimensions. + """ + powers = unit.to_dict().get('powers', {}) + if not powers: + return sc.units.dimensionless + return sc.Unit('*'.join(f'{base}^{power}' for base, power in powers.items())) + + +def normalisation_target(unit: sc.Unit, has_spelling: bool = False) -> Optional[str]: + """ + Return the unit to convert to so that no magnitude is left inside + the unit. + + A unit which reduces to a pure number, such as 'm/mm', is always + folded away. + + Beyond that, only units with nothing better to display are + converted. If the user's own spelling is being kept + (``has_spelling``), then nothing numeric is on show and there is + nothing to fix, so a parameter created with '1/meV^2' keeps both its + spelling and its value, even though scipp would print it as + '3.9e+43/J^2'. + + Parameters + ---------- + unit : sc.Unit + Unit to inspect. + has_spelling : bool, default=False + Whether a clean spelling for this unit is being displayed in its + place. + + Returns + ------- + Optional[str] + The unit to convert to, or None if there is nothing to fix, or + if no safe target could be determined. + """ + if unit.to_dict().get('e_flag'): + # Offset units such as degC cannot be converted this way. + return None + if not unit.to_dict().get('powers'): + # A pure number, such as the 1000 that 'm/mm' reduces to. + return None if unit == sc.units.dimensionless else 'dimensionless' + if has_spelling or not has_numeric_factor(unit): + return None + try: + base_unit = si_base_unit(unit) + target = str(base_unit) + if sc.Unit(target) != base_unit: + # The target does not survive a round trip, so it is not safe to use. + return None + except Exception: + return None + return target diff --git a/tests/unit/global_object/test_integration_comprehensive.py b/tests/unit/global_object/test_integration_comprehensive.py index 61268954..a9ac4a17 100644 --- a/tests/unit/global_object/test_integration_comprehensive.py +++ b/tests/unit/global_object/test_integration_comprehensive.py @@ -422,6 +422,7 @@ def test_concurrent_access_simulation(self, clear_all): # Given global_obj = GlobalObject() results = [] + created = [] # The map holds only weak references, so keep the objects alive errors = [] def create_objects(thread_id, count=10): @@ -429,6 +430,7 @@ def create_objects(thread_id, count=10): try: for i in range(count): param = Parameter(name=f'thread_{thread_id}_param_{i}', value=float(i)) + created.append(param) results.append(param.unique_name) time.sleep(0.001) # Small delay to encourage race conditions except Exception as e: diff --git a/tests/unit/variable/test_descriptor_array.py b/tests/unit/variable/test_descriptor_array.py index 73bb0857..a7b7b4c2 100644 --- a/tests/unit/variable/test_descriptor_array.py +++ b/tests/unit/variable/test_descriptor_array.py @@ -226,19 +226,21 @@ def test_copy(self, descriptor: DescriptorArray): assert descriptor_copy._array.unit == descriptor._array.unit @pytest.mark.parametrize( - 'unit_string, expected', - [('1e+9', 'dimensionless'), ('1000', 'dimensionless'), ('10dm^2', 'm^2')], + 'unit_string, expected_unit, factor', + [ + ('1e+9', 'dimensionless', 1e9), + ('1000', 'dimensionless', 1000.0), + ('10dm^2', 'm^2', 0.1), + ], ids=['scientific_notation', 'numbers', 'unit_prefix'], ) - def test_base_unit(self, unit_string, expected): + def test_numeric_factor_is_folded_into_value(self, unit_string, expected_unit, factor): # When descriptor = DescriptorArray(name='name', value=[[1.0, 2.0], [3.0, 4.0]], unit=unit_string) - # Then - base_unit = descriptor._base_unit() - - # Expect - assert base_unit == expected + # Expect: the magnitude ends up in the values, never inside the unit + assert descriptor.unit == expected_unit + assert descriptor.value == pytest.approx(np.array([[1.0, 2.0], [3.0, 4.0]]) * factor) @pytest.mark.parametrize( 'test, expected, raises_warning', @@ -662,7 +664,7 @@ def test_reverse_subtraction_dimensionless( ( DescriptorNumber('test', 1, 'kg', 10), DescriptorArray( - 'test * name', [[1.0, 2.0], [3.0, 4.0]], 'kg*m', [[10.1, 40.2], [90.3, 160.4]] + 'test * name', [[1.0, 2.0], [3.0, 4.0]], 'm*kg', [[10.1, 40.2], [90.3, 160.4]] ), True, ), @@ -795,7 +797,7 @@ def test_multiplication_dimensionless( ( DescriptorNumber('test', 1, 'kg', 10), DescriptorArray( - 'test * name', [[1.0, 2.0], [3.0, 4.0]], 'kg*m', [[10.1, 40.2], [90.3, 160.4]] + 'test * name', [[1.0, 2.0], [3.0, 4.0]], 'm*kg', [[10.1, 40.2], [90.3, 160.4]] ), True, ), diff --git a/tests/unit/variable/test_descriptor_number.py b/tests/unit/variable/test_descriptor_number.py index 6abd3029..9bb64d6f 100644 --- a/tests/unit/variable/test_descriptor_number.py +++ b/tests/unit/variable/test_descriptor_number.py @@ -213,19 +213,21 @@ def test_copy(self, descriptor: DescriptorNumber): assert descriptor_copy._scalar.unit == descriptor._scalar.unit @pytest.mark.parametrize( - 'unit_string, expected', - [('1e+9', 'dimensionless'), ('1000', 'dimensionless'), ('10dm^2', 'm^2')], + 'unit_string, expected_unit, expected_value', + [ + ('1e+9', 'dimensionless', 1e9), + ('1000', 'dimensionless', 1000.0), + ('10dm^2', 'm^2', 0.1), + ], ids=['scientific_notation', 'numbers', 'unit_prefix'], ) - def test_base_unit(self, unit_string, expected): + def test_numeric_factor_is_folded_into_value(self, unit_string, expected_unit, expected_value): # When descriptor = DescriptorNumber(name='name', value=1, unit=unit_string) - # Then - base_unit = descriptor._base_unit() - - # Expect - assert base_unit == expected + # Expect: the magnitude ends up in the value, never inside the unit + assert descriptor.unit == expected_unit + assert descriptor.value == pytest.approx(expected_value) @pytest.mark.parametrize( 'test, expected', diff --git a/tests/unit/variable/test_parameter.py