fdatools 1.1.0__tar.gz

fdatools-1.1.0/.gitignore

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+__pycache__/
+*.py[cod]
+.venv/
+dist/
+build/
+*.egg-info/
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.hypothesis/
+.coverage
+coverage.xml
+htmlcov/
+.benchmarks/
+site/
+.ipynb_checkpoints/
+.env
+.DS_Store
+~/.cache/
+notebooks/_figures/
+
+# Full-precision dataset dumps for the datasets agent (generated by
+# tools/export_datasets.R); not committed -- large, regenerable, not golden
+# test data.
+data_export/
+
+# Staging area for the GitHub "data-v1" release assets (generated by
+# tools/build_data_release.py from data_export/); not committed -- see
+# docs/dev/data-release.md for the human upload step.
+data_release/
+
+# Local knowledge graph of the repo (graphify); regenerable.
+graphify-out/

fdatools-1.1.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project are documented here. Format follows
+[Keep a Changelog](https://keepachangelog.com/en/1.1.0/); versions follow SemVer.
+
+## [1.1.0] - 2026-09-28
+
+First release under the name **fdatools** (the first one on PyPI).
+
+### Changed
+- The project is renamed from **fabel** to **fdatools**: `pip install fdatools`,
+  `import fdatools as fdt`. The GitHub repository moves to
+  `hameddavodi/fdatools` and the documentation to
+  <https://hameddavodi.github.io/fdatools>. The environment variables
+  `FABEL_DATA_DIR` / `FABEL_RUN_NETWORK_TESTS` become `FDATOOLS_DATA_DIR` /
+  `FDATOOLS_RUN_NETWORK_TESTS`, and the dataset cache moves to
+  `~/.cache/fdatools`. The 1.0.0 entry below describes the release published
+  under the old name.
+- `rpy2` moved from the `dev` extra to a new `golden` extra (only
+  `tools/make_golden.py` uses it), so the development install no longer needs R.
+
+### Fixed
+- `PACE(sigma2=...)` no longer raises a `RuntimeWarning` about a non-positive
+  measurement-error estimate: with `sigma2` given, the estimate is kept in
+  `cov_estimate_` but not used, so it is not worth a warning.
+- `FPCA`, `FCCA` and `PACE` reject a NumPy bool for `n` on every NumPy version
+  (NumPy 2.2 only warned in `operator.index`).
+
+### Added
+- `notebooks/tour.ipynb`: a full tour that uses every public module on the
+  bundled data sets, records 131 checks, and compares key results live with R
+  `fda` (through `Rscript`). Built from `notebooks/tour.py` by
+  `tools/build_tour_notebook.py`.
+
+## [1.0.0] - 2026-09-27
+
+First public release: a clean-room Python rewrite of R `fda` 6.3.0 with
+golden-file parity (`rtol = 1e-8`, `1e-5` for iterative fits).
+
+### Added
+- Basis systems (`fabel.basis`): `BSpline`, `Fourier`, `Monomial`, `Exponential`,
+  `Power`, `Constant`, `Polygonal`, with evaluation and derivatives, roughness
+  penalties for any `LDO`, cached Gram matrices and exact basis products.
+- Core objects (`fabel.core`): `FData` (callable curves, exact derivatives,
+  arithmetic, `mean` / `std` / `center` / `cov`, indexing, `@` inner product),
+  `BiFData`, `LDO` (including the harmonic accelerator) and `inprod`.
+- Smoothing (`fabel.smoothing`): `smooth()` with GCV or degrees-of-freedom
+  selection of λ, positive / monotone / morph constraints, observation weights
+  and irregular per-curve designs; `SmoothResult`; the scikit-learn `Smoother`;
+  `gcv_curve`, `lambda_to_df`, `df_to_lambda`.
+- Decomposition (`fabel.decomposition`): `FPCA` (with roughness-penalised
+  harmonics and varimax rotation) and `FCCA`, both scikit-learn estimators.
