From 75c02bb48962fc543108aeaeb5e311e76ca819db Mon Sep 17 00:00:00 2001 From: Leah Wasser Date: Thu, 12 Jan 2023 10:13:33 -0700 Subject: [PATCH 1/6] Add Pangeo as a partner --- .github/ISSUE_TEMPLATE/presubmission-inquiry.md | 7 +++++++ .github/ISSUE_TEMPLATE/submit-software-for-review.md | 7 +++++++ 2 files changed, 14 insertions(+) diff --git a/.github/ISSUE_TEMPLATE/presubmission-inquiry.md b/.github/ISSUE_TEMPLATE/presubmission-inquiry.md index 2ed353b..b2d698b 100644 --- a/.github/ISSUE_TEMPLATE/presubmission-inquiry.md +++ b/.github/ISSUE_TEMPLATE/presubmission-inquiry.md @@ -18,6 +18,13 @@ Repository Link (if existing): - Include a brief paragraph describing what your package does: +## Community Partnerships +We partner with communities to support peer review with an additional layer of +checks that satisfy community requirements. If your package fits into an +existing community please check below: + +- [ ] Pangeo + ## Scope - Please indicate which [category or categories][PackageCategories] this package falls under: diff --git a/.github/ISSUE_TEMPLATE/submit-software-for-review.md b/.github/ISSUE_TEMPLATE/submit-software-for-review.md index 45222e8..81b39d3 100644 --- a/.github/ISSUE_TEMPLATE/submit-software-for-review.md +++ b/.github/ISSUE_TEMPLATE/submit-software-for-review.md @@ -26,6 +26,13 @@ Date accepted (month/day/year): TBD - Include a brief paragraph describing what your package does: +## Community Partnerships +We partner with communities to support peer review with an additional layer of +checks that satisfy community requirements. If your package fits into an +existing community please check below: + +- [ ] Pangeo + ## Scope - Please indicate which [category or categories][PackageCategories] this package falls under: - [ ] Data retrieval From 56d5f0e558a6d0f2c6b786ca8ef7be2e2959f6ca Mon Sep 17 00:00:00 2001 From: Leah Wasser Date: Mon, 23 Jan 2023 17:31:17 -0700 Subject: [PATCH 2/6] Add: pangeo links to submission guide --- .github/ISSUE_TEMPLATE/submit-software-for-review.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/.github/ISSUE_TEMPLATE/submit-software-for-review.md b/.github/ISSUE_TEMPLATE/submit-software-for-review.md index 81b39d3..884879c 100644 --- a/.github/ISSUE_TEMPLATE/submit-software-for-review.md +++ b/.github/ISSUE_TEMPLATE/submit-software-for-review.md @@ -31,7 +31,8 @@ We partner with communities to support peer review with an additional layer of checks that satisfy community requirements. If your package fits into an existing community please check below: -- [ ] Pangeo +- [ ] [Pangeo][pangeoWebsite] + - [ ] My package adheres to the [Pangeo standards listed in the pyOpenSci peer review guidebook][PangeoCollaboration] ## Scope - Please indicate which [category or categories][PackageCategories] this package falls under: @@ -127,3 +128,7 @@ The [review template can be found here][Review Template]. [Review Template]: https://www.pyopensci.org/peer-review-guide/software-peer-review-guide/reviewer-guide.html#peer-review-template [Comments]: https://github.com/pyOpenSci/governance/issues/8 + +[PangeoCollaboration]: https://www.pyopensci.org/scientific-communities/pangeo-collaboration + +[pangeoWebsite]: https://www.pangeo.io From 36d0879f01a17a76604839b70fd38f0d0478532a Mon Sep 17 00:00:00 2001 From: Leah Wasser Date: Wed, 1 Feb 2023 09:18:15 -0700 Subject: [PATCH 3/6] Fix conflicts and links --- .github/ISSUE_TEMPLATE/help-request.md | 6 +-- .../ISSUE_TEMPLATE/presubmission-inquiry.md | 18 ++++--- .../submit-software-for-review.md | 53 ++++++++++--------- 3 files changed, 43 insertions(+), 34 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/help-request.md b/.github/ISSUE_TEMPLATE/help-request.md index 77d4704..ff62175 100644 --- a/.github/ISSUE_TEMPLATE/help-request.md +++ b/.github/ISSUE_TEMPLATE/help-request.md @@ -57,8 +57,8 @@ Repository Link (if existing): **P.S.** *Have feedback/comments about our review process? Leave a comment [here][Comments] -[PackagingGuide]: https://www.pyopensci.org/contributing-guide/authoring/index.html#packaging-guide +[PackagingGuide]: https://www.pyopensci.org/python-package-guide/ -[PackageCategories]: https://www.pyopensci.org/contributing-guide/open-source-software-peer-review/aims-and-scope.html?highlight=data#package-categories +[PackageCategories]: https://www.pyopensci.org/software-peer-review/about/package-scope.html -[Comments]: https://github.com/pyOpenSci/governance/issues/8 +[Comments]: https://pyopensci.discourse.group/ diff --git a/.github/ISSUE_TEMPLATE/presubmission-inquiry.md b/.github/ISSUE_TEMPLATE/presubmission-inquiry.md index b2d698b..5e189ef 100644 --- a/.github/ISSUE_TEMPLATE/presubmission-inquiry.md +++ b/.github/ISSUE_TEMPLATE/presubmission-inquiry.md @@ -14,6 +14,8 @@ Repository Link (if existing): --- +- [ ]I have read and will commit to package maintenance after the review as per the [pyOpenSci Policies Guidelines][Commitment]. + ## Description - Include a brief paragraph describing what your package does: @@ -23,7 +25,8 @@ We partner with communities to support peer review with an additional layer of checks that satisfy community requirements. If your package fits into an existing community please check below: -- [ ] Pangeo +- [ ] [Pangeo][pangeoWebsite] + - [ ] My package adheres to the [Pangeo standards listed in the pyOpenSci peer review guidebook][PangeoCollaboration] ## Scope @@ -47,17 +50,18 @@ existing community please check below: - Any other questions or issues we should be aware of: -- [ ] Please make sure that you took notice of our [Community Code of Conduct][Conduct] and are able to commit to the package maintainance as per our [Policies Guidelines][Commitment]. +**P.S.** *Have feedback/comments about our review process? Leave a comment [here][Comments] +[PackageCategories]: https://www.pyopensci.org/software-peer-review/about/package-scope.html -**P.S.** *Have feedback/comments about our review process? Leave a comment [here][Comments] +[Conduct]: https://www.pyopensci.org/governance/CODE_OF_CONDUCT +[Commitment]: https://www.pyopensci.org/software-peer-review/our-process/policies.html#after-acceptance-package-ownership-and-maintenance -[PackageCategories]: https://www.pyopensci.org/contributing-guide/open-source-software-peer-review/aims-and-scope.html?highlight=data#package-categories +[Comments]: https://pyopensci.discourse.group/ -[Conduct]: https://www.pyopensci.org/peer-review-guide/about-peer-review/code-of-conduct.html +[PangeoCollaboration]: https://www.pyopensci.org/software-peer-review/partners/pangeo -[Commitment]: https://www.pyopensci.org/peer-review-guide/about-peer-review/policies-guidelines.html#after-acceptance-package-ownership-and-maintenance +[pangeoWebsite]: https://www.pangeo.io -[Comments]: https://github.com/pyOpenSci/governance/issues/8 diff --git a/.github/ISSUE_TEMPLATE/submit-software-for-review.md b/.github/ISSUE_TEMPLATE/submit-software-for-review.md index 884879c..46fafd9 100644 --- a/.github/ISSUE_TEMPLATE/submit-software-for-review.md +++ b/.github/ISSUE_TEMPLATE/submit-software-for-review.md @@ -26,26 +26,36 @@ Date accepted (month/day/year): TBD - Include a brief paragraph describing what your package does: -## Community Partnerships -We partner with communities to support peer review with an additional layer of -checks that satisfy community requirements. If your package fits into an -existing community please check below: - -- [ ] [Pangeo][pangeoWebsite] - - [ ] My package adheres to the [Pangeo standards listed in the pyOpenSci peer review guidebook][PangeoCollaboration] ## Scope -- Please indicate which [category or categories][PackageCategories] this package falls under: +- Please indicate which [category or categories][PackageCategories] this package falls under (If you are unsure of which category you fit, we suggest you make a pre-submission inquiry): + - [ ] Data retrieval - [ ] Data extraction - - [ ] Data munging + - [ ] Data processing/munging - [ ] Data deposition - - [ ] Reproducibility + - [ ] Data validation and testing + - [ ] Data visualization ** + - [ ] Workflow automation + - [ ] Citation management and bibliometrics + - [ ] Scientific software wrappers + - [ ] Database interoperability + +Domain Specific & Community Partnerships + - [ ] Geospatial - [ ] Education - - [ ] Data visualization* + - [ ] Pangeo + + +## Community Partnerships +If your package is associated with an +existing community please check below: +- [ ] [Pangeo][pangeoWebsite] + - [ ] My package adheres to the [Pangeo standards listed in the pyOpenSci peer review guidebook][PangeoCollaboration] -> *Please fill out a pre-submission inquiry before submitting a data visualization package. For more info, see [notes on categories][NotesOnCategories] of our guidebook.