b/tests/unit/variable/test_parameter.py index 1ac05b45..95d6ee8d 100644 --- a/tests/unit/variable/test_parameter.py +++ b/tests/unit/variable/test_parameter.py @@ -1678,7 +1678,7 @@ def test_division_with_parameter_remaining_cases(self, first, second, expected): ( 2, Parameter('name / 2', 0.5, 'm', 0.0025, 0, 5), - Parameter('2 / name', 2, 'm**-1', 0.04, 0.2, np.inf), + Parameter('2 / name', 2, '1/m', 0.04, 0.2, np.inf), ), ], ids=['descriptor_number', 'number'], diff --git a/tests/unit/variable/test_units.py b/tests/unit/variable/test_units.py new file mode 100644 index 00000000..60bf754d --- /dev/null +++ b/tests/unit/variable/test_units.py @@ -0,0 +1,252 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + +import pytest +import scipp as sc +from scipp import UnitError + +from easyscience import DescriptorNumber +from easyscience import Parameter +from easyscience import global_object +from easyscience.variable.units import has_numeric_factor +from easyscience.variable.units import normalisation_target +from easyscience.variable.units import si_base_unit + + +class TestUnitHelpers: + @pytest.mark.parametrize( + 'unit_string, expected', + [ + ('m', False), + ('mm', False), + ('meV', False), + ('m/s', False), + ('counts', False), + ('1/m', False), + ('1/meV', False), + ('1/J**2', False), + ('mm*mm', False), + ('nm*m/s', False), + ('degC', False), + ('deg', False), + ('1000', True), + ('1e+9', True), + ('m/mm', True), + ('dm*m', True), + ('10dm^2', True), + ('meV*meV', True), + ('1/meV**2', True), + ], + ) + def test_has_numeric_factor(self, unit_string, expected): + assert has_numeric_factor(sc.Unit(unit_string)) is expected + + @pytest.mark.parametrize( + 'unit_string, expected', + [ + ('m', 'm'), + ('mm', 'm'), + ('dm*m', 'm^2'), + ('m/mm', 'dimensionless'), + ('1000', 'dimensionless'), + ('nm*m/s', 'm^2/s'), + ('meV', 'J'), + ('counts/s', 'counts/s'), + ], + ) + def test_si_base_unit(self, unit_string, expected): + assert str(si_base_unit(sc.Unit(unit_string))) == expected + + @pytest.mark.parametrize('unit_string', ['degC', 'deg', 'm', 'mm', 'counts']) + def test_normalisation_target_leaves_clean_units_alone(self, unit_string): + # Offset units such as degC must not be touched either: they cannot be + # converted to their base unit this way. + assert normalisation_target(sc.Unit(unit_string)) is None + + +class TestNumericFactorFolding: + @pytest.mark.parametrize( + 'unit_string, expected_unit, expected_value', + [ + ('1e+9', 'dimensionless', 1e9), + ('1000', 'dimensionless', 1000.0), + ('m/mm', 'dimensionless', 1000.0), + ('10dm^2', 'm^2', 0.1), + ], + ids=['scientific_notation', 'number', 'cancelling_prefixes', 'unit_prefix'], + ) + def test_construction_folds_the_factor(self, unit_string, expected_unit, expected_value): + descriptor = DescriptorNumber(name='name', value=1.0, unit=unit_string) + + assert descriptor.unit == expected_unit + assert descriptor.value == pytest.approx(expected_value) + + @pytest.mark.parametrize( + 'left, right, expected_unit, expected_value', + [ + ('m', 'mm', 'dimensionless', 1000.0), + ('m', 'm', 'dimensionless', 1.0), + ('m', 's', 'm/s', 1.0), + ], + ids=['cancelling_prefixes', 'identical', 'unrelated'], + ) + def test_division_folds_the_factor(self, left, right, expected_unit, expected_value): + result = DescriptorNumber('a', 1.0, left) / DescriptorNumber('b', 1.0, right) + + assert result.unit == expected_unit + assert result.value == pytest.approx(expected_value) + + @pytest.mark.parametrize( + 'left, right, expected_unit, expected_value', + [ + ('dm', 'm', 'm^2', 0.2), + ('mm', 'mm', 'mm^2', 2.0), + ('cm', 'm', 'dm^2', 2.0), + ], + ids=['scaled', 'already_named', 'already_named_prefix'], + ) + def test_multiplication_folds_only_when_needed( + self, left, right, expected_unit, expected_value + ): + # A unit scipp can name is left exactly as it names it; only a unit displayed + # with a numeric factor is converted. + result = DescriptorNumber('a', 2.0, left) * DescriptorNumber('b', 1.0, right) + + assert result.unit == expected_unit + assert result.value == pytest.approx(expected_value) + + def test_bounds_are_folded_with_the_value(self): + parameter = Parameter(name='name', value=1.0, min=0.0, max=10.0, unit='m/mm') + + assert parameter.unit == 'dimensionless' + assert parameter.value == pytest.approx(1000.0) + assert parameter.min == pytest.approx(0.0) + assert parameter.max == pytest.approx(10000.0) + + def test_invalid_unit_still_raises(self): + with pytest.raises(UnitError): + DescriptorNumber(name='name', value=1.0, unit='not_a_unit') + + +class TestUnitSpelling: + @pytest.mark.parametrize( + 'unit_string', + ['angstrom', 'nm*m/s', '1/meV^2', 'dm*m', 'Hz'], + ) + def test_unit_is_reported_as_written(self, unit_string): + descriptor = DescriptorNumber(name='name', value=1.0, unit=unit_string) + + assert descriptor.unit == unit_string + # The spelling is a display concern only; the meaning is unchanged. + assert descriptor._scalar.unit == sc.Unit(unit_string) + + def test_spellings_are_per_object(self): + # The property a global alias table could not provide: scipp permits only one + # alias per unit, so one of these two would have had to report the other's + # spelling. + angstrom = DescriptorNumber(name='a', value=1.0, unit='angstrom') + symbol = DescriptorNumber(name='b', value=1.0, unit='Å') + + assert angstrom.unit == 'angstrom' + assert symbol.unit == 'Å' + + @pytest.mark.parametrize('unit_string', ['', 'dimensionless', 'one']) + def test_dimensionless_is_always_reported_as_dimensionless(self, unit_string): + # Reporting '' or 'one' would break the comparisons against 'dimensionless' + # made throughout DescriptorNumber. + descriptor = DescriptorNumber(name='name', value=1.0, unit=unit_string) + + assert descriptor.unit == 'dimensionless' + assert (descriptor + 1.0).value == pytest.approx(2.0) + + def test_derived_units_use_scipps_spelling(self): + result = DescriptorNumber('a', 1.0, 'm') * DescriptorNumber('b', 1.0, 'm') + + assert result.unit == 'm^2' + + @pytest.mark.parametrize('unit_string', ['angstrom', '1/meV^2', 'dm*m']) + def test_unit_preserving_operations_keep_the_spelling(self, unit_string): + # An operation which leaves the unit alone should leave its spelling alone too, + # and must not disturb the value on the way. + a = DescriptorNumber('a', 2.0, unit_string) + b = DescriptorNumber('b', 3.0, unit_string) + + assert (a + b).unit == unit_string + assert (a + b).value == pytest.approx(5.0, rel=0, abs=0) + assert (a * 2).unit == unit_string + assert (a * 2).value == pytest.approx(4.0, rel=0, abs=0) + assert (-a).unit == unit_string + assert abs(a).unit == unit_string + + def test_a_new_unit_is_never_relabelled(self): + # Only an exactly equal unit is inherited from an operand. + a = DescriptorNumber('a', 2.0, 'dm') + b = DescriptorNumber('b', 1.0, 'm') + + assert (a * b).unit == 'm^2' + assert (a * b).value == pytest.approx(0.2) + + def test_bounds_follow_an_inherited_spelling(self): + parameter = Parameter(name='p', value=1.0, min=0.0, max=10.0, unit='angstrom') + + result = parameter * 2 + + assert result.unit == 'angstrom' + assert result.max == pytest.approx(20.0) + + def test_spelling_falls_back_when_the_scalar_changes_underneath(self): + descriptor = DescriptorNumber(name='name', value=1.0, unit='angstrom') + assert descriptor.unit == 'angstrom' + + # Bypass convert_unit entirely, as Parameter._update does. + descriptor._scalar = descriptor._scalar.to(unit='m') + + assert descriptor.unit == 'm' + + def test_convert_unit_adopts_the_new_spelling(self): + descriptor = DescriptorNumber(name='name', value=1.0, unit='m') + + descriptor.convert_unit('angstrom') + + assert descriptor.unit == 'angstrom' + assert descriptor.value == pytest.approx(1e10) + + def test_serialisation_round_trip_preserves_the_spelling(self): + descriptor = DescriptorNumber(name='name', value=1.0, unit='nm*m/s') + + restored = DescriptorNumber.from_dict(descriptor.as_dict(skip=['unique_name'])) + + assert restored.unit == 'nm*m/s' + assert restored._scalar.unit == descriptor._scalar.unit + + +class TestUnitUndoRedo: + def test_undo_restores_value_bounds_and_spelling_together(self): + global_object.stack.enabled = True + try: + parameter = Parameter(name='name', value=1.0, min=0.0, max=10.0, unit='m') + parameter.convert_unit('mm') + assert parameter.unit == 'mm' + assert parameter.value == pytest.approx(1000.0) + assert parameter.max == pytest.approx(10000.0) + + global_object.stack.undo() + + # One undo, and everything the conversion touched comes back with it. + assert parameter.unit == 'm' + assert parameter.value == pytest.approx(1.0) + assert parameter.min == pytest.approx(0.0) + assert parameter.max == pytest.approx(10.0) + finally: + global_object.stack.enabled = False + + def test_construction_does_not_record_an_undo_entry(self): + global_object.stack.enabled = True + try: + global_object.stack.clear() + # A unit needing normalisation must not leave anything to undo. + DescriptorNumber(name='name', value=1.0, unit='m/mm') + + assert global_object.stack.canUndo() is False + finally: + global_object.stack.enabled = False From b8ad51e7a0e2005622c6cdcf43c03e75b407aed5 Mon Sep 17 00:00:00 2001 From: henrikjacobsenfys Date: Thu, 17 Sep 2026 15:08:46 +0200 Subject: [PATCH 2/3] fix linting error --- CONTRIBUTING.md | 3 +- src/easyscience/variable/descriptor_number.py | 153 ++++++++++-------- 2 files changed, 87 insertions(+), 69 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index ca8a1bc1..64104f8c 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -42,8 +42,7 @@ Please make sure you follow the EasyScience organization-wide If you are not planning to contribute code, you may want to: - 🐞 Report a bug — see [Reporting Issues](#11-reporting-issues) -- 🛡 Report a security issue — see - [Security Issues](#12-security-issues) +- 🛡 Report a security issue — see [Security Issues](#12-security-issues) - 💬 Ask a question or start a discussion at [Project Discussions](https://github.com/easyscience/core/discussions) diff --git a/src/easyscience/variable/descriptor_number.py b/src/easyscience/variable/descriptor_number.py index 465cd59b..c2122f0a 100644 --- a/src/easyscience/variable/descriptor_number.py +++ b/src/easyscience/variable/descriptor_number.py @@ -80,7 +80,7 @@ def __init__( self, name: str, value: numbers.Number, - unit: Optional[Union[str, sc.Unit]] = '', + unit: Optional[Union[str, sc.Unit]] = "", variance: Optional[numbers.Number] = None, unique_name: Optional[str] = None, description: Optional[str] = None, @@ -103,20 +103,20 @@ def __init__( self._observers: List[DescriptorNumber] = [] # Extract serializer_id if provided during deserialization - if '__serializer_id' in kwargs: - self.__serializer_id = kwargs.pop('__serializer_id') + if "__serializer_id" in kwargs: + self.