Merge pull request #89 from brown-ccv/php2560_fall

PHP2560

.github/workflows/php2560-fall-tag.yml

@@ -3,18 +3,18 @@ on: [workflow_dispatch]
 
 env:
   CLASS: php2560
-  TARGET: r_lang
+  TARGET: r_julia
   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: ${{ secrets.GCP_SA_KEY_JH_DOCKER }}
@@ -28,8 +28,8 @@ jobs:
       - name: Upload Julia Env Files to Google Storage Bucket
         if: env.TARGET == 'r_julia'
         run: |
-          gsutil cp -r requirements/classes/php2560/julia_env gs://jupyterhub-environment-files/fall-2022/php2560/past/${GITHUB_SHA}/julia
-          gsutil cp -r requirements/classes/php2560/julia_env gs://jupyterhub-environment-files/fall-2022/php2560/latest/julia
+          gsutil cp -r requirements/classes/php2560/julia_env gs://jupyterhub-environment-files/fall-2023/php2560/past/${GITHUB_SHA}/julia
+          gsutil cp -r requirements/classes/php2560/julia_env gs://jupyterhub-environment-files/fall-2023/php2560/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/php2560:${GITHUB_REF##*/}
           docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/php2560:${GITHUB_SHA}
           docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/php2560:latest
-          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/php2560:fall-2022
+          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/php2560:fall-2023
           docker push gcr.io/jupyterhub-docker-images/php2560:latest
-          docker push gcr.io/jupyterhub-docker-images/php2560:fall-2022
+          docker push gcr.io/jupyterhub-docker-images/php2560:fall-2023
           docker push gcr.io/jupyterhub-docker-images/php2560:${GITHUB_REF##*/}
           docker push gcr.io/jupyterhub-docker-images/php2560:${GITHUB_SHA}
 
       - name: Upload Conda Env Files to Google Storage Bucket
         run: |
-          gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2022/php2560/past/${GITHUB_SHA}/conda
-          gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2022/php2560/latest/conda
+          gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2023/php2560/past/${GITHUB_SHA}/conda
+          gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2023/php2560/latest/conda

.github/workflows/php2560.yml

@@ -7,21 +7,22 @@ on:
       - 'docker-compose.yml'
       - 'scripts/**'
       - '.github/workflows/php2560.yml'
+  workflow_dispatch:
 
 env:
   CLASS: php2560
-  TARGET: r_lang
+  TARGET: r_julia
   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 }}
@@ -34,9 +35,9 @@ jobs:
 
       - name: Configure Docker
         run: gcloud auth configure-docker
-      - uses: satackey/[email protected]
+#      - uses: satackey/[email protected]
         # Ignore the failure of a step and avoid terminating the job.
-        continue-on-error: true
+#        continue-on-error: true
       - name: Build and Push JH Image
         run: |
           COMPOSE_DOCKER_CLI_BUILD=1 DOCKER_BUILDKIT=1 docker-compose up jh_image

requirements/classes/php2560/condarc

@@ -12,4 +12,4 @@ channels:
 show_channel_urls: True
 
 # For more information about this file see:
-# https://conda.io/docs/user-guide/configuration/use-condarc.html
+# https://conda.io/docs/user-guide/configuration/use-condarc.html

requirements/classes/php2560/packages.R

@@ -4,11 +4,9 @@
 # the standard install.packages() function; for Bioconductor packages, however, you 
 # must first install BiocManager and then use that for installs. 
 
-install.packages('fivethirtyeightdata', 
-                  dependencies = TRUE,
-                  repos = 'https://fivethirtyeightdata.github.io/drat/', 
-                  type = 'source')
-
-install.packages(c("docstring"), 
-                 dependencies = TRUE, 
-                 repos = 'http://cran.rstudio.com/')
+# 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"))

requirements/classes/php2560/requirements.txt

@@ -1,11 +1,11 @@
 # add class-specific packages here:
+r-gt
+r-gtsummary
 r-gridextra
 r-ggally
-r-knitr
-r-irdisplay
+r-patchwork
 
 # these are the scipy base packages ( YOU PROBABLY DON'T WANT TO REMOVE THESE )
-numpy
 dask 
 pandas
 numexpr
@@ -15,34 +15,42 @@ seaborn
 scikit-learn
 scikit-image
 sympy
+cython
+patsy
 statsmodels
+cloudpickle
+dill
+numba
 bokeh
+sqlalchemy
 hdf5
 vincent
+beautifulsoup4
+protobuf
+xlrd
+bottleneck
 pytables
-cython
 
 # 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
-r-caret
-r-crayon
-r-devtools
-r-forecast
-r-hexbin
-r-htmltools
-r-htmlwidgets
-r-nycflights13
-r-randomforest
-r-rcurl
-r-rmarkdown
-r-rodbc
-r-irkernel
-r-rsqlite
-r-shiny
+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
-r-tidymodels
-
+unixodbc=2.*
+r-tidymodels=1.*
 
 # required for environment and plugins ( DO NOT REMOVE THESE!!! )
 ipython