tirl merge requestshttps://git.fmrib.ox.ac.uk/ihuszar/tirl/-/merge_requests2023-08-03T20:36:17+01:00https://git.fmrib.ox.ac.uk/ihuszar/tirl/-/merge_requests/2Pad mask bug2023-08-03T20:36:17+01:00Sean FitzgibbonPad mask bug- pad function will now retain and pad the image mask
- also added auxlib dependency to- pad function will now retain and pad the image mask
- also added auxlib dependency tohttps://git.fmrib.ox.ac.uk/ihuszar/tirl/-/merge_requests/4A couple of necessary changes required to allow TIRL to be built as a python/...2024-01-30T15:53:46+00:00Paul McCarthyA couple of necessary changes required to allow TIRL to be built as a python/conda package - The `tirl` package cannot be imported in `setup.py` because `setup.py` is executed at *build* time - when `setup.py` is executed, tirl will not have been installed into the environment in which `setup.py` is being executed, and there ... - The `tirl` package cannot be imported in `setup.py` because `setup.py` is executed at *build* time - when `setup.py` is executed, tirl will not have been installed into the environment in which `setup.py` is being executed, and there is no guarantee that it will be available on the python module path. Instead, in order to extract the TIRL version number, `tirl/__init__.py` is read in as a text file.
- Move TIRL config file initialisation from `setup.py` into `tirl/settings.py` - for reasons related to the above, `setup.py` is executed at *build* time, and is almost certainly executed on a different machine than that on which TIRL will be installed and used. So it doesn't make sense to install and initialise user-specific configuration files in `setup.py` - this must be done at installation or run-time.
- Move the `tirl.yml` and `tirlscripts.yml` templates into the `tirl/` package directory so that they are installed into the TIRL package, and can be used for one-time initialisation of the user-specific TIRL configuration file and tirlscripts registry.
- Use `$TMPDIR` rather than `/tmp/` for the TIRL working directory
- Add a `pyproject.toml` file so that build-time dependencies (cython and numpy) can be installed before `setup.py` is executedhttps://git.fmrib.ox.ac.uk/ihuszar/tirl/-/merge_requests/3MNT: Compatibility with newer versions of imageio2022-06-08T21:56:31+01:00Paul McCarthyMNT: Compatibility with newer versions of imageio`imageio.config.plugins.PluginConfig` instances don't seem to have an `extensions` attribute, at least as of `imageio` 2.16`imageio.config.plugins.PluginConfig` instances don't seem to have an `extensions` attribute, at least as of `imageio` 2.16https://git.fmrib.ox.ac.uk/ihuszar/tirl/-/merge_requests/1MNT: Updates to conda recipe2021-01-28T18:02:33+00:00Paul McCarthyMNT: Updates to conda recipeHi Istvan,
Would you be able to update the TIRL conda recipe to fix a few small issues for getting TIRL into FSL 6.0.4:
1. Link to, rather than move, the TIRL data directory from `$FSLDIR` - the root conda environment will cache the un...Hi Istvan,
Would you be able to update the TIRL conda recipe to fix a few small issues for getting TIRL into FSL 6.0.4:
1. Link to, rather than move, the TIRL data directory from `$FSLDIR` - the root conda environment will cache the un-tarred TIRL package, and modifying it by removing the data directory can cause conda to complain about it being corrupted.
2. Do not invoke `python` or `conda` from `post-link.sh`, as there is no guarantee that they are the `python`/`conda` commands associated with the environment into which TIRL is being installed. Furthermore, running `python -c "import tirl..."` may have unintended side effects<sup>*</sup>. I've replaced your `python` invocations with `sed`, and have removed the line which sets up the `$TIRLHOME` environment variable. From what I could see, `$TIRLHOME` is not actually used anywhere, and it would be easiest if we could just omit it for the time being.
3. Clean up installed data in the `pre-unlink.sh` script.
4. Renamed the `conda-recipies` directory, to get rid of the typo in the name.
Thanks!
<sup>*</sup>For example: https://git.fmrib.ox.ac.uk/ihuszar/tirl/-/blob/master/src/tirl/settings.py#L26 . As an aside, I would suggest that you use the built-in `tempfile` module, rather than hard-coding `/tmp/TIRLTWD`, because the temporary directory is not guaranteed to be located at `/tmp/`, so this call may not succceed in all environments.