include v1.3.0-dev1 schema; adjust updater

Author: mr-c

MANIFEST.in

@@ -53,6 +53,10 @@ include cwltool/schemas/v1.2/*.yml
 include cwltool/schemas/v1.2/*.md
 include cwltool/schemas/v1.2/salad/schema_salad/metaschema/*.yml
 include cwltool/schemas/v1.2/salad/schema_salad/metaschema/*.md
+include cwltool/schemas/v1.3.0-dev1/*.yml
+include cwltool/schemas/v1.3.0-dev1/*.md
+include cwltool/schemas/v1.3.0-dev1/salad/schema_salad/metaschema/*.yml
+include cwltool/schemas/v1.3.0-dev1/salad/schema_salad/metaschema/*.md
 include cwltool/extensions.yml
 include cwltool/extensions-v1.1.yml
 include cwltool/extensions-v1.2.yml

cwltool/schemas/v1.3.0-dev1/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 Leadership 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/v1.3.0-dev1/CONFORMANCE_TESTS.md

@@ -0,0 +1,220 @@
+# Common workflow language conformance test suite
+
+The conformance tests are intended to test feature coverage of a CWL
+implementation.  It uses the module cwltest from https://github.com/common-workflow-language/cwltest/.
+
+## Pre-requisites
+
+You will need both the `cwltest` Python package  and the CWL runner you would like to test installed.
+
+Installing the `cwltest` Python package using a virtualenv:
+
+```
+$ python3 -m venv cwltest_env
+$ source cwltest_env/bin/activate
+$ pip install cwltest
+```
+
+or via `bioconda`
+
+```
+$ conda install -c bioconda cwltest
+```
+
+## Usage
+
+```bash
+$ ./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.
+
+### Test Selection
+
+`--tags`
+
+A comma separated list of [tags](#tags-for-conformance-tests); only tests with these tags will be tested.
+`--tags shell_command` will run all tests with `shell_command` in their `tags` list.
+
+`-n{test_range}`
+
+Run only the specific test numbers. `{test_range}` is a comma separated list of
+single test numbers and/or numeric ranges.
+`-n5-7,15` == only runs the 5th, 6th, 7th, and 15th tests.
+
+`-N{test_range}`
+
+Like the lowercase `-n` option, except that the specified tests will not be run.
+Can be mixed with the other test selectors: `-n5-7,15 -N6` == only runs the 5th, 7th, and 15th tests, skipping the 6th test.
+
+`-s{test_names}`
+
+Run the specific tests according to their `id`s. `{test_names}` is a comma separated list of
+test identifiers (the `id` field). `-scl_optional_bindings_provided,stdout_redirect_docker,expression_any_null`
+achieves the same effect as `-n5-7,15 -N6` and it will still work if the tests are re-ordered.
+
+`-S{test_names}`
+
+Excludes specific tests according to their `id`s. `{test_names}` is a comma separated list of
+test identifiers (the `id` field). `--tags shell_command -Sstderr_redirect_shortcut`
+will run all tests with `expression_tool` in their `tags` list except the test
+with the `id` of `stderr_redirect_shortcut`.
+
+### Misc
+
+`EXTRA="--parallel --singularity"`
+
+Extra options to pass to the CWL runner (check your runner for exact options)
+
+`-j=4`
+
+The number of different tests to run at the same time
+
+`--junit-xml=FILENAME`
+
+Store results in JUnit XML format using the given FILENAME.
+
+`--classname=CLASSNAME`
+
+In the JUnit XML, tag the results with the given CLASSNAME.
+Can be useful when multiple test runs are combined to document the differences in `EXTRA=`.
+
+---
+
+For example, to run conformance test 15,16,17, and 20 against the "cwltool"
+reference implementation using the `podman` container engine
+and parallel execution of workflow steps
+
+```bash
+$ ./run_test.sh RUNNER=cwltool -n15-17,20 EXTRA="--parallel --podman"
+Test [15/49]
+Test [16/49]
+Test [17/49]
+Test [20/49]
+All tests passed
+```
+
+## OS X / macOS 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`
+
+## Format of the conformance test file
+
+A single conformance test consist of the path to an input CWL document plus an input CWL object
+and the expected outputs (or `should_fail: true` if the test is deliberately broken)
+
+They are stored in [`conformance_tests.yaml`](https://github.com/common-workflow-language/cwl-v1.2/blob/main/conformance_tests.yaml)
+(or a file `$import`ed into that one)
+
+You can examine [the formal schema of this file](https://github.com/common-workflow-language/cwltest/blob/main/cwltest/cwltest-schema.yml),
+or just continue reading here for an explanation.
+
+The conformance test file is a YAML document: a list of key-value pairs.
+
+We will use this single entry to explain the format
+``` yaml
+- doc: Test command line with optional input (missing)
+   id: cl_optional_inputs_missing
+   tool: tests/cat1-testcli.cwl  
+   job: tests/cat-job.json
+   output:
+     args: [cat, hello.txt]
+   tags: [ required, command_line_tool ]
+```
+- `doc`: A unique, single-line sentence that explain what is being tested.
+     Will be printed at test execution time, so please don't make it too long!
+     Additional documentation can go as comments in the CWL document itself.
+- `id`: a short list of  underscore (`_`) separated words that succinctly identifies and explains the test.
+- `tool` the path to the CWL document to run
+- `job`: the CWL input object in YAML/JSON format. If there are no inputs then use `tests/empty.json`.
+- `output` [the CWL output object expected.](#output-matching)
+- `tags`: a yaml list of tag names, see [the list of canonical tags below](#tags-for-conformance-tests).
+     Must include one or more of the following tags: `command_line_tool`, `expression_tool` or `workflow`.
+     If the test does not test any optional features, the tag `required` is required.
+
+Because `conformance_tests.yaml` is a `schema-salad` processed document, [`$import`](https://www.commonwl.org/v1.2/SchemaSalad.html#Import)
+can be used to organize the tests into separate files.
+
+Currently, the main file is too big (over 3400 lines); we are slowly re-organizing it.
+
+Eventually it would be good to organize the tests so that the test for each optional feature and other logical groups of tests are in their own separate file;
+with the supporting CWL documents and their inputs in separate sub-folders of `tests` as well.
+
+Example: [`- $import: tests/string-interpolation/test-index.yaml`](https://github.com/common-workflow-language/cwl-v1.2/blob/5f27e234b4ca88ed1280dedf9e3391a01de12912/conformance_tests.yaml#L3395)
+adds all the entries in [`tests/string-interpolation/test-index.yaml`](https://github.com/common-workflow-language/cwl-v1.2/blob/main/tests/string-interpolation/test-index.yaml)
+as entries in the main conformance test file.
+
+## Output matching
+
+In each test entry there is an `output` field that contains a mapping of the expected outputs names and their values.
+
+If a particular value could vary and it doesn't matter to the proper functioning of the test, then it can be represented by the special token `Any`.
+
+At any level, if there is an extra field, then that will be considered an error.
+An exception to this is `class: File` and `class: Directory` objects, the `cwl-runner` under test can add additional fields here without causing a test to fail.
+Likewise, if you don't want to test some aspect of a `class: File` or `class: Directory` object (like `nameext`) you can just omit it.
+
+[According to the CWL standards](https://www.commonwl.org/v1.2/CommandLineTool.html#File), the format of the `location` field in 
+`class: File` and `class: Directory` is implementation specific and we should not be testing them.
+Please remember to use `location: Any` for them.
+
+Currently, we do [test the contents of the location field in some older tests, but we should stop](https://github.com/common-workflow-language/common-workflow-language/issues/930)
+If you are editing those old tests, you may be interested in some special processing for  `class: File` and `class: Directory` output objects:
+any `location` value specified will succeed if there is either an exact match to the real output, or it matches the end of the real output.
+Additionally, for `class: Directory` the location reported by the actual execution will have any trailing forward slash (`/`) trimmed off before comparison.
+
+Likewise, please do not test the `path` for `class: File` and `class: Directory`.
+
+## Writing a new conformance test
+
+To add a new conformance test:
+1. Ensure the CWL document you have tests the desired feature or aspect.
+2. All `CommandLineTool`s need a software container (via `DockerRequirement`) for better reproducibility, preferably under `hints`.
+     Please limit your container usage to the following: 
+     - `dockerPull: docker.io/alpine:latest`
+     - `dockerPull: docker.io/bash:4.4`
+     - `dockerPull: docker.io/debian:stable-slim`
+     - `dockerPull: docker.io/python:3-slim`
+4. Run your test using the CWL reference runner (`cwltool`) or another CWL runner
+     that shows the correct behavior to collect the output, or confirm that validation/execution fails as expected
+3. Add the CWL document and output object to the subdirectory `tests` in this repository.
+4. Fill out a new entry in [conformance_tests.yaml](conformance_tests.yaml) following the [format of the conformance test file](#format-of-the-conformance-test-file)
+5. Send a pull request to [current staging branch for the next revision of the CWL standards](https://github.com/common-workflow-language/cwl-v1.2/tree/1.2.1_proposed) 
+     with your changes
+
+## Tags for conformance tests
+
+Each test in the [conformance_tests.yaml](conformance_tests.yaml) should be tagged with one or more tags.
+
+1. A `command_line_tool`, `expression_tool` or `workflow` tag to identify whether a CommandLineTool, ExpressionTool
+   or Workflow is being tested
+2. If the test does not test any optional features, the tag `required`
+3. The name of any features that are being tested:
+    1. `docker` for DockerRequirement
+    1. `env_var` for EnvVarRequirement
+    1. `format_checking` for checking format requirement annotation on File inputs
+    1. `initial_work_dir` for InitialWorkDirRequirements
+    1. `inline_javascript` for InlineJavascriptRequirement
+    1. `inplace_update` for InplaceUpdateRequirement
+    1. `input_object_requirements` for tests that use cwl:requirements in the input object
+    1. `multiple_input` for MultipleInputFeatureRequirement
+    1. `networkaccess` for NetworkAccess
+    1. `resource` for ResourceRequirement
+    1. `scatter` for ScatterFeatureRequirement
+    1. `schema_def` for SchemaDefRequirement
+    1. `shell_command` for ShellCommandRequirement
+    1. `step_input` for StepInputExpressionRequirement
+    1. `subworkflow` for SubworkflowRequirement
+    1. `timelimit` for ToolTimeLimit

cwltool/schemas/v1.3.0-dev1/CommandLineTool-standalone.yml

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