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Cdkharris/big merge #32

Merged
merged 149 commits into from
Oct 1, 2024
Merged

Cdkharris/big merge #32

merged 149 commits into from
Oct 1, 2024

Commits on Jun 16, 2022

  1. revise 'Transferring Files' to use Amdahl code

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Commits on Jun 22, 2022

  1. Concrete data transfer examples; update Parallel episode for Amdahl

    @tkphd
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  2. hpc-intro-code supercedes hpc-intro-data

    @tkphd
    tkphd committed Jun 22, 2022
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Commits on Jun 23, 2022

  1. Add second point and basic scaling discussion

    @tkphd
    tkphd committed Jun 23, 2022
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  2. fix CTCMS shebang

    @tkphd
    tkphd committed Jun 23, 2022
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  3. drop accidentally committed file

    @tkphd
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  4. missed a relative URL in jargon

    @tkphd
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  5. Merge pull request carpentries-incubator#407 from tkphd/amdahl-code 

    Amdahl code
    @reid-a
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  6. Revert "Amdahl code"

    @reid-a
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  7. Merge pull request carpentries-incubator#410 from carpentries-incubat… 

    …or/revert-407-amdahl-code

Revert "Amdahl code"
    @tkphd
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  8. Revert "Merge pull request carpentries-incubator#410 from carpentries… 

    …-incubator/revert-407-amdahl-code"

This reverts commit bdf8529, reversing
changes made to 86229eb.
    @tkphd
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Commits on Jun 30, 2022

  1. Removes typo

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  2. Merge pull request carpentries-incubator#412 from Kerleyark/Episode11… 

    …Corrections

Removes typo
    @tkphd
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Commits on Jul 5, 2022

  1. Removes unneeded comma, redundant word, and changes to active voice

    @juleskerley
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  2. Changes the wording to add clarification 

    There is an implication that `ls` can be used to read the file.
This disambiguates that implication.
    @juleskerley
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  3. Corrects the name to match the squeue result 

    Upon reviewing everyone's current job-with-name-status.snip, I realized that they all had "new_name" instead of "hello-world".
If "hello-world" is preferred, that would mean updating everyone's snip instead of the one line here.
    @juleskerley
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  4. Merge pull request carpentries-incubator#413 from Kerleyark/Episode12… 

    …Corrections

Removes unneeded comma, redundant word, and changes to active voice
    @tkphd
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Commits on Jul 13, 2022

  1. Merge branch 'carpentries-incubator:gh-pages' into Episode13Corrections

    @juleskerley
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  2. Changes wording to be more clear and less clunky 

    I had to move the structure of the paragraph around.
Only the first two lines had important changes.
    @juleskerley
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Commits on Jul 19, 2022

  1. Revert "Corrects the name to match the squeue result" 

    This reverts commit a38da5b.
    Avery Kerley committed Jul 19, 2022
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  2. Updates to "hello-world" or equivalent to match given name

    Avery Kerley committed Jul 19, 2022
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Commits on Jul 21, 2022

  1. Merge pull request carpentries-incubator#414 from Kerleyark/Episode13… 

    …Corrections

Episode13 corrections
    @tkphd
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  2. Merge branch 'carpentries-incubator:gh-pages' into Episode17Corrections

    @juleskerley
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  3. Merge pull request carpentries-incubator#416 from Kerleyark/Episode17… 

    …Corrections

Episode17 corrections
    @tkphd
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Commits on Jul 22, 2022

  1. config options for Birmingham Baskerville slurm

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Commits on Jul 25, 2022

  1. Adds comma to separate run-on sentence (carpentries-incubator#417)

    @juleskerley
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Commits on Sep 14, 2022

  1. Merge branch 'gh-pages' into baskerville

    @jnywong
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  2. update _config.yml

    Jenny Wong (Advanced Research Computing) committed Sep 14, 2022
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  3. restore _config.yml

    Jenny Wong (Advanced Research Computing) committed Sep 14, 2022
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Commits on Sep 22, 2022

  1. correct spelling

    Jenny Wong (Advanced Research Computing) committed Sep 22, 2022
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Commits on Sep 23, 2022

  1. Updating cluster computer slide presenter notes. 

    Updating presenter notes for cluster computer that were duplicated from the "cloud computing" slides. Attempting to address issue [419](carpentries-incubator#419).
    @lcoghill
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Commits on Sep 26, 2022

