Release notes from hpc_submit_scripts

v0.5.0

2024-02-02T08:39:25Z

What's Changed

New Features

New Slurm job scripts densmap-z_Li.sh, densmap-z_NBT.sh, densmap-z_OBT.sh, densmap-z_OE.sh, densmap-z_NTf2.sh, densmap-z_ether.sh that run the MDTools script scripts/structure/densmap.py for different compounds by @andthum in #144
Slurm job scripts discrete-z_Li_back_jump_prob_discrete.sh, renewal_events_Li-ether_back_jump_prob_discrete.sh and renewal_events_Li-NTf2_back_jump_prob_discrete.sh: Use the new command-line option of the MDTools script back_jump_prob_discrete.py, --norm-out, to receive an output file with the normalization factors used to calculate the back-jump probabilities (see andthum/mdtools#201) by @andthum in #142

Bug Fixes

Python submit scripts submit_gmx_analyses_lintf2_ether.py and submit_mdt_analyses_lintf2_ether.py: Use absolute path to Slurm job scripts by @andthum in #144 and #145
Python submit scripts submit_gmx_analyses_lintf2_ether.py and submit_mdt_analyses_lintf2_ether.py: Fix the function _submit_discretized: Reset the submit command after each loop instead of appending it by @andthum in #143 and #145
Python submit script submit_mdt_analyses_lintf2_ether.py: Convert the box length that is read from the .gro file from nanometers to Angstrom by @andthum in #143

Code Refactoring

Slurm job scripts discrete-hex_*.sh: Increase time limit by @andthum in #149
Slurm job scripts analysis/lintf2_ether/mdt/lifetime_autocorr_Li-*.sh: Decrease time limit and increase memory limit by @andthum in #148 and #150
Bash script .cleanup_mdt_analyses.sh: Change how specific analyses are gathered/ordered into sub-directories. This affects axial_hex_dist, discrete-hex, contact_hist_at_pos_change and lig_change_at_pos_change* by @andthum in #147 and #153
Slurm job scripts lig_change_at_pos_change_blocks_*.sh: Increase memory limit by @andthum in #144

Full Changelog: v0.4.0...v0.5.0

v0.4.0

2023-11-18T15:31:39Z

What's Changed

Bug fixes

Slurm job script axial_hex_dist_1nn_OBT.sh: Fix typo in analysis name by @andthum in #137
Bash script .cleanup_mdt_analyses.sh: Fix typo in cleanup of discrete-hex by @andthum in #136
Slurm job scripts discrete_hex_*.sh: Fix cleanup and the path to the MDTools script discrete_hex.py by @andthum in #136 and #137
Slurm job scripts axial_hex_dist_*nn_*.sh: Fix cleanup by @andthum in #136 and #137
Slurm job scripts contact_hist_slab-z_Li-*.sh: Fix cleanup by @andthum in #136 and #137
Slurm job scripts densmap-z_*.sh: Fix cleanup by @andthum in #136 and #137
Slurm job scripts *rdf_slab-z_*.sh: Fix cleanup by @andthum in #136 and #137

Code refactoring

Change time and memory limits of various scripts by @andthum in various pull requests

Full Changelog: v0.3.0...v0.4.0

v0.3.0

2023-10-30T08:39:37Z

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/gmx-users@gromacs.org/msg35903.html and https://www.mail-archive.com/gmx-users@gromacs.org/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

v0.2.0

2023-02-15T16:12:03Z

There have been quite some of changes since version 0.1.0. From now on, I will try to publish new releases already when there have been only small changes, so that the change log will not become overwhelming. And I will try to make the changelog more human-friendly.

