0.3.4

Major points

• We fixed a bug where in template matching the combination of a restricted search in xyz (--search-x option, etc.) and volume split would lead to incorrect merging of subvolumes.
• Installation instructions favor building cupy against local cuda-toolkit, but for robustness also highlight the option to put a cuda-toolkit with prebuild cupy in the conda environment. However, building cupy can provide almost 2x better performance on our systems.
• We added a workaround for cupy 13.0.0 which currently broke a custom kernel.

List of PRs

• Improved installation instructions by @thorstenwagner in #69
• Update install instruction p2 by @McHaillet in #71
• Terminate other processes if one breaks by @McHaillet in #75
• parallel manager in a separate test file by @McHaillet in #78
• unittest discover requirest testfiles to start with 'test' by @sroet in #79
• calculate spectrum whitening filter only in the search region by @McHaillet in #81
• Standard deviation cut-off lower threshold by @McHaillet in #82
• Subvolume indexing bug by @McHaillet in #83
• Add scipy to requirements in setup.py by @sroet in #87
• Add tutorial wiki link to the README.md by @sroet in #86
• make json writing OS agnostic in tmjob.py by @sroet in #90
• Template.py: make filter warnings conditional and allow for no ctf_params by @sroet in #98
• experimental tophat filtering for constraining score volume peaks at extraction by @McHaillet in #91
• add docstrings to all functions by @McHaillet in #100
• Convert to pyproject.toml by @sroet in #104
• Cupy13 workaround by @McHaillet in #107
• update install instructions to prefer building cupy by @McHaillet in #108

New Contributors

• @thorstenwagner made their first contribution in #69

Full Changelog: 0.3.3...0.3.4