* + +> ** Please fill out a pre-submission inquiry before submitting a data visualization package.* - **For all submissions**, explain how the and why the package falls under the categories you indicated above. In your explanation, please address the following points (briefly, 1-2 sentences for each): @@ -68,7 +78,7 @@ For details about the pyOpenSci packaging requirements, see our [packaging guide - [ ] has a test suite. - [ ] has continuous integration, such as Travis CI, AppVeyor, CircleCI, and/or others. -## Publication options +## Publication Options - [ ] Do you wish to automatically submit to the [Journal of Open Source Software][JournalOfOpenSourceSoftware]? If so: @@ -106,12 +116,9 @@ The [editor template can be found here][Editor Template]. The [review template can be found here][Review Template]. -[PackagingGuide]: https://www.pyopensci.org/contributing-guide/authoring/index.html#packaging-guide - -[PackageCategories]: https://www.pyopensci.org/contributing-guide/open-source-software-peer-review/aims-and-scope.html?highlight=data#package-categories - -[NotesOnCategories]: https://www.pyopensci.org/contributing-guide/open-source-software-peer-review/aims-and-scope.html?highlight=data#notes-on-categories +[PackagingGuide]: https://www.pyopensci.org/python-package-guide/ +[PackageCategories]: https://www.pyopensci.org/software-peer-review/about/package-scope.html [JournalOfOpenSourceSoftware]: http://joss.theoj.org/ @@ -119,16 +126,14 @@ The [review template can be found here][Review Template]. [JossPaperRequirements]: https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain -[PyOpenSciCodeOfConduct]: https://www.pyopensci.org/contributing-guide/open-source-software-peer-review/code-of-conduct.html?highlight=code%20conduct +[PyOpenSciCodeOfConduct]: https://www.pyopensci.org/governance/CODE_OF_CONDUCT [OsiApprovedLicense]: https://opensource.org/licenses -[Editor Template]: https://www.pyopensci.org/peer-review-guide/software-peer-review-guide/editors-guide.html#respond-to-the-submitter-in-the-github-issue - -[Review Template]: https://www.pyopensci.org/peer-review-guide/software-peer-review-guide/reviewer-guide.html#peer-review-template +[Templates]: https://www.pyopensci.org/software-peer-review/appendices/templates.html -[Comments]: https://github.com/pyOpenSci/governance/issues/8 +[Comments]: https://pyopensci.discourse.group/ -[PangeoCollaboration]: https://www.pyopensci.org/scientific-communities/pangeo-collaboration +[PangeoCollaboration]: https://www.pyopensci.org/software-peer-review/partners/pangeo [pangeoWebsite]: https://www.pangeo.io From 491dc525d48fc3819bc0b92af43309e10a3e3670 Mon Sep 17 00:00:00 2001 From: Leah Wasser Date: Wed, 1 Feb 2023 09:00:43 -0700 Subject: [PATCH 4/6] Add: ci to check links and clearer categories --- .../ISSUE_TEMPLATE/submit-software-for-review.md | 16 ++++++++++------ .github/workflows/check-links.yml | 14 ++++++++++++++ 2 files changed, 24 insertions(+), 6 deletions(-) create mode 100644 .github/workflows/check-links.yml diff --git a/.github/ISSUE_TEMPLATE/submit-software-for-review.md b/.github/ISSUE_TEMPLATE/submit-software-for-review.md index 46fafd9..55ae17b 100644 --- a/.github/ISSUE_TEMPLATE/submit-software-for-review.md +++ b/.github/ISSUE_TEMPLATE/submit-software-for-review.md @@ -54,7 +54,6 @@ existing community please check below: - [ ] [Pangeo][pangeoWebsite] - [ ] My package adheres to the [Pangeo standards listed in the pyOpenSci peer review guidebook][PangeoCollaboration] - > ** Please fill out a pre-submission inquiry before submitting a data visualization package.