[med-svn] [Git][med-team/python-pyani][upstream] New upstream version 0.2.13
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Tue Mar 18 07:27:51 GMT 2025
Nilesh Patra pushed to branch upstream at Debian Med / python-pyani
Commits:
786145df by Nilesh Patra at 2025-03-18T11:46:04+05:30
New upstream version 0.2.13
- - - - -
627 changed files:
- − .all-contributorsrc
- + .circleci/config.yml
- .codecov.yml
- .flake8
- − .github/ISSUE_TEMPLATE.txt
- − .github/PULL_REQUEST_TEMPLATE.md
- − .github/requirements-rtd.txt
- − .github/workflows/build-linux.yml
- − .github/workflows/build-macos.yml
- .gitignore
- .pre-commit-config.yaml
- − .readthedocs.yml
- CHANGES.md
- CITATIONS
- − CODEOWNERS
- − CONTRIBUTING.md
- CONTRIBUTORS.md
- + Dockerfile-average_nucleotide_identity
- + Dockerfile-genbank_get_genomes_by_taxon
- LICENSE
- Makefile
- + README-docker.md
- README.md
- − README_v_0_2_x.md
- − bandit.yml
- pyani/scripts/average_nucleotide_identity.py → bin/average_nucleotide_identity.py
- pyani/scripts/subcommands/subcmd_createdb.py → bin/delta_filter_wrapper.py
- pyani/scripts/genbank_get_genomes_by_taxon.py → bin/genbank_get_genomes_by_taxon.py
- − docs/Makefile
- − docs/about.rst
- − docs/api/Makefile
- − docs/api/conf.py
- − docs/api/index.rst
- − docs/api/make.bat
- − docs/api/pyani.anib.rst
- − docs/api/pyani.aniblastall.rst
- − docs/api/pyani.anim.rst
- − docs/api/pyani.blast.rst
- − docs/api/pyani.dependencies.rst
- − docs/api/pyani.download.rst
- − docs/api/pyani.logger.rst
- − docs/api/pyani.nucmer.rst
- − docs/api/pyani.pyani_classify.rst
- − docs/api/pyani.pyani_config.rst
- − docs/api/pyani.pyani_files.rst
- − docs/api/pyani.pyani_graphics.mpl.rst
- − docs/api/pyani.pyani_graphics.rst
- − docs/api/pyani.pyani_graphics.sns.rst
- − docs/api/pyani.pyani_jobs.rst
- − docs/api/pyani.pyani_orm.rst
- − docs/api/pyani.pyani_report.rst
- − docs/api/pyani.pyani_tools.rst
- − docs/api/pyani.rst
- − docs/api/pyani.run_multiprocessing.rst
- − docs/api/pyani.run_sge.rst
- − docs/api/pyani.scripts.average_nucleotide_identity.rst
- − docs/api/pyani.scripts.delta_filter_wrapper.rst
- − docs/api/pyani.scripts.genbank_get_genomes_by_taxon.rst
- − docs/api/pyani.scripts.logger.rst
- − docs/api/pyani.scripts.parsers.anib_parser.rst
- − docs/api/pyani.scripts.parsers.aniblastall_parser.rst
- − docs/api/pyani.scripts.parsers.anim_parser.rst
- − docs/api/pyani.scripts.parsers.classify_parser.rst
- − docs/api/pyani.scripts.parsers.common_parser.rst
- − docs/api/pyani.scripts.parsers.createdb_parser.rst
- − docs/api/pyani.scripts.parsers.download_parser.rst
- − docs/api/pyani.scripts.parsers.index_parser.rst
- − docs/api/pyani.scripts.parsers.listdeps_parser.rst
- − docs/api/pyani.scripts.parsers.plot_parser.rst
- − docs/api/pyani.scripts.parsers.report_parser.rst
- − docs/api/pyani.scripts.parsers.rst
- − docs/api/pyani.scripts.parsers.run_common_parser.rst
- − docs/api/pyani.scripts.parsers.scheduling_parser.rst
- − docs/api/pyani.scripts.pyani_script.rst
- − docs/api/pyani.scripts.rst
- − docs/api/pyani.scripts.subcommands.rst
- − docs/api/pyani.scripts.subcommands.subcmd_anib.rst
- − docs/api/pyani.scripts.subcommands.subcmd_aniblastall.rst
- − docs/api/pyani.scripts.subcommands.subcmd_anim.rst
- − docs/api/pyani.scripts.subcommands.subcmd_classify.rst
