derivkit 1.0.0__tar.gz

derivkit-1.0.0/.github/ISSUE_TEMPLATE/derivkit-adoption.yml

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+name: DerivKit adoption entry
+description: Request that a software project or publication using DerivKit be listed in the docs.
+title: "[Adoption] "
+labels: ["adoption"]
+body:
+  - type: dropdown
+    id: entry_type
+    attributes:
+      label: Entry type
+      description: Where should this be listed on the Citation page?
+      options:
+        - Software / pipeline
+        - Publication
+    validations:
+      required: true
+
+  - type: input
+    id: name
+    attributes:
+      label: Name
+      placeholder: "e.g. Augur, COCOA, or Paper title"
+    validations:
+      required: true
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description
+      description: >
+        Required. This text will appear on the Citation page. Please write 2–5 lines.
+      placeholder: |
+        Software example:
+        A short description of what the package/pipeline does, and how DerivKit is used
+        (e.g. Fisher forecasts, DALI expansion, numerical derivatives for likelihoods).
+
+        Publication example:
+        A short description of what the paper does, and where DerivKit enters the analysis
+        (e.g. derivative evaluation, forecasting, validation, etc.).
+    validations:
+      required: true
+
+  - type: input
+    id: link
+    attributes:
+      label: Link (required)
+      description: >
+        Required. For software: repository URL. For publications: arXiv or DOI URL.
+      placeholder: |
+        Software: https://github.com/org/repo
+        Publication: https://arxiv.org/abs/XXXX.XXXXX  (or https://doi.org/...)
+    validations:
+      required: true
+
+  - type: textarea
+    id: citation
+    attributes:
+      label: Citation (publications only)
+      description: >
+        Optional but recommended for publications. Free-form reference text (journal/venue + DOI/arXiv).
+        BibTeX is fine too.
+      placeholder: |
+        Author A., Author B. (YEAR), Journal/venue, DOI or arXiv:XXXX.XXXXX
+    validations:
+      required: true
+
+  - type: input
+    id: contact
+    attributes:
+      label: Contact (optional)
+      description: Email or GitHub handle in case maintainers need clarification.
+      placeholder: "@username or name@example.com"
+    validations:
+      required: true

derivkit-1.0.0/.github/scripts/adoption_from_issue.py

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+"""Create adoption YAML entries from GitHub adoption issues.
+
+This script is used by a GitHub Action. It parses the issue form body and writes a
+YAML file into ``docs/adoption/`` so the docs can render the adoption list.
+"""
+
+from __future__ import annotations
+
+import os
+import re
+from dataclasses import dataclass
+from pathlib import Path
+
+
+@dataclass(frozen=True)
+class AdoptionIssue:
+    """Structured fields extracted from a DerivKit adoption issue."""
+    entry_type: str  # "software" or "publication"
+    name: str
+    description: str
+    link: str | None
+    citation: str | None
+    contact: str | None
+    issue_number: int
+    issue_url: str
+
+
+_FIELD_RE = re.compile(r"^###\s+(?P<label>.+?)\s*$")
+
+
+def _normalize_type(s: str) -> str:
+    """Normalize entry type string to lowercase and remove "software" / "publication"."""
+    s = s.strip().lower()
+    if "software" in s:
+        return "software"
+    if "publication" in s:
+        return "publication"
+    raise ValueError(f"Unrecognized entry type: {s!r}")
+
+
+def _slugify(name: str) -> str:
+    """Generate a slug for a given entry name."""
+    slug = name.strip().lower()
+    slug = re.sub(r"[^a-z0-9]+", "-", slug).strip("-")
+    return slug or "adoption-entry"
+
+
+def _parse_issue_form(body: str) -> dict[str, str]:
+    """Parse a GitHub issue-form body into a mapping of field labels to values.
+
+    The issue form is rendered as markdown sections of the form:
+
+        ### Field label
+        value
+    """
+    out: dict[str, str] = {}
+    current: str | None = None
+    lines: list[str] = []
+    for raw in body.splitlines():
+        m = _FIELD_RE.match(raw)
+        if m:
+            if current is not None:
+                out[current] = "\n".join(lines).strip()
+            current = m.group("label").strip()
+            lines = []
+            continue
+        if current is not None:
+            lines.append(raw)
+    if current is not None:
+        out[current] = "\n".join(lines).strip()
+    return out
+
+
+def _yaml_quote_block(s: str) -> str:
+    # use YAML folded style
+    s = s.rstrip()
+    # indent by two spaces under key
+    return ">\n" + "\n".join(f"  {line}".rstrip() for line in s.splitlines())
+
+
+def build_yaml(issue: AdoptionIssue) -> str:
+    """Render a single adoption entry as YAML text."""
+    if issue.entry_type == "software":
+        if not issue.link:
+            raise ValueError("Software entry requires a repository URL (repo).")
+    if issue.entry_type == "publication":
+        if not issue.citation:
+            raise ValueError("Publication entries require a citation line.")
+
+    reference = [
+            f"name: {issue.name}",
+            f"kind: {issue.entry_type}",
+            "description: " + _yaml_quote_block(issue.description),
+            f"link: {issue.link}",
+            f"source_issue: {issue.issue_url}",
+    ]
+
+    if issue.citation:
+        reference.append("citation: " + _yaml_quote_block(issue.citation))
+    reference.append("")
+    return "\n".join(reference)
+
+
+def main() -> None:
+    """Entry point for GitHub Actions to generate the adoption YAML file."""
+    issue_body = os.environ["ISSUE_BODY"]
+    issue_number = int(os.environ["ISSUE_NUMBER"])
+    issue_url = os.environ["ISSUE_URL"]
+
+    fields = _parse_issue_form(issue_body)
+
+    entry_type = _normalize_type(fields.get("Entry type", ""))
+    name = fields.get("Name", "").strip()
+    description = fields.get("Description", "").strip()
+    link = fields.get("Link (required)", "").strip() or None
+    citation = fields.get("Citation (publications only)", "").strip() or None
+    contact = fields.get("Contact (optional)", "").strip() or None
+
+    if not name:
+        raise ValueError("Missing required field: Name")
+    if not description:
+        raise ValueError("Missing required field: Description")
+
+    issue = AdoptionIssue(
+        entry_type=entry_type,
+        name=name,
+        description=description,
+        link=link,
+        citation=citation,
+        contact=contact,
+        issue_number=issue_number,
+        issue_url=issue_url,
+    )
+
+    slug = _slugify(name)
+    suffix = f"-{issue_number}"
+
+    if entry_type == "software":
+        base = Path("docs/adoption/software") / slug
+    elif entry_type == "publication":
+        base = Path("docs/adoption/publications") / slug
+    else:
+        raise ValueError("Unsupported adoption type")
+
+    out = base.with_suffix(".yml")
+    if out.exists():
+        out = Path(f"{base}{suffix}.yml")
+
+    out.parent.mkdir(parents=True, exist_ok=True)
+    out.write_text(build_yaml(issue), encoding="utf-8")
+    print(str(out))
+
+
+if __name__ == "__main__":
+    main()

