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glotaran / pyglotaran

A Python library for Global and Target Analysis of time-resolved spectroscopy data
GNU Lesser General Public License v3.0
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Bump the runtime-dependencies group with 3 updates #1497

Closed dependabot[bot] closed 2 months ago

dependabot[bot] commented 2 months ago

Bumps the runtime-dependencies group with 3 updates: netcdf4, openpyxl and scipy.

Updates netcdf4 from 1.7.0 to 1.7.1.post1

Changelog

Sourced from netcdf4's changelog.

version 1.7.2 (tag v1.7.2rel)

  • add static type hints (PR #1302)

version 1.7.1 (tag v1.7.1rel)

  • include nc_complex source code from v0.2.0 tag (instead of using submodule).
  • add aarch64 wheels.
Commits


Updates openpyxl from 3.1.4 to 3.1.5

Updates scipy from 1.13.1 to 1.14.0

Release notes

Sourced from scipy's releases.

SciPy 1.14.0 Release Notes

SciPy 1.14.0 is the culmination of 3 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with python -Wd and check for DeprecationWarning s). Our development attention will now shift to bug-fix releases on the 1.14.x branch, and on adding new features on the main branch.

This release requires Python 3.10+ and NumPy 1.23.5 or greater.

For running on PyPy, PyPy3 6.0+ is required.

Highlights of this release

  • SciPy now supports the new Accelerate library introduced in macOS 13.3, and has wheels built against Accelerate for macOS >=14 resulting in significant performance improvements for many linear algebra operations.
  • A new method, cobyqa, has been added to scipy.optimize.minimize - this is an interface for COBYQA (Constrained Optimization BY Quadratic Approximations), a derivative-free optimization solver, designed to supersede COBYLA, developed by the Department of Applied Mathematics, The Hong Kong Polytechnic University.
  • scipy.sparse.linalg.spsolve_triangular is now more than an order of magnitude faster in many cases.

New features

scipy.fft improvements

  • A new function, scipy.fft.prev_fast_len, has been added. This function finds the largest composite of FFT radices that is less than the target length. It is useful for discarding a minimal number of samples before FFT.

scipy.io improvements

  • wavfile now supports reading and writing of wav files in the RF64 format, allowing files greater than 4 GB in size to be handled.

scipy.constants improvements

  • Experimental support for the array API standard has been added.

... (truncated)

Commits
  • 87c4664 REL: SciPy 1.14.0 rel commit [wheel build]
  • ac63c81 Merge pull request #21019 from tylerjereddy/treddy_1.14.0_final_backports
  • 541003f DOC: update 1.14 relnotes [wheel build]
  • a08d1ff MAINT: stats.gstd: warn when an observation is <= 0
  • a4f7119 DEP: special.perm: deprecate non-integer N and k with exact=True (#20909)
  • 73339fb TST: stats: fix use of np.testing to compare xp-arrays
  • 0542df6 DOC: Update 1.14.0 release notes
  • f8e530c STY: _lib._util: silence mypy
  • e2cbda2 TST:sparse.linalg: Skip test due to sensitivity to numerical noise
  • 4fb2e6a TST: robustify test_nnls_inner_loop_case1
  • Additional commits viewable in compare view


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sonarcloud[bot] commented 2 months ago

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

github-actions[bot] commented 2 months ago

Binder :point_left: Launch a binder notebook on branch glotaran/pyglotaran/dependabot/pip/runtime-dependencies-d271523be6

github-actions[bot] commented 2 months ago

Benchmark is done. Checkout the benchmark result page. Benchmark differences below 5% might be due to CI noise.

Benchmark diff v0.7.2 vs. main ``` All benchmarks: | Change | Before [1fb14bbc] | After [477a7e92] | Ratio | Benchmark (Parameter) | |----------|------------------------------|---------------------|---------|-----------------------------------------| | | 239M | 237M | 0.99 | IntegrationTwoDatasets.peakmem_optimize | | | 1.53±0.03s | 1.45±0.07s | 0.95 | IntegrationTwoDatasets.time_optimize | ```
Benchmark diff main vs. PR ``` All benchmarks: | Change | Before [477a7e92] | After [44475818] | Ratio | Benchmark (Parameter) | |----------|----------------------|---------------------|---------|-----------------------------------------| | | 237M | 238M | 1.01 | IntegrationTwoDatasets.peakmem_optimize | | | 1.45±0.07s | 1.41±0.01s | 0.97 | IntegrationTwoDatasets.time_optimize | ```