From ffb2ffb1904efb5f03bfe34575087cdc5dd5924b Mon Sep 17 00:00:00 2001
From: Prasad Bandarkar <bandarkar.prasad@gmail.com>
Date: Sun, 27 Aug 2023 19:41:52 -0400
Subject: [PATCH 1/8] Added base python packages

---
 .github/workflows/neur1630-fall-tag.yml       | 52 +++++++++++++++++++
 .github/workflows/neur1630.yml                | 47 +++++++++++++++++
 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         | 52 +++++++++++++++++++
 7 files changed, 185 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..47abf1b0
--- /dev/null
+++ b/.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/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: ${{ secrets.GCP_SA_KEY_JH_DOCKER }}
+          export_default_credentials: true
+
+      - name: Create Julia Environment Files
+        if: env.TARGET == 'r_julia'
+        run: |
+          sudo --preserve-env=CLASS docker-compose up julia_build
+
+      - name: Upload Julia Env Files to Google Storage Bucket
+        if: env.TARGET == 'r_julia'
+        run: |
+          gsutil cp -r requirements/classes/neur1630/julia_env gs://jupyterhub-environment-files/fall-2023/neur1630/past/${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
\ No newline at end of file
diff --git a/.github/workflows/neur1630.yml b/.github/workflows/neur1630.yml
new file mode 100644
index 00000000..96fdf3d2
--- /dev/null
+++ b/.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/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: ${{ secrets.GCP_SA_KEY_JH_DOCKER }}
+          export_default_credentials: true
+
+      - name: Create Julia Environment Files
+        if: env.TARGET == 'r_julia'
+        run: |
+          sudo --preserve-env=CLASS docker-compose up julia_build
+
+      - name: Configure Docker
+        run: gcloud auth configure-docker
+      - uses: satackey/action-docker-layer-caching@v0.0.11
+        # Ignore the failure of a step and avoid terminating the job.
+        continue-on-error: true
+      - name: Build and Push JH Image
+        run: |
+          COMPOSE_DOCKER_CLI_BUILD=1 DOCKER_BUILDKIT=1 docker-compose up jh_image
+          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/neur1630:${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##*/}
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..e0689d67
--- /dev/null
+++ b/requirements/classes/neur1630/requirements.txt
@@ -0,0 +1,52 @@
+# 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 )
+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

From eb3a7fef54c0360425d4b002a608ab9949df0502 Mon Sep 17 00:00:00 2001
From: Prasad Bandarkar <bandarkar.prasad@gmail.com>
Date: Sun, 24 Sep 2023 22:29:21 -0400
Subject: [PATCH 2/8] Adding Tuan's packages

---
 requirements/classes/neur1630/condarc             |  2 ++
 .../classes/neur1630/requirements.pip.txt         |  6 +++++-
 requirements/classes/neur1630/requirements.txt    | 15 +++++++++++++++
 3 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/requirements/classes/neur1630/condarc b/requirements/classes/neur1630/condarc
index d2a82925..af9e69f3 100644
--- a/requirements/classes/neur1630/condarc
+++ b/requirements/classes/neur1630/condarc
@@ -5,7 +5,9 @@
 # (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.
diff --git a/requirements/classes/neur1630/requirements.pip.txt b/requirements/classes/neur1630/requirements.pip.txt
index 43719b70..2a1ad037 100644
--- a/requirements/classes/neur1630/requirements.pip.txt
+++ b/requirements/classes/neur1630/requirements.pip.txt
@@ -1,2 +1,6 @@
 # add class-specific classes here:
-
+scanpy
+harmonypy
+rpy2
+nwbwidgets
+pynapple
\ No newline at end of file
diff --git a/requirements/classes/neur1630/requirements.txt b/requirements/classes/neur1630/requirements.txt
index e0689d67..80d94f9e 100644
--- a/requirements/classes/neur1630/requirements.txt
+++ b/requirements/classes/neur1630/requirements.txt
@@ -1,4 +1,19 @@
 # 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 

