Releases: deepmodeling/reacnetgenerator
Releases · deepmodeling/reacnetgenerator
v1.6.14
What's Changed
Bugfix
- fix: use rdkit API to remove implicit hydrogens by @njzjz in #2278
- fix: fix test result sha256 by @njzjz in #2256
- fix: remove ref-names from .git_archival.txt by @njzjz-bot in #2253
Documentation
- docs: update example of read_species by @njzjz in #2238
- docs: pin sphinx-argparse to < 0.5.0 by @njzjz-bot in #2257
- docs: fix home page rendering by @njzjz in #2258
Dependencies update
- build(deps-dev): bump sass from 1.77.0 to 1.77.1 in /reacnetgenerator/static/webpack by @dependabot in #2228
- build(deps): bump pypa/cibuildwheel from 2.17 to 2.18 by @dependabot in #2229
- build(deps): bump braces from 3.0.2 to 3.0.3 in /reacnetgenerator/static/webpack by @dependabot in #2245
- build(deps): bump magnific-popup from 1.1.0 to 1.2.0 in /reacnetgenerator/static/webpack by @dependabot in #2243
- build(deps): bump CodSpeedHQ/action from 2 to 3 by @dependabot in #2259
- build(deps): bump pypa/cibuildwheel from 2.19 to 2.20 by @dependabot in #2260
- build(deps-dev): bump cssnano-preset-advanced from 7.0.1 to 7.0.5 in /reacnetgenerator/static/webpack by @dependabot in #2262
- build(deps-dev): bump css-loader from 7.1.1 to 7.1.2 in /reacnetgenerator/static/webpack by @dependabot in #2234
- build(deps): bump pypa/cibuildwheel from 2.20 to 2.21 by @dependabot in #2271
- build(deps): bump docker/build-push-action from 5 to 6 by @dependabot in #2247
- build(deps-dev): bump sass from 1.77.1 to 1.79.4 in /reacnetgenerator/static/webpack by @dependabot in #2277
- build(deps): bump jsrender from 1.0.14 to 1.0.15 in /reacnetgenerator/static/webpack by @dependabot in #2269
- build(deps-dev): bump cssnano from 7.0.1 to 7.0.6 in /reacnetgenerator/static/webpack by @dependabot in #2268
- build(deps-dev): bump postcss from 8.4.38 to 8.4.47 in /reacnetgenerator/static/webpack by @dependabot in #2272
- build(deps-dev): bump webpack from 5.91.0 to 5.95.0 in /reacnetgenerator/static/webpack by @dependabot in #2276
- build(deps-dev): bump cssnano-preset-advanced from 7.0.5 to 7.0.6 in /reacnetgenerator/static/webpack by @dependabot in #2279
- build(deps-dev): bump mini-css-extract-plugin from 2.9.0 to 2.9.1 in /reacnetgenerator/static/webpack by @dependabot in #2280
- build(deps-dev): bump sass-loader from 14.2.1 to 16.0.2 in /reacnetgenerator/static/webpack by @dependabot in #2281
- chore: bump pyright to 1.1.363 by @njzjz in #2232
CI/CD
- ci(docker): fix docker image tags by @njzjz in #2226
- build(conda): update conda file by @njzjz in #2227
- ci: use Python 3.12 for benchmark by @njzjz in #2231
- ci(wheel): use build[uv] frontend by @njzjz in #2244
Full Changelog: v1.6.13...v1.6.14
Contributors
njzjz, dependabot, and njzjz-bot
Assets 2
v1.6.13
What's Changed
Enhancement
- feat: add NumPy 2.0 support by @njzjz in #2183
- feat(build): Add Git archives version files by @njzjz-bot in #2194
- chore: faster check_zero_signal by @njzjz in #2213
- chore: temporarily use pure Python implementation of
idx_to_signalby @njzjz in #2214 - support
python -m reacnetgeneratorby @njzjz in #2212 - refact: refactor merging iso using VF2 by @njzjz in #2221
- feat: lazy import to ensure cli performance by @njzjz in #2224
- test: add benchmark for cli by @njzjz in #2222
Build
- build: migrate to scikit-build-core by @njzjz in #2203
- build: enable Python limited API by @njzjz in #2215
Documentation
- add RTD config by @njzjz in #2151
- remove
