nmrglue-ng 1.0.0__tar.gz

nmrglue_ng-1.0.0/.github/scripts/check_installed_wheel.py

@@ -0,0 +1,100 @@
+"""Validate a runtime wheel with functional tests staged from its sdist."""
+
+from importlib import import_module, metadata
+from pathlib import Path
+import shutil
+import sys
+import sysconfig
+from tempfile import TemporaryDirectory
+
+from packaging.version import Version
+
+
+EXPECTED_CASES = 65
+
+
+class InstalledOriginGuard:
+    def __init__(self, source_root, staged_tests):
+        self.source_root = source_root.resolve()
+        self.staged_tests = staged_tests.resolve()
+        self.site_packages = {
+            Path(path).resolve()
+            for path in (sysconfig.get_path("purelib"), sysconfig.get_path("platlib"))
+            if path
+        }
+        self.collected = 0
+
+    def _assert_origin(self, module):
+        path = getattr(module, "__file__", None)
+        if path is None:
+            return
+        path = Path(path).resolve()
+        if path.is_relative_to(self.source_root) or path.is_relative_to(self.staged_tests):
+            raise RuntimeError(f"nmrglue imported from test source: {path}")
+        if not any(path.is_relative_to(site) for site in self.site_packages):
+            raise RuntimeError(f"nmrglue import is outside site-packages: {path}")
+
+    def _assert_origins(self):
+        import nmrglue
+
+        self._assert_origin(nmrglue)
+        for module in tuple(sys.modules.values()):
+            if module is not None and getattr(module, "__name__", "").startswith("nmrglue"):
+                self._assert_origin(module)
+        for package_path in nmrglue.__path__:
+            path = Path(package_path).resolve()
+            if not any(path.is_relative_to(site) for site in self.site_packages):
+                raise RuntimeError(f"nmrglue package path is outside site-packages: {path}")
+
+    def pytest_sessionstart(self, session):
+        self._assert_origins()
+
+    def pytest_collection_finish(self, session):
+        self.collected = len(session.items)
+        if self.collected != EXPECTED_CASES:
+            raise RuntimeError(
+                f"expected {EXPECTED_CASES} wheel functional cases, collected {self.collected}"
+            )
+        self._assert_origins()
+
+    def pytest_sessionfinish(self, session, exitstatus):
+        self._assert_origins()
+
+
+def main(sdist_root, report):
+    import pytest
+    import nmrglue
+
+    sdist_root = Path(sdist_root).resolve()
+    package_path = Path(nmrglue.__file__).resolve()
+    if Version(metadata.version("nmrglue-ng")) != Version(nmrglue.__version__):
+        raise SystemExit("Distribution and import versions differ")
+    for module in ("analysis", "fileio", "process", "process.nmrtxt.rance_kay", "util"):
+        import_module(f"nmrglue.{module}")
+    print(f"Installed nmrglue-ng {nmrglue.__version__}: {package_path}", flush=True)
+
+    report = Path(report).resolve()
+    with TemporaryDirectory(prefix="nmrglue-wheel-", dir=report.parent) as directory:
+        directory = Path(directory)
+        staged_tests = directory / "tests"
+        shutil.copytree(sdist_root / "tests", staged_tests)
+        config = sdist_root / "pytest.ini"
+        guard = InstalledOriginGuard(sdist_root, staged_tests)
+        status = pytest.main(
+            [
+                "--import-mode=importlib",
+                "--rootdir", str(staged_tests),
+                "-c", str(config),
+                str(staged_tests / "fileio" / "test_pipe.py"),
+                str(staged_tests / "fileio" / "test_bruker.py"),
+                "--strict-markers", "--strict-config", "-ra",
+                f"--junitxml={report}",
+            ],
+            plugins=[guard],
+        )
+        if status:
+            raise SystemExit(status)
+
+
+if __name__ == "__main__":
+    main(sys.argv[1], sys.argv[2])

