Bump prov from 1.5.1 to 2.0.0

cwltool/command_line_tool.py

@@ -765,6 +765,7 @@ def calc_checksum(location: str) -> Optional[str]:
 
             interesting = {
                 "DockerRequirement",
+                "DockerGpuRequirement",
                 "EnvVarRequirement",
                 "InitialWorkDirRequirement",
                 "ShellCommandRequirement",
@@ -940,6 +941,9 @@ def update_status_output_callback(
             j.tmpdir = builder.tmpdir
             j.stagedir = builder.stagedir
 
+        dockerGpuReq, _ = self.get_requirement("DockerGpuRequirement")
+        j.docker_gpu_flag = (dockerGpuReq is not None)
+
         inplaceUpdateReq, _ = self.get_requirement("InplaceUpdateRequirement")
         if inplaceUpdateReq is not None:
             j.inplace_update = cast(bool, inplaceUpdateReq["inplaceUpdate"])

cwltool/docker.py

@@ -341,6 +341,8 @@ def create_runtime(
                 runtime = [user_space_docker_cmd, "run"]
         else:
             runtime = ["docker", "run", "-i"]
+        if getattr(self, 'docker_gpu_flag', False):
+            runtime.append('--gpus=all')
         self.append_volume(
             runtime, os.path.realpath(self.outdir), self.builder.outdir, writable=True
         )

cwltool/process.py

@@ -98,6 +98,7 @@ def filter(self, record: logging.LogRecord) -> bool:
 
 supportedProcessRequirements = [
     "DockerRequirement",
+    "DockerGpuRequirement",
     "SchemaDefRequirement",
     "EnvVarRequirement",
     "ScatterFeatureRequirement",
@@ -1055,7 +1056,7 @@ def validate_hints(
                         strict=strict,
                         vocab=self.doc_loader.vocab,
                     )
-                elif r["class"] in ("NetworkAccess", "LoadListingRequirement"):
+                elif r["class"] in ("NetworkAccess", "LoadListingRequirement", "DockerGpuRequirement"):
                     pass
                 else:
                     _logger.info(str(sl.makeError("Unknown hint %s" % (r["class"]))))

cwltool/singularity.py

@@ -388,6 +388,8 @@ def create_runtime(
             "--ipc",
             "--cleanenv",
         ]
+        if getattr(self, 'docker_gpu_flag', False):
+            runtime.append('--nv')
         if _singularity_supports_userns():
             runtime.append("--userns")
         else:

requirements.txt

@@ -3,7 +3,7 @@ ruamel.yaml>=0.15,<0.17.11
 rdflib>=4.2.2,<6.1
 shellescape>=3.4.1,<3.9
 schema-salad>=8.1.20210627200047,<9
-prov==1.5.1
+prov==2.0.0
 bagit==1.8.1
 mypy-extensions
 psutil>=5.6.6

setup.py

@@ -116,7 +116,7 @@
         "schema-salad >= 8.1.20210627200047, < 9",
         "mypy-extensions",
         "psutil >= 5.6.6",
-        "prov == 1.5.1",
+        "prov == 2.0.0",
         "bagit >= 1.6.4",
         "typing-extensions",
         "coloredlogs",