Update all methods for the new dynwrap

[rcannood]

overview

• [x] angle
• [x] calista
• [x] cellrouter
• [x] celltrails
• [x] celltree_gibbs
• [x] celltree_maptpx
• [x] celltree_vem
• [x] comp1
• [x] dpt
• [x] elpicycle
• [x] elpigraph
• [x] elpilinear
• [x] embeddr
• [x] error
• [x] fateid
• [x] forks
• [x] gng
• [x] gpfates
• [x] grandprix
• [x] identity
• [x] matcher
• [x] merlot
• [x] mfa
• [x] monocle_ddrtree
• [x] monocle_ica
• [x] mpath
• [x] mst
• [x] ouija
• [x] ouijaflow
• [x] paga
• [x] paga_tree
• [x] pcreode
• [x] periodpc
• [x] phenopath
• [x] projected_dpt
• [x] projected_monocle
• [x] projected_paga
• [x] projected_slingshot
• [x] projected_tscan
• [x] pseudogp
• [x] raceid_stemid
• [x] random
• [x] recat
• [x] scimitar
• [x] scorpius
• [x] scoup
• [x] scuba
• [x] shuffle
• [x] sincell
• [x] slice
• [x] slicer
• [x] slingshot
• [x] stemnet
• [x] topslam
• [x] tscan
• [x] urd
• [x] wanderlust
• [x] waterfall
• [x] wishbone

[rcannood]

slicer

• [ ] Write new Dockerfile:
  • Depend on dynwrapr/dynwrappy
  • Remove version label
  • Use COPY instead of ADD
  • Update ENTRYPOINT
  • Create example h5:

    Rscript ./example.R /tmp/example.h5

  • Build docker container

    docker build -t dynverse/ti_slicer .

  • Turn off docker automated builds: go to https://cloud.docker.com/u/dynverse/repository/docker/dynverse/ti_slicer/builds/edit
  • Remove Singularity file
• [ ] Write new definition.yml and create version file with version 1.0.0
  • Test with dynwrap::create_ti_method_definition("ti_slicer/definition.yml")
• [ ] Write new run.R/py and chmod +x run.R
• [ ] Write new example.R (see ti_angle example) and chmod +x
• [ ] Rebuild!
• [ ] Verify that method works:

  docker run -v /tmp:/mnt dynverse/ti_slicer --dataset /mnt/example.h5 --output /mnt/output.h5
  dyncli::read_h5("/tmp/output.h5") %>% dynplot::plot_dimred()
  sudo rm /tmp/example.h5 /tmp/output.h5

  If it doesn't…:

  docker run -it -v /tmp:/mnt --entrypoint R dynverse/ti_slicer --dataset /mnt/example.h5 --output /mnt/output.h5

• [ ] Run travis_enc_all
• [ ] Create pull request and merge once travis has finished successfully

[rcannood]

slingshot

• [x] Write new Dockerfile:
  • Depend on dynwrapr/dynwrappy
  • Remove version label
  • Use COPY instead of ADD
  • Update ENTRYPOINT
  • Create example h5:

    Rscript ./example.R /tmp/example.h5

  • Build docker container

    docker build -t dynverse/ti_slingshot .

  • Turn off docker automated builds: go to https://cloud.docker.com/u/dynverse/repository/docker/dynverse/ti_slingshot/builds/edit
  • Remove Singularity file
• [x] Write new definition.yml and create version file with version 1.0.0
  • Test with dynwrap::create_ti_method_definition("ti_slingshot/definition.yml")
• [x] Write new run.R/py and chmod +x run.R
• [x] Write new example.R (see ti_angle example) and chmod +x
• [x] Rebuild!
• [x] Verify that method works:

  docker run -v /tmp:/mnt dynverse/ti_slingshot --dataset /mnt/example.h5 --output /mnt/output.h5
  dyncli::read_h5("/tmp/output.h5") %>% dynplot::plot_dimred()
  sudo rm /tmp/example.h5 /tmp/output.h5

  If it doesn't…:

  docker run -it -v /tmp:/mnt --entrypoint R dynverse/ti_slingshot --dataset /mnt/example.h5 --output /mnt/output.h5

• [x] Run travis_enc_all
• [x] Create pull request and merge once travis has finished successfully

[rcannood]

stemnet

• [x] Write new Dockerfile:
  • Depend on dynwrapr/dynwrappy
  • Remove version label
  • Use COPY instead of ADD
  • Update ENTRYPOINT
  • Create example h5:

    Rscript ./example.R /tmp/example.h5

  • Build docker container

    docker build -t dynverse/ti_stemnet .

