Age | Commit message (Collapse) | Author |
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*
ravanan/command-line-tool.scm (build-command-line-tool-script)[canonicalize-file-value]:
Separate out file copying into ...
[copy-file-value]: ... new function.
[capture-outputs-gexp, capture-secondary-file, path->value]: Call
copy-file-value after canonicalize-file-value.
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* ravanan/utils.scm: Move to ...
* ravanan/work/utils.scm (json-ref): ... here.
* ravanan/slurm-api.scm: Import (ravanan work utils) instead
of (ravanan utils).
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* ravanan/command-line-tool.scm (build-command-line-tool-script): Add
missing workflow-output-directory argument to canonicalize-file-value.
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* ravanan/work/utils.scm (alist=?): New public function.
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* ravanan/propnet.scm (run-propnet): Add comment describing state
machine implementation.
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* bin/ravanan (read-jwt): Explain why we support the SLURM_JWT=token
format.
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* bin/ravanan: Import (srfi srfi-26) and (ravanan utils).
(read-jwt): Support SLURM_JWT=token format.
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* bin/ravanan (read-jwt): New function.
(main): Call read-jwt.
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* ravanan/utils.scm (string-trim-prefix): New public function.
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*
ravanan/command-line-tool.scm (resolve-inputs)[canonicalize-file-value],
(build-command-line-tool-script)[canonicalize-file-value]: Add
nameroot and nameext fields.
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* ravanan/command-line-tool.scm (collect-input-files): Delete
function.
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stdout-output->value cannot access the inputs variable, and thus
will fail when stdout-filename is a parameter reference that needs to
be evaluated. To avoid this, pass it in as an argument.
*
ravanan/command-line-tool.scm (build-command-line-tool-script)[stdout-output->value]:
Accept stdout-filename as argument instead of G-expression embedding.
Pass stdout-filename as argument to stdout-output->value.
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* ravanan/command-line-tool.scm (resolve-inputs)[resolve]: When
recursing, create a vector of secondary files.
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* ravanan/job-state.scm (job-state-status): Pass on slurm API endpoint
and jwt recursively.
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* Makefile (config_file): Delete variable.
(sources): Remove $(config_file).
(all, %.go): Do not depend on $(config_file).
(clean): Do not delete $(config_file).
* ravanan/config.scm, ravanan/config.scm.in: Delete files.
* ravanan/command-line-tool.scm: Do not import (ravanan config).
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*
ravanan/command-line-tool.scm (resolve-inputs)[canonicalize-file-input,
match-secondary-file-pattern, check-secondary-files]: New functions.
[resolve]: Accept maybe-secondary-files argument.
Check that secondary files are provided with File type inputs.
(copy-input-files-gexp)[copy-input-files]: New function.
Copy secondary files to inputs directory.
(build-command-line-tool-script)[capture-outputs-gexp]: Pass
maybe-secondary-files argument to other-output->value.
[capture-secondary-file]: New function.
[path->value]: Call capture-secondary-file. Accept
maybe-secondary-files argument.
[stdout-output->value]: Pass maybe-secondary-files argument to
path->value.
[other-output->value]: Accept maybe-secondary-files argument and pass
it on to path->value.
Add TODO note about updating paths of staged files in inputs objects.
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* ravanan/work/vectors.scm (vector-filter-map): New public function.
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* ravanan/work/command-line-tool.scm (match-type): Comment on cond
ladder clauses.
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* ravanan/work/command-line-tool.scm (formal-parameter-type): Comment
on cond ladder clauses.
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* ravanan/vectors.scm: Move to ravanan/work/vectors.scm.
* ravanan/command-line-tool.scm, ravanan/job-state.scm,
ravanan/reader.scm, ravanan/workflow.scm: Import (ravanan work
vectors) instead of (ravanan vectors).
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* ravanan/monads.scm: Move to ravanan/work/monads.scm.
* ravanan/command-line-tool.scm, ravanan/propnet.scm,
ravanan/reader.scm, ravanan/workflow.scm: Import (ravanan work
vectors) instead of (ravanan vectors).
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* ravanan/utils.scm: Do not import (rnrs base). Move assoc-ref* to ...
