Ecosyste.ms: Issues

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GitHub / sparks-baird/xtal2png issues and pull requests

#218 - chore(deps): bump pillow from 9.3.0 to 10.0.1

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#215 - fixup lower_tri test

Pull Request - State: closed - Opened by sgbaird over 1 year ago - 1 comment

#214 - add masking to intro tutorial

Issue - State: open - Opened by sgbaird over 1 year ago

#213 - try iterating through 3d matrix

Pull Request - State: closed - Opened by sgbaird over 1 year ago

#212 - fix docstring for mask_types and lower_tri functionality

Pull Request - State: closed - Opened by sgbaird over 1 year ago

#211 - lower_tri mask type zeros out everything

Issue - State: open - Opened by sgbaird over 1 year ago

#210 - add github source link to index.md

Pull Request - State: closed - Opened by sgbaird over 1 year ago

#209 - add github link

Pull Request - State: open - Opened by sgbaird over 1 year ago

#208 - chore(deps): bump pillow from 9.1.1 to 9.3.0

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#206 - local variable 'arr' referenced before assignment due to list of lists

Issue - State: open - Opened by sgbaird over 2 years ago
Labels: bug

#204 - use `xtal2png` with `imagen-pytorch` and `matbench-genmetrics`

Issue - State: open - Opened by sgbaird over 2 years ago - 6 comments

#203 - Update AUTHORS.md

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#201 - fixup REF for JOSS

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#200 - Generalization to building blocks rather than only atoms

Issue - State: open - Opened by sgbaird over 2 years ago - 1 comment
Labels: enhancement

#199 - avoid repeat calculations of distance_matrix

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#198 - Are the distance matrices periodic by default?

Issue - State: open - Opened by sgbaird over 2 years ago - 1 comment
Labels: question

#197 - add T.D.S. in acknowledgment statements

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#196 - docs: update affiliation and acknowledgements

Pull Request - State: closed - Opened by kjappelbaum over 2 years ago

#195 - grant acknowledgements for Hasan and Colton

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#194 - update authors, including adding Faris Khan

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#193 - Any acknowledgements that need to be added to `paper.md`?

Issue - State: closed - Opened by sgbaird over 2 years ago - 6 comments

#192 - response to rkurchin's editorial review

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#191 - add Berend as co-author

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#190 - interpretability of models trained on xtal2png

Issue - State: open - Opened by kjappelbaum over 2 years ago - 3 comments
Labels: manuscript-enhancements

#189 - Revert imports until conda-forge is bumped

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#188 - chore: test example

Pull Request - State: closed - Opened by kjappelbaum over 2 years ago - 6 comments

#187 - JOSS paper review - Docs

Pull Request - State: closed - Opened by kjappelbaum over 2 years ago

#186 - fix: spacegroup fallback and installation docs

Pull Request - State: closed - Opened by kjappelbaum over 2 years ago

#185 - JOSS paper review - Docs

Issue - State: closed - Opened by kjappelbaum over 2 years ago

#184 - JOSS paper review - Installation docs

Issue - State: closed - Opened by kjappelbaum over 2 years ago - 8 comments

#183 - paper: update software paper

Pull Request - State: closed - Opened by kjappelbaum over 2 years ago

#182 - fix: catch partial occupancy

Pull Request - State: closed - Opened by kjappelbaum over 2 years ago

#181 - feat: add `max_sites` to CLI

Pull Request - State: closed - Opened by kjappelbaum over 2 years ago

#180 - Bug: `xtal2png` error with fractional occupancy

Issue - State: closed - Opened by PeterKraus over 2 years ago - 1 comment

#179 - Suggestion: Add CLI parameter for `max_sites`

Issue - State: closed - Opened by PeterKraus over 2 years ago

#177 - Created using Colaboratory

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#176 - Revert "cnn-classification notebook (Created using Colaboratory)"

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#175 - cnn-classification notebook (Created using Colaboratory)

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#174 - Add `element-coder` to `conda-forge`

Issue - State: closed - Opened by sgbaird over 2 years ago - 4 comments
Labels: dependencies

#173 - convert colab badges from html to markdown for nbsphinx compatibility

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#172 - fixup joss badge, remove leftover \autoref command

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#171 - split large block of README text into subsections

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#170 - maxdepth should be 2 for the examples toctree

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#169 - rm code graveyard in core.py

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#168 - Create 2.1-xtal2png-cnn-regression-faris.ipynb

Pull Request - State: closed - Opened by sgbaird over 2 years ago - 2 comments

#167 - normalize lengths by the cubed root of the number of atoms

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#166 - Create parameters-notes.txt

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#165 - remove leftover sys.stdout restoration

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#164 - split xtal2png_test into multiple modules and test loading saved images

Pull Request - State: closed - Opened by sgbaird over 2 years ago - 1 comment

#161 - touching up presentation of notebooks within docs

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#160 - add title to imagen-pytorch nb