- − docs/api/pyani.scripts.subcommands.subcmd_createdb.rst
- − docs/api/pyani.scripts.subcommands.subcmd_download.rst
- − docs/api/pyani.scripts.subcommands.subcmd_index.rst
- − docs/api/pyani.scripts.subcommands.subcmd_listdeps.rst
- − docs/api/pyani.scripts.subcommands.subcmd_plot.rst
- − docs/api/pyani.scripts.subcommands.subcmd_report.rst
- − docs/api/pyani.scripts.tools.rst
- − docs/api/pyani.tetra.rst
- − docs/basic_use.rst
- − docs/citations.rst
- − docs/conf.py
- − docs/contributing.rst
- − docs/createdb.rst
- − docs/download.rst
- − docs/examples.rst
- − docs/images/bioconda-badge-compact.svg
- − docs/images/bioconda-badge-tall.svg
- − docs/images/bioconda-badge-very-compact.svg
- − docs/images/bioconda-badge-wide.svg
- − docs/images/distribution_identity_run3.png
- − docs/images/matrix_coverage_1.png
- − docs/images/matrix_identity_1.png
- − docs/images/scatterplot.png
- − docs/index.rst
- − docs/indexing.rst
- − docs/installation.rst
- − docs/interpreting_plots.rst
- − docs/licensing.rst
- − docs/quickstart.rst
- − docs/requirements.rst
- − docs/run_anib.rst
- − docs/run_anim.rst
- − docs/run_fastani.rst
- − docs/scheduler.rst
- − docs/subcmd_anib.rst
- − docs/subcmd_anim.rst
- − docs/subcmd_classify.rst
- − docs/subcmd_createdb.rst
- − docs/subcmd_download.rst
- − docs/subcmd_fastani.rst
- − docs/subcmd_index.rst
- − docs/subcmd_listdeps.rst
- − docs/subcmd_plot.rst
- − docs/subcmd_report.rst
- − docs/subcommands.rst
- − docs/testing.rst
- − docs/using_a_scheduler.rst
- pyani/__init__.py
- pyani/anib.py
- − pyani/aniblastall.py
- pyani/anim.py
- − pyani/blast.py
- − pyani/dependencies.py
- − pyani/download.py
- − pyani/fastani.py
- − pyani/logger.py
- − pyani/nucmer.py
- − pyani/pyani_classify.py
- pyani/pyani_config.py
- pyani/pyani_files.py
- pyani/pyani_graphics/mpl/__init__.py → pyani/pyani_graphics.py
- − pyani/pyani_graphics/__init__.py
- − pyani/pyani_graphics/sns/__init__.py
- pyani/pyani_jobs.py
- − pyani/pyani_orm.py
- − pyani/pyani_report.py
- pyani/pyani_tools.py
- pyani/run_multiprocessing.py
- pyani/run_sge.py
- − pyani/scripts/__init__.py
- − pyani/scripts/delta_filter_wrapper.py
- − pyani/scripts/parsers/__init__.py
- − pyani/scripts/parsers/anib_parser.py
- − pyani/scripts/parsers/aniblastall_parser.py
- − pyani/scripts/parsers/anim_parser.py
- − pyani/scripts/parsers/classify_parser.py
- − pyani/scripts/parsers/common_parser.py
- − pyani/scripts/parsers/createdb_parser.py
- − pyani/scripts/parsers/download_parser.py
- − pyani/scripts/parsers/fastani_parser.py
- − pyani/scripts/parsers/index_parser.py
- − pyani/scripts/parsers/listdeps_parser.py
- − pyani/scripts/parsers/plot_parser.py
- − pyani/scripts/parsers/report_parser.py
- − pyani/scripts/parsers/run_common_parser.py
- − pyani/scripts/parsers/scheduling_parser.py
- − pyani/scripts/pyani_script.py
- − pyani/scripts/subcommands/__init__.py
- − pyani/scripts/subcommands/subcmd_anib.py
- − pyani/scripts/subcommands/subcmd_aniblastall.py
- − pyani/scripts/subcommands/subcmd_anim.py
- − pyani/scripts/subcommands/subcmd_classify.py
- − pyani/scripts/subcommands/subcmd_download.py
- − pyani/scripts/subcommands/subcmd_fastani.py
- − pyani/scripts/subcommands/subcmd_index.py
- − pyani/scripts/subcommands/subcmd_listdeps.py
