From 4c47fbfd3691e1b1de43668c5e15c8ece87e992f Mon Sep 17 00:00:00 2001 From: Stefanie Butland Date: Tue, 7 Jan 2025 16:35:06 -0800 Subject: [PATCH 1/7] fixes #136 --- inst/agendas/_open_communities.Rmd | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/inst/agendas/_open_communities.Rmd b/inst/agendas/_open_communities.Rmd index 6f914d5..91a7580 100644 --- a/inst/agendas/_open_communities.Rmd +++ b/inst/agendas/_open_communities.Rmd @@ -15,10 +15,7 @@ params: - - (pause recording) - **Breakout groups** (12 min) – All (groups of 3-4, same as reflections) - - **Prompt: Explore communities resources & tutorials relevant for your next Seaside Chat** - - Explore a few communities of interest / from the slides - - What communities are you already a part of? - - What would you like to learn with your research group? How does this fit with your Pathway? + - **Prompt: Where do you go to learn? How do you find what you need? What is one resource or tutorial you might explore in your next Seaside Chat?** - ‎ - - From d9ae3734defb99837a9e7b6369d7f352270506f6 Mon Sep 17 00:00:00 2001 From: Stefanie Butland Date: Tue, 7 Jan 2025 16:42:01 -0800 Subject: [PATCH 2/7] tweak communities prompt --- inst/agendas/_open_communities.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/agendas/_open_communities.Rmd b/inst/agendas/_open_communities.Rmd index 91a7580..4b137ca 100644 --- a/inst/agendas/_open_communities.Rmd +++ b/inst/agendas/_open_communities.Rmd @@ -16,7 +16,7 @@ params: - (pause recording) - **Breakout groups** (12 min) – All (groups of 3-4, same as reflections) - **Prompt: Where do you go to learn? How do you find what you need? What is one resource or tutorial you might explore in your next Seaside Chat?** - - ‎ + - Add your notes here‎ - - - From 85831bb03f4faf2a72aa077c3cb60219decc50c2 Mon Sep 17 00:00:00 2001 From: Stefanie Butland Date: Tue, 7 Jan 2025 17:41:08 -0800 Subject: [PATCH 3/7] addressing #116 --- .../skeleton/skeleton.Rmd | 55 +++++++++++-------- 1 file changed, 31 insertions(+), 24 deletions(-) diff --git a/inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd index fe9b400..8243877 100644 --- a/inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd +++ b/inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd @@ -10,52 +10,59 @@ library(knitr) db <- kyber:::readme_setup(params) ``` - + # `r db$cr$cohort_name_long` -Welcome to the `r db$cr$cohort_name_long` Cohort! This is a Cohort for [TODO: who is this cohort for?]. Learn more about Openscapes and the Champions Program: . +Welcome to the `r db$cr$cohort_name_long` Cohort! This is a Cohort for [TODO: who is this cohort for?]. To learn more about the program, what to expect, and outcomes, and lessons, please see the [Champions Program Lesson Series](https://openscapes.github.io/series). - + ## Cohort Agendas -We will meet as a Cohort via Zoom five times over two months for 1.5 hours each: +We will meet as a Cohort via Zoom five times over two months for 1.5 hours each: -- **Dates:** `r kyber:::pretty_date_sequence(db$date_range)` -- **Times:** `r kyber:::fmt_duration(db$cr$time_start, 90)` -- **Location:** remotely, via Zoom +- **Dates:** `r kyber:::pretty_date_sequence(db$date_range)` +- **Times:** `r kyber:::fmt_duration(db$cr$time_start, 90)` +- **Location:** remotely, via Zoom -Agendas are accessible to Cohort participants in our [Cohort Google Drive Folder](`r db$cr$google_drive_folder`); they are also an archive of our live google-docing. Please see to view blank versions of the agendas. +Agendas are accessible to Cohort participants in our [Cohort Google Drive Folder](%60r%20db$cr$google_drive_folder%60); they are also an archive of our live google-docing. Please see to view blank versions of the agendas. + -## Co-working times (optional) +Cohort Call Topics | Lesson Series Chapters | Seaside Chat Topics +------------------|----------------------|--------------------------- +1. Openscapes mindset | [mindset](https://openscapes.github.io/series/mindset), [better science for future us](https://openscapes.github.io/series/core-lessons/better-science) | Seaside Chat (trailhead) +2. GitHub for publishing & project management | [publishing](https://openscapes.github.io/series/github-pub), [project management](https://openscapes.github.io/series/github-issues) | Seaside Chat: shared organizing with GitHub +3. Team culture and data strategies for future us | [team culture](https://openscapes.github.io/series/team-culture), [data strategies](https://openscapes.github.io/series/core-lessons/data-strategies) | Seaside Chat (code of conduct);
