This is an automated email from the ASF dual-hosted git repository.
yasith pushed a change to branch cybershuttle-dev
in repository https://gitbox.apache.org/repos/asf/airavata.git
discard bfadd4da5b Merge branch 'cybershuttle-staging' into cybershuttle-dev
discard 05d0105105 gather all dependency versions to /pom.xml. fix bugs.
discard 8943a9dd70 update airavata distribution module to match deployment
structure
discard 4daf7e5672 fix deprecations, cleanup code. add placeholders for job
monitor email/pw in airavata-server.properties
discard 76244f5a02 fix issues with helix participant and job engine starter
discard 31d15360d6 get hibernate orm to validate against test db. manually
specify catalog for conflicting entities.
discard 639ded3860 migrate openjpa to hibernate, update pool and dbcp deps to
pool2 and dbcp2.
discard c5fe7a33c2 parametrize pom versions. add maven-enforcer rule for
dependency convergence and fix version issues.
discard efe6fcb751 regenerated thrift stubs with version 0.21.0 and fix issues
discard a417d4ac8c bump JDK to v17. create devcontainer setup. bump rabbitmq
and proto versions. consolidate maven-compiler plugin versions. migrate openjpa
to 4.0.1. update javax to jakarta. regenerate certs. fix bugs.
add e8f73d7a51 move old deployments into examples/, and app scripts into
dev-tools/app-scripts
add 50b71a954e move cybershuttle examples to cyber-shuttle org and add
links instead
new b6363142d2 bump JDK to v17. create devcontainer setup. bump rabbitmq
and proto versions. consolidate maven-compiler plugin versions. migrate openjpa
to 4.0.1. update javax to jakarta. regenerate certs. fix bugs.
new f7ce266948 regenerated thrift stubs with version 0.21.0 and fix issues
new a22e55cd31 parametrize pom versions. add maven-enforcer rule for
dependency convergence and fix version issues.
new 582e78a996 migrate openjpa to hibernate, update pool and dbcp deps to
pool2 and dbcp2.
new 4c2c874b55 get hibernate orm to validate against test db. manually
specify catalog for conflicting entities.
new 27cf8c0309 fix issues with helix participant and job engine starter
new 9eabe24a3d fix deprecations, cleanup code. add placeholders for job
monitor email/pw in airavata-server.properties
new dbe10b3f9c update airavata distribution module to match deployment
structure
new d83cfb4e23 gather all dependency versions to /pom.xml. fix bugs.
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Summary of changes:
.../app-scripts/expanse_af2.sh | 0
.../app-scripts/expanse_namd.sh | 0
examples/projects_using_airavata.md | 35 +
examples/python_sdk_experiment_tracking.md | 2 +
examples/python_sdk_jupyter_notebooks.md | 2 +
.../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/agent-sample/Dockerfile | 9 -
.../deployments/agent-sample/Makefile | 10 -
.../deployments/agent-sample/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 -
.../data/experiment_sdk/1_experiment_sdk.ipynb | 401 -
.../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 -
.../deployments/jupyterhub/data/md_demo/.gitignore | 2 -
.../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 1129976 -> 0 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 4716544 -> 0 bytes
.../jupyterhub/data/md_demo/data/namd/b4pull.pdb | 97198 ------------
.../data/md_demo/data/namd/b4pull.restart.coor | Bin 2332708 -> 0 bytes
.../data/md_demo/data/namd/b4pull.restart.vel | Bin 2332708 -> 0 bytes
.../data/md_demo/data/namd/b4pull.restart.xsc | 3 -
.../data/md_demo/data/namd/par_all36_water.prm | 115 -
.../data/md_demo/data/namd/par_all36m_prot.prm | 3435 -
.../data/md_demo/data/namd/pull_cpu.conf | 100 -
.../data/md_demo/data/namd/pull_gpu.conf | 100 -
.../data/md_demo/data/namd/structure.pdb | 97198 ------------
.../data/md_demo/data/namd/structure.psf | 147335 ------------------
.../data/md_demo/molecular_dynamics.ipynb | 1706 -
.../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 ------------------
.../jupyterhub/data/namd_workshop/settings.ini | 17 -
.../jupyterhub/data/namd_workshop/smd_cpu.ipynb | 401 -
.../jupyterhub/data/namd_workshop/smd_gpu.ipynb | 401 -
.../deployments/jupyterhub/docker-compose.yaml | 24 -
.../deployments/jupyterhub/jupyterhub_config.py | 71 -
.../deployments/jupyterhub/nginx-conf | 36 -
94 files changed, 39 insertions(+), 1029028 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%)
create mode 100644 examples/projects_using_airavata.md
create mode 100644 examples/python_sdk_experiment_tracking.md
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