8000 Release v*.*.* by github-actions[bot] · Pull Request #2 · romerogroup/MatGraphDB · GitHub
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Release v*.*.* #2

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Release v*.*.* #2

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@github-actions github-actions bot commented May 8, 2025

Automated Release PR for next-release

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github-actions bot commented May 8, 2025

PR #1 Summary - Added to Release PR

Generated on: 2025-05-08 13:49:59

Bugs
  • No changes
New Features
  • Added a GitHub Actions workflow to auto-generate and upload a draft PDF for the JOSS paper, committing updates back to main
  • Introduced Python scripts powered by OpenAI’s API to classify and summarize PR commits and comments for automated release notes
  • Created a workflow to trigger these summarization scripts on merges to main
  • Implemented CI workflows that run tests across multiple OSes and Python versions and build Sphinx documentation on pull requests
Documentation
  • Restructured docs: moved Sphinx source to docs/, removed outdated files, and added .readthedocs.yaml for Read the Docs
  • Added CONTRIBUTING.md with setup, testing, and contribution guidelines and updated README to link to it
Maintenance
  • Removed obsolete workflows (Python package upload and draft PDF generation) and deleted unused environment files (env.yml, my_env.yml) and legacy scripts
  • Updated .gitignore to exclude logs, notes, my_tests/, and data/ directories
  • Refined pyproject.toml dependencies: added pytest, pytest-cov, Sphinx packages; removed unused llm deps; moved dev deps to the dev section
  • Deleted redundant _version.py file as versioning is managed elsewhere

This comment was automatically generated by the release workflow.

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github-actions bot commented May 9, 2025

PR #3 Summary - Added to Release PR

Generated on: 2025-05-09 15:58:12

Bugs
  • None identified
New features
  • Implemented a continuous pytest script that logs failures with timestamps and supports graceful shutdown.
Documentation updates
  • Clarified ML installation steps in README and pyproject.toml, covering both CPU and GPU setups.
  • Restructured API docs for materials and node generators; relocated MatGraphDB documentation to a new file.
  • Updated notebook imports and metadata (Getting Started and Graph Generators) to align with the refactored core package and disable execution during builds.
Maintenance
  • Migrated GraphDB to the parquetdb package as ParquetGraphDB and refactored MatGraphDB into a wrapper.
  • Consolidated MaterialStore and MatGraphDB into the core package and updated all import paths.
  • Cleaned up pyproject.toml optional dependencies: added an ML group, reordered entries, and removed unused packages.
  • Refactored tests to use ParquetGraphDB, HeteroGraphBuilder, and Path-based temporary directories.
  • Renamed the data module to builders and updated GraphBuilder references to HeteroGraphBuilder.
  • Removed the verbosity parameter from MaterialStore methods and adjusted related tests.
  • Renamed matgraphdb_base.py to matgraphdb.py and updated corresponding imports.
  • Updated .gitignore to exclude tmp.py and refreshed the material_0.parquet test data.

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github-actions bot commented May 9, 2025

PR #4 Summary - Added to Release PR

Generated on: 2025-05-09 17:29:01

Bugs
  • None identified
New Features
  • None identified
Documentation
  • None identified
Maintenance
  • Refactored logging and configuration: added custom formatter, auto-generate user config, and removed deprecated YAML settings
  • Removed unused calculations module and its files
  • Deleted redundant graph_kit module and its files
  • Reorganized edge/node generators: updated import paths, moved to matgraphdb.generators, and created MaterialStore
  • Standardized logging utility: replaced set_verbosity with set_verbose_level in log_utils
  • Updated material_0.parquet test data to reflect directory restructure

This comment was automatically generated by the release workflow.

lllangWV and others added 13 commits May 10, 2025 11:09
Refactored the documentation configuration in `conf.py` to use
Pathlib for better path management. Updated the logic for copying
example files and the CONTRIBUTING.md file to the documentation
source directory. Removed the old CONTRIBUTING.rst file as part
of this update, streamlining the documentation structure and
ensuring all necessary files are correctly referenced.