__serializer_id = kwargs.pop("__serializer_id") if not isinstance(value, numbers.Number) or isinstance(value, bool): - raise TypeError(f'{value=} must be a number') + raise TypeError(f"{value=} must be a number") if variance is not None: if not isinstance(variance, numbers.Number) or isinstance(variance, bool): - raise TypeError(f'{variance=} must be a number or None') + raise TypeError(f"{variance=} must be a number or None") if variance < 0: - raise ValueError(f'{variance=} must be positive') + raise ValueError(f"{variance=} must be positive") variance = float(variance) if not isinstance(unit, sc.Unit) and not isinstance(unit, str): raise TypeError( - f'{unit=} must be a scipp unit or a string representing a valid scipp unit' + f"{unit=} must be a scipp unit or a string representing a valid scipp unit" ) try: self._scalar = sc.scalar(float(value), unit=unit, variance=variance) @@ -175,9 +175,9 @@ def from_scipp( If ``full_value`` is not a scalar scipp ``Variable``. """ if not isinstance(full_value, Variable): - raise TypeError(f'{full_value=} must be a scipp scalar') + raise TypeError(f"{full_value=} must be a scipp scalar") if len(full_value.dims) != 0: - raise TypeError(f'{full_value=} must be a scipp scalar') + raise TypeError(f"{full_value=} must be a scipp scalar") return cls( name=name, value=full_value.value, @@ -189,7 +189,7 @@ def from_scipp( def _attach_observer(self, observer: DescriptorNumber) -> None: """Attach an observer to the descriptor.""" self._observers.append(observer) - if not hasattr(self, '_DescriptorNumber__serializer_id'): + if not hasattr(self, "_DescriptorNumber__serializer_id"): self.__serializer_id = str(uuid.uuid4()) def _detach_observer(self, observer: DescriptorNumber) -> None: @@ -221,9 +221,9 @@ def _validate_dependencies(self, origin: Optional[str] = None) -> None: """ if origin == self.unique_name: raise RuntimeError( - '\n Cyclic dependency detected!\n' - + f'An update of {self.unique_name} leads to it updating itself.\n' - + 'Please check your dependencies.' + "\n Cyclic dependency detected!\n" + + f"An update of {self.unique_name} leads to it updating itself.\n" + + "Please check your dependencies." ) if origin is None: origin = self.unique_name @@ -247,7 +247,7 @@ def full_value(self) -> Variable: @full_value.setter def full_value(self, full_value: Variable) -> None: raise AttributeError( - f'Full_value is read-only. Change the value and variance seperately. Or create a new {self.__class__.__name__}.' + f"Full_value is read-only. Change the value and variance seperately. Or create a new {self.__class__.__name__}." ) @property @@ -286,7 +286,7 @@ def value(self, value: numbers.Number) -> None: If ``value`` is not a number. """ if not isinstance(value, numbers.Number) or isinstance(value, bool): - raise TypeError(f'{value=} must be a number') + raise TypeError(f"{value=} must be a number") self._scalar.value = float(value) @property @@ -305,7 +305,10 @@ def unit(self) -> str: str Unit as a string. """ - if self._input_unit_parsed is not None and self._input_unit_parsed == self._scalar.unit: + if ( + self._input_unit_parsed is not None + and self._input_unit_parsed == self._scalar.unit + ): return self._input_unit return str(self._scalar.unit) @@ -313,8 +316,8 @@ def unit(self) -> str: def unit(self, unit_str: str) -> None: raise AttributeError( ( - f'Unit is read-only. Use convert_unit to change the unit between allowed types ' - f'or create a new {self.__class__.__name__} with the desired unit.' + f"Unit is read-only. Use convert_unit to change the unit between allowed types " + f"or create a new {self.__class__.__name__} with the desired unit." ) ) # noqa: E501 @@ -351,9 +354,9 @@ def variance(self, variance_float: float) -> None: """ if variance_float is not None: if not isinstance(variance_float, numbers.Number): - raise TypeError(f'{variance_float=} must be a number or None') + raise TypeError(f"{variance_float=} must be a number or None") if variance_float < 0: - raise ValueError(f'{variance_float=} must be positive') + raise ValueError(f"{variance_float=} must be positive") variance_float = float(variance_float) self._scalar.variance = variance_float @@ -392,9 +395,9 @@ def error(self, value: float) -> None: """ if value is not None: if not isinstance(value, numbers.Number): - raise TypeError(f'{value=} must be a number or None') + raise TypeError(f"{value=} must be a number or None") if value < 0: - raise ValueError(f'{value=} must be positive') + raise ValueError(f"{value=} must be positive") value = float(value) self._scalar.variance = value**2 else: @@ -421,9 +424,11 @@ def _convert_unit(self, unit_str: str, record_undo: bool = True) -> None: If ``unit_str`` is not a string. UnitError If the unit conversion fails. - """ + """ # noqa: DOC503. UnitError re-raised after restoring the unit state if not isinstance(unit_str, str): - raise TypeError(f'{unit_str=} must be a string representing a valid scipp unit') + raise TypeError( + f"{unit_str=} must be a string representing a valid scipp unit" + ) new_unit = sc.Unit(unit_str) # Save the current state for undo/redo @@ -444,7 +449,7 @@ def _convert_unit(self, unit_str: str, record_undo: bool = True) -> None: _set_unit_state, old_state, self._unit_state(), - text=f'Convert unit to {unit_str}', + text=f"Convert unit to {unit_str}", ) ) @@ -470,7 +475,7 @@ def _apply_unit_conversion(self, new_unit: sc.Unit) -> None: try: self._scalar = self._scalar.to(unit=new_unit) except Exception as e: - raise UnitError(f'Failed to convert unit: {e}') from e + raise UnitError(f"Failed to convert unit: {e}") from e @staticmethod def _spelling_from_sources(unit: sc.Unit, sources: tuple) -> Union[str, sc.Unit]: @@ -499,7 +504,7 @@ def _spelling_from_sources(unit: sc.Unit, sources: tuple) -> Union[str, sc.Unit] offers one. """ for source in sources: - parsed_unit = getattr(source, '_input_unit_parsed', None) + parsed_unit = getattr(source, "_input_unit_parsed", None) if parsed_unit is not None and parsed_unit == unit: return source._input_unit return unit @@ -577,43 +582,45 @@ def __copy__(self) -> DescriptorNumber: def __repr__(self) -> str: """Return printable representation.""" - string = '<' - string += self.__class__.__name__ + ' ' + string = "<" + string += self.__class__.