From 6de48e53c7397e6ef3b7a7497f07ae78de90ff5b Mon Sep 17 00:00:00 2001 From: Prasad Bandarkar Date: Sun, 27 Aug 2023 19:08:15 -0400 Subject: [PATCH] Adding additional softwares in req.txt --- .github/workflows/php2560-fall-tag.yml | 20 +++---- .github/workflows/php2560.yml | 9 ++-- requirements/classes/php2560/condarc | 2 +- requirements/classes/php2560/packages.R | 14 +++-- requirements/classes/php2560/requirements.txt | 54 +++++++++++-------- 5 files changed, 53 insertions(+), 46 deletions(-) diff --git a/.github/workflows/php2560-fall-tag.yml b/.github/workflows/php2560-fall-tag.yml index 5fb55c51..2ded0771 100644 --- a/.github/workflows/php2560-fall-tag.yml +++ b/.github/workflows/php2560-fall-tag.yml @@ -3,18 +3,18 @@ on: [workflow_dispatch] env: CLASS: php2560 - TARGET: r_lang + TARGET: r_julia SQLITE: false - PYTHON_VERSION: "3.10" + PYTHON_VERSION: "3.9.17" jobs: build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3.5.3 - name: Set Up GCloud - uses: google-github-actions/setup-gcloud@v0.6.0 + uses: google-github-actions/setup-gcloud@v0.6.2 with: project_id: ${{ secrets.GCP_PROJECT_ID_JH_DOCKER }} service_account_key: ${{ secrets.GCP_SA_KEY_JH_DOCKER }} @@ -28,8 +28,8 @@ jobs: - name: Upload Julia Env Files to Google Storage Bucket if: env.TARGET == 'r_julia' run: | - gsutil cp -r requirements/classes/php2560/julia_env gs://jupyterhub-environment-files/fall-2022/php2560/past/${GITHUB_SHA}/julia - gsutil cp -r requirements/classes/php2560/julia_env gs://jupyterhub-environment-files/fall-2022/php2560/latest/julia + gsutil cp -r requirements/classes/php2560/julia_env gs://jupyterhub-environment-files/fall-2023/php2560/past/${GITHUB_SHA}/julia + gsutil cp -r requirements/classes/php2560/julia_env gs://jupyterhub-environment-files/fall-2023/php2560/latest/julia - name: Configure Docker run: gcloud auth configure-docker @@ -40,13 +40,13 @@ jobs: docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/php2560:${GITHUB_REF##*/} docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/php2560:${GITHUB_SHA} docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/php2560:latest - docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/php2560:fall-2022 + docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/php2560:fall-2023 docker push gcr.io/jupyterhub-docker-images/php2560:latest - docker push gcr.io/jupyterhub-docker-images/php2560:fall-2022 + docker push gcr.io/jupyterhub-docker-images/php2560:fall-2023 docker push gcr.io/jupyterhub-docker-images/php2560:${GITHUB_REF##*/} docker push gcr.io/jupyterhub-docker-images/php2560:${GITHUB_SHA} - name: Upload Conda Env Files to Google Storage Bucket run: | - gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2022/php2560/past/${GITHUB_SHA}/conda - gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2022/php2560/latest/conda \ No newline at end of file + gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2023/php2560/past/${GITHUB_SHA}/conda + gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2023/php2560/latest/conda \ No newline at end of file diff --git a/.github/workflows/php2560.yml b/.github/workflows/php2560.yml index ccb052bb..7390c4e1 100644 --- a/.github/workflows/php2560.yml +++ b/.github/workflows/php2560.yml @@ -7,21 +7,22 @@ on: - 'docker-compose.yml' - 'scripts/**' - '.github/workflows/php2560.yml' + workflow_dispatch: env: CLASS: php2560 - TARGET: r_lang + TARGET: r_julia SQLITE: false - PYTHON_VERSION: "3.10" + PYTHON_VERSION: "3.9.17" jobs: build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3.5.3 - name: Set Up GCloud - uses: google-github-actions/setup-gcloud@v0.6.0 + 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 }} diff --git a/requirements/classes/php2560/condarc b/requirements/classes/php2560/condarc index 09142931..d2a82925 100644 --- a/requirements/classes/php2560/condarc +++ b/requirements/classes/php2560/condarc @@ -12,4 +12,4 @@ channels: show_channel_urls: True # For more information about this file see: -# https://conda.io/docs/user-guide/configuration/use-condarc.html +# 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 index 595904bf..e1dced38 100644 --- a/requirements/classes/php2560/packages.R +++ b/requirements/classes/php2560/packages.R @@ -4,11 +4,9 @@ # the standard install.packages() function; for Bioconductor packages, however, you # must first install BiocManager and then use that for installs. -install.packages('fivethirtyeightdata', - dependencies = TRUE, - repos = 'https://fivethirtyeightdata.github.io/drat/', - type = 'source') - -install.packages(c("docstring"), - dependencies = TRUE, - repos = 'http://cran.rstudio.com/') \ No newline at end of file +# 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.txt b/requirements/classes/php2560/requirements.txt index c5e3ee0f..ef3b3695 100644 --- a/requirements/classes/php2560/requirements.txt +++ b/requirements/classes/php2560/requirements.txt @@ -1,11 +1,11 @@ # add class-specific packages here: +r-gt +r-gtsummary r-gridextra r-ggally -r-knitr -r-irdisplay +r-patchwork # these are the scipy base packages ( YOU PROBABLY DON'T WANT TO REMOVE THESE ) -numpy dask pandas numexpr @@ -15,34 +15,42 @@ seaborn scikit-learn scikit-image sympy +cython +patsy statsmodels +cloudpickle +dill +numba bokeh +sqlalchemy hdf5 vincent +beautifulsoup4 +protobuf +xlrd +bottleneck pytables -cython # 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 -r-caret -r-crayon -r-devtools -r-forecast -r-hexbin -r-htmltools -r-htmlwidgets -r-nycflights13 -r-randomforest -r-rcurl -r-rmarkdown -r-rodbc -r-irkernel -r-rsqlite -r-shiny +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 -r-tidymodels - +unixodbc=2.* +r-tidymodels=1.* # required for environment and plugins ( DO NOT REMOVE THESE!!! ) ipython