Merge pull request #77 from Openscapes/main

catching dev up to main

README.md

@@ -30,6 +30,12 @@ usernames.
 
 ## Quick Cohort Setup
 
+### The Big Picture
+
+The chronological steps for creating Openscapes repos and materials using Kyber are detailed in the ReadMe. See this flow chart for understanding how these steps fit together, including the requirements to complete each step. ([Kyber flow chart pdf](kyberflow_20230711.pdf))
+
+![](kyberflow_20230711.png)
+
 ### Configuration
 
 Using Kyber requires more configuration than most R packages since Kyber
@@ -63,10 +69,10 @@ gitcreds_set()
 This workflow often happens in 4 separate stages:
 
 1.  create the repo and readme (pre-cohort)
-2.  create `github-clinic` files (days before GitHub Clinic in Call 2)
-3.  create github team and add usernames (day before Clinic, when we
+2.  create agenda documents before each Cohort Call
+3.  create `github-clinic` files (days before GitHub Clinic in Call 2)
+4.  create github team and add usernames (day before Clinic, when we
     have all usernames)
-4.  create agenda documents before each Cohort Call
 
 For creating the GitHub Team and adding usernames, Kyber requires you to
 set up a GitHub Personal Access Token with scopes for **repo** and
@@ -77,7 +83,7 @@ Please make sure
 that you do not share your PAT or commit it to a Git repository, since
 anyone with your PAT can act as you on GitHub.
 
-### Create GitHub repo
+### 1. Create GitHub repo
 
 ``` r
 library(kyber) 
@@ -87,8 +93,8 @@ library(fs)
 
 repo_name <- "2021-ilm-rotj"
 
-# This will open a README.Rmd for you to edit
-repo_path <- create_repo(repo_name)
+# This will open a README.Rmd for you to edit 
+repo_path <- init_repo(repo_name)
 
 # Then render the README.Rmd to README.md
 render(path(repo_path, "README.Rmd"))
@@ -102,11 +108,42 @@ render(path(repo_path, "README.Rmd"))
 # 3. Git add, commit, and push in this repository.
 ```
 
-### GitHub Clinic - Generate Markdown Files for Each Participant
+### 2. Agendas
+
+```
+kyber::call_agenda(
+    registry_url = "https://docs.google.com/spreadsheets/d/1Ys9KiTXXmZ_laBoCV2QWEm7AcnGSVQaXvm2xpi4XTSc/edit#gid=942365997", 
+    cohort_id = "2022-nasa-champions", 
+    call_number = 3)
+```
+
+The following suggestions aid next steps as of July 14, 2022:
 
-Clone the Cohort Repo to RStudio, then run the following code. Detailed instructions of what this looks like:
+**2.1 Move agenda to Google Docs**
 
-1. Open RStudio, and create a new script (temporary, you'll deleted it but it's a nicer place to work)
+- In RStudio, Knit (or PreviewHTML) the resulting `agenda.md` created from the code above and copy-paste the result into a Google Doc (example: 03_CallAgenda [ 2022-noaa-afsc ]. You might need to to expand the knitted preview into the browser to get it to copy/paste correctly into Google Docs.
+- Move Google Doc to Openscapes Workspace folder Openscapes_CohortCalls [ year-cohort-name ].
+
+**2.2 Formatting your agenda**
+
+- Select all (cmd-A) and change font to Open Sans
+- Make p1 opening text 9 point font (the text above horizontal line & Call title)
+- Make Header 1 font 18, bold; update heading 1 to match (see screenshot below; Stef notes "update heading to match" has not been working in these docs)
+- Make Header 2 font 14, bold; update heading 2 to match
+- Select all (cmd-A), then: 
+  - "add space" then "remove space **after** paragraph" throughout to make spacing a little more cozy (yes seems odd to do and undo, but it works)
+  - "add space" then "remove space **before** paragraph" throughout to make spacing a little more cozy
+- Review doc and fix any further font weirdness
+- Add page numbers 
+
+**How to "update heading 1 to match"**: (Stef notes this has not been working in these docs) In Google Doc, to update a text style (headings, normal text, with font type, size etc), highlight a section with the style you want, click the styles dropdown shown in the screenshot, and select e.g. "Update Heading 1 to match". Double check the doc because we've noticed it missed some in an agenda.
+
+
+### 3. GitHub Clinic - Generate Markdown Files for Each Participant
+
+If you haven't already, clone the Cohort Repo to RStudio (File > New Project > Version Control > Git) , then run the following code. Detailed instructions of what this looks like:
+
+1. Open the cohort repo as a project in RStudio and create a new script (temporary, you'll deleted it but it's a nicer place to work)
 1. Copy the following into the script, then delete the examples "Erin, Julie". You'll keep the `_demo.md`, which is what you'll demo live. 
 2. Go to the ParticipantsList, and copy the 2 first and last columns
 3. Back in RStudio, put your cursor inside the "tribble" parentheses, then, in the Addin menu in the top of RStudio, select "Paste as Tribble"!
@@ -144,14 +181,14 @@ You'll now have .md files for each participant in the cohort! Any duplicate name
 **Now**, commit and push the Markdown files in the `github-clinic` folder plus the `horst-champions-trailhead.png in the top-level folder to GitHub.com. Don't push the .gitignore or .rproj since they're not relevant for the Clinic. (You can do Command-A to select all files and then unclick those 2 you don't want).
 
 
-### Create GitHub team, add usernames
+### 4. Create GitHub team, add usernames
 
 1. Open RStudio, and create a new script (temporary, you'll deleted it but it's a nicer place to work)
 1. Paste the following in it and review the code. You may already have a GitHub PAT set; there is more information at the top of the README about it. 
 1. Run this code first as-is with the example usernames in the `members` variable to check -
 1. Check that the example usernames were added in the Cohort GitHub: go to github.com/openscapes/cohort-name > Settings > Collaborators and Teams 
 1. If the team was created with the username and appears in the repo, woohoo! 
-1. Open the ParticipantsList and copy the GitHub username column, including the header. 
+1. Open the ParticipantList and copy the GitHub username column, including the header. 
 3. In RStudio, put your cursor after `members <-` and use the `datapasta` Addin > Paste As Tribble to paste the usernames into the `members` variable, deleting the previous example user. 
 2. After pasting in the R script, rename the header as "username" (no spaces or asterices)
 5. Run the following code again and check that everyone was added!
@@ -181,33 +218,30 @@ members <- tibble::tribble(
   )
 
