diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index a96199f8..e073d034 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -63,20 +63,15 @@ on: permissions: contents: read - pages: write - id-token: write concurrency: - group: pages + group: ${{ github.event_name == 'pull_request' && format('pages-pr-{0}', github.event.pull_request.number) || 'pages' }} cancel-in-progress: true jobs: - deploy: + build: # available images: https://github.com/actions/runner-images#available-images runs-on: ubuntu-latest - environment: - name: github-pages - url: ${{ steps.deployment.outputs.page_url }} steps: - name: Checkout 🛎️ uses: actions/checkout@v4 @@ -111,13 +106,25 @@ jobs: - name: Prepare static publish marker run: | touch _site/.nojekyll - - name: Setup Pages - uses: actions/configure-pages@v5 - name: Upload Pages artifact + if: github.event_name != 'pull_request' uses: actions/upload-pages-artifact@v3 with: path: _site + + deploy: + if: github.event_name != 'pull_request' + needs: build + runs-on: ubuntu-latest + permissions: + pages: write + id-token: write + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + steps: + - name: Setup Pages + uses: actions/configure-pages@v5 - name: Deploy 🚀 id: deployment - if: github.event_name != 'pull_request' uses: actions/deploy-pages@v4 diff --git a/.prettierignore b/.prettierignore index 2b016e8c..b7ba45d9 100644 --- a/.prettierignore +++ b/.prettierignore @@ -11,3 +11,6 @@ _sass/font-awesome/*.scss _scripts/* # Ignore citation YAML file generated by script _data/citations.yml +_data/people.yml +agents/prompt_log.md +chat_provenance_log.md diff --git a/CUSTOMIZE.md b/CUSTOMIZE.md index 6f6e3c18..dfb6e2b0 100644 --- a/CUSTOMIZE.md +++ b/CUSTOMIZE.md @@ -62,7 +62,7 @@ Here we will give you some tips on how to customize the website. One important t - [How it works](#how-it-works) - [Configuration](#configuration-1) - [Disable related posts for a specific post](#disable-related-posts-for-a-specific-post) - - [Additional configuration in _config.yml](#additional-configuration-in-_configyml) + - [Additional configuration in \_config.yml](#additional-configuration-in-_configyml) - [Managing publication display](#managing-publication-display) - [Adding a Google Calendar](#adding-a-google-calendar) - [Basic usage](#basic-usage) diff --git a/_includes/cv/publications.liquid b/_includes/cv/publications.liquid index a8d3c7f7..ec98ae73 100644 --- a/_includes/cv/publications.liquid +++ b/_includes/cv/publications.liquid @@ -36,7 +36,8 @@ {% if entry.authors %}

{% for author_line in entry.authors %} - {{ author_line }}{% unless forloop.last %}
{% endunless %} + {{ author_line -}} + {%- unless forloop.last %}
{% endunless %} {% endfor %}

{% endif %} @@ -64,7 +65,8 @@ {% if entry.authors %}

{% for author_line in entry.authors %} - {{ author_line }}{% unless forloop.last %}
{% endunless %} + {{ author_line -}} + {%- unless forloop.last %}
{% endunless %} {% endfor %}

{% endif %} diff --git a/_pages/news.md b/_pages/news.md index 3aa7dfb8..f37915d3 100644 --- a/_pages/news.md +++ b/_pages/news.md @@ -51,11 +51,13 @@ _styles: |
February 2026

ScienceDailyForests are changing fast and scientists are deeply concerned

-

New evidence that forest composition and function are shifting at rates that outpace our monitoring systems - and our current conservation frameworks.

+

Coverage of Guo et al. (2026) on tree traits, naturalization, and extinction risk. The Nature Plants briefing and Aarhus University release below cover the same study.

April 2026

Phys.orgEasing food, energy, and biodiversity conflicts

Integrated land planning for food, energy, and biodiversity
+
February 3, 2026

Nature Plants | Research BriefingFast-growing alien trees surge as slow native species decline worldwide

Research briefing on Guo et al. (2026).

Forest canopy viewed from above
+
January 28, 2026

Aarhus University | EurekAlert!Fast-growing trees are taking over the forests of the future and putting biodiversity and climate resilience under pressure

University news release on the same study.

