From caba56e799c44e079a451eab9b9982527271c8f8 Mon Sep 17 00:00:00 2001 From: Christy Melucci <43284496+christymelucci@users.noreply.github.com> Date: Tue, 1 Nov 2022 10:17:09 -0400 Subject: [PATCH 1/9] Move Duane Mengo from Core Members to Past Members --- content/people/index.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/content/people/index.md b/content/people/index.md index c209bc623..cab7503ef 100644 --- a/content/people/index.md +++ b/content/people/index.md @@ -516,7 +516,8 @@ people: image: duane-mengo.jpg affiliation: CMU/MLD team: - - core + - past + note: Core member, April-September 2022 - key: lmorinishi firstName: Leanna lastName: Morinishi From d9c6e95100113eebdcf1f51e9945e698731a1eb3 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 1 Nov 2022 21:01:49 +0000 Subject: [PATCH 2/9] chore(deps-dev): bump hugo-bin from 0.92.3 to 0.93.0 Bumps [hugo-bin](https://github.com/fenneclab/hugo-bin) from 0.92.3 to 0.93.0. - [Release notes](https://github.com/fenneclab/hugo-bin/releases) - [Commits](https://github.com/fenneclab/hugo-bin/compare/v0.92.3...v0.93.0) --- updated-dependencies: - dependency-name: hugo-bin dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- package-lock.json | 6 +++--- package.json | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/package-lock.json b/package-lock.json index bd61f1f1e..d5dfae410 100644 --- a/package-lock.json +++ b/package-lock.json @@ -822,9 +822,9 @@ "dev": true }, "hugo-bin": { - "version": "0.92.3", - "resolved": "https://registry.npmjs.org/hugo-bin/-/hugo-bin-0.92.3.tgz", - "integrity": "sha512-gM121hh7C5ZXRNITQdk/rPWeZ7eh0PqQAVjebQ7uA5eu/Xbk8YH6bsq8A11T3po+RmzCkeh178eJkXiRDRScag==", + "version": "0.93.0", + "resolved": "https://registry.npmjs.org/hugo-bin/-/hugo-bin-0.93.0.tgz", + "integrity": "sha512-tuuTvjyjZGMZlx80eKubX/GJkQkibr4AXzSPaRcDIBpr0FoiT2oURNgeY6Zm5axkgm07DuACNQmFw85KdcvBHw==", "dev": true, "requires": { "bin-wrapper": "^4.1.0", diff --git a/package.json b/package.json index 178e244e6..28c89ca03 100644 --- a/package.json +++ b/package.json @@ -12,7 +12,7 @@ "www-epivis": "https://github.com/cmu-delphi/www-epivis/releases/download/v2.0.3/www-epivis-2.0.3.tgz" }, "devDependencies": { - "hugo-bin": "^0.92.3", + "hugo-bin": "^0.93.0", "husky": "^8.0.1", "lint-staged": "^13.0.3", "prettier": "^2.7.1", From 3cc0193aa6c40309c77342c143a052d441f681d0 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 1 Nov 2022 21:02:09 +0000 Subject: [PATCH 3/9] chore(deps): bump katex from 0.16.2 to 0.16.3 Bumps [katex](https://github.com/KaTeX/KaTeX) from 0.16.2 to 0.16.3. - [Release notes](https://github.com/KaTeX/KaTeX/releases) - [Changelog](https://github.com/KaTeX/KaTeX/blob/main/CHANGELOG.md) - [Commits](https://github.com/KaTeX/KaTeX/compare/v0.16.2...v0.16.3) --- updated-dependencies: - dependency-name: katex dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- package-lock.json | 6 +++--- package.json | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/package-lock.json b/package-lock.json index bd61f1f1e..96f8c91a3 100644 --- a/package-lock.json +++ b/package-lock.json @@ -981,9 +981,9 @@ "dev": true }, "katex": { - "version": "0.16.2", - "resolved": "https://registry.npmjs.org/katex/-/katex-0.16.2.tgz", - "integrity": "sha512-70DJdQAyh9EMsthw3AaQlDyFf54X7nWEUIa5W+rq8XOpEk//w5Th7/8SqFqpvi/KZ2t6MHUj4f9wLmztBmAYQA==", + "version": "0.16.3", + "resolved": "https://registry.npmjs.org/katex/-/katex-0.16.3.tgz", + "integrity": "sha512-3EykQddareoRmbtNiNEDgl3IGjryyrp2eg/25fHDEnlHymIDi33bptkMv6K4EOC2LZCybLW/ZkEo6Le+EM9pmA==", "requires": { "commander": "^8.0.0" } diff --git a/package.json b/package.json index 178e244e6..f87873067 100644 --- a/package.json +++ b/package.json @@ -5,7 +5,7 @@ "dependencies": { "@fortawesome/fontawesome-free": "^6.2.0", "highlight.js": "^11.6.0", - "katex": "^0.16.2", + "katex": "^0.16.3", "uikit": "^3.15.10", "www-covidcast": "https://github.com/cmu-delphi/www-covidcast/releases/download/v3.2.3/www-covidcast-3.2.3.tgz", "www-covidcast-classic": "https://github.com/cmu-delphi/www-covidcast-classic/releases/download/v2.6.3/www-covidcast-classic-2.6.3.tgz", From f307987bb4b39bbcda795699a81eed4e6592a4aa Mon Sep 17 00:00:00 2001 From: Katie Mazaitis Date: Wed, 5 Oct 2022 14:34:57 -0400 Subject: [PATCH 4/9] Workaround for weird miniconda environment - Switch to Mambaforge - Switch to caching the environment, not the packages --- .github/workflows/blog.yaml | 50 +++++++++++++++++++++---------------- environment.yml | 1 + 2 files changed, 30 insertions(+), 21 deletions(-) diff --git a/.github/workflows/blog.yaml b/.github/workflows/blog.yaml index 0bdb031bb..351d4bcbb 100644 --- a/.github/workflows/blog.yaml +++ b/.github/workflows/blog.yaml @@ -7,39 +7,50 @@ on: - "environment.yml" - "dependencies.R" - ".github/workflows/blog.yaml" + workflow_dispatch: jobs: blog: runs-on: ubuntu-latest + defaults: + run: + shell: bash -l {0} + env: + RETICULATE_PYTHON: /usr/share/miniconda3/envs/www-main/bin/python steps: - uses: actions/checkout@v3 with: # submodules: true # Fetch Hugo themes (true OR recursive) fetch-depth: 3 - - name: Cache Conda - uses: actions/cache@v3.0.2 - with: - path: ~/conda_pkgs_dir - key: ${{ runner.os }}-conda6-${{ hashFiles('environment.yml') }} - restore-keys: | - ${{ runner.os }}-conda6- - uses: conda-incubator/setup-miniconda@v2 with: python-version: 3.9 - mamba-version: "*" - channels: conda-forge,defaults - channel-priority: true activate-environment: www-main - environment-file: environment.yml - auto-activate-base: false + miniforge-variant: Mambaforge + miniforge-version: latest + use-mamba: true use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! - # - name: Conda info - # shell: bash -l {0} - # run: | - # conda info - # conda list + - name: Get Date + id: get-date + run: echo "name=today::$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT + shell: bash + - name: Cache Conda env + uses: actions/cache@v3 + with: + path: ${{ env.CONDA }}/envs + key: conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ hashFiles('environment.yml') }}-${{ env.CACHE_NUMBER }} + env: + # Increase this value to reset cache if etc/example-environment.yml has not changed + CACHE_NUMBER: 0 + id: cache + - name: Update environment + run: mamba env update -n www-main -f environment.yml + if: steps.cache.outputs.cache-hit != 'true' + - name: Conda info + run: | + conda info + conda list - name: Install R dependencies - shell: bash -l {0} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} run: | @@ -54,10 +65,8 @@ jobs: ${{ runner.os }}-blogdown2-${{ hashFiles('environment.yml') }}- ${{ runner.os }}-blogdown2- - name: Build site - shell: bash -l {0} run: | npm run build:blog - - uses: actions/upload-artifact@v3 with: name: blog @@ -79,7 +88,6 @@ jobs: run: npm run lint - name: Build run: npm run build - - uses: actions/upload-artifact@v3 with: name: website diff --git a/environment.yml