PyCDFt 0.1.0__tar.gz

pycdft-0.1.0/.github/workflows/ci.yml

@@ -0,0 +1,44 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  test-core:
+    name: core tests (Python ${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install
+        run: |
+          python -m pip install --upgrade pip
+          pip install numpy pytest
+          pip install -e .
+      - name: Run core tests (numpy only)
+        run: pytest -m "not cross" -q
+
+  test-cross:
+    name: cross-validation (ibicus + R port, Python 3.11)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install
+        run: |
+          python -m pip install --upgrade pip
+          pip install numpy pytest
+          pip install -e .
+          pip install ibicus
+      - name: Run cross tests (skipped when ibicus is missing)
+        run: pytest -m cross -q

pycdft-0.1.0/CHANGELOG.md

@@ -0,0 +1,77 @@
+# Changelog
+
+All notable changes to this project are documented here. The format follows
+[Keep a Changelog](https://keepachangelog.com/) and versioning follows
+[Semantic Versioning](https://semver.org/).
+
+## [Unreleased]
+
+### Documentation
+
+- README: added a Documentation section (links to `docs/design.md`,
+  `docs/gpu.md` and `docs/guide.html`), a glossary note for the CDF-t
+  notation, a Limitations section, and honest cross-test skip wording;
+  fixed the grid-field example ("per-cell drift" was a field-wide offset)
+  and the calibration-reuse example (was a no-op); removed the
+  maintainer-only PyPI-name paragraph and the multivariate references
+  unrelated to the package; added a note that the R `CDFt` source is GPL
+  and reproduced in the tests for validation only.
+- `docs/design.md`: replaced unverifiable "measured" claims with the
+  actual numbers and test references; removed informal wording and
+  un-attributed "reference implementation" / "parent project" phrasing;
+  cross-referenced the README comparison table.
+- `docs/gpu.md`: added the measured MI210 speedup table (23× vs numpy);
+  corrected the hardware/test-count claims to what the logs show.
+- `docs/guide.html`: linked from the README, removed the hardcoded version
+  badge, removed the invented "verification period" inputs, fixed the
+  no-op quick-start example, trimmed the reference list.
+- `CONTRIBUTING.md`: fixed the release instructions (version is
+  single-sourced), the setup comment, added the GPU test command and a
+  documentation-maintenance note.
+- `docs/guide.html`: removed the duplication with the README — quick start
+  shrunk to a teaser, the comparison table and measured numbers dropped
+  (README/`docs/design.md` §4 only), the reference list replaced by a
+  pointer, the FAQ removed (its answers restated earlier sections), and the
+  GPU install table removed (see `docs/gpu.md`). The notation table now ties
+  the symbols to the `obs`/`cm_hist`/`cm_future` names.
+- `README.md`: removed the "Memory-lean design", "Tail semantics" and
+  "NaN semantics" sections (conventions live in `docs/design.md` and the
+  plain-language guide §6) and the measured comparison table (now
+  `docs/design.md` §4 only); kept the aspect comparison table and trimmed
+  the low-level API example.
+
+### Changed
+
+- The package is now called **PyCDFt**. The import name stays `pycdft`
+  (lowercase, Python module convention), so existing imports are unchanged.
+
+### Packaging
+
+- Added `MANIFEST.in` so the sdist ships the docs, examples, benchmarks,
+  the CI workflow and **all** test helpers (`tests/naive_cdft.py`,
+  `tests/r_cdft_reference.py`), which the previous sdist silently omitted
+  (tests from the sdist failed at collection).
+- Added the `py.typed` marker: the package is fully type-annotated, so
+  type checkers now treat it as typed.
+- Switched to the SPDX license expression (`license = "Apache-2.0"` +
+  `license-files`) and bumped the setuptools build requirement to `>=77`
+  (the deprecated `license = { text = ... }` form is gone).
+- Single-sourced the version: `pycdft/__init__.py` is now the only place
+  that defines it (`[tool.setuptools.dynamic] version`).
+- Extended the CI matrix to Python 3.9–3.13.
+- Added the `dev` extra (pytest + pyflakes).
+
+## [0.1.0] - 2026-10-12
+
+### Added
+
+- Vectorized CDF-t (Michelangeli, Vrac & Loukos 2009) on a numpy core:
+  `pycdft.CDFt`, `calibrate` / `apply_cdft` / `calibrate_hist` /
+  `apply_cdft_hist`, `cdft_transform`, `transfer`.
+- Grid-ready kernels (sorted ECDF, type-7 quantiles, windowed-slope tails,
+  histogram path), NaN conventions, float32 support, chunked processing and
+  a `workers` thread pool.
+- Optional torch GPU backend `pycdft.gpu` (CUDA / ROCm / MPS / CPU)
+  mirroring the numpy API, verified numerically identical to the numpy core.
+- Cross-validation against ibicus and a reference R CDFt port; tests,
+  benchmarks, examples and this documentation set.

