v0.3.0

What's Changed

Breaking changes

• Python submit script submit_gmx_analyses_lintf2_ether.py: Replace the --every option ("read every n-th frame from the trajectory") by a --skip and --dt option. The new options mirror the -skip and -dt options of Gromacs analysis tools and therefore should by less confusing by @andthum in #126
• Slurm job scripts gmx/trjconv_*.sh: Replace the -dt option with -skip, which should be more robust (see https://www.mail-archive.com/[email protected]/msg35903.html and https://www.mail-archive.com/[email protected]/msg06868.html) by @andthum in #119
• Compress all created text output files with gzip by @andthum in #119

New features

• New Slurm job scripts renewal_events_Li-*_kaplan_meier*.sh by @andthum in #132
• New Slurm job scripts renewal_events_Li-*_back_jump_prob*.sh by @andthum in #132
• New Slurm job script discrete-z_Li_kaplan_meier_discrete.sh by @andthum in #132
• New Slurm job script discrete-z_Li_back_jump_prob_discrete.sh by @andthum in #132
• Slurm job script discrete-hex_*.sh: Additionally run the MDTools scripts scripts/discretization/back_jump_prob and scripts/discretization/kaplan_meier by @andthum in #132
• Python submit script submit_mdt_analyses_lintf2_ether.py: Submit the msd_layer* scripts together with all other bulk scripts (command-line option --scritps 1), because the issue that has prevented the msd_layer* scripts to work on bulk simulations has been fixed (see andthum/mdtools#181) by @andthum in #132
• Slurm job script gmx/energy.sh: Add -skip option by @andthum in #126

Bug fixes

• Adjust memory and time limits of various Slurm job scripts by @andthum in #123
• Increase robustness of the Bash cleanup scripts .cleanup_gmx_analyses.sh and .cleanup_mdt_analyses.sh by @andthum in #123
• Increase memory limits of some Slurm job scripts by @andthum in #122

Documentation updates

• Python submit script submit_gmx_analyses_lintf2_ether.py: Format docstring and fix error in the argparse help text that led to an error when calling the script with the -h option by @andthum in #127
• Python submit script submit_mdt_analyses_lintf2_ether.py: Fix wrong length unit: --binwidth must be given in Angstrom not nanometers by @andthum in #122

Project maintenance

• Fix Development Tools by @andthum in #122
• Include Sphinx linkcheck in CI workflow by @andthum in #118

Full Changelog: v0.2.0...v0.3.0