b/environment.yml index b4b839fd3..8c3ca478a 100644 --- a/environment.yml +++ b/environment.yml @@ -50,6 +50,7 @@ dependencies: - r-vroom - r-urltools - r-base64url + - r-readr - pandoc - fiona - geopandas From 1f78fcca4c93c46c3f8cd0331a4a166d4fae0f39 Mon Sep 17 00:00:00 2001 From: Katie Mazaitis Date: Wed, 2 Nov 2022 16:41:30 -0400 Subject: [PATCH 5/9] Need newer version of readr --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 8c3ca478a..226152e8e 100644 --- a/environment.yml +++ b/environment.yml @@ -50,7 +50,7 @@ dependencies: - r-vroom - r-urltools - r-base64url - - r-readr + - r-readr >=2 - pandoc - fiona - geopandas From a956621a54748cac742ec271da6519c97cdfaa7c Mon Sep 17 00:00:00 2001 From: Kathryn M Mazaitis Date: Thu, 3 Nov 2022 12:51:48 -0400 Subject: [PATCH 6/9] Resolved several build errors locally --- content/blog/2021-01-22-holiday-surveys.Rmd | 2 +- dependencies.R | 6 +++--- environment.yml | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/content/blog/2021-01-22-holiday-surveys.Rmd b/content/blog/2021-01-22-holiday-surveys.Rmd index 23ed46348..87952ef1e 100644 --- a/content/blog/2021-01-22-holiday-surveys.Rmd +++ b/content/blog/2021-01-22-holiday-surveys.Rmd @@ -108,7 +108,7 @@ regionmap <- travel %>% filter(geo_value %in% str_to_lower(statelist)) %>% mutate(value = plyr::mapvalues(geo_value, str_to_lower(statelist), regions), value = as.integer(factor(value))) - +attr(regionmap, "metadata") <- list(geo_type = "state") grid_label <- textGrob("Data from Delphi COVIDcast, delphi.cmu.edu", hjust = 1, x = 1, gp = gpar(fontsize = 9)) diff --git a/dependencies.R b/dependencies.R index 9407717a7..f388cc8dc 100644 --- a/dependencies.R +++ b/dependencies.R @@ -8,6 +8,6 @@ install.packages("covidcast", repo="http://cran.rstudio.com/") # upgrade = 'never', # subdir = "R-packages/covidcast") -devtools::install_github("reichlab/zoltr", upgrade = 'never', quick = TRUE) -devtools::install_github("reichlab/covidData", upgrade = 'never', quick = TRUE) -devtools::install_github("reichlab/covidHubUtils", upgrade = 'never', quick = TRUE) +devtools::install_github("reichlab/zoltr", upgrade = 'never') +devtools::install_github("reichlab/covidData", upgrade = 'never') +devtools::install_github("reichlab/covidHubUtils", upgrade = 'never') diff --git a/environment.yml b/environment.yml index 226152e8e..7654a9816 100644 --- a/environment.yml +++ b/environment.yml @@ -6,7 +6,7 @@ dependencies: - gdal - python=3.9.1 - pip - - r-base=3.6.3 + - r-base - glib - mscorefonts - r-cairo From c1d1f1f15c925bf48ce972e2f578fb4633ec0d2d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 3 Nov 2022 19:51:38 +0000 Subject: [PATCH 7/9] chore(deps): bump uikit from 3.15.10 to 3.15.11 Bumps [uikit](https://github.com/uikit/uikit) from 3.15.10 to 3.15.11. - [Release notes](https://github.com/uikit/uikit/releases) - [Changelog](https://github.com/uikit/uikit/blob/develop/CHANGELOG.md) - [Commits](https://github.com/uikit/uikit/compare/v3.15.10...v3.15.11) --- updated-dependencies: - dependency-name: uikit dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- package-lock.json | 6 +++--- package.json | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/package-lock.json b/package-lock.json index 96f8c91a3..ce31f8760 100644 --- a/package-lock.json +++ b/package-lock.json @@ -2068,9 +2068,9 @@ "dev": true }, "uikit": { - "version": "3.15.10", - "resolved": "https://registry.npmjs.org/uikit/-/uikit-3.15.10.tgz", - "integrity": "sha512-vAM9net9CIYkXXo2xVS2drs7garbJrgnMzO87QgilMgf8kQswOUW4BvUztFzw8CJVUF+3TKdHx6+hnHmjNEcTQ==" + "version": "3.15.11", + "resolved": "https://registry.npmjs.org/uikit/-/uikit-3.15.11.tgz", + "integrity": "sha512-3qJJsfSHiq1iFelumosXCvVT1HvcCZArRCewtOcyRz8m4KbcliymwKn+J5MfgshN9yBkozQvwNv8kVgJbvW7OA==" }, "ulid": { "version": "2.3.0", diff --git a/package.json b/package.json index f87873067..5af98fea9 100644 --- a/package.json +++ b/package.json @@ -6,7 +6,7 @@ "@fortawesome/fontawesome-free": "^6.2.0", "highlight.js": "^11.6.0", "katex": "^0.16.3", - "uikit": "^3.15.10", + "uikit": "^3.15.11", "www-covidcast": "https://github.com/cmu-delphi/www-covidcast/releases/download/v3.2.3/www-covidcast-3.2.3.tgz", "www-covidcast-classic": "https://github.com/cmu-delphi/www-covidcast-classic/releases/download/v2.6.3/www-covidcast-classic-2.6.3.tgz", "www-epivis": "https://github.com/cmu-delphi/www-epivis/releases/download/v2.0.3/www-epivis-2.0.3.tgz" From de34835fba07f70f7c1dbb9f1f0b0555249cbf29 Mon Sep 17 00:00:00 2001 From: Alex Reinhart Date: Mon, 7 Nov 2022 13:14:22 -0500 Subject: [PATCH 8/9] New citation Yet another survey citation. --- content/covid19/ctis.md | 1 + 1 file changed, 1 insertion(+) diff --git a/content/covid19/ctis.md b/content/covid19/ctis.md index 3f3fc5d73..7aaf5aa41 100644 --- a/content/covid19/ctis.md +++ b/content/covid19/ctis.md @@ -59,6 +59,7 @@ Our primary description of the survey and its results over the first year of ope Other research publications using the survey data include: +- C. Lupton-Smith, E. Badillo Goicoechea, M. Collins, J. Lessler, M. K. Grabowski & E. A. Stuart (2022). [Consistency between Household and County Measures of Onsite Schooling during the COVID-19 Pandemic](https://doi.org/10.1080/19345747.2022.2131660). *Journal of Research on Educational Effectiveness*. - Nguyen, Q.C., Yardi, I., Gutierrez, F.X.M. et al. (2022). [Leveraging 13 million responses to the U.S. COVID-19 Trends and Impact Survey to examine vaccine hesitancy, vaccination, and mask wearing, January 2021-February 2022](https://doi.org/10.1186/s12889-022-14286-3). *BMC Public Health* 22, 1911. - J. G. Lu (2022). [Two large-scale global studies on COVID-19 vaccine hesitancy over time: Culture, uncertainty avoidance, and vaccine side-effect concerns](https://doi.org/10.1037/pspa0000320). *Journal of Personality and Social Psychology*. - J. M. Cox-Ganser, P. K. Henneberger, D. N. Weissman, G. Guthrie, and C. P. Groth (2022). [COVID-19 test positivity by occupation using the Delphi US COVID-19 Trends and Impact Survey, September–November 2020](https://doi.org/10.1002/ajim.23410). *American Journal of Industrial Medicine* 65 (9), 721-730. From 6fbb47e04db3362912cb323a1862d09dfd68bb17 Mon Sep 17 00:00:00 2001 From: krivard Date: Tue, 8 Nov 2022 20:52:40 +0000 Subject: [PATCH 9/9] chore: release v3.0.26 --- package-lock.json | 2 +- package.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/package-lock.json b/package-lock.json index 845f23a9d..6c82858e5 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "www-main", - "version": "3.0.25", + "version": "3.0.26", "lockfileVersion": 1, "requires": true, "dependencies": { diff --git a/package.json b/package.json index 78c9c999b..e832b023f 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "www-main", - "version": "3.0.25", + "version": "3.0.26", "private": true, "dependencies": { "@fortawesome/fontawesome-free": "^6.2.0",