illumina-interop: enable Python bindings; add license. #40431

cbrueffer · 2023-04-13T09:14:46Z

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matrulda · 2024-05-02T08:52:51Z

@cbrueffer What is the status here? Let me know if I can do anything to help.

cbrueffer · 2024-05-07T07:58:36Z

I've made some progress since your last ping. The blocker is that the package is not being correctly installed, e.g. no interop package files in the site-packages directory (hence the ls tests in the recipe) . I'll try to look into it again in a few days.

matrulda · 2024-05-08T06:18:17Z

Thank you!

SPPearce · 2024-06-29T20:12:24Z

@cbrueffer , are you able to look at this please?

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

recipes/illumina-interop/meta.yaml

martin-g · 2024-07-01T08:46:30Z

@BiocondaBot please fetch artifacts

BiocondaBot · 2024-07-01T08:46:55Z

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	illumina-interop-1.3.1-hdbdd923_2.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the LinuxArtifacts directory: `conda install -c ./packages <package name>`
linux-aarch64	illumina-interop-1.3.1-h7021222_2.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/07596237-5c0f-492d-8405-caad4cb310d2/artifacts/0/tmp/artifacts/packages <package name>`

Docker image(s) built:

Package	Tag	CI	Install with `docker`
illumina-interop	1.3.1--hdbdd923_2	Azure	show Images for Azure are in the LinuxArtifacts zip file above.`gzip -dc LinuxArtifacts/images/illumina-interop:1.3.1--hdbdd923_2.tar.gz \| docker load`

martin-g · 2024-07-01T08:50:00Z

@cbrueffer Here is a list of the installed files:

❯ tar xvf illumina-interop-1.3.1-h7021222_2.tar.bz2                                                                                                                                                        (test123) 
info/test/test_time_dependencies.json
info/run_exports.json
info/hash_input.json
info/recipe/build.sh
info/index.json
info/test/run_test.sh
info/recipe/meta.yaml.template
info/recipe/meta.yaml
info/recipe/conda_build_config.yaml
info/about.json
info/files
info/licenses/LICENSE
info/paths.json
info/git
interop/lib64/python/_py_interop_run.so
interop/lib64/python/_py_interop_comm.so
interop/lib64/python/_py_interop_table.so
interop/lib64/python/_py_interop_run_metrics.so
interop/lib64/python/_py_interop_plot.so
interop/lib64/python/_py_interop_summary.so
interop/lib64/python/_py_interop_metrics.so
interop/share/illumina/interop/src/python/interop/__pycache__/__init__.cpython-310.pyc
interop/share/illumina/interop/src/python/interop/__pycache__/__main__.cpython-310.pyc
interop/lib64/python/__pycache__/py_interop_comm.cpython-310.pyc
interop/share/illumina/interop/src/python/interop/__pycache__/py_interop_comm.cpython-310.pyc
interop/lib64/python/__pycache__/py_interop_run_metrics.cpython-310.pyc
interop/share/illumina/interop/src/python/interop/__pycache__/py_interop_run_metrics.cpython-310.pyc
interop/lib64/python/__pycache__/py_interop_table.cpython-310.pyc
interop/share/illumina/interop/src/python/interop/__pycache__/py_interop_table.cpython-310.pyc
interop/lib64/python/__pycache__/py_interop_plot.cpython-310.pyc
interop/share/illumina/interop/src/python/interop/__pycache__/py_interop_plot.cpython-310.pyc
interop/lib64/python/__pycache__/py_interop_summary.cpython-310.pyc
interop/share/illumina/interop/src/python/interop/__pycache__/py_interop_summary.cpython-310.pyc
interop/lib64/python/__pycache__/py_interop_run.cpython-310.pyc
interop/share/illumina/interop/src/python/interop/__pycache__/py_interop_run.cpython-310.pyc
interop/lib64/python/__pycache__/py_interop_metrics.cpython-310.pyc
interop/share/illumina/interop/src/python/interop/__pycache__/py_interop_metrics.cpython-310.pyc
interop/share/illumina/interop/src/python/interop/__init__.py
interop/share/illumina/interop/src/python/interop/__main__.py
interop/lib64/python/py_interop_comm.py
interop/share/illumina/interop/src/python/interop/py_interop_comm.py
interop/share/illumina/interop/src/python/interop/py_interop_run_metrics.py
interop/lib64/python/py_interop_run_metrics.py
interop/share/illumina/interop/src/python/interop/py_interop_table.py
interop/lib64/python/py_interop_table.py
interop/lib64/python/py_interop_plot.py
interop/share/illumina/interop/src/python/interop/py_interop_plot.py
interop/share/illumina/interop/src/python/interop/py_interop_summary.py
interop/lib64/python/py_interop_summary.py
interop/share/illumina/interop/src/python/interop/py_interop_run.py
interop/lib64/python/py_interop_run.py
interop/share/illumina/interop/src/python/interop/py_interop_metrics.py
interop/lib64/python/py_interop_metrics.py
interop/include/interop/version.h
interop/include/interop/config.h
interop/include/interop/util/exception_specification.h
interop/include/interop/util/timer.h
interop/include/interop/util/base_exception.h
interop/include/interop/logic/metric/index_metric.h
interop/include/interop/logic/metric/extended_tile_metric.h
interop/include/interop/util/static_assert.h
interop/include/interop/model/table/table_exceptions.h
interop/include/interop/model/plot/plot_exceptions.h
interop/include/interop/util/self_registration.h
interop/include/interop/interop.h
interop/include/interop/model/metric_base/metric_exceptions.h
interop/include/interop/io/format/generic_layout.h
interop/include/interop/constants/typedefs.h
interop/include/interop/logic/plot/plot_sample_qc.h
interop/include/interop/io/format/stream_membuf.h
interop/include/interop/logic/metric/extraction_metric.h
interop/include/interop/util/map.h
interop/include/interop/logic/plot/plot_metric_list.h
interop/include/interop/logic/logic.h
interop/include/interop/logic/summary/run_summary.h
interop/include/interop/logic/plot/plot_qscore_histogram.h
interop/include/interop/model/run/image_dimensions.h
interop/include/interop/model/summary/metric_average.h
interop/include/interop/logic/metric/dynamic_phasing_metric.h
interop/include/interop/model/model_exceptions.h
interop/include/interop/util/assert.h
interop/include/interop/logic/plot/plot_qscore_heatmap.h
interop/include/interop/constants/enum_description.h
interop/include/interop/util/length_of.h
interop/include/interop/model/metric_base/point2d.h
interop/include/interop/util/math.h
interop/include/interop/util/cstdint.h
interop/include/interop/logic/table/create_imaging_table_columns.h
interop/include/interop/logic/summary/index_summary.h
interop/include/interop/model/run/run_exceptions.h
interop/include/interop/util/exception.h
interop/include/interop/logic/plot/plot_point.h
interop/include/interop/util/unique_ptr.h
interop/include/interop/io/format/default_layout.h
interop/include/interop/model/plot/bar_point.h
interop/include/interop/io/format/abstract_text_format.h
interop/include/interop/model/summary/surface_summary.h
interop/include/interop/util/filesystem.h
interop/include/interop/logic/table/create_imaging_table.h
interop/include/interop/util/xml_exceptions.h
interop/include/interop/logic/table/table_util.h
interop/include/interop/io/stream_exceptions.h
interop/include/interop/model/metrics/q_by_lane_metric.h
interop/include/interop/logic/plot/plot_by_lane.h
interop/include/interop/model/plot/data_point.h
interop/include/interop/io/format/metric_format_factory.h
interop/include/interop/io/format/text_format.h
interop/include/interop/model/summary/metric_stat.h
interop/include/interop/model/run/read_info.h
interop/include/interop/logic/plot/plot_by_cycle.h
interop/include/interop/util/linear_hierarchy.h
interop/include/interop/model/metrics/phasing_metric.h
interop/include/interop/model/summary/cycle_state_summary.h