formats:allin the RTD config file by @njzjz in #2152 - docs: update urls by @njzjz in #2153
- docs: fix links after documentation migration by @njzjz in #2164
- docs: add the link to conda faq by @njzjz in #2168
- docs: setup uv for read the docs by @njzjz in #2200
- docs: add example for cell by @njzjz in #2223
- chore: add release configuration by @njzjz in #2225
CI/CD
- setup dependabot by @njzjz in #2155
- fix docker publish by @njzjz in #2154
- docker: set the master branch as the latest tag by @njzjz in #2159
- ci: setup concurrency by @njzjz in #2179
- ci: add linter for markdown, yaml, CSS, html by @njzjz in #2176
- CI: Mirror the repository to Gitee by @njzjz-bot in #2191
- CI: accelerate CI using uv by @njzjz in #2195
- ci: tidy bibtex by @njzjz in #2199
- ci(build): use uv for cibuildwheel by @njzjz in #2201
- ci: benchmark using codspeed by @njzjz in #2218
- ci(wheel): enable linux aarch64 wheel by @njzjz in #2216
Dependencies update
- chore(deps): lock file maintenance by @renovate in #2104
- chore(deps): lock file maintenance by @renovate in #2105
- chore(deps): update dependency style-loader to v3.3.4 by @renovate in #2106
- chore(deps): update dependency css-loader to v6.9.0 by @renovate in #2107
- chore(deps): update dependency mini-css-extract-plugin to v2.7.7 by @renovate in #2108
- chore(deps): lock file maintenance by @renovate in #2109
- chore(deps): lock file maintenance by @renovate in #2110
- chore(deps): update jakebailey/pyright-action action to v2 by @renovate in #2116
- chore(deps): update actions/cache action to v4 by @renovate in #2114
- chore(deps): update dependency sass to v1.70.0 by @renovate in #2117
- chore(deps): update dependency css-loader to v6.9.1 by @renovate in #2118
- chore(deps): lock file maintenance by @renovate in #2120
- chore(deps): update dependency webpack to v5.90.0 by @renovate in #2121
- chore(deps): lock file maintenance by @renovate in #2122
- chore(deps): update dependency css-loader to v6.10.0 by @renovate in #2123
- chore(deps): update dependency mini-css-extract-plugin to v2.8.0 by @renovate in #2126
- chore(deps): update dependency webpack to v5.90.1 by @renovate in #2127
- chore(deps): lock file maintenance by @renovate in #2128
- chore(deps): lock file maintenance by @renovate in #2129
- chore(deps): update dependency postcss to v8.4.34 by @renovate in #2130
- chore(deps): update dependency postcss to v8.4.35 by @renovate in #2131
- chore(deps): update yarn to v4.1.0 by @renovate in #2124
- chore(deps): lock file maintenance by @renovate in #2132
- chore(deps): update dependency postcss-import to v16.0.1 by @renovate in #2133
- chore(deps): update dependency webpack to v5.90.2 by @renovate in #2134
- chore(deps): update dependency sass to v1.71.0 by @renovate in #2135
- chore(deps): update dependency sass-loader to v14 by @renovate in #2111
- chore(deps): lock file maintenance by @renovate in #2136
- chore(deps): lock file maintenance by @renovate in #2137
- chore(deps): update dependency webpack to v5.90.3 by @renovate in #2138
- chore(deps): update dependency sass-loader to v14.1.1 by @renovate in #2139
- chore(deps): update dependency postcss-loader to v8 by @renovate in #2112
- chore(deps): update dependency css-minimizer-webpack-plugin to v6 by @renovate in #2115
- chore(deps): update dependency sass to v1.71.1 by @renovate in #2141
- chore(deps): update dependency bootstrap to v5.3.3 by @renovate in #2140
- chore(deps): update dependency cssnano to v6.0.4 by @renovate in #2142