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#159 - fixup files and content for nbsphinx_link

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#158 - Update 2.1-xtal2png-cnn-classification.ipynb

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#157 - add ipykernel as docs req

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#156 - nbsphinx_link and scripts in examples tab

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#155 - fixup toctree syntax

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#154 - feat: implement click CLI

Pull Request - State: closed - Opened by kjappelbaum over 2 years ago

#153 - docs: paper edits

Pull Request - State: closed - Opened by kjappelbaum over 2 years ago - 4 comments

#152 - move toctree to examples.md and use nbsphinx recommended format

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#151 - jupyter notebooks and python scripts surfaced in docs via nbsphinx

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#150 - mention XtalConverter as top-level API, and other links to API

Pull Request - State: closed - Opened by sgbaird over 2 years ago - 1 comment

#149 - `func:` syntax issue in API docs

Issue - State: closed - Opened by sgbaird over 2 years ago - 2 comments
Labels: documentation

#148 - Add Kevin Jablonka and Colton Seegmiller as co-authors

Pull Request - State: closed - Opened by sgbaird over 2 years ago - 1 comment

#147 - Response to PeterKraus software paper review comments

Pull Request - State: closed - Opened by sgbaird over 2 years ago - 1 comment

#146 - JOSS paper review - Documentation

Issue - State: closed - Opened by PeterKraus over 2 years ago - 3 comments

#145 - `xtal2png` without arguments throws `ValueError`

Issue - State: closed - Opened by PeterKraus over 2 years ago - 2 comments

#144 - JOSS paper review - Software paper

Issue - State: closed - Opened by PeterKraus over 2 years ago - 4 comments

#143 - public api / top-level imports since not using namespace packages

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#142 - Consider making `mod_pettifor` the default elemental scale

Issue - State: open - Opened by sgbaird over 2 years ago - 2 comments

#141 - replace volume with num_sites and use num_sites as a mask

Pull Request - State: closed - Opened by sgbaird over 2 years ago - 1 comment

#140 - test_max_sites

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#139 - max_sites error msg: note about encode/decode_cell_type kwargs

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#138 - allow for masking out redundant info from representation

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#137 - png2xtal: if not isinstance(images, list) raise ValueError

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#135 - Allow for zero-ing out pairwise distance matrix or other redundant info

Issue - State: closed - Opened by sgbaird over 2 years ago
Labels: hyperparameter

#134 - consider retaining only the lower (or upper triangle) data, and setting rest to zeros

Issue - State: closed - Opened by sgbaird over 2 years ago
Labels: hyperparameter

#130 - encode/decode as primitive True by default (temporary fix)

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#129 - consider using niggli unit cells

Issue - State: closed - Opened by sgbaird over 2 years ago - 1 comment
Labels: hyperparameter

#128 - Consider normalizing "the lengths of lattice vectors with [N^(1/3)]" (inspired by CDVAE)

Issue - State: closed - Opened by sgbaird over 2 years ago - 1 comment
Labels: hyperparameter

#127 - replace erroneous "made with pymatviz" with ase in paper.md

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#126 - fixup badges in index.md

Pull Request - State: closed - Opened by sgbaird over 2 years ago

#122 - Enable forcing use of conventional cell for encoding and decoding

Issue - State: closed - Opened by sgbaird over 2 years ago - 1 comment
Labels: hyperparameter

#119 - Coordinate convolutions (e.g. CoordConv) for use in downstream convolutional models

Issue - State: open - Opened by sgbaird over 2 years ago - 1 comment
Labels: manuscript-enhancements

#117 - [WIP] feat: encode and decode using `element_coder`

Pull Request - State: closed - Opened by kjappelbaum over 2 years ago - 1 comment

#114 - materials project feature ranges based on conventional unit cells

Pull Request - State: closed - Opened by hasan-sayeed over 2 years ago - 6 comments

#98 - OOM on `matbench_mp_e_form` conversion

Issue - State: closed - Opened by sgbaird over 2 years ago - 1 comment
Labels: enhancement

#94 - Consider using Wyckoff positions instead of atomic sites

Issue - State: closed - Opened by sgbaird over 2 years ago - 4 comments
Labels: hyperparameter

#83 - consider reconstructing fractional coordinates from distance matrix (via MDS or neural network)

Issue - State: open - Opened by sgbaird over 2 years ago - 6 comments
Labels: hyperparameter

#82 - consider kwarg for mapping noble gases to a "nearby" element or (better) using different elemental featurizer

Issue - State: closed - Opened by sgbaird over 2 years ago - 13 comments
Labels: enhancement, hyperparameter

#79 - Generated, decoded structures all seem to be of P(1) symmetry

Issue - State: open - Opened by sgbaird over 2 years ago - 4 comments
Labels: bug

#75 - Permutation invariance - site ordering and data augmentation

Issue - State: open - Opened by sgbaird over 2 years ago - 4 comments
Labels: hyperparameter