This is an automated email from the ASF dual-hosted git repository.
lahirujayathilake pushed a change to branch cybershuttle-dev
in repository https://gitbox.apache.org/repos/asf/airavata.git
from 9a02f2faf3 enabled micromamba base when starting the kernel
new 5ab0aaff6a fix bugs in airavata-jupyter-magic package
new 496fcd84f6 fix dependency issue in cyberfaces agent
new 2cc7c666cd organize code, add other deployment files, partially redo
airavata_jupyter_magic for runtime switching
new 63f8ff76c7 refine code flow in airavata_jupyter_magic. bump version to
1.0.5, update notebook, fix bugs
new 3debcbcc4b updated notebooks
new 9d696d9d4b rename platform x86_64 -> amd64. fix issues in cyberfaces
dockerfile. update notebooks. move environment files.
The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "add" were already present in the repository and have only
been added to this reference.
Summary of changes:
modules/agent-framework/airavata-agent/Dockerfile | 2 +-
modules/agent-framework/airavata-agent/Makefile | 2 +-
.../airavata-jupyter-magic/.gitignore | 3 +-
.../airavata_jupyter_magic.py | 751 +
.../airavata-jupyter-magic/airavata_magics.py | 403 -
.../airavata-jupyter-magic/pyproject.toml | 11 +-
.../deployments/agent-cerebrum/Makefile | 2 +-
.../deployments/agent-cyberfaces/Dockerfile | 61 +-
.../deployments/agent-cyberfaces/Makefile | 9 +-
.../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-i-guide/Makefile | 2 +-
.../agent-framework/deployments/agent-md/Makefile | 2 +-
.../deployments/agent-sample/Makefile | 2 +-
.../deployments/jupyterhub/Dockerfile-jl-base | 2 +-
.../deployments/jupyterhub/Dockerfile-jl-iguide | 2 +-
.../cyberfaces/Solution_DA3_DEM_Access_v4.ipynb | 601 +
.../Solution_DP6_DEM_Processing_v2.ipynb | 882 +
.../{ => experiment_sdk}/1_experiment_sdk.ipynb | 0
.../jupyterhub/data/iguide/cyberfaces.ipynb | 868 +
.../md_demo/data/alphafold2/Abeta42_Dimer.fasta | 4 +
.../data/md_demo/data/amber/RAMP1.prmtop | 52609 +++++++++++
.../data/md_demo/data/amber/RAMP1_equil.rst7 | Bin 0 -> 1129976 bytes
.../jupyterhub/data/md_demo/data/amber/md.in | 9 +
.../md_demo/data/gaussian/NOR0N-RAD21-freq.gjf | 89 +
.../jupyterhub/data/md_demo/data/gromacs/md.mdp | 46 +
.../jupyterhub/data/md_demo/data/gromacs/npt.gro | 93291 +++++++++++++++++++
.../jupyterhub/data/md_demo/data/gromacs/npt.tpr | Bin 0 -> 4716544 bytes
.../data/{md => md_demo/data/namd}/b4pull.pdb | 0
.../{md => md_demo/data/namd}/b4pull.restart.coor | Bin
.../{md => md_demo/data/namd}/b4pull.restart.vel | Bin
.../{md => md_demo/data/namd}/b4pull.restart.xsc | 0
.../{md => md_demo/data/namd}/par_all36_water.prm | 0
.../{md => md_demo/data/namd}/par_all36m_prot.prm | 0
.../data/{md => md_demo/data/namd}/pull_cpu.conf | 2 +-
.../data/{md => md_demo/data/namd}/pull_gpu.conf | 2 +-
.../data/{md => md_demo/data/namd}/structure.pdb | 0
.../data/{md => md_demo/data/namd}/structure.psf | 0
.../data/md_demo/molecular_dynamics.ipynb | 1706 +
.../jupyterhub/data/{ => md_demo}/settings.ini | 18 +-
.../data/{md => namd_workshop/data}/b4pull.pdb | 0
.../{md => namd_workshop/data}/b4pull.restart.coor | Bin
.../{md => namd_workshop/data}/b4pull.restart.vel | Bin
.../{md => namd_workshop/data}/b4pull.restart.xsc | 0
.../{md => namd_workshop/data}/par_all36_water.prm | 0
.../{md => namd_workshop/data}/par_all36m_prot.prm | 0
.../data/{md => namd_workshop/data}/pull_cpu.conf | 0
.../data/{md => namd_workshop/data}/pull_gpu.conf | 0
.../data/{md => namd_workshop/data}/structure.pdb | 0
.../data/{md => namd_workshop/data}/structure.psf | 0
.../data/{ => namd_workshop}/settings.ini | 0
.../data/{ => namd_workshop}/smd_cpu.ipynb | 0
.../data/{ => namd_workshop}/smd_gpu.ipynb | 0
55 files changed, 151073 insertions(+), 466 deletions(-)
create mode 100644
modules/agent-framework/airavata-jupyter-magic/airavata_jupyter_magic.py
delete mode 100644
modules/agent-framework/airavata-jupyter-magic/airavata_magics.py
create mode 100644