+- Regression (`fabel.regression`): `fregress()` for scalar and functional
+  responses with scalar and functional covariates (model type read from the
+  arguments, or an R-style formula string with treatment-coded factors), with
+  `predict()`, `stderr()` and `cv()`; the scikit-learn `FRegress` estimator.
+- Registration (`fabel.registration`): continuous registration `register()`
+  (Newton with the exact Hessian, optional periodic shift), landmark registration
+  (`landmarks=` or `landmark_register()`), the amplitude/phase decomposition
+  `RegistrationResult.decompose()` and the scikit-learn `Registrator`.
+- Dynamics (`fabel.dynamics`): principal differential analysis `PDA` for single
+  equations and coupled systems, with an ODE `solve()` and `plot_overlay()`, and
+  the `phase_plane()` plot.
+- Statistics (`fabel.stats`): `cov`, `cor`, functional depth (MBD, BD2, FM),
+  the functional `boxplot`, and the permutation tests `t_test` and `f_test`.
+  `f_test` takes either raw inputs `(y, x, basis=, lam=, penalty=)` like R
+  `Fperm.fd`, or a fitted `fregress` model: `f_test(model, n_perm=, q=, t=,
+  random_state=)`.
+- scikit-learn: `check_estimator` passes for `Smoother`, `FPCA`, `FRegress` and
+  `Registrator` with no exemptions. `FRegress` validates `y` as scikit-learn does
+  (finite, column vectors flattened with a warning, at least 2 samples).
+  `Registrator` has `n_iter_`, and its default basis for an n-column coefficient
+  matrix is `BSpline(n_basis=n, order=min(4, n))`, the same rule as `FPCA`.
+- PyTorch layers (`fabel.nn`, optional `fabel[torch]` extra): `BasisLayer`,
+  `SmoothingLayer` (learnable λ) and `FDataDataset`. `import fabel` does not
+  import PyTorch; `fabel.nn` loads on first use.
+- Top-level exports: `smooth`, `Smoother`, `SmoothResult`, `FPCA`, `FCCA`,
+  `fregress`, `FRegress`, `register`, `landmark_register`, `Registrator`, `PDA`,
+  `phase_plane`, and the `stats` module.
+- Datasets (`fabel.datasets`): 14 loaders for the FDA book datasets; `growth`,
+  `gait` and `pinch` ship in the package, the others download once with SHA-256
+  verification and a `FABEL_DATA_DIR`-overridable cache.
+- I/O (`fabel.io`): `from_pandas`, `to_pandas`, `to_xarray` and `read_rds` for R
+  `fd` / `bifd` / `basisfd` objects.
+- Array API backend: NumPy and PyTorch inputs, with gradients flowing through
+  evaluation, products and inner products.
+- Golden-file parity suite against R `fda` 6.3.0, and `tools/parity_report.py`,
+  which measures every parity check and writes `PARITY_REPORT.md`.
+- Documentation site (MkDocs Material + mkdocstrings): quickstart, R migration
+  table, API reference for every module, and six tutorials (smoothing, FPCA,
+  registration, regression, dynamics, machine learning). Tests run every
+  tutorial block and check that every public symbol is rendered.
+- `notebooks/book_figures.ipynb`: figures of Ramsay, Hooker & Graves (2009),
+  assembled from `notebooks/book/ch*.py` by `tools/build_book_notebook.py`
+  (`make book`) and run in CI with `nbmake`.
+- Packaging: typed (`py.typed`) wheel and sdist for Python 3.10 to 3.13,
+  BSD-3-Clause license, `CITATION.cff`.
+- `register()` accepts an `FData` with PyTorch coefficients and returns PyTorch
+  results; gradients flow from the registered curves to the input coefficients
+  (autodiff Newton path; the optimal warps are held fixed).
+- Build: the Makefile uses the `.venv` Python and has new `sync` and `gate5`
+  targets.