  • Turn off docker automated builds: go to https://cloud.docker.com/u/dynverse/repository/docker/dynverse/ti_stemnet/builds/edit
  • Remove Singularity file
• [x] Write new definition.yml and create version file with version 1.0.0
  • Test with dynwrap::create_ti_method_definition("ti_stemnet/definition.yml")
• [x] Write new run.R/py and chmod +x run.R
• [x] Write new example.R (see ti_angle example) and chmod +x
• [x] Rebuild!
• [x] Verify that method works:

  docker run -v /tmp:/mnt dynverse/ti_stemnet --dataset /mnt/example.h5 --output /mnt/output.h5
  dyncli::read_h5("/tmp/output.h5") %>% dynplot::plot_dimred()
  sudo rm /tmp/example.h5 /tmp/output.h5

  If it doesn't…:

  docker run -it -v /tmp:/mnt --entrypoint R dynverse/ti_stemnet --dataset /mnt/example.h5 --output /mnt/output.h5

• [x] Run travis_enc_all
• [ ] Create pull request and merge once travis has finished successfully

[rcannood]

topslam

• [x] Write new Dockerfile:
  • Depend on dynwrapr/dynwrappy
  • Remove version label
  • Use COPY instead of ADD
  • Update ENTRYPOINT
  • Create example h5:

    Rscript ./example.R /tmp/example.h5

  • Build docker container

    docker build -t dynverse/ti_topslam .

  • Turn off docker automated builds: go to https://cloud.docker.com/u/dynverse/repository/docker/dynverse/ti_topslam/builds/edit
  • Remove Singularity file
• [x] Write new definition.yml and create version file with version 1.0.0
  • Test with dynwrap::create_ti_method_definition("ti_topslam/definition.yml")
• [x] Write new run.R/py and chmod +x run.R
• [x] Write new example.R (see ti_angle example) and chmod +x
• [x] Rebuild!
• [x] Verify that method works:

  docker run -v /tmp:/mnt dynverse/ti_topslam --dataset /mnt/example.h5 --output /mnt/output.h5
  dyncli::read_h5("/tmp/output.h5") %>% dynplot::plot_dimred()
  sudo rm /tmp/example.h5 /tmp/output.h5

  If it doesn't…:

  docker run -it -v /tmp:/mnt --entrypoint R dynverse/ti_topslam --dataset /mnt/example.h5 --output /mnt/output.h5

• [x] Run travis_enc_all
• [ ] Create pull request and merge once travis has finished successfully

[rcannood]

tscan

• [x] Write new Dockerfile:
  • Depend on dynwrapr/dynwrappy
  • Remove version label
  • Use COPY instead of ADD
  • Update ENTRYPOINT
  • Create example h5:

    Rscript ./example.R /tmp/example.h5

  • Build docker container

    docker build -t dynverse/ti_tscan .

  • Turn off docker automated builds: go to https://cloud.docker.com/u/dynverse/repository/docker/dynverse/ti_tscan/builds/edit
  • Remove Singularity file
• [x] Write new definition.yml and create version file with version 1.0.0
  • Test with dynwrap::create_ti_method_definition("ti_tscan/definition.yml")
• [x] Write new run.R/py and chmod +x run.R
• [x] Write new example.R (see ti_angle example) and chmod +x
• [x] Rebuild!
• [x] Verify that method works:

  docker run -v /tmp:/mnt dynverse/ti_tscan --dataset /mnt/example.h5 --output /mnt/output.h5
  dyncli::read_h5("/tmp/output.h5") %>% dynplot::plot_dimred()
  sudo rm /tmp/example.h5 /tmp/output.h5

