From 518183c70cb51169ee50523ce7da4b11f9b3f72c Mon Sep 17 00:00:00 2001
From: Anna Murphy <anna_murphy1@brown.edu>
Date: Mon, 5 Aug 2024 14:43:21 -0400
Subject: [PATCH 1/4] Add class NEUR1630.

Requirements copied from 2023 class as per the ticket information
---
 .github/workflows/neur1630-fall-tag.yml       | 56 +++++++++++++++
 .github/workflows/neur1630.yml                | 54 ++++++++++++++
 requirements/classes/neur1630/condarc         | 15 ++++
 requirements/classes/neur1630/packages.R      | 12 ++++
 requirements/classes/neur1630/requirements.jl |  5 ++
 .../classes/neur1630/requirements.pip.txt     |  2 +
 .../classes/neur1630/requirements.txt         | 70 +++++++++++++++++++
 7 files changed, 214 insertions(+)
 create mode 100644 .github/workflows/neur1630-fall-tag.yml
 create mode 100644 .github/workflows/neur1630.yml
 create mode 100644 requirements/classes/neur1630/condarc
 create mode 100644 requirements/classes/neur1630/packages.R
 create mode 100644 requirements/classes/neur1630/requirements.jl
 create mode 100644 requirements/classes/neur1630/requirements.pip.txt
 create mode 100644 requirements/classes/neur1630/requirements.txt

diff --git a/.github/workflows/neur1630-fall-tag.yml b/.github/workflows/neur1630-fall-tag.yml
new file mode 100644
index 00000000..636031c4
--- /dev/null
+++ b/.github/workflows/neur1630-fall-tag.yml
@@ -0,0 +1,56 @@
+name: tag-image-neur1630
+on: [workflow_dispatch]
+
+env:
+  CLASS: neur1630
+  TARGET: base
+  SQLITE: false
+  PYTHON_VERSION: "3.9.17"
+  PROJECT_ID: jupyterhub-docker-images
+  REGION: us-east1
+  GAR_LOCATION: us-east1-docker.pkg.dev/jupyterhub-docker-images/all-classes/neur1630
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3.5.3
+
+      - name: Set Up GCloud
+        uses: google-github-actions/setup-gcloud@v0.6.2
+        with:
+          project_id: ${{ secrets.GCP_PROJECT_ID_JH_DOCKER }}
+          service_account_key: ${{ secrets.GCP_SA_KEY_JH_DOCKER }}
+          export_default_credentials: true
+
+      - name: Create Julia Environment Files
+        if: env.TARGET == 'r_julia'
+        run: |
+          sudo --preserve-env=CLASS docker compose up julia_build
+
+      - name: Upload Julia Env Files to Google Storage Bucket
+        if: env.TARGET == 'r_julia'
+        run: |
+          gsutil cp -r requirements/classes/neur1630/julia_env gs://jupyterhub-environment-files/fall-2024/neur1630/past/${GITHUB_SHA}/julia
+          gsutil cp -r requirements/classes/neur1630/julia_env gs://jupyterhub-environment-files/fall-2024/neur1630/latest/julia
+
+      - name: Configure Docker
+        run: gcloud auth configure-docker
+      - 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 }}:fall-2024
+      - 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 ${{ env.GAR_LOCATION }}:fall-2024
+
+      - name: Upload Conda Env Files to Google Storage Bucket
+        run: |
+          gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2024/neur1630/past/${GITHUB_SHA}/conda
+          gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2024/neur1630/latest/conda
\ No newline at end of file
diff --git a/.github/workflows/neur1630.yml b/.github/workflows/neur1630.yml
new file mode 100644
index 00000000..84c90615
--- /dev/null
+++ b/.github/workflows/neur1630.yml
@@ -0,0 +1,54 @@
+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"
+  PROJECT_ID: jupyterhub-docker-images
+  REGION: us-east1
+  GAR_LOCATION: us-east1-docker.pkg.dev/jupyterhub-docker-images/all-classes/neur1630
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3.5.3
+
+      - name: Set Up GCloud
+        uses: google-github-actions/setup-gcloud@v0.6.2
+        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
+
+      - 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##*/}
\ No newline at end of file
diff --git a/requirements/classes/neur1630/condarc b/requirements/classes/neur1630/condarc
new file mode 100644
index 00000000..d2a82925
--- /dev/null
+++ b/requirements/classes/neur1630/condarc
@@ -0,0 +1,15 @@
+# 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
\ No newline at end of file
diff --git a/requirements/classes/neur1630/packages.R b/requirements/classes/neur1630/packages.R
new file mode 100644
index 00000000..e1dced38
--- /dev/null
+++ b/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"))
diff --git a/requirements/classes/neur1630/requirements.jl b/requirements/classes/neur1630/requirements.jl
new file mode 100644
index 00000000..87635a43
--- /dev/null
+++ b/requirements/classes/neur1630/requirements.jl
@@ -0,0 +1,5 @@
+const julia_packages = [
+                    "IJulia", # DO NOT REMOVE
+                   # add class specific classes here:
+
+                    ]
\ No newline at end of file
diff --git a/requirements/classes/neur1630/requirements.pip.txt b/requirements/classes/neur1630/requirements.pip.txt
new file mode 100644
index 00000000..43719b70
--- /dev/null
+++ b/requirements/classes/neur1630/requirements.pip.txt
@@ -0,0 +1,2 @@
+# add class-specific classes here:
+
diff --git a/requirements/classes/neur1630/requirements.txt b/requirements/classes/neur1630/requirements.txt
new file mode 100644
index 00000000..7901ac0e
--- /dev/null
+++ b/requirements/classes/neur1630/requirements.txt
@@ -0,0 +1,70 @@
+# add class-specific packages here:
+
+# 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