+- Sparse / longitudinal FPCA (`fabel.sparse`, PACE): `sparse_mean`
+  (R `smooth.sparse.mean`), `sparse_cov` / `SparseCov` (R `covPACE`, with the
+  measurement-error variance `sigma2`), and the `PACE` estimator (R `pcaPACE`)
+  with conditional-expectation (BLUP) scores in `transform` (replaces R's
+  defective `scoresPACE`) and `inverse_transform`.
+- Density and intensity estimation (`fabel.density`): `fit_density` (R
+  `density.fd`, no longer shipped in fda 6.3.0) and `fit_intensity` (R
+  `intensity.fd`), damped Newton with the exact Hessian and exact integrals;
+  `DensityResult`, `IntensityResult`.
+- Generalized profiling for ODE parameters (`fabel.profiling`, replaces the R
+  CSTR family): `ODEModel` (analytic, finite-difference or torch-autodiff
+  derivatives), `ProfiledODE`, `profile_ode`, `ProfileResult`, built-in
+  `cstr_model` / `cstr_inputs` and `fitzhugh_nagumo_model`, and `simpson_rule`
+  (R `quadset`). Unobserved states are allowed.
+- Regression: `linmod()` / `LinmodResult` for a functional response on a
+  functional covariate with a bivariate coefficient beta(s, t) (R `linmod`),
+  with weights and a `predict()` method. `fregress` now computes in the input's
+  array namespace: torch tensors in give torch results, with gradients to the
+  response, covariates and weights.
+- Registration: `register()` accepts multivariate curves (one warp per curve,
+  new `var_weights=` keyword; `var_weights=[1, 0, ...]` reproduces R, which uses
+  the first variable only); landmark registration and `decompose()` accept
+  multivariate curves; new `RegistrationResult.apply(fd)` (R `register.newfd`).
+- Dynamics: `PDA` forcing functions (`forcing_basis=`, `forcing_lam=`,
+  `fit(X, forcing=u)`, `forcing_weights_`; R `pda.fd` `awtlist` / `ufdlist`) and
+  `PDA.stability()` returning `PDAStability` (R `eigen.pda`, with the true
+  equilibrium limits).
+- Smoothing: monotone, positive and morph `SmoothResult`s evaluate exact
+  derivatives of any order (Faà di Bruno / complete Bell polynomials; R
+  `eval.monfd`, `eval.posfd`, `predict.monfd`).
+- Statistics: pointwise `confidence_band()` / `ConfidenceBand` for a smooth
+  (via `y2c_map`) or an `fregress` result (via `stderr`), and the plots
+  `plot_beta` (R `plotbeta`), `cycleplot` (R `cycleplot.fd`) and `plot_scores`
+  (R `plotscores`).
+- Top-level exports added: `PACE`, `SparseCov`, `sparse_mean`, `sparse_cov`,
+  `fit_density`, `fit_intensity`, `DensityResult`, `IntensityResult`,
+  `ODEModel`, `ProfiledODE`, `profile_ode`, `linmod`, `LinmodResult`,
+  `PDAStability`, and the `sparse`, `density` and `profiling` modules.
+
+### Fixed
+- `register(lam=0, criterion='eigen')` no longer raises `LinAlgError`: it warns
+  (`RuntimeWarning`) when a curve has no finite optimum, and raises `ValueError`
+  on NaN or infinite input.
+- `FPCA` and `FCCA` accept any integer-like `n` (`SupportsIndex`).
+- `FData.std` samples the pointwise standard deviation on
+  `max(201, 10 * n_basis + 1)` points, matching R `sd.fd` to 1.8e-15.
+
+### Documentation
+- Dataset docstrings state the unit of every value and time field.
+- Observation weights: behaviour compared with R `fRegress(wt=)` and
+  `Fperm.fd` in the `fregress` / `f_test` notes and the R migration page.
+
+### Known differences from R `fda`
+- Where R `fda` 6.3.0 is demonstrably less accurate (for example `deriv.fd`,
+  `times.fd`, B-spline penalties with no interior knots, `smooth.pos` stopping
+  one iteration short), Fabel returns the exact value. Each case is a strict
+  expected failure in the test suite with its measured error; see
+  `PARITY_REPORT.md`.

