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ModuleNotFoundError: No module named 'omero_zarr._version' #154

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will-moore opened this issue Nov 30, 2023 · 10 comments
Open

ModuleNotFoundError: No module named 'omero_zarr._version' #154

will-moore opened this issue Nov 30, 2023 · 10 comments

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@will-moore
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I'm seeing an import Error using a conda environment on ome-zarr-dev1 machine (but I don't see any error on a local env): e.g.

(omero_zarr_export) [wmoore@ome-zarr-dev1 idr0001]$ omero login
Error loading: /lifesci/groups/jrs/wmoore/miniconda3/envs/omero_zarr_export/lib/python3.9/site-packages/omero/plugins/zarr.py
Traceback (most recent call last):
  File "/lifesci/groups/jrs/wmoore/miniconda3/envs/omero_zarr_export/lib/python3.9/site-packages/omero/cli.py", line 1690, in loadpath
    execfile(str(pathobj), loc)
  File "/lifesci/groups/jrs/wmoore/miniconda3/envs/omero_zarr_export/lib/python3.9/site-packages/past/builtins/misc.py", line 87, in execfile
    exec_(code, myglobals, mylocals)
  File "/lifesci/groups/jrs/wmoore/miniconda3/envs/omero_zarr_export/lib/python3.9/site-packages/omero/plugins/zarr.py", line 1, in <module>
    from omero_zarr.cli import HELP, ZarrControl
  File "/lifesci/groups/jrs/wmoore/miniconda3/envs/omero_zarr_export/lib/python3.9/site-packages/omero_zarr/__init__.py", line 21, in <module>
    from ._version import version as __version__
ModuleNotFoundError: No module named 'omero_zarr._version'

I tried a different pattern to import __version__ within __init__.py:

from . import _version

__version__ = _version.version

Again, this works on my local machine but not on the ome-zarr-dev1 server env:

(omero_zarr_export) [wmoore@ome-zarr-dev1 ~]$ python
Python 3.9.0 | packaged by conda-forge | (default, Nov 26 2020, 07:57:39) 
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from omero_zarr.cli import HELP, ZarrControl
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/lifesci/groups/jrs/wmoore/miniconda3/envs/omero_zarr_export/lib/python3.9/site-packages/omero_zarr/__init__.py", line 21, in <module>
    from . import _version
ImportError: cannot import name '_version' from partially initialized module 'omero_zarr' (most likely due to a circular import) (/lifesci/groups/jrs/wmoore/miniconda3/envs/omero_zarr_export/lib/python3.9/site-packages/omero_zarr/__init__.py)
@will-moore
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Seems this may only be an issue when installing this from github:

pip install git+https://github.com/ome/omero-cli-zarr.git@master

Installing directly from pypi fixes this issue.

@will-moore
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Having released omero-cli-zarr v0.5.4 and upgraded to this on my remote ome-zarr-dev1 environment, I now see this import Error with that installed from pypi, but downgrading back to v0.5.3 fixes the issue (with no other dependency changes).

Comparing the releases, I don't see any code changes that would cause this issue:
v0.5.3...v0.5.4

@will-moore
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Returning to a conda env on pilot-zarr1-dev where I have previously been exporting NGFF for IDR conversions, with ecf5a3e, without changing the version installed, I now find that I get the ModuleNotFoundError above, when I haven't seen this before on this environment!?

@will-moore
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cc @jburel @joshmoore - Any ideas what's going on here? Seems the 0.5.4 release is broken, so we need to fix or revert the release (if that's possible)?

@joshmoore
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joshmoore commented Dec 7, 2023

pip install . in a fresh clone also shows this issue.

