Merge pull request #95 from brown-ccv/ccv_bootcamp_2024

updating the ccv_bootcamp workflow and requirements files for summer …

.github/workflows/ccv_bootcamp-summer-tag.yml

@@ -4,17 +4,17 @@ on: [workflow_dispatch]
 env:
   CLASS: ccv_bootcamp
   TARGET: r_julia
-  SQLITE: true
-  PYTHON_VERSION: 3.7
+  SQLITE: false
+  PYTHON_VERSION: "3.9.17"
 
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-        #https://github.blog/changelog/2022-09-22-github-actions-all-actions-will-begin-running-on-node16-instead-of-node12/
+      - uses: actions/checkout@v4
+
       - 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: ${{ secrets.GCP_SA_KEY_JH_DOCKER }}
@@ -28,8 +28,8 @@ jobs:
       - name: Upload Julia Env Files to Google Storage Bucket
         if: env.TARGET == 'r_julia'
         run: |
-          gsutil cp -r requirements/classes/ccv_bootcamp/julia_env gs://jupyterhub-environment-files/summer-2023/ccv_bootcamp/past/${GITHUB_SHA}/julia
-          gsutil cp -r requirements/classes/ccv_bootcamp/julia_env gs://jupyterhub-environment-files/summer-2023/ccv_bootcamp/latest/julia
+          gsutil cp -r requirements/classes/ccv_bootcamp/julia_env gs://jupyterhub-environment-files/summer-2024/ccv_bootcamp/past/${GITHUB_SHA}/julia
+          gsutil cp -r requirements/classes/ccv_bootcamp/julia_env gs://jupyterhub-environment-files/summer-2024/ccv_bootcamp/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/ccv_bootcamp:${GITHUB_REF##*/}
           docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/ccv_bootcamp:${GITHUB_SHA}
           docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/ccv_bootcamp:latest
-          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/ccv_bootcamp:summer-2023
+          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/ccv_bootcamp:summer-2024
           docker push gcr.io/jupyterhub-docker-images/ccv_bootcamp:latest
-          docker push gcr.io/jupyterhub-docker-images/ccv_bootcamp:summer-2023
+          docker push gcr.io/jupyterhub-docker-images/ccv_bootcamp:summer-2024
           docker push gcr.io/jupyterhub-docker-images/ccv_bootcamp:${GITHUB_REF##*/}
           docker push gcr.io/jupyterhub-docker-images/ccv_bootcamp:${GITHUB_SHA}
 
       - name: Upload Conda Env Files to Google Storage Bucket
         run: |
-          gsutil cp -r requirements/out gs://jupyterhub-environment-files/summer-2023/ccv_bootcamp/past/${GITHUB_SHA}/conda
-          gsutil cp -r requirements/out gs://jupyterhub-environment-files/summer-2023/ccv_bootcamp/latest/conda
+          gsutil cp -r requirements/out gs://jupyterhub-environment-files/summer-2024/ccv_bootcamp/past/${GITHUB_SHA}/conda
+          gsutil cp -r requirements/out gs://jupyterhub-environment-files/summer-2024/ccv_bootcamp/latest/conda

.github/workflows/ccv_bootcamp.yml

@@ -12,16 +12,17 @@ on:
 env:
   CLASS: ccv_bootcamp
   TARGET: r_julia
-  SQLITE: true
-  PYTHON_VERSION: 3.7
+  SQLITE: false
+  PYTHON_VERSION: "3.9.17"
 
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+
       - 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]
-#        # Ignore the failure of a step and avoid terminating the job.
-#        continue-on-error: true
+      - uses: satackey/[email protected]
+        # Ignore the failure of a step and avoid terminating the job.
+        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/ccv_bootcamp/packages.R