fdatools-1.1.0/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use fdatools, please cite it as below, together with Ramsay & Silverman (2005)."
+type: software
+title: "fdatools: functional data analysis for Python"
+abstract: >-
+  fdatools is a clean-room Python rewrite of the R package fda (version 6.3.0):
+  basis expansions, penalised smoothing, functional principal component and
+  canonical correlation analysis, functional regression, curve registration
+  and principal differential analysis, with numerical parity against R.
+version: 1.1.0
+date-released: 2026-09-28
+license: BSD-3-Clause
+authors:
+  - family-names: Davodi
+    given-names: Hamed
+    email: hamed.davodi94@gmail.com
+repository-code: "https://github.com/hameddavodi/fdatools"
+url: "https://hameddavodi.github.io/fdatools"
+keywords:
+  - functional data analysis
+  - fda
+  - splines
+  - smoothing
+  - functional PCA
+references:
+  - type: book
+    title: "Functional Data Analysis"
+    edition: "2nd"
+    authors:
+      - family-names: Ramsay
+        given-names: J. O.
+      - family-names: Silverman
+        given-names: B. W.
+    year: 2005
+    publisher:
+      name: Springer
+  - type: book
+    title: "Functional Data Analysis with R and MATLAB"
+    authors:
+      - family-names: Ramsay
+        given-names: J. O.
+      - family-names: Hooker
+        given-names: Giles
+      - family-names: Graves
+        given-names: Spencer
+    year: 2009
+    publisher:
+      name: Springer
+  - type: software
+    title: "fda: Functional Data Analysis (R package)"
+    version: 6.3.0
+    authors:
+      - family-names: Ramsay
+        given-names: J. O.
+      - family-names: Graves
+        given-names: Spencer
+      - family-names: Hooker
+        given-names: Giles
+    url: "https://cran.r-project.org/package=fda"

fdatools-1.1.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2026, Hamed Davodi
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

fdatools-1.1.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: fdatools
+Version: 1.1.0
+Summary: Functional data analysis for Python: a clean-room rewrite of R's fda package.
+Project-URL: Homepage, https://github.com/hameddavodi/fdatools
+Project-URL: Documentation, https://hameddavodi.github.io/fdatools
+Project-URL: Source, https://github.com/hameddavodi/fdatools
+Project-URL: Issues, https://github.com/hameddavodi/fdatools/issues
+Project-URL: Changelog, https://github.com/hameddavodi/fdatools/blob/main/CHANGELOG.md
+Author-email: Hamed Davodi <hamed.davodi94@gmail.com>
+License-Expression: BSD-3-Clause
+License-File: LICENSE
+Keywords: fda,fpca,functional data analysis,smoothing,splines
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Requires-Dist: array-api-compat>=1.11
+Requires-Dist: numpy>=2.1
+Requires-Dist: scikit-learn>=1.4
+Requires-Dist: scipy>=1.14
+Provides-Extra: dev
+Requires-Dist: build>=1.2; extra == 'dev'
+Requires-Dist: hypothesis>=6.100; extra == 'dev'
+Requires-Dist: jupyter>=1.0; extra == 'dev'
+Requires-Dist: mkdocs-material>=9.5; extra == 'dev'
+Requires-Dist: mkdocs<2,>=1.6; extra == 'dev'
+Requires-Dist: mkdocstrings[python]>=0.25; extra == 'dev'
+Requires-Dist: mypy>=1.11; extra == 'dev'
+Requires-Dist: nbmake>=1.5; extra == 'dev'
+Requires-Dist: pandas-stubs>=2.2; extra == 'dev'
+Requires-Dist: pip-audit>=2.7; extra == 'dev'
+Requires-Dist: pyright>=1.1.403; extra == 'dev'
+Requires-Dist: pytest-benchmark>=4.0; extra == 'dev'
