Aiida-shell

Fixes

- `ShellJob`: Fix bug when `metadata.options.output_filename` is specified [[437f2b3]](https://github.com/sphuber/aiida-shell/commit/437f2b3c656fec275ff8a5a4f710b469f6c3264c)

Fixes
- `ShellJob`: Fix `RemoteData` inputs shadowing job's own input files [[9d32bf8]](https://github.com/sphuber/aiida-shell/commit/9d32bf8b94ca30bf3657abd6cbca541151e53f56)

Dependencies
- Update requirement `aiida-core~=2.6` [[b41d007]](https://github.com/sphuber/aiida-shell/commit/b41d007231080450be58cabb020cfcbbde00d56b)

Devops
- Package: Change `Development Status` from `Alpha` to `Beta` [[fcfce35]](https://github.com/sphuber/aiida-shell/commit/fcfce35d80bba3ae3070125dea52f1ac1e0b8cfa)
- Make use of the improved `pytest` fixtures in `aiida-core` [[27a6393]](https://github.com/sphuber/aiida-shell/commit/27a63932eeca3ca80356dc0a9a0f9ef9b7b78295)

Fixes
- `ShellParser`: Prefix output filenames starting with a number [[352c309]](https://github.com/sphuber/aiida-shell/commit/352c309c0b4b5fd2c6af78dcf01013bfb6def6a6)

Docs
- Docs: Add hint on retrieving outputs from daemon submitted jobs [[31ebfbc]](https://github.com/sphuber/aiida-shell/commit/31ebfbcde77f30a34a5495f349c19424d8dc1984)

Features
- `PickledData`: Allow passing kwargs to pickler [[f94f030]](https://github.com/sphuber/aiida-shell/commit/f94f030abb36fd8f0dee60190c71b9df5e0a8a6c)
- `ShellJob`: Automatically serialize string for `arguments` [[4518221]](https://github.com/sphuber/aiida-shell/commit/451822157d9bc585254fded0352863258a7a7290)
- `launch_shell_job`: Add option to keep skip resolving of `command` [[d4ad9e7]](https://github.com/sphuber/aiida-shell/commit/d4ad9e72b26b3fd6591501e29fab2c9d70046d88)

Fixes
- Fix `InvalidOperation` raised by `aiida-core` when pickling [[0458966]](https://github.com/sphuber/aiida-shell/commit/045896653ab3f7459a6400039596400f22bb2004)
- `prepare_computer`: Check whether `default_mpiprocs_per_machine` is set [[97f0b55]](https://github.com/sphuber/aiida-shell/commit/97f0b55404f81b8020591773075721f9efd34776)
- `ShellJob`: Detect and prevent filename clashes [[415b27e]](https://github.com/sphuber/aiida-shell/commit/415b27e1ab69e98afba27a2179c095f8feca6c4b)

Changes
- Set default localhost scratch to `$TMP/aiida_shell_scratch` [[beeab21]](https://github.com/sphuber/aiida-shell/commit/beeab21f87ecb89d798fa9a142e099b8689bd478)

Dependencies
- Add support for Python 3.12 [[0ddb9c3]](https://github.com/sphuber/aiida-shell/commit/0ddb9c3178a0b76719f20d8a2ba869eb31e0147c)
- Drop support for Python 3.8 [[ab97ef7]](https://github.com/sphuber/aiida-shell/commit/ab97ef796d365c4ecd30edd2c0556f3c701c7a8d)
- Update minimum requirement `aiida-core~=2.5` (69) [[d61dd00]](https://github.com/sphuber/aiida-shell/commit/d61dd00db66a3d2d82cb18a1907da2c510272ac0)

Docs
- Add a favicon [[c439b5f]](https://github.com/sphuber/aiida-shell/commit/c439b5f592884ccb3d407d48fe8bc0f2f4a74f4c)
- Add how-to on use of `prepend_text` metadata option (67) [[d20edd1]](https://github.com/sphuber/aiida-shell/commit/d20edd1b56f7738daa2de1a03c06d4d7f19cef18)
- Add section on how to run with MPI [[adf491d]](https://github.com/sphuber/aiida-shell/commit/adf491d9973d0ecb5b9d42c6bb0fc7c63e2b73ca)
- Add section with examples [[2d9ae56]](https://github.com/sphuber/aiida-shell/commit/2d9ae56c7514e3ea290e3bafbdeb7cfb1e1c8764)
- Fix typos `option` instead of `options` [[825aad1]](https://github.com/sphuber/aiida-shell/commit/825aad1fcf2c9f94034c2f4f1e4737c6b17c635a)
- Link to AiiDA's docs for creating custom codes [[0cfbe4c]](https://github.com/sphuber/aiida-shell/commit/0cfbe4c72a0560f41af345ea4ebfab10079c5f69)

