ipyrad2 0.1.9__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- ipyrad2-0.1.9/.github/workflows/publish-pypi.yml +51 -0
- ipyrad2-0.1.9/.gitignore +14 -0
- ipyrad2-0.1.9/LICENSE.txt +674 -0
- ipyrad2-0.1.9/PKG-INFO +749 -0
- ipyrad2-0.1.9/README.md +47 -0
- ipyrad2-0.1.9/TODO.md +106 -0
- ipyrad2-0.1.9/conda.recipe/meta.yaml +57 -0
- ipyrad2-0.1.9/docs/_templates/README.md +28 -0
- ipyrad2-0.1.9/docs/_templates/command-reference.md +51 -0
- ipyrad2-0.1.9/docs/_templates/concept-guide.md +39 -0
- ipyrad2-0.1.9/docs/_templates/section-landing.md +32 -0
- ipyrad2-0.1.9/docs/analyses/dapc.md +282 -0
- ipyrad2-0.1.9/docs/analyses/index.md +35 -0
- ipyrad2-0.1.9/docs/analyses/pca.md +327 -0
- ipyrad2-0.1.9/docs/analyses/popgen.md +369 -0
- ipyrad2-0.1.9/docs/assembly/assemble.md +309 -0
- ipyrad2-0.1.9/docs/assembly/demux.md +192 -0
- ipyrad2-0.1.9/docs/assembly/denovo.md +385 -0
- ipyrad2-0.1.9/docs/assembly/index.md +72 -0
- ipyrad2-0.1.9/docs/assembly/map.md +222 -0
- ipyrad2-0.1.9/docs/assembly/trim.md +223 -0
- ipyrad2-0.1.9/docs/css/notebook-markdown.css +114 -0
- ipyrad2-0.1.9/docs/getting-started/ethos.md +28 -0
- ipyrad2-0.1.9/docs/getting-started/files-and-data-types.md +187 -0
- ipyrad2-0.1.9/docs/getting-started/installation.md +96 -0
- ipyrad2-0.1.9/docs/getting-started/what-is-ipyrad.md +43 -0
- ipyrad2-0.1.9/docs/index.md +36 -0
- ipyrad2-0.1.9/docs/recipes/index.md +28 -0
- ipyrad2-0.1.9/docs/recipes/sample-name-parsing.md +136 -0
- ipyrad2-0.1.9/docs/writing-outputs/index.md +67 -0
- ipyrad2-0.1.9/docs/writing-outputs/lex.md +51 -0
- ipyrad2-0.1.9/docs/writing-outputs/snpex.md +178 -0
- ipyrad2-0.1.9/docs/writing-outputs/wex.md +290 -0
- ipyrad2-0.1.9/environment.yml +21 -0
- ipyrad2-0.1.9/ipyrad2/__init__.py +16 -0
- ipyrad2-0.1.9/ipyrad2/_version.py +24 -0
- ipyrad2-0.1.9/ipyrad2/analysis/__init__.py +61 -0
- ipyrad2-0.1.9/ipyrad2/analysis/converters/__init__.py +22 -0
- ipyrad2-0.1.9/ipyrad2/analysis/converters/vcf_to_hdf5.py +656 -0
- ipyrad2-0.1.9/ipyrad2/analysis/extracters/__init__.py +33 -0
- ipyrad2-0.1.9/ipyrad2/analysis/extracters/locus_extracter.py +472 -0
- ipyrad2-0.1.9/ipyrad2/analysis/extracters/sequence_common.py +230 -0
- ipyrad2-0.1.9/ipyrad2/analysis/extracters/snps_extracter.py +1399 -0
- ipyrad2-0.1.9/ipyrad2/analysis/extracters/window_extracter.py +991 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/__init__.py +47 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/admixture.py +346 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/baba/__init__.py +21 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/baba/models.py +79 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/baba/runner.py +1822 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/bpp.py +756 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/bpp_posteriors.py +105 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/bpp_summary.py +123 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/common.py +688 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/dapc.py +256 