__name__ + " " string += f"'{self._name}': " if np.abs(self._scalar.value) > 1e4 or ( np.abs(self._scalar.value) < 1e-4 and self._scalar.value != 0 ): # Use scientific notation for large or small values - string += f'{self._scalar.value:.3e}' + string += f"{self._scalar.value:.3e}" if self.variance: - string += f' \u00b1 {self.error:.3e}' + string += f" \u00b1 {self.error:.3e}" else: - string += f'{self._scalar.value:.4f}' + string += f"{self._scalar.value:.4f}" if self.variance: - string += f' \u00b1 {self.error:.4f}' + string += f" \u00b1 {self.error:.4f}" obj_unit = self.unit - if obj_unit == 'dimensionless': - obj_unit = '' + if obj_unit == "dimensionless": + obj_unit = "" else: - obj_unit = f' {obj_unit}' + obj_unit = f" {obj_unit}" string += obj_unit - string += '>' + string += ">" return string # return f"<{class_name} '{obj_name}': {obj_value:0.04f}{obj_unit}>" def as_dict(self, skip: Optional[List[str]] = None) -> Dict[str, Any]: raw_dict = super().as_dict(skip=skip) - raw_dict['value'] = self._scalar.value - raw_dict['unit'] = self.unit - raw_dict['variance'] = self._scalar.variance - if hasattr(self, '_DescriptorNumber__serializer_id'): - raw_dict['__serializer_id'] = self.__serializer_id + raw_dict["value"] = self._scalar.value + raw_dict["unit"] = self.unit + raw_dict["variance"] = self._scalar.variance + if hasattr(self, "_DescriptorNumber__serializer_id"): + raw_dict["__serializer_id"] = self.__serializer_id return raw_dict - def __add__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorNumber: + def __add__( + self, other: Union[DescriptorNumber, numbers.Number] + ) -> DescriptorNumber: if isinstance(other, numbers.Number): - if self.unit != 'dimensionless': - raise UnitError('Numbers can only be added to dimensionless values') + if self.unit != "dimensionless": + raise UnitError("Numbers can only be added to dimensionless values") new_value = self.full_value + other elif type(other) is DescriptorNumber: original_unit = other.unit @@ -621,7 +628,7 @@ def __add__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorN other._convert_unit(self.unit) except UnitError: raise UnitError( - f'Values with units {self.unit} and {other.unit} cannot be added' + f"Values with units {self.unit} and {other.unit} cannot be added" ) from None new_value = self.full_value + other.full_value other._convert_unit(original_unit) @@ -635,8 +642,8 @@ def __add__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorN def __radd__(self, other: numbers.Number) -> DescriptorNumber: if isinstance(other, numbers.Number): - if self.unit != 'dimensionless': - raise UnitError('Numbers can only be added to dimensionless values') + if self.unit != "dimensionless": + raise UnitError("Numbers can only be added to dimensionless values") new_value = other + self.full_value else: return NotImplemented @@ -646,10 +653,14 @@ def __radd__(self, other: numbers.Number) -> DescriptorNumber: descriptor_number.name = descriptor_number.unique_name return descriptor_number - def __sub__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorNumber: + def __sub__( + self, other: Union[DescriptorNumber, numbers.Number] + ) -> DescriptorNumber: if isinstance(other, numbers.Number): - if self.unit != 'dimensionless': - raise UnitError('Numbers can only be subtracted from dimensionless values') + if self.unit != "dimensionless": + raise UnitError( + "Numbers can only be subtracted from dimensionless values" + ) new_value = self.full_value - other elif type(other) is DescriptorNumber: original_unit = other.unit @@ -657,7 +668,7 @@ def __sub__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorN other._convert_unit(self.unit) except UnitError: raise UnitError( - f'Values with units {self.unit} and {other.unit} cannot be subtracted' + f"Values with units {self.unit} and {other.unit} cannot be subtracted" ) from None new_value = self.full_value - other.full_value other._convert_unit(original_unit) @@ -671,8 +682,10 @@ def __sub__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorN def __rsub__(self, other: numbers.Number) -> DescriptorNumber: if isinstance(other, numbers.Number): - if self.unit != 'dimensionless': - raise UnitError('Numbers can only be subtracted from dimensionless values') + if self.unit != "dimensionless": + raise UnitError( + "Numbers can only be subtracted from dimensionless values" + ) new_value = other - self.full_value else: return NotImplemented @@ -682,7 +695,9 @@ def __rsub__(self, other: numbers.Number) -> DescriptorNumber: descriptor.name = descriptor.unique_name return descriptor - def __mul__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorNumber: + def __mul__( + self, other: Union[DescriptorNumber, numbers.Number] + ) -> DescriptorNumber: if isinstance(other, numbers.Number): new_value = self.full_value * other elif type(other) is DescriptorNumber: @@ -706,14 +721,16 @@ def __rmul__(self, other: numbers.Number) -> DescriptorNumber: descriptor_number.name = descriptor_number.unique_name return descriptor_number - def __truediv__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorNumber: + def __truediv__( + self, other: Union[DescriptorNumber, numbers.Number] + ) -> DescriptorNumber: if isinstance(other, numbers.Number): if other == 0: - raise ZeroDivisionError('Cannot divide by zero') + raise ZeroDivisionError("Cannot divide by zero") new_value = self.full_value / other elif type(other) is DescriptorNumber: if other.value == 0: - raise ZeroDivisionError('Cannot divide by zero') + raise ZeroDivisionError("Cannot divide by zero") new_value = self.full_value / other.full_value else: return NotImplemented @@ -726,7 +743,7 @@ def __truediv__(self, other: Union[DescriptorNumber, numbers.Number]) -> Descrip def __rtruediv__(self, other: numbers.Number) -> DescriptorNumber: if isinstance(other, numbers.Number): if self.value == 0: - raise ZeroDivisionError('Cannot divide by zero') + raise ZeroDivisionError("Cannot divide by zero") new_value = other / self.full_value else: return NotImplemented @@ -736,14 +753,16 @@ def __rtruediv__(self, other: numbers.Number) -> DescriptorNumber: descriptor_number.name = descriptor_number.unique_name return descriptor_number - def __pow__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorNumber: + def __pow__( + self, other: Union[DescriptorNumber, numbers.Number] + ) -> DescriptorNumber: if isinstance(other, numbers.Number): exponent = other elif type(other) is DescriptorNumber: - if other.unit != 'dimensionless': - raise UnitError('Exponents must be dimensionless') + if other.unit != "dimensionless": + raise UnitError("Exponents must be dimensionless") if other.variance is not None: - raise ValueError('Exponents must not have variance') + raise ValueError("Exponents must not have variance") exponent = other.value else: return NotImplemented @@ -752,7 +771,7 @@ def __pow__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorN except Exception as message: raise message from None if np.isnan(new_value.value): - raise ValueError('The result of the exponentiation is not a number') + raise ValueError("The result of the exponentiation is not a number") descriptor_number = DescriptorNumber.from_scipp( name=self.name, full_value=new_value, sources=(self, other) ) @@ -761,10 +780,10 @@ def __pow__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorN def __rpow__(self, other: numbers.Number) -> numbers.Number: if isinstance(other, numbers.Number): - if self.unit != 'dimensionless': - raise UnitError('Exponents must be dimensionless') + if self.unit != "dimensionless": + raise UnitError("Exponents must be dimensionless") if self.variance is not None: - raise ValueError('Exponents must not have variance') + raise ValueError("Exponents must not have variance") new_value = other**self.value else: return NotImplemented From ca5b265c6e3978eabd05634b26b295151a77f8d0 Mon Sep 17 00:00:00 2001 From: henrikjacobsenfys Date: Fri, 18 Sep 2026 06:55:16 +0200 Subject: [PATCH 3/3] fix errors --- pixi.lock | 6462 ++++++++--------- src/easyscience/variable/descriptor_number.py | 151 +- 2 files changed, 3265 insertions(+), 3348 deletions(-) diff --git a/pixi.lock b/pixi.lock index 96a470ca..eb033db0 100644 --- a/pixi.lock +++ b/pixi.lock @@ -27,51 +27,51 @@ environments: packages: p1: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-26.1.0-py314h89acca1_1.conda - 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coverage ; extra == 'test' + - asteval[dev,doc,test] ; extra == 'all' + requires_python: '>=3.10' diff --git a/src/easyscience/variable/descriptor_number.py b/src/easyscience/variable/descriptor_number.py index c2122f0a..aa8810d3 100644 --- a/src/easyscience/variable/descriptor_number.py +++ b/src/easyscience/variable/descriptor_number.py @@ -80,7 +80,7 @@ def __init__( self, name: str, value: numbers.Number, - unit: Optional[Union[str, sc.Unit]] = "", + unit: Optional[Union[str, sc.Unit]] = '', variance: Optional[numbers.Number] = None, unique_name: Optional[str] = None, description: Optional[str] = None, @@ -103,20 +103,20 @@ def __init__( self._observers: List[DescriptorNumber] = [] # Extract serializer_id if provided during deserialization - if "__serializer_id" in kwargs: - self.__serializer_id = kwargs.pop("__serializer_id") + if '__serializer_id' in kwargs: + self.__serializer_id = kwargs.pop('__serializer_id') if not isinstance(value, numbers.Number) or isinstance(value, bool): - raise TypeError(f"{value=} must be a number") + raise TypeError(f'{value=} must be a number') if variance is not None: if not isinstance(variance, numbers.Number) or isinstance(variance, bool): - raise TypeError(f"{variance=} must be a number or None") + raise TypeError(f'{variance=} must be a number or None') if variance < 0: - raise ValueError(f"{variance=} must be positive") + raise ValueError(f'{variance=} must be positive') variance = float(variance) if not isinstance(unit, sc.Unit) and not isinstance(unit, str): raise TypeError( - f"{unit=} must be a scipp unit or a string representing a valid scipp unit" + f'{unit=} must be a scipp unit or a string representing a valid scipp unit' ) try: self._scalar = sc.scalar(float(value), unit=unit, variance=variance) @@ -175,9 +175,9 @@ def from_scipp( If ``full_value`` is not a scalar scipp ``Variable``. """ if not isinstance(full_value, Variable): - raise TypeError(f"{full_value=} must be a scipp scalar") + raise TypeError(f'{full_value=} must be a scipp scalar') if len(full_value.dims) != 0: - raise TypeError(f"{full_value=} must be a scipp scalar") + raise TypeError(f'{full_value=} must be a scipp scalar') return cls( name=name, value=full_value.value, @@ -189,7 +189,7 @@ def from_scipp( def _attach_observer(self, observer: DescriptorNumber) -> None: """Attach an observer to the descriptor.""" self._observers.append(observer) - if not hasattr(self, "_DescriptorNumber__serializer_id"): + if not hasattr(self, '_DescriptorNumber__serializer_id'): self.__serializer_id = str(uuid.uuid4()) def _detach_observer(self, observer: DescriptorNumber) -> None: @@ -221,9 +221,9 @@ def _validate_dependencies(self, origin: Optional[str] = None) -> None: """ if origin == self.unique_name: raise RuntimeError( - "\n Cyclic dependency detected!\n" - + f"An update of {self.unique_name} leads to it updating itself.\n" - + "Please check your dependencies." + '\n Cyclic dependency detected!\n' + + f'An update of {self.unique_name} leads to it updating itself.