  If it doesn't…:

  docker run -it -v /tmp:/mnt --entrypoint R dynverse/ti_tscan --dataset /mnt/example.h5 --output /mnt/output.h5

• [x] Run travis_enc_all
• [x] Create pull request and merge once travis has finished successfully

[rcannood]

urd

• [x] Write new Dockerfile:
  • Depend on dynwrapr/dynwrappy
  • Remove version label
  • Use COPY instead of ADD
  • Update ENTRYPOINT
  • Create example h5:

    Rscript ./example.R /tmp/example.h5

  • Build docker container

    docker build -t dynverse/ti_urd .

  • Turn off docker automated builds: go to https://cloud.docker.com/u/dynverse/repository/docker/dynverse/ti_urd/builds/edit
  • Remove Singularity file
• [x] Write new definition.yml and create version file with version 1.0.0
  • Test with dynwrap::create_ti_method_definition("ti_urd/definition.yml")
• [x] Write new run.R/py and chmod +x run.R
• [x] Write new example.R (see ti_angle example) and chmod +x
• [x] Rebuild!
• [x] Verify that method works:

  docker run -v /tmp:/mnt dynverse/ti_urd --dataset /mnt/example.h5 --output /mnt/output.h5
  dyncli::read_h5("/tmp/output.h5") %>% dynplot::plot_dimred()
  sudo rm /tmp/example.h5 /tmp/output.h5

  If it doesn't…:

  docker run -it -v /tmp:/mnt --entrypoint R dynverse/ti_urd --dataset /mnt/example.h5 --output /mnt/output.h5

• [x] Run travis_enc_all
• [x] Create pull request and merge once travis has finished successfully

[rcannood]

wanderlust

• [x] Write new Dockerfile:
  • Depend on dynwrapr/dynwrappy
  • Remove version label
  • Use COPY instead of ADD
  • Update ENTRYPOINT
  • Create example h5:

    Rscript ./example.R /tmp/example.h5

  • Build docker container

    docker build -t dynverse/ti_wanderlust .

  • Turn off docker automated builds: go to https://cloud.docker.com/u/dynverse/repository/docker/dynverse/ti_wanderlust/builds/edit
  • Remove Singularity file
• [x] Write new definition.yml and create version file with version 1.0.0
  • Test with dynwrap::create_ti_method_definition("ti_wanderlust/definition.yml")
• [x] Write new run.R/py and chmod +x run.R
• [x] Write new example.R (see ti_angle example) and chmod +x
• [x] Rebuild!
• [x] Verify that method works:

  docker run -v /tmp:/mnt dynverse/ti_wanderlust --dataset /mnt/example.h5 --output /mnt/output.h5
  dyncli::read_h5("/tmp/output.h5") %>% dynplot::plot_dimred()
  sudo rm /tmp/example.h5 /tmp/output.h5

  If it doesn't…:

  docker run -it -v /tmp:/mnt --entrypoint R dynverse/ti_wanderlust --dataset /mnt/example.h5 --output /mnt/output.h5

• [x] Run travis_enc_all
• [ ] Create pull request and merge once travis has finished successfully

Waiting on travis to rebuild dynwrap_containers

[rcannood]

waterfall

• [x] Write new Dockerfile:
  • Depend on dynwrapr/dynwrappy
  • Remove version label
  • Use COPY instead of ADD
  • Update ENTRYPOINT
  • Create example h5:

    Rscript ./example.R /tmp/example.h5

  • Build docker container

    docker build -t dynverse/ti_waterfall .