Devops
- Add pre-commit hooks to format TOML and YAML files [[1cfb428]](https://github.com/sphuber/aiida-shell/commit/1cfb42890dac545785d4235a9fd187ee6fbd69bd)

Features
- `ShellJob`: Add support for `RemoteData` nodes [[4a60253]](https://github.com/sphuber/aiida-shell/commit/4a60253210b455869e285685dfc53984204fe11c)

The `nodes` input of the `launch_shell_job` and `ShellJob` now allow `RemoteData` nodes.
Their content will be copied to the working directory of the job, just as with `SinglefileData` nodes.
See [the how-to example in the documentation](https://aiida-shell.readthedocs.io/en/latest/howto.html#running-a-shell-command-with-remote-data) for details.

- `ShellJob`: Allow entry point strings for the `parser` input [[2f4fb3d]](https://github.com/sphuber/aiida-shell/commit/2f4fb3df8e419228cf2b70ddf1aa5bd25b0ae708)
- Add the `EntryPointData` data plugin [[161cfef]](https://github.com/sphuber/aiida-shell/commit/161cfef271b4b97150c747447a9b51e28afd592d)

Fixes
- `ShellJob`: Do not copy contents of `nodes` to repository [[5d46235]](https://github.com/sphuber/aiida-shell/commit/5d4623504cb36387334356d5bfb131f30153efc8)

Changes
- `launch_shell_job`: Move `arguments` to be the second argument [[8957f59]](https://github.com/sphuber/aiida-shell/commit/8957f594405e05bfe87e0d285e771b30d8953b6f)
- Add top-level imports explicitly to `__all__` [[7fc9ba5]](https://github.com/sphuber/aiida-shell/commit/7fc9ba5aaa89f1f9c2595b3c35c35d16f70c3d6d)
- Move module `engine.launchers.shell_job` to `launch` [[a0dac1e]](https://github.com/sphuber/aiida-shell/commit/a0dac1e2f34db6cd13eafb4ebf4ac0ba2143ecba)

Docs
- Update the styling to custom theme [[0588076]](https://github.com/sphuber/aiida-shell/commit/0588076b13c8e4d818ded72c88cc899e77a771ac)
- Add example showcase of `pdb-tools` [[ae6b919]](https://github.com/sphuber/aiida-shell/commit/ae6b919492300091aa3fedbf061b50cbbbd2a5bf)
- Add the changelog to the documentation [[6bc435b]](https://github.com/sphuber/aiida-shell/commit/6bc435bece7c38ad0d8b555a0cebe3936382b637)
- Improve the logo [[42fd0de]](https://github.com/sphuber/aiida-shell/commit/42fd0def21ac9a9234fc136b582fef98ae1a0f7d)
- Fix outdated markdown style header [[a2a9294]](https://github.com/sphuber/aiida-shell/commit/a2a929478c2137726045e251fa47b3b09eb10ebb)

Devops
- Migrate to `ruff` and cleanup pre-commit config [[a591f2a]](https://github.com/sphuber/aiida-shell/commit/a591f2ab0f4d81d07eb617404df058ddd6a1f351)
- Update `setup-python` dependency in CI/CD to v4 [[3788672]](https://github.com/sphuber/aiida-shell/commit/37886727bf583e35ae7e9ea9db06ce2984cff5d7)
- Update dependency requirement `mypy==1.6.1` [[5ddb83e]](https://github.com/sphuber/aiida-shell/commit/5ddb83eef22d01ca98dc099635a0f63333129d03)

Features
- `ShellJob`: Add support for `FolderData` in `nodes` input [[9587c33]](https://github.com/sphuber/aiida-shell/commit/9587c337cd70b2dadb26a723dfa1ad4691570272)