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Merge pull request #350 from GeoStat-Framework/prepare_1.5.2
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perpare v1.5.2
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MuellerSeb authored May 19, 2024
2 parents fd05229 + 8ad73c7 commit b80d8bb
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25 changes: 13 additions & 12 deletions .github/workflows/main.yml
Original file line number Diff line number Diff line change
Expand Up @@ -53,27 +53,21 @@ jobs:
cython-lint src/gstools/
build_wheels:
name: wheels for ${{ matrix.cfg.os }} / ${{ matrix.cfg.arch }}
runs-on: ${{ matrix.cfg.os }}
name: wheels for ${{ matrix.os }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
cfg:
- { os: ubuntu-latest, arch: x86_64 }
- { os: windows-latest, arch: AMD64 }
- { os: macos-latest, arch: x86_64 }
- { os: macos-latest, arch: arm64 }
- { os: macos-latest, arch: universal2 }
# macos-13 is an intel runner, macos-14 is apple silicon
os: [ubuntu-latest, windows-latest, macos-13, macos-14]

steps:
- uses: actions/checkout@v4
with:
fetch-depth: '0'

- name: Build wheels
uses: pypa/[email protected]
env:
CIBW_ARCHS: ${{ matrix.cfg.arch }}
uses: pypa/[email protected]
with:
output-dir: dist

Expand All @@ -87,7 +81,7 @@ jobs:
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest, windows-latest, macos-latest]
os: [ubuntu-latest, windows-latest, macos-13, macos-14]
# https://github.com/scipy/oldest-supported-numpy/blob/main/setup.cfg
ver:
- {py: '3.8', np: '==1.20.0', sp: '==1.5.4'}
Expand All @@ -96,6 +90,13 @@ jobs:
- {py: '3.11', np: '==1.23.2', sp: '==1.9.2'}
- {py: '3.12', np: '==1.26.2', sp: '==1.11.2'}
- {py: '3.12', np: '>=2.0.0rc1', sp: '>=1.13.0'}
exclude:
- os: macos-14
ver: {py: '3.8', np: '==1.20.0', sp: '==1.5.4'}
- os: macos-14
ver: {py: '3.9', np: '==1.20.0', sp: '==1.5.4'}
- os: macos-14
ver: {py: '3.10', np: '==1.21.6', sp: '==1.7.2'}
steps:
- uses: actions/checkout@v4
with:
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12 changes: 9 additions & 3 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,23 +2,28 @@

All notable changes to **GSTools** will be documented in this file.

## [Unreleased] - ?
## [1.5.2] - Nifty Neon - 2024-05

### Enhancements

- added global variable `config.NUM_THREADS` to select number of threads for parallel computation ([#336](https://github.com/GeoStat-Framework/GSTools/pull/336))
- speed up sampling with emcee by setting `vectorize=True` in `EnsembleSampler` ([#346](https://github.com/GeoStat-Framework/GSTools/pull/346))
- prepare numpy 2 support ([#340](https://github.com/GeoStat-Framework/GSTools/pull/340))
- numpy 2.0.0rc1 for building extensions (for Python 3.9 and above)
- at least numpy 2.0.0rc1 for building extensions (for Python 3.9 and above)
- check multiple numpy and scipy versions in CI
- fixed minimal versions for numpy
- use `np.asarray` everywhere with `np.atleast_(n)d`
- fix long/longlong integer issue in cython on windows by always using 64bit integers

### Bugfixes
- build docs with latest sphinx version ([#340](https://github.com/GeoStat-Framework/GSTools/pull/340))
- fixed zero division error in spectral density of Integral model ([#347](https://github.com/GeoStat-Framework/GSTools/pull/347))
- minor pylint fixes for used-before-assignment issues ([#350](https://github.com/GeoStat-Framework/GSTools/pull/350))

### Changes
- require pyvista 0.40 at least ([#340](https://github.com/GeoStat-Framework/GSTools/pull/340))
- require matplotlib 3.7 at least ([#350](https://github.com/GeoStat-Framework/GSTools/pull/350))
- remove universal2 wheels for macos (we already provide separate intel and arm64 wheels) ([#350](https://github.com/GeoStat-Framework/GSTools/pull/350))


## [1.5.1] - Nifty Neon - 2023-11
Expand Down Expand Up @@ -435,7 +440,8 @@ See: [#197](https://github.com/GeoStat-Framework/GSTools/issues/197)
First release of GSTools.


