salishseacast/nemo-cmd

NEMO command processor, a command line tool for doing various operations associated with the running NEMO (and other) ocean models. This an extensible tool built on the OpenStack cliff (Command Line Interface Formulation Framework) package. As such, it can be used as the basis for a NEMO domain-specific command processor tool.

NEMO Command Processor

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The NEMO command processor, nemo, is a command line tool for doing various operations associated with running the NEMO ocean model.

Use nemo --help to get a list of the sub-commands available. Use nemo help <sub-command> to get a synopsis of what a sub-command does, what its required arguments are, and what options are available to control it.

Documentation for the command processor is in the docs/ directory and is rendered at https://nemo-cmd.readthedocs.io/en/latest/.

This an extensible tool built on the OpenStack cliff (Command Line Interface Formulation Framework) package. As such, it can be used as the basis for a NEMO domain-specific command processor tool.

The NEMO-Cmd is based on v2.2 of the SalishSeaCast NEMO model project's tools/SalishSeaCmd package.

License

The NEMO command processor and documentation are copyright 2013 – present by the SalishSeaCast Project Contributors and The University of British Columbia.

They are licensed under the Apache License, Version 2.0. https://www.apache.org/licenses/LICENSE-2.0 Please see the LICENSE file for details of the license.

nemo-cmd's Issues

Add `nemo run --no-deflate` option

For use with XIOS-2 on-the-fly deflation

Port from SalishSeaCmd; see https://bitbucket.org/salishsea/salishseacmd/commits/a263a1ff734a3dda8e1caab4487704296c7740ec

Combine & rename XIOS-2 stdout/stderr files

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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XIOS-2 produces per-processor xios_client_\d*.[out|err] and per-server xios_server_\d*.[out|err] files.
They need to be concatenated to produce 4 files:

• xios_client.stdout
• xios_client.stderr
• xios_server.stdout
• xios_server.stderr

Change GitHub Actions jobs to use reusable workflows

Reusable workflows are in UBC-MOAD/gha-workflows

• Add .github/dependabot.yaml to check for action version updated and generate PRs
• Add editable VCS installs of SalishSeaCast and MOAD pkgs to environment-test.yaml Already done in this repo
• Update codeql-analysis.yaml
• Update and rename docs-linkcheck.yaml
• Update and rename pytest-coverage.yaml
• Confirm badge URLs in README and dev docs
• Delete repo secrets in favour of org secrets

Change run results_dir arg to Path() object

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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Change cmd.split() to shlex.split(cmd) in run

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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Add --delete-restart option to gather

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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Expose combine. _find_rebuild_nemo_script() the API

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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So that it can be used by packages like SalishSeaCmd that extend NEMO-Cmd to confirm the existence of the rebuild_nemo tool executable during run preparation.

See issue #19 and https://bitbucket.org/salishsea/salishseacmd/issues/4

Enable use of ref namelists other than from CONFIG/SHARED/

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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See https://bitbucket.org/salishsea/tools/commits/dbc0c38d350916d102e35f55021725fae3985576?at=salishseacmdTRACE

VCS recording should ignore CONFIG/cfg.txt and TOOLS/COMPILE/full_key_list.txt files

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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The NEMO CONFIG/cfg.txt and TOOLS/COMPILE/full_key_list.txt files change when configs or tools are built, but the changes are generally of no consequence (e.g. line order changes).

So, they should be ignored by the VCS revision and status recording feature.

Proposed by @sea_susanallen

Add --ignore-restart option to combine

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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Gracefully handle empty stanzas in YAML run description

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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Known problem stanzas:

• forcing:
• restart:
• vcs revisions: hg:

Add PBS feature directives to run script via stanza in YAML run description file

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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Add HPC module loads to run script via stanza in YAML run description file

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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Port run_id prepended to temporary run dir uuid/name in from SalishSeaCmd

See https://bitbucket.org/salishsea/salishseacmd/issues/8/

Prepare should confirm existence of rebuild_nemo tool executable

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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Requested by @mdunphy

Allow absolute paths to coordinates & bathymetry files

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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Add unit tests for vcs revision & status recording feature

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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Add docs re: building tools that extend NEMO-Cmd

Use bash to launch run script if qsub doesn't exist

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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If bash is to be used, need to use $HOME rather than $PBS_O_HOME in run script.

Coordinates & bathymetry paths containing $HOME and $USER don't work

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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Might be a Python 2.7 issue - seen while helping Idalia get running on orcinus.

Allow more widespread use of ~, $USER, and $HOME in paths

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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VCS revision & status recording fails w/ unicode/str error under Python 2.7

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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Seen when helping Idalia get running on orcinus.

Add environment-hpc.yaml

Now that we can use conda envs with --user package installation on HPC clusters (sockeye, graham, optimum) we should have an environment description that provides just the required for installation dependencies (unlike the dev, test & rtd envs).

• Add environment-hpc.yaml file
• Update installation docs

Minimize environment-rtd.yaml

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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Most packages can be replaced by mock directives in conf.py.

Port AGRIF handling in from SalishSeaCmd

gather fails when restart/ dir exists in results dir

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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This comes up if GoMSS nowcast runs have to be repeated. Not sure if it is a bug or a safety feature since it (annoyingly) prevents overwrites.

Temporary run dir path may appear twice at end of prepare

Original report by Doug Latornell (Bitbucket: douglatornell, GitHub: douglatornell).

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Review use of reStructuredText :kbd: role in docs

sphinx-rtd-theme has change styling of :kdb: items to look like a keycap. That is not appropriate for things like machine names; e.g. :kbd:'salish'.