  1. Typo fix for README.md. 

    This is slightly mysterious -- it *is* an actual error, "script"
is meant there, but it's apparently been accepted by the CI
for a long time, but now is not being accepted.  "Scrip" is a
perfectly legitimate English word, though not what is meant
here, so the CI rejection is a bit puzzling also. Maybe the
dictionary changed?
    @reid-a
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  2. Merge pull request carpentries-incubator#423 from reid-a/scrip-fix 

    Typo fix for README.md.
    @ocaisa
    ocaisa authored Sep 26, 2022
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Commits on Sep 29, 2022

  1. Merge branch 'gh-pages' into update-jargon-presentation-notes

    @reid-a
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Commits on Oct 6, 2022

  1. Merge pull request carpentries-incubator#421 from baskerville-hpc/bas… 

    …kerville

Config options for Birmingham Baskerville slurm
    @reid-a
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  2. Grammar fix for the jargon file.

    @reid-a
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  3. Merge branch 'gh-pages' into update-jargon-presentation-notes

    @reid-a
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  4. Merge pull request carpentries-incubator#422 from lcoghill/update-jar… 

    …gon-presentation-notes

Updating cluster computer slide presenter notes.
    @reid-a
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Commits on Nov 17, 2022

  1. Properly template Python file URL 

    Closes carpentries-incubator#427.
    @tkphd
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Commits on Nov 18, 2022

  1. Merge pull request carpentries-incubator#429 from carpentries-incubat… 

    …or/issue427-broken-link-to-python-code

Properly template Python file URL
    @ocaisa
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Commits on Dec 3, 2022

  1. Revert "Merge pull request carpentries-incubator#410 from carpentries… 

    …-incubator/revert-407-amdahl-code"

This reverts commit bdf8529, reversing
changes made to 86229eb.
    @tkphd
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Commits on Jan 19, 2023

  1. Substitute Amdahl tarball for lesson files

    @tkphd
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  2. Merge branch 'amdahl-code-redux' of github:tkphd/hpc-intro into amdah… 

    …l-code-redux
    @tkphd
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  3. pip install amdahl in parallel episode

    @tkphd
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  4. fix missing blockquote tags

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  5. see amdahl not cpi in history

    @tkphd
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  6. update Python version

    @tkphd
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  7. updated server name

    @tkphd
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  8. a few readability fixes

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Commits on Jan 31, 2023

  1. remove unused tarball, consolidate pi code in new tarball

    @tkphd
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  2. Ask learners to think about why a transfer may not work 

    Co-authored-by: ocaisa <alan.ocais@cecam.org>
    @tkphd @ocaisa
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  3. Expand on the remote_destination for scp 

    Co-authored-by: ocaisa <alan.ocais@cecam.org>
    @tkphd @ocaisa
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  4. Clarify that remote_path may not exist 

    Co-authored-by: ocaisa <alan.ocais@cecam.org>
    @tkphd @ocaisa
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  5. discuss the tarball before transferring it

    @tkphd
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  6. Merge branch 'amdahl-code-redux' of github:tkphd/hpc-intro into amdah… 

    …l-code-redux
    @tkphd
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Commits on Feb 2, 2023

  1. Ask learners to think about why a transfer may not work 

    Co-authored-by: ocaisa <alan.ocais@cecam.org>
    @tkphd @ocaisa
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  2. Expand on the remote_destination for scp 

    Co-authored-by: ocaisa <alan.ocais@cecam.org>
    @tkphd @ocaisa
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  3. Clarify that remote_path may not exist 

    Co-authored-by: ocaisa <alan.ocais@cecam.org>
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  4. remove unused tarball, consolidate pi code in new tarball

    @tkphd
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  5. discuss the tarball before transferring it

    @tkphd
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Commits on Feb 3, 2023

  1. Merge branch 'amdahl-bad-merge' into amdahl-code-redux

    @tkphd
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Commits on Feb 10, 2023

  1. clean up & clarify a thing or two

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Commits on Feb 15, 2023

  1. revised discussion of tar and scp flags & fields

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Commits on Feb 16, 2023

  1. use nano to edit bashrc

    @tkphd
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  2. substitute previously-seen example job ID

    @tkphd
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  3. resolve build failure

    @tkphd
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  4. Update _episodes/16-parallel.md

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  5. Merge pull request carpentries-incubator#411 from tkphd/amdahl-code-r… 

    …edux

Amdahl code, redux
    @ocaisa
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Commits on Mar 20, 2023

  1. Update 13-scheduler.md 

    The HISAT2 website was moved to a new place.
    @eckhrd
    eckhrd authored Mar 20, 2023
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  2. Merge pull request carpentries-incubator#431 from eckhrd/patch-1 

