sync with template; fix lesson-check

Author: mr-c

CONDUCT.md renamed to CODE_OF_CONDUCT.md

@@ -1,7 +1,6 @@
 ---
 layout: page
 title: "Contributor Code of Conduct"
-permalink: /conduct/
 ---
 As contributors and maintainers of this project,
 we pledge to respect all people who contribute through reporting issues,

CONTRIBUTING.md

@@ -27,7 +27,7 @@ This is a good way to introduce yourself
 and to meet some of our community members.
 
 1.  If you do not have a [GitHub][github] account,
-    you can [send us comments by email][contact].
+    you can [send us comments by email][discuss-list].
     However,
     we will be able to respond more quickly if you use one of the other methods described below.
 

Makefile

@@ -63,7 +63,7 @@ RMD_DST = $(patsubst _episodes_rmd/%.Rmd,_episodes/%.md,$(RMD_SRC))
 # Lesson source files in the order they appear in the navigation menu.
 MARKDOWN_SRC = \
   index.md \
-  CONDUCT.md \
+  CODE_OF_CONDUCT.md \
   setup.md \
   $(sort $(wildcard _episodes/*.md)) \
   reference.md \
@@ -88,27 +88,17 @@ ${RMD_DST} : ${RMD_SRC}
 	@bin/knit_lessons.sh ${RMD_SRC}
 
 ## lesson-check     : validate lesson Markdown.
-lesson-check :
+lesson-check : lesson-fixme
 	@bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md
 
 ## lesson-check-all : validate lesson Markdown, checking line lengths and trailing whitespace.
 lesson-check-all :
 	@bin/lesson_check.py -s . -p ${PARSER} -l -w
 
-## lesson-figures   : re-generate inclusion displaying all figures.
-lesson-figures :
-	@bin/extract_figures.py -p ${PARSER} ${MARKDOWN_SRC} > _includes/all_figures.html
-
 ## unittest         : run unit tests on checking tools.
 unittest :
 	python bin/test_lesson_check.py
 
-RUNNER=cwl-runner
-
-## unittest-examples: run unit tests for the examples
-unittest-examples :
-	cd _includes/cwl; cwltest --test=conformance-test.yml --tool=${RUNNER}
-
 ## lesson-files     : show expected names of generated files for debugging.
 lesson-files :
 	@echo 'RMD_SRC:' ${RMD_SRC}

_config.yml

@@ -11,7 +11,7 @@ title: "Common Workflow Language User Guide"
 # Contact.  This *must* include the protocol: if it's an email
 # address, it must look like "mailto:lessons@software-carpentry.org",
 # or if it's a URL, "https://gitter.im/username/ProjectName".
-contact: "http://www.commonwl.org/#Support"
+email: "http://www.commonwl.org/#Support"
 
 #------------------------------------------------------------
 # Generic settings (should not need to change).
@@ -34,8 +34,8 @@ repository: common-workflow-language/user-guide
 # template_repo: "https://github.com/swcarpentry/styles"
 # example_repo: "https://github.com/swcarpentry/lesson-example"
 # example_site: "https://swcarpentry.github.com/lesson-example"
-# workshop_repo: "https://github.com/swcarpentry/workshop-template"
-# workshop_site: "https://swcarpentry.github.io/workshop-template"
+workshop_repo: "https://github.com/swcarpentry/workshop-template"
+workshop_site: "https://swcarpentry.github.io/workshop-template"
 # training_site: "https://swcarpentry.github.io/instructor-training"
 
 # Surveys.
@@ -50,24 +50,34 @@ start_time: 0
 collections:
   episodes:
     output: true
-    permalink: /:path/
+    permalink: /:path/index.html
   extras:
     output: true
+    permalink: /:path/index.html
 
 # Set the default layout for things in the episodes collection.
 defaults:
   - values:
-      root: ..
+      root: .
+      layout: page
   - scope:
       path: ""
       type: episodes
     values:
+      root: ..
       layout: episode
+  - scope:
+      path: ""
+      type: extras
+    values:
+      root: ..
+      layout: page
 