+Requires-Dist: pytest-cov>=5.0; extra == 'dev'
+Requires-Dist: pytest>=8.0; extra == 'dev'
+Requires-Dist: ruff>=0.6; extra == 'dev'
+Requires-Dist: scipy-stubs>=1.14; (python_version >= '3.10') and extra == 'dev'
+Requires-Dist: twine>=5.0; extra == 'dev'
+Provides-Extra: golden
+Requires-Dist: rpy2>=3.5; extra == 'golden'
+Provides-Extra: io
+Requires-Dist: rdata>=0.11; extra == 'io'
+Provides-Extra: pandas
+Requires-Dist: pandas>=2.2; extra == 'pandas'
+Requires-Dist: xarray>=2024.1; extra == 'pandas'
+Provides-Extra: plot
+Requires-Dist: matplotlib>=3.8; extra == 'plot'
+Provides-Extra: torch
+Requires-Dist: torch>=2.2; extra == 'torch'
+Description-Content-Type: text/markdown
+
+# fdatools
+
+[![CI](https://github.com/hameddavodi/fdatools/actions/workflows/ci.yml/badge.svg)](https://github.com/hameddavodi/fdatools/actions/workflows/ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/fdatools.svg)](https://pypi.org/project/fdatools/)
+[![Python versions](https://img.shields.io/pypi/pyversions/fdatools.svg)](https://pypi.org/project/fdatools/)
+[![License: BSD-3-Clause](https://img.shields.io/badge/license-BSD--3--Clause-blue.svg)](https://github.com/hameddavodi/fdatools/blob/main/LICENSE)
+[![Docs](https://img.shields.io/badge/docs-hameddavodi.github.io%2Ffdatools-blue.svg)](https://hameddavodi.github.io/fdatools)
+
+**Functional data analysis for Python.** fdatools is a clean-room Python rewrite of
+R's [`fda`](https://cran.r-project.org/package=fda) package (Ramsay, Hooker &
+Graves): basis expansions, penalised smoothing, functional PCA and CCA,
+functional regression, curve registration and principal differential analysis.
+
+- **Same numbers as R.** Every public function is tested against golden output
+  from R `fda` 6.3.0 at `rtol = 1e-8` (`1e-5` for iterative fits). See the
+  [parity report](https://github.com/hameddavodi/fdatools/blob/main/PARITY_REPORT.md).
+- **About 40 symbols instead of 515 functions.** Curves are callable (`fd(t)`),
+  arithmetic is plain Python (`fd1 + fd2`, `fd1 @ fd2`), and there is one
+  `smooth()`, one `register()`, one `.plot()`.
+- **Fits the Python stack.** scikit-learn estimators, NumPy or PyTorch arrays
+  through the Array API (gradients flow), pandas and xarray I/O.
+
+## Install
+
+```bash
+pip install fdatools
+```
+
+Optional extras: `fdatools[plot]` (matplotlib), `fdatools[pandas]` (pandas + xarray),
+`fdatools[io]` (read R `.rds` files), `fdatools[torch]` (PyTorch). Python 3.10 to 3.13.
+
+## Quickstart
+
+```python
+import numpy as np
+import fdatools as fdt
+
+growth = fdt.datasets.load_growth()                   # Berkeley growth study, ships with fdatools
+basis = fdt.BSpline(domain=(1.0, 18.0), n_basis=12)   # cubic B-splines on ages 1-18
+coefs, *_ = np.linalg.lstsq(basis(growth.age), growth.hgtf, rcond=None)
+girls = fdt.FData(coefs, basis)                       # 54 height curves in one object
+speed = girls.derivative()                           # growth speed in cm/year, exact
+print(speed.mean()(np.array([5.0, 12.0])))           # curves are callable: evaluate anywhere
+print(fdt.inprod(girls[0], girls[0]))                 # L2 inner product of one curve
+```
+
+Next steps: penalised smoothing with automatic λ (`smooth`), functional PCA
+(`FPCA`) and more in the [quickstart guide](https://hameddavodi.github.io/fdatools/quickstart/).
+Coming from R? The [migration table](https://hameddavodi.github.io/fdatools/r-migration/)
+maps every `fda` function to its fdatools equivalent.