    HISAT2 website moved
    @tkphd
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Commits on Apr 20, 2023

  1. Update 17-resources.md 

    I needed to use `less -S`, otherwise less (v. 530) would wrap the text, making it impossible to read.
    @eckhrd
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  2. Merge pull request carpentries-incubator#434 from eckhrd/patch-2 

    Make sure `sacct` job output is not wrapped in `less`
    @tkphd
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Commits on Jul 6, 2023

  1. Generate HPCC Cluster library, fix some random lesson deficiencies

    @tkphd
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Commits on Sep 21, 2023

  1. Update using-nodes-interactively.snip

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  2. Merge pull request carpentries-incubator#436 from carpentries-incubat… 

    …or/cluster.hpc-carpentry.org

Generate HPCC Cluster library, fix some random lesson deficiencies
    @ocaisa
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  3. Switch default config to HPCC cluster

    @ocaisa
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  4. Retain other lesson info

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  5. Retain other useful info

    @ocaisa
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  6. Update _config.yml

    @ocaisa
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  7. Update _config.yml

    @ocaisa
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  8. Update _config.yml

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  9. Update _config.yml

    @ocaisa
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  10. Update _config.yml

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  11. Update _config.yml

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  12. Merge pull request carpentries-incubator#440 from carpentries-incubat… 

    …or/ocaisa-patch-1

Switch default config to HPCC cluster
    @tkphd
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Commits on Jan 10, 2024

  1. Update Gemfile and fix some typos

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  2. codespell args are hard

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  3. cleanup crufty text from another lib

    @tkphd
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  4. Use packaged codespell instead of pip

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  5. Create missing file

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  6. cache bundle

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  7. missing file

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  8. Overhaul markdownlint using config file

    @tkphd
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  9. Missed a file

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  10. Figuring out how GH Actions work.

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  11. Long URLs should maybe be ref-links?

    @tkphd
    tkphd committed Jan 10, 2024
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  12. Complete listing of mdl rules

    @tkphd
    tkphd committed Jan 10, 2024
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  13. Merge pull request carpentries-incubator#444 from tkphd/update-workflows 

    Update Gemfile and fix some typos
    @ocaisa
    ocaisa authored Jan 10, 2024
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  14. Added all changes associated with EPCC_Cirrus_slurm.

    @mbareford @tkphd
    mbareford authored and tkphd committed Jan 10, 2024
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  15. Removed references to Cirrus PBS.

    @mbareford @tkphd
    mbareford authored and tkphd committed Jan 10, 2024
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  16. Update episode list

    @tkphd
    tkphd committed Jan 10, 2024
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  17. Repair some Markdown, prune some files

    @tkphd
    tkphd committed Jan 10, 2024
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  18. Restore a couple missing files

    @tkphd
    tkphd committed Jan 10, 2024
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  19. Fold templated stuff into core lesson

    @tkphd
    tkphd committed Jan 10, 2024
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  20. Restore rule: blanks around headings

    @tkphd
    tkphd committed Jan 10, 2024
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  21. Populate missing config flag, fix broken link

    @tkphd
    tkphd committed Jan 10, 2024
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  22. Merge pull request carpentries-incubator#445 from tkphd/epcc-cirrus-s… 

    …lurm

EPCC Cirrus (slurm)
    @ocaisa
    ocaisa authored Jan 10, 2024
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Commits on Jan 26, 2024

  1. Add episode on environment variables

    @ocaisa
    ocaisa committed Jan 26, 2024
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  2. Pass linter

    @ocaisa
    ocaisa committed Jan 26, 2024
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Commits on Jan 27, 2024

  1. Fix code block naming

    @ocaisa
    ocaisa committed Jan 27, 2024
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  2. Fix linting again

    @ocaisa
    ocaisa committed Jan 27, 2024
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  3. Some tweaks

    @ocaisa
    ocaisa committed Jan 27, 2024
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  4. Further tweaks

    @ocaisa
    ocaisa committed Jan 27, 2024
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Commits on Jan 28, 2024

  1. Make sure environment variables are not referenced before we cover them

    @ocaisa
    ocaisa committed Jan 28, 2024
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Commits on Feb 1, 2024

  1. Update snippet lib episode lists

    @tkphd
    tkphd committed Feb 1, 2024
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  2. Teeny little typo

    @tkphd
    tkphd committed Feb 1, 2024
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  3. Merge pull request carpentries-incubator#446 from ocaisa/runtime_env 

    Add episode on environment variables
    @tkphd
    tkphd authored Feb 1, 2024
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Commits on Apr 16, 2024