modules/agent-framework/deployments/agent-cyberfaces/envs/aiml.yml
create mode 100644
modules/agent-framework/deployments/agent-cyberfaces/envs/fair.yml
create mode 100644
modules/agent-framework/deployments/agent-cyberfaces/envs/justiceindata.yml
create mode 100644
modules/agent-framework/deployments/agent-cyberfaces/envs/rs.yml
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/cyberfaces/Solution_DA3_DEM_Access_v4.ipynb
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/cyberfaces/Solution_DP6_DEM_Processing_v2.ipynb
rename modules/agent-framework/deployments/jupyterhub/data/{ =>
experiment_sdk}/1_experiment_sdk.ipynb (100%)
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/iguide/cyberfaces.ipynb
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/alphafold2/Abeta42_Dimer.fasta
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/amber/RAMP1.prmtop
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/amber/RAMP1_equil.rst7
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/amber/md.in
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/gaussian/NOR0N-RAD21-freq.gjf
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/gromacs/md.mdp
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/gromacs/npt.gro
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/gromacs/npt.tpr
copy modules/agent-framework/deployments/jupyterhub/data/{md =>
md_demo/data/namd}/b4pull.pdb (100%)
copy modules/agent-framework/deployments/jupyterhub/data/{md =>
md_demo/data/namd}/b4pull.restart.coor (100%)
copy modules/agent-framework/deployments/jupyterhub/data/{md =>
md_demo/data/namd}/b4pull.restart.vel (100%)
copy modules/agent-framework/deployments/jupyterhub/data/{md =>
md_demo/data/namd}/b4pull.restart.xsc (100%)
copy modules/agent-framework/deployments/jupyterhub/data/{md =>
md_demo/data/namd}/par_all36_water.prm (100%)
copy modules/agent-framework/deployments/jupyterhub/data/{md =>
md_demo/data/namd}/par_all36m_prot.prm (100%)
copy modules/agent-framework/deployments/jupyterhub/data/{md =>
md_demo/data/namd}/pull_cpu.conf (99%)
copy modules/agent-framework/deployments/jupyterhub/data/{md =>
md_demo/data/namd}/pull_gpu.conf (99%)
copy modules/agent-framework/deployments/jupyterhub/data/{md =>
md_demo/data/namd}/structure.pdb (100%)
copy modules/agent-framework/deployments/jupyterhub/data/{md =>
md_demo/data/namd}/structure.psf (100%)
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/md_demo/molecular_dynamics.ipynb
copy modules/agent-framework/deployments/jupyterhub/data/{ =>
md_demo}/settings.ini (85%)
rename modules/agent-framework/deployments/jupyterhub/data/{md =>
namd_workshop/data}/b4pull.pdb (100%)
rename modules/agent-framework/deployments/jupyterhub/data/{md =>
namd_workshop/data}/b4pull.restart.coor (100%)
rename modules/agent-framework/deployments/jupyterhub/data/{md =>
namd_workshop/data}/b4pull.restart.vel (100%)
rename modules/agent-framework/deployments/jupyterhub/data/{md =>
namd_workshop/data}/b4pull.restart.xsc (100%)
rename modules/agent-framework/deployments/jupyterhub/data/{md =>
namd_workshop/data}/par_all36_water.prm (100%)
rename modules/agent-framework/deployments/jupyterhub/data/{md =>
namd_workshop/data}/par_all36m_prot.prm (100%)
rename modules/agent-framework/deployments/jupyterhub/data/{md =>
namd_workshop/data}/pull_cpu.conf (100%)
rename modules/agent-framework/deployments/jupyterhub/data/{md =>
namd_workshop/data}/pull_gpu.conf (100%)
rename modules/agent-framework/deployments/jupyterhub/data/{md =>
namd_workshop/data}/structure.pdb (100%)
rename modules/agent-framework/deployments/jupyterhub/data/{md =>
namd_workshop/data}/structure.psf (100%)
rename modules/agent-framework/deployments/jupyterhub/data/{ =>
namd_workshop}/settings.ini (100%)
rename modules/agent-framework/deployments/jupyterhub/data/{ =>
namd_workshop}/smd_cpu.ipynb (100%)
rename modules/agent-framework/deployments/jupyterhub/data/{ =>
namd_workshop}/smd_gpu.ipynb (100%)