- chore(deps): update dependency cssnano to v6.0.5 by @renovate in #2144
- chore(deps): lock file maintenance by @renovate in #2145
- chore(deps): lock file maintenance by @renovate in #2146
- chore(deps): update dependency mini-css-extract-plugin to v2.8.1 by @renovate in #2147
- chore(deps): update dependency postcss-loader to v8.1.1 by @renovate in #2148
- chore(deps): lock file maintenance by @renovate in #2149
- chore(deps): lock file maintenance by @renovate in #2150
- build(deps-dev): bump postcss from 8.4.35 to 8.4.37 in /reacnetgenerator/static/webpack by @dependabot in #2172
- build(deps): bump pypa/cibuildwheel from 2.16 to 2.17 by @dependabot in #2169
- Bump cssnano-preset-advanced from 6.0.3 to 6.1.0 in /reacnetgenerator/static/webpack by @dependabot in #2162
- Bump sass from 1.71.1 to 1.72.0 in /reacnetgenerator/static/webpack by @dependabot in #2167
- build(deps-dev): bump webpack from 5.90.3 to 5.91.0 in /reacnetgenerator/static/webpack by @dependabot in #2173
- build(deps-dev): bump cssnano from 6.0.5 to 6.1.1 in /reacnetgenerator/static/webpack by @dependabot in #2174
- build(deps-dev): bump postcss-import from 16.0.1 to 16.1.0 in /reacnetgenerator/static/webpack by @dependabot in #2177
- build(deps-dev): bump cssnano-preset-advanced from 6.1.0 to 6.1.1 in /reacnetgenerator/static/webpack by @dependabot in https://github.com/deepmodeling/reacnetge...
Contributors
renovate, njzjz, and 2 other contributors
Assets 2
v1.6.12
Breaking change
- breaking: remove implicit Hs from RDKit SMILES by @njzjz in #2102
As pointed out by #2087, the current output SMILES contains implicit Hs, making the output SMILES unclear. They are removed now.
Bugfix
CI/CD
Dependency update
- chore(deps): lock file maintenance by @renovate in #2074
- chore(deps): update dependency cssnano to v6.0.2 by @renovate in #2077
- chore(deps): update dependency regenerator-runtime to v0.14.1 by @renovate in #2081
- chore(deps): lock file maintenance by @renovate in #2082
- chore(deps): lock file maintenance by @renovate in #2083
- chore(deps): update dependency html-webpack-plugin to v5.6.0 by @renovate in #2084
- chore(deps): lock file maintenance by @renovate in #2089
- chore(deps): update dependency sass-loader to v13.3.3 by @renovate in #2090
- chore(deps): update dependency cssnano-preset-advanced to v6.0.2 by @renovate in #2078
- [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #2075
- chore(deps): update dependency postcss-loader to v7.3.4 by @renovate in #2091
- chore(deps): update dependency terser-webpack-plugin to v5.3.10 by @renovate in #2092
- chore(deps): update dependency sass to v1.69.6 by @renovate in #2093
- chore(deps): lock file maintenance by @renovate in #2094
- chore(deps): update dependency sass to v1.69.7 by @renovate in #2096
- chore(deps): update dependency cssnano to v6.0.3 by @renovate in #2098
- chore(deps): update dependency cssnano-preset-advanced to v6.0.3 by @renovate in #2099
- chore(deps): update dependency postcss to v8.4.33 by @renovate in #2100
- chore(deps): update dependency postcss-import to v16 by @renovate in #2097
- chore(deps): update actions/deploy-pages action to v4 by @renovate in #2085
- chore(deps): update actions/download-artifact action to v4 by @renovate in #2079
- chore(deps): update github/codeql-action action to v3 by @renovate in #2076
- deprecate query-string by @njzjz in #2103
Full Changelog: v1.6.11...v1.6.12
Contributors
renovate, njzjz, and pre-commit-ci
Assets 2
v1.6.11
Enhancement