I'm inclined to move to verioneer as in German-BioImaging/omero-rdf#4

joshmoore added a commit to joshmoore/omero-cli-zarr that referenced this issue Dec 7, 2023
Move to the use of https://github.com/python-versioneer/python-versioneer
for defining a version from the current tag. This also removes the need
to use bump2version, therefore releases can be handled completely from
the GH UI.
joshmoore added a commit to joshmoore/omero-cli-zarr that referenced this issue Dec 7, 2023
Move to the use of https://github.com/python-versioneer/python-versioneer
for defining a version from the current tag. This also removes the need
to use bump2version, therefore releases can be handled completely from
the GH UI.
@jburel
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jburel commented Dec 7, 2023

the problem is coming from scm itself.
Error in the action

Requirement already satisfied: wheel in /usr/lib/python3/dist-packages (0.37.1)
/usr/lib/python3/dist-packages/setuptools/installer.py:2[7](https://github.com/ome/omero-cli-zarr/actions/runs/7045520856/job/19175424186#step:5:8): SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.
  warnings.warn(
/home/runner/work/omero-cli-zarr/omero-cli-zarr/.eggs/setuptools_scm-[8](https://github.com/ome/omero-cli-zarr/actions/runs/7045520856/job/19175424186#step:5:9).0.4-py3.10.egg/setuptools_scm/_integration/setuptools.py:30: RuntimeWarning: 
ERROR: setuptools==59.6.0 is used in combination with setuptools_scm>=8.x

Your build configuration is incomplete and previously worked by accident!
setuptools_scm requires setuptools>=61

Suggested workaround if applicable:
 - migrating from the deprecated setup_requires mechanism to pep517/518
   and using a pyproject.toml to declare build dependencies
   which are reliably pre-installed before running the build tools

  warnings.warn(
/home/runner/work/omero-cli-zarr/omero-cli-zarr/.eggs/setuptools_scm-8.0.4-py3.10.egg/setuptools_scm/_integration/setuptools.py:[9](https://github.com/ome/omero-cli-zarr/actions/runs/7045520856/job/19175424186#step:5:10)0: UserWarning: version of omero-cli-zarr already set
  warnings.warn(f"version of {dist_name} already set")

@joshmoore
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Heh. Nice find. If you'd prefer the more immediate fix, no objection. I do have the feeling that we should be migrating setup.py to pyproject.toml everywhere when possible.

@jburel
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jburel commented Dec 7, 2023

I have been thinking about that migration too. This is a new repo so it will make sense to start with that one

@will-moore
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@jburel Where are you seeing that error? All the recent PRs have been 'green' when merged?

@will-moore
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Ah - you're talking about Josh's PR, not the ModuleNotFoundError from this PR!

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Repository: ome/omero-cli-zarr
Excluded PRs:
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  - PR 118 sbesson 'Allow to use bioformats2raw to export HCS data' (stage: draft)
Already up-to-date.

Merged PRs:
  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'
  - PR 157 will-moore 'Pixel type fix'

Conflicting PRs (not included):
  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'

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  - PR 118 sbesson 'Allow to use bioformats2raw to export HCS data' (stage: draft)
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Merged PRs:
  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'
  - PR 157 will-moore 'Pixel type fix'

Conflicting PRs (not included):
  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'

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  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'
  - PR 157 will-moore 'Pixel type fix'

Conflicting PRs (not included):
  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'

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Already up-to-date.

Merged PRs:
  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'
  - PR 157 will-moore 'Pixel type fix'

Conflicting PRs (not included):
  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'

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Already up-to-date.

Merged PRs:
  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'
  - PR 157 will-moore 'Pixel type fix'

Conflicting PRs (not included):
  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'

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Merged PRs:
  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'
  - PR 157 will-moore 'Pixel type fix'

Conflicting PRs (not included):
  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'

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Already up-to-date.

Merged PRs:
  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'
  - PR 157 will-moore 'Pixel type fix'

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Already up-to-date.

Merged PRs:
  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'
  - PR 157 will-moore 'Pixel type fix'

Conflicting PRs (not included):
  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'

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  - PR 118 sbesson 'Allow to use bioformats2raw to export HCS data' (stage: draft)
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Merged PRs:
  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'
  - PR 157 will-moore 'Pixel type fix'

Conflicting PRs (not included):
  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'

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  - PR 118 sbesson 'Allow to use bioformats2raw to export HCS data' (stage: draft)
Already up-to-date.