- − pyani/scripts/subcommands/subcmd_plot.py
- − pyani/scripts/subcommands/subcmd_report.py
- pyani/tetra.py
- − pytest.ini
- requirements-dev.txt
- − requirements-fastani-linux.txt
- − requirements-fastani-macos.txt
- requirements-pip.txt
- − requirements-pyqt-conda.txt
- − requirements-pyqt-pip.txt
- − requirements-thirdparty-linux.txt
- − requirements-thirdparty-macos.txt
- requirements.txt
- + setup.cfg
- setup.py
- + test-requirements.txt
- − tests/conftest.py
- − tests/fixtures/C_blochmannia/GCF_000011745.1_ASM1174v1_genomic.fna
- − tests/fixtures/C_blochmannia/GCF_000011745.1_ASM1174v1_genomic.fna.gz
- − tests/fixtures/C_blochmannia/GCF_000011745.1_ASM1174v1_genomic.md5
- − tests/fixtures/C_blochmannia/GCF_000011745.1_ASM1174v1_hashes.txt
- − tests/fixtures/C_blochmannia/GCF_000043285.1_ASM4328v1_genomic.fna
- − tests/fixtures/C_blochmannia/GCF_000043285.1_ASM4328v1_genomic.fna.gz
- − tests/fixtures/C_blochmannia/GCF_000043285.1_ASM4328v1_genomic.md5
- − tests/fixtures/C_blochmannia/GCF_000043285.1_ASM4328v1_hashes.txt
- − tests/fixtures/C_blochmannia/GCF_000185985.2_ASM18598v2_genomic.fna
- − tests/fixtures/C_blochmannia/GCF_000185985.2_ASM18598v2_genomic.fna.gz
- − tests/fixtures/C_blochmannia/GCF_000185985.2_ASM18598v2_genomic.md5
- − tests/fixtures/C_blochmannia/GCF_000185985.2_ASM18598v2_hashes.txt
- − tests/fixtures/C_blochmannia/GCF_000331065.1_ASM33106v1_genomic.fna
- − tests/fixtures/C_blochmannia/GCF_000331065.1_ASM33106v1_genomic.fna.gz
- − tests/fixtures/C_blochmannia/GCF_000331065.1_ASM33106v1_genomic.md5
- − tests/fixtures/C_blochmannia/GCF_000331065.1_ASM33106v1_hashes.txt
- − tests/fixtures/C_blochmannia/GCF_000973505.1_ASM97350v1_genomic.fna
- − tests/fixtures/C_blochmannia/GCF_000973505.1_ASM97350v1_genomic.fna.gz
- − tests/fixtures/C_blochmannia/GCF_000973505.1_ASM97350v1_genomic.md5
- − tests/fixtures/C_blochmannia/GCF_000973505.1_ASM97350v1_hashes.txt
- − tests/fixtures/C_blochmannia/GCF_000973545.1_ASM97354v1_genomic.fna
- − tests/fixtures/C_blochmannia/GCF_000973545.1_ASM97354v1_genomic.fna.gz
- − tests/fixtures/C_blochmannia/GCF_000973545.1_ASM97354v1_genomic.md5
- − tests/fixtures/C_blochmannia/GCF_000973545.1_ASM97354v1_hashes.txt
- − tests/fixtures/C_blochmannia/GCF_009827135.1_ASM982713v1_genomic.fna
- − tests/fixtures/C_blochmannia/GCF_009827135.1_ASM982713v1_genomic.fna.gz
- − tests/fixtures/C_blochmannia/GCF_009827135.1_ASM982713v1_genomic.md5
- − tests/fixtures/C_blochmannia/GCF_009827135.1_ASM982713v1_hashes.txt
- − tests/fixtures/C_blochmannia/GCF_014857065.1_ASM1485706v1_genomic.fna
- − tests/fixtures/C_blochmannia/GCF_014857065.1_ASM1485706v1_genomic.fna.gz
- − tests/fixtures/C_blochmannia/GCF_014857065.1_ASM1485706v1_genomic.md5
- − tests/fixtures/C_blochmannia/GCF_014857065.1_ASM1485706v1_hashes.txt
- − tests/fixtures/C_blochmannia/GCF_023016305.1_ASM2301630v1_genomic.fna
- − tests/fixtures/C_blochmannia/GCF_023016305.1_ASM2301630v1_genomic.fna.gz
- − tests/fixtures/C_blochmannia/GCF_023016305.1_ASM2301630v1_genomic.md5
- − tests/fixtures/C_blochmannia/GCF_023016305.1_ASM2301630v1_hashes.txt
- − tests/fixtures/C_blochmannia/classes.txt
- − tests/fixtures/C_blochmannia/labels.txt
- − tests/fixtures/C_blochmannia_kraken/GCF_000011745.1_ASM1174v1_genomic.fna
