xtal2png - v0.9.4

What's Changed

• fixup REF for JOSS by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/201

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.9.3...v0.9.4

Scientific Software - Peer-reviewed - Python
Published by sgbaird almost 4 years ago

xtal2png - v0.9.3

Fixup references for JOSS manuscript. https://github.com/openjournals/joss-reviews/issues/4528#issuecomment-1199942110

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.9.2...v0.9.3

Scientific Software - Peer-reviewed - Python
Published by sgbaird almost 4 years ago

xtal2png - v0.9.2

What's Changed

• avoid repeat calculations of distance_matrix by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/199

Other Changes

• update authors, including adding Faris Khan by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/194
• grant acknowledgements for Hasan and Colton by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/195
• docs: update affiliation and acknowledgements by @kjappelbaum in https://github.com/sparks-baird/xtal2png/pull/196
• chore: test example by @kjappelbaum in https://github.com/sparks-baird/xtal2png/pull/188
• add T.D.S. in acknowledgment statements by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/197

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.9.1...v0.9.2

Scientific Software - Peer-reviewed - Python
Published by sgbaird almost 4 years ago

xtal2png - v0.9.1

What's Changed

• cnn-classification notebook (Created using Colaboratory) by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/175
• add regression notebook and change classification Colab badge to markdown for compatibility with nbsphinx by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/178
• fix: catch partial occupancy by @kjappelbaum in https://github.com/sparks-baird/xtal2png/pull/182
• fix: spacegroup fallback and installation docs by @kjappelbaum in https://github.com/sparks-baird/xtal2png/pull/186
• feat: add max_sites to CLI by @kjappelbaum in https://github.com/sparks-baird/xtal2png/pull/181

Other Changes

• fixup joss badge, remove leftover \autoref command by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/172
• split large block of README text into subsections by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/171
• convert colab badges from html to markdown for nbsphinx compatibility by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/173
• Revert "cnn-classification notebook (Created using Colaboratory)" by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/176
• Created using Colaboratory by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/177
• paper: update software paper by @kjappelbaum in https://github.com/sparks-baird/xtal2png/pull/183
• JOSS paper review - Docs by @kjappelbaum in https://github.com/sparks-baird/xtal2png/pull/187
• add Berend as co-author by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/191
• Revert imports until conda-forge is bumped by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/189
• response to rkurchin's editorial review by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/192

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.8.0...v0.9.1

Scientific Software - Peer-reviewed - Python
Published by sgbaird almost 4 years ago

xtal2png - v0.8.0

What's Changed

• allow for masking out redundant info from representation by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/138
• feat: encode and decode using element_coder by @kjappelbaum in https://github.com/sparks-baird/xtal2png/pull/117
• public api / top-level imports since not using namespace packages by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/143 (note still need to use original import statements until element-coder conda-forge dependency is resolved)
• feat: implement click CLI by @kjappelbaum in https://github.com/sparks-baird/xtal2png/pull/154

Other Changes

• png2xtal: if not isinstance(images, list) raise ValueError by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/137
• maxsites error msg: note about encode/decodecell_type kwargs by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/139
• testmaxsites by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/140
• replace volume with numsites and use numsites as a mask by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/141
• Response to PeterKraus software paper review comments by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/147
• Add Kevin Jablonka and Colton Seegmiller as co-authors by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/148
• mention XtalConverter as top-level API, and other links to API by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/150
• jupyter notebooks and python scripts surfaced in docs via nbsphinx by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/151
• move toctree to examples.md and use nbsphinx recommended format by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/152
• docs: paper edits by @kjappelbaum in https://github.com/sparks-baird/xtal2png/pull/153
• fixup toctree syntax by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/155
• nbsphinx_link and scripts in examples tab by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/156
• Update 2.1-xtal2png-cnn-classification.ipynb by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/158
• add ipykernel as docs req by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/157
• fixup files and content for nbsphinx_link by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/159
• add title to imagen-pytorch nb by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/160
• touching up presentation of notebooks within docs by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/161
• fix typo (as --> and) and syntax error in 2 references for smiles/selfies by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/163
• split xtal2png_test into multiple modules and test loading saved images by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/164
• Create parameters-notes.txt by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/166
• remove leftover sys.stdout restoration by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/165
• rm code graveyard in core.py by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/169
• maxdepth should be 2 for the examples toctree by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/170

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.7.0...v0.8.0

Scientific Software - Peer-reviewed - Python
Published by sgbaird almost 4 years ago

xtal2png - v0.7.0

What's Changed

• convert encode/decodeasprimitive kwargs to encode/decodecelltype kwargs by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/131

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.6.3...v0.7.0

Scientific Software - Peer-reviewed - Python
Published by sgbaird almost 4 years ago

xtal2png - v0.6.3

What's Changed

• encode/decode as primitive True by default (temporary fix) by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/130
• update imagen-pytorch example by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/123

Other Changes

• Update CONTRIBUTING.md by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/121
• remove todo's from CONTRIBUTING.md by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/124
• add badges and other image-to-image models to index.md by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/125
• fixup badges in index.md by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/126
• materials project feature ranges based on conventional unit cells by @hasan-sayeed in https://github.com/sparks-baird/xtal2png/pull/114
• replace erroneous "made with pymatviz" with ase in paper.md by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/127

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.6.2...v0.6.3

Scientific Software - Peer-reviewed - Python
Published by sgbaird almost 4 years ago

xtal2png - v0.6.2

What's Changed

Other Changes

• try except for m3gnet import if relaxondecode by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/110
• refactor to use rgb_scaling=False in imagen-pytorch example by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/107
• support RGB (3-channel) averaging in addition to grayscale images by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/111
• add num_sites and a note about displaying plotly figures by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/115
• flat is better than nested (fit refactor) by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/113
• commented "shuffle" code (might test later) and add channels variable to example scripts by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/112
• make m3gnet an optional dep and relaxondecode False by default by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/118
• tqdmifverbose wrapper fn by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/120

