Leighton Pritchard

Same here, occurred with the update to 1.29.0

I see the same issue as @deprekate, with Java 18: ```bash % java --version [3:09:29] java 18.0.1.1 2022-04-22 Java(TM) SE Runtime Environment (build 18.0.1.1+2-6) Java HotSpot(TM) 64-Bit Server VM (build...

I don't know if it would, either. It's hard to beat O(1) for efficiency, so we'd gain nothing from changing to a set at this point, I think (though it...

I looked at `pyani_orm.py` for comparison - `filter_existing_comparisons()` seems to append the same number of tuples to a list without losing efficiency.

`gc.disable()`/`gc.enable()` didn't appear to have an effect, nor did substituting a `deque` for a list. Replacing the `list` with a `set` makes it substantially slower. The rate of appending drops...

Batching gave an average speed-up of about 100x - very fast! -until it fell over at 400k jobs. I don't yet understand why that happened.

With batching, it appears that the script enters a `D` (uninterruptible IO) state when `joblist` in `generate_joblist()` reaches ≈450000 elements. I had the function batch jobs into lists of 10k,...

I've used `pyani compare` in anger now, and it's _awesome_. But I do have some notes. *Edited by Bailey to create a checklist.* - [x] In Bland-Altman plots, we should...

I agree, a `--dry-run` option would be useful for a number of subcommands. However, the ANIm commands already show up in my logs, e.g. ```text [...] [INFO] [pyani.scripts.pyani_script]: command-line: /mnt/shared/scratch/lpritcha/apps/conda/envs/pyani_py38/bin/pyani...

> I don't think so. They show up even the second time you run an analysis? No. `pyani` does not repeat alignment runs that are already present in the database....