From a320d554a0477112aeffa7a77ebaf73b2c2baa0b Mon Sep 17 00:00:00 2001 From: kathsherratt Date: Tue, 2 Jun 2026 21:53:56 +0100 Subject: [PATCH 1/4] update readme --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index abbaf0ce..a8054662 100755 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ The source for the [web page](https://cmmid.github.io/) advertising assorted [CM # Adding NEW posts -To add a new post to the website, add a new markdown or html file to `/topics/covid19/_posts` using the template [/topics/YYYY-MM-DD-post-template.md](https://github.com/cmmid/cmmid.github.io/blob/master/topics/YYYY-MM-DD-post-template.md).. +To add a new post to the website, add a new markdown or html file to `/topics/{topic}/_posts` using the template [/topics/YYYY-MM-DD-post-template.md](https://github.com/cmmid/cmmid.github.io/blob/master/topics/YYYY-MM-DD-post-template.md). Front-matter variables are optional, but the following are available: @@ -42,12 +42,12 @@ authors: If you want to use mathjax, tabs, or other objects regularly used in Rmarkdown html files: 1. set 'output: html_fragment' in your rmarkdown file 2. set rmarkdown_html_fragment: true in the front-matter of your post - # Figures and attachments -Copy your figures and attachments into the `/topics/covid19/figures` and `/topics/covid19/reports` directories accordingly. Make sure they have a unique name (chances are someone else has already generated a `figure1.png` file), or create under `/topics/covid19/figures` specifically for your figures. The template contains some example markup demonstrating this. - +Copy your figures and attachments into the `/topics/{topic}/figures` and `/topics/{topic}/reports` directories accordingly. +Make sure they have a unique name (chances are someone else has already generated a `figure1.png` file), or create under `/topics/{topic}/figures` specifically for your figures. +The template contains some example markup demonstrating this. # Adding TRANSLATED posts From dcaa6f1edfd54331f08602b9181cb079cbbfb42d Mon Sep 17 00:00:00 2001 From: kathsherratt Date: Tue, 2 Jun 2026 21:54:24 +0100 Subject: [PATCH 2/4] add a CLAUDE.md --- CLAUDE.md | 72 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 CLAUDE.md diff --git a/CLAUDE.md b/CLAUDE.md new file mode 100644 index 00000000..f910785f --- /dev/null +++ b/CLAUDE.md @@ -0,0 +1,72 @@ +# CMMID site — dev guide + +Jekyll site, deploys to https://cmmid.github.io via GitHub Pages on push to `master`. + +Use the README for detailed instructions to add new posts. + +## Local dev + +```bash +make setup # first time: bundle install +make run # bundle exec jekyll serve -w → http://localhost:4000 +``` + +Requires Ruby + Bundler. + +## Adding a post + +1. Create `topics/{topic}/_posts/YYYY-MM-DD-{slug}.md` +2. Copy front-matter from `topics/YYYY-MM-DD-post-template.md` +3. Place figures in `topics/{topic}/figures/`, reports in `topics/{topic}/reports/` (use unique filenames) + +Minimal front-matter: + +```yaml +--- +title: "Post title" +description: One-line summary +status: paper-under-peer-review +update: YYYY-MM-DD +tags: [transmission-dynamics] +authors: + - id: author_id +--- +``` + +**Status options:** `paper-under-peer-review`, `paper-accepted-at-journal`, `paper-published-at-journal`, `real-time-report`, `report`, `comment-opinion-online`, `comment-opinion-journal` + +**Tags:** `transmission-dynamics`, `severity`, `lmic-considerations`, `control-measures`, `mixing-patterns`, `healthcare-settings`, `comments-opinions`, `forecasts-and-projections` + +Author IDs come from `_data/authors.yml`. Special group IDs: `ncov-group` (CMMID COVID-19 working group, 48 members), `chil-group`. + +For R Markdown HTML fragment output: set `rmarkdown_html_fragment: true` in front-matter. + +## Adding a Shiny app + +Copy `_shinyapp/template.md` to a new file in `_shinyapp/`, edit `shinyurl` and `title` only. + +## Adding a tag + +Two steps required — both must be present before tag appears: +1. Create topic page in `topics/{topic}/` with `tag_filter` matching the new tag +2. Add entry to `_data/translations.yml` with `id` matching the tag and `en-gb` value + +## PR workflow + +No PR template or CI. Branch from `master`, open PR against `master`. + +Key maintainers/reviewers (use GitHub handles or tag by email): +- Adam Kucharski — adam.kucharski@lshtm.ac.uk +- Sebastian Funk — sebastian.funk@lshtm.ac.uk +- Rosalind Eggo — r.eggo@lshtm.ac.uk +- John Edmunds — john.edmunds@lshtm.ac.uk + +## Key files + +| Path | Purpose | +|------|---------| +| `_config.yml` | Site config, plugins, permalink structure | +| `_data/authors.yml` | All author IDs and metadata | +| `_data/translations.yml` | Tag display names and i18n strings | +| `topics/YYYY-MM-DD-post-template.md` | Post template | +| `Makefile` | `make run` / `make setup` | From c4783f31e28d297cff242b924f3a8c1aeec6793e Mon Sep 17 00:00:00 2001 From: kathsherratt Date: Tue, 2 Jun 2026 21:57:35 +0100 Subject: [PATCH 3/4] minor clarifications --- CLAUDE.md | 6 +++--- README.md | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CLAUDE.md b/CLAUDE.md index f910785f..84cdbbd7 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -16,14 +16,14 @@ Requires Ruby + Bundler. ## Adding a post 1. Create `topics/{topic}/_posts/YYYY-MM-DD-{slug}.md` -2. Copy front-matter from `topics/YYYY-MM-DD-post-template.md` +2. Copy front-matter from `/topics/YYYY-MM-DD-post-template.md` 3. Place figures in `topics/{topic}/figures/`, reports in `topics/{topic}/reports/` (use unique filenames) -Minimal front-matter: +Front-matter example: ```yaml --- -title: "Post title" +title: Post title description: One-line summary status: paper-under-peer-review update: YYYY-MM-DD diff --git a/README.md b/README.md index a8054662..00d9cb62 100755 --- a/README.md +++ b/README.md @@ -46,7 +46,7 @@ If you want to use mathjax, tabs, or other objects regularly used in Rmarkdown h # Figures and attachments Copy your figures and attachments into the `/topics/{topic}/figures` and `/topics/{topic}/reports` directories accordingly. -Make sure they have a unique name (chances are someone else has already generated a `figure1.png` file), or create under `/topics/{topic}/figures` specifically for your figures. +Make sure they have a unique name (chances are someone else has already generated a `figure1.png` file), or create a subdirectory under `/topics/{topic}/figures` specifically for your figures. The template contains some example markup demonstrating this. # Adding TRANSLATED posts From 24991da09ec65143a5a8362c7a57974f359d68c3 Mon Sep 17 00:00:00 2001 From: kathsherratt Date: Tue, 2 Jun 2026 22:15:15 +0100 Subject: [PATCH 4/4] drop unnecessary PR info --- CLAUDE.md | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/CLAUDE.md b/CLAUDE.md index 84cdbbd7..7b7016d3 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -51,16 +51,6 @@ Two steps required — both must be present before tag appears: 1. Create topic page in `topics/{topic}/` with `tag_filter` matching the new tag 2. Add entry to `_data/translations.yml` with `id` matching the tag and `en-gb` value -## PR workflow - -No PR template or CI. Branch from `master`, open PR against `master`. - -Key maintainers/reviewers (use GitHub handles or tag by email): -- Adam Kucharski — adam.kucharski@lshtm.ac.uk -- Sebastian Funk — sebastian.funk@lshtm.ac.uk -- Rosalind Eggo — r.eggo@lshtm.ac.uk -- John Edmunds — john.edmunds@lshtm.ac.uk - ## Key files | Path | Purpose |