- set default nproc to the number of logical CPUs the current process can use by @njzjz in #2062
- requires numpy<2 since oldest-supported-numpy is used by @njzjz in #2073
Bugfix
Documentation
CI/CD
Dependencies
- chore(deps): update dependency sass to v1.69.5 by @renovate in #2047
- chore(deps): update yarn to v4.0.1 by @renovate in #2049
- chore(deps): lock file maintenance by @renovate in #2050
- chore(deps): lock file maintenance by @renovate in #2051
- chore(deps): lock file maintenance by @renovate in #2054
- chore(deps): lock file maintenance by @renovate in #2059
- chore(deps): lock file maintenance by @renovate in #2060
- chore(deps): update yarn to v4.0.2 by @renovate in #2061
- chore(deps): lock file maintenance by @renovate in #2063
- chore(deps): lock file maintenance by @renovate in #2064
- chore(deps): lock file maintenance by @renovate in #2065
- chore(deps): update dependency animejs to v3.2.2 by @renovate in #2066
- chore(deps): lock file maintenance by @renovate in #2068
- chore(deps): lock file maintenance by @renovate in #2069
- chore(deps): update dependency html-webpack-plugin to v5.5.4 by @renovate in #2072
- chore(deps): update actions/setup-python action to v5 by @renovate in #2071
- chore(deps): update actions/deploy-pages action to v3 by @renovate in #2070
- chore(deps): update dependency postcss to v8.4.32 by @renovate in #2067
- [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #2052
Full Changelog: v1.6.10...v1.6.11
Contributors
renovate, njzjz, and pre-commit-ci
Assets 2
v1.6.10
v1.6.9
Support Python 3.12
- remove distutils by @njzjz in #2014
- drop pkg_resources by @njzjz in #2042
- build Python 3.12 wheels by @njzjz in #2017
- chore(deps): update python docker tag to v3.12 by @renovate in #2023
Enhancement
- disable the progress bar when stderr is redirected by @njzjz in #1789
- disable compactDrawing for smilesDrawer by @njzjz in #1814
- add SPDX id to each file by @njzjz in #1967
- Update setup.py by @SilentJMA in #2016
- set --dump and --type to be exclusive by @njzjz in #2041
- improve
.paginationjsstyle by @njzjz in #1833
Documentation
Tests/CI/CD
- update test configures by @njzjz in #1790
- enable python 3.11 tests by @njzjz in #1792
- ignore typing error by @njzjz in #1798
- fix tox 4 compatibility by @njzjz in #1808
- migrate coverage configs from tox.ini to pyproject.toml by @njzjz in #1791
- add pre-commit and lint by @njzjz in #1834
- add isort by @njzjz in #1839
- format numpydoc by @njzjz in #1841
- use ruff to lint codes by @njzjz in #1852
- apply more lint rules by @njzjz in #1855
- always pass codecov status by @njzjz in #1874
- fix pyright errors by @njzjz in #1920
- apply C4 rule by @njzjz in #1953
- use OIDC to publish packages by @njzjz in #1960
- improve codeql workflow by @njzjz in #1972
- enable ruff and npy rules by @njzjz in #1998
- use GitHub native depoly action and enable merge queue by @njzjz in #2027
- pyright: exclude the version file by @njzjz in #2015
- skip cp37 tests by @njzjz in #2045
Dependencies
- chore(deps): lock file maintenance by @renovate in #1782
- chore(deps): update yarn to v3.3.0 by @renovate in #1783
- chore(deps): update dependency mini-css-extract-plugin to v2.7.0 by @renovate in #1784
- chore(deps): update dependency regenerator-runtime to v0.13.11 by @renovate in #1786
- chore(deps): lock file maintenance by @renovate in #1787
- chore(deps): update dependency bootstrap to v5.2.3 by @renovate in #1788
- chore(deps): update dependency webpack-cli to v5 by @renovate in #1785