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/pca.py +800 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/pca_drawing.py +286 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/popgen/__init__.py +21 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/popgen/common.py +193 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/popgen/estimators.py +406 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/popgen/models.py +185 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/popgen/runner.py +451 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/popgen/seq_backend.py +1314 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/popgen/snp_backend.py +296 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/snmf.py +635 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/snps_imputer.py +182 -0
- ipyrad2-0.1.9/ipyrad2/analysis/methods/treeslider.py +1140 -0
- ipyrad2-0.1.9/ipyrad2/analysis/utils.py +163 -0
- ipyrad2-0.1.9/ipyrad2/assembler/__init__.py +3 -0
- ipyrad2-0.1.9/ipyrad2/assembler/assemble.py +2257 -0
- ipyrad2-0.1.9/ipyrad2/assembler/beds.py +826 -0
- ipyrad2-0.1.9/ipyrad2/assembler/hdf5_utils.py +163 -0
- ipyrad2-0.1.9/ipyrad2/assembler/loci.py +1897 -0
- ipyrad2-0.1.9/ipyrad2/assembler/paralogs.py +913 -0
- ipyrad2-0.1.9/ipyrad2/assembler/read_filters.py +352 -0
- ipyrad2-0.1.9/ipyrad2/assembler/sort_utils.py +12 -0
- ipyrad2-0.1.9/ipyrad2/assembler/variants.py +1495 -0
- ipyrad2-0.1.9/ipyrad2/assembler/write_seqs.py +384 -0
- ipyrad2-0.1.9/ipyrad2/assembler/write_snps.py +700 -0
- ipyrad2-0.1.9/ipyrad2/classic/__init__.py +3 -0
- ipyrad2-0.1.9/ipyrad2/classic/cli_classic.py +234 -0
- ipyrad2-0.1.9/ipyrad2/cli/__init__.py +3 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_admixture.py +139 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_analysis.py +570 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_assemble.py +217 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_baba.py +149 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_bpp.py +167 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_dapc.py +135 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_demux.py +169 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_denovo.py +166 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_lex.py +114 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_main.py +483 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_map.py +100 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_pca.py +163 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_popgen.py +152 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_snmf.py +158 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_snpex.py +147 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_treeslider.py +153 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_trim.py +179 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_vcf_to_hdf5.py +65 -0
- ipyrad2-0.1.9/ipyrad2/cli/cli_wex.py +113 -0
- ipyrad2-0.1.9/ipyrad2/cli/command_log.py +68 -0
- ipyrad2-0.1.9/ipyrad2/cli/common.py +24 -0