nmrglue_ng-1.0.0/.github/scripts/check_test_report.py

@@ -0,0 +1,22 @@
+"""Reject empty, skipped, or failing test runs in required CI profiles."""
+
+import sys
+import xml.etree.ElementTree as ET
+
+
+def check_report(path, expected_count=None):
+    cases = list(ET.parse(path).getroot().iter("testcase"))
+    if not cases:
+        raise SystemExit("Required profile executed no tests")
+    if expected_count is not None and len(cases) != expected_count:
+        raise SystemExit(
+            f"Required profile executed {len(cases)} tests, expected {expected_count}"
+        )
+    for case in cases:
+        if any(case.find(tag) is not None for tag in ("skipped", "failure", "error")):
+            raise SystemExit(f"Required test did not pass: {case.attrib}")
+    print(f"Required profile: {len(cases)} tests passed, no skips")
+
+
+if __name__ == "__main__":
+    check_report(sys.argv[1], int(sys.argv[2]) if len(sys.argv) == 3 else None)

nmrglue_ng-1.0.0/INSTALL.txt

@@ -0,0 +1,54 @@
+==================
+Installation Guide
+==================
+
+The distribution is named ``nmrglue-ng``. The Python package and import name
+remain ``nmrglue`` for compatibility with existing code.
+
+Installing from PyPI
+--------------------
+
+Install the stable release with::
+
+    python -m pip install nmrglue-ng
+
+Conda packages are planned after the stable 1.0.0 release.
+
+Requirements
+------------
+
+``nmrglue-ng`` requires Python 3.10 or newer. Runtime dependencies and their
+supported versions are declared in ``pyproject.toml``, which is the source of
+truth for packaging metadata.
+
+Installing from source
+----------------------
+
+Using a virtual environment is recommended but not required. For example::
+
+    python -m venv .venv
+    source .venv/bin/activate
+
+Clone and install the project with::
+
+    git clone https://github.com/spectrochempy/nmrglue-ng.git
+    cd nmrglue-ng
+    python -m pip install .
+
+Development installation
+------------------------
+
+Install the project in editable mode with its test dependencies::
+
+    python -m pip install -e ".[test]"
+
+Documentation dependencies are available through the ``docs`` extra::
+
+    python -m pip install -e ".[docs]"
+
+Importing the package
+---------------------
+
+The installed distribution is imported with::
+
+    import nmrglue as ng

nmrglue_ng-1.0.0/LICENSE.txt

@@ -0,0 +1,38 @@
+Copyright Notice and Statement for the nmrglue Project
+
+
+Copyright (c) 2010-2015 Jonathan J. Helmus
+All rights reserved.
+
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+
+a. Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+
+
+b. 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.
+
+
+c. Neither the name of the author nor the names of 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
+OWNER 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.

nmrglue_ng-1.0.0/MANIFEST.in

@@ -0,0 +1,10 @@
+include *.txt
+include *.rst
+include pytest.ini
+include maintainer/testdata-manifest.toml
+include .github/scripts/check_test_report.py
+include .github/scripts/check_installed_wheel.py
+include scripts/generate_testdata_manifest.py
+include scripts/verify_testdata.py
+recursive-include tests *
+global-exclude __pycache__ *.py[cod]

