Mols2grid

Added
- A proper documentation page with tutorials can now be accessed online.
- Added a `single_highlight=False` parameter to only highlight a single match per
molecule in substructure queries.
- Added a *"Check matching"* button that only selects items that match the current search
and/or filters.
- Added `custom_css`, `custom_header` and `sort_by` to the "table" template
Changed
- Compounds matching a substructure search are now aligned to the query molecule before
rendering the image.
- When doing a substructure search, all matches are now highlighted by default. To only
show a single one, use `single_highlight=True`.
- The *Check all*, *Uncheck all* and *Invert* selection buttons have been fixed. They now
actually check/uncheck ALL items, and not just the ones matching the current search. A
*Check matching* button has been added to reproduce the old behaviour.
- If both `subset` and `tooltip` are `None`, the index and image will be directly
displayed on the grid while the remaining fields will be in the tooltip. This makes the
default representation much more readable.
- The default number of columns is now 5 for `template="table"` (same as the other default
template)
Fixed
- `template="table"` now correctly displays images when `prerender=True` (Issue 27)
- Displaying the grid with `template="table"` in a notebook now automatically fits to the
content of the table.

Fixed
- Field names containing spaces are now correctly delt with
- The text search now looks for matches inside the values of the tooltip fields, rather
than inside the HTML code of the tooltip which included tags and other irrelevant text
- Fixed an encoding bug when saving the grid as an HTML file on French Windows, which uses
CP-1252 encoding instead of UTF-8

Added
- `cache_selection=True` allows to retrieve the checkbox state when re-displaying a grid,
as long as they have the same name. Fixes 22
- `prerender=False` moves the rendering of molecule images from Python to the browser and
only when the molecule is on the current page, giving a performance boost and allowing
to process much larger files. Fixes 17
- `substruct_highlight=True` highlight the atoms that matched the substructure query when
using the SMARTS search (only available when `prerender=False`). Fixes 18
- Added CSV save option. Exports all the data present in `subset` and `tooltip` for the
current selection
- Support for `.sdf.gz` files
- Added automated tests of the interface, which should prevent future updates from
breaking things
Changed
- Python 3.6 is no longer supported
- Molecule images are now generated by the web browser (see `prerender=False` argument)
- The coordinates of the input file are now ignored by default (`use_coords=False`). This
change was made to comply with generating images from SMILES string with the browser by
default.
- Python callbacks are now automatically registered in Google Colab
- Javascript callbacks can access RDKit as either `RDKit` or `RDKitModule`
- The "img" field is now available from the callback data
- The `subset` parameter now throws an error if "img" is not present
- Clicking "Check all"/"Uncheck all" should now be faster
- Bumped RDKit JS version to `2021.9.4` to better support moldrawoptions
- Installation now requires `jinja2>=2.11.0` to prevent an error when given a pathlib.Path
object instead of a string
Fixed
- Callbacks now work when `selection=False`. Fixes: Issue 22
- Using both `transform` and `style` should now display the labels as expected in the
tooltip
- Fixed a race condition when clicking checkboxes on different grids
- Fixed the `gap` argument not being properly taken into account
- Automatic resizing of the iframe (used in `mols2Grid.display`) should now work even
better

Added
- The grid can be filtered using pandas DataFrame's `query` and `loc` logic (mostly
useful to combine with ipywidgets) with `MolGrid.filter_by_index` and `MolGrid.filter`.
- Selections can now be modified (select and unselect all, or invert) and exported (to
clipboard or a SMILES file) even without a notebook kernel. Fixes: Issue 16.
- The grid can be sorted according to the selection status and to values in the tooltips.
- Added tracking the selection in multiple grids at the same time (i.e. it's not a
global object that get's overwritten anymore).
- Added support for executing custom JavaScript code or Python function when clicking on
a molecule's image through the `callback` argument.
- Added the `mols2grid.make_popup_callback` helper function to create a popup-like window
as a JavaScript callback.
- Added styling for the whole cell through `style={"__all__": userfunction}`.
- Added `mols2grid.get_selection()` allowing users to specify which grid selection should
be returned. Without argument, the most recently updated grid is returned.
- Added `mols2grid.list_grids()` to return a list of grid names available.
- Added the `mols2grid.sdf_to_dataframe` function to easily convert an SDF file to a
pandas DataFrame.
- Added the `custom_css` argument to pass custom CSS for the HTML document.
- Added the `sort_by` argument to change how the grid elements are ordered
Changed
- The functions in `style` and `transform` are now also applied to tooltips.
- The sizing of the iframe displaying the grid is now fully automated and more precise.
- Reorganized the code to separate the JS, CSS and HTML templates.
Fixed
- Fixed `mols2grid.save` that returned an error about missing the `output` argument.
- The tooltip is now compatible with the "focus" mode: `tooltip_trigger="focus"`.
- Fixed rendering SVG images in tooltips.
Deprecated
- Deprecated `mols2grid.selection` in favor of `mols2grid.get_selection()`.
- Deprecated `mapping` in favor of `rename` in the MolGrid class and `mols2grid.display`.

Changed
- Javascript module for RDKit is now sourced from `unpkg.com` and pinned to `v2021.3.2`

Added
- New `transform` parameter that accepts a dictionary of field-function items where each
function transforms the input value that will be displayed. Fixes: Issue 10
Fixed
- Running mols2grid could throw an ImportError (instead of ModuleNotFoundError) if the
`google` module was installed, but not `google.colab`. Solved by PR 11
- Private molecule properties (i.e properties starting with `_`) were not registered when
reading properties from RDKit molecules (SDF or list of mols).