interop/include/interop/io/format/abstract_metric_format.h
interop/include/interop/logic/summary/map_cycle_to_read.h
interop/include/interop/util/time.h
interop/include/interop/model/plot/data_point_collection.h
interop/include/interop/io/table/imaging_table_csv.h
interop/include/interop/model/run/parameters.h
interop/include/interop/io/format/text_format_factory.h
interop/include/interop/model/run/cycle_range.h
interop/include/interop/model/plot/chart_data.h
interop/include/interop/logic/utils/metrics_to_load.h
interop/include/interop/util/constant_mapping.h
interop/include/interop/io/table/csv_format.h
interop/include/interop/util/string.h
interop/include/interop/model/metrics/dynamic_phasing_metric.h
interop/include/interop/model/metric_base/base_read_metric.h
interop/include/interop/model/plot/series.h
interop/include/interop/util/object_list.h
interop/include/interop/model/summary/index_count_summary.h
interop/include/interop/model/plot/plot_data.h
interop/include/interop/model/metrics/extended_tile_metric.h
interop/include/interop/util/type_traits.h
interop/include/interop/model/plot/candle_stick_point.h
interop/include/interop/logic/summary/cycle_state_summary.h
interop/include/interop/logic/summary/extraction_summary.h
interop/include/interop/model/plot/axes.h
interop/include/interop/model/summary/index_flowcell_summary.h
interop/include/interop/logic/summary/phasing_summary.h
interop/include/interop/model/metric_base/base_cycle_metric.h
interop/include/interop/io/format/stream_util.h
interop/include/interop/logic/plot/plot_flowcell_map.h
interop/include/interop/logic/utils/metric_type_ext.h
interop/include/interop/logic/plot/plot_metric_proxy.h
interop/include/interop/model/metrics/summary_run_metric.h
interop/include/interop/model/summary/read_summary.h
interop/include/interop/model/table/imaging_table.h
interop/include/interop/logic/plot/plot_data.h
interop/include/interop/io/layout/base_metric.h
interop/include/interop/util/indirect_range_iterator.h
interop/include/interop/model/summary/lane_summary.h
interop/include/interop/logic/metric/tile_metric.h
interop/include/interop/model/run/flowcell_layout.h
interop/include/interop/model/summary/metric_summary.h
interop/include/interop/logic/utils/channel.h
interop/include/interop/model/metrics/q_collapsed_metric.h
interop/include/interop/util/lexical_cast.h
interop/include/interop/model/plot/heatmap_data.h
interop/include/interop/io/paths.h
interop/include/interop/util/xml_parser.h
interop/include/interop/logic/table/check_imaging_table_column.h
interop/include/interop/model/plot/flowcell_data.h
interop/include/interop/logic/table/table_populator.h
interop/include/interop/model/metrics/image_metric.h
interop/include/interop/model/metrics/error_metric.h
interop/include/interop/model/summary/index_lane_summary.h
interop/include/interop/util/option_parser.h
interop/include/interop/logic/summary/summary_statistics.h
interop/include/interop/model/metrics/index_metric.h
interop/include/interop/logic/metric/q_metric.h
interop/include/interop/model/table/imaging_column.h
interop/include/interop/logic/metric/metric_value.h
interop/include/interop/io/format/metric_format.h
interop/include/interop/model/run/info.h
interop/include/interop/logic/summary/error_summary.h
interop/include/interop/model/summary/run_summary.h
interop/include/interop/constants/enums.h
interop/include/interop/logic/utils/enums.h
interop/include/interop/logic/summary/quality_summary.h
interop/include/interop/io/format/map_io.h
interop/include/interop/io/metric_stream.h
interop/include/interop/io/metric_file_stream.h
interop/include/interop/io/plot/gnuplot.h
interop/include/interop/model/metric_base/base_metric.h
interop/include/interop/model/summary/stat_summary.h
interop/include/interop/model/metrics/extraction_metric.h
interop/include/interop/model/run_metrics.h
interop/include/interop/model/metrics/tile_metric.h
interop/include/interop/logic/summary/tile_summary.h
interop/include/interop/model/metrics/q_metric.h
interop/include/interop/util/statistics.h
interop/include/interop/util/pstdint.h
interop/include/interop/model/metrics/corrected_intensity_metric.h
interop/include/interop/model/metric_base/metric_set.h
interop/include/interop/model/plot/filter_options.h
interop/include/interop/external/rapidxml_utils.hpp
interop/include/interop/external/rapidxml_iterators.hpp
interop/include/interop/external/rapidxml_print.hpp
interop/include/interop/external/rapidxml.hpp
interop/lib64/libinterop_lib.a
interop/lib64/libinterop_fpic_lib.a
interop/share/illumina/interop/src/python/interop/tablePYTHON_wrap.cxx
interop/share/illumina/interop/src/python/interop/run_metricsPYTHON_wrap.cxx
interop/share/illumina/interop/src/python/interop/commPYTHON_wrap.cxx
interop/share/illumina/interop/src/python/interop/plotPYTHON_wrap.cxx
interop/share/illumina/interop/src/python/interop/summaryPYTHON_wrap.cxx
interop/share/illumina/interop/src/python/interop/runPYTHON_wrap.cxx
interop/share/illumina/interop/src/python/interop/metricsPYTHON_wrap.cxx
interop/bin/aggregate
interop/bin/dumptext
interop/bin/dumpbin
interop/bin/imaging_table
interop/bin/index-summary
interop/bin/plot_flowcell
interop/bin/plot_qscore_heatmap
interop/bin/plot_sample_qc
interop/bin/plot_qscore_histogram
interop/bin/plot_by_lane
interop/bin/plot_by_cycle
interop/bin/summary
interop/include/interop/config.h.in
interop/README.md
interop/changes.md
interop/share/illumina/interop/examples/example1
interop/share/illumina/interop/examples/example2
interop/share/illumina/interop/examples/example3
interop/share/illumina/interop/examples/example4
interop/share/illumina/interop/examples/example_q_metric
interop/share/illumina/interop/examples/example_populate_qmetricset
bin/interop_dumpbin
bin/interop_summary
bin/interop_dumptext
bin/interop_aggregate
bin/interop_plot_by_lane
bin/interop_plot_by_cycle
bin/interop_plot_flowcell
bin/interop_index-summary
bin/interop_imaging_table
bin/interop_plot_sample_qc
bin/interop_plot_qscore_heatmap
bin/interop_plot_qscore_histogram

