This is an automated email from the ASF dual-hosted git repository.
yasith pushed a change to branch cybershuttle-staging
in repository https://gitbox.apache.org/repos/asf/airavata.git
from 34abbfb222 Merge branch 'master' into cybershuttle-staging
add e8f73d7a51 move old deployments into examples/, and app scripts into
dev-tools/app-scripts
No new revisions were added by this update.
Summary of changes:
.../app-scripts/expanse_af2.sh | 0
.../app-scripts/expanse_namd.sh | 0
.../01_extending_airavata_agent}/Dockerfile | 0
.../01_extending_airavata_agent}/Makefile | 0
.../01_extending_airavata_agent}/README.md | 0
.../02_using_python_sdk}/.gitignore | 0
.../data/alphafold2/Abeta42_Dimer.fasta | 0
.../02_using_python_sdk}/data/amber/RAMP1.prmtop | 0
.../data/amber/RAMP1_equil.rst7 | Bin
.../02_using_python_sdk}/data/amber/md.in | 0
.../data/gaussian/NOR0N-RAD21-freq.gjf | 0
.../02_using_python_sdk}/data/gromacs/md.mdp | 0
.../02_using_python_sdk}/data/gromacs/npt.gro | 0
.../02_using_python_sdk}/data/gromacs/npt.tpr | Bin
.../02_using_python_sdk}/data/namd/b4pull.pdb | 0
.../data/namd/b4pull.restart.coor | Bin
.../data/namd/b4pull.restart.vel | Bin
.../data/namd/b4pull.restart.xsc | 0
.../data/namd/par_all36_water.prm | 0
.../data/namd/par_all36m_prot.prm | 0
.../02_using_python_sdk}/data/namd/pull_cpu.conf | 0
.../02_using_python_sdk}/data/namd/pull_gpu.conf | 0
.../02_using_python_sdk}/data/namd/structure.pdb | 0
.../02_using_python_sdk}/data/namd/structure.psf | 0
examples/02_using_python_sdk/data/sample.txt | 1 +
.../02_using_python_sdk/experiment_sdk.ipynb | 0
.../02_using_python_sdk}/molecular_dynamics.ipynb | 0
.../02_using_python_sdk/namd_workshop_cpu.ipynb | 22 +-
.../02_using_python_sdk/namd_workshop_gpu.ipynb | 22 +-
.../02_using_python_sdk}/settings.ini | 0
.../deployments/agent-cerebrum/Dockerfile | 36 -
.../deployments/agent-cerebrum/Makefile | 17 -
.../deployments/agent-cerebrum/README.md | 13 -
.../deployments/agent-cyberfaces/Dockerfile | 53 -
.../deployments/agent-cyberfaces/Makefile | 17 -
.../deployments/agent-cyberfaces/README.md | 13 -
.../deployments/agent-cyberfaces/envs/aiml.yml | 44 -
.../deployments/agent-cyberfaces/envs/fair.yml | 82 -
.../agent-cyberfaces/envs/justiceindata.yml | 9 -
.../deployments/agent-cyberfaces/envs/rs.yml | 23 -
.../deployments/agent-gkeyll/Dockerfile | 6 -
.../deployments/agent-gkeyll/Makefile | 17 -
.../deployments/agent-gkeyll/README.md | 13 -
.../deployments/agent-i-guide/Dockerfile | 15 -
.../deployments/agent-i-guide/Makefile | 10 -
.../deployments/agent-i-guide/README.md | 13 -
.../deployments/agent-md/Dockerfile | 12 -
.../agent-framework/deployments/agent-md/Makefile | 10 -
.../agent-framework/deployments/agent-md/README.md | 13 -
.../deployments/app-scripts/anvil_agent.sh | 41 -
.../deployments/app-scripts/expanse_agent.sh | 40 -
.../deployments/jupyterhub/Dockerfile | 13 -
.../deployments/jupyterhub/Dockerfile-jl-base | 28 -
.../deployments/jupyterhub/Dockerfile-jl-iguide | 30 -
.../deployments/jupyterhub/Makefile | 13 -
.../deployments/jupyterhub/README.md | 1 -
.../deployments/jupyterhub/data/allen-v1 | 1 -
.../data/cerebrum/bkg/bkg_spikes_250Hz_3s.h5 | Bin 133346 -> 0 bytes
.../jupyterhub/data/cerebrum/config_nest.json | 54 -
.../data/cerebrum/description/config.json | 537 -
.../data/cerebrum/description/config_template.json | 283 -
.../data/cerebrum/description/custom_mod.json | 5858 -
.../cerebrum/description/db_connect_output.json | 70675 ---------
.../data/cosyne/cosyne_tutorial_part_1.ipynb | 1 -
.../data/cosyne/cosyne_tutorial_part_2.ipynb | 2470 -
.../jupyterhub/data/cosyne/cybershuttle.yml | 64 -
.../cyberfaces/Solution_DA3_DEM_Access_v4.ipynb | 601 -
.../Solution_DP6_DEM_Processing_v2.ipynb | 882 -
.../deployments/jupyterhub/data/functional-network | 1 -
.../jupyterhub/data/gkeyll/plotE_z.ipynb | 164 -
.../data/iguide/NID_FIM_MH_F/MH_F_CA10022.tiff | Bin 365941 -> 0 bytes
.../data/iguide/NID_FIM_NH_F/NH_F_CA10022.tiff | Bin 27506 -> 0 bytes
.../data/iguide/NID_FIM_TAS_F/TAS_F_CA10022.tiff | Bin 232386 -> 0 bytes
.../data/iguide/census_geometry/census_data.csv | 83510 ----------
.../census_geometry/census_tract_from_api.geojson | 9115 --
.../census_geometry/tl_2020_06_tabblock20.geojson | 12896 --
.../jupyterhub/data/iguide/cyberfaces.ipynb | 868 -
