Add scatter plot #37

Pepe-Marquez · 2024-11-21T08:52:50Z

Summary by Sourcery

Add a scatter plot feature to the perovskite ions app and enhance the documentation with new guides and acknowledgments. Refactor widget layout configuration for better readability and update tests to accommodate changes.

New Features:

Introduce a scatter plot feature in the perovskite ions app, allowing visualization of data with customizable axes and markers.

Enhancements:

Refactor the layout configuration for widgets in the perovskite ions app to improve readability and maintainability.

Documentation:

Update the documentation to include new sections on creating perovskite compositions, adding new ions, exporting cation structures, and searching for ions.
Add badges and acknowledgments to the documentation, enhancing its presentation and providing credit to contributors.

Tests:

Modify the test for importing the solar cell app to ignore type checking, ensuring compatibility with the updated code.

sourcery-ai · 2024-11-21T08:52:54Z

Reviewer's Guide by Sourcery

This PR adds a scatter plot widget to the perovskite ions app and reorganizes the documentation structure. The scatter plot visualizes the relationship between A cation molar mass and number of atoms, with structural type as a color marker. The documentation changes include improved organization, new how-to guides, and additional resources.

No diagrams generated as the changes look simple and do not need a visual representation.

File-Level Changes

Change	Details	Files
Added a new scatter plot widget to visualize perovskite ion relationships	Implemented scatter plot with A cation molar mass vs number of atoms Added color coding based on structural type Configured responsive layout settings for different screen sizes	`src/perovskite_solar_cell_database/apps/perovskite_ions_app.py`
Restructured and enhanced documentation	Added new how-to guides for ion-related operations Reorganized navigation structure Added EU funding and project logos Updated installation instructions Improved homepage content organization	`docs/index.md` `mkdocs.yml` `docs/how_to/install_this_plugin.md` `docs/how_to/create_a_perovskite_composition.md` `docs/how_to/add_a_new_ion.md` `docs/how_to/export_a_cation_structure.md` `docs/how_to/search_for_ions.md` `docs/tutorial/sharing_a_perovskite_composition.md`

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sourcery-ai

Hey @Pepe-Marquez - I've reviewed your changes and they look great!

Here's what I looked at during the review

🟡 General issues: 3 issues found
🟢 Security: all looks good
🟡 Testing: 1 issue found
🟡 Complexity: 1 issue found
🟢 Documentation: all looks good

Sourcery is free for open source - if you like our reviews please consider sharing them ✨

_{Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.}

sourcery-ai · 2024-11-21T08:53:46Z

src/perovskite_solar_cell_database/apps/perovskite_ions_app.py

+                    h: 6
+                    w: 9
+                    y: 0
+                    x: .inf


issue (bug_risk): Invalid x coordinate value '.inf' in xxl layout

The x coordinate value '.inf' is invalid and could cause rendering issues. Please specify a valid numeric value.

sourcery-ai · 2024-11-21T08:53:46Z

tests/apps/test_solar_cell_app.py

+    from perovskite_solar_cell_database.apps.solar_cell_app import (  # type: ignore
        solar_cell_app,  # noqa: F401


issue (testing): Missing tests for the new scatter plot functionality

The PR adds a new scatter plot widget but there are no tests to verify its configuration and behavior. Consider adding tests that verify:

The scatter plot widget is properly configured with the correct search quantities

The layout parameters are correct for different screen sizes

The autorange and marker settings work as expected

sourcery-ai · 2024-11-21T08:53:46Z

docs/index.md


-  [<img src="assets/screenshot_nomad_app.png">](https://nomad-lab.eu/prod/v1/staging/gui/search/solarcells)
+It also contains a database of ions used in halide perovskites and a schema to create standarized perovskite composition entries.


suggestion (typo): Fix typo: 'standarized' should be 'standardized'

Suggested change

It also contains a database of ions used in halide perovskites and a schema to create standarized perovskite composition entries.

It also contains a database of ions used in halide perovskites and a schema to create standardized perovskite composition entries.

sourcery-ai · 2024-11-21T08:53:47Z

docs/index.md

+
+### Acknowledgments
+Special thanks to Jinzhao Li and all contributors who have made this project possible.
+This project is supported by the FAIRmat NFDI initiative and also by by the European Union as part of the SolMates project (Project Nr. 101122288).


suggestion (typo): Remove duplicate word 'by'

The sentence contains a duplicate 'by'. Consider revising to 'supported by the FAIRmat NFDI initiative and also by the European Union'

Suggested change

This project is supported by the FAIRmat NFDI initiative and also by by the European Union as part of the SolMates project (Project Nr. 101122288).

This project is supported by the FAIRmat NFDI initiative and also by the European Union as part of the SolMates project (Project Nr. 101122288).

sourcery-ai · 2024-11-21T08:53:47Z

src/perovskite_solar_cell_database/apps/perovskite_ions_app.py

-                  md: {minH: 8, minW: 12, h: 8, w: 12, y: 0, x: 0}
-                  sm: {minH: 8, minW: 12, h: 8, w: 12, y: 0, x: 0}
-                type: periodictable
+                - type: periodictable


issue (complexity): Consider using YAML anchors and aliases to define reusable layout configurations.

The layout configuration can be simplified using YAML anchors and aliases to reduce repetition while maintaining the same functionality. Here's how:

widgets: - type: periodictable scale: linear search_quantity: results.material.elements layout: # Define base layout template &base_layout minH: 8 minW: 12 y: 0 x: 0 xxl: <<: *base_layout h: 9 w: 13 xl: <<: *base_layout h: 9 w: 12 lg: &standard_size <<: *base_layout h: 8 w: 12 md: <<: *standard_size sm: <<: *standard_size

This approach:

Defines common properties once using &base_layout

Uses <<: *base_layout to inherit common properties

Only specifies values that differ for each screen size

Further reduces duplication by reusing identical sizes with &standard_size

The same pattern can be applied to the scatter_plot widget's layout.

Pepe-Marquez added 3 commits November 20, 2024 16:00

Modified docs structure for the ions database.

2759489

Fixed some typos.

d7e6c10

Added scatter plot widget

5887270

sourcery-ai bot reviewed Nov 21, 2024

View reviewed changes

Pepe-Marquez closed this Nov 21, 2024

Pepe-Marquez deleted the add-scatter-plot branch November 21, 2024 09:00

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Add scatter plot #37

Add scatter plot #37

Pepe-Marquez commented Nov 21, 2024 •

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		from perovskite_solar_cell_database.apps.solar_cell_app import ( # type: ignore
		solar_cell_app, # noqa: F401


		[<img src="assets/screenshot_nomad_app.png">](https://nomad-lab.eu/prod/v1/staging/gui/search/solarcells)
		It also contains a database of ions used in halide perovskites and a schema to create standarized perovskite composition entries.

	This project is supported by the FAIRmat NFDI initiative and also by by the European Union as part of the SolMates project (Project Nr. 101122288).
	This project is supported by the FAIRmat NFDI initiative and also by the European Union as part of the SolMates project (Project Nr. 101122288).

Add scatter plot #37

Add scatter plot #37

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Pepe-Marquez commented Nov 21, 2024 • edited by sourcery-ai bot Loading

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Pepe-Marquez commented Nov 21, 2024 •

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