Merged PRs:
  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'
  - PR 157 will-moore 'Pixel type fix'

Conflicting PRs (not included):
  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'

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  - PR 118 sbesson 'Allow to use bioformats2raw to export HCS data' (stage: draft)
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  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'
  - PR 157 will-moore 'Pixel type fix'

Conflicting PRs (not included):
  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'

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  - PR 118 sbesson 'Allow to use bioformats2raw to export HCS data' (stage: draft)
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Merged PRs:
  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'
  - PR 157 will-moore 'Pixel type fix'

Conflicting PRs (not included):
  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'

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  - PR 118 sbesson 'Allow to use bioformats2raw to export HCS data' (stage: draft)
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Merged PRs:
  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'
  - PR 157 will-moore 'Pixel type fix'

Conflicting PRs (not included):
  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'

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  - PR 118 sbesson 'Allow to use bioformats2raw to export HCS data' (stage: draft)
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  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'
  - PR 157 will-moore 'Pixel type fix'

Conflicting PRs (not included):
  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'

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  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'
  - PR 157 will-moore 'Pixel type fix'

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  - PR 123 will-moore 'Support export of Fileset:ID'

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  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'

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  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'

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  - PR 123 will-moore 'Support export of Fileset:ID'

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  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'

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  - PR 118 sbesson 'Allow to use bioformats2raw to export HCS data' (stage: draft)
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  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'

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  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'

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Already up-to-date.

Merged PRs:
  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'

Conflicting PRs (not included):
  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'

Generated by OMERO-plugins-push#364 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/OMERO-plugins-push/364/)
snoopycrimecop added a commit to snoopycrimecop/omero-cli-zarr that referenced this issue Jan 9, 2024
snoopycrimecop added a commit to snoopycrimecop/omero-cli-zarr that referenced this issue Jan 9, 2024
Repository: ome/omero-cli-zarr
Excluded PRs:
  - PR 158 pre-commit-ci[bot] '[pre-commit.ci] pre-commit autoupdate' (user: pre-commit-ci[bot])
  - PR 118 sbesson 'Allow to use bioformats2raw to export HCS data' (stage: draft)
Already up-to-date.

Merged PRs:
  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'

Conflicting PRs (not included):
  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'

Generated by OMERO-plugins-push#365 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/OMERO-plugins-push/365/)
snoopycrimecop added a commit to snoopycrimecop/omero-cli-zarr that referenced this issue Jan 10, 2024
snoopycrimecop added a commit to snoopycrimecop/omero-cli-zarr that referenced this issue Jan 10, 2024
Repository: ome/omero-cli-zarr
Excluded PRs:
  - PR 158 pre-commit-ci[bot] '[pre-commit.ci] pre-commit autoupdate' (user: pre-commit-ci[bot])
  - PR 118 sbesson 'Allow to use bioformats2raw to export HCS data' (stage: draft)
Already up-to-date.

Merged PRs:
  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'

Conflicting PRs (not included):
  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'
  - PR 159 will-moore 'scm version fix'

Generated by OMERO-plugins-push#366 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/OMERO-plugins-push/366/)
snoopycrimecop added a commit to snoopycrimecop/omero-cli-zarr that referenced this issue Jan 11, 2024
snoopycrimecop added a commit to snoopycrimecop/omero-cli-zarr that referenced this issue Jan 11, 2024
Repository: ome/omero-cli-zarr
Excluded PRs:
  - PR 158 pre-commit-ci[bot] '[pre-commit.ci] pre-commit autoupdate' (user: pre-commit-ci[bot])
  - PR 118 sbesson 'Allow to use bioformats2raw to export HCS data' (stage: draft)
Already up-to-date.

Merged PRs:
  - PR 147 will-moore 'Name option'
  - PR 156 joshmoore 'Use versioneer for tagging (Fix ome#154)'

Conflicting PRs (not included):
  - PR 102 will-moore 'Zarr export tests'
  - PR 123 will-moore 'Support export of Fileset:ID'
  - PR 159 will-moore 'scm version fix'

Generated by OMERO-plugins-push#367 (https://snoopycrimecop-ci.openmicroscopy.org/jenkins/job/OMERO-plugins-push/367/)
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@joshmoore @will-moore @jburel and others