What's Changed

Breaking changes

[submit_gmx_mdrun.py]: Change Default Backup Behavior by @andthum in #61
[Feat]: Support Compressed Files by @andthum in #64
Change Default of --every Option of submit_gmx_analyses_lintf2_ether.py by @andthum in #74
[energy_dist.py]: Adopt to Changed CLI of plot_energy_dist.py by @andthum in #116

New features

Create Bash Scripts to Load Compression Tools on Palma2 by @andthum in #59
[gmx energy]: Also Calculate Conserved Energy by @andthum in #60
[submit_mdt_analyses_lintf2_ether.py]: Additional --scripts Options by @andthum in #84
[submit_mdt_analyses_lintf2_ether.py]: Support .npz Archives by @andthum in #85
New Slurm Job Script subvolume charg.sh by @andthum in #87
[Feat]: New Job Script energy_dist.sh by @andthum in #92
Create Source Script vmd1-9-4_foss_cuda.sh by @andthum in #98
New Slurm Job Scripts: attribute hist* by @andthum in #104
[create_mda_universe.sh]: Create Universe for .trr Trajectory by @andthum in #115

Bug fixes

Fix Cleanup Step in msd_layer*.py Analysis Scripts by @andthum in #57
[gmx_mdrun.sh]: Add --ntasks 1 to the srun Call of gzip by @andthum in #68
[gmx_mdrun.sh]: Exit When gmx mdrun Fails by @andthum in #69
[gmx_mdrun.sh]: Exit Slurm Script with Gromacs Exit Code by @andthum in #70
Fix Log-File Search in submit_gmx_analyses_lintf2_ether.py by @andthum in #71
Fix Search for Compressed Files in submit_gmx_analyses_lintf2_ether.py by @andthum in #72
[energy.sh]: Fix Call of decompres.sh by @andthum in #82
[submit_mdt_analyses_lintf2_ether.py]: Fix Submit Option 11.3 / 11.4 by @andthum in #86
[subvolume_charge.sh]: Fix Argument Parsing by @andthum in #89
Update pre-commit Config and pyproject.toml by @andthum in #99
Fix Typo in submit_mdt_analyses_lintf2_ether.py by @andthum in #105

Dependency updates

Update flake8 by @andthum in #77
Update Config Files by @andthum in #108

Documentation updates

Fix Typos in the Developer's Guide by @andthum in #67
Add Badge "Doc Style NumPy" by @andthum in #103
Update Documentation by @andthum in #113
[submit_mdt_analyses.py]: Correct Documentation of the --mdt-path Option by @andthum in #114

Code refactoring

Refactor Analysis Scripts in analysis/lintf2_ether/* by @andthum in #62
[subvolume_charge.sh]: Change sbatch Options by @andthum in #88
[hpcssrc.ini]: Remove Unused Section by @andthum in #90
energy_dist.sh: Increase Memory Limit from 2G to 4G by @andthum in #93

Project maintenance

Grant the PR-Labeler Write Access to Pull Requests by @andthum in #58
[pull_request_template.md]: Link PR to Issue Correctly by @andthum in #63
PR Template: Change Mark for Unrelated Checkboxes by @andthum in #76
Rename shellcheckrc to .shellcheckrc by @andthum in #78
Create Config Files for VSCode by @andthum in #83
Update Project-Specific VSCode Settings by @andthum in #100
Update pre-commit-config.yaml by @andthum in #102
Fix Wrong Glob Patterns in .gitignore and settings.json by @andthum in #109
Update Configuration of Development Tools by @andthum in #110
Update GitHub Actions by @andthum in #112
Prepare Release 0.2.0 by @andthum in #117

Other changes

Unskip All pre-commit Hooks for the CI Workflow by @andthum in #52
[dependabot.yml]: Add Search Directories for pip by @andthum in #53
[dependabot.yml]: Fix directory Key by @andthum in #54
Clarify Docs about the Config File by @andthum in #55
Automatically label pull requests using issue-labler by @andthum in #56
Update flake8-isort requirement from <5.0,>=4.0 to >=4.0,<6.0 by @dependabot in #80
Update flake8-builtins requirement from <2.0,>=1.0 to >=1.0,<3.0 by @dependabot in #81
Update flake8-isort requirement from <6.0,>=4.2 to >=4.2,<7.0 by @dependabot in #94
Update sphinx requirement from <6.0,>=3.0 to >=3.0,<7.0 in /docs by @dependabot in #96
Bump github/issue-labeler from 2.5 to 2.6 by @dependabot in #106

Full Changelog: v0.1.0...v0.2.0

v0.1.0: Release of HPC Submit Scripts version 0.1.0

2022-07-15T08:29:09Z

Everything should work stable now and apply to the style guide defined in our
Developer's Guide.

Note that the analysis/lintf2_ether/pyemma has been removed. To go back to
the last state before the removal, checkout commit
2695182.