Merge branch 'master' into singularity23_fix

Author: mr-c

MANIFEST.in

@@ -15,6 +15,10 @@ include cwltool/schemas/v1.0/*.yml
 include cwltool/schemas/v1.0/*.md
 include cwltool/schemas/v1.0/salad/schema_salad/metaschema/*.yml
 include cwltool/schemas/v1.0/salad/schema_salad/metaschema/*.md
+include cwltool/schemas/v1.1/*.yml
+include cwltool/schemas/v1.1/*.md
+include cwltool/schemas/v1.1/salad/schema_salad/metaschema/*.yml
+include cwltool/schemas/v1.1/salad/schema_salad/metaschema/*.md
 include cwltool/schemas/v1.1.0-dev1/*.yml
 include cwltool/schemas/v1.1.0-dev1/*.md
 include cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/*.yml

cwltool/builder.py

@@ -313,6 +313,7 @@ def _capture_files(f):
                         else:
                             sf_required = True
 
+
                         if "$(" in sf["pattern"] or "${" in sf["pattern"]:
                             sfpath = self.do_eval(sf["pattern"], context=datum)
                         else:

cwltool/executors.py

@@ -81,8 +81,7 @@ def execute(self,
                 raise WorkflowException(
                     "`cwl:requirements` in the input object is not part of CWL "
                     "v1.0. You can adjust to use `cwltool:overrides` instead; or you "
-                    "can set the cwlVersion to v1.1.0-dev1 or greater and re-run with "
-                    "--enable-dev.")
+                    "can set the cwlVersion to v1.1")
             job_reqs = job_order_object["https://w3id.org/cwl/cwl#requirements"]
         elif ("cwl:defaults" in process.metadata
               and "https://w3id.org/cwl/cwl#requirements"
@@ -91,8 +90,7 @@ def execute(self,
                 raise WorkflowException(
                     "`cwl:requirements` in the input object is not part of CWL "
                     "v1.0. You can adjust to use `cwltool:overrides` instead; or you "
-                    "can set the cwlVersion to v1.1.0-dev1 or greater and re-run with "
-                    "--enable-dev.")
+                    "can set the cwlVersion to v1.1")
             job_reqs = process.metadata["cwl:defaults"]["https://w3id.org/cwl/cwl#requirements"]
         if job_reqs is not None:
             for req in job_reqs:

cwltool/load_tool.py

@@ -259,12 +259,11 @@ def resolve_and_validate_document(loadingContext,
         del jobobj["http://commonwl.org/cwltool#overrides"]
 
     if isinstance(jobobj, CommentedMap) and "https://w3id.org/cwl/cwl#requirements" in jobobj:
-        if cwlVersion not in ("v1.1.0-dev1",):
+        if cwlVersion not in ("v1.1.0-dev1","v1.1"):
             raise ValidationException(
                     "`cwl:requirements` in the input object is not part of CWL "
                     "v1.0. You can adjust to use `cwltool:overrides` instead; or you "
-                    "can set the cwlVersion to v1.1.0-dev1 or greater and re-run with "
-                    "--enable-dev.")
+                    "can set the cwlVersion to v1.1 or greater.")
         loadingContext.overrides_list.append({"overrideTarget": uri,
                                               "requirements": jobobj["https://w3id.org/cwl/cwl#requirements"]})
         del jobobj["https://w3id.org/cwl/cwl#requirements"]

cwltool/schemas/v1.1/CITATION

@@ -0,0 +1,28 @@
+To cite the Common Workflow Language standard in a publication, please use:
+
+Amstutz, Peter; Crusoe, Michael R; Tijanić, Nebojša; Chapman, Brad;
+Chilton, John; Heuer, Michael; Kartashov, Andrey; Kern, John; Leehr, Dan;
+Ménager, Hervé; Nedeljkovich, Maya; Scales, Matt; Soiland-Reyes, Stian;
+Stojanovic, Luka (2016): Common Workflow Language, v1.0. Specification,
+Common Workflow Language working group. https://w3id.org/cwl/v1.0/
+https://doi.org/10.6084/m9.figshare.3115156.v2
+
+@data{cwl,
+  doi = {10.6084/m9.figshare.3115156.v2},
+  url = {https://doi.org/10.6084/m9.figshare.3115156.v2},
+  author = {Peter Amstutz; Michael R. Crusoe; Nebojša Tijanić; Brad Chapman;
+John Chilton; Michael Heuer; Andrey Kartashov; John Kern; Dan Leehr;
+Hervé Ménager; Maya Nedeljkovich; Matt Scales; Stian Soiland-Reyes;
+Luka Stojanovic
+ },
+  publisher = {Figshare},
+  institution = {Common Workflow Language working group},
+  title = {Common Workflow Language, v1.0},
+  year = {2016}
+}
+
+# Are you editing this file?
+# Synchronize any changes made with
+# README.md
+# and
+# https://github.com/common-workflow-language/user_guide/blob/gh-pages/CITATION

cwltool/schemas/v1.1/CODE_OF_CONDUCT.md

@@ -0,0 +1,108 @@
+CWL Code of Conduct
+===================
+
+The CWL Project is dedicated to providing a harassment-free experience for
+everyone. We do not tolerate harassment of participants in any form.
+
+This code of conduct applies to all CWL Project spaces both online and off: the
+Google Group, the Gitter chat room, the Google Hangouts chats, and any other
+CWL spaces. Anyone who violates this code of conduct may be sanctioned or
+expelled from these spaces at the discretion of the CWL Leadership Team.
+
+Some CWL Project spaces may have additional rules in place, which will be
+made clearly available to participants. Participants are responsible for
+knowing and abiding by these rules.
+
+Harassment includes, but is not limited to:
+
+ - Offensive comments related to gender, gender identity and expression, sexual
+orientation, disability, mental illness, neuro(a)typicality, physical
+appearance, body size, age, race, or religion.
+ - Unwelcome comments regarding a person’s lifestyle choices and practices,
+including those related to food, health, parenting, drugs, and employment.
+ - Deliberate misgendering or use of [dead](https://www.quora.com/What-is-deadnaming/answer/Nancy-C-Walker)
+or rejected names.
+ - Gratuitous or off-topic sexual images or behaviour  in spaces where they’re not
+appropriate.
+ - Physical contact and simulated physical contact (eg, textual descriptions like
+“\*hug\*” or “\*backrub\*”) without consent or after a request to stop.
+ - Threats of violence.
+ - Incitement of violence towards any individual, including encouraging a person
+to commit suicide or to engage in self-harm.
+ - Deliberate intimidation.
+ - Stalking or following.
+ - Harassing photography or recording, including logging online activity for
+harassment purposes.
+ - Sustained disruption of discussion.
+ - Unwelcome sexual attention.
+ - Pattern of inappropriate social contact, such as requesting/assuming
+inappropriate levels of intimacy with others
+ - Continued one-on-one communication after requests to cease.
+ - Deliberate “outing” of any aspect of a person’s identity without their consent
+except as necessary to protect vulnerable people from intentional abuse.
+ - Publication of non-harassing private communication.
+
+The CWL Project prioritizes marginalized people’s safety over privileged
+people’s comfort. The CWL Leadeship Team will not act on complaints regarding:
+
+ - ‘Reverse’ -isms, including ‘reverse racism,’ ‘reverse sexism,’ and ‘cisphobia’
+ - Reasonable communication of boundaries, such as “leave me alone,” “go away,” or
+“I’m not discussing this with you.”
+ - Communicating in a [tone](http://geekfeminism.wikia.com/wiki/Tone_argument)
+you don’t find congenial
+
+Reporting
+---------
+
+If you are being harassed by a member of the CWL Project, notice that someone
+else is being harassed, or have any other concerns, please contact the CWL
+Leadership Team at [email protected]. If person who is harassing
+you is on the team, they will recuse themselves from handling your incident. We
+will respond as promptly as we can.
+
+This code of conduct applies to CWL Project spaces, but if you are being
+harassed by a member of CWL Project outside our spaces, we still want to
+know about it. We will take all good-faith reports of harassment by CWL Project
+members, especially the CWL Leadership Team, seriously. This includes harassment
+outside our spaces and harassment that took place at any point in time. The
+abuse team reserves the right to exclude people from the CWL Project based on
+their past behavior, including behavior outside CWL Project spaces and
+behavior towards people who are not in the CWL Project.
+
+In order to protect volunteers from abuse and burnout, we reserve the right to
+reject any report we believe to have been made in bad faith. Reports intended
+to silence legitimate criticism may be deleted without response.
+
+We will respect confidentiality requests for the purpose of protecting victims
+of abuse. At our discretion, we may publicly name a person about whom we’ve
+received harassment complaints, or privately warn third parties about them, if
+we believe that doing so will increase the safety of CWL Project members or
+the general public. We will not name harassment victims without their
+affirmative consent.
+
+Consequences
+------------
+
+Participants asked to stop any harassing behavior are expected to comply
+immediately.
+
+If a participant engages in harassing behavior, the CWL Leadership Team may
+take any action they deem appropriate, up to and including expulsion from all
+CWL Project spaces and identification of the participant as a harasser to other
+CWL Project members or the general public.
+
+This anti-harassment policy is based on the [example policy from the Geek
+Feminism wiki](http://geekfeminism.wikia.com/wiki/Community_anti-harassment/Policy),
+created by the Geek Feminism community.
+
+CWL Leadership Team
+-------------------
+
+As a stop gap measure until a more formal governance structure is adopted, the
+following individuals make up the leadership of the CWL Project: Peter Amstutz,
+John Chilton, Michael R. Crusoe, and Nebojša Tijanić.
+
+To report an issue with anyone on the team you can escalate to Ward Vandewege
+ (Curoverse) [email protected], Anton Nekrutenko (Galaxy)
+anton AT bx DOT psu DOT edu, C. Titus Brown (UC Davis) [email protected], or
+Brandi Davis-Dusenbery (Seven Bridges Genomics) [email protected].

cwltool/schemas/v1.1/CONFORMANCE_TESTS.md

@@ -0,0 +1,42 @@
+# Common workflow language conformance test suite
+
+The conformance tests are intended to test feature coverage of a CWL
+implementation.  It uses the module "cwltool.cwltest" from the cwltool
+reference implementation.
+
+## Usage
+
+```
+$ ./run_test.sh
+--- Running conformance test draft-3 on cwl-runner ---
+Test [49/49]
+All tests passed
+```
+
+
+## Options
+
+RUNNER=other-cwl-runner
+
+The CWL implementation to be tested.
+
+-nN
+
+Run a single specific test number N.
+
+For example, to run conformance test 15 against the "cwltool"
+reference implementation:
+
+```
+$ ./run_test.sh RUNNER=cwltool -n15
+Test [15/49]
+All tests passed
+```
+
+## Notes
+
+_NOTE_: For running on OSX systems, you'll need to install coreutils via brew. This will add to your
+system some needed GNU-like tools like `greadlink`.
+
+1. If you haven't already, install [brew](http://brew.sh/) package manager in your mac
+2. Run `brew install coreutils`

cwltool/schemas/v1.1/CommandLineTool-standalone.yml

@@ -0,0 +1,2 @@
+- $import: Process.yml
+- $import: CommandLineTool.yml