+
+## Documentation
+
+Full documentation, API reference and tutorials: <https://hameddavodi.github.io/fdatools>.
+
+## Citing
+
+If you use fdatools in published work, please cite it together with Ramsay &
+Silverman (2005); see [`CITATION.cff`](https://github.com/hameddavodi/fdatools/blob/main/CITATION.cff).
+
+## License
+
+BSD 3-Clause. fdatools is a clean-room implementation written from the published
+mathematics (Ramsay & Silverman 2005; Ramsay, Hooker & Graves 2009) and the
+public behaviour of R `fda`; it contains no R source code.

fdatools-1.1.0/README.md

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+# fdatools
+
+[![CI](https://github.com/hameddavodi/fdatools/actions/workflows/ci.yml/badge.svg)](https://github.com/hameddavodi/fdatools/actions/workflows/ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/fdatools.svg)](https://pypi.org/project/fdatools/)
+[![Python versions](https://img.shields.io/pypi/pyversions/fdatools.svg)](https://pypi.org/project/fdatools/)
+[![License: BSD-3-Clause](https://img.shields.io/badge/license-BSD--3--Clause-blue.svg)](https://github.com/hameddavodi/fdatools/blob/main/LICENSE)
+[![Docs](https://img.shields.io/badge/docs-hameddavodi.github.io%2Ffdatools-blue.svg)](https://hameddavodi.github.io/fdatools)
+
+**Functional data analysis for Python.** fdatools is a clean-room Python rewrite of
+R's [`fda`](https://cran.r-project.org/package=fda) package (Ramsay, Hooker &
+Graves): basis expansions, penalised smoothing, functional PCA and CCA,
+functional regression, curve registration and principal differential analysis.
+
+- **Same numbers as R.** Every public function is tested against golden output
+  from R `fda` 6.3.0 at `rtol = 1e-8` (`1e-5` for iterative fits). See the
+  [parity report](https://github.com/hameddavodi/fdatools/blob/main/PARITY_REPORT.md).
+- **About 40 symbols instead of 515 functions.** Curves are callable (`fd(t)`),
+  arithmetic is plain Python (`fd1 + fd2`, `fd1 @ fd2`), and there is one
+  `smooth()`, one `register()`, one `.plot()`.
+- **Fits the Python stack.** scikit-learn estimators, NumPy or PyTorch arrays
+  through the Array API (gradients flow), pandas and xarray I/O.
+
+## Install
+
+```bash
+pip install fdatools
+```
+
+Optional extras: `fdatools[plot]` (matplotlib), `fdatools[pandas]` (pandas + xarray),
+`fdatools[io]` (read R `.rds` files), `fdatools[torch]` (PyTorch). Python 3.10 to 3.13.
+
+## Quickstart
+
+```python
+import numpy as np
+import fdatools as fdt
+
+growth = fdt.datasets.load_growth()                   # Berkeley growth study, ships with fdatools
+basis = fdt.BSpline(domain=(1.0, 18.0), n_basis=12)   # cubic B-splines on ages 1-18
+coefs, *_ = np.linalg.lstsq(basis(growth.age), growth.hgtf, rcond=None)
+girls = fdt.FData(coefs, basis)                       # 54 height curves in one object
+speed = girls.derivative()                           # growth speed in cm/year, exact
+print(speed.mean()(np.array([5.0, 12.0])))           # curves are callable: evaluate anywhere
+print(fdt.inprod(girls[0], girls[0]))                 # L2 inner product of one curve
+```
+
+Next steps: penalised smoothing with automatic λ (`smooth`), functional PCA
+(`FPCA`) and more in the [quickstart guide](https://hameddavodi.github.io/fdatools/quickstart/).
+Coming from R? The [migration table](https://hameddavodi.github.io/fdatools/r-migration/)
+maps every `fda` function to its fdatools equivalent.
+
+## Documentation
+
+Full documentation, API reference and tutorials: <https://hameddavodi.github.io/fdatools>.
