From f854ea6c4d1a6876d5be4f195c6627a085cb5dbd Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Fri, 20 Sep 2024 12:03:55 -0700 Subject: [PATCH 1/8] update slides for getting credit lesson --- .../site_libs/revealjs/dist/theme/quarto.css | 2 +- lessons/10-get-credit/slides.qmd | 50 +++++++++++++++---- 2 files changed, 40 insertions(+), 12 deletions(-) diff --git a/_freeze/site_libs/revealjs/dist/theme/quarto.css b/_freeze/site_libs/revealjs/dist/theme/quarto.css index e96ab76..c35eaa0 100644 --- a/_freeze/site_libs/revealjs/dist/theme/quarto.css +++ b/_freeze/site_libs/revealjs/dist/theme/quarto.css @@ -5,4 +5,4 @@ * we also add `bright-[color]-` synonyms for the `-[color]-intense` classes since * that seems to be what ansi_up emits * 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!important}blockquote::before{content:"“";font-size:75px;font-weight:bold;color:#aeaeae;position:absolute;left:10px;top:5px}blockquote::after{content:""}/*# sourceMappingURL=f95d2bded9c28492b788fe14c3e9f347.css.map */ diff --git a/lessons/10-get-credit/slides.qmd b/lessons/10-get-credit/slides.qmd index d97a314..5d1a06d 100644 --- a/lessons/10-get-credit/slides.qmd +++ b/lessons/10-get-credit/slides.qmd @@ -5,7 +5,7 @@ date: "2024-10-03" date-format: long format: uaz-revealjs: - reference-location: document + reference-location: section link-external-newwindow: true chalkboard: true logo: "../../logo.png" @@ -27,7 +27,7 @@ Figure 2 from @maitner Figure 2: Predicted impacts of code-sharing on cumulative citations. Predicted values shown are for the mean Impact Factor (3.0) across the publications analyzed. Fully open = open code and open-access publication; fully closed = closed-access publication and no publicly available code. -Predictions are based on estimated model coe cients (Table 2) +Predictions are based on estimated model coeficients (Table 2) ::: ## Getting credit for your code @@ -59,7 +59,7 @@ Make it **easier** for people to cite your code ## Options for archiving {.smaller} | Service | Versioned DOIs? | Free? | GitHub integration? | Notes | -|--------------|--------------|--------------|--------------|----------------| +|---------------|---------------|---------------|---------------|---------------| | Zenodo | Yes | Yes | Yes | Backed by CERN, built with code and data in mind | | Dryad | Yes | No, but some publishers cover cost | No | Intended for data, not code. Partners with Zenodo | | Figshare | Yes | Yes | Yes | Can't choose your license | @@ -69,7 +69,17 @@ Make it **easier** for people to cite your code More detailed comparisons [here](https://www.agu.org/-/media/Files/Publications/Generalist-Data-Repository-Grid.pdf) ::: -# Zenodo Archiving Demo +## Zenodo Archiving Demo + +1. Log in to sandbox.zenodo.org using GitHub[^1] +2. In drop-down menu with your username, select "GitHub" +3. Find your repo in the list and flip the switch next to it +4. Go to your repo on GitHub and make a release +5. On sandbox.zenodo.org, get markdown to add a badge to README.md + +::: notes +Demo archiving a repo with sandbox.zenodo.org and have everyone follow along with the repo they've been using for notes. +::: ## Reproducible computational environments @@ -113,9 +123,14 @@ To deactivate `renv`, run `renv::deactivate()`. To also remove all the files it created, run `renv::deactivate(clean = TRUE)` instead. ::: +::: notes +Briefly discuss the contents of `renv.lock`, `.Rprofile`, and `renv/`. +Point out `renv/.gitignore` — trust it about which files should go on GitHub. +::: + ## Limitations of `renv` -- Only tracks R packages [^1] +- Only tracks R packages [^2] - Can't reproduce operating system or system libraries @@ -159,7 +174,7 @@ RUN Rscript /02_code/install_packages.R ## Hold up, what *is* reproducibility again? -There is a reproducibility **tradeoff** for using `renv` and Docker---robust computational reproducibility **but** harder for novices to reproduce +There is a reproducibility **trade-off** for using `renv` and Docker---robust computational