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7 dayscommand-line-tool: Stage secondary files too.Arun Isaac
* ravanan/command-line-tool.scm (build-command-line-tool-script): Stage secondary files too.
7 daysreader: Use canonicalize-file-value.Arun Isaac
* ravanan/reader.scm (normalize-input): Use canonicalize-file-value.
7 dayswork/command-line-tool: Comment on trusting the checksum.Arun Isaac
* ravanan/work/command-line-tool.scm (canonicalize-file-value): Comment on trusting the checksum.
7 dayswork/command-line-tool: Canonicalize secondary files too.Arun Isaac
* ravanan/work/command-line-tool.scm (canonicalize-file-value): Canonicalize secondary files too.
7 dayswork/command-line-tool: Handle absent path and location correctly.Arun Isaac
* ravanan/work/command-line-tool.scm (canonicalize-file-value): Handle absent path and location correctly.
7 daysreader: Move location->path to work module.Arun Isaac
* ravanan/reader.scm (location->path): Move to ... * ravanan/work/command-line-tool.scm (location->path): ... here.
7 dayscommand-line-tool: Move canonicalize-file-value to work module.Arun Isaac
* ravanan/command-line-tool.scm (build-command-line-tool-script): Move canonicalize-file-value to ... * ravanan/work/command-line-tool.scm (canonicalize-file-value): ... here.
12 dayscommand-line-tool: Abstract out handling of SecondaryFile pattern.Arun Isaac
* ravanan/command-line-tool.scm (build-command-line-tool-script)[secondary-path]: New function. [capture-secondary-file]: Use secondary-path.
12 dayscommand-line-tool: Abstract out file staging into its own function.Arun Isaac
* ravanan/command-line-tool.scm (build-command-line-tool-script)[stage-file]: New function. [stage-files]: Use stage-file.
2025-04-14store: Intern secondary files.Arun Isaac
* ravanan/store.scm: Import (srfi srfi-26) and (ravanan work vectors). (intern-file): Intern secondary files. (%store-hash-length): New variable. (store-item-name): New public function. * ravanan/workflow.scm (resolve-inputs)[match-secondary-file-pattern]: Strip store hashes before matching secondary file patterns.
2025-04-14dir-locals: Indent call-with-atomic-output-file correctly.Arun Isaac
* .dir-locals.el (scheme-mode): Indent call-with-atomic-output-file correctly.
2025-03-18tests: Fix typo in test.Arun Isaac
* tests/reader.scm ("Normalize array of File arrays type formal output"): Replace normalize-formal-input with normalize-formal-output.
2025-03-18tests: Tolerate only path or location in File type inputs.Arun Isaac
* tests/reader.scm: Import (ice-9 filesystem), (web uri), (ravanan work command-line-tool) and (ravanan work utils). (normalize-input): New variable. ("Normalize inputs with only location", "Normalize inputs with only path"): New tests.
2025-03-18reader: Canonicalize File inputs completely in reader.Arun Isaac
It is the reader's job to completely canonicalize File type inputs. This should not be done later when the workflow is executing. * ravanan/reader.scm: Import (web uri). (normalize-formal-input): Normalize default value. (location->path): New function. (normalize-input): Canonicalize File type input completely. * ravanan/workflow.scm (workflow-scheduler): Update comment about partially specified File objects. (location->path): Delete function. (resolve-inputs): Do not canonicalize File type inputs; they already are.
2025-03-18reader: Spin off input normalization into separate function.Arun Isaac
Separate functions are easier to test. * ravanan/reader.scm (read-inputs): Spin off input normalization into ... (normalize-input): ... new function.
2025-02-28README: Add Contributing section.Arun Isaac
* README.md (Contributing): New section.
2025-02-24command-line-tool: Pass package versions separately to inferior.Arun Isaac
* ravanan/command-line-tool.scm (software-packages->environment): Pass package versions as separate argument to lookup-inferior-packages.