Co-working +4. Open communities and coding strategies for future us | [open communities](https://openscapes.github.io/series/core-lessons/communities), [coding strategies](https://openscapes.github.io/series/core-lessons/coding-strategies) | Seaside Chat (pathway); Coworking +5. Pathways share and next steps | [pathways](https://openscapes.github.io/series/core-lessons/pathways) | -Co-working sessions are where we work at the same time together. Sometimes, this means quiet work with check-ins to break up focused work and get feedback, and sometimes this involves asking questions and screensharing to learn and problem solve. +## Coworking times (optional) -- **Dates:** -- **Times:** -- **Location:** remotely, via Zoom +Coworking sessions are where get our own work done at the same time together. Sometimes, this means quiet work with check-ins to break up focused work and get feedback, and sometimes this involves asking questions and screensharing to learn and problem solve. We will make breakout rooms in Zoom so people working on related themes can meet and learn from each other. -## Participating teams -Some brief information about participating teams. Please add any edits directly (we'll learn how in our GitHub Clinic!) +- **Dates:** +- **Times:** +- **Location:** remotely, via Zoom -## Openscapes Team +## Participating teams and individuals -[TODO: Add Planning Google Folder] +Some brief information about participating teams and individuals. Please add any edits directly (we'll learn how in our GitHub Clinic!) -[Planning Google Folder]() +## Our Team -Julie Lowndes, Openscapes Co-Lead, NCEAS, UCSB, is co-leading -Erin Robinson, Openscapes Co-Lead, Metadata Game Changers, is co-leading +Julie Lowndes (@jules32), Openscapes +Stefanie Butland (@stefaniebutland), Openscapes +Andy Teucher (@teucher), Openscapes ## More about Openscapes and the Champions program: -* **[Our path to better science in less time using open data science tools](https://www.nature.com/articles/s41559-017-0160)** (Lowndes et al 2017, _Nature Ecology & Evolution_) - this paper greatly influences the whole Champions program and we’ll ask that everyone participating reads it before our first Cohort Call on September 9. -* **[Openscapes: Better Science for Future Us](https://docs.google.com/presentation/d/1HGw4P095-lblHiGQHXYidHiVysjrPxuojxTxKtE13vk/edit#slide=id.ge2b7c2f974_0_2017)** - 2021 plenary talk at the Society for Open, Reliable, and Transparent Ecology and Evolutionary biology (SORTEE) inaugural conference -* **[Openscapes embraces kindness and inclusion in open science](https://sparcopen.org/impact-story/openscapes-embraces-kindness-and-inclusion-of-open-science/)** - 2021 article about Openscapes -* **[openscapes.org](https://openscapes.org/)** – Openscapes is operated at the National Center for Ecological Analysis & Synthesis, UC Santa Barbara +- [**Our path to better science in less time using open data science tools**](https://www.nature.com/articles/s41559-017-0160) (Lowndes et al. 2017) - This describes a marine science team’s transition to open collaborative teamwork. It was the original inspiration for creating the Champions Program and heavily influences the Core Lessons. We’ll ask that everyone participating reads it before our first Cohort Call. +- [**Supercharge your research: a ten-week plan for open data science**](https://openscapes.github.io/supercharge-research/) (Lowndes