derivkit-1.0.0/.github/workflows/adoption-issue-to-pr.yml

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+name: Adoption issue -> PR
+
+"on":
+  issues:
+    types: [labeled]
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  create_pr:
+    # Safer gate: only run when a maintainer adds this label
+    if: github.event.label.name == 'adoption-approved'
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install pyyaml
+
+      - name: Generate adoption YAML from issue
+        env:
+          ISSUE_BODY: ${{ github.event.issue.body }}
+          ISSUE_NUMBER: ${{ github.event.issue.number }}
+          ISSUE_URL: ${{ github.event.issue.html_url }}
+        run: |
+          python .github/scripts/adoption_from_issue.py
+
+      - name: Create PR
+        uses: peter-evans/create-pull-request@v6
+        with:
+          branch: automation/adoption-${{ github.event.issue.number }}
+          title: "docs: add adoption entry (#${{ github.event.issue.number }})"
+          commit-message: "docs: add adoption entry (#${{ github.event.issue.number }})"
+          body: |
+            Auto-generated from adoption issue #${{ github.event.issue.number }}.
+          add-paths: |
+            docs/adoption/**
+          labels: |
+            adoption

derivkit-1.0.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+  pull_request:
+    branches:
+      - main
+  schedule:
+    - cron: '23 1 * * 0'
+  workflow_dispatch:
+
+jobs:
+  testing:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up uv with Python ${{ matrix.python-version }}
+        uses: astral-sh/setup-uv@v7
+        with:
+          version: "0.8.22" # Fix the version of uv
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --extra test
+
+      - name: Run tests
+        run: uv run tox -m test
+
+  linting:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.12"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up uv with Python 3.12
+        uses: astral-sh/setup-uv@v7
+        with:
+          version: "0.8.22" # Fix the version of uv
+
+      - name: Install dependencies
+        run: uv sync --extra lint
+
+      - name: Run ruff
+        run: uv run tox -e lint -- --output-format github
+
+  finalise:
+    runs-on: ubuntu-latest
+    needs: [testing, linting]
+    steps:
+      - name: finalise
+        run: echo "All done"

derivkit-1.0.0/.github/workflows/docs.yml

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+name: Deploy Sphinx Documentation
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  publish_sphinx_docs:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v3
+        with:
+          python-version: "3.13"
+
+      - name: Install dependencies
+        run: |
+          pip install -e .
+
+      - name: Sphinx build
+        run: |
+          tox -e docs-releases
+
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/_build/html
+          cname: docs.derivkit.org
+          force_orphan: true