nmrglue_ng-1.0.0/PKG-INFO

@@ -0,0 +1,224 @@
+Metadata-Version: 2.4
+Name: nmrglue-ng
+Version: 1.0.0
+Summary: An independent continuation of nmrglue for working with NMR data in Python
+Author-email: "Jonathan J. Helmus" <jjhelmus@gmail.com>
+License-Expression: BSD-3-Clause
+Project-URL: Homepage, https://github.com/spectrochempy/nmrglue-ng
+Project-URL: Repository, https://github.com/spectrochempy/nmrglue-ng
+Project-URL: Issues, https://github.com/spectrochempy/nmrglue-ng/issues
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Programming Language :: Python :: 3
+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: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX :: Linux
+Requires-Python: >=3.10
+Description-Content-Type: text/x-rst
+License-File: LICENSE.txt
+Requires-Dist: numpy>=1.21.2
+Requires-Dist: scipy>=1.7.2
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-book-theme; extra == "docs"
+Requires-Dist: sphinx-design; extra == "docs"
+Requires-Dist: sphinx_rtd_theme; extra == "docs"
+Requires-Dist: myst-nb; extra == "docs"
+Requires-Dist: numpydoc; extra == "docs"
+Requires-Dist: matplotlib; extra == "docs"
+Requires-Dist: sphinx-intl; extra == "docs"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: tomli; python_version < "3.11" and extra == "test"
+Dynamic: license-file
+
+==========
+nmrglue-ng
+==========
+
+**An independent continuation of nmrglue for processing and working with NMR data in Python.**
+
+``nmrglue-ng`` is an independent fork of `nmrglue <https://github.com/jjhelmus/nmrglue>`_, originally developed by Jonathan J. Helmus and contributors.
+
+The project aims to preserve the simplicity, scientific capabilities, and established API of nmrglue while providing ongoing maintenance, reproducible testing, up-to-date documentation, and a predictable contribution and release process.
+
+.. important::
+
+   ``nmrglue-ng`` is an independent project. It is not the official nmrglue distribution and is not maintained or endorsed by the maintainers of the original project.
+
+Why nmrglue-ng?
+===============
+
+nmrglue has provided the NMR community with a lightweight and powerful Python toolkit for reading, writing, converting, processing, and analysing NMR data for more than a decade.
+
+Its broad support for NMR formats and its NumPy-oriented API make it particularly valuable for scientific scripting and interoperability.
+
+``nmrglue-ng`` builds on that work rather than replacing it.
+
+The main goals of this fork are:
+
+* preserve compatibility with the established nmrglue API wherever practical;
+* maintain and test existing NMR file-format support;
+* fix confirmed bugs and scientific inconsistencies;
+* provide reproducible test datasets for critical I/O operations;
+* maintain compatibility with current Python, NumPy, and SciPy releases;
+* keep packaging and continuous integration up to date;
+* maintain and continuously build the documentation;
+* establish a clear process for reviewing contributions as the project grows;
+* document important scientific and API decisions.
+
+Large API redesigns are explicitly **not** an initial objective.
+
+Compatibility
+=============
+
+Backward compatibility with existing nmrglue code is a primary goal.
+
+Existing code should, whenever possible, continue to work unchanged::
+
+    import nmrglue as ng
+
+    dic, data = ng.bruker.read("experiment")
+
+The distribution name and Python import name are intentionally distinct::
+
+    distribution: nmrglue-ng
+    import:       nmrglue
+
+Compatibility cannot be guaranteed indefinitely when correcting scientifically incorrect behaviour. Such changes will be documented, tested, and introduced through an explicit compatibility policy.
+
+Scientific scope
+================
+
+The project retains nmrglue's established scope, including:
+
+* reading and writing NMR data;
+* vendor and interchange file formats;
+* conversion between formats;
+* spectral processing;
+* unit and axis conversion;
+* peak picking and fitting;
+* low-memory access to large datasets.
+
+Scientific correctness and preservation of acquisition and processing metadata are considered part of the public behaviour of the library, not implementation details.
+
+Development priorities
+======================
+
+The initial development effort focuses on maintenance rather than redesign.
+
+Reliability
+-----------
+
+* reproducible test fixtures for supported NMR formats;
+* read/write and conversion round-trip tests;
+* regression tests for confirmed bugs;
+* validation of spectral axes and metadata.
+
+Scientific consistency
+----------------------
+
+Particular attention is being given to the relationships between:
+
+* observation frequency;
+* reference frequency;
+* carrier frequency and offset;
+* spectral width;
+* point, Hz, and ppm coordinates;
+* quadrature and complex-data conventions.
+
+Infrastructure
+--------------
+
+* modern Python packaging;
+* current Python/NumPy/SciPy compatibility;
+* Linux, macOS, and Windows CI;
+* automated documentation builds;
+* reproducible releases.
+
+File formats
+------------
+
+Existing format support will be preserved and progressively strengthened with real and synthetic reference datasets.
+
+Changes to parsers are expected to include regression tests demonstrating the corresponding format convention.
+
+Relationship with upstream nmrglue
+==================================
+
+``nmrglue-ng`` retains the complete Git history of nmrglue and acknowledges the original authors and all contributors whose work forms the basis of this project.
+
+Where practical, fixes developed here that are applicable to the original nmrglue project may also be proposed upstream through pull requests or reported as issues in the original repository. This may include bug fixes, regression tests, documentation improvements, compatibility updates, and clarifications of scientific or format-specific behaviour.
+
+Before opening an upstream contribution, the proposed change will be reviewed for relevance to the original project, compatibility with its maintenance policy, and consistency with its existing API and scope. Changes that are specific to ``nmrglue-ng``, or that depend on its independent development direction, will remain in this project.
+
+Likewise, useful upstream developments may be incorporated into ``nmrglue-ng`` with their original authorship and attribution preserved.
+
+The intention is not to obscure or replace the history of nmrglue, but to continue building on it transparently and, where appropriate, to contribute improvements back to the original project.
+
+Contributions
+=============
+
+Contributions are welcome, particularly:
+
+* reproducible bug reports;
+* regression tests;
+* small NMR datasets that can legally be redistributed for testing;
+* fixes for file-format readers and writers;
+* documentation improvements;
+* scientific validation against vendor software or documented format specifications;
+* performance improvements accompanied by correctness tests and benchmarks.
+
+Changes affecting scientific conventions or public API semantics may require a short design discussion before implementation.
+
+As the project develops, contribution and maintenance practices may evolve to make it easier for additional maintainers to participate.
+
+Installation
+============
+
+Install ``nmrglue-ng`` with pip::
+
+    python -m pip install nmrglue-ng
+
+Conda packages are planned after the stable 1.0.0 release. See
+`INSTALL.txt <INSTALL.txt>`_ for source and development installation options.
+
+The distribution is named ``nmrglue-ng``, while the Python import remains::
+
+    import nmrglue as ng
+
+Citation and attribution
+========================
+
+nmrglue-ng is derived from **nmrglue**, created by Jonathan J. Helmus and contributors.
+
+Users should continue to acknowledge the original nmrglue work where appropriate:
+
+    Jonathan J. Helmus and Christopher P. Jaroniec,
+
+    *Nmrglue: an open source Python package for the analysis of multidimensional NMR data*,
+
+    Journal of Biomolecular NMR (2013).
+
+A citation specific to ``nmrglue-ng`` will be provided if and when an appropriate archival release or publication becomes available.
+
+License
+=======
+
+``nmrglue-ng`` is distributed under the BSD 3-Clause License inherited from nmrglue.
+
+The original copyright notices and contributor history are preserved.
+
+See ``LICENSE.txt`` for details.
+
+----
+
+**nmrglue-ng is an independent continuation of nmrglue.**
+
+Its objective is deliberately conservative: preserve a useful and established NMR toolkit while making its maintenance, testing, documentation, and evolution sustainable.

