Fixed the linting and formatting #3
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* Add container universe support This allows the executor to specify an HTCondor universe, and a container image when the universe is set to container/docker. These values are passed to the executor via the executor's CLI, e.g.: `snakemake --executor htcondor --htcondor-universe container --htcondor-container-image docker://foo:latest I chose to add these to the CLI instead of to the job's resources dict, because I think these will likely be applied to all jobs in a workflow. * Add job wrappers and HTCondor ftransfers when running w/o shared FS This commit adds a new CLI to specify a job wrapper (i.e. an HTCondor executable). When provided, the script should pass all of the executor's generated args to the snakemake executable, i.e. it should contain something like: ``` python -m snakemake $@ ``` This commit also takes a first pass at allowing HTCondor to manage its own file transfers, and makes use of the `can_transfer_local_files` executor interface introduced in PRs snakemake-interface-executor-plugins:67 and snakemake:2921. * Cleanup whitespace * Add creds and forgotten SHOULD_TRANFER_FILES attrs * Transfer Snakefile when no shared FS * Name jobs in queue according to snakemake job.name-job.jobid * Add traceback for debugging failed submissions * Move submit requests from CLI to resources * Allow custom classads * Update documentation and build toml * Update further docs with an example of non-shared fs usage * Upgrade to the V2 bindings to resolve credentials error These changes have been tested, but not rigorously, by a user at CHTC. * Move creds call into try block --------- Co-authored-by: Justin Hiemstra <[email protected]> Co-authored-by: Justin Hiemstra <[email protected]>
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I think there is a syntax error in the code creating the custom ClassAds: Instead it should be |
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