et al. 2019) - This was co-authored with the inaugural Champions Cohort, capturing the most valuable take-aways for marine and environmental science early career faculty. +- [**Shifting institutional culture to develop climate solutions with Open Science**](https://onlinelibrary.wiley.com/doi/10.1002/ece3.11341) (Lowndes et al. 2024) - This was co-authored by Openscapes mentors across organizations – including NASA Earthdata, NOAA Fisheries, EPA, California Water Boards, Pathways to Open Science, Fred Hutch Cancer Center. From 3aa4b2dda8c54a6b727d6f71b2da1b63458ddf24 Mon Sep 17 00:00:00 2001 From: Stefanie Butland Date: Wed, 8 Jan 2025 11:53:20 -0800 Subject: [PATCH 4/7] updates to cohort readme skeleton --- .../skeleton/skeleton.Rmd | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd index 8243877..67805b7 100644 --- a/inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd +++ b/inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd @@ -14,9 +14,9 @@ db <- kyber:::readme_setup(params) # `r db$cr$cohort_name_long` -Welcome to the `r db$cr$cohort_name_long` Cohort! This is a Cohort for [TODO: who is this cohort for?]. To learn more about the program, what to expect, and outcomes, and lessons, please see the [Champions Program Lesson Series](https://openscapes.github.io/series). +Welcome to the `r db$cr$cohort_name_long` Cohort! This is a Cohort for [TODO: who is this cohort for?] To learn more about the program, what to expect, and outcomes, and lessons, please see the [Champions Program Lesson Series](https://openscapes.github.io/series). - + ## Cohort Agendas @@ -26,7 +26,7 @@ We will meet as a Cohort via Zoom five times over two months for 1.5 hours each: - **Times:** `r kyber:::fmt_duration(db$cr$time_start, 90)` - **Location:** remotely, via Zoom -Agendas are accessible to Cohort participants in our [Cohort Google Drive Folder](%60r%20db$cr$google_drive_folder%60); they are also an archive of our live google-docing. Please see to view blank versions of the agendas. +Agendas are accessible to Cohort participants in our [Cohort Google Drive Folder] [TODO:link to folder]; they are also an archive of our live google-docing. Please see to view blank versions of the agendas. + ## Coworking times (optional) -Coworking sessions are where get our own work done at the same time together. Sometimes, this means quiet work with check-ins to break up focused work and get feedback, and sometimes this involves asking questions and screensharing to learn and problem solve. We will make breakout rooms in Zoom so people working on related themes can meet and learn from each other. +Coworking sessions are where get our own work done at the same time together. Sometimes, this means quiet work with check-ins to break up focused work and get feedback, and sometimes this involves asking questions and screensharing to learn and problem solve. We will make breakout rooms so people working on related themes can meet and learn from each other. - **Dates:** - **Times:** From 991f893e0d269775ba08f5657e71ca07a37dda5a Mon Sep 17 00:00:00 2001 From: Stefanie Butland Date: Wed, 8 Jan 2025 12:05:59 -0800 Subject: [PATCH 5/7] syncing local and remote kyber/readme.md updates several updates were made by me direct to main --- README.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index b51e168..3ca1875 100644 --- a/README.md +++ b/README.md @@ -103,6 +103,8 @@ repo_path <- init_repo(repo_name) # Then render the README.Rmd to README.md render(path(repo_path, "README.Rmd")) +# To create a readme independently of creating a repo use: `kyber::create_readme()`, which is called by `init_repo()`. Then knit the README.Rmd to README.md. + # We still need to work out the next part of the workflow and the extent to # which it should be automated, but I imagine something like: # @@ -282,10 +284,12 @@ kyber::call_agenda( call_number = 4) ``` -1. To review the call agenda, open `agenda.md`, click Preview, and view it in the Viewer Tab. +6. To review