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Merged
tristan-f-r merged 4 commits into from
Sep 6, 2025
Merged

chore: bump spras #45

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3a29361
chore: bump spras
tristan-f-r Sep 6, 2025
0225a62
chore: downgrade snakemake
tristan-f-r Sep 6, 2025
8692acf
fix configs
tristan-f-r Sep 6, 2025
011727f
fix: rm run from reconstruction_settings
tristan-f-r Sep 6, 2025
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3 changes: 0 additions & 3 deletions configs/dmmm.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,13 +10,10 @@ container_registry:
reconstruction_settings:
locations:
reconstruction_dir: "output"
run: true

analysis:
summary:
include: false
graphspace:
include: false
cytoscape:
include: false
ml:
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3 changes: 0 additions & 3 deletions configs/pra.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,10 @@ container_registry:
reconstruction_settings:
locations:
reconstruction_dir: "output"
run: true

analysis:
summary:
include: false
graphspace:
include: false
cytoscape:
include: false
ml:
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -13,7 +13,7 @@ dependencies = [
[dependency-groups]
dev = [
"pre-commit>=4.2.0",
"snakemake>=9.6.0",
"snakemake==9.9.0",
]

[tool.ruff]
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4 changes: 2 additions & 2 deletions run_snakemake.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,8 @@ set -o nounset
cd "$(dirname "$0")"

main() {
uv tool run snakemake --cores 1 -d datasets/yeast-osmotic-stress -s datasets/yeast-osmotic-stress/Snakefile
uv tool run snakemake --cores 1 -d datasets/hiv -s datasets/hiv/Snakefile
uv run snakemake --cores 1 -d datasets/yeast-osmotic-stress -s datasets/yeast-osmotic-stress/Snakefile
uv run snakemake --cores 1 -d datasets/hiv -s datasets/hiv/Snakefile
}

main "$@"
2 changes: 1 addition & 1 deletion spras
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Submodule spras updated 87 files
+20 −0 .devcontainer/Dockerfile
+31 −0 .devcontainer/README.md
+17 −0 .devcontainer/devcontainer.json
+2 −2 .github/workflows/build-and-remove-template.yml
+1 −1 .github/workflows/build-containers.yml
+46 −13 .github/workflows/test-spras.yml
+6 −3 .pre-commit-config.yaml
+146 −0 .test_durations
+0 −311 CONTRIBUTING.md
+62 −16 Snakefile
+4 −0 _typos.toml
+0 −2 config/config.yaml
+0 −1 config/egfr.yaml
+1 −1 docker-wrappers/OmicsIntegrator1/README.md
+1 −1 docker-wrappers/RWR/README.md
+7 −10 docker-wrappers/SPRAS/example_config.yaml
+1 −1 docker-wrappers/ST_RWR/README.md
+6 −0 docs/conf.py
+0 −10 docs/contributing.rst
+493 −0 docs/contributing/index.rst
+60 −0 docs/contributing/maintain.rst
+2 −1 docs/index.rst
+7 −1 docs/prms/allpairs.rst
+11 −0 docs/prms/bowtiebuilder.rst
+7 −1 docs/prms/domino.rst
+11 −1 docs/prms/meo.rst
+16 −1 docs/prms/mincostflow.rst
+24 −2 docs/prms/oi1.rst
+18 −2 docs/prms/oi2.rst
+14 −1 docs/prms/pathlinker.rst
+29 −0 docs/prms/prms.rst
+11 −0 docs/prms/responsenet.rst
+13 −0 docs/prms/rwr.rst
+12 −0 docs/prms/strwr.rst
+32 −24 environment.yml
+18 −17 pyproject.toml
+2 −4 spras/allpairs.py
+3 −3 spras/analysis/ml.py
+35 −2 spras/analysis/summary.py
+3 −5 spras/btb.py
+0 −0 spras/config/__init__.py
+109 −128 spras/config/config.py
+168 −0 spras/config/schema.py
+19 −0 spras/config/util.py
+1 −1 spras/containers.py
+9 −5 spras/dataset.py
+4 −6 spras/domino.py
+165 −79 spras/evaluation.py
+6 −5 spras/meo.py
+5 −8 spras/mincostflow.py
+14 −6 spras/omicsintegrator1.py
+14 −6 spras/omicsintegrator2.py
+3 −5 spras/pathlinker.py
+7 −1 spras/prm.py
+5 −9 spras/responsenet.py
+3 −5 spras/rwr.py
+4 −6 spras/strwr.py
+2 −2 test/AllPairs/test_ap.py
+13 −1 test/BowTieBuilder/test_btb.py
+1 −1 test/DOMINO/test_domino.py
+1 −1 test/LocalNeighborhood/test_ln.py
+1 −1 test/MEO/test_meo.py
+1 −1 test/MinCostFlow/test_mcf.py
+1 −1 test/OmicsIntegrator1/test_oi1.py
+1 −1 test/OmicsIntegrator2/test_oi2.py
+1 −1 test/PathLinker/test_pathlinker.py
+1 −1 test/RWR/test_RWR.py
+1 −1 test/ResponseNet/test_rn.py
+1 −1 test/ST_RWR/test_STRWR.py
+10 −0 test/analysis/expected_output/expected_egfr_summary.txt
+13 −0 test/analysis/expected_output/expected_example_summary.txt
+0 −10 test/analysis/expected_output/test_egfr_summary.txt
+0 −13 test/analysis/expected_output/test_example_summary.txt
+0 −1 test/analysis/input/config.yaml
+0 −1 test/analysis/input/egfr.yaml
+1 −1 test/analysis/test_cytoscape.py
+3 −3 test/analysis/test_summary.py
+0 −0 test/evaluate/expected/expected-pr-pca-chosen-not-provided.txt
+2 −0 test/evaluate/expected/expected-pr-per-pathway-empty.txt
+5 −0 test/evaluate/expected/expected-pr-per-pathway.txt
+87 −40 test/evaluate/test_evaluate.py
+7 −0 test/ml/expected/expected-pca-coordinates-kde-negated.tsv
+5 −0 test/ml/expected/expected-pca-coordinates-sorted-negated.tsv
+5 −0 test/ml/expected/expected-pca-coordinates-sorted.tsv
+10 −4 test/ml/test_ml.py
+30 −6 test/test_config.py
+1 −1 test/test_util.py
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