requirements and action workflows for biol1435

.github/workflows/biol1435-spring-tag.yml

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+name: tag-image-biol1435
+on: [workflow_dispatch]
+
+env:
+  CLASS: biol1435
+  TARGET: r_julia
+  SQLITE: false
+  PYTHON_VERSION: "3.9"
+  PROJECT_ID: jupyterhub-docker-images
+  REGION: us-east1
+  GAR_LOCATION: us-east1-docker.pkg.dev/jupyterhub-docker-images/all-classes/biol1435
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+
+      - name: Set Up GCloud
+        uses: google-github-actions/[email protected]
+        with:
+          project_id: ${{ secrets.GCP_PROJECT_ID_JH_DOCKER }}
+          service_account_key: ${{ secrets.GCP_SA_KEY_JH_DOCKER }}
+          export_default_credentials: true
+
+      - name: Create Julia Environment Files
+        if: env.TARGET == 'r_julia'
+        run: |
+          sudo --preserve-env=CLASS docker compose up julia_build
+
+      - name: Upload Julia Env Files to Google Storage Bucket
+        if: env.TARGET == 'r_julia'
+        run: |
+          gsutil cp -r requirements/classes/biol1435/julia_env gs://jupyterhub-environment-files/spring-2025/biol1435/past/${GITHUB_SHA}/julia
+          gsutil cp -r requirements/classes/biol1435/julia_env gs://jupyterhub-environment-files/spring-2025/biol1435/latest/julia
+
+      - name: Configure Docker
+        run: gcloud auth configure-docker ${{ env.REGION }}-docker.pkg.dev --quiet
+      - name: Build JH Image
+        run: |
+          COMPOSE_DOCKER_CLI_BUILD=1 DOCKER_BUILDKIT=1 docker compose up jh_image
+          docker tag ${{ env.CLASS }}:latest ${{ env.GAR_LOCATION }}:latest
+          docker tag ${{ env.CLASS }}:latest ${{ env.GAR_LOCATION }}:${GITHUB_REF##*/}
+          docker tag ${{ env.CLASS }}:latest ${{ env.GAR_LOCATION }}:${GITHUB_SHA}
+          docker tag ${{ env.CLASS }}:latest ${{ env.GAR_LOCATION }}:spring-2025
+      - name: Push JH Image
+        run: |
+          docker push ${{ env.GAR_LOCATION }}:latest
+          docker push ${{ env.GAR_LOCATION }}:${GITHUB_REF##*/}
+          docker push ${{ env.GAR_LOCATION }}:${GITHUB_SHA}
+          docker push ${{ env.GAR_LOCATION }}:spring-2025
+
+      - name: Upload Conda Env Files to Google Storage Bucket
+        run: |
+          gsutil cp -r requirements/out gs://jupyterhub-environment-files/spring-2025/biol1435/past/${GITHUB_SHA}/conda
+          gsutil cp -r requirements/out gs://jupyterhub-environment-files/spring-2025/biol1435/latest/conda

.github/workflows/biol1435.yml

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+name: build-image-biol1435
+on: 
+  push:
+      paths:
+      - 'requirements/classes/biol1435/**'
+      - 'Dockerfile'
+      - 'docker-compose.yml'
+      - 'scripts/**'
+      - '.github/workflows/biol1435.yml'
+  workflow_dispatch:
+
+env:
+  CLASS: biol1435
+  TARGET: r_julia
+  SQLITE: false
+  PYTHON_VERSION: "3.9"
+  PROJECT_ID: jupyterhub-docker-images
+  REGION: us-east1
+  GAR_LOCATION: us-east1-docker.pkg.dev/jupyterhub-docker-images/all-classes/biol1435
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+
+      - name: Set Up GCloud
+        uses: google-github-actions/[email protected]
+        with:
+          project_id: ${{ secrets.GCP_PROJECT_ID_JH_DOCKER }}
+          service_account_key: ${{ secrets.GCP_SA_KEY_JH_DOCKER }}
+          export_default_credentials: true
+
+      - name: Create Julia Environment Files
+        if: env.TARGET == 'r_julia'
+        run: |
+          sudo --preserve-env=CLASS docker compose up julia_build
+
+      - name: Configure Docker
+        run: gcloud auth configure-docker ${{ env.REGION }}-docker.pkg.dev --quiet
+
+      - name: Build JH Image
+        run: |
+          COMPOSE_DOCKER_CLI_BUILD=1 DOCKER_BUILDKIT=1 docker compose up jh_image
+
+      - name: Tag JH Image
+        run: |
+          docker tag ${{ env.CLASS }}:latest ${{ env.GAR_LOCATION }}:${GITHUB_REF##*/}
+          docker tag ${{ env.CLASS }}:latest ${{ env.GAR_LOCATION }}:latest
+
+      - name: Push JH Image
+        run: |
+          docker push ${{ env.GAR_LOCATION }}:latest
+          docker push ${{ env.GAR_LOCATION }}:${GITHUB_REF##*/}