\n' + + 'Please check your dependencies.' ) if origin is None: origin = self.unique_name @@ -247,7 +247,7 @@ def full_value(self) -> Variable: @full_value.setter def full_value(self, full_value: Variable) -> None: raise AttributeError( - f"Full_value is read-only. Change the value and variance seperately. Or create a new {self.__class__.__name__}." + f'Full_value is read-only. Change the value and variance seperately. Or create a new {self.__class__.__name__}.' ) @property @@ -286,7 +286,7 @@ def value(self, value: numbers.Number) -> None: If ``value`` is not a number. """ if not isinstance(value, numbers.Number) or isinstance(value, bool): - raise TypeError(f"{value=} must be a number") + raise TypeError(f'{value=} must be a number') self._scalar.value = float(value) @property @@ -305,10 +305,7 @@ def unit(self) -> str: str Unit as a string. """ - if ( - self._input_unit_parsed is not None - and self._input_unit_parsed == self._scalar.unit - ): + if self._input_unit_parsed is not None and self._input_unit_parsed == self._scalar.unit: return self._input_unit return str(self._scalar.unit) @@ -316,8 +313,8 @@ def unit(self) -> str: def unit(self, unit_str: str) -> None: raise AttributeError( ( - f"Unit is read-only. Use convert_unit to change the unit between allowed types " - f"or create a new {self.__class__.__name__} with the desired unit." + f'Unit is read-only. Use convert_unit to change the unit between allowed types ' + f'or create a new {self.__class__.__name__} with the desired unit.' ) ) # noqa: E501 @@ -354,9 +351,9 @@ def variance(self, variance_float: float) -> None: """ if variance_float is not None: if not isinstance(variance_float, numbers.Number): - raise TypeError(f"{variance_float=} must be a number or None") + raise TypeError(f'{variance_float=} must be a number or None') if variance_float < 0: - raise ValueError(f"{variance_float=} must be positive") + raise ValueError(f'{variance_float=} must be positive') variance_float = float(variance_float) self._scalar.variance = variance_float @@ -395,9 +392,9 @@ def error(self, value: float) -> None: """ if value is not None: if not isinstance(value, numbers.Number): - raise TypeError(f"{value=} must be a number or None") + raise TypeError(f'{value=} must be a number or None') if value < 0: - raise ValueError(f"{value=} must be positive") + raise ValueError(f'{value=} must be positive') value = float(value) self._scalar.variance = value**2 else: @@ -426,9 +423,7 @@ def _convert_unit(self, unit_str: str, record_undo: bool = True) -> None: If the unit conversion fails. """ # noqa: DOC503. UnitError re-raised after restoring the unit state if not isinstance(unit_str, str): - raise TypeError( - f"{unit_str=} must be a string representing a valid scipp unit" - ) + raise TypeError(f'{unit_str=} must be a string representing a valid scipp unit') new_unit = sc.Unit(unit_str) # Save the current state for undo/redo @@ -449,7 +444,7 @@ def _convert_unit(self, unit_str: str, record_undo: bool = True) -> None: _set_unit_state, old_state, self._unit_state(), - text=f"Convert unit to {unit_str}", + text=f'Convert unit to {unit_str}', ) ) @@ -475,7 +470,7 @@ def _apply_unit_conversion(self, new_unit: sc.Unit) -> None: try: self._scalar = self._scalar.to(unit=new_unit) except Exception as e: - raise UnitError(f"Failed to convert unit: {e}") from e + raise UnitError(f'Failed to convert unit: {e}') from e @staticmethod def _spelling_from_sources(unit: sc.Unit, sources: tuple) -> Union[str, sc.Unit]: @@ -504,7 +499,7 @@ def _spelling_from_sources(unit: sc.Unit, sources: tuple) -> Union[str, sc.Unit] offers one. """ for source in sources: - parsed_unit = getattr(source, "_input_unit_parsed", None) + parsed_unit = getattr(source, '_input_unit_parsed', None) if parsed_unit is not None and parsed_unit == unit: return source._input_unit return unit @@ -582,45 +577,43 @@ def __copy__(self) -> DescriptorNumber: def __repr__(self) -> str: """Return printable representation.""" - string = "<" - string += self.__class__.__name__ + " " + string = '<' + string += self.__class__.__name__ + ' ' string += f"'{self._name}': " if np.abs(self._scalar.value) > 1e4 or ( np.abs(self._scalar.value) < 1e-4 and self._scalar.value != 0 ): # Use scientific notation for large or small values - string += f"{self._scalar.value:.3e}" + string += f'{self._scalar.value:.3e}' if self.variance: - string += f" \u00b1 {self.error:.3e}" + string += f' \u00b1 {self.error:.3e}' else: - string += f"{self._scalar.value:.4f}" + string += f'{self._scalar.value:.4f}' if self.variance: - string += f" \u00b1 {self.error:.4f}" + string += f' \u00b1 {self.error:.4f}' obj_unit = self.unit - if obj_unit == "dimensionless": - obj_unit = "" + if obj_unit == 'dimensionless': + obj_unit = '' else: - obj_unit = f" {obj_unit}" + obj_unit = f' {obj_unit}' string += obj_unit - string += ">" + string += '>' return string # return f"<{class_name} '{obj_name}': {obj_value:0.04f}{obj_unit}>" def as_dict(self, skip: Optional[List[str]] = None) -> Dict[str, Any]: raw_dict = super().as_dict(skip=skip) - raw_dict["value"] = self._scalar.value - raw_dict["unit"] = self.unit - raw_dict["variance"] = self._scalar.variance - if hasattr(self, "_DescriptorNumber__serializer_id"): - raw_dict["__serializer_id"] = self.__serializer_id + raw_dict['value'] = self._scalar.value + raw_dict['unit'] = self.unit + raw_dict['variance'] = self._scalar.variance + if hasattr(self, '_DescriptorNumber__serializer_id'): + raw_dict['__serializer_id'] = self.