* @@ -68,15 +67,15 @@ existing community please check below: ## Technical checks -For details about the pyOpenSci packaging requirements, see our [packaging guide][PackagingGuide]. Confirm each of the following by checking the box. This package: +For details about the pyOpenSci packaging requirements, see our [packaging guide][PackagingGuide]. Confirm each of the following by checking the box. This package: - [ ] does not violate the Terms of Service of any service it interacts with. -- [ ] has an [OSI approved license][OsiApprovedLicense]. +- [ ] uses an [OSI approved license][OsiApprovedLicense]. - [ ] contains a README with instructions for installing the development version. - [ ] includes documentation with examples for all functions. -- [ ] contains a vignette with examples of its essential functions and uses. +- [ ] contains a tutorial with examples of its essential functions and uses. - [ ] has a test suite. -- [ ] has continuous integration, such as Travis CI, AppVeyor, CircleCI, and/or others. +- [ ] has continuous integration setup, such as GitHub Actions CircleCI, and/or others. ## Publication Options @@ -99,7 +98,12 @@ This option will allow reviewers to open smaller issues that can then be linked - [x] Yes I am OK with reviewers submitting requested changes as issues to my repo. Reviewers will then link to the issues in their submitted review. -## Code of conduct +Confirm each of the following by checking the box. + +- [ ] I have read the [author guide](https://www.pyopensci.org/software-peer-review/how-to/author-guide.html). +- [ ] I expect to maintain this package for at least 2 years and can help find a replacement for the maintainer (team) if needed. + +## Code of Conduct - [ ] I agree to abide by [pyOpenSci's Code of Conduct][PyOpenSciCodeOfConduct] during the review process and in maintaining my package should it be accepted. diff --git a/.github/workflows/check-links.yml b/.github/workflows/check-links.yml new file mode 100644 index 0000000..a8e7641 --- /dev/null +++ b/.github/workflows/check-links.yml @@ -0,0 +1,14 @@ +name: check links + +on: + pull_request: + push: + branches: + - main + +jobs: + markdown-link-check: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@master + - uses: gaurav-nelson/github-action-markdown-link-check@v1 \ No newline at end of file From 6e23496f42901555bf1980bfd3a47aa360c86a1b Mon Sep 17 00:00:00 2001 From: Leah Wasser Date: Wed, 1 Feb 2023 09:19:52 -0700 Subject: [PATCH 5/6] Rebase fix conflict --- .../ISSUE_TEMPLATE/presubmission-inquiry.md | 19 ++++++++++++++++--- .../submit-software-for-review.md | 13 +++++++------ 2 files changed, 23 insertions(+), 9 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/presubmission-inquiry.md b/.github/ISSUE_TEMPLATE/presubmission-inquiry.md index 5e189ef..919d597 100644 --- a/.github/ISSUE_TEMPLATE/presubmission-inquiry.md +++ b/.github/ISSUE_TEMPLATE/presubmission-inquiry.md @@ -14,6 +14,9 @@ Repository Link (if existing): --- +## Code of Conduct & Commitment to Maintain Package + +- [ ] I agree to abide by [pyOpenSci's Code of Conduct][PyOpenSciCodeOfConduct] during the review process and in maintaining my package after should it be accepted. - [ ]I have read and will commit to package maintenance after the review as per the [pyOpenSci Policies Guidelines][Commitment]. ## Description @@ -31,14 +34,23 @@ existing community please check below: ## Scope - Please indicate which [category or categories][PackageCategories] this package falls under: + - [ ] Data retrieval - [ ] Data extraction - - [ ] Data munging + - [ ] Data processing/munging - [ ] Data deposition - - [ ] Data visualization - - [ ] Reproducibility + - [ ] Data validation and testing + - [ ] Data visualization ** + - [ ] Workflow automation + - [ ] Citation management and bibliometrics + - [ ] Scientific software wrappers + - [ ] Database interoperability + +Domain Specific & Community Partnerships + - [ ] Geospatial - [ ] Education + - [ ] Pangeo - [ ] Unsure/Other (explain below) - Explain how and why the package falls under these categories (briefly, 1-2 sentences). Please note any areas you are unsure of: @@ -65,3 +77,4 @@ existing community please check below: [pangeoWebsite]: https://www.pangeo.io +[PyOpenSciCodeOfConduct]: https://www.pyopensci.org/governance/CODE_OF_CONDUCT diff --git a/.github/ISSUE_TEMPLATE/submit-software-for-review.md b/.github/ISSUE_TEMPLATE/submit-software-for-review.md index 55ae17b..640afe5 100644 --- a/.github/ISSUE_TEMPLATE/submit-software-for-review.md +++ b/.github/ISSUE_TEMPLATE/submit-software-for-review.md @@ -22,13 +22,19 @@ Date accepted (month/day/year): TBD --- +## Code of Conduct + +- [ ] I agree to abide by [pyOpenSci's Code of Conduct][PyOpenSciCodeOfConduct] during the review process and in maintaining my package should it be accepted. + ## Description - Include a brief paragraph describing what your package does: ## Scope -- Please indicate which [category or categories][PackageCategories] this package falls under (If you are unsure of which category you fit, we suggest you make a pre-submission inquiry): +- Please indicate which category or categories. +Check out our [package scope page][PackageCategories] to learn more about our +scope. (If you are unsure of which category you fit, we suggest you make a pre-submission inquiry): - [ ] Data retrieval - [ ] Data extraction @@ -56,7 +62,6 @@ existing community please check below: > ** Please fill out a pre-submission inquiry before submitting a data visualization package.* - - **For all submissions**, explain how the and why the package falls under the categories you indicated above. In your explanation, please address the following points (briefly, 1-2 sentences for each): - Who is the target audience and what are scientific applications of this package? @@ -103,10 +108,6 @@ Confirm each of the following by checking the box. - [ ] I have read the [author guide](https://www.pyopensci.org/software-peer-review/how-to/author-guide.html). - [ ] I expect to maintain this package for at least 2 years and can help find a replacement for the maintainer (team) if needed. -## Code of Conduct - -- [ ] I agree to abide by [pyOpenSci's Code of Conduct][PyOpenSciCodeOfConduct] during the review process and in maintaining my package should it be accepted. - ## Please fill out our survey - [ ] [Last but not least please fill out our pre-review survey](https://forms.gle/F9mou7S3jhe8DMJ16). This helps us track submission and improve our peer review process. We will also ask our reviewers From 1f9661aab878f881f6bb39efe9cd0ad064a6acb5 Mon Sep 17 00:00:00 2001 From: Leah Wasser Date: Wed, 1 Feb 2023 09:21:14 -0700 Subject: [PATCH 6/6] Fix: categories on both templates --- .github/ISSUE_TEMPLATE/presubmission-inquiry.md | 5 +++++ .github/ISSUE_TEMPLATE/submit-software-for-review.md | 6 ++++-- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/presubmission-inquiry.md b/.github/ISSUE_TEMPLATE/presubmission-inquiry.md index 919d597..d4c943a 100644 --- a/.github/ISSUE_TEMPLATE/presubmission-inquiry.md +++ b/.github/ISSUE_TEMPLATE/presubmission-inquiry.md @@ -35,6 +35,11 @@ existing community please check below: - Please indicate which [category or categories][PackageCategories] this package falls under: +## Scope +- Please indicate which category or categories. +Check out our [package scope page][PackageCategories] to learn more about our +scope. (If you are unsure of which category you fit, we suggest you make a pre-submission inquiry): + - [ ] Data retrieval - [ ] Data extraction - [ ] Data processing/munging diff --git a/.github/ISSUE_TEMPLATE/submit-software-for-review.md b/.github/ISSUE_TEMPLATE/submit-software-for-review.md index 640afe5..1823813 100644 --- a/.github/ISSUE_TEMPLATE/submit-software-for-review.md +++ b/.github/ISSUE_TEMPLATE/submit-software-for-review.md @@ -22,9 +22,10 @@ Date accepted (month/day/year): TBD --- -## Code of Conduct +## Code of Conduct & Commitment to Maintain Package -- [ ] I agree to abide by [pyOpenSci's Code of Conduct][PyOpenSciCodeOfConduct] during the review process and in maintaining my package should it be accepted. +- [ ] I agree to abide by [pyOpenSci's Code of Conduct][PyOpenSciCodeOfConduct] during the review process and in maintaining my package after should it be accepted. +- [ ]I have read and will commit to package maintenance after the review as per the [pyOpenSci Policies Guidelines][Commitment]. ## Description @@ -142,3 +143,4 @@ The [review template can be found here][Review Template]. [PangeoCollaboration]: https://www.pyopensci.org/software-peer-review/partners/pangeo [pangeoWebsite]: https://www.pangeo.io +[Commitment]: https://www.pyopensci.org/software-peer-review/our-process/policies.html#after-acceptance-package-ownership-and-maintenance \ No newline at end of file