From c425d831e7eed05cb67ba8b28d94a7878644d0bd Mon Sep 17 00:00:00 2001 From: Anna Murphy Date: Mon, 26 Aug 2024 10:57:17 -0400 Subject: [PATCH 1/5] php2560 & php 1560 --- .github/workflows/php1560-fall-tag.yml | 56 +++++++++++++++ .github/workflows/php1560.yml | 54 ++++++++++++++ .github/workflows/php2560-fall-tag.yml | 56 +++++++++++++++ .github/workflows/php2560.yml | 54 ++++++++++++++ requirements/classes/php1560/condarc | 15 ++++ requirements/classes/php1560/packages.R | 12 ++++ requirements/classes/php1560/requirements.jl | 5 ++ .../classes/php1560/requirements.pip.txt | 2 + requirements/classes/php1560/requirements.txt | 72 +++++++++++++++++++ requirements/classes/php2560/condarc | 15 ++++ requirements/classes/php2560/packages.R | 12 ++++ requirements/classes/php2560/requirements.jl | 5 ++ .../classes/php2560/requirements.pip.txt | 2 + requirements/classes/php2560/requirements.txt | 72 +++++++++++++++++++ 14 files changed, 432 insertions(+) create mode 100644 .github/workflows/php1560-fall-tag.yml create mode 100644 .github/workflows/php1560.yml create mode 100644 .github/workflows/php2560-fall-tag.yml create mode 100644 .github/workflows/php2560.yml create mode 100644 requirements/classes/php1560/condarc create mode 100644 requirements/classes/php1560/packages.R create mode 100644 requirements/classes/php1560/requirements.jl create mode 100644 requirements/classes/php1560/requirements.pip.txt create mode 100644 requirements/classes/php1560/requirements.txt create mode 100644 requirements/classes/php2560/condarc create mode 100644 requirements/classes/php2560/packages.R create mode 100644 requirements/classes/php2560/requirements.jl create mode 100644 requirements/classes/php2560/requirements.pip.txt create mode 100644 requirements/classes/php2560/requirements.txt diff --git a/.github/workflows/php1560-fall-tag.yml b/.github/workflows/php1560-fall-tag.yml new file mode 100644 index 00000000..11fbdd77 --- /dev/null +++ b/.github/workflows/php1560-fall-tag.yml @@ -0,0 +1,56 @@ +name: tag-image-php1560 +on: [workflow_dispatch] + +env: + CLASS: php1560 + 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/php1560 + +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: ${{ secrets.GCP_SA_KEY_JH_DOCKER }} + export_default_credentials: true + + - name: Create Julia Environment Files + if: env.TARGET == 'r_julia' + run: | + sudo --preserve-env=CLASS docker compose up julia_build + + - name: Upload Julia Env Files to Google Storage Bucket + if: env.TARGET == 'r_julia' + run: | + gsutil cp -r requirements/classes/php1560/julia_env gs://jupyterhub-environment-files/fall-2024/php1560/past/${GITHUB_SHA}/julia + gsutil cp -r requirements/classes/php1560/julia_env gs://jupyterhub-environment-files/fall-2024/php1560/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 }}: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 ${{ env.GAR_LOCATION }}:fall-2024 + + - name: Upload Conda Env Files to Google Storage Bucket + run: | + gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2024/php1560/past/${GITHUB_SHA}/conda + gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2024/php1560/latest/conda \ No newline at end of file diff --git a/.github/workflows/php1560.yml b/.github/workflows/php1560.yml new file mode 100644 index 00000000..128b794f --- /dev/null +++ b/.github/workflows/php1560.yml @@ -0,0 +1,54 @@ +name: build-image-php1560 +on: + push: + paths: + - 'requirements/classes/php1560/**' + - 'Dockerfile' + - 'docker-compose.yml' + - 'scripts/**' + - '.github/workflows/php1560.yml' + workflow_dispatch: + +env: + CLASS: php1560 + 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/php1560 + +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 ${{ 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##*/} \ No newline at end of file diff --git a/.github/workflows/php2560-fall-tag.yml