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docs: point Snakemake install docs at 2.5.0

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Update AlphaPulldown README snippets to deploy AlphaPulldownSnakemake 2.5.0
and align the shared input-parser dependency with the public 0.5.0 parser API.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
This commit is contained in:
Dima Molodenskiy
2026-05-26 16:22:27 +02:00
parent 4577f56b2f
commit 1d940d0b6a
2 changed files with 6 additions and 5 deletions
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9
README.md
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@@ -12,7 +12,7 @@ Install required dependencies:
```bash ```bash
conda env create \ conda env create \
-n snake \ -n snake \
-f https://raw.githubusercontent.com/KosinskiLab/AlphaPulldownSnakemake/2.4.0/workflow/envs/alphapulldown.yaml -f https://raw.githubusercontent.com/KosinskiLab/AlphaPulldownSnakemake/2.5.0/workflow/envs/alphapulldown.yaml
conda activate snake conda activate snake
``` ```
@@ -28,7 +28,7 @@ Create a new processing directory for your project:
snakedeploy deploy-workflow \ snakedeploy deploy-workflow \
https://github.com/KosinskiLab/AlphaPulldownSnakemake \ https://github.com/KosinskiLab/AlphaPulldownSnakemake \
AlphaPulldownSnakemake \ AlphaPulldownSnakemake \
--tag 2.4.0 --tag 2.5.0
cd AlphaPulldownSnakemake cd AlphaPulldownSnakemake
``` ```
@@ -70,8 +70,9 @@ selection and keeps the AF3 JSON feature input as one discontinuous polymer
chain with preserved residue-number gaps. For the AlphaFold 3 backend this chain with preserved residue-number gaps. For the AlphaFold 3 backend this
means chopped regions stay intra-chain, so template contacts between retained means chopped regions stay intra-chain, so template contacts between retained
fragments are not masked as inter-chain interactions. fragments are not masked as inter-chain interactions.
For workflow deployments, make sure the execution environment also carries This syntax is parsed by the shared `alphapulldown-input-parser` package used by
`alphapulldown-input-parser>=0.4.0`. both AlphaPulldown and AlphaPulldownSnakemake. For workflow deployments, make
sure the execution environment carries `alphapulldown-input-parser>=0.5.0`.
</details> </details>

2
pyproject.toml
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@@ -19,7 +19,7 @@ classifiers = [
dynamic = ["version"] dynamic = ["version"]
dependencies = [ dependencies = [
"absl-py>=0.13.0", "absl-py>=0.13.0",
"alphapulldown-input-parser>=0.4.0", "alphapulldown-input-parser>=0.5.0",
"dm-haiku", "dm-haiku",
"dm-tree>=0.1.6", "dm-tree>=0.1.6",
"h5py>=3.1.0", "h5py>=3.1.0",