reproducibility **but** harder for novices to reproduce . . . @@ -169,17 +184,30 @@ If you use these tools, provide: - Where to go for help troubleshooting - Ways to access your code *without* extra layers -## Drop-in Session & Showcase +## Resources -- Next week (10/10, 10/12): No workshops! +- [Reproducible computational environments with Docker](https://reproducibility.rocks/materials/day4/01-docker/) -- Tuesday 10/17: Drop-in help session +- [`renv` website](https://rstudio.github.io/renv/articles/renv.html) -- Tuesday 10/24: Reproducibility show & tell +- [CFF INIT helper](https://citation-file-format.github.io/cff-initializer-javascript/#/) + +## Next week + +- Tuesday 10/18: **Drop-in co-working session**. + + - Come and work on your reproducibility colloquium project/presentation + +- Thursday 10/10: **Reproducibility Colloquium!** + + - Invite your lab-mates, PI, friends! ## References ::: refs ::: -[^1]: `renv` can also be set up to track [Python dependencies](https://rstudio.github.io/renv/articles/python.html) +[^1]: sandbox.zenodo.org is just for practice. + Use zenodo.org when you're ready to get a *real* DOI! + +[^2]: `renv` can also be set up to track [Python dependencies](https://rstudio.github.io/renv/articles/python.html) From 58c3edd466f8ae56a8f6a82362a508fb1ad38bf8 Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Fri, 20 Sep 2024 12:13:14 -0700 Subject: [PATCH 2/8] update notes --- lessons/10-get-credit/notes.qmd | 19 ++++++++++--------- lessons/10-get-credit/slides.qmd | 8 ++++++++ 2 files changed, 18 insertions(+), 9 deletions(-) diff --git a/lessons/10-get-credit/notes.qmd b/lessons/10-get-credit/notes.qmd index 3cd99a9..119bb5e 100644 --- a/lessons/10-get-credit/notes.qmd +++ b/lessons/10-get-credit/notes.qmd @@ -8,9 +8,11 @@ bibliography: references.bib ## Objective -Learn the wrap-up steps to publish/archive a research compendium with a DOI. -Understand reproducible computational environment. -Learn `renv` and discuss Docker (concept). +- Learn the wrap-up steps to publish/archive a research compendium with a DOI. + +- Understand concept of a reproducible computational environment. + +- Learn `renv` and discuss Docker (concept). ## Lesson Outline @@ -32,21 +34,20 @@ Learn `renv` and discuss Docker (concept). - Show CITATION.cff files for this repo and maybe one for a research compendium - Show "cite this" button on GitHub - Show CITATION.cff creation tool [CFFINIT](https://citation-file-format.github.io/cff-initializer-javascript/#/) - - Maybe mention `cffr::cff_validate()` + - *Maybe* mention `cffr::cff_validate()` - Archiving - - Most participants probably won't be ready to follow along with their own repos, but we will be there to help when they are ready - - Demo archiving a repo with Zenodo using this repo + - Demo archiving a repo with Zenodo using sandbox.zenodo.org - Add DOI badge to readme - Update CITATION.cff with DOI - `renv` - Discuss why - - Ask students to activate `renv` for a project and inspect files it creates (have co-instructor share screen) + - Ask students to activate `renv` for a project and inspect files it creates - Explain how `renv` works, especially `renv::status()` , and `renv::snapshot()` - - Clone co-instructor's repo with `renv` files + - Clone demo repo with `renv` files - Show that no packages are available initially (project is isolated) - run `renv::restore()` @@ -58,4 +59,4 @@ Learn `renv` and discuss Docker (concept). ## Homework -- Prep for showcase session +- Prep for reproducibility colloquium diff --git a/lessons/10-get-credit/slides.qmd b/lessons/10-get-credit/slides.qmd index 5d1a06d..b6a13c8 100644 --- a/lessons/10-get-credit/slides.qmd +++ b/lessons/10-get-credit/slides.qmd @@ -81,6 +81,14 @@ More detailed comparisons [here](https://www.agu.org/-/media/Files/Publications/ Demo archiving a repo with sandbox.zenodo.org and have everyone follow along with the repo they've been using for notes. ::: +## When to archive? + +No hard rules on this, but my preference: + +1. Just before