 # Files and directories that are not to be copied.
 exclude:
   - Makefile
-  - bin
+  - bin/
+  - .Rproj.user/
 
-# Turn off built-in syntax highlighting.
-highlighter: false
+# Turn on built-in syntax highlighting.
+highlighter: rouge

_episodes/01-introduction.md

@@ -28,3 +28,5 @@ technologies such as Docker and be used with CWL implementations from different
 vendors. CWL is well suited for describing large-scale workflows in cluster,
 cloud and high performance computing environments where tasks are scheduled in
 parallel across many nodes.
+
+{% include links.md %}

_episodes/02-1st-example.md

@@ -82,3 +82,4 @@ This tool has no formal output, so the `outputs` section is an empty list.
 
 [json]: http://json.org
 [yaml]: http://yaml.org
+{% include links.md %}

_episodes/03-input.md

@@ -151,3 +151,4 @@ is optional.  The default position is 0.
 The `baseCommand` field will always appear in the final command line before the parameters.
 
 [touch]: http://www.linfo.org/touch.html
+{% include links.md %}

_episodes/04-output.md

@@ -44,7 +44,7 @@ wrapper and the input object on the command line:
 $ touch hello.txt && tar -cvf hello.tar hello.txt
 $ cwl-runner tar.cwl tar-job.yml
 [job tar.cwl] /tmp/tmpqOeawQ$ tar \
-    xf \
+    --extract --file \
     /tmp/tmpGDk8Y1/stg80bbad20-494d-47af-8075-dffc32df03a3/hello.tar
 [job tar.cwl] completed success
 {
@@ -77,3 +77,5 @@ outputs:
 
 The `glob` field consists of the name of a file in the output directory.
 If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`.
+
+{% include links.md %}

_episodes/05-stdout.md

@@ -52,3 +52,4 @@ Final process status is success
 
 ~~~
 {: .output}
+{% include links.md %}

_episodes/06-params.md

@@ -37,12 +37,12 @@ input object on the command line:
 $ rm hello.tar || true && touch goodbye.txt && tar -cvf hello.tar goodbye.txt
 $ cwl-runner tar-param.cwl tar-param-job.yml
 [job tar-param.cwl] /tmp/tmpwH4ouT$ tar \
-    xf \
+    --extract --file \
     /tmp/tmpREYiEt/stgd7764383-99c9-4848-af51-7c2d6e5527d9/hello.tar \
     goodbye.txt
 [job tar-param.cwl] completed success
 {
-    "example_out": {
+    "extracted_file": {
         "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
         "basename": "goodbye.txt",
         "nameroot": "goodbye",
@@ -62,7 +62,7 @@ These are evaluated and replaced with value being referenced.
 
 ~~~
 outputs:
-  example_out:
+  extracted_out:
     type: File
     outputBinding:
       glob: $(inputs.extractfile)
@@ -80,3 +80,5 @@ Note that because `File` parameters are objects, to get the path to an
 input file you must reference the path field on a file object; to
 reference the path to the tar file in the above example you would write
 `$(inputs.tarfile.path)`.
+
+{% include links.md %}

_episodes/07-containers.md

@@ -89,3 +89,4 @@ the container, as reflected in the invocation of the `node` command.
 
 
 [docker]: https://docker.io
+{% include links.md %}

_episodes/08-arguments.md

@@ -92,3 +92,4 @@ designated output directory.  Other parameters include `$(runtime.tmpdir)`,
 CWL specification for details.
 
 [runtime]: http://www.commonwl.org/v1.0/CommandLineTool.html#Runtime_environment
+{% include links.md %}

_episodes/09-array-inputs.md

@@ -77,3 +77,5 @@ Note that the arrays of inputs are specified inside square brackets `[]` in `arr
 array values that are not defined with an associated key is marked by a leading
 `-`, as demonstrated in the next lesson. 
 You can specify arrays of arrays, arrays of records, and other complex types.
+
+{% include links.md %}

