Merge pull request #91 from brown-ccv/eeps1430F23

Eeps1430 class for Fall 2023
brown-ccv · Sep 14, 2023 · ecd9b5e · ecd9b5e
2 parents bf159da + a214271
commit ecd9b5e
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Showing 4 changed files with 45 additions and 13 deletions.
diff --git a/.github/workflows/eeps1430-fall-tag.yml b/.github/workflows/eeps1430-fall-tag.yml
@@ -5,16 +5,16 @@ env:
   CLASS: eeps1430
   TARGET: base
   SQLITE: false
-  PYTHON_VERSION: "3.10"
+  PYTHON_VERSION: "3.9.17"
 
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3.5.3
 
       - name: Set Up GCloud
-        uses: google-github-actions/[email protected].0
+        uses: google-github-actions/[email protected].2
         with:
           project_id: ${{ secrets.GCP_PROJECT_ID_JH_DOCKER }}
           service_account_key: ${{ secrets.GCP_SA_KEY_JH_DOCKER }}
@@ -28,8 +28,8 @@ jobs:
       - name: Upload Julia Env Files to Google Storage Bucket
         if: env.TARGET == 'r_julia'
         run: |
-          gsutil cp -r requirements/classes/eeps1430/julia_env gs://jupyterhub-environment-files/fall-2022/eeps1430/past/${GITHUB_SHA}/julia
-          gsutil cp -r requirements/classes/eeps1430/julia_env gs://jupyterhub-environment-files/fall-2022/eeps1430/latest/julia
+          gsutil cp -r requirements/classes/eeps1430/julia_env gs://jupyterhub-environment-files/fall-2023/eeps1430/past/${GITHUB_SHA}/julia
+          gsutil cp -r requirements/classes/eeps1430/julia_env gs://jupyterhub-environment-files/fall-2023/eeps1430/latest/julia
 
       - name: Configure Docker
         run: gcloud auth configure-docker
@@ -40,13 +40,13 @@ jobs:
           docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/eeps1430:${GITHUB_REF##*/}
           docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/eeps1430:${GITHUB_SHA}
           docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/eeps1430:latest
-          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/eeps1430:fall-2022
+          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/eeps1430:fall-2023
           docker push gcr.io/jupyterhub-docker-images/eeps1430:latest
-          docker push gcr.io/jupyterhub-docker-images/eeps1430:fall-2022
+          docker push gcr.io/jupyterhub-docker-images/eeps1430:fall-2023
           docker push gcr.io/jupyterhub-docker-images/eeps1430:${GITHUB_REF##*/}
           docker push gcr.io/jupyterhub-docker-images/eeps1430:${GITHUB_SHA}
 
       - name: Upload Conda Env Files to Google Storage Bucket
         run: |
-          gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2022/eeps1430/past/${GITHUB_SHA}/conda
-          gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2022/eeps1430/latest/conda
+          gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2023/eeps1430/past/${GITHUB_SHA}/conda
+          gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2023/eeps1430/latest/conda
diff --git a/.github/workflows/eeps1430.yml b/.github/workflows/eeps1430.yml
@@ -13,16 +13,16 @@ env:
   CLASS: eeps1430
   TARGET: base
   SQLITE: false
-  PYTHON_VERSION: "3.10"
+  PYTHON_VERSION: "3.9.17"
 
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3.5.3
 
       - name: Set Up GCloud
-        uses: google-github-actions/[email protected].0
+        uses: google-github-actions/[email protected].2
         with:
           project_id: ${{ secrets.GCP_PROJECT_ID_JH_DOCKER }}
           service_account_key: ${{ secrets.GCP_SA_KEY_JH_DOCKER }}

diff --git a/requirements/classes/eeps1430/packages.R b/requirements/classes/eeps1430/packages.R
@@ -0,0 +1,12 @@
+# Use this script to install packages via CRAN, for example: 
+
+# NOTE: Code below shows how you install R packages from CRAN and Bioconductor. For CRAN packages, you can use 
+# the standard install.packages() function; for Bioconductor packages, however, you 
+# must first install BiocManager and then use that for installs. 
+
+# install.packages("BiocManager", dependencies=TRUE, repos='http://cran.rstudio.com/')
+# install.packages(c("ggplot2", "pheatmap", "RColorBrewer", "PoiClaClu",
+#                    "patchwork", "tidyr", "GGally"), dependencies=TRUE, 
+#                  repos='http://cran.rstudio.com/')
+# BiocManager::install(c("airway", "DESeq2", "vsn", "biomaRt",
+#                        "AnnotationHub", "SummarizedExperiment"))
diff --git a/requirements/classes/eeps1430/requirements.txt b/requirements/classes/eeps1430/requirements.txt
@@ -1,5 +1,4 @@
 # add class-specific packages here:
-# for eeps1430
 netCDF4
 metpy
 cartopy
@@ -31,6 +30,27 @@ xlrd
 bottleneck
 pytables
 
+# these are the base r packages in the r-notebook image ( YOU PROBABLY WANT THESE IF YOUR TARGET IN DOCKER IS r_lang OR r_julia )
+r-base=4.2.*
+r-caret=6.*
+r-crayon=1.*
+r-devtools=2.*
+r-forecast=8.*
+r-hexbin=1.*
+r-htmltools=0.*
+r-htmlwidgets=1.*
+r-irkernel=1.*
+r-nycflights13=1.*
+r-randomforest=4.*
+r-rcurl=1.98*
+r-rmarkdown=2.*
+r-rodbc=1.*
+r-rsqlite=2.*
+r-shiny=1.*
+r-tidyverse
+unixodbc=2.*
+r-tidymodels=1.*
+
 # required for environment and plugins ( DO NOT REMOVE THESE!!! )
 ipython 
 ipykernel