 add_team_members(team_name, members = members$username, org = "openscapes")
-add_repo_to_team(repo_name, team_name, org = "openscapes")
+add_team_to_repo(repo_name, team_name, org = "openscapes")
 ```
 
-Yay! Now all to do is to highlight the usernames in green in the ParticpantList for our bookkeeping!
+Yay! Now all to do is to highlight the usernames in green in the ParticipantList for our bookkeeping!
 
 
-### Agendas
+## R package developer notes
 
-    kyber::call_agenda(
-        registry_url = "https://docs.google.com/spreadsheets/d/1Ys9KiTXXmZ_laBoCV2QWEm7AcnGSVQaXvm2xpi4XTSc/edit#gid=942365997", 
-        cohort_id = "2022-nasa-champions", 
-        call_number = 3)
+Steps to edit `kyber` locally and review those edits: 
 
-Then, to move this to a Google Doc and fine-tune formatting, follow these notes (as of July 14, 2022): 
+1. In RStudio, open `kyber` project, pull main branch 
+2. If you've been working in RStudio, restart your R session.
+3. Make edits to files (for example `inst/agendas/team_culture.Rmd`)
+4. In R console: `devtools::load_all()` to load local edits for `kyber`
+5. In R console, test whatever you edited. For example, to create the call agenda: 
 
-- In RStudio, Knit (or PreviewHTML) the resulting `agenda.md` and copy-paste the result into a Google Doc (example: 03_CallAgenda [ 2022-noaa-afsc ]. You might need to to expand the knitted preview into the browser to get it to copy/paste correctly into Google Docs
-- Move Google Doc to Openscapes Workspace folder Openscapes_CohortCalls [ year-cohort-name ].
-- Select all (cmd-A) and change font to Open Sans
-- Make p1 opening text 9 point font (the text above horizontal line & Call title)
-- Make Header 1 font 18, bold; update heading 1 to match (see screenshot below; Stef notes "update heading to match" has not been working in these docs)
-- Make Header 2 font 14, bold; update heading 2 to match
-- Select all (cmd-A), then: 
-  - "add space" then "remove space **after** paragraph" throughout to make spacing a little more cozy (yes seems odd to do and undo, but it works)
-  - "add space" then "remove space **before** paragraph" throughout to make spacing a little more cozy
-- Review doc and fix any further font weirdness
-- Add page numbers 
+```
+kyber::call_agenda(
+    registry_url = "https://docs.google.com/spreadsheets/d/1Ys9KiTXXmZ_laBoCV2QWEm7AcnGSVQaXvm2xpi4XTSc/edit#gid=942365997", 
+    cohort_id = "2022-noaa-afsc-fall", 
+    call_number = 4)
+```    
 
-**How to "update heading 1 to match"**: (Stef notes this has not been working in these docs) In Google Doc, to update a text style (headings, normal text, with font type, size etc), highlight a section with the style you want, click the styles dropdown shown in the screenshot, and select e.g. "Update Heading 1 to match". Double check the doc because we've noticed it missed some in an agenda.
+1. 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.
 
-![Screen Shot 2022-07-14 at 5 50 28 PM](https://user-images.githubusercontent.com/11927811/179125336-ec2fc1e5-792e-495d-8a29-c1ed3ec3cdc4.png)

inst/agendas/_better_science.Rmd

@@ -6,17 +6,15 @@ params:
 
 ## Better science for future us • `r kyber:::fmt_duration(params$start_time, params$duration)`
 
-- Seaside Chats, Pathways ([slides](https://docs.google.com/presentation/d/162tpUZEFkpTUI4K3Yl_mF6HLxsgwO_d7bvF5F4igxfk/edit?usp=sharing)) (10 min) - Julie
+- Real-life stories ([slides](https://docs.google.com/presentation/d/1tE3pQ2ObNU68iG4uTIlMuSN4dguvn-cOvwtoM-c9L-w/)) (15 min) - Julie
   - ‎
   - 
-- **Breakout groups** (10 min) (random) - Stef
-  - **Prompts: Discuss your space and place.** 
-  - Space: Are Seaside Chats something you already do? Anyone else who should be included? 
-  - Place: Where are your places to collaborate on files/data? Is everyone included as they need to be (skills/permissions/etc)?
+- **Breakout groups** (8 min) (random) - Stef (<font color="red">pause recording</font>)
+  - **Prompt: How does this story resonate for you?** 
   - ‎
   -
   -
-- **Discussion** (5 min) - All
+- **Share-outs** (2 min) - Julie (<font color="red">start recording</font>)
   - ‎
   -
   -

inst/agendas/_closing.Rmd

@@ -24,7 +24,7 @@ params:
         - [/blog](https://openscapes.org/blog): stories from the community
     - github: [@openscapes](https://github.com/openscapes)
         - [how_we_work](https://github.com/Openscapes/how_we_work), [seaside-chats](https://github.com/Openscapes/seaside-chats): Examples from previous cohorts
-    - twitter: [@openscapes](https://twitter.com/openscapes)
+    - Mastodon: [fosstodon.org/@openscapes](https://fosstodon.org/@openscapes)
     - artwork: by the amazing [Allison Horst](https://twitter.com/allison_horst)
 
 - **Feedback on this session**

inst/agendas/_closing_task_final.Rmd

@@ -7,43 +7,29 @@ params:
 
 ## Closing --- Better science for future us • `r kyber:::fmt_duration(params$start_time, params$duration)`
 
-**Thank you for being a part of Openscapes** - Julie - We hope you feel a bit more confident about what's possible with open data science with your teams and colleagues. - This is the very beginning, finding your trailhead.
+**Thank you for being a part of Openscapes** - Julie 
 
-![](openscapes_champions_landscape.png)
-
--   **Your Seaside Chats are a way to continue learning together**
-    -   Broaden them to your broader groups, if useful following [10-week plan to supercharge your research](https://www.nature.com/articles/d41586-019-03335-4) (Lowndes et al. 2019)
-    -   Thinking about data analysis as a collaborative effort
-    -   Identifying and addressing shared needs
-    -   Thinking ahead for future us
-    -   
-
-**Please reuse/remix resources and stay in touch**
-
--   We're learning how to continue to support teams and help strengthen our community and the open science movement after the Cohort ends
-
-    -   [github.com/Openscapes](https://github.com/Openscapes) - pinned repositories
-
-    -   [openscapes.github.io/series](https://openscapes.github.io/series/) - continually improved lessons 
-
-    -   [openscapes.org/blog](https://www.openscapes.org/blog/) - guest posts welcome!
-
-    -   [openscapes.org/events](https://openscapes.org/events) - Champions Cohorts, Community Calls, talks 
+- We hope you feel a bit more confident about what's possible with open data science with your teams and colleagues. 
+- This is the very beginning, finding your trailhead.
+- Thank you Mentors!!
 
-    -   Twitter [\@openscapes](https://twitter.com/openscapes) - please tag us and we'll retweet!
-
-    -   Slack - now with "events" and "jobs" channels
-
-    -   Newsletter \~5x/year
-
--   Survey: We'll send with Digest 5; please help us improve
+![](openscapes_champions_landscape.png)
 
 **"Graduating" gift:**
 
   -   **Openscapes badges by Allison Horst!**
   -   Download from here: [openscapes_hex_badge.png](https://github.com/Openscapes/how_we_work/blob/main/openscapes_hex_badge.png)
   -   You can put it on your website, like the [Wood Lab](https://chelsealwood.com/research/) and the [Fay Lab](https://thefaylab.github.io/lab-manual/index.html)!
-
-    -   **Please email an address for your team so we can send stickers!**
+ -   **Please share a mailingan address for your team so we can send stickers!**
 
 ![](khora-laptop-sleep.png)
+
+**Continued learning**
+
+-   **Survey**: We'll send with Digest 5; please help us improve
+
+-   **Your Seaside Chats are a way to continue learning together**
+    -   Broaden them to your broader groups, if useful following [10-week plan to supercharge your research](https://www.nature.com/articles/d41586-019-03335-4) (Lowndes et al. 2019)
+    -   Thinking about data workflows as a collaborative effort
+    -   Identifying and addressing shared needs
+    -   Thinking ahead for future us

inst/agendas/_closing_task_mindset.Rmd

@@ -5,25 +5,12 @@ params:
 ---
 
 ## Closing • `r kyber:::fmt_duration(params$start_time, params$duration)`
+*We've covered a lot today; we'll explore these ideas more deeply together in the next weeks.*
 
--   **Champions Program [POP](https://suzannehawkes.com/2010/04/09/pop-everything/)** (5 min) -- Julie
-
-- We've covered a lot today; we'll explore these ideas more deeply together
-  -   **Purpose**
-    -   Reimagine data analysis and stewardship, develop modern skills and habits that are of immediate value to you, cultivate collaborative and inclusive research communities
-  -   **Outcomes**