_episodes/10-array-outputs.md

@@ -38,13 +38,13 @@ Final process status is success
   "output": [
     {
       "size": 0,
-      "location": "/home/peter/work/common-workflow-language/draft-3/examples/foo.txt",
+      "location": "foo.txt",
       "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
       "class": "File"
     },
     {
       "size": 0,
-      "location": "/home/peter/work/common-workflow-language/draft-3/examples/baz.txt",
+      "location": "baz.txt",
       "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
       "class": "File"
     }
@@ -56,3 +56,5 @@ Final process status is success
 The array of expected outputs is specified in `array-outputs-job.yml` with each
 entry marked by a leading `-`. This format can also be used in CWL descriptions
 to mark entries in arrays, as demonstrated in several of the upcoming sections.
+
+{% include links.md %}

_episodes/11-records.md

@@ -113,3 +113,5 @@ $ cat output.txt
 
 In the third example, only `itemD` is provided, so it appears on the
 command line.
+
+{% include links.md %}

_episodes/12-env.md

@@ -55,3 +55,4 @@ HOME=/home/example
 TMPDIR=/tmp/tmp63Obpk
 ~~~
 {: .output}
+{% include links.md %}

_episodes/13-expressions.md

@@ -114,3 +114,4 @@ You can only use expressions in certain fields.  These are:
 
 [file-prop]: http://www.commonwl.org/v1.0/CommandLineTool.html#File
 [rec-practices]: http://www.commonwl.org/user_guide/rec-practices/
+{% include links.md %}

_episodes/14-runtime.md

@@ -52,3 +52,4 @@ $ cat output.txt
 CONFIGVAR=Hello world!
 ~~~
 {: .output}
+{% include links.md %}

_episodes/15-staging.md

@@ -49,3 +49,4 @@ Final process status is success
 }
 ~~~
 {: .output}
+{% include links.md %}

_episodes/16-file-formats.md

@@ -85,3 +85,4 @@ Final process status is success
 
 [IANA]: https://www.iana.org/assignments/media-types/media-types.xhtml
 [EDAM]: http://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_1915
+{% include links.md %}

_episodes/17-metadata.md

@@ -45,3 +45,4 @@ requirements in order to use the tool, and a few more metadata fields.
 {: .source}
 
 [schema-salad]: http://www.commonwl.org/v1.0/SchemaSalad.html#Explicit_context
+{% include links.md %}

_episodes/19-custom-types.md

@@ -98,3 +98,4 @@ the software that the description was written for and other useful metadata.
 These features are discussed further in other chapters of this user guide.
 
 [biom]: http://biom-format.org/
+{% include links.md %}

_episodes/20-software-requirements.md

@@ -57,3 +57,4 @@ include the DOI for the main tool citation and the URL to the tool.
 [dependencies]: https://github.com/common-workflow-language/cwltool#leveraging-softwarerequirements-beta
 [identifiers]: https://identifiers.org/
 [scicrunch-add-tool]: https://scicrunch.org/page/tutorials/336
+{% include links.md %}

_episodes/21-1st-workflow.md

@@ -23,7 +23,9 @@ compiles it.
 ~~~
 {: .source}
 
-<a href="https://view.commonwl.org/workflows/github.com/common-workflow-language/user_guide/blob/gh-pages/_includes/cwl/21-1st-workflow/1st-workflow.cwl"><img src="https://view.commonwl.org/graph/svg/github.com/common-workflow-language/user_guide/blob/gh-pages/_includes/cwl/21-1st-workflow/1st-workflow.cwl" alt="Visualization of 1st-workflow.cwl" /></a>
+> ## Visualization of 1st-workflow.cwl
+> <a href="https://view.commonwl.org/workflows/github.com/common-workflow-language/user_guide/blob/gh-pages/_includes/cwl/21-1st-workflow/1st-workflow.cwl"><img src="https://view.commonwl.org/graph/svg/github.com/common-workflow-language/user_guide/blob/gh-pages/_includes/cwl/21-1st-workflow/1st-workflow.cwl" alt="Visualization of 1st-workflow.cwl" /></a>
+{: .callout}
 
 Use a JSON object in a separate file to describe the input of a run:
 