b/.github/workflows/php2560-fall-tag.yml new file mode 100644 index 00000000..4a7b0ea2 --- /dev/null +++ b/.github/workflows/php2560-fall-tag.yml @@ -0,0 +1,56 @@ +name: tag-image-php2560 +on: [workflow_dispatch] + +env: + CLASS: php2560 + 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/php2560 + +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: ${{ secrets.GCP_SA_KEY_JH_DOCKER }} + export_default_credentials: true + + - name: Create Julia Environment Files + if: env.TARGET == 'r_julia' + run: | + sudo --preserve-env=CLASS docker compose up julia_build + + - name: Upload Julia Env Files to Google Storage Bucket + if: env.TARGET == 'r_julia' + run: | + gsutil cp -r requirements/classes/php2560/julia_env gs://jupyterhub-environment-files/fall-2024/php2560/past/${GITHUB_SHA}/julia + gsutil cp -r requirements/classes/php2560/julia_env gs://jupyterhub-environment-files/fall-2024/php2560/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 }}: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 ${{ env.GAR_LOCATION }}:fall-2024 + + - name: Upload Conda Env Files to Google Storage Bucket + run: | + gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2024/php2560/past/${GITHUB_SHA}/conda + gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2024/php2560/latest/conda \ No newline at end of file diff --git a/.github/workflows/php2560.yml b/.github/workflows/php2560.yml new file mode 100644 index 00000000..2bf93fe9 --- /dev/null +++ b/.github/workflows/php2560.yml @@ -0,0 +1,54 @@ +name: build-image-php2560 +on: + push: + paths: + - 'requirements/classes/php2560/**' + - 'Dockerfile' + - 'docker-compose.yml' + - 'scripts/**' + - '.github/workflows/php2560.yml' + workflow_dispatch: + +env: + CLASS: php2560 + 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/php2560 + +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 ${{ 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##*/} \ No newline at end of file diff --git a/requirements/classes/php1560/condarc b/requirements/classes/php1560/condarc new file mode 100644 index 00000000..d2a82925 --- /dev/null +++ b/requirements/classes/php1560/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/php1560/packages.R b/requirements/classes/php1560/packages.R new file mode 100644 index 00000000..e1dced38 --- /dev/null +++ b/requirements/classes/php1560/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/php1560/requirements.jl b/requirements/classes/php1560/requirements.jl new file mode 100644 index 00000000..87635a43 --- /dev/null +++ b/requirements/classes/php1560/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/php1560/requirements.pip.txt b/requirements/classes/php1560/requirements.pip.txt new file mode 100644 index 00000000..43719b70 --- /dev/null +++ b/requirements/classes/php1560/requirements.pip.txt @@ -0,0 +1,2 @@ +# add class-specific classes here: + diff --git a/requirements/classes/php1560/requirements.txt b/requirements/classes/php1560/requirements.txt new file mode 100644 index 00000000..59164746 --- /dev/null +++ b/requirements/classes/php1560/requirements.txt @@ -0,0 +1,72 @@ +# add class-specific packages here: +r-ggplot2 +r-dplyr + +# 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 diff --git a/requirements/classes/php2560/condarc b/requirements/classes/php2560/condarc new file mode 100644 index 00000000..d2a82925 --- /dev/null +++ b/requirements/classes/php2560/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/php2560/packages.R b/requirements/classes/php2560/packages.R new file mode 100644 index 00000000..e1dced38 --- /dev/null +++ b/requirements/classes/php2560/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/php2560/requirements.jl b/requirements/classes/php2560/requirements.jl new file mode 100644 index 00000000..87635a43 --- /dev/null +++ b/requirements/classes/php2560/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/php2560/requirements.pip.txt