[WIP] Updating for Bacting 0.0.40 by egonw · Pull Request #9 · BlueObelisk/pybacting

egonw · 2022-07-02T17:13:49Z

This brings in @bioregistry support:

xref = bridgedb.compactIdentifier("ncbigene:1234");

egonw · 2022-07-04T07:46:08Z

@cthoyt, I have some problems with the internal logic. The dependencies do not seem to be downloaded properly. Do you have any clue what is going on?

==================================== ERRORS ====================================
____________________ ERROR collecting tests/test_trivial.py ____________________
tests/test_trivial.py:9: in <module>
    import pybacting
.tox/py/lib/python3.10/site-packages/pybacting/__init__.py:5: in <module>
    from .api import (  # noqa:F401
.tox/py/lib/python3.10/site-packages/pybacting/api.py:49: in <module>
    start_jvm()
.tox/py/lib/python3.10/site-packages/scyjava/__init__.py:116: in start_jvm
    _, workspace = jgo.resolve_dependencies(
.tox/py/lib/python3.10/site-packages/jgo/jgo.py:665: in resolve_dependencies
    raise e
.tox/py/lib/python3.10/site-packages/jgo/jgo.py:[63](https://github.com/cthoyt/pybacting/runs/7163960021?check_suite_focus=true#step:5:64)6: in resolve_dependencies
    mvn_out = run_and_combine_outputs(mvn, *mvn_args)
.tox/py/lib/python3.10/site-packages/jgo/jgo.py:274: in run_and_combine_outputs
    return subprocess.check_output(command_string, stderr=subprocess.STDOUT)
/opt/hostedtoolcache/Python/3.10.5/x[64](https://github.com/cthoyt/pybacting/runs/7163960021?check_suite_focus=true#step:5:65)/lib/python3.10/subprocess.py:420: in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
/opt/hostedtoolcache/Python/3.10.5/x64/lib/python3.10/subprocess.py:524: in run
    raise CalledProcessError(retcode, process.args,
E   subprocess.CalledProcessError: Command '('/usr/bin/mvn', '-B', '-f', '/home/runner/.jgo/io.github.egonw.bacting/managers-inchi/0.0.38/caba08eef1528fc425331118385026b51eda6dea99bcd0282efeb94aba4153fc/pom.xml', 'dependency:resolve')' returned non-zero exit status 1.
=========================== short test summary info ============================
ERROR tests/test_trivial.py - subprocess.CalledProcessError: Command '('/usr/...
!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!
============================== 1 error in 28.16s ===============================
ERROR: InvocationError for command /home/runner/work/pybacting/pybacting/.tox/py/bin/coverage run -p -m pytest --durations=20 tests (exited with code 2)
___________________________________ summary ____________________________________
ERROR:   py: commands failed
Error: Process completed with exit code 1.

egonw · 2022-07-09T16:10:16Z

Seems Google Colab has the same problem with a previously released version:

cthoyt · 2022-07-09T17:50:16Z

So this is probably an upstream issue with scijava

egonw · 2022-07-10T09:19:45Z

Maybe I'm making progress on other fronts... now running into this issue: sphinx-doc/sphinx#10491

cthoyt · 2022-07-10T11:43:32Z

Maybe I'm making progress on other fronts... now running into this issue: sphinx-doc/sphinx#10491

Yes, indeed, thanks for finding that fix. Unfortunately the implicit default for english was removed and every repository needs this update :/

cthoyt · 2022-07-10T11:51:39Z

As far as the maven resolution, it seems that something is relying on a version of org.osgi.service.prefs that no longer exists

[ERROR] Failed to execute goal on project managers-inchi-BOOTSTRAPPER: Could not resolve dependencies for project io.github.egonw.bacting-BOOTSTRAPPER:managers-inchi-BOOTSTRAPPER:jar:0: Failed to collect dependencies at io.github.egonw.bacting:managers-inchi:jar:0.0.34 -> io.github.egonw.bacting:bacting-core:jar:0.0.34 -> io.github.egonw.bacting:bioclipse-core:jar:2.8.0.13 -> org.eclipse.platform:org.eclipse.core.runtime:jar:3.24.100 -> org.eclipse.platform:org.eclipse.equinox.preferences:jar:3.10.0 -> org.osgi.service:org.osgi.service.prefs:jar:[1.1.0,1.2.0): No versions available for org.osgi.service:org.osgi.service.prefs:jar:[1.1.0,1.2.0) within specified range -> [Help 1]