__serializer_id return raw_dict - def __add__( - self, other: Union[DescriptorNumber, numbers.Number] - ) -> DescriptorNumber: + def __add__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorNumber: if isinstance(other, numbers.Number): - if self.unit != "dimensionless": - raise UnitError("Numbers can only be added to dimensionless values") + if self.unit != 'dimensionless': + raise UnitError('Numbers can only be added to dimensionless values') new_value = self.full_value + other elif type(other) is DescriptorNumber: original_unit = other.unit @@ -628,7 +621,7 @@ def __add__( other._convert_unit(self.unit) except UnitError: raise UnitError( - f"Values with units {self.unit} and {other.unit} cannot be added" + f'Values with units {self.unit} and {other.unit} cannot be added' ) from None new_value = self.full_value + other.full_value other._convert_unit(original_unit) @@ -642,8 +635,8 @@ def __add__( def __radd__(self, other: numbers.Number) -> DescriptorNumber: if isinstance(other, numbers.Number): - if self.unit != "dimensionless": - raise UnitError("Numbers can only be added to dimensionless values") + if self.unit != 'dimensionless': + raise UnitError('Numbers can only be added to dimensionless values') new_value = other + self.full_value else: return NotImplemented @@ -653,14 +646,10 @@ def __radd__(self, other: numbers.Number) -> DescriptorNumber: descriptor_number.name = descriptor_number.unique_name return descriptor_number - def __sub__( - self, other: Union[DescriptorNumber, numbers.Number] - ) -> DescriptorNumber: + def __sub__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorNumber: if isinstance(other, numbers.Number): - if self.unit != "dimensionless": - raise UnitError( - "Numbers can only be subtracted from dimensionless values" - ) + if self.unit != 'dimensionless': + raise UnitError('Numbers can only be subtracted from dimensionless values') new_value = self.full_value - other elif type(other) is DescriptorNumber: original_unit = other.unit @@ -668,7 +657,7 @@ def __sub__( other._convert_unit(self.unit) except UnitError: raise UnitError( - f"Values with units {self.unit} and {other.unit} cannot be subtracted" + f'Values with units {self.unit} and {other.unit} cannot be subtracted' ) from None new_value = self.full_value - other.full_value other._convert_unit(original_unit) @@ -682,10 +671,8 @@ def __sub__( def __rsub__(self, other: numbers.Number) -> DescriptorNumber: if isinstance(other, numbers.Number): - if self.unit != "dimensionless": - raise UnitError( - "Numbers can only be subtracted from dimensionless values" - ) + if self.unit != 'dimensionless': + raise UnitError('Numbers can only be subtracted from dimensionless values') new_value = other - self.full_value else: return NotImplemented @@ -695,9 +682,7 @@ def __rsub__(self, other: numbers.Number) -> DescriptorNumber: descriptor.name = descriptor.unique_name return descriptor - def __mul__( - self, other: Union[DescriptorNumber, numbers.Number] - ) -> DescriptorNumber: + def __mul__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorNumber: if isinstance(other, numbers.Number): new_value = self.full_value * other elif type(other) is DescriptorNumber: @@ -721,16 +706,14 @@ def __rmul__(self, other: numbers.Number) -> DescriptorNumber: descriptor_number.name = descriptor_number.unique_name return descriptor_number - def __truediv__( - self, other: Union[DescriptorNumber, numbers.Number] - ) -> DescriptorNumber: + def __truediv__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorNumber: if isinstance(other, numbers.Number): if other == 0: - raise ZeroDivisionError("Cannot divide by zero") + raise ZeroDivisionError('Cannot divide by zero') new_value = self.full_value / other elif type(other) is DescriptorNumber: if other.value == 0: - raise ZeroDivisionError("Cannot divide by zero") + raise ZeroDivisionError('Cannot divide by zero') new_value = self.full_value / other.full_value else: return NotImplemented @@ -743,7 +726,7 @@ def __truediv__( def __rtruediv__(self, other: numbers.Number) -> DescriptorNumber: if isinstance(other, numbers.Number): if self.value == 0: - raise ZeroDivisionError("Cannot divide by zero") + raise ZeroDivisionError('Cannot divide by zero') new_value = other / self.full_value else: return NotImplemented @@ -753,16 +736,14 @@ def __rtruediv__(self, other: numbers.Number) -> DescriptorNumber: descriptor_number.name = descriptor_number.unique_name return descriptor_number - def __pow__( - self, other: Union[DescriptorNumber, numbers.Number] - ) -> DescriptorNumber: + def __pow__(self, other: Union[DescriptorNumber, numbers.Number]) -> DescriptorNumber: if isinstance(other, numbers.Number): exponent = other elif type(other) is DescriptorNumber: - if other.unit != "dimensionless": - raise UnitError("Exponents must be dimensionless") + if other.unit != 'dimensionless': + raise UnitError('Exponents must be dimensionless') if other.variance is not None: - raise ValueError("Exponents must not have variance") + raise ValueError('Exponents must not have variance') exponent = other.value else: return NotImplemented @@ -771,7 +752,7 @@ def __pow__( except Exception as message: raise message from None if np.isnan(new_value.value): - raise ValueError("The result of the exponentiation is not a number") + raise ValueError('The result of the exponentiation is not a number') descriptor_number = DescriptorNumber.from_scipp( name=self.name, full_value=new_value, sources=(self, other) ) @@ -780,10 +761,10 @@ def __pow__( def __rpow__(self, other: numbers.Number) -> numbers.Number: if isinstance(other, numbers.Number): - if self.unit != "dimensionless": - raise UnitError("Exponents must be dimensionless") + if self.unit != 'dimensionless': + raise UnitError('Exponents must be dimensionless') if self.variance is not None: - raise ValueError("Exponents must not have variance") + raise ValueError('Exponents must not have variance') new_value = other**self.value else: return NotImplemented