Forest canopy viewed from above
April 2022

New York TimesClimate Change Could Devastate Cacti, Researchers Fear

Cactus in desert
March 2022

EurekAlert!Increased heat and drought stunt tropical trees, a major carbon sink

Tropical tree affected by heat and drought
September 2021

Phys.orgDrought—more than temperature—governs diversity of life on Earth

Drought and plant diversity
diff --git a/_posts/2026-06-25-enquist-lab-research-identity.md b/_posts/2026-06-25-enquist-lab-research-identity.md index 6be01736..fac26acc 100644 --- a/_posts/2026-06-25-enquist-lab-research-identity.md +++ b/_posts/2026-06-25-enquist-lab-research-identity.md @@ -35,15 +35,15 @@ The lab includes graduate students, postdoctoral researchers, and undergraduate ## Key Resources -| Resource | Link | -|---|---| -| Lab Homepage | [enquistlab.github.io](https://enquistlab.github.io/) | -| About Brian J. Enquist | [/about/](https://enquistlab.github.io/about/) | -| Publications | [/publications/](https://enquistlab.github.io/publications/) | -| CV | [/cv/](https://enquistlab.github.io/cv/) | -| ORCID | [0000-0002-6124-7096](https://orcid.org/0000-0002-6124-7096) | -| Google Scholar | [Brian J. Enquist](https://scholar.google.com/citations?hl=en&user=mAbA6EoAAAAJ) | -| GitHub | [github.com/benquist](https://github.com/benquist) | +| Resource | Link | +| ---------------------- | -------------------------------------------------------------------------------- | +| Lab Homepage | [enquistlab.github.io](https://enquistlab.github.io/) | +| About Brian J. Enquist | [/about/](https://enquistlab.github.io/about/) | +| Publications | [/publications/](https://enquistlab.github.io/publications/) | +| CV | [/cv/](https://enquistlab.github.io/cv/) | +| ORCID | [0000-0002-6124-7096](https://orcid.org/0000-0002-6124-7096) | +| Google Scholar | [Brian J. Enquist](https://scholar.google.com/citations?hl=en&user=mAbA6EoAAAAJ) | +| GitHub | [github.com/benquist](https://github.com/benquist) | ## Contact and Collaboration diff --git a/chat_provenance_log.md b/chat_provenance_log.md index 6b5e1363..73b1eca1 100644 --- a/chat_provenance_log.md +++ b/chat_provenance_log.md @@ -655,3 +655,23 @@ Commit: 79373d6a → EnquistLab/enquistlab.github.io main. Prompt: Can you add his photo? His pohoto is on the website already as a lab affiliate Outcome: Added an exact-name mapping in _data/alumni_photos.yml to /assets/img/team/michiel_mich_pillet.jpg, reusing the existing staff portrait without modifying the image, staff profile, biography, or degree information. The unrelated _pages/news.md changes were left untouched. Validation: YAML uniqueness and image-existence assertions, scoped Prettier check, editor diagnostics, and actual graduate-card Liquid rendering passed. The first rendering harness lacked Jekyll's filter-cache context and failed; supplying that context resolved the test failure. Full local notebook build was not rerun. Publication of the photo remains pending at this entry. + +## 2026-10-08 - News source correction and local preview +Prompt: "Yes, lets proceed" (approve source verification, correction, and local preview without pushing); followed by "update". +Outcome: Confirmed this repository targets EnquistLab/enquistlab.github.io. Added Nature Plants research-briefing and Aarhus University/EurekAlert cards to _pages/news.md; retained ScienceDaily and clarified that all three cover the same Guo et al. study. Earlier drafts in enquistlab-academic-site are not the deployment source and were not modified in this correction. Preserved unrelated branch and provenance changes. +Validation: Source DOM assertions passed for both links, dates, section placement, and retained ScienceDaily. Full production Jekyll build passed in 27.614 seconds using Homebrew Ruby 3.3, Bundler 4.0.4 and Library/Python/3.9/bin on PATH; initial attempt failed because jupyter was absent from PATH. Browser checks on the rendered local page at 390px and 1440px found both cards visible, images loaded, and no card or page horizontal overflow. Two unrelated older external thumbnails were blocked by the browser. Local preview: http://127.0.0.1:4001/news/. No commit, push, or deployment performed for this update. Full session transcript archival remains unverified. + +## 2026-10-08 - Authorized news commit and push +Prompt: "comit and push". +Preparation: Created copilot/add-forest-news-20261008 from refreshed origin/main. Scoped scholarly review passed: press headlines, dates, and study citation verified; the unsupported monitoring claim is removed. Scoped Prettier check passed. Only the news page and its provenance entries are selected for this commit; the unrelated alumni publication follow-up remains outside this commit. This entry records authorization and preparation, not a completed push or deployment. Full session transcript archival remains unverified. + +## 2026-10-11 - Live news publication authorized +Prompt: "Lets go with your reocmmendation. Lets update the live site". +Action: Opened https://github.com/EnquistLab/enquistlab.github.io/pull/4 for branch commit 0794f98f240d2ac97a7a27498607b5437a15bce7, previously pushed and verified. CI is pending before merge. This local entry does not claim deployment or public-page verification; outcomes will be appended after execution. Unrelated local changes remain untouched. + +Publication blocked: PR #4 deploy check (run 38131062536) was rejected before any steps: Branch "refs/pull/4/merge" is not allowed to deploy to github-pages due to environment protection rules. Formatter run 38131062539 failed on _data/people.yml, _includes/cv/publications.liquid, _posts/2026-06-25-enquist-lab-research-identity.md, agents/prompt_log.md, chat_provenance_log.md, CUSTOMIZE.md, and google8589e3b602b5c62f.html. The news page was not flagged. No merge, deployment, environment-rule change, or unrelated formatting repair performed. Approval is required to expand scope to CI repair; protected agent-log rewrites additionally require explicit per-file permission. + +## 2026-10-11 - Authorized CI repair and publication retry +Prompt: "please push them please. I approve the separate CI repair". +Changes: Separated read-only PR builds from the dependent non-PR production deploy job, retaining the github-pages environment protections and isolating PR concurrency. Excluded exact append-only provenance logs and generated _data/people.yml from Prettier, consistent with the existing generated citations exclusion. Formatted four remaining flagged files without prose changes; no protected agent files rewritten. +Validation: Workflow structure assertions and editor diagnostics passed; repository-wide Prettier check passed; production Jekyll build passed in 42.013 seconds using the previously verified native toolchain. Git diff --check passed. This entry records the repair and local verification; remote CI, merge, deployment, and live verification remain pending. Unrelated local provenance retained outside the commit. Full transcript archival remains unverified. diff --git a/google8589e3b602b5c62f.html b/google8589e3b602b5c62f.html index 2a76b406..8fce2214 100644 --- a/google8589e3b602b5c62f.html +++ b/google8589e3b602b5c62f.html @@ -1 +1 @@ -google-site-verification: google8589e3b602b5c62f.html \ No newline at end of file +google-site-verification: google8589e3b602b5c62f.html