submitting a manuscript: release v 0.1.0 +2. After responding to reviewers or re-submitting: increment "minor" version, e.g. v 0.2.0 +3. After acceptance: release v 1.0.0 + ## Reproducible computational environments Congrats! From b09559e1a8ec6a32427df45373fa2d54d4781030 Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Fri, 20 Sep 2024 12:15:36 -0700 Subject: [PATCH 3/8] update syllabus --- _freeze/index/execute-results/html.json | 4 ++-- index.qmd | 2 +- schedule.csv | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/_freeze/index/execute-results/html.json b/_freeze/index/execute-results/html.json index 5fb3bf9..f283b38 100644 --- a/_freeze/index/execute-results/html.json +++ b/_freeze/index/execute-results/html.json @@ -1,8 +1,8 @@ { - "hash": "bd5e899c4855a84d6ccaf8793ad30381", + "hash": "806e3893af8c23dccd9ccbf04251750e", "result": { "engine": "knitr", - "markdown": "---\ntitle: Reproducibility and Data Science in R\nsubtitle: \"Fall 2024\"\nformat: html\ncitation:\n title: Syllabus\n---\n\n\n\n\nWelcome to the syllabus for the CCT Data Science fall workshop series: **Reproducibility and Data Science in R.** If you didn't register for the course this year, sign up for our [mailing list](https://datascience.cct.arizona.edu/contact) to be notified when enrollment opens for next year's iteration and to be notified of our other monthly workshops.\n\n## Schedule\n\nWe'll meet on Tuesdays and Thursdays from 11am to 1pm via Zoom (link pinned in Slack channel)\n\n\n\n\n\n\n::: {.cell}\n::: {.cell-output-display}\n\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
LessonDateThemeTopicLinks
1Tue, 9/3Manage & OrganizeProject managment and documentation
\n
2Thu, 9/5Document & PublishLiterate programming with Quarto
\n
3Tue, 9/10Share & CollaborateFile systems and command line
\n
4Thu, 9/12Share & CollaborateVersion control with git
\n
5Tue, 9/17Share & CollaborateDeveloping code on GitHub
\n
6Thu, 9/19Share & CollaborateCollaborating with GitHub
\n
7Tue, 9/24Tidy & WrangleData manipulation & coding best practices
\n
8Thu, 9/26Repeat & ReproduceIntermediate R programming I
\n
9Tue, 10/1Repeat & ReproduceIntermediate R programming II—
10Thu, 10/3Document & PublishGetting credit for your hard work—
11Tue, 10/8ReviewDrop-in co-working—
12Thu, 10/10Reproducibility ColloquiumAn opportunity for you to show off what you've learned
\n
\n```\n\n:::\n:::\n\n\n\n\n## Code of Conduct\n\n> Our group's mission is to enable scientists.\n> This means treating people with respect and responding in a polite and helpful way.\n>\n> Our group is committed to ensuring a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.\n>\n> Examples of unacceptable behavior by members, collaborators, and contributors include: the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.\n\nRead our full [code of conduct](https://cct-datascience.github.io/group-procedures/code-of-conduct.html) and please report any violations or concerns to the course instructors or to Kristina Riemer ([kristinariemer\\@arizona.edu](mailto:kristinariemer@arizona.edu)).\n\n## Helpful Reads\n\nThis workshop series doesn't have anything like \"required reading\", but we think these books and websites are good companions.\n\nData analysis in R:\n\n- [R for Data Science (2e)](https://r4ds.hadley.nz/)\n- [Building reproducible analytical pipelines with R](https://raps-with-r.dev/) \n\nBest practices for reproducibility:\n\n- [Good enough practices in scientific computing](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510)\n- [Data organization in spreadsheets](https://doi.org/10.1080/00031305.2017.1375989)\n- [A beginner's guide to conducting reproducible research](https://doi.org/10.1002/bes2.1801)\n- [The Turing Way: Guide for Reproducible Research](https://the-turing-way.netlify.app/reproducible-research/reproducible-research)\n- [6 Steps Toward Reproducible Research](https://zenodo.org/records/12744715)\n\nVersion control:\n\n- [Excuse me, do you have a moment to talk about version control?](https://doi.org/10.7287/peerj.preprints.3159v2)\n- [Happy Git and GitHub for the useR](https://happygitwithr.com/)\n", + "markdown": "---\ntitle: Reproducibility and Data Science in R\nsubtitle: \"Fall 2024\"\nformat: html\ncitation:\n title: Syllabus\n---\n\n\n\n\nWelcome to the syllabus for the CCT Data Science fall workshop series: **Reproducibility and Data Science in R.