requirements/classes/biol1435/condarc

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+# channel locations. These override conda defaults, i.e., conda will
+# search *only* the channels listed here, in the order given.
+# Use "defaults" to automatically include all default channels.
+# Non-url channels will be interpreted as Anaconda.org usernames
+# (this can be changed by modifying the channel_alias key; see below).
+# The default is just 'defaults'.
+channels:
+  - conda-forge
+
+# Show channel URLs when displaying what is going to be downloaded
+# and in 'conda list'. The default is False.
+show_channel_urls: True
+
+# For more information about this file see:
+# https://conda.io/docs/user-guide/configuration/use-condarc.html

requirements/classes/biol1435/packages.R

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+# 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"))

requirements/classes/biol1435/requirements.jl

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+const julia_packages = [
+                    "IJulia", # DO NOT REMOVE
+                   # add class specific classes here:
+
+                    ]

requirements/classes/biol1435/requirements.pip.txt

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+# add class-specific classes here:
+ete3

requirements/classes/biol1435/requirements.txt

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+# add class-specific packages here:
+msprime
+tskit
+stdpopsim
+pyslim
+demes
+demesdraw
+sage
+
+# these are the scipy base packages ( YOU PROBABLY DON'T WANT TO REMOVE THESE )
+dask 
+pandas
+numexpr
+matplotlib
+scipy
+seaborn
+scikit-learn
+scikit-image
+sympy
+cython
+patsy
+statsmodels
+cloudpickle
+dill
+numba
+bokeh
+sqlalchemy
+hdf5
+vincent
+beautifulsoup4
+protobuf
+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 )
+# https://stat.ethz.ch/R-manual/R-devel/library/base/html/00Index.html
+r-base=4.2.*
+# https://github.com/topepo/caret/releases/tag/v6.0-93
+r-caret=6.*
+# https://cran.r-project.org/web/packages/crayon/index.html
+r-crayon=1.*
+# https://cran.r-project.org/web/packages/devtools/index.html
+r-devtools=2.*
+# https://cran.r-project.org/web/packages/forecast/index.html
+r-forecast=8.*
+# https://cran.r-project.org/web/packages/hexbin/index.html
+r-hexbin=1.*
+# https://cran.r-project.org/web/packages/htmltools/index.html
+r-htmltools=0.*
+# https://cran.r-project.org/web/packages/htmlwidgets/index.html
+r-htmlwidgets=1.*
+# https://github.com/IRkernel/IRkernel/releases/tag/1.3.2
+r-irkernel=1.*
+# https://cran.r-project.org/web/packages/nycflights13/index.html
+r-nycflights13=1.*
+# https://cran.r-project.org/web/packages/randomForest/index.html
+r-randomforest=4.*
+# https://cran.r-project.org/web/packages/RCurl/index.html
+r-rcurl=1.98*
+# https://cran.r-project.org/web/packages/rmarkdown/index.html
+r-rmarkdown=2.*
+# https://cran.r-project.org/web/packages/odbc/index.html
+r-rodbc=1.*
+# https://cran.r-project.org/web/packages/RSQLite/index.html
+r-rsqlite=2.*
+# https://cran.r-project.org/web/packages/shiny/index.html
+r-shiny=1.*
+# https://cran.r-project.org/web/packages/tidyverse/index.html
+r-tidyverse
+unixodbc=2.*
+# https://cran.r-project.org/web/packages/tidymodels/index.html
+r-tidymodels=1.*
+
+# required for environment and plugins ( DO NOT REMOVE THESE!!! )
+ipython 
+ipykernel