2025-02-24command-line-tool: Handle SoftwarePackage in helper function.Arun Isaac
* ravanan/command-line-tool.scm (specifications->environment): Rename to software-packages->environment. (software-packages->environment): Accept vector of SoftwarePackage association lists. (build-command-line-tool-script): Move into software-packages->environment. Pass vector of SoftwarePackage association lists to software-packages->environment.
2025-02-24guix: Inherit ravanan package from Guix upstream.Arun Isaac
* .guix/ravanan-package.scm: Do no import (gnu packages package-management), (gnu packages gnupg), (gnu packages guile), (gnu packages guile-xyz), (gnu packages node), (guix build-system gnu), (guix licenses) and (guix profiles). Import ravanan from (gnu packages bioinformatics) with a guix: prefix. * .guix/ravanan-package.scm (ravanan): Inherit from guix:ravanan.
2025-02-01Revert "bin: Remove unused (ravanan command-line-tool) import."Arun Isaac
This reverts commit 17b88bd2ca1411fbf2799e0e194d7052c059a36b. (ravanan command-line-tool) is required for manifest-file-error?.
2025-01-28README: Mention use of caching for developing workflows.Arun Isaac
* README.md: Mention use of caching for developing workflows.
2025-01-28images: Crop image of Ravanan.Arun Isaac
We crop the image to remove Siva and Parvathi. * images/ravanan-king-of-lanka.jpg: Crop.
2025-01-28releases: Add v0.1.0 release tarball.Arun Isaac
* releases/ravanan-0.1.0.tar.lz, releases/ravanan-0.1.0.tar.lz.asc: New files.
2025-01-28bin: Add newline after usage message.v0.1.0Arun Isaac
* bin/ravanan (print-usage): Add newline at the end.
2025-01-28Makefile: Add release tarball generation rules.Arun Isaac
* Makefile (GIT, GPG, LZIP, config_file_template, distribute_files, dist_archive): New variables. (dist, distsign, $(dist_archive), %.asc): New rules.
2025-01-28Makefile: Treat config.scm distinctly from sources.Arun Isaac
config.scm is a generated source file. Treat it the same as a hand-written source file creates problems when generating release tarballs. * Makefile (sources): Remove $(config_file). (objects): Add $(config_file:.scm=.go). (install): Depend on $(config_file) and install it.
2025-01-27README: Add table of contents.Arun Isaac
* README.md: Add table of contents.
2025-01-27README: Add image of Ravanan.Arun Isaac
* README.md: Add image of Ravanan. (License): Mention license and attribution for image. * images/ravanan-king-of-lanka.jpg, images/LICENSE.md: New files.
2025-01-27README: Fix grammar.Arun Isaac
* README.md (Building from source): Change "do" to "do so".
2025-01-27README: Restructure introduction.Arun Isaac
* README.md: Restructure introduction.
2025-01-27README: Add "Building from source" section.Arun Isaac
* README.md (Building from source): New section.
2025-01-27README: Fill out "How to use" section.Arun Isaac
* README.md (How to use): Fill out section. * doc/hello-world-inputs.json, doc/hello-world.cwl: New files.
2025-01-27bin: Create store directory when it does not exist.Arun Isaac
* bin/ravanan: Import (ravanan store). (main): Create store directory when it does not exist. * ravanan/store.scm (make-store): New public function.
2025-01-27store: Move store interning code to (ravanan store).Arun Isaac
* ravanan/store.scm: Import (ravanan work command-line-tool) and (ravanan work monads). * ravanan/workflow.scm (same-filesystem?, intern-file): Move to (ravanan store).
2025-01-27bin: Remove unused (ravanan command-line-tool) import.Arun Isaac
* bin/ravanan: Do not import (ravanan command-line-tool).
2025-01-27store: Move store path related code to new module.Arun Isaac
* ravanan/command-line-tool.scm: Import (ravanan store). (%store-files-directory, %store-data-directory, %store-logs-directory, script->store-files-directory, script->store-data-file, script->store-stdout-file, script->store-stderr-file): Move to ... * ravanan/store.scm: ... new file. * ravanan/workflow.scm (ravanan): Import (ravanan store).