- − tests/fixtures/C_blochmannia_kraken/GCF_000011745.1_ASM1174v1_genomic.fna.gz
- − tests/fixtures/C_blochmannia_kraken/GCF_000011745.1_ASM1174v1_genomic.md5
- − tests/fixtures/C_blochmannia_kraken/GCF_000011745.1_ASM1174v1_hashes.txt
- − tests/fixtures/C_blochmannia_kraken/GCF_000043285.1_ASM4328v1_genomic.fna
- − tests/fixtures/C_blochmannia_kraken/GCF_000043285.1_ASM4328v1_genomic.fna.gz
- − tests/fixtures/C_blochmannia_kraken/GCF_000043285.1_ASM4328v1_genomic.md5
- − tests/fixtures/C_blochmannia_kraken/GCF_000043285.1_ASM4328v1_hashes.txt
- − tests/fixtures/C_blochmannia_kraken/GCF_000185985.2_ASM18598v2_genomic.fna
- − tests/fixtures/C_blochmannia_kraken/GCF_000185985.2_ASM18598v2_genomic.fna.gz
- − tests/fixtures/C_blochmannia_kraken/GCF_000185985.2_ASM18598v2_genomic.md5
- − tests/fixtures/C_blochmannia_kraken/GCF_000185985.2_ASM18598v2_hashes.txt
- − tests/fixtures/C_blochmannia_kraken/GCF_000331065.1_ASM33106v1_genomic.fna
- − tests/fixtures/C_blochmannia_kraken/GCF_000331065.1_ASM33106v1_genomic.fna.gz
- − tests/fixtures/C_blochmannia_kraken/GCF_000331065.1_ASM33106v1_genomic.md5
- − tests/fixtures/C_blochmannia_kraken/GCF_000331065.1_ASM33106v1_hashes.txt
- − tests/fixtures/C_blochmannia_kraken/GCF_000973505.1_ASM97350v1_genomic.fna
- − tests/fixtures/C_blochmannia_kraken/GCF_000973505.1_ASM97350v1_genomic.fna.gz
- − tests/fixtures/C_blochmannia_kraken/GCF_000973505.1_ASM97350v1_genomic.md5
- − tests/fixtures/C_blochmannia_kraken/GCF_000973505.1_ASM97350v1_hashes.txt
- − tests/fixtures/C_blochmannia_kraken/GCF_000973545.1_ASM97354v1_genomic.fna
- − tests/fixtures/C_blochmannia_kraken/GCF_000973545.1_ASM97354v1_genomic.fna.gz
- − tests/fixtures/C_blochmannia_kraken/GCF_000973545.1_ASM97354v1_genomic.md5
- − tests/fixtures/C_blochmannia_kraken/GCF_000973545.1_ASM97354v1_hashes.txt
- − tests/fixtures/C_blochmannia_kraken/GCF_009827135.1_ASM982713v1_genomic.fna
- − tests/fixtures/C_blochmannia_kraken/GCF_009827135.1_ASM982713v1_genomic.fna.gz
- − tests/fixtures/C_blochmannia_kraken/GCF_009827135.1_ASM982713v1_genomic.md5
- − tests/fixtures/C_blochmannia_kraken/GCF_009827135.1_ASM982713v1_hashes.txt
- − tests/fixtures/C_blochmannia_kraken/GCF_014857065.1_ASM1485706v1_genomic.fna
- − tests/fixtures/C_blochmannia_kraken/GCF_014857065.1_ASM1485706v1_genomic.fna.gz
- − tests/fixtures/C_blochmannia_kraken/GCF_014857065.1_ASM1485706v1_genomic.md5
- − tests/fixtures/C_blochmannia_kraken/GCF_014857065.1_ASM1485706v1_hashes.txt
- − tests/fixtures/C_blochmannia_kraken/GCF_023016305.1_ASM2301630v1_genomic.fna
- − tests/fixtures/C_blochmannia_kraken/GCF_023016305.1_ASM2301630v1_genomic.fna.gz
- − tests/fixtures/C_blochmannia_kraken/GCF_023016305.1_ASM2301630v1_genomic.md5
- − tests/fixtures/C_blochmannia_kraken/GCF_023016305.1_ASM2301630v1_hashes.txt
- − tests/fixtures/anib/NC_002696-fragments.fna
- − tests/fixtures/anib/NC_002696_vs_NC_010338.blast_tab
- − tests/fixtures/anib/NC_002696_vs_NC_011916.blast_tab
- − tests/fixtures/anib/blastall/NC_002696_vs_NC_010338.blast_tab
- − tests/fixtures/anib/blastall/NC_002696_vs_NC_011916.blast_tab
- − tests/fixtures/anib/blastall/NC_002696_vs_NC_014100.blast_tab
- − tests/fixtures/anib/blastall/NC_010338_vs_NC_002696.blast_tab
- − tests/fixtures/anib/blastall/NC_010338_vs_NC_011916.blast_tab
- − tests/fixtures/anib/blastall/NC_010338_vs_NC_014100.blast_tab