pycdft-0.1.0/CONTRIBUTING.md

@@ -0,0 +1,51 @@
+# Contributing to PyCDFt
+
+Thanks for contributing! This package is intentionally small, numpy-only and
+dependency-light: keep it that way.
+
+## Setup
+
+```bash
+pip install -e .[test]        # numpy + pytest (matplotlib via .[examples])
+pip install ibicus            # only needed for the ibicus cross tests
+```
+
+## Tests
+
+```bash
+pytest                        # everything
+pytest -m "not cross"         # core suite (no external deps, CI runs this)
+pytest -m cross -s            # cross-validation (ibicus + R port, prints metrics)
+pytest -m gpu                 # torch GPU backend (skipped without torch)
+```
+
+- New kernels go in `pycdft/math.py` (numpy only, vectorized over the cell
+  axis, docstrings with the convention); the pipeline in `pycdft/core.py`;
+  the public API in `pycdft/api.py`.
+- Any change to the numerics must keep the conventions documented in
+  `docs/design.md` (step ECDF, type-7 quantiles, delta shift, grid, tails,
+  NaN semantics) — and the cross-test tolerances must stay honest: if a
+  tolerance is loosened, update the numbers in `README.md` and
+  `docs/design.md` (they are reproduced by `pytest -m cross -s`).
+- Documentation: the public docs are `README.md`, `docs/design.md`,
+  `docs/gpu.md` and `docs/guide.html` (the plain-language companion).
+  Any API or convention change must update all of them consistently —
+  `docs/guide.html` is hand-maintained, so check it for drift too.
+
+## Conventions
+
+- numpy only in the core; scipy/xarray/pandas/matplotlib must stay optional.
+- 1-D series and `(T, N)` fields both supported (any trailing dims are
+  flattened into cells).
+- Never mutate the caller's arrays (`np.sort` only on private copies).
+- Deterministic: `workers > 1` must not change results.
+- No project-specific paths, no network access in the tests.
+
+## Releasing (maintainers)
+
+1. Bump `__version__` in `pycdft/__init__.py` (single-sourced:
+   `pyproject.toml` reads it via `[tool.setuptools.dynamic]`).
+2. `python -m build` (or `pip install build && python -m build`).
+3. `twine check dist/* && twine upload dist/*` (the name `pycdft` was free
+   at the time of writing; re-check `https://pypi.org/pypi/pycdft/json`
+   before publishing).

pycdft-0.1.0/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but not
+      limited to compiled object code, generated documentation, and
+      conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including the
+      original version of the Work and any modifications or additions to
+      that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright 2026 pycdft contributors
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

pycdft-0.1.0/MANIFEST.in

@@ -0,0 +1,18 @@
+# Files that must reach the source distribution (sdist).
+# README.md, LICENSE and pyproject.toml are included automatically.
+
+include CHANGELOG.md
+include Makefile
+include CONTRIBUTING.md
+recursive-include docs *
+recursive-include examples *.py
+recursive-include examples/figures *.png
+recursive-include benchmarks *
+recursive-include tests *.py
+recursive-include .github *
+
+# Internal notes and machine-local artifacts: never ship these.
+exclude HANDOFF.md
+prune .hybrid_logs
+prune .pytest_cache
+global-exclude *.py[cod]

pycdft-0.1.0/Makefile

@@ -0,0 +1,33 @@
+# Convenience targets for development.
+# The package core is pure numpy; the cross tests additionally need ibicus.
+
+PYTHON ?= python
+
+.PHONY: test test-core test-cross lint install editable clean examples
+
+test:
+	$(PYTHON) -m pytest
+
+test-core:
+	$(PYTHON) -m pytest -m "not cross"
+
+test-cross:
+	$(PYTHON) -m pytest -m cross -s
+
+lint:
+	$(PYTHON) -m pyflakes pycdft tests examples || true
+
+install:
+	$(PYTHON) -m pip install .
+
+editable:
+	$(PYTHON) -m pip install -e .[test]
+
+examples:
+	$(PYTHON) examples/example_r_gaussian.py
+	$(PYTHON) examples/example_skewed.py
+	$(PYTHON) examples/example_grid.py
+
+clean:
+	rm -rf build dist *.egg-info .pytest_cache .coverage htmlcov
+	find . -name __pycache__ -type d -prune -exec rm -rf {} \;