** If you didn't register for the course this year, sign up for our [mailing list](https://datascience.cct.arizona.edu/contact) to be notified when enrollment opens for next year's iteration and to be notified of our other monthly workshops.\n\n## Schedule\n\nWe'll meet on Tuesdays and Thursdays from 11am to 1pm via Zoom (link pinned in Slack channel)\n\n\n\n\n\n\n::: {.cell}\n::: {.cell-output-display}\n\n```{=html}\n
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n\n\n\n\n \n \n \n
LessonDateThemeTopicLinks
1Tue, 9/3Manage & OrganizeProject managment and documentation
\n
2Thu, 9/5Document & PublishLiterate programming with Quarto
\n
3Tue, 9/10Share & CollaborateFile systems and command line
\n
4Thu, 9/12Share & CollaborateVersion control with git
\n
5Tue, 9/17Share & CollaborateDeveloping code on GitHub
\n
6Thu, 9/19Share & CollaborateCollaborating with GitHub
\n
7Tue, 9/24Tidy & WrangleData manipulation & coding best practices
\n
8Thu, 9/26Repeat & ReproduceIntermediate R programming I
\n
9Tue, 10/1Repeat & ReproduceIntermediate R programming II—
10Thu, 10/3Document & PublishGetting credit for your hard work
\n
11Tue, 10/8ReviewDrop-in co-working—
12Thu, 10/10Reproducibility ColloquiumAn opportunity for you to show off what you've learned
\n
\n```\n\n:::\n:::\n\n\n\n\n## Code of Conduct\n\n> Our group's mission is to enable scientists.\n> This means treating people with respect and responding in a polite and helpful way.\n>\n> Our group is committed to ensuring a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.\n>\n> Examples of unacceptable behavior by members, collaborators, and contributors include: the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.\n\nRead our full [code of conduct](https://cct-datascience.github.io/group-procedures/code-of-conduct.html) and please report any violations or concerns to the course instructors or to Kristina Riemer ([kristinariemer\\@arizona.edu](mailto:kristinariemer@arizona.edu)).\n\n## Helpful Reads\n\nThis workshop series doesn't have anything like \"required reading\", but we think these books and websites are good companions.\n\nData analysis in R:\n\n- [R for Data Science (2e)](https://r4ds.hadley.nz/)\n- [Building reproducible analytical pipelines with R](https://raps-with-r.dev/) \n\nBest practices for reproducibility:\n\n- [Good enough practices in scientific computing](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510)\n- [Data organization in spreadsheets](https://doi.org/10.1080/00031305.2017.1375989)\n- [A beginner's guide to conducting reproducible research](https://doi.org/10.1002/bes2.1801)\n- [The Turing Way: Guide for Reproducible Research](https://the-turing-way.netlify.app/reproducible-research/reproducible-research)\n- [6 Steps Toward Reproducible Research](https://zenodo.org/records/12744715)\n\nVersion control:\n\n- [Excuse me, do you have a moment to talk about version control?](https://doi.org/10.7287/peerj.preprints.3159v2)\n- [Happy Git and GitHub for the useR](https://happygitwithr.com/)\n", "supporting": [], "filters": [ "rmarkdown/pagebreak.lua" diff --git a/index.qmd b/index.qmd index 8b686dc..5d9a39d 100644 --- a/index.qmd +++ b/index.qmd @@ -12,7 +12,7 @@ Welcome to the syllabus for the CCT Data Science fall workshop series: **Reprodu We'll meet on Tuesdays and Thursdays from 11am to 1pm via Zoom (link pinned in Slack channel) - + ```{r} #| echo: false diff --git a/schedule.csv b/schedule.csv index bf16b9f..ace6f2f 100644 --- a/schedule.csv +++ b/schedule.csv @@ -8,6 +8,6 @@ Lesson,Date,Theme,Topic,Links,Notes 7,2024-09-24,Tidy & Wrangle,Data manipulation & coding best practices,[slides](lessons/7-data-manipulation/slides.html),data carpentry R ecology episodes 2 & 3 8,2024-09-26,Repeat & Reproduce,Intermediate R programming I,[slides](lessons/8-intermediate-r-1/slides.html),functions 9,2024-10-01,Repeat & Reproduce,Intermediate R programming II,,iteration (and anonymous functions) -10,2024-10-03,Document & Publish,Getting credit for your hard work,,"renv, LICENSE, CITATION.cff, Zenodo, GitHub releases" +10,2024-10-03,Document & Publish,Getting credit for your hard work,[slides](lessons/10-get-credit/slides.html),"renv, LICENSE, CITATION.cff, Zenodo, GitHub releases" 11,2024-10-08,Review,Drop-in co-working,, 12,2024-10-10,Reproducibility Colloquium,An opportunity for you to show off what you've learned,[guidelines](colloquium.html), From 14f284dade81ca6b2d34f080fabbcc85a2515ac4 Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Wed, 25 Sep 2024 09:42:06 -0700 Subject: [PATCH 4/8] adds github icon to navbar that links to source --- _freeze/site_libs/revealjs/dist/theme/quarto.css | 2 +- _quarto.yml | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/_freeze/site_libs/revealjs/dist/theme/quarto.css b/_freeze/site_libs/revealjs/dist/theme/quarto.css index e96ab76..c35eaa0 100644 --- a/_freeze/site_libs/revealjs/dist/theme/quarto.css +++ b/_freeze/site_libs/revealjs/dist/theme/quarto.css @@ -5,4 +5,4 @@ * we also add `bright-[color]-` synonyms for the `-[color]-intense` classes since * that seems to be what ansi_up emits * -*/.ansi-black-fg{color:#3e424d}.ansi-black-bg{background-color:#3e424d}.ansi-black-intense-black,.ansi-bright-black-fg{color:#282c36}.ansi-black-intense-black,.ansi-bright-black-bg{background-color:#282c36}.ansi-red-fg{color:#e75c58}.ansi-red-bg{background-color:#e75c58}.ansi-red-intense-red,.ansi-bright-red-fg{color:#b22b31}.ansi-red-intense-red,.ansi-bright-red-bg{background-color:#b22b31}.ansi-green-fg{color:#00a250}.ansi-green-bg{background-color:#00a250}.ansi-green-intense-green,.ansi-bright-green-fg{color:#007427}.ansi-green-intense-green,.ansi-bright-green-bg{background-color:#007427}.ansi-yellow-fg{color:#ddb62b}.ansi-yellow-bg{background-color:#ddb62b}.ansi-yellow-intense-yellow,.ansi-bright-yellow-fg{color:#b27d12}.ansi-yellow-intense-yellow,.ansi-bright-yellow-bg{background-color:#b27d12}.ansi-blue-fg{color:#208ffb}.ansi-blue-bg{background-color:#208ffb}.ansi-blue-intense-blue,.ansi-bright-blue-fg{color:#0065ca}.ansi-blue-intense-blue,.ansi-bright-blue-bg{background-color:#0065ca}.ansi-magenta-fg{color:#d160c4}.ansi-magenta-bg{background-color:#d160c4}.ansi-magenta-intense-magenta,.ansi-bright-magenta-fg{color:#a03196}.ansi-magenta-intense-magenta,.ansi-bright-magenta-bg{background-color:#a03196}.ansi-cyan-fg{color:#60c6c8}.ansi-cyan-bg{background-color:#60c6c8}.ansi-cyan-intense-cyan,.ansi-bright-cyan-fg{color:#258f8f}.ansi-cyan-intense-cyan,.ansi-bright-cyan-bg{background-color:#258f8f}.ansi-white-fg{color:#c5c1b4}.ansi-white-bg{background-color:#c5c1b4}.ansi-white-intense-white,.ansi-bright-white-fg{color:#a1a6b2}.ansi-white-intense-white,.ansi-bright-white-bg{background-color:#a1a6b2}.ansi-default-inverse-fg{color:#fff}.ansi-default-inverse-bg{background-color:#000}.ansi-bold{font-weight:bold}.ansi-underline{text-decoration:underline}:root{--quarto-body-bg: 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!important}blockquote::before{content:"“";font-size:75px;font-weight:bold;color:#aeaeae;position:absolute;left:10px;top:5px}blockquote::after{content:""}/*# sourceMappingURL=f95d2bded9c28492b788fe14c3e9f347.css.map */ diff --git a/_quarto.yml b/_quarto.yml index 92e7ac8..282fbe4 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -12,6 +12,10 @@ website: repo-actions: [edit, issue] site-url: https://cct-datascience.github.io/repro-data-sci/ navbar: + tools: + - icon: github + text: Source #shows on hover + href: https://github.com/cct-datascience/repro-data-sci left: - href: index.qmd text: Home From 32bc6d6d951d51f0c6244153a75e8931e8b1d4f5 Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Wed, 