I don't see any site_packages here.

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

martin-g · 2024-07-01T08:56:51Z

https://dev.azure.com/bioconda/25074ded-3133-43ca-af80-895ab87b53cb/_apis/build/builds/62523/logs/21 contains logs with debug ls -Ra

cbrueffer added the WIP label Apr 13, 2023

cbrueffer mentioned this pull request Mar 20, 2024

checkqc: InterOp is not installed in docker image #46558

Open

cbrueffer added 2 commits March 20, 2024 12:24

Enable Python bindings; add license.

15cf5e0

WIP: Require Python for tests

51bcfa5

cbrueffer force-pushed the interop-python branch from a24d25f to 51bcfa5 Compare March 20, 2024 11:32

cbrueffer added 8 commits March 20, 2024 13:35

Add more requirements

7654f03

More depends fixes

116611a

More depends

f231b06

Debug

6caf8ca

debug

fdcbd15

debug

31c165b

debug

7bebd3f

debug

e81a8ec

matrulda mentioned this pull request May 14, 2024

New module: checkqc nf-core/modules#4158

Merged

13 tasks

martin-g and others added 2 commits July 1, 2024 09:37

Merge branch 'master' into interop-python

9bd4e8f

Bump build number

2f1e841

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

martin-g reviewed Jul 1, 2024

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martin-g force-pushed the interop-python branch from 1d4d48c to a68cc6a Compare July 1, 2024 07:22

List the files of the installed Python version

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martin-g force-pushed the interop-python branch from a68cc6a to 351aad4 Compare July 1, 2024 07:47

List the contents of /opt/mambaforge/envs/bioconda/lib/python3*/

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Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

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illumina-interop: enable Python bindings; add license. #40431

illumina-interop: enable Python bindings; add license. #40431

cbrueffer commented Apr 13, 2023

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martin-g commented Jul 1, 2024

illumina-interop: enable Python bindings; add license. #40431

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