nmrglue_ng-1.0.0/README.rst

@@ -0,0 +1,184 @@
+==========
+nmrglue-ng
+==========
+
+**An independent continuation of nmrglue for processing and working with NMR data in Python.**
+
+``nmrglue-ng`` is an independent fork of `nmrglue <https://github.com/jjhelmus/nmrglue>`_, originally developed by Jonathan J. Helmus and contributors.
+
+The project aims to preserve the simplicity, scientific capabilities, and established API of nmrglue while providing ongoing maintenance, reproducible testing, up-to-date documentation, and a predictable contribution and release process.
+
+.. important::
+
+   ``nmrglue-ng`` is an independent project. It is not the official nmrglue distribution and is not maintained or endorsed by the maintainers of the original project.
+
+Why nmrglue-ng?
+===============
+
+nmrglue has provided the NMR community with a lightweight and powerful Python toolkit for reading, writing, converting, processing, and analysing NMR data for more than a decade.
+
+Its broad support for NMR formats and its NumPy-oriented API make it particularly valuable for scientific scripting and interoperability.
+
+``nmrglue-ng`` builds on that work rather than replacing it.
+
+The main goals of this fork are:
+
+* preserve compatibility with the established nmrglue API wherever practical;
+* maintain and test existing NMR file-format support;
+* fix confirmed bugs and scientific inconsistencies;
+* provide reproducible test datasets for critical I/O operations;
+* maintain compatibility with current Python, NumPy, and SciPy releases;
+* keep packaging and continuous integration up to date;
+* maintain and continuously build the documentation;
+* establish a clear process for reviewing contributions as the project grows;
+* document important scientific and API decisions.
+
+Large API redesigns are explicitly **not** an initial objective.
+
+Compatibility
+=============
+
+Backward compatibility with existing nmrglue code is a primary goal.
+
+Existing code should, whenever possible, continue to work unchanged::
+
+    import nmrglue as ng
+
+    dic, data = ng.bruker.read("experiment")
+
+The distribution name and Python import name are intentionally distinct::
+
+    distribution: nmrglue-ng
+    import:       nmrglue
+
+Compatibility cannot be guaranteed indefinitely when correcting scientifically incorrect behaviour. Such changes will be documented, tested, and introduced through an explicit compatibility policy.
+
+Scientific scope
+================
+
+The project retains nmrglue's established scope, including:
+
+* reading and writing NMR data;
+* vendor and interchange file formats;
+* conversion between formats;
+* spectral processing;
+* unit and axis conversion;
+* peak picking and fitting;
+* low-memory access to large datasets.
+
+Scientific correctness and preservation of acquisition and processing metadata are considered part of the public behaviour of the library, not implementation details.
+
+Development priorities
+======================
+
+The initial development effort focuses on maintenance rather than redesign.
+
+Reliability
+-----------
+
+* reproducible test fixtures for supported NMR formats;
+* read/write and conversion round-trip tests;
+* regression tests for confirmed bugs;
+* validation of spectral axes and metadata.
+
+Scientific consistency
+----------------------
+
+Particular attention is being given to the relationships between:
+
+* observation frequency;
+* reference frequency;
+* carrier frequency and offset;
+* spectral width;
+* point, Hz, and ppm coordinates;
+* quadrature and complex-data conventions.
+
+Infrastructure
+--------------
+
+* modern Python packaging;
+* current Python/NumPy/SciPy compatibility;
+* Linux, macOS, and Windows CI;
+* automated documentation builds;
+* reproducible releases.
+
+File formats
+------------
+
+Existing format support will be preserved and progressively strengthened with real and synthetic reference datasets.
+
+Changes to parsers are expected to include regression tests demonstrating the corresponding format convention.
+
+Relationship with upstream nmrglue
+==================================
+
+``nmrglue-ng`` retains the complete Git history of nmrglue and acknowledges the original authors and all contributors whose work forms the basis of this project.
+
+Where practical, fixes developed here that are applicable to the original nmrglue project may also be proposed upstream through pull requests or reported as issues in the original repository. This may include bug fixes, regression tests, documentation improvements, compatibility updates, and clarifications of scientific or format-specific behaviour.
+
+Before opening an upstream contribution, the proposed change will be reviewed for relevance to the original project, compatibility with its maintenance policy, and consistency with its existing API and scope. Changes that are specific to ``nmrglue-ng``, or that depend on its independent development direction, will remain in this project.
+
+Likewise, useful upstream developments may be incorporated into ``nmrglue-ng`` with their original authorship and attribution preserved.
+
+The intention is not to obscure or replace the history of nmrglue, but to continue building on it transparently and, where appropriate, to contribute improvements back to the original project.
+
+Contributions
+=============
+
+Contributions are welcome, particularly:
+
+* reproducible bug reports;
+* regression tests;
+* small NMR datasets that can legally be redistributed for testing;
+* fixes for file-format readers and writers;
+* documentation improvements;
+* scientific validation against vendor software or documented format specifications;
+* performance improvements accompanied by correctness tests and benchmarks.
+
+Changes affecting scientific conventions or public API semantics may require a short design discussion before implementation.
+
+As the project develops, contribution and maintenance practices may evolve to make it easier for additional maintainers to participate.
+
+Installation
+============
+
+Install ``nmrglue-ng`` with pip::
+
+    python -m pip install nmrglue-ng
+
+Conda packages are planned after the stable 1.0.0 release. See
+`INSTALL.txt <INSTALL.txt>`_ for source and development installation options.
+
+The distribution is named ``nmrglue-ng``, while the Python import remains::
+
+    import nmrglue as ng
+
+Citation and attribution
+========================
+
+nmrglue-ng is derived from **nmrglue**, created by Jonathan J. Helmus and contributors.
+
+Users should continue to acknowledge the original nmrglue work where appropriate:
+
+    Jonathan J. Helmus and Christopher P. Jaroniec,
+
+    *Nmrglue: an open source Python package for the analysis of multidimensional NMR data*,
+
+    Journal of Biomolecular NMR (2013).
+
+A citation specific to ``nmrglue-ng`` will be provided if and when an appropriate archival release or publication becomes available.
+
+License
+=======
+
+``nmrglue-ng`` is distributed under the BSD 3-Clause License inherited from nmrglue.
+
+The original copyright notices and contributor history are preserved.
+
+See ``LICENSE.txt`` for details.
+
+----
+
+**nmrglue-ng is an independent continuation of nmrglue.**
+
+Its objective is deliberately conservative: preserve a useful and established NMR toolkit while making its maintenance, testing, documentation, and evolution sustainable.