b/requirements/classes/php2560/requirements.pip.txt new file mode 100644 index 00000000..43719b70 --- /dev/null +++ b/requirements/classes/php2560/requirements.pip.txt @@ -0,0 +1,2 @@ +# add class-specific classes here: + diff --git a/requirements/classes/php2560/requirements.txt b/requirements/classes/php2560/requirements.txt new file mode 100644 index 00000000..59164746 --- /dev/null +++ b/requirements/classes/php2560/requirements.txt @@ -0,0 +1,72 @@ +# add class-specific packages here: +r-ggplot2 +r-dplyr + +# 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 488e9ab419c3947520e74c9617a2a864d3f76627 Mon Sep 17 00:00:00 2001 From: Anna Murphy Date: Tue, 3 Sep 2024 11:24:41 -0400 Subject: [PATCH 2/5] change base to rlang --- .github/workflows/php1560-fall-tag.yml | 2 +- .github/workflows/php1560.yml | 2 +- .github/workflows/php2560-fall-tag.yml | 2 +- .github/workflows/php2560.yml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/php1560-fall-tag.yml b/.github/workflows/php1560-fall-tag.yml index 11fbdd77..5bc793dd 100644 --- a/.github/workflows/php1560-fall-tag.yml +++ b/.github/workflows/php1560-fall-tag.yml @@ -3,7 +3,7 @@ on: [workflow_dispatch] env: CLASS: php1560 - TARGET: base + TARGET: r_lang SQLITE: false PYTHON_VERSION: "3.9.17" PROJECT_ID: jupyterhub-docker-images diff --git a/.github/workflows/php1560.yml b/.github/workflows/php1560.yml index 128b794f..2250a96c 100644 --- a/.github/workflows/php1560.yml +++ b/.github/workflows/php1560.yml @@ -11,7 +11,7 @@ on: env: CLASS: php1560 - TARGET: base + TARGET: r_lang SQLITE: false PYTHON_VERSION: "3.9.17" PROJECT_ID: jupyterhub-docker-images diff --git a/.github/workflows/php2560-fall-tag.yml b/.github/workflows/php2560-fall-tag.yml index 4a7b0ea2..c0f0b8dd 100644 --- a/.github/workflows/php2560-fall-tag.yml +++ b/.github/workflows/php2560-fall-tag.yml @@ -3,7 +3,7 @@ on: [workflow_dispatch] env: CLASS: php2560 - TARGET: base + TARGET: r_lang SQLITE: false PYTHON_VERSION: "3.9.17" PROJECT_ID: jupyterhub-docker-images diff --git a/.github/workflows/php2560.yml b/.github/workflows/php2560.yml index 2bf93fe9..6f4271e4 100644 --- a/.github/workflows/php2560.yml +++ b/.github/workflows/php2560.yml @@ -11,7 +11,7 @@ on: env: CLASS: php2560 - TARGET: base + TARGET: r_lang SQLITE: false PYTHON_VERSION: "3.9.17" PROJECT_ID: jupyterhub-docker-images From 1f30d68a87fad031f63532ed9acd2efe0d3c8c9b Mon Sep 17 00:00:00 2001 From: Anna Murphy Date: Tue, 3 Sep 2024 11:24:47 -0400 Subject: [PATCH 3/5] add requriements --- requirements/classes/php1560/requirements.txt | 14 ++++++++++++++ requirements/classes/php2560/requirements.txt | 14 ++++++++++++++ 2 files changed, 28 insertions(+) diff --git a/requirements/classes/php1560/requirements.txt b/requirements/classes/php1560/requirements.txt index 59164746..47c105a4 100644 --- a/requirements/classes/php1560/requirements.txt +++ b/requirements/classes/php1560/requirements.txt @@ -1,6 +1,20 @@ # add class-specific packages here: r-ggplot2 r-dplyr +r-HDSinRdata +r-GGally +r-gt +r-gtsummary +r-tidyverse +r-patchwork +r-usmap +r-car +r-broom +r-pROC +r-lmtest +r-glmnet +r-testthat +r-microbenchmark # these are the scipy base packages ( YOU PROBABLY DON'T WANT TO REMOVE THESE ) dask diff --git a/requirements/classes/php2560/requirements.txt b/requirements/classes/php2560/requirements.txt index 59164746..47c105a4 100644 --- a/requirements/classes/php2560/requirements.txt +++ b/requirements/classes/php2560/requirements.txt @@ -1,6 +1,20 @@ # add class-specific packages here: r-ggplot2 r-dplyr +r-HDSinRdata +r-GGally +r-gt +r-gtsummary +r-tidyverse +r-patchwork +r-usmap +r-car +r-broom +r-pROC +r-lmtest +r-glmnet +r-testthat +r-microbenchmark # these are the scipy base packages ( YOU PROBABLY DON'T WANT TO REMOVE THESE ) dask From 9ac1b42f3c27a50f8067ba4243225488afd4bd8c Mon Sep 17 00:00:00 2001 From: Anna Murphy Date: Tue, 3 Sep 2024 11:59:13 -0400 Subject: [PATCH 4/5] move r dependencies to packages.R --- requirements/classes/php1560/packages.R | 5 +++++ requirements/classes/php1560/requirements.txt | 15 +-------------- requirements/classes/php2560/packages.R | 4 ++++ requirements/classes/php2560/requirements.txt | 14 -------------- 4 files changed, 10 insertions(+), 28 deletions(-) diff --git a/requirements/classes/php1560/packages.R b/requirements/classes/php1560/packages.R index e1dced38..f6a0a7f0 100644 --- a/requirements/classes/php1560/packages.R +++ b/requirements/classes/php1560/packages.R @@ -10,3 +10,8 @@ # repos='http://cran.rstudio.com/') # BiocManager::install(c("airway", "DESeq2", "vsn", "biomaRt", # "AnnotationHub", "SummarizedExperiment")) + +install.packages( + c("HDSinRdata", "GGally", "gt", "gtsummary", "tidyverse", "patchwork", "usmap", "car", "broom", "pROC", "lmtest", "glmnet", "testthat", "microbenchmark"), + dependencies=TRUE, + repos='http://cran.rstudio.com/') diff --git a/requirements/classes/php1560/requirements.txt b/requirements/classes/php1560/requirements.txt index 47c105a4..353a999a 100644 --- a/requirements/classes/php1560/requirements.txt +++ b/requirements/classes/php1560/requirements.txt @@ -1,20 +1,7 @@ # add class-specific packages here: r-ggplot2 r-dplyr -r-HDSinRdata -r-GGally -r-gt -r-gtsummary -r-tidyverse -r-patchwork -r-usmap -r-car -r-broom -r-pROC -r-lmtest -r-glmnet -r-testthat -r-microbenchmark + # these are the scipy base packages ( YOU PROBABLY DON'T WANT TO REMOVE THESE ) dask diff --git a/requirements/classes/php2560/packages.R b/requirements/classes/php2560/packages.R index e1dced38..65c0f489 100644 --- a/requirements/classes/php2560/packages.R +++ b/requirements/classes/php2560/packages.R @@ -10,3 +10,7 @@ # repos='http://cran.rstudio.com/') # BiocManager::install(c("airway", "DESeq2", "vsn", "biomaRt", # "AnnotationHub", "SummarizedExperiment")) +install.packages( + c("HDSinRdata", "GGally", "gt", "gtsummary", "tidyverse", "patchwork", "usmap", "car", "broom", "pROC", "lmtest", "glmnet", "testthat", "microbenchmark"), + dependencies=TRUE, + repos='http://cran.rstudio.com/') diff --git a/requirements/classes/php2560/requirements.txt b/requirements/classes/php2560/requirements.txt index 47c105a4..59164746 100644 --- a/requirements/classes/php2560/requirements.txt +++ b/requirements/classes/php2560/requirements.txt @@ -1,20 +1,6 @@ # add class-specific packages here: r-ggplot2 r-dplyr -r-HDSinRdata -r-GGally -r-gt -r-gtsummary -r-tidyverse -r-patchwork -r-usmap -r-car -r-broom -r-pROC -r-lmtest -r-glmnet -r-testthat -r-microbenchmark # these are the scipy base packages ( YOU PROBABLY DON'T WANT TO REMOVE THESE ) dask From 5af021c48fe098f1f169ba82361e3075d9bf169d Mon Sep 17 00:00:00 2001 From: Anna Murphy Date: Tue, 3 Sep 2024 16:11:00 -0400 Subject: [PATCH 5/5] add r-sf dependency to be installed by conda --- requirements/classes/php1560/requirements.txt | 2 +- requirements/classes/php2560/requirements.txt | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/requirements/classes/php1560/requirements.txt b/requirements/classes/php1560/requirements.txt index 353a999a..f015ce28 100644 --- a/requirements/classes/php1560/requirements.txt +++ b/requirements/classes/php1560/requirements.txt @@ -1,7 +1,7 @@ # add class-specific packages here: r-ggplot2 r-dplyr - +r-sf # these are the scipy base packages ( YOU PROBABLY DON'T WANT TO REMOVE THESE ) dask diff --git a/requirements/classes/php2560/requirements.txt b/requirements/classes/php2560/requirements.txt index 59164746..f015ce28 100644 --- a/requirements/classes/php2560/requirements.txt +++ b/requirements/classes/php2560/requirements.txt @@ -1,6 +1,7 @@ # add class-specific packages here: r-ggplot2 r-dplyr +r-sf # these are the scipy base packages ( YOU PROBABLY DON'T WANT TO REMOVE THESE ) dask