25 Sep 2024 10:38:31 -0700 Subject: [PATCH 5/8] add robots.txt --- _quarto.yml | 2 ++ robots.txt | 30 ++++++++++++++++++++++++++++++ 2 files changed, 32 insertions(+) create mode 100644 robots.txt diff --git a/_quarto.yml b/_quarto.yml index 282fbe4..72e1c3d 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -1,5 +1,7 @@ project: type: website + resources: + - "robots.txt" render: - "*.qmd" diff --git a/robots.txt b/robots.txt new file mode 100644 index 0000000..6c017a7 --- /dev/null +++ b/robots.txt @@ -0,0 +1,30 @@ +User-agent: CCBot +Disallow: / + +User-agent: ChatGPT-User +Disallow: / + +User-agent: GPTBot +Disallow: / + +User-agent: Google-Extended +Disallow: / + +User-agent: Omgilibot +Disallow: / + +User-agent: Omgili +Disallow: / + +User-agent: FacebookBot +Disallow: / + +User-agent: PerplexityBot +Disallow: / + +User-agent: anthropic-ai +Disallow: / +‍User-agent: Claude-Web +Disallow: / +User-agent: ClaudeBot +Disallow: / From bc126207f748a2c685c25ed6ee0f92ddaa8e57a0 Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Wed, 25 Sep 2024 10:49:47 -0700 Subject: [PATCH 6/8] update with comments --- robots.txt | 29 +++++++++++++++++++++++++---- 1 file changed, 25 insertions(+), 4 deletions(-) diff --git a/robots.txt b/robots.txt index 6c017a7..d7fc4b7 100644 --- a/robots.txt +++ b/robots.txt @@ -1,30 +1,51 @@ +# sources: +# https://www.cyberciti.biz/web-developer/block-openai-bard-bing-ai-crawler-bots-using-robots-txt-file/ +# https://neil-clarke.com/block-the-bots-that-feed-ai-models-by-scraping-your-website/ + +# Data from Common Crawl is used to train ChatGPT, Bard, etc. User-agent: CCBot Disallow: / +# Stops ChatGPT users from instructing ChatGPT to access our site User-agent: ChatGPT-User Disallow: / +# Don't add any content to the GPT model User-agent: GPTBot Disallow: / +# Blocks Bard and VertexAI. Does not impact search indexing. User-agent: Google-Extended Disallow: / +# webz.io. They sell data for training LLMs User-agent: Omgilibot Disallow: / User-agent: Omgili Disallow: / +# Specific to AI. Won't prevent previews from showing up correctly on Facebook posts User-agent: FacebookBot Disallow: / -User-agent: PerplexityBot -Disallow: / - +# Anthropic AI (Claude) User-agent: anthropic-ai Disallow: / -‍User-agent: Claude-Web + +User-agent: Claude-Web Disallow: / + User-agent: ClaudeBot Disallow: / + +# ByteDance's bot for gathering LLM training data +User-agent: Bytespider +Disallow: / + +User-agent: ImagesiftBot +Disallow: / + +# Takes content and re-writes it using genAI +User-agent: PerplexityBot +Disallow: / From 765446be67dc676729b17c50e4a68e4df97c8101 Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Mon, 30 Sep 2024 11:16:07 -0700 Subject: [PATCH 7/8] finish updating slides --- lessons/10-get-credit/slides.qmd | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/lessons/10-get-credit/slides.qmd b/lessons/10-get-credit/slides.qmd index b6a13c8..9b4e58d 100644 --- a/lessons/10-get-credit/slides.qmd +++ b/lessons/10-get-credit/slides.qmd @@ -43,7 +43,7 @@ Make it **easier** for people to cite your code ## CITATION.cff ::: incremental -- Citation File Format are plain text files written in YAML +- A `CITATION.cff` file contains citation information written in YAML - Adding a `CITATION.cff` file to your repo... @@ -51,19 +51,19 @@ Make it **easier** for people to cite your code - Helps code archive tools fill out metadata correctly when you archive your repo -- Create a CITATION.cff file with this [helper](https://citation-file-format.github.io/cff-initializer-javascript/#/) +- Learn more and create your own: - See example [here](https://github.com/cct-datascience/repro-data-sci/blob/main/CITATION.cff) ::: ## Options for archiving {.smaller} -| Service | Versioned DOIs? | Free? | GitHub integration? | Notes | +| Service | Versioned DOIs? | Free? | GitHub integration? | Notes | |---------------|---------------|---------------|---------------|---------------| -| Zenodo | Yes | Yes | Yes | Backed by CERN, built