* ravanan/work/utils.scm: ... here. Import assertion-violation
from (rnrs base).
* ravanan/command-line-tool.scm, ravanan/workflow.scm: Do not
import (ravanan utils).
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* ravanan/command-line-tool.scm (intern-file): Intern file only if it
is not already in the store.
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* ravanan/command-line-tool.scm (copy-input-files-gexp): Make
G-expression singular.
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* ravanan/command-line-tool.scm (build-command-line-tool-script):
Coerce expressions in glob patterns.
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* ravanan/command-line-tool.scm (build-command-line-tool-script):
Import (ravanan work ui) into G-expression.
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* ravanan/ui.scm: Move to ravanan/work/ui.scm.
* ravanan/command-line-tool.scm, ravanan/workflow.scm: Import (ravanan
work ui) instead of (ravanan ui).
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* ravanan/reader.scm (normalize-workflow)[normalize-secondary-files]:
New function.
[normalize-formal-input]: Use normalize-secondary-files.
[normalize-formal-output]: New function.
Call normalie-formal-output from main body.
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* ravanan/vectors.scm (vector-append-map): New public function.
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* ravanan/reader.scm (normalize-formals): Refactor type normalization
into ...
[normalize-type]: ... new function.
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This resolves the warning about importing (ice-9 filesystem) from the
host.
* ravanan/command-line-tool.scm: Import guile-filesystem from (gnu
packages guile-xyz).
(build-command-line-tool-script): Use with-extensions, not
with-imported-modules, to import guile-filesystem.
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* ravanan/command-line-tool.scm (build-command-line-tool-script):
Support File type staging entries.
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* ravanan/command-line-tool.scm (javascript-expression?): Return #t
even for parameter references mixed with literals.
(interpolate-parameter-references): New function.
(strip-javascript-expression): Delete function.
(coerce-expression): Use interpolate-parameter-references instead of
strip-javascript-expression.
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* ravanan/command-line-tool.scm (build-command-line-tool-script):
Import (rnrs io ports).
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* ravanan/command-line-tool.scm (build-command-line-tool-script):
Replace call-with-output-file with call-with-input-file.
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*
ravanan/command-line-tool.scm (build-command-line-tool-script)[files-to-stage]:
Use coerce-expression.
Adapt calling expression.
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* ravanan/command-line-tool.scm (build-command-line-tool-script):
Wrap result of files-to-stage in a maybe monad.
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*
ravanan/command-line-tool.scm (build-command-line-tool-script)[files-to-stage]:
Use vector-map->list.
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* ravanan/ui.scm (warning, user-error): Add docstrings.
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* ravanan/workflow.scm: Import (ravanan ui).
(run-workflow): Error out when required inputs are not specified.
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* ravanan/workflow.scm (optional-input?): New function.
(command-line-tool->propagator): Use optional-input?.
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error collides with a core binding.
* ravanan/ui.scm (error): Rename to user-error.
* ravanan/command-line-tool.scm: Import error without renaming to
raise-error. Replace calls to error with user-error, and calls to
raise-error with error.
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* ravanan/command-line-tool.scm: Import (ravanan ui).
(warning, error): Move to (ravanan ui).
* ravanan/ui.scm: New file.
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* ravanan/job-state.scm: New file.
* ravanan/command-line-tool.scm: Import (ravanan job-state).
(<single-machine-job-state>, <slurm-job-state>): Move to (ravanan
job-state).
(command-line-tool-scheduler): Use job-state-status and
job-state-script.
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* ravanan/slurm-api.scm (submit-job): Accept name argument and set it
as the job name.
* ravanan/command-line-tool.scm (run-command-line-tool): Pass name to
submit-job.
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* ravanan/propnet.scm (run-propnet): Pre-schedule all propagators.
* tests/propnet.scm: New file.
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* ravanan/workflow.scm (%supported-requirements): Add
ScatterFeatureRequirement.
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* .dir-locals.el (scheme-mode): Do not set scheme-indent-function on
call-with-temporary-directory.
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For other major modes, especially in magit commit message buffers, we
want the default fill-column of 70.
* .dir-locals.el (nil)[fill-column]: Move to scheme-mode.
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* tests/work/command-line-tool.scm: New file.
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