Merge pull request #90 from brown-ccv/neur1630_fall

Neur1630

.github/workflows/neur1630-fall-tag.yml

@@ -0,0 +1,52 @@
+name: tag-image-neur1630
+on: [workflow_dispatch]
+
+env:
+  CLASS: neur1630
+  TARGET: base
+  SQLITE: false
+  PYTHON_VERSION: "3.9.17"
+
+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: ${{ secrets.GCP_SA_KEY_JH_DOCKER }}
+          export_default_credentials: true
+
+      - name: Create Julia Environment Files
+        if: env.TARGET == 'r_julia'
+        run: |
+          sudo --preserve-env=CLASS docker-compose up julia_build
+
+      - name: Upload Julia Env Files to Google Storage Bucket
+        if: env.TARGET == 'r_julia'
+        run: |
+          gsutil cp -r requirements/classes/neur1630/julia_env gs://jupyterhub-environment-files/fall-2023/neur1630/past/${GITHUB_SHA}/julia
+          gsutil cp -r requirements/classes/neur1630/julia_env gs://jupyterhub-environment-files/fall-2023/neur1630/latest/julia
+
+      - name: Configure Docker
+        run: gcloud auth configure-docker
+
+      - name: Build and Push JH Image
+        run: |
+          COMPOSE_DOCKER_CLI_BUILD=1 DOCKER_BUILDKIT=1 docker-compose up jh_image
+          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/neur1630:${GITHUB_REF##*/}
+          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/neur1630:${GITHUB_SHA}
+          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/neur1630:latest
+          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/neur1630:fall-2023
+          docker push gcr.io/jupyterhub-docker-images/neur1630:latest
+          docker push gcr.io/jupyterhub-docker-images/neur1630:fall-2023
+          docker push gcr.io/jupyterhub-docker-images/neur1630:${GITHUB_REF##*/}
+          docker push gcr.io/jupyterhub-docker-images/neur1630:${GITHUB_SHA}
+
+      - name: Upload Conda Env Files to Google Storage Bucket
+        run: |
+          gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2023/neur1630/past/${GITHUB_SHA}/conda
+          gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2023/neur1630/latest/conda

.github/workflows/neur1630.yml

@@ -0,0 +1,47 @@
+name: build-image-neur1630
+on: 
+  push:
+      paths:
+      - 'requirements/classes/neur1630/**'
+      - 'Dockerfile'
+      - 'docker-compose.yml'
+      - 'scripts/**'
+      - '.github/workflows/neur1630.yml'
+  workflow_dispatch:
+
+env:
+  CLASS: neur1630
+  TARGET: base
+  SQLITE: false
+  PYTHON_VERSION: "3.9.17"
+
+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: ${{ secrets.GCP_SA_KEY_JH_DOCKER }}
+          export_default_credentials: true
+
+      - name: Create Julia Environment Files
+        if: env.TARGET == 'r_julia'
+        run: |
+          sudo --preserve-env=CLASS docker-compose up julia_build
+
+      - name: Configure Docker
+        run: gcloud auth configure-docker
+#      - uses: satackey/[email protected]
+#        # Ignore the failure of a step and avoid terminating the job.
+#        continue-on-error: true
+      - name: Build and Push JH Image
+        run: |
+          COMPOSE_DOCKER_CLI_BUILD=1 DOCKER_BUILDKIT=1 docker-compose up jh_image
+          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/neur1630:${GITHUB_REF##*/}
+          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/neur1630:latest
+          docker push gcr.io/jupyterhub-docker-images/neur1630:latest
+          docker push gcr.io/jupyterhub-docker-images/neur1630:${GITHUB_REF##*/}

Dockerfile

@@ -143,6 +143,7 @@ RUN jupyter kernelspec remove -f python3
 
 COPY --chown=${NB_UID}:${NB_GID} requirements/classes/${CLASS} /home/$NB_USER/tmp/
 COPY --chown=${NB_UID}:${NB_GID} requirements/classes/${CLASS}/condarc /home/$NB_USER/.mambarc
+COPY --chown=${NB_UID}:${NB_GID} requirements/classes/${CLASS}/condarc /home/$NB_USER/.condarc
 
 RUN mamba create --quiet --yes -p ${CONDA_DIR}/envs/${CLASS} python=${PYTHON_VERSION} && \
     mamba install -y --name ${CLASS} --file /home/$NB_USER/tmp/requirements.txt && \

requirements/classes/neur1630/condarc

@@ -0,0 +1,17 @@
+# 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:
+  - bioconda
+  - conda-forge
+#  - defaults
+
+# 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/neur1630/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"))

requirements/classes/neur1630/requirements.jl

@@ -0,0 +1,5 @@
+const julia_packages = [
+                    "IJulia", # DO NOT REMOVE
+                   # add class specific classes here:
+
+                    ]

requirements/classes/neur1630/requirements.pip.txt

@@ -0,0 +1,9 @@
+# add class-specific classes here:
+scanpy
+harmonypy
+rpy2
+nwbwidgets
+pynapple
+pybiomart
+pyranges
+gseapy

requirements/classes/neur1630/requirements.txt

@@ -0,0 +1,67 @@
+# add class-specific packages here:
+ipywidgets
+zarr
+requests
+aiohttp
+louvain
+anndata
+umap-learn
+loompy
+scrublet
+bioconductor-scran
+anndata2ri
+fastcluster
+tqdm
+pynwb
+dandi
+
+# 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 )
+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