2025-01-26slurm-api: Handle all slurm job state codes.Arun Isaac
* ravanan/slurm-api.scm: Import assertion-violation from (rnrs base). (slurm-state-codes->job-state): New function. (job-state): Use slurm-state-codes->job-state. * tests/slurm-api.scm: New file.
2025-01-25workflow: Hard link instead of copying when interning into the store.Arun Isaac
* ravanan/workflow.scm (same-filesystem?): New function. (intern-file): Hard link files if on the same filesystem. Else, copy.
2025-01-25slurm-api: Handle failed state when polling job state.Arun Isaac
* ravanan/slurm-api.scm (job-state): Handle failed state.
2025-01-24slurm-api: Translate slurm job states correctly.Arun Isaac
The job states returned by the slurm API are not the same as that expected by ravanan code. * ravanan/slurm-api.scm (job-state): Translate PENDING and RUNNING to pending state. Translate SUCCESS to completed state.
2025-01-24slurm-api: Error out when all options have been exhausted.Arun Isaac
Prior to this, job-state could still return a value if there were no errors described in the JSON. This is quite unlikely, but in the interest of rigour… * ravanan/slurm-api.scm (job-state): Error out when all options have been exhausted.
2025-01-24slurm-api: Support tracing.Arun Isaac
* ravanan/slurm-api.scm: Import (ravanan verbosity). (submit-job, job-state): Add traces. * bin/ravanan (%options): Support slurm-api in --trace option. (print-usage): Document it.
2025-01-24verbosity: Implement subsystem tracing.Arun Isaac
* ravanan/verbosity.scm: New file. * bin/ravanan: Import (ravanan verbosity). (%options): Add trace. (print-usage): Document it. (main): Set default value of traces. Parameterize %traces when running workflow.
2025-01-24command-line-tool: Support float and double types.Arun Isaac
* ravanan/work/command-line-tool.scm (object-type, match-type): Support float and double types. * ravanan/command-line-tool.scm (command-line-binding->args): Handle float arguments.
2025-01-24command-line-tool: Import (ravanan work types) into the job script.Arun Isaac
We need (ravanan work types) for array-type?. * ravanan/command-line-tool.scm (build-command-line-tool-script): Import (ravanan work types) into the job script.
2025-01-23command-line-tool: Handle G-exp args when joining with item separator.Arun Isaac
* ravanan/command-line-tool.scm (command-line-binding->args): Handle G-exp args when joining with item separator.
2025-01-23workflow: Handle exceptions in run-workflow.Arun Isaac
Since our scheduler is now state-monadic, the exception handler must guard the context in which the monad is actually run. * ravanan/workflow.scm (workflow-scheduler): Move exception handler to ... (run-workflow): ... here.
2025-01-23slurm-api: Bind return value of slurm-http-get in the state monad.Arun Isaac
* ravanan/slurm-api.scm (job-state): Bind return value of slurm-http-get in the state monad.
2025-01-22reader: Normalize File array type formals too.Arun Isaac
* ravanan/reader.scm: Import (ravanan work types). (some-file-type?): New function. (normalize-formal-input, normalize-formal-output): Normalize File array type formals too. * tests/reader.scm: Import (srfi srfi-1) and (ice-9 match). (normalize-formal-input, normalize-formal-output): New variables. (json=?): New function. ("Normalize File type formal input", "Normalize File array type formal input", "Normalize array of File arrays type formal input", "Normalize File type formal output", "Normalize File array type formal output", "Normalize array of File arrays type formal output"): New tests.
2025-01-22reader: Promote normalize functions to top level.Arun Isaac
It is easier to test top-level functions. * ravanan/reader.scm (normalize-workflow)[normalize-secondary-files, normalize-formal-input, normalize-formal-output, normalize-base-command, normalize-arguments, normalize-steps]: Promote to top level.
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