Py2

[joshmoore]

This PR intends to add the necessary infrastructure on top of a decoupled versions of https://github.com/ome/openmicroscopy/releases/tag/v5.5.1 (c21d65e) such that python setup.py leads to a package that can then be pip-installed.

[joshmoore]

This is now getting to the point where I think I can try removing lib/python from an OMERO 5.5.1 installation and seeing if pip install omero-py will be fully functional. If that works, I'd propose tagging this as 5.5.1 and pushing it out to PyPI. Then the team can start adding PRs for 5.5.x while I work against a py3 integration branch that will become 5.6 or later.

Unfortunately, users will need to rm -rf lib/python to consume 5.5.1+ but perhaps that's worth it to some until another OMERO release changes the prepend behavior of:

https://github.com/ome/openmicroscopy/blob/develop/components/tools/OmeroPy/bin/omero#L77-L84

cc: @olatarkowska @manics @sbesson @will-moore

[joshmoore]

Three (not necessarily mutually exclusive options) with various pros and cons are:

1. delete lib/python, pip install, set OMERODIR, use old dist/bin/omero 👍
2. pip install with new venv/bin/omero, set OMERODIR 👍
3. ship new OMERO 5.5.2 with updated dist/bin/omero which appends lib/python rather than prepending it 👍

[joshmoore]

Changes to omero-server-docker for option 1 above:

...
USER root
RUN rm -rf /opt/omero/server/OMERO.server/lib/python
COPY omero-py-5.5.1.tar.gz /tmp/
RUN pip install /tmp/omero-py-5.5.1.tar.gz
RUN mkdir /opt/omero/server/OMERO.server/lib/python # Dummy for omego
ENV OMERODIR /opt/omero/server/OMERO.server
USER omero-server

Changes to omero-server-docker for option 2 above:

...
USER root
COPY omero-py-5.5.1.tar.gz /tmp/
RUN pip install /tmp/omero-py-5.5.1.tar.gz
ENV OMERODIR /opt/omero/server/OMERO.server
USER omero-server

Additionally for option 2, I'd suggest we add:

index fe2d47b..f9f619f 100755
--- a/bin/omero
+++ b/bin/omero
@@ -75,20 +75,22 @@ else:
 # This list needs to be kept in line with omero.cli.CLI._env
 #
 top = os.path.normpath(top)
 lib = os.path.join(top, "lib")
 lpy = os.path.join(top, "lib","python")
 ipy = os.path.join(top, "lib","fallback")
 var = os.path.join(top, "var")
 vlb = os.path.join(var, "lib")
-sys.path.insert(0,vlb);
-sys.path.insert(0,lpy);
+sys.path.append(lpy);
+sys.path.append(vlb);
 sys.path.append(ipy)

but note that the referenced _env already appends rather than prepends so that the new code is picked up.

[manics]

Since they all require an openmicroscopy release option 2 seems the cleanest

[joshmoore]

Definitely agree that 2 is the cleanest, but I was hoping option 1 and option 2 didn't require an ome/openmicroscopy release.

[joshmoore]

Note: one thing that can't be controlled is that if the user explicitly has set PYTHONPATH then that will be preferred. ctx._env likely has the same problem, but I only see it being used by admin.py and therefore might be ignorable (or deprecatable).

[joshmoore]

Summary:

• Option 2 looks to be a viable way to add omero-py from pypi to an existing OMERO installation
• The primary downside is the requirement to set OMERODIR
• I propose that this get reviewed and then released as a pre-release on PyPI for more thorough testing (docker, etc)
• I'd then move on to handle omero-web in the same way.

[joshmoore]

General 👍 up: during the call. Only outstanding TODO is likely to strip out the integration tests and rebase, which I forgot to do. Otherwise, looking to get this pre-released to pypi (propose: 5.5.dev1) ASAP and then to move on to omero-web in the same fashion. Once that's done, those directories can be deleted from ome/openmicroscopy and all unmerged PRs closed.

[joshmoore]

Re-opening to kick off travis

[joshmoore]

Merging and releasing this to PyPI now. Follow-up items include:

• running tests
• moving to bumpversion
• extracting gateway & plugins

Other suggestions/ideas welcome either as a card on https://github.com/orgs/ome/projects/5 or as a new PR against this repository.

[joshmoore]

Note: origin/master was force-pushed after this was merged since I forgot to run bfg first to strip out large files. The only change was:

/opt/omero-py $bash size.sh
All sizes are in kB's. The pack column is the size of the object, compressed, inside the pack file.
size   SHA                                       location
35852  3d57f7ae1bd728b6e320741ea980cc7cfc228cad  src/omero/gateway/scripts/imgs/CHOBI_d3d.dv

[sbesson]

As a minimal validation, I have been using the state of this repository within the context of IDR/idr-metadata#380 (comment):

$ pip install --user omero-py
$ omero login demo@localhost
$ python pyidr/study_parser.py --set ...

Everything worked as expected with the projects and datasets being annotated as expected using the pip-installed library

[joshmoore]

Does that imply we should go ahead and tag 5.5.1? cc: @ome/python