[pre-commit.ci] pre-commit autoupdate #206
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
![pre-commit-ci[bot]](https://avatars.githubusercontent.com/in/68672?s=60&v=4){kind=small}
updates: - [github.com/psf/black: 23.12.0 → 23.12.1](psf/black@23.12.0...23.12.1) - [github.com/astral-sh/ruff-pre-commit: v0.1.8 → v0.1.9](astral-sh/ruff-pre-commit@v0.1.8...v0.1.9)
Ali-Tehrani
pushed a commit
that referenced
this pull request
Jan 17, 2024
updates: - [github.com/psf/black: 23.12.0 → 23.12.1](psf/black@23.12.0...23.12.1) - [github.com/astral-sh/ruff-pre-commit: v0.1.8 → v0.1.9](astral-sh/ruff-pre-commit@v0.1.8...v0.1.9) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Ali-Tehrani
added a commit
that referenced
this pull request
Jan 17, 2024
* Add Cubic grid tutorial from Quickstart.ipynb * Combine the two cubic grids together * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Remove warning in notebook and labels * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Remove cubic grid notebook * Make var names consistent * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Disable zero division warning in BeckeRTransform BeckeRTransform of certain OneDGrids with points at 1.0 (like Trapezoidal) resulted in RuntimeWarning: divide by zero encountered in deriv and deriv2 methods. To avoid printing a warning message, the zero devision was disabled. * Add class attribute name to various OneDGrid subclasses To simply tutorials and make it easier to keep track of the name of 1-dimensional grids, name was added as a class attribute. * Improve One_dimensional_grids.ipynb notebook * Update oned notebook - Add relative error for [0, infty) integration - Added log plot to one of the plots * [pre-commit.ci] pre-commit autoupdate (#206) updates: - [github.com/psf/black: 23.12.0 → 23.12.1](psf/black@23.12.0...23.12.1) - [github.com/astral-sh/ruff-pre-commit: v0.1.8 → v0.1.9](astral-sh/ruff-pre-commit@v0.1.8...v0.1.9) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Minor changes to the One_dimensional_grids.ipynb * Add interpolated derivative example * Update quickstart notebook - Fix some typos - Fix the headings for the website * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Minor changes to Quickstart.ipynb * Add little things to radial \rho example 1. The explanation on the angular integration was improved 2. The maxima of the radial electron density distribution were found using scipy. * Update gbasis from_iodata API change This API change is described in theochem/gbasis#140 * Add a comment for finding local maxima of radial density * Add default PowerRTransform params to utils * Add default rgrid to from_preset in atomgrid * Fix that default rgrid is in angstorm * Add helper function to generate default rgrid * Add default rgrid to from_preset in molgrid - Also change tests * Add default rgrid to mol from_size and from_pruned - Change tests as well * Fix bug in atomgrid with default rgrid * Decrease accuracy of ode test - Failed because it was on the boundary of accuracy * Fix def rgrid in molgrid and add tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix linters issue * Change random test so that it passes in ode * Add aim_weights default for Molgrid.from_preset * Add default aim_weights to MolGrid.from_size * Add default aim_weights to MolGrid.from_pruned * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix ruff linter * Clarification on converting A^o to a.u. * Remove *_ from MolGrid.from_preset * Fix improt for scipy.constants * Remove * from AtomicGrid class * Add angstrom scipy conversion * Remove sub-test where ode doesn't converge - Happens multiple times, note test is randomized * Fix ruff linter * Define ang2bohr conversion factor * Add example of local(atomic) property integation Added an example showing how to extratct a local or atomic grid from a molecular grid and integrate the local property. * Update gbasis from_iodata API change This API change is described in theochem/gbasis#140 * Minor updates to doc/notebooks/Molecular_Grid.ipynb * Add method to define uniform grid from cube file The method has two options, that depend on the `grid_only` parameter. If `grid_only` is True, only the grid is returned else the tuple (atnums, atcorrds, grid) is returned. * Add method to UniformGrid to save cubes * Change return of from_cube method * Add test for uniform grid from cube * Add test for UniformGrid:generate_cube * Add cube file for test * Rename grid_only argument to return_date This name is more consistent with other Python packages. * Fix typo * Parse and return the data section of cube file * Add the line that was not added in the previous commit * Remove example from docstring * Enhance 'Angular_grid' notebook This commit refines the 'Angular_grid' notebook by: 1. Adding examples of grid creation for symmetric spherical grids. 2. Improving the output formatting of select cells for readability. 3. Introducing test statements to validate cell results. * Remove tests from notebook * Minor improvements to Angular_grid.ipynb * [pre-commit.ci] pre-commit autoupdate (#217) updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.1.11](astral-sh/ruff-pre-commit@v0.1.9...v0.1.11) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add JCP_Paper Jupyter notebook * Add open in colab badge * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix colab link to point to main repo * Added missing square root to real spherical harmonics equation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.11 → v0.1.13](astral-sh/ruff-pre-commit@v0.1.11...v0.1.13) * Fix Poisson example * Refactor docs website (#218) * Move jupyter notebooks to examples folder in main * Update year in conf * Add nbsphinx-link to conf.py to link notebooks - Needed to link website to notebooks outside of the doc folder * Construct nblink for every externel jup notebook * Add toc link to jupyter notebook via nbsphinx-link * Add nbsphinx-link to requirements.txt * Fix weird typo introduced in onedgrid examples * Rename table of contents title * Remove unused Becke reference - Removes warning message in sphinx - Updated to current api for .from_* methods * Update documentation to remove some sphinx errors * Add talbe link to oned juypter notebooks * Update hyperlinks and title in atom_grid_construct * Change get_rgrid_size to private - So it doesn't show up in the documentation * Fix wrong solution to Poisson example - The error is incredibly small after fix * Fix spacing in equation so it fits into page - The equations go out of page in the webstie * Fix so that bullet points show up - Docutils need to be version 0.16 - Extensions need to have the theme - stackoverflow: 67542699/readthedocs-sphinx-not-rendering-bullet-list-from-rst-file * Fix table to show angular grids link correctly * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add instructions on how to build the website * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix ruff linters on cubic and test_cubic * Update citations * Update atom grid notebook to match new api * Add jupyter notebook * Update jupyter github action workflow * Remove .png from gitignore for jup notebooks - Jupyter notebooks create .png files and so we need them for the website * Try website github actions push * Try again * Try again but with artifacts removed * Remove pip install with editable mode on * Try upgrading pip because installation UNKNOWN * Try again forgot html keyword * Add new extensions to pyproject.toml * Try again: Add pandoc installation fix * Try again: Add pandoc installation fix 2 * Try again: add explicit pandoc installation * Try again: add github token * Try again: add github token2 * Try again: add permission to github token * Try again: add permission to github token2 * Try again: add permission to github token3 * Try again: add permission to github token4 * Try again:update website * Try again: create gh-page branch * Update multipole moment notebook * Update JCP paper to match paper * Update hoe website is automatically updated * Update pre-commit to exclude certain directories * Update juypter notebook * Update molecular grid to include iodata/gbasis * Decreaes accuracy of certain test --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Update README.md * Update installation.rst * Combine the two cubic grids together * Remove warning in notebook and labels * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Delete moved notebooks * Update cubic grid to new gbasis API * Fix correupt Cubic grid notebook * Update cubic grid --------- Co-authored-by: Marco Martínez González <[email protected]> Co-authored-by: Ali-Tehrani <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Sebastian Pujalte <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
updates: