├── .bumpversion.cfg ├── .github └── workflows │ ├── codeql.yml │ └── workflow.yml ├── .gitignore ├── .mailmap ├── .readthedocs.yml ├── CHANGELOG.md ├── LICENSE.txt ├── README.rst ├── docs ├── Makefile ├── conf.py ├── index.rst ├── make.bat ├── omero.all.rst ├── omero.api.rst ├── omero.callbacks.rst ├── omero.cli.rst ├── omero.clients.rst ├── omero.columns.rst ├── omero.config.rst ├── omero.conversions.rst ├── omero.gateway.pytest_fixtures.rst ├── omero.gateway.rst ├── omero.gateway.scripts.dbhelpers.rst ├── omero.gateway.scripts.rst ├── omero.gateway.scripts.testdb_create.rst ├── omero.gateway.utils.rst ├── omero.grid.monitors.rst ├── omero.grid.rst ├── omero.hdfstorageV2.rst ├── omero.install.bzip2_tool.rst ├── omero.install.config_parser.rst ├── omero.install.jvmcfg.rst ├── omero.install.logs_library.rst ├── omero.install.perf_test.rst ├── omero.install.python_warning.rst ├── omero.install.rst ├── omero.install.versions.rst ├── omero.install.win_set_path.rst ├── omero.install.windows_warning.rst ├── omero.java.rst ├── omero.main.rst ├── omero.min.rst ├── omero.model.rst ├── omero.plugins.admin.rst ├── omero.plugins.basics.rst ├── omero.plugins.chgrp.rst ├── omero.plugins.chown.rst ├── omero.plugins.db.rst ├── omero.plugins.delete.rst ├── omero.plugins.download.rst ├── omero.plugins.export.rst ├── omero.plugins.fs.rst ├── omero.plugins.group.rst ├── omero.plugins.hql.rst ├── omero.plugins.import.rst ├── omero.plugins.ldap.rst ├── omero.plugins.node.rst ├── omero.plugins.obj.rst ├── omero.plugins.perf.rst ├── omero.plugins.prefs.rst ├── omero.plugins.rst ├── omero.plugins.script.rst ├── omero.plugins.search.rst ├── omero.plugins.sessions.rst ├── omero.plugins.submit.rst ├── omero.plugins.tag.rst ├── omero.plugins.user.rst ├── omero.processor.rst ├── omero.romio.rst ├── omero.rst ├── omero.rtypes.rst ├── omero.scripts.rst ├── omero.tables.rst ├── omero.testlib.cli.rst ├── omero.testlib.rst ├── omero.testlib.script.rst ├── omero.util.OmeroPopo.rst ├── omero.util.ROIDrawingUtils.rst ├── omero.util.ROI_utils.rst ├── omero.util.cleanse.rst ├── omero.util.concurrency.rst ├── omero.util.decorators.rst ├── omero.util.figureUtil.rst ├── omero.util.imageUtil.rst ├── omero.util.image_utils.rst ├── omero.util.import_candidates.rst ├── omero.util.importperf.rst ├── omero.util.metadata_mapannotations.rst ├── omero.util.metadata_utils.rst ├── omero.util.pixelstypetopython.rst ├── omero.util.populate_metadata.rst ├── omero.util.populate_roi.rst ├── omero.util.pydict_text_io.rst ├── omero.util.roi_handling_utils.rst ├── omero.util.rst ├── omero.util.script_utils.rst ├── omero.util.sessions.rst ├── omero.util.temp_files.rst ├── omero.util.text.rst ├── omero.util.tiles.rst └── omero.util.upgrade_check.rst ├── examples ├── createSession.py ├── load.omero ├── projection_1.py ├── submit.omero └── upload.omero ├── ice.config ├── manualtests ├── README.txt └── populate_roi_test.py ├── pytest.ini ├── setup.py ├── src ├── IceImport.py ├── omero │ ├── __init__.py │ ├── all.py │ ├── api │ │ └── __init__.py │ ├── callbacks.py │ ├── cli.py │ ├── clients.py │ ├── columns.py │ ├── config.py │ ├── conversions.py │ ├── fs │ │ └── __init__.py │ ├── gateway │ │ ├── __init__.py │ │ ├── pilfonts │ │ │ ├── B08.pbm │ │ │ ├── B08.pil │ │ │ ├── B10.pbm │ │ │ ├── B10.pil │ │ │ ├── B12.pbm │ │ │ ├── B12.pil │ │ │ ├── B14.pbm │ │ │ ├── B14.pil │ │ │ ├── B18.pbm │ │ │ ├── B18.pil │ │ │ ├── B20.pbm │ │ │ ├── B20.pil │ │ │ ├── B24.pbm │ │ │ ├── B24.pil │ │ │ ├── B32.pbm │ │ │ ├── B32.pil │ │ │ ├── B40.pbm │ │ │ ├── B40.pil │ │ │ ├── B48.pbm │ │ │ ├── B48.pil │ │ │ ├── B56.pbm │ │ │ ├── B56.pil │ │ │ ├── B64.pbm │ │ │ ├── B64.pil │ │ │ ├── FreeSans.ttf │ │ │ ├── FreeSansBold.ttf │ │ │ ├── FreeSansBoldOblique.ttf │ │ │ └── FreeSansOblique.ttf │ │ ├── pytest_fixtures.py │ │ ├── scripts │ │ │ ├── __init__.py │ │ │ ├── dbhelpers.py │ │ │ ├── imgs │ │ │ │ ├── 32float.fake │ │ │ │ ├── 32float.fake.ini │ │ │ │ ├── bigimg.fake │ │ │ │ ├── bigimg.fake.ini │ │ │ │ ├── testimg.fake │ │ │ │ ├── testimg.fake.ini │ │ │ │ ├── tinyimg.fake │ │ │ │ └── tinyimg.fake.ini │ │ │ └── testdb_create.py │ │ └── utils.py │ ├── grid │ │ ├── __init__.py │ │ └── monitors │ │ │ └── __init__.py │ ├── hdfstorageV2.py │ ├── install │ │ ├── __init__.py │ │ ├── bzip2_tool.py │ │ ├── config_parser.py │ │ ├── jvmcfg.py │ │ ├── logs_library.py │ │ ├── perf_test.py │ │ ├── python_warning.py │ │ ├── versions.py │ │ ├── win_set_path.py │ │ └── windows_warning.py │ ├── java.py │ ├── main.py │ ├── min.py │ ├── model │ │ └── __init__.py │ ├── plugins │ │ ├── __init__.py │ │ ├── _duplicate_deprecated.py │ │ ├── _metadata_deprecated.py │ │ ├── _upload_deprecated.py │ │ ├── admin.py │ │ ├── basics.py │ │ ├── chgrp.py │ │ ├── chown.py │ │ ├── db.py │ │ ├── delete.py │ │ ├── download.py │ │ ├── export.py │ │ ├── fs.py │ │ ├── group.py │ │ ├── hql.py │ │ ├── import.py │ │ ├── ldap.py │ │ ├── node.py │ │ ├── obj.py │ │ ├── perf.py │ │ ├── prefs.py │ │ ├── script.py │ │ ├── search.py │ │ ├── sessions.py │ │ ├── submit.py │ │ ├── tag.py │ │ └── user.py │ ├── processor.py │ ├── romio │ │ └── __init__.py │ ├── rtypes.py │ ├── scripts.py │ ├── sys │ │ └── __init__.py │ ├── tables.py │ ├── testlib │ │ ├── __init__.py │ │ ├── cli.py │ │ └── script.py │ └── util │ │ ├── OmeroPopo.py │ │ ├── ROIDrawingUtils.py │ │ ├── ROI_utils.py │ │ ├── __init__.py │ │ ├── _process_defaultxml.py │ │ ├── cleanse.py │ │ ├── concurrency.py │ │ ├── decorators.py │ │ ├── figureUtil.py │ │ ├── imageUtil.py │ │ ├── image_utils.py │ │ ├── import_candidates.py │ │ ├── importperf.py │ │ ├── metadata_mapannotations.py │ │ ├── metadata_utils.py │ │ ├── pixelstypetopython.py │ │ ├── populate_metadata.py │ │ ├── populate_roi.py │ │ ├── pydict_text_io.py │ │ ├── roi_handling_utils.py │ │ ├── script_utils.py │ │ ├── sessions.py │ │ ├── temp_files.py │ │ ├── text.py │ │ ├── tiles.py │ │ └── upgrade_check.py ├── omero_ext │ ├── __init__.py │ ├── argparse.py │ ├── killableprocess.py │ ├── path.py │ ├── pyinotify.py │ ├── stubout.py │ ├── which.py │ └── winprocess.py ├── omero_model_DetailsI.py ├── omero_model_ElectricPotentialI.py ├── omero_model_FrequencyI.py ├── omero_model_LengthI.py ├── omero_model_PermissionsI.py ├── omero_model_PowerI.py ├── omero_model_PressureI.py ├── omero_model_TemperatureI.py ├── omero_model_TimeI.py ├── omero_model_UnitBase.py ├── omero_sys_ParametersI.py ├── omero_version.py ├── runProcessor.py └── runTables.py ├── test ├── __init__.py ├── conftest.py └── unit │ ├── __init__.py │ ├── clitest │ ├── bulk_import │ │ ├── test_bad │ │ │ └── bulk.yml │ │ ├── test_cols │ │ │ ├── 1.fake │ │ │ ├── bulk.tsv │ │ │ └── bulk.yml │ │ ├── test_dryrun │ │ │ ├── 1.fake │ │ │ ├── bulk.tsv │ │ │ └── bulk.yml │ │ ├── test_include │ │ │ ├── bulk.yml │ │ │ └── inner │ │ │ │ ├── bulk.tsv │ │ │ │ ├── bulk.yml │ │ │ │ └── foo.fake │ │ ├── test_javaargs │ │ │ ├── 1.fake │ │ │ ├── bulk.tsv │ │ │ └── bulk.yml │ │ ├── test_name │ │ │ ├── 1.fake │ │ │ ├── bulk.tsv │ │ │ └── bulk.yml │ │ ├── test_simple │ │ │ ├── 1.fake │ │ │ ├── bulk.tsv │ │ │ └── bulk.yml │ │ └── test_skip │ │ │ ├── 1.fake │ │ │ ├── all.yml │ │ │ ├── bulk.tsv │ │ │ ├── checksum.yml │ │ │ ├── minmax.yml │ │ │ ├── thumbnails.yml │ │ │ └── upgrade.yml │ ├── readers │ │ ├── no_fakes.txt │ │ └── only_fakes.txt │ ├── test_admin.py │ ├── test_admin_noomerodir.py │ ├── test_basics.py │ ├── test_chgrp.py │ ├── test_cli.py │ ├── test_db.py │ ├── test_download.py │ ├── test_export.py │ ├── test_fs.py │ ├── test_group.py │ ├── test_hql.py │ ├── test_import.py │ ├── test_ldap.py │ ├── test_obj.py │ ├── test_prefs.py │ ├── test_rcode.py │ ├── test_script.py │ ├── test_sess.py │ ├── test_sessions.py │ ├── test_tag.py │ └── test_user.py │ ├── fstest │ ├── __init__.py │ └── test_model.py │ ├── gatewaytest │ ├── test_argument_errors.py │ ├── test_build_query.py │ └── test_utils.py │ ├── old_templates.xml │ ├── scriptstest │ ├── test_parse.py │ ├── test_processor.py │ └── test_prototypes.py │ ├── tablestest │ ├── library.py │ ├── test_hdfstorage.py │ └── test_servants.py │ ├── test_clients.py │ ├── test_config.py │ ├── test_conversions.py │ ├── test_gateway.py │ ├── test_jvmcfg.json │ ├── test_jvmcfg.py │ ├── test_metadata_mapannotations.py │ ├── test_metadata_utils.py │ ├── test_model.py │ ├── test_parameters.py │ ├── test_path.py │ ├── test_permissions.py │ ├── test_python_only.py │ ├── test_rois.py │ ├── test_rtypes.py │ ├── test_tempfiles.py │ └── test_util.py └── tox.ini /.bumpversion.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ome/omero-py/HEAD/.bumpversion.cfg -------------------------------------------------------------------------------- /.github/workflows/codeql.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ome/omero-py/HEAD/.github/workflows/codeql.yml -------------------------------------------------------------------------------- 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