From 3b81de78141f2e5638e5351f2e335a528d340f3a Mon Sep 17 00:00:00 2001
From: Anna Murphy <anna_murphy1@brown.edu>
Date: Mon, 5 Aug 2024 14:43:38 -0400
Subject: [PATCH 2/4] Add requirements

---
 .../classes/neur1630/requirements.pip.txt        |  8 ++++++++
 requirements/classes/neur1630/requirements.txt   | 16 ++++++++++++++++
 2 files changed, 24 insertions(+)

diff --git a/requirements/classes/neur1630/requirements.pip.txt b/requirements/classes/neur1630/requirements.pip.txt
index 43719b70..3d4fcb08 100644
--- a/requirements/classes/neur1630/requirements.pip.txt
+++ b/requirements/classes/neur1630/requirements.pip.txt
@@ -1,2 +1,10 @@
 # add class-specific classes here:
 
+scanpy
+harmonypy
+rpy2
+nwbwidgets
+pynapple
+pybiomart
+pyranges
+gseapy
diff --git a/requirements/classes/neur1630/requirements.txt b/requirements/classes/neur1630/requirements.txt
index 7901ac0e..a9e46cc6 100644
--- a/requirements/classes/neur1630/requirements.txt
+++ b/requirements/classes/neur1630/requirements.txt
@@ -1,5 +1,21 @@
 # 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

From c018ec9299c6f5ead051ca7c23344680abca9115 Mon Sep 17 00:00:00 2001
From: Anna Murphy <anna_murphy1@brown.edu>
Date: Mon, 12 Aug 2024 09:58:51 -0400
Subject: [PATCH 3/4] add bioconda to condarc

---
 requirements/classes/neur1630/condarc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements/classes/neur1630/condarc b/requirements/classes/neur1630/condarc
index d2a82925..30ac9f6c 100644
--- a/requirements/classes/neur1630/condarc
+++ b/requirements/classes/neur1630/condarc
@@ -6,6 +6,7 @@
 # The default is just 'defaults'.
 channels:
   - conda-forge
+  - bioconda
 
 # Show channel URLs when displaying what is going to be downloaded
 # and in 'conda list'. The default is False.

From 2eb3587b89be97e5b306499bd2a5833d695ee1cb Mon Sep 17 00:00:00 2001
From: Anna Murphy <anna_murphy1@brown.edu>
Date: Mon, 12 Aug 2024 11:35:07 -0400
Subject: [PATCH 4/4] fix gcloud auth

---
 .github/workflows/neur1630-fall-tag.yml | 2 +-
 .github/workflows/neur1630.yml          | 2 +-
 dev/templates/class_tag.yml             | 2 +-
 dev/templates/class_workflow.yml        | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/neur1630-fall-tag.yml b/.github/workflows/neur1630-fall-tag.yml
index 636031c4..63e548b6 100644
--- a/.github/workflows/neur1630-fall-tag.yml
+++ b/.github/workflows/neur1630-fall-tag.yml
@@ -35,7 +35,7 @@ jobs:
           gsutil cp -r requirements/classes/neur1630/julia_env gs://jupyterhub-environment-files/fall-2024/neur1630/latest/julia
 
       - name: Configure Docker
-        run: gcloud auth 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
diff --git a/.github/workflows/neur1630.yml b/.github/workflows/neur1630.yml
index 84c90615..a1458b2b 100644
--- a/.github/workflows/neur1630.yml
+++ b/.github/workflows/neur1630.yml
@@ -37,7 +37,7 @@ jobs:
           sudo --preserve-env=CLASS docker compose up julia_build
 
       - name: Configure Docker
-        run: gcloud auth configure-docker
+        run: gcloud auth configure-docker ${{ env.REGION }}-docker.pkg.dev --quiet
 
       - name: Build JH Image
         run: |
diff --git a/dev/templates/class_tag.yml b/dev/templates/class_tag.yml
index 22c580da..b4b28b80 100644
--- a/dev/templates/class_tag.yml
+++ b/dev/templates/class_tag.yml
@@ -35,7 +35,7 @@ jobs:
           gsutil cp -r requirements/classes/${CLASS}/julia_env gs://jupyterhub-environment-files/${SEASON}-${YEAR}/${CLASS}/latest/julia
 
       - name: Configure Docker
-        run: gcloud auth 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
diff --git a/dev/templates/class_workflow.yml b/dev/templates/class_workflow.yml
index 093b6710..139825fd 100644
--- a/dev/templates/class_workflow.yml
+++ b/dev/templates/class_workflow.yml
@@ -37,7 +37,7 @@ jobs:
           sudo --preserve-env=CLASS docker compose up julia_build
 
       - name: Configure Docker
-        run: gcloud auth configure-docker
+        run: gcloud auth configure-docker ${{ env.REGION }}-docker.pkg.dev --quiet
 
       - name: Build JH Image
         run: |