@@ -1,90 +1,35 @@
+# 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"))
+
 install.packages("BiocManager", dependencies=TRUE, repos='http://cran.rstudio.com/')
 install.packages(c("tidyverse"), dependencies=TRUE, repos='http://cran.rstudio.com/')
-install.packages(c(
-"ape",
-"arrow",
-"deldir",
-"devtools",
-"doMC",
-"doRNG",
-"DT",
-"enrichR",
-"ggrepel",
-"hdf5r",
-"kableExtra",
-"knitr",
-"maps",
-"Matrix",
-"metap",
-"mixtools",
-"NMF",
-"openxlsx",
-"parallel",
-"patchwork",
-"pdftools",
-"pheatmap",
-"plotly",
-"PoiClaClu",
-"purrr",
-"R.utils",
-"R2HTML",
-"RColorBrewer",
-"RcppArmadillo",
-"remotes",
-"Rfast2",
-"rgeos",
-"rsvd",
-"Rtsne",
-"sctransform",
-"Seurat",
-"spatstat.explore",
-"spatstat.geom",
-"stringr",
-"VGAM",
-"viridis",
-"zoo"),
- repos = "http://cran.rstudio.com/",
- dependencies = TRUE)
-BiocManager::install(c(
-"airpart",
-"airway",
-"AnnotationHub",
-"AUCell",
-"batchelor",
-"Biobase",
-"BiocGenerics",
-"biomaRt",
-"BSgenome",
-"BSgenome.Hsapiens.UCSC.hg19",
-"clusterProfiler",
-"ComplexHeatmap",
-"DelayedArray",
-"DelayedMatrixStats",
-"DESeq2",
-"DOSE",
-"enrichplot",
-"ensembldb",
-"GENIE3",
-"GenomicFeatures",
-"GenomeInfoDb",
-"GenomicRanges",
-"glmGamPoi",
-"IRanges",
-"JASPAR2018",
-"limma",
-"MAST",
-"monocle",
-"multtest",
-"RcisTarget",
-"RnaSeqSampleSize",
-"rtracklayer",
-"S4Vectors",
-"scater",
-"SingleCellExperiment",
-"SummarizedExperiment",
-"TFBSTools",
-"vsn",
-"WGCNA"))
+install.packages(c( "ape", "arrow", "deldir", "devtools", "doMC", 
+                    "doRNG", "DT", "enrichR", "ggrepel", "hdf5r",
+                    "kableExtra", "knitr", "maps", "Matrix", "metap", 
+                    "mixtools", "NMF", "openxlsx", "parallel", "patchwork", 
+                    "pdftools", "pheatmap", "plotly", "PoiClaClu", "purrr", 
+                    "R.utils", "R2HTML", "RColorBrewer", "RcppArmadillo", "remotes", 
+                    "Rfast2", "rgeos", "rsvd", "Rtsne", "sctransform", "Seurat", 
+                    "spatstat.explore", "spatstat.geom", "stringr", "VGAM", "viridis",
+                    "zoo"),  repos = "http://cran.rstudio.com/",  dependencies = TRUE)
+BiocManager::install(c("airpart", "airway", "AnnotationHub", "AUCell", "batchelor", 
+                       "Biobase", "BiocGenerics", "biomaRt", "BSgenome", "BSgenome.Hsapiens.UCSC.hg19",
+                       "clusterProfiler", "ComplexHeatmap", "DelayedArray", "DelayedMatrixStats", "DESeq2", 
+                       "DOSE", "enrichplot", "ensembldb", "GENIE3", "GenomicFeatures", 
+                       "GenomeInfoDb", "GenomicRanges", "glmGamPoi", "IRanges", 
+                       "JASPAR2022", "limma", "MAST", "monocle", "multtest", 
+                       "RcisTarget", "RnaSeqSampleSize", "rtracklayer", "S4Vectors", "scater", 
+                       "SingleCellExperiment", "SummarizedExperiment", "TFBSTools", "vsn", "WGCNA"))
 remotes::install_github("mojaveazure/seurat-disk")
 remotes::install_github("satijalab/seurat-data")
-remotes::install_github("brendankelly/micropower")
+remotes::install_github("brendankelly/micropower")

requirements/classes/ccv_bootcamp/requirements.jl

@@ -1,5 +1,5 @@
 const julia_packages = [
-                   "IJulia", # DO NOT REMOVE
+                    "IJulia", # DO NOT REMOVE
                    # add class specific classes here:
                    "CSV",
                    "DataFrames",
@@ -35,4 +35,4 @@ const julia_packages = [
                    "MLDatasets",
                    "StatsPlots",
                    "Tidier"
-                    ]
+                    ]

requirements/classes/ccv_bootcamp/requirements.pip.txt

@@ -1,2 +1,2 @@
-# add class-specific packages here:
+# add class-specific classes here:
 

requirements/classes/ccv_bootcamp/requirements.txt

@@ -32,20 +32,20 @@ r-caret=6.*
 r-crayon=1.*
 r-devtools=2.*
 r-forecast=8.*
-r-hexbin=1.28*
-r-htmltools
-r-htmlwidgets=1.5*
+r-hexbin=1.*
+r-htmltools=0.*
+r-htmlwidgets=1.*
 r-irkernel=1.*
-r-nycflights13=1.0*
+r-nycflights13=1.*
 r-randomforest=4.*
 r-rcurl=1.98*
 r-rmarkdown=2.*
-r-rodbc=1.3*
-r-rsqlite=2.2*
+r-rodbc=1.*
+r-rsqlite=2.*
 r-shiny=1.*
-r-tidyverse=1.3*
-unixodbc=2.3.*
-r-tidymodels
+r-tidyverse
+unixodbc=2.*
+r-tidymodels=1.*
 
 # required for environment and plugins ( DO NOT REMOVE THESE!!! )
 ipython