Remove io.LoadScan._spm_px_to_nm_scaling()
#1036
Comments
ns-rse
changed the title
io.LoadScan._spm_px_to_nm_scaling()
ns-rse
added a commit
that referenced
this issue
Dec 11, 2024
Closes #1036 With the delegation of much I/O (Input/Output) functionality to @SylviaWhittle `AFMReader` (see #1031) we have removed most of the methods to the `io.LoadScan()` class. One that slipped through was `_spm_pixel_to_nm_scaling()` and this commit removes it along with its associated test. Further the delegation of reading AFM files using `AFMReader` means `TopoStats` no longer has explicit dependencies on the `igor2`, `pySPM` or `tifffile` packages and so these have been removed from the `dependencies` section of `pyproject.toml`. These are dependencies of `AFMReader` and will still be installed in virtual environments.
2 tasks
ns-rse
added a commit
that referenced
this issue
Dec 11, 2024
Closes #1036 With the delegation of much I/O (Input/Output) functionality to @SylviaWhittle `AFMReader` (see #1031) we have removed most of the methods to the `io.LoadScan()` class. One that slipped through was `_spm_pixel_to_nm_scaling()` and this commit removes it along with its associated test. Further the delegation of reading AFM files using `AFMReader` means `TopoStats` no longer has explicit dependencies on the `igor2`, `pySPM` or `tifffile` packages and so these have been removed from the `dependencies` section of `pyproject.toml`. These are dependencies of `AFMReader` and will still be installed in virtual environments.
ns-rse
added a commit
that referenced
this issue
Dec 11, 2024
Closes #1036 With the delegation of much I/O (Input/Output) functionality to @SylviaWhittle `AFMReader` (see #1031) we have removed most of the methods to the `io.LoadScan()` class. One that slipped through was `_spm_pixel_to_nm_scaling()` and this commit removes it along with its associated test. Further the delegation of reading AFM files using `AFMReader` means `TopoStats` no longer has explicit dependencies on the `igor2`, `pySPM` or `tifffile` packages and so these have been removed from the `dependencies` section of `pyproject.toml`. These are dependencies of `AFMReader` and will still be installed in virtual environments. Moved `pytest-testmon` from `tests` to `dev` under optional dependencies as its not used when running the test suite, only when making commits locally.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
See AFMReader #83 where this method needs to be part of that package so that scans are correctly loaded.
Ideally we should have tests that cover all of the pixel scaling units are correctly loaded in the TopoStats pipeline (although I would be happy to have them covered by unit tests in AFMReader which is probably where they belong).
The text was updated successfully, but these errors were encountered: