Added artifacts_json to git ignore and deleting, closing #15. Deleted old YAML files. Added hints on the config template.

.gitignore

@@ -3,6 +3,7 @@ output/*
 cache/*
 examples/*
 .snakemake/*
+artifacts_json/*
 pkglist.csv
 log.txt
 build_status.csv

artifacts_json/breitweiser_high.json

@@ -1,38 +0,0 @@
-{
-  "artifact_url": "https://zenodo.org/record/7544675/files/SF2-code.tar.gz",
-  "dockerfile_location": "bdm-paper-examples/docker",
-  "doi": "10.1145/3572848.3577480",
-  "git_packages": [
-    {
-      "location": "~/.pyenv",
-      "name": "pyenv"
-    }
-  ],
-  "image_name": "bdm-publication-image-v7",
-  "misc_packages": [
-    {
-      "name": "NetLogo-6.2.0-64",
-      "type": "tar",
-      "url": "http://ccl.northwestern.edu/netlogo/6.2.0/NetLogo-6.2.0-64.tgz"
-    },
-    {
-      "name": "root_v6.22.06_python3.9_ubuntu-20.04",
-      "type": "tar",
-      "url": "http://biodynamo-lfs.web.cern.ch/biodynamo-lfs/third-party/root_v6.22.06_python3.9_ubuntu-20.04.tar.gz"
-    },
-    {
-      "name": "qt_v5.12.10_ubuntu-20.04",
-      "type": "tar",
-      "url": "http://biodynamo-lfs.web.cern.ch/biodynamo-lfs/third-party/qt_v5.12.10_ubuntu-20.04.tar.gz"
-    },
-    {
-      "name": "paraview_v5.9.0_ubuntu-20.04_default",
-      "type": "tar",
-      "url": "http://biodynamo-lfs.web.cern.ch/biodynamo-lfs/third-party/paraview_v5.9.0_ubuntu-20.04_default.tar.gz"
-    }
-  ],
-  "package_managers": [
-    "dpkg"
-  ],
-  "type": "tar"
-}

artifacts_json/isakov_taxonomy.json

@@ -1,13 +0,0 @@
-{
-  "artifact_url": "https://zenodo.org/record/6632461/files/SC22_artifacts_submission.zip",
-  "dockerfile_location": "SC22_artifacts_submission",
-  "doi": "10.5555/3571885.3571906",
-  "git_packages": [],
-  "image_name": "taxo:artefact",
-  "misc_packages": [],
-  "package_managers": [
-    "dpkg",
-    "pip"
-  ],
-  "type": "zip"
-}

artifacts_json/moses_high.json

@@ -1,24 +0,0 @@
-{
-  "artifact_url": "https://zenodo.org/record/7508499/files/wsmoses/PolygeistGPU-Docker-v0.2.1.zip",
-  "dockerfile_location": "wsmoses-PolygeistGPU-Docker-ba18197/MocCUDA",
-  "doi": "10.1145/3572848.3577475",
-  "git_packages": [
-    {
-      "location": "/root/MocCUDA",
-      "name": "MocCUDA"
-    }
-  ],
-  "image_name": "polygeist:artefact",
-  "misc_packages": [
-    {
-      "name": "cmake-3.23.1",
-      "type": "tar",
-      "url": "https://github.com/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1.tar.gz"
-    }
-  ],
-  "package_managers": [
-    "dpkg",
-    "pip"
-  ],
-  "type": "zip"
-}

artifacts_json/parasyris_approximate.json

@@ -1,19 +0,0 @@
-{
-  "artifact_url": "https://zenodo.org/record/6926481/files/koparasy/HPAC-v0.0.0-Puppeteer.zip",
-  "dockerfile_location": "koparasy-HPAC-2723bb8/approx/puppeteer/container",
-  "doi": "10.5555/3571885.3571974",
-  "git_packages": [],
-  "image_name": "puppeteer:artefact",
-  "misc_packages": [
-    {
-      "name": "HPAC",
-      "type": "zip",
-      "url": "https://github.com/koparasy/HPAC/archive/refs/heads/develop.zip"
-    }
-  ],
-  "package_managers": [
-    "dpkg",
-    "pip"
-  ],
-  "type": "zip"
-}

artifacts_json/template.json

@@ -1,23 +0,0 @@
-{
-  "artifact_url": "https://example.com/artifact.zip",
-  "dockerfile_location": "path/to/docker/folder",
-  "doi": "...",
-  "git_packages": [
-    {
-      "location": "path/to/git/repo",
-      "name": "pkg1"
-    }
-  ],
-  "image_name": "image:version",
-  "misc_packages": [
-    {
-      "name": "mpkg1",
-      "type": "zip",
-      "url": "https://"
-    }
-  ],
-  "package_managers": [
-    "dpkg"
-  ],
-  "type": "zip"
-}

artifacts_json/test.json

@@ -1,24 +0,0 @@
-{
-  "artifact_url": "http://localhost/artifact.zip",
-  "dockerfile_location": "./",
-  "doi": "...",
-  "git_packages": [
-    {
-      "location": "/pkg1",
-      "name": "pkg1"
-    }
-  ],
-  "image_name": "prog:latest",
-  "misc_packages": [
-    {
-      "name": "mpkg1",
-      "type": "zip",
-      "url": "http://localhost/package1.zip"
-    }
-  ],
-  "package_managers": [
-    "dpkg",
-    "pip"
-  ],
-  "type": "zip"
-}

artifacts_json/wang_tgopt.json

@@ -1,19 +0,0 @@
-{
-  "artifact_url": "https://zenodo.org/record/7328505/files/tgopt-artifact.tgz",
-  "dockerfile_location": "tgopt-artifact",
-  "doi": "10.1145/3572848.3577490",
-  "git_packages": [],
-  "image_name": "tgopt:artefact",
-  "misc_packages": [
-    {
-      "name": "Miniconda3-py37_4.12.0-Linux-x86_64",
-      "type": "zip",
-      "url": "https://repo.anaconda.com/miniconda/Miniconda3-py37_4.12.0-Linux-x86_64.sh"
-    }
-  ],
-  "package_managers": [
-    "dpkg",
-    "conda"
-  ],
-  "type": "tar"
-}

artifacts_json/ziogas_deinsum-cpu.json

@@ -1,37 +0,0 @@
-{
-  "artifact_url": "https://zenodo.org/record/7004393/files/deinsum/sc22-artifact-0.4.zip",
-  "dockerfile_location": "deinsum-sc22-artifact-7559901/docker_cpu",
-  "doi": "10.5555/3571885.3571918",
-  "git_packages": [
-    {
-      "location": "/dace",
-      "name": "dace"
-    },
-    {
-      "location": "/multilinear-algebra-sc22-artifact",
-      "name": "multilinear-algebra-sc22-artifact"
-    },
-    {
-      "location": "/ctf",
-      "name": "ctf"
-    }
-  ],
-  "image_name": "deinsum:artefact-cpu",
-  "misc_packages": [
-    {
-      "name": "mpich-3.1.4",
-      "type": "tar",
-      "url": "http://www.mpich.org/static/downloads/3.1.4/mpich-3.1.4.tar.gz"
-    },
-    {
-      "name": "Python-3.10.2",
-      "type": "tar",
-      "url": "https://www.python.org/ftp/python/3.10.2/Python-3.10.2.tgz"
-    }
-  ],
-  "package_managers": [
-    "dpkg",
-    "pip"
-  ],
-  "type": "zip"
-}

artifacts_json/ziogas_deinsum-gpu.json

@@ -1,32 +0,0 @@
-{
-  "artifact_url": "https://zenodo.org/record/7004393/files/deinsum/sc22-artifact-0.4.zip",
-  "dockerfile_location": "deinsum-sc22-artifact-7559901/docker_gpu",
-  "doi": "10.5555/3571885.3571918",
-  "git_packages": [
-    {
-      "location": "/dace",
-      "name": "dace"
-    },
-    {
-      "location": "/multilinear-algebra-sc22-artifact",
-      "name": "multilinear-algebra-sc22-artifact"
-    },
-    {
-      "location": "/ctf",
-      "name": "ctf"
-    }
-  ],
-  "image_name": "deinsum:artefact_gpu",
-  "misc_packages": [
-    {
-      "name": "pip",
-      "type": "zip",
-      "url": "https://bootstrap.pypa.io/get-pip.py"
-    }
-  ],
-  "package_managers": [
-    "dpkg",
-    "pip"
-  ],
-  "type": "zip"
-}

artifacts_nickel/template.ncl

@@ -1,15 +1,15 @@
 let { Artifact, .. } = import "../workflow/nickel/artifact_contract.ncl" in
 {
   artifact_url = "https://example.com/artifact.zip",
-  type = "zip",
+  type = "zip", # Possible values: zip, tar
   doi = "...",
   image_name = "image:version",
   dockerfile_location = "path/to/docker/folder",
-  package_managers = [ "dpkg" ],
+  package_managers = [ "dpkg" ], # Possible values: dpkg, rpm, pacman, pip, conda
   git_packages = [
     { name = "pkg1", location = "path/to/git/repo"}
   ],
   misc_packages = [
-    { name = "mpkg1", url = "http://example.com/package.zip", type = "zip" }
+    { name = "mpkg1", url = "http://example.com/package.zip", type = "zip" # Possible values: zip, tar }
   ]
 } | Artifact

artifacts_yaml/ppopp23/gpu_to_cpu_transpilation_and_optimization_via_high_level_parallel_constructs.yaml