- ipyrad2-0.1.9/ipyrad2/demuxer/__init__.py +3 -0
- ipyrad2-0.1.9/ipyrad2/demuxer/demux.py +1162 -0
- ipyrad2-0.1.9/ipyrad2/demuxer/demux_pipeline.py +869 -0
- ipyrad2-0.1.9/ipyrad2/demuxer/demux_report.py +471 -0
- ipyrad2-0.1.9/ipyrad2/demuxer/match.py +975 -0
- ipyrad2-0.1.9/ipyrad2/demuxer/sample_names.py +37 -0
- ipyrad2-0.1.9/ipyrad2/denovo/__init__.py +2 -0
- ipyrad2-0.1.9/ipyrad2/denovo/align.py +1346 -0
- ipyrad2-0.1.9/ipyrad2/denovo/cluster.py +163 -0
- ipyrad2-0.1.9/ipyrad2/denovo/common.py +75 -0
- ipyrad2-0.1.9/ipyrad2/denovo/denovo.py +1702 -0
- ipyrad2-0.1.9/ipyrad2/denovo/graph.py +1334 -0
- ipyrad2-0.1.9/ipyrad2/denovo/graph_split.py +269 -0
- ipyrad2-0.1.9/ipyrad2/mapper/__init__.py +8 -0
- ipyrad2-0.1.9/ipyrad2/mapper/legacy_map_bams.py +453 -0
- ipyrad2-0.1.9/ipyrad2/mapper/map_samples_prep.py +304 -0
- ipyrad2-0.1.9/ipyrad2/mapper/map_stats.py +604 -0
- ipyrad2-0.1.9/ipyrad2/mapper/mapper.py +599 -0
- ipyrad2-0.1.9/ipyrad2/trimmer/__init__.py +2 -0
- ipyrad2-0.1.9/ipyrad2/trimmer/adapters.fa +14 -0
- ipyrad2-0.1.9/ipyrad2/trimmer/trim_fastqs.py +730 -0
- ipyrad2-0.1.9/ipyrad2/utils/__init__.py +0 -0
- ipyrad2-0.1.9/ipyrad2/utils/exceptions.py +11 -0
- ipyrad2-0.1.9/ipyrad2/utils/jit_funcs.py +91 -0
- ipyrad2-0.1.9/ipyrad2/utils/kmers.py +1177 -0
- ipyrad2-0.1.9/ipyrad2/utils/logger.py +104 -0
- ipyrad2-0.1.9/ipyrad2/utils/names.py +699 -0
- ipyrad2-0.1.9/ipyrad2/utils/parallel/__init__.py +22 -0
- ipyrad2-0.1.9/ipyrad2/utils/parallel/pipeline.py +681 -0
- ipyrad2-0.1.9/ipyrad2/utils/parallel/pool.py +544 -0
- ipyrad2-0.1.9/ipyrad2/utils/params.py +222 -0
- ipyrad2-0.1.9/ipyrad2/utils/pops.py +228 -0
- ipyrad2-0.1.9/ipyrad2/utils/profiling.py +83 -0
- ipyrad2-0.1.9/ipyrad2/utils/progress.py +58 -0
- ipyrad2-0.1.9/ipyrad2/utils/seqs.py +46 -0
- ipyrad2-0.1.9/ipyrad2.egg-info/PKG-INFO +749 -0
- ipyrad2-0.1.9/ipyrad2.egg-info/SOURCES.txt +189 -0
- ipyrad2-0.1.9/ipyrad2.egg-info/dependency_links.txt +1 -0
- ipyrad2-0.1.9/ipyrad2.egg-info/entry_points.txt +3 -0
- ipyrad2-0.1.9/ipyrad2.egg-info/requires.txt +14 -0
- ipyrad2-0.1.9/ipyrad2.egg-info/scm_file_list.json +184 -0
- ipyrad2-0.1.9/ipyrad2.egg-info/scm_version.json +8 -0
- ipyrad2-0.1.9/ipyrad2.egg-info/top_level.txt +1 -0
- ipyrad2-0.1.9/pyproject.toml +63 -0
- ipyrad2-0.1.9/scripts/benchmark_denovo_split.py +204 -0
- ipyrad2-0.1.9/scripts/migrate_legacy_map_bams.py +73 -0
- ipyrad2-0.1.9/setup.cfg +4 -0
- ipyrad2-0.1.9/tests/test_analysis_admixture.py +319 -0
- ipyrad2-0.1.9/tests/test_analysis_baba.py +525 -0
- ipyrad2-0.1.9/tests/test_analysis_bpp.py +288 -0
- ipyrad2-0.1.9/tests/test_analysis_cluster_tools.py +315 -0
- ipyrad2-0.1.9/tests/test_analysis_extractors.py +1001 -0
- ipyrad2-0.1.9/tests/test_analysis_pca.py +966 -0
- ipyrad2-0.1.9/tests/test_analysis_popgen.py +888 -0
- ipyrad2-0.1.9/tests/test_analysis_snmf.py +136 -0
- ipyrad2-0.1.9/tests/test_analysis_snp_imputer.py +213 -0
- ipyrad2-0.1.9/tests/test_analysis_snp_tools.py +956 -0
- ipyrad2-0.1.9/tests/test_analysis_treeslider.py +724 -0