with code and data in mind | -| Dryad | Yes | No, but some publishers cover cost | No | Intended for data, not code. Partners with Zenodo | -| Figshare | Yes | Yes | Yes | Can't choose your license | -| UA ReDATA | Yes | Yes (for UA researchers) | No | University of Arizona Libraries | +| Zenodo | Yes | Yes | Yes | Backed by CERN, built with code and data in mind | +| Dryad | Yes | No, but some publishers cover cost | No | Intended for data, not code. Partners with Zenodo | +| Figshare | Yes | Yes | Yes | Can't choose your license | +| UA ReDATA | Yes | Yes (for UA researchers) | No | University of Arizona Libraries | ::: aside More detailed comparisons [here](https://www.agu.org/-/media/Files/Publications/Generalist-Data-Repository-Grid.pdf) @@ -71,7 +71,7 @@ More detailed comparisons [here](https://www.agu.org/-/media/Files/Publications/ ## Zenodo Archiving Demo -1. Log in to sandbox.zenodo.org using GitHub[^1] +1. Log in to [sandbox.zenodo.org](https://sandbox.zenodo.org) using GitHub[^1] 2. In drop-down menu with your username, select "GitHub" 3. Find your repo in the list and flip the switch next to it 4. Go to your repo on GitHub and make a release @@ -144,7 +144,7 @@ Point out `renv/.gitignore` — trust it about which files should go on GitHub. - Sometimes quite annoying to use (but it's getting better!) -## Reproducible Everything with Docker +## *More* Reproducibility with Docker Docker containers... @@ -158,7 +158,7 @@ Docker containers... - Can be downloaded and run from the command line ::: -## Making a Docker Container +## Making a Docker Container {visibility="hidden"} A **Dockerfile** holds instructions on what to install and what code to run. Actually creating a Docker container is beyond the scope of this workshop, but you can [learn how](https://www.r-bloggers.com/2019/02/running-your-r-script-in-docker/)! @@ -194,11 +194,13 @@ If you use these tools, provide: ## Resources -- [Reproducible computational environments with Docker](https://reproducibility.rocks/materials/day4/01-docker/) - - [`renv` website](https://rstudio.github.io/renv/articles/renv.html) -- [CFF INIT helper](https://citation-file-format.github.io/cff-initializer-javascript/#/) +- CITATION.cff [info](https://citation-file-format.github.io/) and [creator tool](https://citation-file-format.github.io/cff-initializer-javascript/#/) + +- [Zenodo-GitHub integration](https://zenodo.org/account/settings/github/) + +- [Reproducible computational environments with Docker](https://reproducibility.rocks/materials/day4/01-docker/) ## Next week From 2e7b2404e90c750088c60874ae25ab77d3d5d3da Mon Sep 17 00:00:00 2001 From: Eric Scott Date: Mon, 30 Sep 2024 11:18:36 -0700 Subject: [PATCH 8/8] update notes --- lessons/10-get-credit/notes.qmd | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/lessons/10-get-credit/notes.qmd b/lessons/10-get-credit/notes.qmd index 119bb5e..564ba92 100644 --- a/lessons/10-get-credit/notes.qmd +++ b/lessons/10-get-credit/notes.qmd @@ -8,7 +8,9 @@ bibliography: references.bib ## Objective -- Learn the wrap-up steps to publish/archive a research compendium with a DOI. +- Add a basic CITATION.cff file to your repo + +- Practice the wrap-up steps to publish/archive a research compendium with a DOI. - Understand concept of a reproducible computational environment. @@ -33,12 +35,12 @@ bibliography: references.bib - Show CITATION.cff files for this repo and maybe one for a research compendium - Show "cite this" button on GitHub - - Show CITATION.cff creation tool [CFFINIT](https://citation-file-format.github.io/cff-initializer-javascript/#/) + - Everyone use CITATION.cff creation tool [CFFINIT](https://citation-file-format.github.io/cff-initializer-javascript/#/) to create a *basic* CITATION.cff - *Maybe* mention `cffr::cff_validate()` - Archiving - - Demo archiving a repo with Zenodo using sandbox.zenodo.org + - Exercise: guide everyone through archiving a repo with Zenodo using sandbox.zenodo.org - Add DOI badge to readme - Update CITATION.cff with DOI