the call agenda, open `agenda.md`, click Preview, and view it in the Viewer Tab. Usually you can repeat steps 3-5 whenever you make edits you want to review, however if there are problems try restarting you R session. +To update the template for all Cohort README.Rmd's, edit [`inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd`](https://github.com/Openscapes/kyber/blob/main/inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd) + ## Contributing to Kyber To contribute to Kyber, fork the repo, unchecking the "Copy the main branch only" box. Start working from the `dev` branch, create a new branch like `new-branch dev`, and then submit Pull Requests to `dev`. If using Git on the command line the workflow would look like: @@ -298,5 +302,4 @@ To contribute to Kyber, fork the repo, unchecking the "Copy the main branch only - then `git push origin new-branch` - keep adding, committing, and pushing, then when you're ready open a PR -We started using this workflow when the [California Water Boards Openscapes]((https://cawaterboarddatacenter.github.io/swrcb-openscapes/) team began using Kyber to create Agendas from some unique source Rmd files. For example, Water Boards Cohort Calls are 2 hours, not the default 1.5 hrs, their lesson order is different from Openscapes Core Lessons, and includes a new lesson on Documentation. - +We started using this workflow when the [California Water Boards Openscapes](https://cawaterboarddatacenter.github.io/swrcb-openscapes/) team began using Kyber to create Agendas from some unique source Rmd files. For example, Water Boards Cohort Calls are 2 hours, not the default 1.5 hrs, their lesson order is different from Openscapes Core Lessons, and includes a new lesson on Documentation. From cd66ee20e1d5965ad42136d67c64255bc3116992 Mon Sep 17 00:00:00 2001 From: Stefanie Butland Date: Wed, 8 Jan 2025 16:37:22 -0800 Subject: [PATCH 6/7] Update inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd --- .../templates/openscapes-cohort-readme/skeleton/skeleton.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd index 67805b7..7a9cf3c 100644 --- a/inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd +++ b/inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd @@ -14,7 +14,7 @@ db <- kyber:::readme_setup(params) # `r db$cr$cohort_name_long` -Welcome to the `r db$cr$cohort_name_long` Cohort! This is a Cohort for [TODO: who is this cohort for?] To learn more about the program, what to expect, and outcomes, and lessons, please see the [Champions Program Lesson Series](https://openscapes.github.io/series). +Welcome to the `r db$cr$cohort_name_long` Cohort! This is a Cohort for [TODO: who is this cohort for?]. Please see the [Champions Program Lesson Series](https://openscapes.github.io/series) for what to expect, outcomes, and to browse the open lesson materials. From 4e2d3a8006c1d9949904c4c50b0931a1f51d1527 Mon Sep 17 00:00:00 2001 From: Stefanie Butland Date: Wed, 8 Jan 2025 16:50:23 -0800 Subject: [PATCH 7/7] improve cohort preamble based on fred hutch cohort readme --- .../templates/openscapes-cohort-readme/skeleton/skeleton.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd index 7a9cf3c..6717221 100644 --- a/inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd +++ b/inst/rmarkdown/templates/openscapes-cohort-readme/skeleton/skeleton.Rmd @@ -14,7 +14,7 @@ db <- kyber:::readme_setup(params) # `r db$cr$cohort_name_long` -Welcome to the `r db$cr$cohort_name_long` Cohort! This is a Cohort for [TODO: who is this cohort for?]. Please see the [Champions Program Lesson Series](https://openscapes.github.io/series) for what to expect, outcomes, and to browse the open lesson materials. +Welcome to the `r db$cr$cohort_name_long` Cohort! This is a Cohort for [TODO: who is this cohort for?]. To learn more about what to expect (the purpose, outcomes, and process of our Cohort) and to browse the open lesson materials, please see the [Champions Program Lesson Series](https://openscapes.github.io/series).