+
+## Citing
+
+If you use fdatools in published work, please cite it together with Ramsay &
+Silverman (2005); see [`CITATION.cff`](https://github.com/hameddavodi/fdatools/blob/main/CITATION.cff).
+
+## License
+
+BSD 3-Clause. fdatools is a clean-room implementation written from the published
+mathematics (Ramsay & Silverman 2005; Ramsay, Hooker & Graves 2009) and the
+public behaviour of R `fda`; it contains no R source code.

fdatools-1.1.0/pyproject.toml

@@ -0,0 +1,181 @@
+[build-system]
+requires = ["hatchling>=1.27"]
+build-backend = "hatchling.build"
+
+[project]
+name = "fdatools"
+version = "1.1.0"
+description = "Functional data analysis for Python: a clean-room rewrite of R's fda package."
+readme = "README.md"
+license = "BSD-3-Clause"
+license-files = ["LICENSE"]
+requires-python = ">=3.10"
+authors = [{ name = "Hamed Davodi", email = "hamed.davodi94@gmail.com" }]
+keywords = ["functional data analysis", "fda", "splines", "smoothing", "fpca"]
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "Intended Audience :: Developers",
+  "Intended Audience :: Science/Research",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Topic :: Scientific/Engineering :: Mathematics",
+  "Topic :: Scientific/Engineering :: Information Analysis",
+  "Typing :: Typed",
+]
+dependencies = [
+  "numpy>=2.1",
+  "scipy>=1.14",
+  "array-api-compat>=1.11",
+  "scikit-learn>=1.4",
+]
+
+[project.optional-dependencies]
+torch = ["torch>=2.2"]
+pandas = ["pandas>=2.2", "xarray>=2024.1"]
+plot = ["matplotlib>=3.8"]
+io = ["rdata>=0.11"]
+# Only for tools/make_golden.py (it falls back to Rscript without it). Needs R to build.
+golden = ["rpy2>=3.5"]
+dev = [
+  "pytest>=8.0",
+  "pytest-cov>=5.0",
+  "pytest-benchmark>=4.0",
+  "hypothesis>=6.100",
+  "ruff>=0.6",
+  "mypy>=1.11",
+  "pyright>=1.1.403",
+  "nbmake>=1.5",
+  "jupyter>=1.0",
+  # MkDocs 2.0 drops the plugin system that mkdocs-material and mkdocstrings need.
+  "mkdocs>=1.6,<2",
+  "mkdocs-material>=9.5",
+  "mkdocstrings[python]>=0.25",
+  "build>=1.2",
+  "twine>=5.0",
+  "pip-audit>=2.7",
+  "pandas-stubs>=2.2",
+  "scipy-stubs>=1.14; python_version >= '3.10'",
+]
+
+[project.urls]
+Homepage = "https://github.com/hameddavodi/fdatools"
+Documentation = "https://hameddavodi.github.io/fdatools"
+Source = "https://github.com/hameddavodi/fdatools"
+Issues = "https://github.com/hameddavodi/fdatools/issues"
+Changelog = "https://github.com/hameddavodi/fdatools/blob/main/CHANGELOG.md"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/fdatools"]
+
+[tool.hatch.build.targets.sdist]
+include = ["src/fdatools", "README.md", "LICENSE", "CHANGELOG.md", "CITATION.cff"]
+
+[tool.ruff]
+line-length = 100
+target-version = "py310"
+src = ["src", "tests", "tools", "benchmarks"]
+# Markdown is documentation, not source: SPEC.md/WORKFLOW.md snippets are illustrative
+# API sketches and must not be rewritten by the formatter.