- chore(deps): update python docker tag to v3.11 by @renovate in #1753
- chore(deps): lock file maintenance by @renovate in #1793
- chore(deps): update dependency mini-css-extract-plugin to v2.7.1 by @renovate in #1794
- chore(deps): update dependency postcss-loader to v7.0.2 by @renovate in #1795
- chore(deps): update dependency query-string to v7.1.2 by @renovate in #1797
- chore(deps): update dependency query-string to v7.1.3 by @renovate in #1800
- chore(deps): update dependency postcss-import to v15.0.1 by @renovate in #1799
- chore(deps): update dependency paginationjs to v2.3.0 by @renovate in #1796
- chore(deps): update dependency paginationjs to v2.4.1 by @renovate in #1801
- chore(deps): lock file maintenance by @renovate in #1802
- chore(deps): update dependency webpack-cli to v5.0.1 by @renovate in #1803
- chore(deps): update dependency mini-css-extract-plugin to v2.7.2 by @renovate in #1804
- chore(deps): update dependency sass to v1.56.2 by @renovate in #1807
- chore(deps): update dependency postcss-import to v15.1.0 by @renovate in #1806
- chore(deps): update dependency postcss to v8.4.20 by @renovate in #1809
- chore(deps): lock file maintenance by @renovate in #1810
- chore(deps): update dependency paginationjs to v2.4.2 by @renovate in #1811
- chore(deps): update dependency smiles-drawer to v2.1.2 by @renovate in #1812
- Revert "chore(deps): update dependency smiles-drawer to v2.1.2" by @njzjz in #1815
- chore(deps): update dependency jquery to v3.6.2 by @renovate in #1816
- chore(deps): update dependency css-loader to v6.7.3 by @renovate in #1817
- chore(deps): update dependency sass to v1.57.0 by @renovate in #1818
- Update dependency smiles-drawer to v2.1.2 by @renovate in #1819
- Revert "Update dependency smiles-drawer to v2.1.2" by @njzjz in #1820
- chore(deps): disallow upgrade for smiles-drawer by @njzjz in #1821
- chore(deps): lock file maintenance by @renovate in #1822
- chore(deps): update dependency sass to v1.57.1 by @renovate in #1823
- chore(deps): update yarn to v3.3.1 by @renovate in #1824
- chore(deps): update dependency jquery to v3.6.3 by @renovate in #1825
- chore(deps): update dependency paginationjs to v2.5.0 by @renovate in #1826
- chore(deps): lock file maintenance by @renovate in #1827
- chore(deps): update dependency postcss to v8.4.21 by @renovate in #1830
- chore(deps): lock file maintenance by @renovate in #1831
- chore(deps): lock file maintenance by @renovate in #1832
- [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1836
- chore(deps): lock file maintenance by @renovate in #1835
- chore(deps): update dependency sass to v1.58.0 by @renovate in #1837
- chore(deps): update yarn to v3.4.1 by @renovate in #1840
- chore(deps): lock file maintenance by @renovate in #1842
- [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1843
- chore(deps): lock file maintenance by @renovate in #1844
- chore(deps): update dependency sass to v1.58.1 by @renovate in #1845
- chore(deps): update dependency cssnano to v5.1.15 by @renovate in #1847
- chore(deps): update dependency cssnano-preset-advanced to v5.3.10 by @renovate in #1848
- chore(deps): update dependency sass to v1.58.2 by @renovate in #1849
- chore(deps): update dependency sass to v1.58.3 by @renovate in #1850
- [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/tongzhugroup/...
Contributors
renovate, njzjz, and 2 other contributors
Assets 2
v1.6.8
Bugfix
Note: calculate_rate in previous versions gives wrong results. Please upgrade to the new version.
