which does the following. Given paths to environment YAML files, it would
Extract package names and channels from the env.
Run mamba create --dry-run --json -c .
Extract the versions from the packages in the json that also occur in the original env.
Rewrite the env with minor version pinnings derived from the extracted versions.
This can (a) be used to update all environments (except wrappers) in a workflow to the latest minor release, and (b) be used to update all wrapper envs in snakemake/snakemake-wrappers. The latter can be used in a weekly CI job which would automatically create a PR in case of new changes. The same github action can also be offered for workflows actually.
which would bump all wrapper directives in a given Snakefile to the latest stable wrapper release. Again, this can come in combination with a github action that automatically creates a PR.
We should add a subcommand
which does the following. Given paths to environment YAML files, it would
This can (a) be used to update all environments (except wrappers) in a workflow to the latest minor release, and (b) be used to update all wrapper envs in snakemake/snakemake-wrappers. The latter can be used in a weekly CI job which would automatically create a PR in case of new changes. The same github action can also be offered for workflows actually.
In addition, we should have another subcommand
which would bump all wrapper directives in a given Snakefile to the latest stable wrapper release. Again, this can come in combination with a github action that automatically creates a PR.