[Unreleased]: https://github.com/GeoStat-Framework/gstools/compare/v1.5.1...HEAD
[Unreleased]: https://github.com/GeoStat-Framework/gstools/compare/v1.5.2...HEAD
[1.5.2]: https://github.com/GeoStat-Framework/gstools/compare/v1.5.1...v1.5.2
[1.5.1]: https://github.com/GeoStat-Framework/gstools/compare/v1.5.0...v1.5.1
[1.5.0]: https://github.com/GeoStat-Framework/gstools/compare/v1.4.1...v1.5.0
[1.4.1]: https://github.com/GeoStat-Framework/gstools/compare/v1.4.0...v1.4.1
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6 changes: 2 additions & 4 deletions pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ dependencies = [
[project.optional-dependencies]
doc = [
"m2r2>=0.2.8",
"matplotlib>=3",
"matplotlib>=3.7",
"meshzoo>=0.7",
"numpydoc>=1.1",
"pykrige>=1.5,<2",
Expand All @@ -68,7 +68,7 @@ doc = [
"sphinxcontrib-youtube>=1.1",
]
plotting = [
"matplotlib>=3",
"matplotlib>=3.7",
"pyvista>=0.40",
]
rust = ["gstools_core>=0.2.0,<1"]
Expand Down Expand Up @@ -166,5 +166,3 @@ skip = ["cp36-*", "cp37-*", "pp*", "*-win32", "*-manylinux_i686", "*-musllinux_*
# Run the package tests using `pytest`
test-extras = "test"
test-command = "pytest -v {package}/tests"
# Skip trying to test arm64 builds on Intel Macs
test-skip = "*-macosx_arm64 *-macosx_universal2:arm64"
2 changes: 2 additions & 0 deletions src/gstools/covmodel/fit.py
Original file line number Diff line number Diff line change
Expand Up @@ -214,6 +214,7 @@ def fit_variogram(
def _pre_para(model, para_select, sill, anis):
"""Preprocess selected parameters."""
var_last = False
var_tmp = 0.0 # init value
for par in para_select:
if par not in model.arg_bounds:
raise ValueError(f"fit: unknown parameter in selection: {par}")
Expand Down Expand Up @@ -464,6 +465,7 @@ def _post_fitting(model, para, popt, anis, is_dir_vario):
fit_para = {}
para_skip = 0
opt_skip = 0
var_tmp = 0.0 # init value
for par in DEFAULT_PARA:
if para[par]:
if par == "var": # set variance last
Expand Down
10 changes: 2 additions & 8 deletions src/gstools/field/plot.py
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
plot_vec_field
"""

# pylint: disable=C0103, W0613, E1101
# pylint: disable=C0103, W0613, E1101, E0606
import numpy as np
from scipy import interpolate as inter
from scipy.spatial import ConvexHull
Expand Down Expand Up @@ -232,13 +232,6 @@ def plot_nd(
)
rax.set_title(" Plane", loc="left")
radio = RadioButtons(rax, plane_names, activecolor="grey")
# make radio buttons circular
rpos = rax.get_position().get_points()
fh, fw = fig.get_figheight(), fig.get_figwidth()
rscale = (rpos[:, 1].ptp() / rpos[:, 0].ptp()) * (fh / fw)
for circ in radio.circles:
circ.set_radius(0.06)
circ.height /= rscale
elif mesh_type == "unstructured" and convex_hull:
# show convex hull in 2D
hull = ConvexHull(pos.T)
Expand Down Expand Up @@ -291,6 +284,7 @@ def update_plane(label):
s.vline.set_data(2 * [s.valinit], [-0.1, 1.1])
s.reset()
im.set_extent(ax_extents[p])
asp = 1.0 # init value
if aspect == "quad":
asp = ax_rngs[planes[p][0]] / ax_rngs[planes[p][1]]
if aspect is not None:
Expand Down
1 change: 1 addition & 0 deletions src/gstools/krige/base.py
Original file line number Diff line number Diff line change
Expand Up @@ -337,6 +337,7 @@ def _get_krige_vecs(
# determine the chunk size
chunk_size = len(pos[0]) if chunk_slice[1] is None else chunk_slice[1]
chunk_size -= chunk_slice[0]
chunk_pos = None # init value
res = np.empty((self.krige_size, chunk_size), dtype=np.double)
if only_mean:
# set points to limit of the covariance to only get the mean
Expand Down
3 changes: 1 addition & 2 deletions src/gstools/transform/field.py
Original file line number Diff line number Diff line change
Expand Up @@ -262,8 +262,7 @@ def binary(
"""
if not process and divide is None:
_check_for_default_normal(fld)
if divide is None:
mean = 0.0 if process and not keep_mean else fld.mean
mean = 0.0 if process and not keep_mean else fld.mean
divide = mean if divide is None else divide
upper = mean + np.sqrt(fld.model.sill) if upper is None else upper
lower = mean - np.sqrt(fld.model.sill) if lower is None else lower
Expand Down

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