Other changes
- chore(deps): update dependency sass to v1.56.1 by @renovate in #1774
- chore(deps): lock file maintenance by @renovate in #1773
- chore(deps): update dependency postcss to v8.4.19 by @renovate in #1777
- chore(deps): update dependency sass-loader to v13.2.0 by @renovate in #1776
- build macos universal2 wheels by @njzjz in #1778
- chore(deps): update dependency webpack to v5.75.0 by @renovate in #1775
- chore(deps): update dependency jsrender to v1.0.12 by @renovate in #1779
- chore(deps): update dependency css-loader to v6.7.2 by @renovate in #1780
Full Changelog: v1.6.7...v1.6.8
Contributors
renovate and njzjz
Assets 2
v1.6.7
v1.6.6
What's Changed
- limit the size of options in a select to 65536 by @njzjz in #1741
- docs: migrate to sphinx book theme by @njzjz in #1742
- docs: migrate to pydata-sphinx-theme by @njzjz in #1743
- use openbabel native pbc implementation by @njzjz in #1744
- deprecate base64 for compress block by @njzjz in #1745
- fix: fix and minify docker images by @njzjz in #1746
- docs: refactor and improve user guides by @njzjz in #1747
- tests: test OB PBC bonds by @njzjz in #1749
- docs: add text besides logo by @njzjz in #1750
- add type check by @njzjz in #1751
- chore(deps): lock file maintenance by @renovate in #1752
- docs: move ipynb files into docs by @njzjz in #1756
- docs: revise docstring by @njzjz in #1757
- docs: improve citations by @njzjz in #1758
- docs: add an example to calculate_rate by @njzjz in #1759
- removes
basepythonby @njzjz in #1760 - chore(deps): update dependency cssnano to v5.1.14 by @renovate in #1761
- chore(deps): update dependency cssnano-preset-advanced to v5.3.9 by @renovate in #1762
- docs: add link to publications by @njzjz in #1763
- chore(deps): lock file maintenance by @renovate in #1764
- chore(deps): update dependency sass to v1.56.0 by @renovate in #1767
- add time to the route file by @njzjz in #1768
- improve cli help by @njzjz in #1769
- docs: add note about pip and python by @njzjz in #1770
- docs: add analysis.ipynb by @njzjz in #1771
Full Changelog: v1.6.5...v1.6.6
Contributors
renovate and njzjz
Assets 2
v1.6.5
What's Changed
- chore(deps): update dependency postcss to v8.4.17 by @renovate in #1716
- chore(deps): lock file maintenance by @renovate in #1717
- chore(deps): update dependency bootstrap to v5.2.2 by @renovate in #1718
- chore(deps): update dependency sass-loader to v13.1.0 by @renovate in #1719
- chore(deps): lock file maintenance by @renovate in #1720
- chore(deps): update dependency postcss to v8.4.18 by @renovate in #1721
- chore(deps): update dependency regenerator-runtime to v0.13.10 by @renovate in #1722
- fix coverage for multiprocessing by @njzjz in #1723
- fetch nodejs from pypi by @njzjz in #1724
- migrate from setup.py to pyproject.yaml by @njzjz in #1726
- pin nodejs to 16; rollback to manylinux_2014 by @njzjz in #1727
- move cibuildwheel config to pyproject.toml by @njzjz in #1728
- use pypi nodejs to build docs by @njzjz in #1729
- remove precss by @njzjz in #1731
- switch to VF2; fallback when RDKit throws error by @njzjz in #1730
- update project classifiers by @njzjz in #1733
- use specific package level logger; update metadata by @njzjz in #1732
- fix conda recipe; revise docs by @njzjz in #1734
- replace optimize-css-assets-webpack-plugin with css-minimizer-webpack-plugin by @njzjz in #1735
- chore(deps): lock file maintenance by @renovate in #1736
- show formula in selects by @njzjz in #1737
- switch from VF2 to SMILES but fallback to VF2 when failed by @njzjz in #1738
- build wheels on more platforms by @njzjz in #1739
- minify docs by @njzjz in #1740
Full Changelog: v1.6.4...v1.6.5
Contributors
renovate and njzjz