This page says that only version 1.1.1 and 1.1.2 exist - https://search.maven.org/artifact/org.osgi/org.osgi.service.prefs

egonw · 2022-07-10T11:54:39Z

This page says that only version 1.1.1 and 1.1.2 exist - https://search.maven.org/artifact/org.osgi/org.osgi.service.prefs

yes, but far as I know both fall in the range [1.1.0,1.2.0) ... :(

But I am considering this lead and in the progress of releasing Bacting 0.0.40 which depends on the new Eclipse core libraries that came up.

Another lead I have been trying is a comment somewhere that JGO has a hashing issue and mixing up versions in the local cache... that's why I tried deleting /home/running/.jgo at some point, but without success...

egonw · 2022-07-10T12:23:14Z

Okay, we're not the only ones having the issue :(

https://code2care.org/maven/cannot-resolve-no-versions-available-for-org-osgi-service-prefs-jar-1-1-0-1-2-0-within-specified-range

And the root cause if identified here: eclipse-equinox/equinox.bundles#54 They also mention the removal of bundles from Maven Central here.

egonw · 2022-07-10T12:35:13Z

So, Bacting 0.0.40 should fix it. It depends on the fixed libraries, but JGO/ScyJava is not picking up the libraries correctly. Here's the dependencies:

[INFO] ---------------< io.github.egonw.bacting:managers-inchi >---------------
[INFO] Building managers-inchi 0.0.40                                   [11/26]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-dependency-plugin:2.8:tree (default-cli) @ managers-inchi ---
[INFO] io.github.egonw.bacting:managers-inchi:jar:0.0.40
[INFO] +- xom:xom:jar:1.3.7:compile
[INFO] |  +- xerces:xercesImpl:jar:2.8.0:compile
[INFO] |  |  \- xml-apis:xml-apis:jar:1.3.03:compile
[INFO] |  \- xalan:xalan:jar:2.7.2:compile
[INFO] |     \- xalan:serializer:jar:2.7.2:compile
[INFO] +- io.github.egonw.bacting:bacting-core:jar:0.0.40:compile
[INFO] |  \- io.github.egonw.bacting:bioclipse-core:jar:2.8.0.16:compile
[INFO] |     +- org.eclipse.platform:org.eclipse.core.runtime:jar:3.25.0:compile
[INFO] |     |  +- org.eclipse.platform:org.eclipse.osgi:jar:3.18.0:compile (version selected from constraint [3.17.0,4.0.0))
[INFO] |     |  +- org.eclipse.platform:org.eclipse.equinox.common:jar:3.16.100:compile (version selected from constraint [3.16.0,))
[INFO] |     |  +- org.eclipse.platform:org.eclipse.core.jobs:jar:3.13.0:compile (version selected from constraint [3.13.0,4.0.0))
[INFO] |     |  +- org.eclipse.platform:org.eclipse.equinox.registry:jar:3.11.100:compile (version selected from constraint [3.11.0,4.0.0))
[INFO] |     |  +- org.eclipse.platform:org.eclipse.equinox.preferences:jar:3.10.1:compile (version selected from constraint [3.10.0,4.0.0))
[INFO] |     |  |  \- org.osgi:org.osgi.service.prefs:jar:1.1.2:compile (version selected from constraint [1.1.0,1.2.0))
[INFO] |     |  |     \- org.osgi:osgi.annotation:jar:8.0.1:compile
[INFO] |     |  +- org.eclipse.platform:org.eclipse.core.contenttype:jar:3.8.100:compile (version selected from constraint [3.8.0,4.0.0))
[INFO] |     |  \- org.eclipse.platform:org.eclipse.equinox.app:jar:1.6.100:compile (version selected from constraint [1.6.0,))
[INFO] |     \- org.eclipse.platform:org.eclipse.core.resources:jar:3.17.0:compile
[INFO] |        +- org.eclipse.platform:org.eclipse.core.expressions:jar:3.8.100:compile (version selected from constraint [3.2.0,4.0.0))
[INFO] |        \- org.eclipse.platform:org.eclipse.core.filesystem:jar:1.9.400:compile (version selected from constraint [1.3.0,2.0.0))

But note that ScyJava is still looking for the old (wrong: org.osgi.service:org.osgi.service.prefs instead of the correct org.osgi:org.osgi.service.prefs) library... why???

Error: ] Failed to execute goal on project managers-inchi-BOOTSTRAPPER: Could not resolve dependencies for project io.github.egonw.bacting-BOOTSTRAPPER:managers-inchi-BOOTSTRAPPER:jar:0: Failed to collect dependencies at io.github.egonw.bacting:managers-inchi:jar:0.0.40 -> io.github.egonw.bacting:bacting-core:jar:0.0.40 -> io.github.egonw.bacting:bioclipse-core:jar:2.8.0.16 -> org.eclipse.platform:org.eclipse.core.runtime:jar:3.25.0 -> org.eclipse.platform:org.eclipse.equinox.preferences:jar:3.10.0 -> org.osgi.service:org.osgi.service.prefs:jar:[1.1.0,1.2.0): No versions available for org.osgi.service:org.osgi.service.prefs:jar:[1.1.0,1.2.0) within specified range -> [Help 1]

Well, obvious because it's depending on the wrong org.eclipse.platform:org.eclipse.equinox.preferences:jar:3.10.0 instead of the correct org.eclipse.platform:org.eclipse.equinox.preferences:jar:3.10.1) ... sigh

egonw · 2022-07-10T12:55:43Z

On the upside, at least I can reproduce it locally now. Maybe a confounding ScyJava bug after all?

egonw · 2022-07-10T13:23:06Z

I filed an issue to indicate pybacting is currently uninstallable: #11

egonw · 2022-07-10T16:08:42Z

Okay, the workaround for the Eclipse problem worked. But now I got other problems (that should not even exist).

egonw · 2022-07-11T06:02:49Z

Well, at least Bacting is fixed:

Now I just need to figure out how to get pybacting working again too.

egonw · 2022-07-12T07:11:08Z

Replacing this with a clean new PR.

cthoyt · 2022-07-12T12:06:19Z

I do squash and merge exclusively on my projects so it’s not strictly necessary to open a new PR, just for future reference

egonw · 2022-07-13T05:32:46Z

Yeah, I know. It was more for myself, so that I can see better what is happening.

egonw closed this Jul 2, 2022

egonw force-pushed the egonw/update-to-0.0.38 branch from d28c951 to cb0ae7e Compare July 2, 2022 19:16

egonw reopened this Jul 2, 2022

egonw mentioned this pull request Jul 10, 2022

problems downloading dependencies scijava/scyjava#42

Open

egonw force-pushed the egonw/update-to-0.0.38 branch from b03505b to 280fc3d Compare July 10, 2022 08:54

egonw changed the title ~~Updating for Bacting 0.0.38~~ Updating for Bacting 0.0.39 Jul 10, 2022

egonw force-pushed the egonw/update-to-0.0.38 branch 2 times, most recently from e987135 to 3e8a3d7 Compare July 10, 2022 11:18

egonw added 5 commits July 10, 2022 14:10

Bacting 0.0.38

2a7d3ef

Bacting 0.0.39 and added three more recent managers

9238d79

Added boiler plate code for three new managers

72e8d86

Added missing trailing comma

305f78c

Bacting 0.0.40

d921dd6

egonw force-pushed the egonw/update-to-0.0.38 branch from 0448251 to d921dd6 Compare July 10, 2022 12:12

egonw changed the title ~~Updating for Bacting 0.0.39~~ Updating for Bacting 0.0.40 Jul 10, 2022

egonw force-pushed the egonw/update-to-0.0.38 branch from a74e510 to d921dd6 Compare July 10, 2022 12:47

egonw added 3 commits July 10, 2022 16:49

Bacting 0.0.41: Hardcoded org.eclipse.equinox.preferences 3.10.1

bd34db1

Bacting 0.0.42: hardcoded for both Eclipse packages

9ee28d8

Include log4j

8b4860c

Another missing dependency

f58d845

egonw changed the title ~~Updating for Bacting 0.0.40~~ [WIP] Updating for Bacting 0.0.40 Jul 11, 2022

egonw closed this Jul 12, 2022

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