+extend-exclude = ["*.md"]
+
+[tool.ruff.lint]
+select = ["E", "F", "W", "I", "N", "UP", "B", "A", "C4", "SIM", "RUF", "D", "ANN", "S", "PT", "NPY"]
+ignore = ["D203", "D213", "ANN401", "S101", "D105", "D107"]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**" = ["D", "ANN", "S", "PT011"]
+"benchmarks/**" = ["D", "ANN"]
+"tools/**" = ["S603", "S607"]
+"notebooks/**" = ["D", "ANN", "E402", "B018"]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.mypy]
+# 3.12 because numpy >= 2.3 ships stubs written with PEP 695 `type` statements that
+# mypy refuses to parse under an older target. Runtime support stays >= 3.10; ruff
+# target-version = "py310" is what guards against newer syntax in our own sources.
+python_version = "3.12"
+strict = true
+warn_unreachable = true
+
+[[tool.mypy.overrides]]
+module = ["array_api_compat.*", "sklearn.*", "matplotlib.*", "torch.*", "rdata.*", "xarray.*", "hypothesis.*", "rpy2.*"]
+ignore_missing_imports = true
+
+[tool.pyright]
+# Pyright backs the editor/agent language server: code intelligence (jump-to-def,
+# references, document symbols) plus fast control-flow checks. `mypy --strict` stays
+# the authoritative type gate in CI -- pyright is tuned here NOT to re-report what
+# mypy and ruff already own, so that what it does say is signal rather than noise.
+#
+# venvPath/venv are the load-bearing lines: without them pyright resolves no project
+# import at all and every numpy/scipy/sklearn call cascades into a phantom error.
+venvPath = "."
+venv = ".venv"
+# 3.12 for the same reason as [tool.mypy]: numpy >= 2.3 ships stubs written with PEP
+# 695 `type` statements. Runtime support stays >= 3.10, guarded by ruff py310.
+pythonVersion = "3.12"
+# Every directory ruff lints, so code intelligence works outside src/ too.
+include = ["src", "tests", "tools", "benchmarks"]
+exclude = [
+  "**/__pycache__",
+  "**/.ruff_cache",
+  "**/.mypy_cache",
+  "**/.pytest_cache",
+  "**/.hypothesis",
+  ".venv",
+  "notebooks",
+  "data_export",
+  "data_release",
+  "tests/golden",
+]
+typeCheckingMode = "standard"
+# `ignore` suppresses diagnostics but STILL indexes these files, so jump-to-definition
+# and find-references keep working across the tests. (`exclude` would drop them from the
+# index entirely and break code intelligence.) Tests, tools and benchmarks are
+# deliberately unannotated -- ruff already exempts them via per-file-ignores ANN --
+# so type-checking them yields noise, not signal.
+ignore = ["tests", "tools", "benchmarks"]
+# Already enforced by ruff: F401 unused import, F841 unused local.
+reportUnusedImport = "none"
+reportUnusedVariable = "none"
+# Already handled by [[tool.mypy.overrides]] ignore_missing_imports.
+reportMissingTypeStubs = "none"
+# The checks that earn their place: control-flow faults mypy --strict does not
+# report by default. reportPossiblyUnbound caught a real UnboundLocalError path
+# in smoothing._smooth_irregular that no grep or AST scan can see.
+reportPossiblyUnboundVariable = "error"
+reportUnboundVariable = "error"
+# Known, accepted false positives: sklearn's `validate_data` declares a union return type
+# that includes the `"no_validation"` sentinel string, so pyright thinks `.shape`/`.T` may
+# be attribute access on `str` at 3 call sites (decomposition._as_fdata, Smoother.fit).
+# mypy sidesteps this via ignore_missing_imports for sklearn.*. The rule stays ON because
+# it catches real faults elsewhere -- it flagged a genuine bad attribute in io.py.
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-ra --strict-markers"
+markers = [
+  "parity: golden-file parity tests against R fda 6.3.0",
+  "slow: long-running tests",
+  "gpu: requires CUDA",
+  "network: hits the real network, skipped by default",
+]
+filterwarnings = ["error::DeprecationWarning:fdatools.*"]
+
+[tool.coverage.run]
+source = ["fdatools"]
+branch = true
+
+[tool.coverage.report]
+show_missing = true
+exclude_lines = ["pragma: no cover", "if TYPE_CHECKING:", "@overload"]