2022 Week 41 release #281

mr-c · 2022-10-12T09:48:58Z

For review & deploy Friday, October 14th ish.

This PR will update automatically as additional contributions are merged into the main branch.

Outstanding issues:

list previous authors in AUTHORS.md #260
Update https://github.com/common-workflow-language/user_guide/blob/main/.zenodo.json with the information from AUTHORS.md (and maybe move the authors there and moving the funding acknowledgemnts to the README)
README.md should state what this repo is and its goal; move contribution info to CONTRIBUTING.md #305

…ink-fix

* Show cwltool --make-template to users in the chapter where we introduce the inputs objects * Add a troubleshooting section for the cachedir docs Co-authored-by: Michael R. Crusoe <[email protected]>

* Link to #$include in the note * 'Important' box wasn't terminated properly Co-authored-by: Michael R. Crusoe <[email protected]>

…mmand output lines (#247) * Highlight lines of interest in the command outputs * Rename "Advanced Inputs" to "Inclusive and Exclusive Inputs" * Add text about the exclusive input parameters and expressions * explain why itemC was chosen when both are provided Co-authored-by: Michael R. Crusoe <[email protected]>

…into update-content

"pip install -e .[all]" doesn't work if you don't have setup.py. We're using a declarative package config so we need to invoke it slightly differently.

Adjust install instructions

Typo fix

update note content and add windows OS and link to install cwltool

Co-authored-by: Michael R. Crusoe <[email protected]> Co-authored-by: “gathoni-k” <“[email protected]”>

* modified sentence * modified quick-start.md

* Increase navigation depth to 3 * Expand left sidebar * Revert "Expand left sidebar" This reverts commit a3dc19b. Co-authored-by: “gathoni-k” <“[email protected]”>

Co-authored-by: “gathoni-k” <“[email protected]”> Co-authored-by: SWZ <[email protected]>

* Update README with current render * update README with released and RTD user guide

swzCuroverse · 2022-10-15T05:23:11Z

The json file has a different DOI than the readme -- do we want the json to point to the latest release but the readme to point to the general zenodo which houses all the releases, or should they match. Additionally, who is in charge of putting the zenodo entry to match the zenodo.json file in the GitHub repository? I know there exist github actions for zenodo but don't know if he have them set up or not. @kinow perhaps you know?

as we no longer use them

mr-c · 2022-10-16T15:13:34Z

The json file has a different DOI than the readme

The Zenodo JSON file points to multiple related DOIs.

user_guide/.zenodo.json

Line 20 in 0c1df15

    
           "notes": "Based off of the excellent Software/Data Carpentry templates: https://doi.org/10.5281/zenodo.838778",

is a reference to the template we used to use from the Carpentries, and thus can be removed.

user_guide/.zenodo.json

Line 29 in 0c1df15

"identifier": "10.5281/zenodo.840129",

Is a reference to the "all versions of this resource" parent DOI for the User Guide, as detailed at https://help.zenodo.org/#versioning

The badge will show the DOI for the latest release of the user.

-- do we want the json to point to the latest release but the readme to point to the general zenodo which houses all the releases, or should they match. Additionally, who is in charge of putting the zenodo entry to match the zenodo.json file in the GitHub repository? I know there exist github actions for zenodo but don't know if he have them set up or not. @kinow perhaps you know?

So there is no reason to update the Zenodo JSON file. Each new GitHub release automatically uploads to Zenodo.

P.S. You deleted a comment I made in response to your earlier inquiry (and that inquiry itself). Continued deletion of my comments will undermine your retaining write privileges in this and any other CWL repository.

mr-c · 2022-10-17T07:41:06Z

README.md

+[Released User guide for CWL v1.2.0](https://www.commonwl.org/user_guide/) : This is the released version which corresponds to the release branch.  
+[Read The Docs User guide for CWL v1.2.0](https://common-workflow-languageuser-guide.readthedocs.io/en/latest/) : This is the Read The Docs(RTD) version which corresponds to the main branch.


Use plain URL links here, please. The link text is too similar to each other.

RTD is defined here and never used again, so remove that abbreviation.

I believe it was added because we in tickets and other places (like chat) use RTD so people were wondering what that meant. So, I think even though not used in the README again, it might be nice to somehow tell me what common acronyms people are using. Not sure if this is the place to do this - but just an FYI.

swzCuroverse · 2022-10-17T11:51:32Z

The json file has a different DOI than the readme

The Zenodo JSON file points to multiple related DOIs.

user_guide/.zenodo.json

Line 20 in 0c1df15

"notes": "Based off of the excellent Software/Data Carpentry templates: https://doi.org/10.5281/zenodo.838778",

is a reference to the template we used to use from the Carpentries, and thus can be removed.

user_guide/.zenodo.json

Line 29 in 0c1df15

"identifier": "10.5281/zenodo.840129",

Is a reference to the "all versions of this resource" parent DOI for the User Guide, as detailed at https://help.zenodo.org/#versioning

The badge will show the DOI for the latest release of the user.

-- do we want the json to point to the latest release but the readme to point to the general zenodo which houses all the releases, or should they match. Additionally, who is in charge of putting the zenodo entry to match the zenodo.json file in the GitHub repository? I know there exist github actions for zenodo but don't know if he have them set up or not. @kinow perhaps you know?

So there is no reason to update the Zenodo JSON file. Each new GitHub release automatically uploads to Zenodo.

I assume you mean the Zenodo entry since you have a ticket to update the .json file. Documentation of this and the release process would be welcome. Also, it seems like the release is a moving target. So it would be nice to know if we now have a complete list for the release.

Co-authored-by: Michael R. Crusoe <[email protected]>

mr-c · 2022-10-17T13:24:06Z

@bamiwoaluko , @Gathoni-K, and @Mackenzie-OO7: Under which name shall we list you in the AUTHORS.md ?

Co-authored-by: Michael R. Crusoe <[email protected]>

swzCuroverse · 2022-10-17T14:17:50Z

@bamiwoaluko , @Gathoni-K, and @Mackenzie-OO7: Under which name shall we list you in the AUTHORS.md ?

I don't think we should require people to give their formal names to be listed as authors. I think it is fine if they do - but it shouldn't be an obligation. People may for several reasons not be using their legal names and/or not want their names (legal or not) to be made available on a project.

mr-c · 2022-10-17T14:22:18Z

@bamiwoaluko , @Gathoni-K, and @Mackenzie-OO7: Under which name shall we list you in the AUTHORS.md ?

I don't think we should require people to give their formal names to be listed as authors. I think it is fine if they do - but it shouldn't be an obligation. People may for several reasons not be using their legal names and/or not want their names (legal or not) to be made available on a project.

Agreed, I already listed them by their GitHub handles as shown in c757074 ; just giving them a chance to choose how they will be represented.

swzCuroverse · 2022-10-17T14:22:44Z

@bamiwoaluko , @Gathoni-K, and @Mackenzie-OO7: Under which name shall we list you in the AUTHORS.md ?

I don't think we should require people to give their formal names to be listed as authors. I think it is fine if they do - but it shouldn't be an obligation. People may for several reasons not be using their legal names and/or not want their names (legal or not) to be made available on a project.

Agreed, I already listed them by their GitHub handles as shown in c757074 ; just giving them a chance to choose how they will be represented.

Makes sense to me.

remigathoni · 2022-10-18T05:32:00Z

@bamiwoaluko , @Gathoni-K, and @Mackenzie-OO7: Under which name shall we list you in the AUTHORS.md ?

Mary Gathoni

bamiwoaluko · 2022-10-18T15:20:29Z

@bamiwoaluko , @Gathoni-K, and @Mackenzie-OO7: Under which name shall we list you in the AUTHORS.md ?

Bamiwo Aluko

Mackenzie-OO7 · 2022-10-18T15:38:03Z

@bamiwoaluko , @Gathoni-K, and @Mackenzie-OO7: Under which name shall we list you in the AUTHORS.md ?

Levai Mackenzie Agbara

mr-c · 2022-10-19T08:58:18Z

Levai Mackenzie Agbara

@Mackenzie-OO7 To confirm, should it be Agbara or Ágbàrà ?

user_guide/AUTHORS.md

Line 20 in 864f866

* Levai Mackenzie Ágbàrà (@Mackenzie-OO7)

Mackenzie-OO7 · 2022-10-19T09:03:24Z

Levai Mackenzie Agbara

@Mackenzie-OO7 To confirm, should it be Agbara or Ágbàrà ?

user_guide/AUTHORS.md

Line 20 in 864f866

* Levai Mackenzie Ágbàrà (@Mackenzie-OO7)

It should be Ágbàrà, I couldn't get those letters on my device earlier, thanks!

Fienne and others added 30 commits October 9, 2022 22:20

fix: change "core concepts" to "topics"

cc7ea36

Fixed broken link

2e59d13

Fixed broken link

d3f51a3

Merge branch 'link-fix' of https://github.com/Smyja/user_guide into l…

cd18f6d

…ink-fix

Document more features of cwltool (#246)

611c806

* Show cwltool --make-template to users in the chapter where we introduce the inputs objects * Add a troubleshooting section for the cachedir docs Co-authored-by: Michael R. Crusoe <[email protected]>

Add documentation about InlineJavascriptRequirement expressionLib (#242)

76dd547

* Link to #$include in the note * 'Important' box wasn't terminated properly Co-authored-by: Michael R. Crusoe <[email protected]>

feat: add cwl runner source

c3ba19d

Merge branch 'main' into update-content

537a23d

changed br to double break line

9c48683

Merge branch 'update-content' of https://github.com/Fienne/user_guide …

81435f2

…into update-content

fix broken link

3cb3c8a

adjust line break

5c65a81

Typo fix

8d083bc

Merge branch 'common-workflow-language:main' into link-fix

f28b6fa

format syntax

b84279b

Update missing links, edit document

7e25dd0

update note content and add windows OS and link to install cwltool

ac3a656

Adjust install instructions

cf2f6ce

"pip install -e .[all]" doesn't work if you don't have setup.py. We're using a declarative package config so we need to invoke it slightly differently.

Merge pull request #277 from common-workflow-language/use-python-mpip

516da15

Adjust install instructions

Merge branch 'main' into link-fix

66a635d

Merge branch 'main' into improve-introduction

d4f7030

Merge branch 'main' into bug-fix

ae2e308

Merge pull request #273 from Smyja/link-fix

613b021

Typo fix

Merge branch 'main' into improve-introduction

29b7e86

Merge branch 'main' into bug-fix

86d9cb8

Merge branch 'main' into update-content

b4c8c34

Merge pull request #276 from Fienne/improve-introduction

7ebe537

update note content and add windows OS and link to install cwltool

Merge branch 'main' into bug-fix

165a491

Merge branch 'main' into update-content

4109ab8

remigathoni and others added 7 commits October 13, 2022 08:32

Fix broken links (#291)

38fe5df

Co-authored-by: Michael R. Crusoe <[email protected]> Co-authored-by: “gathoni-k” <“[email protected]”>

typo fixes (#292)

bc776b3

pip command was missing "install" (#293)

f871abc

Modified docs (#295)

371d615

* modified sentence * modified quick-start.md

Expand toc nav depth (#296)

05cc06d

* Increase navigation depth to 3 * Expand left sidebar * Revert "Expand left sidebar" This reverts commit a3dc19b. Co-authored-by: “gathoni-k” <“[email protected]”>

Add descriptive link texts (#294)

d59c479

Co-authored-by: “gathoni-k” <“[email protected]”> Co-authored-by: SWZ <[email protected]>

Update README with current render (#297)

0c1df15

* Update README with current render * update README with released and RTD user guide

common-workflow-language deleted a comment from mr-c Oct 14, 2022

remove reference to the Carpentries template

10e6346

as we no longer use them

mr-c commented Oct 17, 2022

View reviewed changes

swzCuroverse closed this Oct 17, 2022

swzCuroverse reopened this Oct 17, 2022

mr-c and others added 3 commits October 17, 2022 15:03

freshen zenodo metadata

9309f3c

Better explain how to update the tutorials list (#302)

031b22f

Co-authored-by: Michael R. Crusoe <[email protected]>

more authors

c757074

add information on which branch to contribute to (#303)

78064c7

Co-authored-by: Michael R. Crusoe <[email protected]>

consolidate contributing information. Fixes #305

9f99f68

mr-c merged commit 61e8478 into release Oct 17, 2022

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2022 Week 41 release #281

2022 Week 41 release #281

mr-c commented Oct 12, 2022 •

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mr-c commented Oct 19, 2022

Mackenzie-OO7 commented Oct 19, 2022 •

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		[Released User guide for CWL v1.2.0](https://www.commonwl.org/user_guide/) : This is the released version which corresponds to the release branch.
		[Read The Docs User guide for CWL v1.2.0](https://common-workflow-languageuser-guide.readthedocs.io/en/latest/) : This is the Read The Docs(RTD) version which corresponds to the main branch.

2022 Week 41 release #281

2022 Week 41 release #281

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