@@ -1,7 +0,0 @@
-artifact_url: "https://zenodo.org/record/7508499/files/wsmoses/PolygeistGPU-Docker-v0.2.1.zip"
-type: "zip"
-doi: "10.1145/3572848.3577475"
-image_name: "polygeist:artefact"
-dockerfile_location: "wsmoses-PolygeistGPU-Docker-ba18197/MocCUDA"
-package_managers:
-  - "dpkg"

artifacts_yaml/ppopp23/high_performance_and_scalable_agent_based_simulation_with_BioDynaMo.yaml

@@ -1,8 +0,0 @@
-artifact_url: "https://zenodo.org/record/7544675/files/SF2-code.tar.gz"
-type: "tar"
-doi: "10.1145/3572848.3577480"
-image_name: "bdm-publication-image-v7"
-dockerfile_location: "bdm-paper-examples/docker"
-package_managers:
-  - "dpkg"
-# Build done by running build.sh and not just docker build, but this is not implemented yet

artifacts_yaml/ppopp23/tgopt_redundancy_aware-optimizations_for_temporal_graph_attention_network.yaml

@@ -1,8 +0,0 @@
-artifact_url: "https://zenodo.org/record/7328505/files/tgopt-artifact.tgz"
-type: "tar"
-doi: "10.1145/3572848.3577490"
-image_name: "tgopt:artefact"
-dockerfile_location: "tgopt-artifact"
-package_managers:
-  - "dpkg"
-  - "conda"

artifacts_yaml/sc22/a_taxonomy_of_error_sources_in_hpc_io_machine_learning_models.yaml

@@ -1,8 +0,0 @@
-artifact_url: "https://zenodo.org/record/6632461/files/SC22_artifacts_submission.zip"
-type: "zip"
-doi: "10.5555/3571885.3571906"
-image_name: "taxo:artefact"
-dockerfile_location: "SC22_artifacts_submission"
-package_managers:
-  - "dpkg"
-  - "pip"

artifacts_yaml/sc22/approximate_copmuting_through_the_lens_of_uncertainty_quantification.yaml

@@ -1,8 +0,0 @@
-artifact_url: "https://zenodo.org/record/6926481/files/koparasy/HPAC-v0.0.0-Puppeteer.zip"
-type: "zip"
-doi: "10.5555/3571885.3571974"
-image_name: "puppeteer:artefact"
-dockerfile_location: "koparasy-HPAC-2723bb8/approx/puppeteer/container"
-package_managers:
-  - "dpkg"
-  - "pip"

artifacts_yaml/sc22/deinsum_practially_io_optimal_multi_linear_algebra-cpu.yaml

@@ -1,7 +0,0 @@
-artifact_url: "https://zenodo.org/record/7004393/files/deinsum/sc22-artifact-0.4.zip"
-type: "zip"
-doi: "10.5555/3571885.3571918"
-image_name: "deinsum:artefact-cpu"
-dockerfile_location: "deinsum-sc22-artifact-7559901/docker_cpu"
-package_managers:
-  - "dpkg"

artifacts_yaml/sc22/deinsum_practially_io_optimal_multi_linear_algebra-gpu.yaml

@@ -1,7 +0,0 @@
-artifact_url: "https://zenodo.org/record/7004393/files/deinsum/sc22-artifact-0.4.zip"
-type: "zip"
-doi: "10.5555/3571885.3571918"
-image_name: "deinsum:artefact_gpu"
-dockerfile_location: "deinsum-sc22-artifact-7559901/docker_gpu"
-package_managers:
-  - "dpkg"

artifacts_yaml/template.yaml

@@ -1,14 +0,0 @@
-artifact_url: "https://example.com/artifact.zip"
-type: "zip" # Possible values: zip, tar
-doi: "XX.XXXX/XXXXXXX.XXXXXXX"
-image_name: "image1:version"
-dockerfile_location: "path/to/docker/folder"
-package_managers:
-  - "dpkg" # Possible values: dpkg, rpm, pacman, pip, conda
-git_packages:
-  - name: "pkg1"
-    location: "path/to/git/repo"
-misc_packages:
-  - name: "mpkg1"
-    url: "https://example.com/package1.zip"
-    type: "zip" # Possible values: zip, tar

artifacts_yaml/test.yaml

@@ -1,15 +0,0 @@
-artifact_url: "http://localhost/artifact.zip"
-type: "zip"
-doi: "XX.XXXX/XXXXXXX.XXXXXXX"
-image_name: "prog:latest"
-dockerfile_location: "./"
-package_managers:
-  - "dpkg"
-  - "pip"
-git_packages:
-  - name: "pkg1"
-    location: "/pkg1"
-misc_packages:
-  - name: "mpkg1"
-    url: "http://localhost/package1.zip"
-    type: "zip"