  1. Merge branch 'gh-pages' into cdkharris/big-merge

    @cdkharris
    cdkharris committed Apr 16, 2024
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  2. Merge UCL-ARC changes into the renamed transferring files episode

    @cdkharris
    cdkharris committed Apr 16, 2024
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  3. Remove the old parallel lesson

    @cdkharris
    cdkharris committed Apr 16, 2024
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  4. Merge the parallel snippets for the overhauled lesson

    @cdkharris
    cdkharris committed Apr 16, 2024
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Commits on Apr 26, 2024

  1. Update 13-scheduler.md to fix wall time directive

    @cdkharris
    cdkharris authored Apr 26, 2024
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Commits on May 29, 2024

  1. Update test_and_build.yml to not run the other sites

    @cdkharris
    cdkharris authored May 29, 2024
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  2. markdown formatting

    @cdkharris
    cdkharris committed May 29, 2024
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Commits on Jul 23, 2024

  1. Create filezilla-remote-instructions.snip

    @heatherkellyucl @dpshelio
    heatherkellyucl authored and dpshelio committed Jul 23, 2024
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Commits on Jul 25, 2024

  1. Reference a site snippet for Filezilla in the transferring-files lesson

    @cdkharris
    cdkharris authored Jul 25, 2024
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  2. Untangle comments about rsync on directories

    @cdkharris
    cdkharris authored Jul 25, 2024
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  3. Removing a redundant comment about scp -r

    @cdkharris
    cdkharris authored Jul 25, 2024
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  4. Merge pull request carpentries-incubator#454 from UCL-ARC/rsync 

    Rsync's behavior when uploading a directory
    @reid-a
    reid-a authored Jul 25, 2024
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  5. fix markdown and relocate UCL snippet

    @cdkharris
    cdkharris authored Jul 25, 2024
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  6. New snippet files for using Fliezilla with SSH tunnels

    @cdkharris
    cdkharris authored Jul 25, 2024
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  7. Merge branch 'gh-pages' into filezilla

    @cdkharris
    cdkharris authored Jul 25, 2024
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  8. Merge pull request carpentries-incubator#453 from UCL-ARC/filezilla 

    Filezilla remote tunneling instructions
    @reid-a
    reid-a authored Jul 25, 2024
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Commits on Aug 5, 2024

  1. Merge branch 'gh-pages-upstream' into cdkharris/big-merge

    @cdkharris
    cdkharris committed Aug 5, 2024
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Commits on Aug 6, 2024

  1. Revert "Update test_and_build.yml to not run the other sites" 

    This reverts commit 24210cd.
    @cdkharris
    cdkharris committed Aug 6, 2024
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Commits on Aug 7, 2024

  1. Add -L option to curl command 

    Fixes carpentries-incubator#455
    @ocaisa
    ocaisa authored Aug 7, 2024
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  2. Try again

    @ocaisa
    ocaisa authored Aug 7, 2024
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  3. Lint

    @ocaisa
    ocaisa authored Aug 7, 2024
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  4. Whoops

    @ocaisa
    ocaisa authored Aug 7, 2024
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  5. Merge pull request carpentries-incubator#456 from carpentries-incubat… 

    …or/ocaisa-patch-1

Add `-L` option to `curl` command
    @reid-a
    reid-a authored Aug 7, 2024
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Commits on Sep 23, 2024

  1. Merge branch 'gh-pages-upstream' into cdkharris/big-merge

    @cdkharris
    cdkharris committed Sep 23, 2024
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  2. Shuffled around some site-specific snippets

    @cdkharris
    cdkharris committed Sep 23, 2024
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  3. No longer needed for the new parallel lesson

    @cdkharris
    cdkharris committed Sep 23, 2024
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  4. Reducing diffs with upstream

    @cdkharris
    cdkharris committed Sep 23, 2024
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  5. Update login and compute node

    @cdkharris
    cdkharris committed Sep 23, 2024
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  6. Update new python scripts with Myriad env setup

    @cdkharris
    cdkharris committed Sep 23, 2024
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  7. Update option flags for Myriad SGE

    @cdkharris
    cdkharris committed Sep 23, 2024
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  8. Merge pull request carpentries-incubator#458 from UCL-ARC/cdkharris/U… 

    …CL-update-site-snippets

Update UCL site snippets
    @reid-a
    reid-a authored Sep 23, 2024
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Commits on Sep 24, 2024

  1. Merge branch 'gh-pages-upstream' into cdkharris/big-merge

    @cdkharris
    cdkharris committed Sep 24, 2024
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