- ipyrad2-0.1.9/tests/test_assemble_callable_regions.py +410 -0
- ipyrad2-0.1.9/tests/test_assemble_paralogs.py +329 -0
- ipyrad2-0.1.9/tests/test_assemble_read_filters.py +6210 -0
- ipyrad2-0.1.9/tests/test_cli_analysis_help.py +852 -0
- ipyrad2-0.1.9/tests/test_cli_assemble_help.py +221 -0
- ipyrad2-0.1.9/tests/test_cli_command_log.py +117 -0
- ipyrad2-0.1.9/tests/test_cli_demux_help.py +213 -0
- ipyrad2-0.1.9/tests/test_cli_denovo_help.py +117 -0
- ipyrad2-0.1.9/tests/test_cli_lazy_imports.py +148 -0
- ipyrad2-0.1.9/tests/test_cli_map_help.py +99 -0
- ipyrad2-0.1.9/tests/test_cli_trim_help.py +153 -0
- ipyrad2-0.1.9/tests/test_demux_interrupt.py +343 -0
- ipyrad2-0.1.9/tests/test_demux_matching.py +2306 -0
- ipyrad2-0.1.9/tests/test_denovo.py +3902 -0
- ipyrad2-0.1.9/tests/test_kmers.py +506 -0
- ipyrad2-0.1.9/tests/test_legacy_map_bams.py +353 -0
- ipyrad2-0.1.9/tests/test_map_samples_prep.py +293 -0
- ipyrad2-0.1.9/tests/test_map_stats.py +157 -0
- ipyrad2-0.1.9/tests/test_mapper.py +582 -0
- ipyrad2-0.1.9/tests/test_names.py +369 -0
- ipyrad2-0.1.9/tests/test_parallel_ctrl_c.py +239 -0
- ipyrad2-0.1.9/tests/test_parallel_pipeline.py +240 -0
- ipyrad2-0.1.9/tests/test_parallel_pool.py +402 -0
- ipyrad2-0.1.9/tests/test_parallel_streaming.py +128 -0
- ipyrad2-0.1.9/tests/test_pops.py +91 -0
- ipyrad2-0.1.9/tests/test_profiling.py +112 -0
- ipyrad2-0.1.9/tests/test_progress_logging.py +100 -0
- ipyrad2-0.1.9/tests/test_trim_fastqs.py +768 -0
- ipyrad2-0.1.9/tests/test_trim_fastqs_outputs.py +1029 -0
- ipyrad2-0.1.9/tests/test_version.py +23 -0
- ipyrad2-0.1.9/zensical.toml +33 -0
|
@@ -0,0 +1,51 @@
|
|
|
1
|
+
name: Publish PyPI Release
|
|
2
|
+
|
|
3
|
+
on:
|
|
4
|
+
push:
|
|
5
|
+
tags:
|
|
6
|
+
- "v*"
|
|
7
|
+
|
|
8
|
+
permissions:
|
|
9
|
+
contents: read
|
|
10
|
+
id-token: write
|
|
11
|
+
|
|
12
|
+
jobs:
|
|
13
|
+
build-and-publish:
|
|
14
|
+
runs-on: ubuntu-latest
|
|
15
|
+
|
|
16
|
+
steps:
|
|
17
|
+
- name: Check out repository
|
|
18
|
+
uses: actions/checkout@v4
|
|
19
|
+
with:
|
|
20
|
+
fetch-depth: 0
|
|
21
|
+
|
|
22
|
+
- name: Set up Python
|
|
23
|
+
uses: actions/setup-python@v5
|
|
24
|
+
with:
|
|
25
|
+
python-version: "3.12"
|
|
26
|
+
|
|
27
|
+
- name: Classify tag
|
|
28
|
+
id: tag_kind
|
|
29
|
+
shell: bash
|
|
30
|
+
run: |
|
|
31
|
+
tag="${GITHUB_REF_NAME}"
|
|
32
|
+
if [[ "$tag" =~ ^v[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
|
|
33
|
+
echo "stable=true" >> "$GITHUB_OUTPUT"
|
|
34
|
+
else
|
|
35
|
+
echo "stable=false" >> "$GITHUB_OUTPUT"
|
|
36
|
+
fi
|
|
37
|
+
|
|
38
|
+
- name: Install build tooling
|
|
39
|
+
run: |
|
|
40
|
+
python -m pip install --upgrade pip
|
|
41
|
+
python -m pip install build
|
|
42
|
+
|
|
43
|
+
- name: Build distributions
|
|
44
|
+
run: python -m build
|
|
45
|
+
|
|
46
|
+
- name: Show built artifacts
|
|
47
|
+
run: ls -lh dist
|
|
48
|
+
|
|
49
|
+
- name: Publish stable release to PyPI
|
|
50
|
+
if: steps.tag_kind.outputs.stable == 'true'
|
|
51
|
+
uses: pypa/gh-action-pypi-publish@release/v1
|