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.5.1...v0.6.2

Scientific Software - Peer-reviewed - Python
Published by sgbaird almost 4 years ago

xtal2png - v0.5.1

What's Changed

Other Changes

• structures <---> arrays functions get rgb_output kwarg, default True by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/104
• imagen-pytorch example by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/106
• Add tests for rgb_scaling=False by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/105

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.5.0...v0.5.1

Scientific Software - Peer-reviewed - Python
Published by sgbaird almost 4 years ago

xtal2png - v0.5.0

What's Changed

• ❗Implement m3gnet's DFT surrogate structure relaxation during decoding and use by default by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/100.
  • (Much thanks to @shyuep for support on this)
• fit method for feature ranges by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/91 as suggested by @kjappelbaum
• encode vs. decode symprec, angle_tolerance, and primitive options by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/97
• Use pymatgen StructureMatcher as initial check and preprocesser before detailed matching by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/85
• Use getrefinedstructure with symprec and angle_tolerance during decoding by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/86
• denoising diffusion notebook and script by @sgbaird and @hasan-sayeed in https://github.com/sparks-baird/xtal2png/pull/70

Other Changes

• Paper by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/67
• remove code graveyards by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/68
• minor joss paper fixes by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/69
• update paper affiliations by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/72
• Update run_grayskull.py with section order sorting by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/71
• replace strange characters with normal characters in chemical formula by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/74
• denoising diffusion probabilistic model script by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/73
• Create 2.2-xgboost-matbench-benchmark.ipynb by @sgbaird and @cseeg in https://github.com/sparks-baird/xtal2png/pull/78
• running ddpm from pretrained model and sampling by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/77
• plot of the equimolar elemental contributions using pymatviz by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/87
• fixup :func: reference by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/88
• Update 2.0-materials-project-feature-ranges.ipynb with output cells by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/90
• add attributions section by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/92
• links to google imagen by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/93
• fill distancematrix diagonals with zeros in arraysto_structures by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/95
• modify structures directly instead of appending to a new list by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/99
• update README and ipynb with m3gnet usage (/fixup syntax) by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/101

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.4.0...v0.5.0

Scientific Software - Peer-reviewed - Python
Published by sgbaird almost 4 years ago

xtal2png - v0.4.0

What's Changed

Other Changes

• available on conda-forge by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/49
• fix colab link in index.md by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/53
• add colab link to README by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/52
• fixup colab link by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/56
• add note about needing development versions of pyscaffold and extensions by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/58
• Support rgb images in png2xtal by converting to grayscale by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/62

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.3.0...v0.4.0

Scientific Software - Peer-reviewed - Python
Published by sgbaird almost 4 years ago

xtal2png - v0.1.3

setup.cfg updated Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.1.2...v0.1.3

Scientific Software - Peer-reviewed - Python
Published by sgbaird almost 4 years ago

xtal2png - v0.3.0

What's Changed

Feature ranges for a, b, c, volume, and distance are chosen based on Materials Project data for all structures with fewer than 52 sites.

Other Changes

• ranges of features by @hasan-sayeed in https://github.com/sparks-baird/xtal2png/pull/39
• Colab feature ranges notebook updates by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/45
• matplotlibify by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/40
• rename to 2.0-materials-project-feature-ranges.ipynb by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/46
• refactor abc to a, b, c to accommodate individual feature ranges by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/43
• Grayskull conda forge by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/48
• replace USERNAME with sparks-baird and conda-forge instructions by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/47

New Contributors

• @hasan-sayeed made their first contribution in https://github.com/sparks-baird/xtal2png/pull/39

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.2.1...v0.3.0

Scientific Software - Peer-reviewed - Python
Published by sgbaird almost 4 years ago

xtal2png - refs/tags/v0.2.1

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.2.0...v0.2.1

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] about 4 years ago

xtal2png - refs/tags/v0.2.0

• no changes

What's Changed

Other Changes

• sphinxrtdtheme, icon / favicon, and other conf.py settings by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/31
• forgot f in f-string in ValueError by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/32
• self.maxsites instead of maxsites by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/33
• use a larger logo by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/34
• use .ico and fixup path by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/35
• working cli via xtal2png --encode ... and xtal2png --decode ... syntax by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/37

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.1.6...v0.2.0

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] about 4 years ago

xtal2png - refs/tags/v0.1.6

What's Changed

Other Changes

• minor typos, clarification by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/29
• Fix png2xtal shape mismatch by np.stack-ing on correct axis (and add unit tests) by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/30

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.1.5...v0.1.6

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] about 4 years ago

xtal2png - v0.1.5

What's Changed

Other Changes

• resolve save_dir not found by making directory if it doesn't exist by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/28

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.1.4...v0.1.5

Scientific Software - Peer-reviewed - Python
Published by sgbaird about 4 years ago

xtal2png - v0.1.4

What's Changed

Other Changes

• Conda forge workflow - use grayskull to create meta.yaml by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/23
• Conda forge workflow, first working pass by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/24
• Create codeql-analysis.yml by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/25
• Create release.yml by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/26
• refactor to latest extension version, uses myst-parser instead by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/27

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.1.3...v0.1.4

Scientific Software - Peer-reviewed - Python
Published by sgbaird about 4 years ago

xtal2png - v0.1.2

What's Changed

• initial release and console script fixups by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/19

Full Changelog: https://github.com/sparks-baird/xtal2png/compare/v0.1.1...v0.1.2

Scientific Software - Peer-reviewed - Python
Published by sgbaird about 4 years ago