This change enhances maintainability and prepares for future
documentation updates.
Eliminated unused commented-out code related to example paths in
`conf.py`. This change helps to clean up the documentation
configuration file, improving readability and maintainability
without affecting functionality.
Changed the assignment of SRC_DIR in `conf.py` to use the parent
directory of the current file. This adjustment improves path
management and aligns with the updated structure established in
previous commits, enhancing maintainability of the documentation
configuration.
Included `myst_parser` in the docu
8000
mentation dependencies within
`pyproject.toml`. This addition enables support for MyST Markdown,
enhancing the documentation capabilities and allowing for more
flexible content formatting.
Replaced multiple individual development dependencies with a single
entry for `matgraphdb[docs,tests]`. This change simplifies the
dependency management in the project and ensures that all necessary
packages for documentation and testing are included in one line,
improving clarity and maintainability of the configuration.
Moved the tutorials form the docs source to the examples directory.

Updated the index.rst file to include links to the new tutorial
notebooks, ensuring easy navigation for users seeking to learn
about MatGraphDB.
Added pyrightconfig.json to .gitignore to prevent tracking of the
configuration file. Removed the existing pyrightconfig.json file as
it was no longer needed, streamlining the project structure and
ensuring unnecessary files are not included in version control.
Enhanced the README by adding documentation and project links for
better navigation. Clarified the relationship with `ParquetGraphDB`
and updated references to the CONTRIBUTING and LICENSE files. This
improves user experience and accessibility of important resources.
Modified the .gitignore file to ensure the data directory is ignored
by adding a wildcard entry for *data/. This change prevents tracking
of any files within the data directory, maintaining a cleaner project
structure and avoiding unnecessary file inclusion in version control.
Introduced a new Jupyter notebook for building a materials graph
database using the MPNearHull dataset. This example demonstrates
the process of importing libraries, downloading data, and setting
up a MatGraphDB instance.

Updated the index.rst files to include links to the new tutorials
and applications sections, improving navigation for users seeking
to explore MatGraphDB functionalities.
Removed links to the tutorials section in index.rst as they are no
longer relevant. This change streamlines the documentation and
improves clarity for users navigating the examples of MatGraphDB.
Changed the title in index.rst from "Getting Started" to "MPNearHull Dataset"
to accurately represent the content of the example. This update improves
navigation and clarity for users exploring the MatGraphDB documentation.
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PR #5 Summary - Added to Release PR

Generated on: 2025-05-15 12:57:13

Bugs
  • None identified
New Features
  • Added myst_parser to enable MyST Markdown support
  • Introduced an MPNearHull dataset example notebook and updated index links
Documentation
  • Restructured conf.py to use pathlib, removed commented-out code, and updated SRC_DIR
  • Migrated tutorials from the docs source to an examples directory and updated index.rst
  • Cleaned up outdated tutorial links and renamed index titles for clarity
  • Enhanced README with clear links to documentation, CONTRIBUTING, LICENSE, and ParquetGraphDB
Maintenance
  • Consolidated development dependencies into a single matgraphdb[docs,tests] entry in pyproject.toml
  • Updated .gitignore to exclude pyrightconfig.json and the data directory; removed the obsolete pyrightconfig.json file

This comment was automatically generated by the release workflow.

lllangWV and others added 2 commits May 15, 2025 09:01
Introduced a new CSS file, notebook.css, to cap output areas at 15 lines
and enable scrolling for better readability in Jupyter notebooks. Updated
conf.py to include this new stylesheet alongside the existing custom.css,
enhancing the visual presentation of output in the documentation.
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PR #6 Summary - Added to Release PR

Generated on: 2025-05-15 13:03:44

Bugs
  • None identified
New features
  • None identified
Documentation updates
  • Added notebook.css to cap output areas at 15 lines and enable scrolling in Jupyter notebook docs; updated conf.py to include it alongside custom.css
Maintenance
  • None identified

This comment was automatically generated by the release workflow.

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