@@ -40,14 +42,14 @@ command line:
 ~~~
 $ echo "public class Hello {}" > Hello.java && tar -cvf hello.tar Hello.java
 $ cwl-runner 1st-workflow.cwl 1st-workflow-job.yml
-[job untar] /tmp/tmp94qFiM$ tar xf /home/example/hello.tar Hello.java
+[job untar] /tmp/tmp94qFiM$ tar --create --file /home/example/hello.tar Hello.java
 [step untar] completion status is success
 [job compile] /tmp/tmpu1iaKL$ docker run -i --volume=/tmp/tmp94qFiM/Hello.java:/var/lib/cwl/job301600808_tmp94qFiM/Hello.java:ro --volume=/tmp/tmpu1iaKL:/var/spool/cwl:rw --volume=/tmp/tmpfZnNdR:/tmp:rw --workdir=/var/spool/cwl --read-only=true --net=none --user=1001 --rm --env=TMPDIR=/tmp java:7 javac -d /var/spool/cwl /var/lib/cwl/job301600808_tmp94qFiM/Hello.java
 [step compile] completion status is success
 [workflow 1st-workflow.cwl] outdir is /home/example
 Final process status is success
 {
-  "classout": {
+  "compiled_class": {
     "location": "/home/example/Hello.class",
     "checksum": "sha1$e68df795c0686e9aa1a1195536bd900f5f417b18",
     "class": "File",
@@ -71,8 +73,8 @@ document.  The `class` field indicates this document describes a workflow.
 
 ~~~
 inputs:
-  inp: File
-  ex: string
+  tarball: File
+  name_of_file_to_extract: string
 ~~~
 {: .source}
 
@@ -83,7 +85,7 @@ specific workflows steps.
 
 ~~~
 outputs:
-  classout:
+  compiled_class:
     type: File
     outputSource: compile/classfile
 ~~~
@@ -92,16 +94,16 @@ outputs:
 The `outputs` section describes the outputs of the workflow.  This is a
 list of output parameters where each parameter consists of an identifier
 and a data type.  The `outputSource` connects the output parameter `classfile`
-of the `compile` step to the workflow output parameter `classout`.
+of the `compile` step to the workflow output parameter `compiled_class`.
 
 ~~~
 steps:
   untar:
     run: tar-param.cwl
     in:
-      tarfile: inp
-      extractfile: ex
-    out: [example_out]
+      tarfile: tarball
+      extractfile: name_of_file_to_extract
+    out: [extracted_file]
 ~~~
 {: .source}
 
@@ -114,13 +116,15 @@ instead the order is determined by the dependencies between steps (using
 another may run in parallel.
 
 The first step, `untar` runs `tar-param.cwl` (described previously in
-[Parameter references][params]).  This tool has two input parameters, `tarfile`
-and `extractfile` and one output parameter `example_out`.
+[Parameter references]({{ page.root }}{% link _episodes/06-params.md %})).
+This tool has two input parameters, `tarfile` and `extractfile` and one output
+parameter `example_out`.
 
 The ``in`` section of the workflow step connects these two input parameters to
-the inputs of the workflow, `inp` and `ex` using `source`.  This means that when
-the workflow step is executed, the values assigned to `inp` and `ex` will be
-used for the parameters `tarfile` and `extractfile` in order to run the tool.
+the inputs of the workflow, `tarball` and `name_of_file_to_extract` using
+`source`.  This means that when the workflow step is executed, the values
+assigned to `tarball` and `name_of_file_to_extract` will be used for the
+parameters `tarfile` and `extractfile` in order to run the tool.
 
 The `out` section of the workflow step lists the output parameters that are
 expected from the tool.
@@ -129,14 +133,14 @@ expected from the tool.
   compile:
     run: arguments.cwl
     in:
-      src: untar/example_out
+      src: untar/extracted_file
     out: [classfile]
 ~~~
 {: .source}
 
 The second step `compile` depends on the results from the first step by
 connecting the input parameter `src` to the output parameter of `untar` using
-`untar/example_out`.  The output of this step `classfile` is connected to the
+`untar/extracted_file`.  The output of this step `classfile` is connected to the
 `outputs` section for the Workflow, described above.
 
-[params]: ../06-params/
+{% include links.md %}