.../jupyterhub/data/iguide/dam_list.csv | 346 -
.../jupyterhub/data/md_demo/settings.ini | 13 -
.../jupyterhub/data/namd_workshop/data/b4pull.pdb | 97198 ------------
.../data/namd_workshop/data/b4pull.restart.coor | Bin 2332708 -> 0 bytes
.../data/namd_workshop/data/b4pull.restart.vel | Bin 2332708 -> 0 bytes
.../data/namd_workshop/data/b4pull.restart.xsc | 3 -
.../data/namd_workshop/data/par_all36_water.prm | 115 -
.../data/namd_workshop/data/par_all36m_prot.prm | 3435 -
.../data/namd_workshop/data/pull_cpu.conf | 100 -
.../data/namd_workshop/data/pull_gpu.conf | 100 -
.../data/namd_workshop/data/structure.pdb | 97198 ------------
.../data/namd_workshop/data/structure.psf | 147335 ------------------
.../deployments/jupyterhub/docker-compose.yaml | 24 -
.../deployments/jupyterhub/jupyterhub_config.py | 71 -
.../deployments/jupyterhub/nginx-conf | 36 -
92 files changed, 23 insertions(+), 534558 deletions(-)
rename {modules/agent-framework/deployments =>
dev-tools}/app-scripts/expanse_af2.sh (100%)
rename {modules/agent-framework/deployments =>
dev-tools}/app-scripts/expanse_namd.sh (100%)
rename {modules/agent-framework/deployments/agent-sample =>
examples/01_extending_airavata_agent}/Dockerfile (100%)
rename {modules/agent-framework/deployments/agent-sample =>
examples/01_extending_airavata_agent}/Makefile (100%)
rename {modules/agent-framework/deployments/agent-sample =>
examples/01_extending_airavata_agent}/README.md (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/.gitignore (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/alphafold2/Abeta42_Dimer.fasta (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/amber/RAMP1.prmtop (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/amber/RAMP1_equil.rst7 (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/amber/md.in (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/gaussian/NOR0N-RAD21-freq.gjf (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/gromacs/md.mdp (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/gromacs/npt.gro (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/gromacs/npt.tpr (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/namd/b4pull.pdb (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/namd/b4pull.restart.coor (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/namd/b4pull.restart.vel (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/namd/b4pull.restart.xsc (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/namd/par_all36_water.prm (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/namd/par_all36m_prot.prm (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/namd/pull_cpu.conf (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/namd/pull_gpu.conf (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/namd/structure.pdb (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/data/namd/structure.psf (100%)
create mode 100644 examples/02_using_python_sdk/data/sample.txt
rename
modules/agent-framework/deployments/jupyterhub/data/experiment_sdk/1_experiment_sdk.ipynb
=> examples/02_using_python_sdk/experiment_sdk.ipynb (100%)
rename {modules/agent-framework/deployments/jupyterhub/data/md_demo =>
examples/02_using_python_sdk}/molecular_dynamics.ipynb (100%)
rename
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/smd_cpu.ipynb
=> examples/02_using_python_sdk/namd_workshop_cpu.ipynb (95%)
rename
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/smd_gpu.ipynb
=> examples/02_using_python_sdk/namd_workshop_gpu.ipynb (95%)
rename {modules/agent-framework/deployments/jupyterhub/data/namd_workshop =>
examples/02_using_python_sdk}/settings.ini (100%)
delete mode 100644
modules/agent-framework/deployments/agent-cerebrum/Dockerfile
delete mode 100644 modules/agent-framework/deployments/agent-cerebrum/Makefile
delete mode 100644 modules/agent-framework/deployments/agent-cerebrum/README.md
delete mode 100644
modules/agent-framework/deployments/agent-cyberfaces/Dockerfile
delete mode 100644
modules/agent-framework/deployments/agent-cyberfaces/Makefile
delete mode 100644
modules/agent-framework/deployments/agent-cyberfaces/README.md
delete mode 100644
modules/agent-framework/deployments/agent-cyberfaces/envs/aiml.yml
delete mode 100644
modules/agent-framework/deployments/agent-cyberfaces/envs/fair.yml
delete mode 100644
