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Auto Generate environment.yml#339

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TimothyWillard wants to merge 44 commits intomainHopkinsIDD/flepiMoP:mainfrom GH-191/auto-generate-environment.ymlHopkinsIDD/flepiMoP:GH-191/auto-generate-environment.ymlCopy head branch name to clipboard

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Commits

Commits on Sep 13, 2024

• Copy slurm_init.sh to slurm_init_longleaf.sh

  TimothyWillard

  committed
  aa0c077

• Restore slurm_init.sh

  TimothyWillard

  committed
  22cb130

• Merge branch 'copy-file' into GH-191/longleaf-batch-submission

  TimothyWillard

  committed
  90e29b2

• Added UNC Longleaf Specific Init/Prerun Scripts

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  TimothyWillard

  committed
  c1d54ef

Commits on Sep 16, 2024

• Draft implementation of HPC install script

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  TimothyWillard

  committed
  e238d66

• Minor changes to hpc_install.sh

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  TimothyWillard

  committed
  2436640

• Added slurm --partition flag to inference script

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  TimothyWillard

  committed
  bba583a

Commits on Oct 2, 2024

• Initial pass at HPC install on rockfish

  TimothyWillard

  committed
  2c8c952

• Remove longleaf specific slurm scripts

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  TimothyWillard

  committed
  194d2e1

• Remove --partion flag

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  TimothyWillard

  committed
  f76d68a

Commits on Oct 3, 2024

• Minor updates to hpc_install.sh

  Show description for 8af3698
  TimothyWillard

  committed
  8af3698

Commits on Oct 9, 2024

• initial tweaks to make flepimop-inference-* runnable

  

  pearsonca

  authored and

  TimothyWillard

  committed
  23d9de1

• further install scripts fixes

  

  pearsonca

  authored and

  TimothyWillard

  committed
  9ac9cf0

• fix reinvocation of inference-slot

  

  pearsonca

  authored and

  TimothyWillard

  committed
  d32a58c

• initial installation for ubuntu re-org

  

  pearsonca

  authored and

  TimothyWillard

  committed
  9f2c085

• updates addressing use of installed r scripts

  

  pearsonca

  authored and

  TimothyWillard

  committed
  e2bc41f

• README revs

  

  pearsonca

  authored and

  TimothyWillard

  committed
  3095ae4

• add arrow installation

  

  pearsonca

  authored and

  TimothyWillard

  committed
  1b33dc3

• Switch R pkg install to use build/setup.R

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  TimothyWillard

  committed
  ec0c479

• Add $WORKDIR to hpc_install.R

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  TimothyWillard

  committed
  e754364

• Add missing flepi path arg to setup.R

  TimothyWillard

  committed
  5e4f398

• Force pin arrow version between python and R

  TimothyWillard

  committed
  0d9f813

• Change rockfish default directories

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  TimothyWillard

  committed
  9ca12ed

• Split hpc_install.sh into init and install

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  TimothyWillard

  committed
  f78ee75

• Use devtools::install in setup.R

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  TimothyWillard

  committed
  6d69186

• Unset error exit around R pkg install

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  TimothyWillard

  committed
  7adbdfa

• Add set +e an exit to flepi_init.sh

  TimothyWillard

  committed
  ae6666f

• install_cli installs to conda bin

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  TimothyWillard

  and

  pearsonca

  committed
  f3fb1a7

• Remove init call from install script

  Show description for e443626
  TimothyWillard

  committed
  e443626

• Remove old version restrictions, add optparse

  TimothyWillard

  committed
  480bfd7

• Move R deps install into conda environment

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  TimothyWillard

  committed
  385eeb5

• Readd inference CLI install

  Show description for f0571ae
  TimothyWillard

  committed
  f0571ae

• Update example command to use installed CLI

  TimothyWillard

  committed
  53f2f49

• Manually install covidcast package

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  TimothyWillard

  committed
  ec7978d

• Downgrade r-base dependency to 4.3

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  TimothyWillard

  committed
  2e6dfca

• Remove symlinks if exists on reinstall

  TimothyWillard

  committed
  42259a2

Commits on Oct 10, 2024

• Script to generate environment.yml

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  TimothyWillard

  committed
  aed8442

• Add dnachun to channels, add r-sf dependency

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  TimothyWillard

  committed
  a4631db

• GitHub action to generate environment.yml

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  TimothyWillard

  committed
  b0685c5

• Remove unneeded comment

  TimothyWillard

  committed
  a9e9f47

• Merge main into GH-191/auto-generate-environment.yml

  TimothyWillard

  committed
  9acda2c

• GitHub action checkout with attached head

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  TimothyWillard

  committed
  ca10838

• Update environment.yml

  TimothyWillard

  committed
  6ad753d

• Make clear source of environment.yml commit

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  TimothyWillard

  committed
  27a80f7