master -> main

Author: mr-c

.travis.yml

@@ -47,6 +47,6 @@ jobs:
 script: tox
 branches:
   only:
-    - master
+    - main
 notifications:
   email: false

CWLProv.rst

@@ -230,7 +230,7 @@ These set which vocabularies ("namespaces") are used by the CWLProv statements::
     prefix wf <arcp://uuid,0e6cb79e-fe70-4807-888c-3a61b9bf232a/workflow/packed.cwl#>
     prefix foaf <http://xmlns.com/foaf/0.1/>
 
-Note that the `arcp <https://tools.ietf.org/id/draft-soilandreyes-arcp-03.html>`__  base URI will correspond to the UUID of each master workflow run.
+Note that the `arcp <https://tools.ietf.org/id/draft-soilandreyes-arcp-03.html>`__  base URI will correspond to the UUID of each main workflow run.
 
 Account who launched cwltool
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Makefile

@@ -89,7 +89,7 @@ pydocstyle_report.txt: $(PYSOURCES)
 	pydocstyle setup.py $^ > $@ 2>&1 || true
 
 diff_pydocstyle_report: pydocstyle_report.txt
-	diff-quality --violations=pycodestyle --fail-under=100 $^
+	diff-quality --compare-branch=main --violations=pycodestyle --fail-under=100 $^
 
 ## format      : check/fix all code indentation and formatting (runs black)
 format:

README.rst

@@ -12,10 +12,10 @@ CWL conformance tests: |Conformance Status| |Linux Status| |Windows Status| |Cov
 .. |Conformance Status| image:: https://ci.commonwl.org/buildStatus/icon?job=cwltool-conformance
    :target: https://ci.commonwl.org/job/cwltool-conformance/
 
-.. |Linux Status| image:: https://img.shields.io/travis/common-workflow-language/cwltool/master.svg?label=Linux%20builds
+.. |Linux Status| image:: https://img.shields.io/travis/common-workflow-language/cwltool/main.svg?label=Linux%20builds
    :target: https://travis-ci.org/common-workflow-language/cwltool
 
-.. |Windows Status| image:: https://img.shields.io/appveyor/ci/mr-c/cwltool/master.svg?label=Windows%20builds
+.. |Windows Status| image:: https://img.shields.io/appveyor/ci/mr-c/cwltool/main.svg?label=Windows%20builds
    :target: https://ci.appveyor.com/project/mr-c/cwltool
 
 .. |Coverage Status| image:: https://img.shields.io/codecov/c/github/common-workflow-language/cwltool.svg
@@ -24,49 +24,49 @@ CWL conformance tests: |Conformance Status| |Linux Status| |Windows Status| |Cov
 .. |Downloads| image:: https://pepy.tech/badge/cwltool/month
    :target: https://pepy.tech/project/cwltool
 
-.. |CommandLineTool Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/command_line_tool.json?icon=commonwl
+.. |CommandLineTool Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/main/cwltool/cwl_v1.0/cwltool_latest/command_line_tool.json?icon=commonwl
    :target: https://ci.commonwl.org/job/cwltool-conformance/
 
-.. |DockerRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/docker.json?icon=commonwl
+.. |DockerRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/main/cwltool/cwl_v1.0/cwltool_latest/docker.json?icon=commonwl
    :target: https://ci.commonwl.org/job/cwltool-conformance/
 
-.. |EnvVarRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/env_var.json?icon=commonwl
+.. |EnvVarRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/main/cwltool/cwl_v1.0/cwltool_latest/env_var.json?icon=commonwl
    :target: https://ci.commonwl.org/job/cwltool-conformance/
 
-.. |ExpressionTool Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/expression_tool.json?icon=commonwl
+.. |ExpressionTool Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/main/cwltool/cwl_v1.0/cwltool_latest/expression_tool.json?icon=commonwl
    :target: https://ci.commonwl.org/job/cwltool-conformance/
 
-.. |InitialWorkDirRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/initial_work_dir.json?icon=commonwl
+.. |InitialWorkDirRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/main/cwltool/cwl_v1.0/cwltool_latest/initial_work_dir.json?icon=commonwl
    :target: https://ci.commonwl.org/job/cwltool-conformance/
 
-.. |InlineJavascriptRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/inline_javascript.json?icon=commonwl
+.. |InlineJavascriptRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/main/cwltool/cwl_v1.0/cwltool_latest/inline_javascript.json?icon=commonwl
    :target: https://ci.commonwl.org/job/cwltool-conformance/
 
-.. |MultipleInputRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/multiple_input.json?icon=commonwl
+.. |MultipleInputRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/main/cwltool/cwl_v1.0/cwltool_latest/multiple_input.json?icon=commonwl
    :target: https://ci.commonwl.org/job/cwltool-conformance/
 
-.. |Core Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/required.json?icon=commonwl
+.. |Core Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/main/cwltool/cwl_v1.0/cwltool_latest/required.json?icon=commonwl
    :target: https://ci.commonwl.org/job/cwltool-conformance/
 
-.. |ResourceRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/resource.json?icon=commonwl
+.. |ResourceRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/main/cwltool/cwl_v1.0/cwltool_latest/resource.json?icon=commonwl
    :target: https://ci.commonwl.org/job/cwltool-conformance/
 
-.. |ScatterRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/scatter.json?icon=commonwl
+.. |ScatterRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/main/cwltool/cwl_v1.0/cwltool_latest/scatter.json?icon=commonwl
    :target: https://ci.commonwl.org/job/cwltool-conformance/
 
-.. |SchemaDefRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/schema_def.json?icon=commonwl
+.. |SchemaDefRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/main/cwltool/cwl_v1.0/cwltool_latest/schema_def.json?icon=commonwl
    :target: https://ci.commonwl.org/job/cwltool-conformance/
 
-.. |ShellCommandequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/shell_command.json?icon=commonwl
+.. |ShellCommandequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/main/cwltool/cwl_v1.0/cwltool_latest/shell_command.json?icon=commonwl
    :target: https://ci.commonwl.org/job/cwltool-conformance/
 
-.. |StepInputRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/step_input.json?icon=commonwl
+.. |StepInputRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/main/cwltool/cwl_v1.0/cwltool_latest/step_input.json?icon=commonwl
    :target: https://ci.commonwl.org/job/cwltool-conformance/
 
-.. |SubWorkflowRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/subworkflow.json?icon=commonwl
+.. |SubWorkflowRequirement Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/main/cwltool/cwl_v1.0/cwltool_latest/subworkflow.json?icon=commonwl
    :target: https://ci.commonwl.org/job/cwltool-conformance/
 
-.. |Workflow Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/workflow.json?icon=commonwl
+.. |Workflow Support| image:: https://badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/main/cwltool/cwl_v1.0/cwltool_latest/workflow.json?icon=commonwl
    :target: https://ci.commonwl.org/job/cwltool-conformance/
 
 
@@ -173,21 +173,21 @@ with the ``--user-space-docker-cmd`` option.
 One such "user space" friendly docker replacement is ``udocker`` https://github.com/indigo-dc/udocker and another
 is ``dx-docker`` https://wiki.dnanexus.com/Developer-Tutorials/Using-Docker-Images
 
-udocker installation: https://github.com/indigo-dc/udocker/blob/master/doc/installation_manual.md#22-install-from-indigo-datacloud-repositories
+udocker installation: https://github.com/indigo-dc/udocker/blob/main/doc/installation_manual.md#22-install-from-indigo-datacloud-repositories
 
 dx-docker installation: start with the DNAnexus toolkit (see https://wiki.dnanexus.com/Downloads for instructions).
 
 Run `cwltool` just as you normally would, but with the new option, e.g. from the conformance tests:
 
 .. code:: bash
 
-  cwltool --user-space-docker-cmd=udocker https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/test-cwl-out2.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/empty.json
+  cwltool --user-space-docker-cmd=udocker https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/main/v1.0/v1.0/test-cwl-out2.cwl https://github.com/common-workflow-language/common-workflow-language/blob/main/v1.0/v1.0/empty.json
 
 or
 
 .. code:: bash
 
-  cwltool --user-space-docker-cmd=dx-docker https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/test-cwl-out2.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/empty.json
+  cwltool --user-space-docker-cmd=dx-docker https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/main/v1.0/v1.0/test-cwl-out2.cwl https://github.com/common-workflow-language/common-workflow-language/blob/main/v1.0/v1.0/empty.json
 
 ``cwltool`` can use `Singularity <http://singularity.lbl.gov/>`_ version 2.6.1
 or later as a Docker container runtime.
@@ -201,7 +201,7 @@ those involving Docker container ENTRYPOINTs.
 
 .. code:: bash
 
-  cwltool --singularity https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/v1.0/cat3-tool-mediumcut.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/cat-job.json
+  cwltool --singularity https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/main/v1.0/v1.0/v1.0/cat3-tool-mediumcut.cwl https://github.com/common-workflow-language/common-workflow-language/blob/main/v1.0/v1.0/cat-job.json
 
 Running a tool or workflow from remote or local locations
 ---------------------------------------------------------
@@ -648,7 +648,7 @@ To run the basic tests after installing `cwltool` execute the following:
   pip install -rtest-requirements.txt
   py.test --ignore cwltool/schemas/ --pyarg cwltool
 
-To run various tests in all supported Python environments we use `tox <https://github.com/common-workflow-language/cwltool/tree/master/tox.ini>`_. To run the test suite in all supported Python environments
+To run various tests in all supported Python environments we use `tox <https://github.com/common-workflow-language/cwltool/tree/main/tox.ini>`_. To run the test suite in all supported Python environments
 first downloading the complete code repository (see the ``git clone`` instructions above) and then run
 the following in the terminal:
 ``pip install tox; tox``
@@ -666,7 +666,7 @@ The GitHub repository for the CWL specifications contains a script that tests a
 implementation against a wide array of valid CWL files using the `cwltest <https://github.com/common-workflow-language/cwltest>`_
 program
 
-Instructions for running these tests can be found in the Common Workflow Language Specification repository at https://github.com/common-workflow-language/common-workflow-language/blob/master/CONFORMANCE_TESTS.md
+Instructions for running these tests can be found in the Common Workflow Language Specification repository at https://github.com/common-workflow-language/common-workflow-language/blob/main/CONFORMANCE_TESTS.md
 
 Import as a module
 ------------------

appveyor.yml

@@ -50,4 +50,4 @@ on_finish:
 
 branches:
   only:
-    - master
+    - main

cwltool/provenance_profile.py

@@ -718,7 +718,7 @@ def finalize_prov_profile(self, name):
         """Transfer the provenance related files to the RO."""
         # NOTE: Relative posix path
         if name is None:
-            # master workflow, fixed filenames
+            # main workflow, fixed filenames
             filename = "primary.cwlprov"
         else:
             # ASCII-friendly filename, avoiding % as we don't want %2520 in manifest.json

cwltool/workflow.py

@@ -80,8 +80,8 @@ def __init__(
         self.provenance_object = None  # type: Optional[ProvenanceProfile]
         if loadingContext.research_obj is not None:
             run_uuid = None  # type: Optional[UUID]
-            is_master = not loadingContext.prov_obj  # Not yet set
-            if is_master:
+            is_main = not loadingContext.prov_obj  # Not yet set
+            if is_main:
                 run_uuid = loadingContext.research_obj.ro_uuid
 
             self.provenance_object = ProvenanceProfile(
@@ -92,8 +92,8 @@ def __init__(
                 orcid=loadingContext.orcid,
                 run_uuid=run_uuid,
                 fsaccess=loadingContext.research_obj.fsaccess,
-            )  # inherit RO UUID for master wf run
-            # TODO: Is Workflow(..) only called when we are the master workflow?
+            )  # inherit RO UUID for main wf run
+            # TODO: Is Workflow(..) only called when we are the main workflow?
             self.parent_wf = self.provenance_object
 
         # FIXME: Won't this overwrite prov_obj for nested workflows?

tests/test_http_input.py

@@ -8,12 +8,12 @@
 
 def test_http_path_mapping() -> None:
 
-    input_file_path = "https://raw.githubusercontent.com/common-workflow-language/cwltool/master/tests/2.fasta"
+    input_file_path = "https://raw.githubusercontent.com/common-workflow-language/cwltool/main/tests/2.fasta"
     tempdir = tempfile.mkdtemp()
     base_file = [
         {
             "class": "File",
-            "location": "https://raw.githubusercontent.com/common-workflow-language/cwltool/master/tests/2.fasta",
+            "location": "https://raw.githubusercontent.com/common-workflow-language/cwltool/main/tests/2.fasta",
             "basename": "chr20.fa",
         }
     ]  # type: List[CWLObjectType]

tests/test_provenance.py

@@ -451,10 +451,10 @@ def check_prov(
         g.serialize(sys.stdout, format="ttl")
     runs = set(g.subjects(RDF.type, WFPROV.WorkflowRun))
 
-    # master workflow run URI (as urn:uuid:) should correspond to arcp uuid part
+    # main workflow run URI (as urn:uuid:) should correspond to arcp uuid part
     uuid = arcp.parse_arcp(arcp_root).uuid
-    master_run = URIRef(uuid.urn)
-    assert master_run in runs, "Can't find run %s in %s" % (master_run, runs)
+    main_run = URIRef(uuid.urn)
+    assert main_run in runs, "Can't find run %s in %s" % (main_run, runs)
     # TODO: we should not need to parse arcp, but follow
     # the has_provenance annotations in manifest.json instead
 
@@ -466,7 +466,7 @@ def check_prov(
     engine = engines.pop()
 
     assert (
-        master_run,
+        main_run,
         PROV.wasAssociatedWith,
         engine,
     ) in g, "Wf run not associated with wf engine"
@@ -483,15 +483,15 @@ def check_prov(
         # than the tool run
         # (NOTE: the WorkflowEngine is also activity, but not declared explicitly)
     else:
-        # Check all process runs were started by the master worklow
+        # Check all process runs were started by the main worklow
         stepActivities = set(g.subjects(RDF.type, WFPROV.ProcessRun))
         # Although semantically a WorkflowEngine is also a ProcessRun,
         # we don't declare that,
         # thus only the step activities should be in this set.
-        assert master_run not in stepActivities
+        assert main_run not in stepActivities
         assert stepActivities, "No steps executed in workflow"
         for step in stepActivities:
-            # Let's check it was started by the master_run. Unfortunately, unlike PROV-N
+            # Let's check it was started by the main_run. Unfortunately, unlike PROV-N
             # in PROV-O RDF we have to check through the n-ary qualifiedStart relation
             starts = set(g.objects(step, PROV.qualifiedStart))
             assert starts, "Could not find qualifiedStart of step %s" % step
@@ -500,8 +500,8 @@ def check_prov(
             assert (
                 start,
                 PROV.hadActivity,
-                master_run,
-            ) in g, "Step activity not started by master activity"
+                main_run,
+            ) in g, "Step activity not started by main activity"
             # Tip: Any nested workflow step executions should not be in this prov file,
             # but in separate file
     if nested:

travis.bash

@@ -8,12 +8,12 @@ venv() {
 }
 
 if [[ "$version" = "v1.0" ]] ; then
-   wget https://github.com/common-workflow-language/common-workflow-language/archive/master.tar.gz
-   tar xzf master.tar.gz && rm master.tar.gz
+   wget https://github.com/common-workflow-language/common-workflow-language/archive/main.tar.gz
+   tar xzf main.tar.gz && rm main.tar.gz
 else
     repo=$(echo $version | sed 's/\(v[0-9]*\.\)\([0-9]*\).*/\1\2/')
-    wget https://github.com/common-workflow-language/cwl-${repo}/archive/master.tar.gz
-    tar xzf master.tar.gz && rm master.tar.gz
+    wget https://github.com/common-workflow-language/cwl-${repo}/archive/main.tar.gz
+    tar xzf main.tar.gz && rm main.tar.gz
 fi
 
 docker pull node:slim
@@ -33,9 +33,9 @@ do
 	if [[ "$version" = "v1.0" ]]
 	then
 		DRAFT="DRAFT=v1.0"
-		pushd common-workflow-language-master || exit 1
+		pushd common-workflow-language-main || exit 1
 	else
-		pushd cwl-${repo}-master || exit 1
+		pushd cwl-${repo}-main || exit 1
 	fi
 	rm -f .coverage* coverage.xml
 	source=$(realpath ../cwltool)
@@ -76,7 +76,7 @@ EOF
 	then
 		EXTRA="EXTRA=${EXTRA}"
 	fi
-	if [ "$GIT_BRANCH" = "origin/master" ] && [[ "$version" = "v1.0" ]] && [[ "$CONTAINER" = "docker" ]] && [ $PYTHON_VERSION -eq 3 ]
+	if [ "$GIT_BRANCH" = "origin/main" ] && [[ "$version" = "v1.0" ]] && [[ "$CONTAINER" = "docker" ]] && [ $PYTHON_VERSION -eq 3 ]
 	then
 		rm -Rf conformance
 		git clone http://"${jenkins_cwl_conformance}"@github.com/common-workflow-language/conformance.git
@@ -122,7 +122,7 @@ EOM
 done
 done
 # build new docker container
-if [ "$GIT_BRANCH" = "origin/master" ] && [[ "$version" = "v1.0" ]]
+if [ "$GIT_BRANCH" = "origin/main" ] && [[ "$version" = "v1.0" ]]
 then
   ./build-cwl-docker.sh || true
 fi