Pyds-cli

This version introduces several enhancements and bug fixes to improve the efficiency and reliability of the CI/CD workflows, testing strategies, and the CLI interface. Notable changes include the refinement of GitHub Actions workflows, the addition of new tests and features for analysis, and updates to the project's dependency management.

New Features

- Introduced a new analysis module with CLI integration for managing analysis projects, including project initialization and dependency management. (c257966) (Eric Ma)
- Enhanced environment setup and gitignore handling by creating a dynamic .env file and ensuring it's added to .gitignore. (882824) (Eric Ma)
- Added tomli 2.0.2 to project dependencies to support better configuration and dependency management. (c4ceb2) (Eric Ma)
- Refactored project initialization and configuration logic for improved error handling and debugging output in CLI commands. (1b6b29) (Eric Ma)
- Added pre-commit configuration for various hooks including YAML checks, end-of-file fixer, trailing whitespace, and more for improved code quality. (52a770) (Eric Ma)
- Implemented running juv in interactive mode to keep the process in the foreground, enhancing the user experience during analysis. (8f9319) (Eric Ma)
- Added new tests for running notebooks with various options, improving the test coverage for analysis functionalities. (026765) (Eric Ma)

Bug Fixes

- Corrected error output stream for nonexistent notebook checks to stderr, ensuring error messages are properly directed. (30be66) (Eric Ma)
- Ensured error message for duplicate notebook creation appears in stderr, improving error handling in CLI tests. (bbbabaf) (Eric Ma)

Deprecations

- Removed lock file update step from PyPI release workflow, streamlining the release process. (3b8d26) (Eric Ma)

This release includes several updates to the CLI configuration and test setup, as well as a version bump.

New Features

- The global git configuration has been moved from the test script to the CI workflow, and direct git command dependencies have been removed from the test scripts. This should improve the reliability and maintainability of the test setup. (b22f168) (Eric Ma)
- The CLI configuration has been updated to use GitHub Tester credentials by default. This should make it easier to use the CLI with GitHub testing. (1564e65) (Eric Ma)

Bug Fixes

- The version of the `pyds-cli` package in the `pixi.lock` file has been updated to 0.6.3 for compatibility. The SHA256 hash for the new version has also been updated. (f7bce31) (Eric Ma)
- The installation instructions in the `README.md` file have been updated to use the `pixi install` command. (7b59f66) (Eric Ma)

Deprecations

- None in this release.

This release includes improvements to the project initialization process and updates to the release notes.

New Features

- Default branch is now set to 'main' during git initialization. The initial commit after project setup is also automated. Additionally, '.pixi' has been added to the .gitignore template. (1320d97) (Eric Ma)
- Release notes for version 0.6.2 have been added. (fc77b05) (github-actions)

Bug Fixes

No bug fixes were included in this release.

Deprecations

No deprecations were included in this release.

This release includes updates to the project setup and dependency management, as well as a version bump.

New Features

- The `pixi` lockfile has been updated to ensure consistent dependency versions (68ca800, Eric Ma)
- The `environment.yml` file has been removed and `pixi-kernel` and `ipython` dependencies have been added to `pyproject.toml` to streamline dependency management (05d9399, Eric Ma)

Bug Fixes

No bug fixes were included in this release.

Deprecations

No deprecations were included in this release.

Note: The commit `c315883` is a version bump and does not contain any new features or bug fixes. The commit `0dc3c14` is the addition of release notes for the previous version and does not contain any new features or bug fixes.

This release includes several updates and improvements to the CUDA dependencies, error messages, and CI/CD system.

New Features

- Updated CUDA dependencies to use jaxlib with CUDA 12 and added system requirements for CUDA 12 on Linux 64-bit platform (0a2a1e3b, Eric Ma)
- Improved error message for missing .pixi directory and suggested running `pixi install` to create environment (29cbc5c9, Eric Ma)
- Updated pyproject.toml dependencies for ruamel.yaml and mkdocstrings (491059a3, Eric Ma)
- Introduced fixes to CI/CD system (eab8f5ff, Eric Ma)

Bug Fixes

- Removed the CUDA feature from pyproject.toml as it is no longer needed (eb8d154c, Eric Ma)
- Updated requires-python version in pyproject.toml, removed llamabot dependency from devtools, added devtools to default dependencies, imported sh.rm in tests/cli/conftest.py, and used rm to clean up temporary directory in tests (8a96bb13, Eric Ma)

Deprecations

- None in this release

This release includes several improvements and new features to enhance the development experience.

New Features

- **Pixi environment setup and adjustments**: Introduced Pixi environment setup for better dependency management and testing across different setups. This includes adding a new `pixi` command in the CLI toolset and updating the `pyproject.toml` file to define Pixi environment configurations. (129cbd7) (Eric Ma)
- **Automatic Pixi installation on ImportError**: Added automatic Pixi installation when it is not found, ensuring seamless availability for users without manual intervention. (27fc2d2) (Eric Ma)
- **Editable installation of pyds-cli in Pixi environment**: Allowed for easier development and testing of the `pyds-cli` package within its own Pixi-managed environment. (48b4b45) (Eric Ma)
- **Pre-commit dependency added**: Included pre-commit in the `pyproject.toml` file to automatically run checks before commits are made, enhancing the development workflow. (00bdac3) (Eric Ma)
- **Added cuda feature**: Introduced a new CUDA feature to support GPU-accelerated computations. (01de9b5) (Eric Ma)
- **Removed dependency on homebrew**: Simplified the environment setup by removing the dependency on Homebrew. (85ee785) (Eric Ma)

Bug Fixes

- **Improved error handling for missing Pixi dependency**: Updated the error handling mechanism when the Pixi dependency is not found, providing users with a clear error message and a link to the installation instructions. (77bebf7) (Eric Ma)
- **Replaced curl command with subprocess.run for Pixi installation**: Ensured compatibility with environments where the `sh` module might not be available or preferred, and improved the portability and security of the installation script. (fab6122) (Eric Ma)
- **Fixed missing blank lines and added extra ones for consistency**: Applied minor style fixes to various Python files in the project to ensure consistency across the codebase according to PEP 8 guidelines. (830d5fdd) (Eric Ma)

Deprecations

- **Removed conda command integration**: Simplified the CLI interface by removing the conda command and its integration from the CLI application. (5ecc31bc) (Eric Ma)
- **Removed llamabot from template**: Removed the llamabot package from the template as it is no longer required. (8abd082) (Eric Ma)
- **Removed cli tooling**: Removed the CLI tooling as it is no longer needed in the project. (03a0d0e) (Eric Ma)
- **Removed unused CLI commands and updated project templates**: Refactored the CLI interface by removing unused commands and updating project templates to reflect the changes. (0b5872b) (Eric Ma)
- **Removed unused `docs` command and `cfgv` dependency**: Simplified the CLI application by removing unused components and dependencies, potentially reducing the maintenance overhead and improving the installation time for users. (68ac4c0) (Eric Ma)