  • Turn off docker automated builds: go to https://cloud.docker.com/u/dynverse/repository/docker/dynverse/ti_waterfall/builds/edit
  • Remove Singularity file
• [x] Write new definition.yml and create version file with version 1.0.0
  • Test with dynwrap::create_ti_method_definition("ti_waterfall/definition.yml")
• [x] Write new run.R/py and chmod +x run.R
• [x] Write new example.R (see ti_angle example) and chmod +x
• [x] Rebuild!
• [x] Verify that method works:

  docker run -v /tmp:/mnt dynverse/ti_waterfall --dataset /mnt/example.h5 --output /mnt/output.h5
  dyncli::read_h5("/tmp/output.h5") %>% dynplot::plot_dimred()
  sudo rm /tmp/example.h5 /tmp/output.h5

  If it doesn't…:

  docker run -it -v /tmp:/mnt --entrypoint R dynverse/ti_waterfall --dataset /mnt/example.h5 --output /mnt/output.h5

• [x] Run travis_enc_all
• [ ] Create pull request and merge once travis has finished successfully

[rcannood]

wishbone

• [x] Write new Dockerfile:
  • Depend on dynwrapr/dynwrappy
  • Remove version label
  • Use COPY instead of ADD
  • Update ENTRYPOINT
  • Create example h5:

    Rscript ./example.R /tmp/example.h5

  • Build docker container

    docker build -t dynverse/ti_wishbone .

  • Turn off docker automated builds: go to https://cloud.docker.com/u/dynverse/repository/docker/dynverse/ti_wishbone/builds/edit
  • Remove Singularity file
• [x] Write new definition.yml and create version file with version 1.0.0
  • Test with dynwrap::create_ti_method_definition("ti_wishbone/definition.yml")
• [x] Write new run.R/py and chmod +x run.R
• [x] Write new example.R (see ti_angle example) and chmod +x
• [x] Rebuild!
• [x] Verify that method works:

  docker run -v /tmp:/mnt dynverse/ti_wishbone --dataset /mnt/example.h5 --output /mnt/output.h5
  dyncli::read_h5("/tmp/output.h5") %>% dynplot::plot_dimred()
  sudo rm /tmp/example.h5 /tmp/output.h5

  If it doesn't…:

  docker run -it -v /tmp:/mnt --entrypoint R dynverse/ti_wishbone --dataset /mnt/example.h5 --output /mnt/output.h5

• [x] Run travis_enc_all
• [ ] Create pull request and merge once travis has finished successfully

Waiting on travis to rebuild dynwrap_containers

[rcannood]

@zouter : I was having an issue that was hard to reproduce outside of the container.

[rcannood@morna ti_cellrouter]$ docker run -v /tmp:/mnt dynverse/ti_cellrouter --dataset /mnt/example.h5 --output /mnt/output.h5
Error in enc2utf8(path) : argument is not a character vector
Calls: <Anonymous> ... eval -> eval -> <Anonymous> -> file_info -> path_expand
Execution halted

I'm trying to debug it with:

[rcannood@morna ti_cellrouter]$ docker run -v /tmp:/mnt --entrypoint /init -e PASSWORD=helphelphelp -p 8787:8787 dynverse/ti_cellrouter

[zouter]

Some useful commands while trying to port:

chmod +x run.py
chmod +x run.R
chmod +x example.R

Rscript example.R example.h5

docker build -t dynverse/ti_scuba .

docker run -it --entrypoint bash -v /tmp:/mnt dynverse/ti_scuba

[zouter]

Updated useful commands (some R is interspersed)

export METHOD=tscan
method = "tscan"

cd ../ti_${METHOD}

chmod +x run.py
chmod +x run.R
chmod +x example.R

Rscript example.R example.h5

docker build -t dynverse/ti_${METHOD} .

docker run -it --entrypoint bash -v /tmp:/mnt dynverse/ti_${METHOD}

dynwrap::create_ti_method_definition(paste0("ti_", method, "/definition.yml"))

docker run -v $(pwd):/mnt dynverse/ti_${METHOD} --dataset /mnt/example.h5 --output /mnt/output.h5
dynutils::read_h5(paste0("ti_", method, "/output.h5")) %>% dynplot::plot_graph()
rm -f output.h5

echo "VERSION=0.9.9" > version

travis_enc_all

git checkout -b dynwrapv2
git add .
git commit -m "dynwrapv2"
git push --set-upstream origin dynwrapv2

[zouter]

All resolved :clap:

Ready for merge in 3 2 1....

[rcannood]

0.5 .... 0.4 ...

[zouter]

0.3999999

[zouter]

0 :confetti_ball: