[WIP] Draft 4.dev3 to v1.0.dev4#114

Merged

mr-c merged 250 commits intomasterfrom

draft-4.dev3-to-v1.0.dev4

Jul 6, 2016

Commits on Mar 18, 2016

Commits on Mar 31, 2016

Add "Creating files at runtime" to UserGuide
Peter Amstutz
committed

Commits on Apr 1, 2016

Add missing files / links. Another section WIP.
Peter Amstutz
committed

Commits on Apr 5, 2016

Add Javascript expression section to UserGuide. Add conformance test for file name conflicts.
Peter Amstutz
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Remove non-participating organization
mr-c
committed

Commits on Apr 8, 2016

Update userguide inputs file.
Peter Amstutz
committed

Commits on Apr 13, 2016

Bump version #
Peter Amstutz
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Talk about Javascript. Fix CWLType.
Peter Amstutz
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Remove redundant example- from examples.
Peter Amstutz
committed

Commits on Apr 14, 2016

Merge pull request #192 from mr-c/citation
mr-c
committed

Commits on Apr 15, 2016

Switch inputs to use yaml instead of json.
Peter Amstutz
committed
Merge branch 'master' of github.com:common-workflow-language/common-workflow-language
Peter Amstutz
committed

Commits on Apr 17, 2016

enable coverage testing
mr-c
committed

Commits on Apr 18, 2016

Update docker.cwl
neevor
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Commits on Apr 19, 2016

Merge pull request #199 from neevor/patch-1
mr-c
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Commits on Apr 21, 2016

Branched draft-4 spec.

Peter Amstutz
authored and
mr-c
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document adding a new draft
mr-c
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Add 'draft-4/salad/' from commit '9c8c36f4defedbd55af1956a915dbf5373ecff3c'
mr-c
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Makedoc detects any ``` for toggling looking for # for section headings.
Peter Amstutz
committed
Merge branch 'master' of github.com:common-workflow-language/schema_salad
Peter Amstutz
committed
Add workflow example to user guide. Add missing files.
Peter Amstutz
committed
Merge branch 'master' of github.com:common-workflow-language/common-workflow-language
Peter Amstutz
committed
Merge commit '37c129d361c788c044d171a9e95a407599d50b43' into draft-4
Peter Amstutz
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Markup fields to take advantage of draft-4 syntax improvements
Peter Amstutz
committed

Commits on May 3, 2016

Commits on May 4, 2016

Comment out 'size' on Directory for now.
Peter Amstutz
committed
Fix "out" to be valid Avro schema.
Peter Amstutz
committed

Commits on May 5, 2016

enable rdfa schema format (#22)
mr-c
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more type checking (#21)
mr-c
committed
Fix draft-3 conformance tests missing 'cwlVersion'. The 'cwlVersion' field is now a @vocab instead of an @id.
Peter Amstutz
committed
Merge branch 'master' into draft-4
Peter Amstutz
committed
cwlVersion is @vocab
Peter Amstutz
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enhance CI
mr-c
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Return metaschema loader from load_schema. Don't crash expanding identifier
Peter Amstutz
committed
Merge branch 'master' of github.com:common-workflow-language/schema_salad
Peter Amstutz
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Bump version.
Peter Amstutz
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Fix tests
Peter Amstutz
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Put prefix back on "cwlVersion: draft-3"
Peter Amstutz
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Put prefix back on "cwlVersion: draft-3"
Peter Amstutz
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Fix draft-3 version symbols in schema.
Peter Amstutz
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split out mypy
mr-c
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Merge branch 'master' into draft-4
Peter Amstutz
committed
Fix version symbols in draft-4
Peter Amstutz
committed
fix diff-cover
mr-c
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Ported draft-2 schema to schema salad proper for validation by current cwltool.
Peter Amstutz
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Merge branch 'master' into draft-4
Peter Amstutz
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Add documentRoot
Peter Amstutz
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Add cwlVersion to draft-2 spec.
Peter Amstutz
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Add CWLVersions to draft-2, and change cwlVersion field to ref CWLVersions enum
Peter Amstutz
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Fixes to pass conformance tests.
Peter Amstutz
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Fix hints
Peter Amstutz
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SchemaDef extends InputSchema
Peter Amstutz
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Fix specialize
Peter Amstutz
committed

Commits on May 6, 2016

Changed name for initial working directory
psaffrey-illumina
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Specialize Binding to CommandLineBinding for SchemaDef.
Peter Amstutz
committed
Make draft-2 SchemaDef name optional.
Peter Amstutz
committed
Merge branch 'draft-4' of github.com:common-workflow-language/common-workflow-language into draft-4
Peter Amstutz
committed
Update conformance tests with draft-4 version number.
Peter Amstutz
committed
Update conformance tests to use draft-4 syntax improvements.
Peter Amstutz
committed
Permit idmaps for hints, envDef
Peter Amstutz
committed
Fix mapSubject fields when $import or $include is provided.
Peter Amstutz
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Commits on May 8, 2016

start documenting the draft-4 changes
mr-c
committed

Commits on May 10, 2016

Commits on May 11, 2016

Add missing files for site generation.
Peter Amstutz
committed

Commits on May 23, 2016

Commits on May 24, 2016

Commits on May 30, 2016

Commits on Jun 2, 2016

Fold link validation into resolve_all() and resolve scoped identifiers.
Peter Amstutz
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Add scopedRef to metaschema. Tweak test.
Peter Amstutz
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New test for scoped ref that better reflects actual desired behavior.
Peter Amstutz
committed
update types

mr-c
authored and
Peter Amstutz
committed
Remove explicit calls to validate_links since it is folded into resolve_all().
Peter Amstutz
committed
Reworking refScope to be fixed instead of search based.
Peter Amstutz
committed
Improve documentation. Add feature of skipping some inner scopes.
Peter Amstutz
committed
fix types
mr-c
committed

Commits on Jun 3, 2016

Merge pull request #28 from common-workflow-language/scoped_ref
mr-c
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Refactor resolve_all into smaller methods.
Peter Amstutz
committed
"type" DSL wip
Peter Amstutz
committed
Merge branch 'resolve_all_refactor'
Peter Amstutz
committed
Merge branch 'master' into type_dsl. Add test for typeDSL.
Peter Amstutz
committed
Update bootstrap context.
Peter Amstutz
committed
Using typeDSL in metaschema.
Peter Amstutz
committed

Commits on Jun 6, 2016

Commits on Jun 7, 2016

Adjust ref scopes
Peter Amstutz
committed
Merge commit '8823aaa11432aa042b3e307891e71ee13e11bfd7' into scoped-ref-and-typedsl
Peter Amstutz
committed
Split minimal base types used in CWL into metaschema_base.yml
Peter Amstutz
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Merge commit '851b3c1302aa5b5d8a80f74c5732a617f62acefe' into scoped-ref-and-typedsl
Peter Amstutz
committed
Detect when an abstract class is used but doesn't have a concrete subtype.
Peter Amstutz
committed
Introducing refScope and typeDSL into CWL schema
Peter Amstutz
committed

Commits on Jun 8, 2016

Commits on Jun 9, 2016

Commits on Jun 10, 2016

Merge pull request #32 from common-workflow-language/type_dsl
mr-c
authored
version bump
mr-c
committed
Merge commit '6ac559ed62780091eb0cfff914018ed101ef46ef' into scoped-ref-and-typedsl
mr-c
committed
Merge pull request #228 from common-workflow-language/scoped-ref-and-typedsl
mr-c
authored
Command line generation tests now work by executing a small script that copies
Peter Amstutz
committed
Port draft-2 changes to command line generation tests to draft-3.
Peter Amstutz
committed
Add missing args.py used by draft-3 tests.
Peter Amstutz
committed
Port draft-3 changes to command line generation tests to draft-4.
Peter Amstutz
committed
Fix last test using "args"
Peter Amstutz
committed
Add listing to directory type
Peter Amstutz
committed
Make path/listing optional (sort of).
Peter Amstutz
committed

Commits on Jun 13, 2016

Commits on Jun 15, 2016

Commits on Jun 16, 2016

Commits on Jun 17, 2016

Commits on Jun 20, 2016

Add initial conformance tests for input and output of directory objects.
Peter Amstutz
committed

Commits on Jun 21, 2016

Add basename, nameroot, nameext to conformance tests.
Peter Amstutz
committed

Commits on Jun 23, 2016

Add location, update text for dirname, basename, nameroot, nameext.
Peter Amstutz
committed
Adjust Directory to also use a `location` field to identify it.
Peter Amstutz
committed
Merge branch 'master' into directory
Peter Amstutz
committed
location field is required on File and Directory. Rename conflicting basename to entryname on Dirent.
Peter Amstutz
committed
Add draft-4.dev3
Peter Amstutz
committed

Commits on Jun 24, 2016

Updating conformance tests to draft-4.dev3, path -> location
Peter Amstutz
committed
Bring up to date with draft-4 changes.
Peter Amstutz
committed

Commits on Jun 26, 2016

Merge pull request #233 from common-workflow-language/cwltype-v-primitivetype
mr-c
authored

Commits on Jun 27, 2016

Commits on Jun 28, 2016

Add InitialWorkDirRequirement, supercedes CreateFileRequirement.
Peter Amstutz
committed
Allow expression to provide full listing for InitialWorkDirRequirement
Peter Amstutz
committed
secondaryFiles has Dirent, not Directory.
Peter Amstutz
committed
Fix syntax error. Update tests to use InitialWorkDirRequirement
Peter Amstutz
committed

Commits on Jun 29, 2016

Update tests to use InitialWorkDirRequirement
Peter Amstutz
committed
Adding directory feature tests.
Peter Amstutz
committed
Unify Directory listing, InitialWorkDir and secondaryFiles to accept equivalent
Peter Amstutz
committed
Update test
Peter Amstutz
committed
Update stderr-shortcut tests.
Peter Amstutz
committed
Remove CreateFileRequirement. Add documentation to InitialWorkDirRequirement.
Peter Amstutz
committed
Delete obsolote initialWorkDir record from previous work on Directory
Peter Amstutz
committed
Add test staging files into output directory for update.
Peter Amstutz
committed

Commits on Jun 30, 2016

Commits on Jul 1, 2016

fix the draft-4 tests
mr-c
committed
Squashed 'draft-4/salad/' changes from 9c8c36f..c509a07
Peter Amstutz
committed
Merge commit '6266928eac323672c0c44d16dca91d808fbc5e68'
Peter Amstutz
committed

Commits on Jul 2, 2016

Updating site generation for draft-4.
Peter Amstutz
committed
Merge branch 'master' of github.com:common-workflow-language/common-workflow-language
Peter Amstutz
committed
Make "location" field optional when "listing" is provided.
Peter Amstutz
committed

Commits on Jul 3, 2016

Site generation works again
Peter Amstutz
committed
Fix ttl and context generation
Peter Amstutz
committed

Commits on Jul 4, 2016

Get rid of Dirent. Update spec for basename. Add contents field to File spec.
Peter Amstutz
committed
Use file content literals for InitialWorkDir.
Peter Amstutz
committed
Fix field name conflict.
Peter Amstutz
committed
Remove mapSubject entryname.
Peter Amstutz
committed
Make location optional to support File contents literals.
Peter Amstutz
committed
Fix basename.
Peter Amstutz
committed
Restore Dirent for InitialWorkDir only.
Peter Amstutz
committed
Using Dirent.
Peter Amstutz
committed
Remove conflicting mapSubject/mapPredicate
Peter Amstutz
committed
Add test of file literals.
Peter Amstutz
committed
Update site generation after removing Dirent from Directory type.
Peter Amstutz
committed

Commits on Jul 6, 2016