modules/agent-framework/deployments/agent-cyberfaces/envs/justiceindata.yml
delete mode 100644
modules/agent-framework/deployments/agent-cyberfaces/envs/rs.yml
delete mode 100644 modules/agent-framework/deployments/agent-gkeyll/Dockerfile
delete mode 100644 modules/agent-framework/deployments/agent-gkeyll/Makefile
delete mode 100644 modules/agent-framework/deployments/agent-gkeyll/README.md
delete mode 100644 modules/agent-framework/deployments/agent-i-guide/Dockerfile
delete mode 100644 modules/agent-framework/deployments/agent-i-guide/Makefile
delete mode 100644 modules/agent-framework/deployments/agent-i-guide/README.md
delete mode 100644 modules/agent-framework/deployments/agent-md/Dockerfile
delete mode 100644 modules/agent-framework/deployments/agent-md/Makefile
delete mode 100644 modules/agent-framework/deployments/agent-md/README.md
delete mode 100644
modules/agent-framework/deployments/app-scripts/anvil_agent.sh
delete mode 100644
modules/agent-framework/deployments/app-scripts/expanse_agent.sh
delete mode 100644 modules/agent-framework/deployments/jupyterhub/Dockerfile
delete mode 100644
modules/agent-framework/deployments/jupyterhub/Dockerfile-jl-base
delete mode 100644
modules/agent-framework/deployments/jupyterhub/Dockerfile-jl-iguide
delete mode 100644 modules/agent-framework/deployments/jupyterhub/Makefile
delete mode 100644 modules/agent-framework/deployments/jupyterhub/README.md
delete mode 160000 modules/agent-framework/deployments/jupyterhub/data/allen-v1
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/bkg/bkg_spikes_250Hz_3s.h5
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/config_nest.json
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/description/config.json
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/description/config_template.json
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/description/custom_mod.json
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cerebrum/description/db_connect_output.json
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cosyne/cosyne_tutorial_part_1.ipynb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cosyne/cosyne_tutorial_part_2.ipynb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cosyne/cybershuttle.yml
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cyberfaces/Solution_DA3_DEM_Access_v4.ipynb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/cyberfaces/Solution_DP6_DEM_Processing_v2.ipynb
delete mode 160000
modules/agent-framework/deployments/jupyterhub/data/functional-network
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/gkeyll/plotE_z.ipynb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/NID_FIM_MH_F/MH_F_CA10022.tiff
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/NID_FIM_NH_F/NH_F_CA10022.tiff
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/NID_FIM_TAS_F/TAS_F_CA10022.tiff
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/census_geometry/census_data.csv
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/census_geometry/census_tract_from_api.geojson
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/census_geometry/tl_2020_06_tabblock20.geojson
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/cyberfaces.ipynb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/dam_list.csv
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/settings.ini
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/b4pull.pdb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/b4pull.restart.coor
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/b4pull.restart.vel
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/b4pull.restart.xsc
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/par_all36_water.prm
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/par_all36m_prot.prm
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/pull_cpu.conf
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/pull_gpu.conf
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/structure.pdb
delete mode 100644
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/data/structure.psf
delete mode 100644
modules/agent-framework/deployments/jupyterhub/docker-compose.yaml
delete mode 100644
modules/agent-framework/deployments/jupyterhub/jupyterhub_config.py
delete mode 100644 modules/agent-framework/deployments/jupyterhub/nginx-conf
