[med-svn] [Git][med-team/macsyfinder][master] 6 commits: d/watch: upgrade to syntax version 5

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / macsyfinder


Commits:
0c9b1da9 by Michael R. Crusoe at 2026-01-31T13:09:34+01:00
d/watch: upgrade to syntax version 5

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9c7f937f by Michael R. Crusoe at 2026-01-31T13:34:14+01:00
New upstream version

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bc360d51 by Michael R. Crusoe at 2026-01-31T13:34:17+01:00
New upstream version 2.1.6
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abd2b24c by Michael R. Crusoe at 2026-01-31T13:38:48+01:00
Update upstream source from tag 'upstream/2.1.6'

Update to upstream version '2.1.6'
with Debian dir 60cb6c533483987c57787d70a271bd508187ab38
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edd1c1d3 by Michael R. Crusoe at 2026-01-31T13:38:49+01:00
Standards-Version: 4.7.3 (routine-update)

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8f28e05a by Michael R. Crusoe at 2026-01-31T13:39:02+01:00
Remove duplicate line from changelog.

Changes-By: lintian-brush

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71 changed files:

- .github/workflows/testing.yml
- CONTRIBUTORS.md
- codemeta.json
- debian/changelog
- debian/control
- debian/watch
- doc/source/modeler_guide/modeling.rst
- doc/source/user_guide/input.rst
- doc/source/user_guide/new_v2.rst
- nextflow.config
- pyproject.toml
- src/macsyfinder/__init__.py
- src/macsyfinder/scripts/macsy_gembase_split.py
- src/macsyfinder/scripts/macsy_merge_results.py
- src/macsyfinder/scripts/macsyconfig.py
- src/macsyfinder/scripts/macsyprofile.py
- src/macsyfinder/scripts/msf.py
- + tests/data/base/test_16.faa
- + tests/data/functional_test_ordered_circular_small/all_best_solutions.tsv
- + tests/data/functional_test_ordered_circular_small/all_systems.tsv
- + tests/data/functional_test_ordered_circular_small/all_systems.txt
- + tests/data/functional_test_ordered_circular_small/best_solution.tsv
- + tests/data/functional_test_ordered_circular_small/best_solution_loners.tsv
- + tests/data/functional_test_ordered_circular_small/best_solution_multisystems.tsv
- + tests/data/functional_test_ordered_circular_small/best_solution_summary.tsv
- + tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_MOBB.res_hmm_extract
- + tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_MOBB.search_hmm.err
- + tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_MOBB.search_hmm.out
- + tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_MOBQ.res_hmm_extract
- + tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_MOBQ.search_hmm.err
- + tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_MOBQ.search_hmm.out
- + tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_t4cp1.res_hmm_extract
- + tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_t4cp1.search_hmm.err
- + tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_t4cp1.search_hmm.out
- + tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_virb4.res_hmm_extract
- + tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_virb4.search_hmm.err
- + tests/data/functional_test_ordered_circular_small/hmmer_results/T4SS_virb4.search_hmm.out
- + tests/data/functional_test_ordered_circular_small/macsyfinder.conf
- + tests/data/functional_test_ordered_circular_small/rejected_candidates.tsv
- + tests/data/functional_test_ordered_circular_small/rejected_candidates.txt
- + tests/data/functional_test_ordered_circular_small_2/all_best_solutions.tsv
- + tests/data/functional_test_ordered_circular_small_2/all_systems.tsv
- + tests/data/functional_test_ordered_circular_small_2/all_systems.txt
- + tests/data/functional_test_ordered_circular_small_2/best_solution.tsv
- + tests/data/functional_test_ordered_circular_small_2/best_solution_loners.tsv
- + tests/data/functional_test_ordered_circular_small_2/best_solution_multisystems.tsv
- + tests/data/functional_test_ordered_circular_small_2/best_solution_summary.tsv
- + tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_MOBB.res_hmm_extract
- + tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_MOBB.search_hmm.err
- + tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_MOBB.search_hmm.out
- + tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_MOBQ.res_hmm_extract
- + tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_MOBQ.search_hmm.err
- + tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_MOBQ.search_hmm.out
- + tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_t4cp1.res_hmm_extract
- + tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_t4cp1.search_hmm.err
- + tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_t4cp1.search_hmm.out
- + tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_virb4.res_hmm_extract
- + tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_virb4.search_hmm.err
- + tests/data/functional_test_ordered_circular_small_2/hmmer_results/T4SS_virb4.search_hmm.out
- + tests/data/functional_test_ordered_circular_small_2/macsyfinder.conf
- + tests/data/functional_test_ordered_circular_small_2/rejected_candidates.tsv
- + tests/data/functional_test_ordered_circular_small_2/rejected_candidates.txt
- + tests/data/models/functional/definitions/MOB_light.xml
- + tests/data/models/functional/definitions/MOB_light_no_loner.xml
- + tests/data/models/functional/profiles/T4SS_MOBB.hmm
- + tests/data/models/functional/profiles/T4SS_MOBQ.hmm
- + tests/data/models/functional/profiles/T4SS_t4cp1.hmm
- + tests/data/models/functional/profiles/T4SS_virb4.hmm
- tests/test_functional_test.py
- tests/test_macsyconfig.py
- tests/test_scripts.py


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/macsyfinder/-/compare/afb0fa41c2ed415a41a0773211da06652e821af8...8f28e05aff7ef409d70238a7f8c125e5e4a56b0c

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View it on GitLab: https://salsa.debian.org/med-team/macsyfinder/-/compare/afb0fa41c2ed415a41a0773211da06652e821af8...8f28e05aff7ef409d70238a7f8c125e5e4a56b0c
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