derivkit-1.0.0/.github/workflows/publish.yml

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+name: "Publish new versions of DerivKit to PyPI"
+
+on:
+  push:
+    tags:
+      - v*
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install Python 3.13
+        run: uv python install 3.13
+      - name: Build
+        run: uv build
+      - name: Publish
+        run: uv publish

derivkit-1.0.0/.gitignore

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+.idea
+*__pycache__
+logs/
+plots_tests/
+*.egg-info
+venv
+build
+dist
+.tox
+.cache
+docs/_build
+
+# Notebooks
+*.ipynb
+.ipynb_checkpoints/
+notebooks/
+notebooks/plots/*.png
+notebooks/plots/*.pdf
+notebooks/logs/
+docs/_generated/

derivkit-1.0.0/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use DerivKit, please cite it as below."
+title: "DerivKit"
+type: software
+authors:
+  - given-names: "Nikolina"
+    family-names: "Šarčević"
+    email: "nikolina.sarcevic@gmail.com"
+    orcid: 0000-0001-7301-6415
+  - given-names: "Matthijs"
+    family-names: "van der Wild"
+    email: "matthijs@vanderwild.com"
+    orcid: 0000-0002-3949-3063
+  - given-names: "Cynthia"
+    family-names: "Trendafilova"
+    email: "cyntrendafilova@gmail.com"
+    orcid: 0000-0001-5500-4058
+license: "MIT"
+repository-code: "https://github.com/derivkit/derivkit"

derivkit-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Nikolina Šarčević
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

derivkit-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: derivkit
+Version: 1.0.0
+Summary: A robust toolkit for stable numerical derivatives
+Author-email: Nikolina Šarčević <nikolina.sarcevic@gmail.com>, Matthijs van der Wild <matthijs@vanderwild.com>, Cynthia Trendafilova <cyntrendafilova@gmail.com>
+License-Expression: MIT
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numdifftools
+Requires-Dist: numpy
+Requires-Dist: multiprocess
+Requires-Dist: scipy
+Requires-Dist: tox
+Requires-Dist: getdist
+Requires-Dist: emcee
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx<9; extra == "docs"
+Requires-Dist: sphinx-design; extra == "docs"
+Requires-Dist: sphinx-multiversion; extra == "docs"
+Requires-Dist: furo; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
+Provides-Extra: lint
+Requires-Dist: ruff; extra == "lint"
+Provides-Extra: jax
+Requires-Dist: jax>=0.4; extra == "jax"
+Requires-Dist: jaxlib>=0.4; extra == "jax"
+Dynamic: license-file
+
+# derivkit
+
+[![CI](https://github.com/derivkit/derivkit/actions/workflows/ci.yml/badge.svg)](https://github.com/derivkit/derivkit/actions/workflows/ci.yml)
+[![Deploy Sphinx Documentation](https://github.com/derivkit/derivkit/actions/workflows/docs.yml/badge.svg)](https://github.com/derivkit/derivkit/actions/workflows/docs.yml)
+[![License](https://img.shields.io/github/license/derivkit/derivkit)](LICENSE)
+
+
+**DerivKit** is a robust Python toolkit for stable numerical derivatives, built for scientific computing, cosmology, and any domain requiring accurate gradients or higher-order expansions.
+
+Detailed documentation, examples, and API reference can be found at the [derivkit documentation](https://docs.derivkit.org).
+
+
+## License
+MIT License © 2025 Niko Šarčević, Matthijs van der Wild, Cynthia Trendafilova and contributors.

derivkit-1.0.0/README.md

@@ -0,0 +1,14 @@
+# derivkit
+
+[![CI](https://github.com/derivkit/derivkit/actions/workflows/ci.yml/badge.svg)](https://github.com/derivkit/derivkit/actions/workflows/ci.yml)
+[![Deploy Sphinx Documentation](https://github.com/derivkit/derivkit/actions/workflows/docs.yml/badge.svg)](https://github.com/derivkit/derivkit/actions/workflows/docs.yml)
+[![License](https://img.shields.io/github/license/derivkit/derivkit)](LICENSE)
+
+
+**DerivKit** is a robust Python toolkit for stable numerical derivatives, built for scientific computing, cosmology, and any domain requiring accurate gradients or higher-order expansions.
+
+Detailed documentation, examples, and API reference can be found at the [derivkit documentation](https://docs.derivkit.org).
+
+
+## License
+MIT License © 2025 Niko Šarčević, Matthijs van der Wild, Cynthia Trendafilova and contributors.

derivkit-1.0.0/docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+clean:
+	@$(SPHINXBUILD) -M clean "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O);
+	cd _build; git worktree add -f html gh-pages
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)