From ac3e93f244e615dbbbfcabe381a09e323bebc18c Mon Sep 17 00:00:00 2001
From: Prasad Bandarkar <bandarkar.prasad@gmail.com>
Date: Sun, 24 Sep 2023 22:59:14 -0400
Subject: [PATCH 3/8] removing defaults channel

---
 requirements/classes/neur1630/condarc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/classes/neur1630/condarc b/requirements/classes/neur1630/condarc
index af9e69f3..26d2ae4b 100644
--- a/requirements/classes/neur1630/condarc
+++ b/requirements/classes/neur1630/condarc
@@ -7,7 +7,7 @@
 channels:
   - bioconda
   - conda-forge
-  - defaults
+#  - defaults
 
 # Show channel URLs when displaying what is going to be downloaded
 # and in 'conda list'. The default is False.

From c7a3ef59d2afd8c56d19eb5849f1f61c16167d6d Mon Sep 17 00:00:00 2001
From: Prasad Bandarkar <bandarkar.prasad@gmail.com>
Date: Sun, 24 Sep 2023 23:17:42 -0400
Subject: [PATCH 4/8] removing caching

---
 .github/workflows/neur1630.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/neur1630.yml b/.github/workflows/neur1630.yml
index 96fdf3d2..b38764dd 100644
--- a/.github/workflows/neur1630.yml
+++ b/.github/workflows/neur1630.yml
@@ -35,9 +35,9 @@ jobs:
 
       - name: Configure Docker
         run: gcloud auth configure-docker
-      - uses: satackey/action-docker-layer-caching@v0.0.11
-        # Ignore the failure of a step and avoid terminating the job.
-        continue-on-error: true
+#      - uses: satackey/action-docker-layer-caching@v0.0.11
+#        # 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

From bdc1b7cb2f0f9911f67dbf8ba570be0d0399cb15 Mon Sep 17 00:00:00 2001
From: Prasad Bandarkar <bandarkar.prasad@gmail.com>
Date: Sun, 24 Sep 2023 23:37:16 -0400
Subject: [PATCH 5/8] temporarily changing dockerfile

---
 Dockerfile | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Dockerfile b/Dockerfile
index 94577c20..aafa9686 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -144,6 +144,8 @@ 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
 
+RUN mamba config --show channels
+
 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 && \
     mamba clean --all -f -y

From 110169ffe1e144c4e682129f04c85316e0623425 Mon Sep 17 00:00:00 2001
From: Prasad Bandarkar <bandarkar.prasad@gmail.com>
Date: Mon, 25 Sep 2023 10:09:30 -0400
Subject: [PATCH 6/8] running mamba info -a

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index aafa9686..ad541842 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -144,7 +144,7 @@ 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
 
-RUN mamba config --show channels
+RUN mamba info -a
 
 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 && \

From 902d28d4fd786430a25ceadd4334f06c37f0431e Mon Sep 17 00:00:00 2001
From: Prasad Bandarkar <bandarkar.prasad@gmail.com>
Date: Mon, 25 Sep 2023 10:45:26 -0400
Subject: [PATCH 7/8] creating .condarc

---
 Dockerfile | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index ad541842..679f7767 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -143,8 +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
-
-RUN mamba info -a
+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 && \

From c71cf27d9b49755781542701c0cce5fdb0f90105 Mon Sep 17 00:00:00 2001
From: Prasad Bandarkar <bandarkar.prasad@gmail.com>
Date: Thu, 12 Oct 2023 17:10:37 -0400
Subject: [PATCH 8/8] Adding additional packages

---
 requirements/classes/neur1630/requirements.pip.txt | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/requirements/classes/neur1630/requirements.pip.txt b/requirements/classes/neur1630/requirements.pip.txt
index 2a1ad037..d100ddc3 100644
--- a/requirements/classes/neur1630/requirements.pip.txt
+++ b/requirements/classes/neur1630/requirements.pip.txt
@@ -3,4 +3,7 @@ scanpy
 harmonypy
 rpy2
 nwbwidgets
-pynapple
\ No newline at end of file
+pynapple
+pybiomart
+pyranges
+gseapy
\ No newline at end of file