- − tests/fixtures/anib/blastall/NC_011916_vs_NC_002696.blast_tab
- − tests/fixtures/anib/blastall/NC_011916_vs_NC_010338.blast_tab
- − tests/fixtures/anib/blastall/NC_011916_vs_NC_014100.blast_tab
- − tests/fixtures/anib/blastall/NC_014100_vs_NC_002696.blast_tab
- − tests/fixtures/anib/blastall/NC_014100_vs_NC_010338.blast_tab
- − tests/fixtures/anib/blastall/NC_014100_vs_NC_011916.blast_tab
- − tests/fixtures/anib/blastn/NC_002696_vs_NC_010338.blast_tab
- − tests/fixtures/anib/blastn/NC_002696_vs_NC_011916.blast_tab
- − tests/fixtures/anib/blastn/NC_002696_vs_NC_014100.blast_tab
- − tests/fixtures/anib/blastn/NC_010338_vs_NC_002696.blast_tab
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- − tests/fixtures/anim/deltadir/NC_011916/out.1delta
- − tests/fixtures/anim/deltadir/NC_011916/out.mcoords
- − tests/fixtures/anim/deltadir/NC_011916/out.mdelta
- − tests/fixtures/anim/deltadir/NC_011916/out.qdiff
- − tests/fixtures/anim/deltadir/NC_011916/out.rdiff
- − tests/fixtures/anim/deltadir/NC_011916/out.report
- − tests/fixtures/anim/deltadir/NC_011916/out.snps
- − tests/fixtures/anim/deltadir/NC_011916/test.filter1
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- − tests/fixtures/anim/sequences/NC_014100.fna.md5
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- − tests/test_targets/legacy_scripts/C_blochmannia/GCF_000973505.1_ASM97350v1_genomic.fna.gz
- − tests/test_targets/legacy_scripts/C_blochmannia/GCF_000973545.1_ASM97354v1_genomic.fna
- − tests/test_targets/legacy_scripts/C_blochmannia/GCF_000973545.1_ASM97354v1_genomic.fna.gz
- − tests/test_targets/legacy_scripts/C_blochmannia/classes.txt
- − tests/test_targets/legacy_scripts/C_blochmannia/labels.txt
- − tests/test_targets/legacy_scripts/TETRA_mpl/TETRA_correlations.pdf
- − tests/test_targets/legacy_scripts/TETRA_mpl/TETRA_correlations.png
- − tests/test_targets/legacy_scripts/TETRA_mpl/TETRA_correlations.tab
- − tests/test_targets/legacy_scripts/TETRA_seaborn/TETRA_correlations.pdf
- − tests/test_targets/legacy_scripts/TETRA_seaborn/TETRA_correlations.png
- − tests/test_targets/legacy_scripts/TETRA_seaborn/TETRA_correlations.tab
- − tests/test_targets/subcmd_index/GCF_000011745.1_ASM1174v1_genomic.fna.md5
- − tests/test_targets/subcmd_index/GCF_000043285.1_ASM4328v1_genomic.fna.md5
- − tests/test_targets/subcmd_index/GCF_000185985.2_ASM18598v2_genomic.fna.md5
- − tests/test_targets/subcmd_index/GCF_000331065.1_ASM33106v1_genomic.fna.md5
- − tests/test_targets/subcmd_index/GCF_000973505.1_ASM97350v1_genomic.fna.md5
- − tests/test_targets/subcmd_index/GCF_000973545.1_ASM97354v1_genomic.fna.md5
- − tests/test_targets/subcmd_index/classes.txt
- − tests/test_targets/subcmd_index/labels.txt
- tests/fixtures/targets/tetra/correlation.tab → tests/test_targets/tetra/correlation.tab
- tests/fixtures/targets/tetra/zscore.json → tests/test_targets/tetra/zscore.json
- tests/test_tetra.py
- − tests/tools.py
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/python-pyani/-/commit/786145dfa8ecbf2170c4de54c9dd23892ae7d3b8
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View it on GitLab: https://salsa.debian.org/med-team/python-pyani/-/commit/786145dfa8ecbf2170c4de54c9dd23892ae7d3b8
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