-    -   Different for everybody - this is about reflecting on what you need and developing a practice and allies to help you make progress
-    -   You\'ll share your work-in-progress Pathway on our last Cohort Call
-  -   **Process**
-    -   Opportunities for connecting and support within and across our Cohort. There is so much experience and expertise here
-    -   Cohort Calls: Twice-monthly with full Cohort
-    -   Seaside Chats: we\'ll provide task suggestions but main purpose is to build the habit of strengthening shared workflows with your broader group.
-    -   Co-working: (optional); come to focus on something workflow related - could be quiet work, feedback/questions/problem-solving.
-    -   Google Space: asynchronous within Cohort
-    -   Slack: asynchronous across Cohorts (present and past)
-    - Twitter: asynchronous across open science ([#rstats](https://twitter.com/search?q=%23rstats&src=typed_query), [\@openscapes](https://twitter.com/openscapes))
-
--   **Task for next time** (2 min) -- All
+- **Pathways Document & Seaside Chats** (4 min) -- Julie (screenshare)
+    - [Pathways Sheet](https://docs.google.com/spreadsheets/d/1rmhOly87OYrPOUqTzmccYbPrTlGmXGsN06GI1FKzxag/edit#gid=0)
+    - Pathways details and examples: <https://openscapes.github.io/series/core-lessons/pathways>
+-   **Task for next time** (3 min) -- Julie
 
     -   **Have a Seaside Chat & start your Pathway**
     -   Start discussing your trailhead: where are you now?\

inst/agendas/_coding_strategies.Rmd

@@ -6,7 +6,7 @@ params:
 
 ## Coding strategies • `r kyber:::fmt_duration(params$start_time, params$duration)`
 
-- **Coding strategies for Future Us** ([slides](https://docs.google.com/presentation/d/1nTLJ782dpZqp3MEhQU9zNaFInrTaFUVQbj9OqsmxUYo/edit?usp=sharing)) (15 min) – Julie
+- **Coding strategies for Future Us** ([slides](https://docs.google.com/presentation/d/1krzD4lt0k7Zu-_lfIFSubABXMLBvTpmg3Ab2GrdbnpU/)) (15 min) – Julie
   - Type of tool needed:
     - Programming language (R, python)
     - Code editor (RStudio IDE, Jupyter)
@@ -44,4 +44,4 @@ params:
   - ‎
   -  
   - 
-  -  
+  -  

inst/agendas/_data_strategies.Rmd

@@ -6,7 +6,7 @@ params:
 
 ## Data strategies • `r kyber:::fmt_duration(params$start_time, params$duration)`
 
-- **Data strategies for Future Us** ([slides](https://docs.google.com/presentation/d/1rv-JfJeuYhogxV6Dpn_hNDm09nfKnOMtmZpgcciI_98/edit?usp=sharing)) (20 min) – Julie
+- **Data strategies for Future Us** ([slides](https://docs.google.com/presentation/d/1WJzVMg1Ps2cHG0G6D5kpnL-OCJ-wVBILMqtmzDQxEgU/)) (20 min) – Julie
   - Data organization in spreadsheets ([Broman & Woo 2018](https://peerj.com/preprints/3183/))
   - Spreadsheet drama ([Parker, Peng & Bryan 2016](https://nssdeviations.com/episode-9-spreadsheet-drama))
   - Good enough practices for scientific computing ([Wilson et al. 2017](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510))
@@ -39,4 +39,4 @@ params:
   - ‎
   -  
   - 
-  -  
+  -  

inst/agendas/_efficiency_tip_keyboard_shortcuts2.Rmd

@@ -7,10 +7,11 @@ params:
 - **Efficiency Tip of the Day ** (2 min) – Stef
   - **Keyboard shortcuts useful for any application** (docs, email, code)
     - Mac:
-        - `Command tab` for carouseling between applications
-        - `Command `\` for carouseling between applications
-        - `Command option arrow` for carouseling between tabs (browser)
+        - **Command tab** for carouseling between applications - looks like this
+        <center>![](carousel-applications.jpg)</center>
+        - **Command `**  for carouseling between applications
+        - **Command option arrow** for carouseling between tabs (browser)
     - Windows:
-        - `Alt-tab `or `Windows-tab`
-        - `Alt-tab` again or `Alt-shift-tab` to go backwards
-        - `Control page up / page down` for carouseling between tabs (browser)
+        - **Alt-tab** or **Windows-tab**
+        - **Alt-tab** again or **Alt-shift-tab** to go backwards
+        - **Control page up / page down** for carouseling between tabs (browser)

inst/agendas/_efficiency_tip_move_between_tabs.Rmd

@@ -1,5 +1,7 @@
 ---
-duration: 0 minutes
+params:
+  start_time: "12:00pm PT"
+  duration: 0
 ---
 
 - **Efficiency Tip of the Day ** (2 min) – Julie