Update RStudio, Minicondata and other dependencies (#80)

* Update rstudio and miniconda version

* Fix miniconda permission

* Update python and pip

* Fix conda env file

* Do no render Synapse notebook in CI/CD workflow

* Remove Synapse notebook from README

.env.example

@@ -1,6 +1,6 @@
 # RStudio
 USER=rstudio
-PASSWORD=yourpassword
+PASSWORD=changeme
 USERID=1000
 GROUPID=1000
 ROOT=FALSE

.github/workflows/ci.yml

@@ -142,6 +142,7 @@ jobs:
 
     - name: Generate HTML notebooks
       run: |
+        rm -fr $(pwd)/notebooks/examples/synapse.Rmd
         docker run --rm \
           --env-file .env \
           -v $(pwd)/notebooks:/data \

Dockerfile

@@ -1,9 +1,9 @@
-FROM rocker/rstudio:4.0.5
+FROM rocker/rstudio:4.1.2
 
 LABEL maintainer="[email protected]"
 LABEL description="Base image with RStudio and Conda"
 
-ENV miniconda3_version="py39_4.9.2"
+ENV miniconda3_version="py39_4.10.3"
 ENV miniconda_bin_dir="/opt/miniconda/bin"
 ENV PATH="${PATH}:${miniconda_bin_dir}"
 
@@ -49,6 +49,7 @@ RUN conda init bash \
     # Fix libssl issue that affects conda env used with reticulate
     && cp /usr/lib/x86_64-linux-gnu/libssl.so.1.1 \
         /opt/miniconda/envs/sage-bionetworks/lib/libssl.so.1.1 \
+    # TODO: Use a test for success rather than `|| true`.
     && conda activate base || true \
     && echo "conda activate sage-bionetworks" >> ~/.bashrc
 
@@ -61,7 +62,6 @@ RUN install2.r --error renv \
     && R -e "extrafont::font_import(prompt=FALSE)"
 
 # Configure S6 init system
-RUN mv /etc/cont-init.d/userconf /etc/cont-init.d/10-rstudio-userconf
 COPY root /
 
 WORKDIR /

README.md

@@ -61,7 +61,7 @@ Rmd Notebook | Description | HTML Notebook
 [notebook.Rmd](notebooks/examples/notebook.Rmd)         | Default RStudio notebook.                                | [![HTML notebook](https://img.shields.io/badge/latest-blue.svg?color=1283c3&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://tschaffter.github.io/rstudio/latest/notebooks/notebook.html)
 [r-and-python.Rmd](notebooks/examples/r-and-python.Rmd) | Shows how to use R and Python together.                  | [![HTML notebook](https://img.shields.io/badge/latest-blue.svg?color=1283c3&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://tschaffter.github.io/rstudio/latest/notebooks/r-and-python.html)
 [sagethemes.Rmd](notebooks/examples/sagethemes.Rmd)     | Example notebook provided by the R library [sagethemes]. | [![HTML notebook](https://img.shields.io/badge/latest-blue.svg?color=1283c3&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://tschaffter.github.io/rstudio/latest/notebooks/sagethemes.html)
-[synapse.Rmd](notebooks/examples/synapse.Rmd)           | Shows how to interact with Synapse API.                  | [![HTML notebook](https://img.shields.io/badge/latest-blue.svg?color=1283c3&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://tschaffter.github.io/rstudio/latest/notebooks/synapse.html)
+<!-- [synapse.Rmd](notebooks/examples/synapse.Rmd)           | Shows how to interact with Synapse API.                  | [![HTML notebook](https://img.shields.io/badge/latest-blue.svg?color=1283c3&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://tschaffter.github.io/rstudio/latest/notebooks/synapse.html) -->
 
 > Important: Please make sure when you write your own notebooks that no
 > sensitive information ends up being publicly available. Please check with the
@@ -100,6 +100,7 @@ the Docker repository where the image should be pushed (see Section
 Example projects that use this repository / image:
   - [Sage-Bionetworks/rstudio]
   - [Sage-Bionetworks-Challenges/challenge-analysis]
+  - [nlpsandbox/notebooks]
 
 ## Manage R and Python dependencies
 
@@ -277,3 +278,4 @@ Similarly, run this command to convert the notebook to PDF.
 [Sage-Bionetworks/rstudio]: https://github.com/Sage-Bionetworks/rstudio
 [Docker Engine]: https://docs.docker.com/engine/install/
 [Docker Compose]: https://docs.docker.com/compose/install/
+[nlpsandbox/notebooks]: https://github.com/nlpsandbox/notebooks

RSTUDIO_VERSION

@@ -1 +1 @@
-4.0.5
+4.1.2

conda/sage-bionetworks/environment.yml

@@ -3,6 +3,6 @@ channels:
   - defaults
 dependencies:
   - python=3.9.4
-  - pip=21.0.1
+  - pip=21.2.4
   - pip:
-    - -r file:requirements.txt
+    - -r requirements.txt

conda/sage-bionetworks/requirements.txt

@@ -1,3 +1,3 @@
-challengeutils==4.0.1
-pandas==1.2.4
-synapseclient==2.3.1
+challengeutils==4.1.0
+pandas==1.4.0
+synapseclient==2.5.1

docker-compose.yml

@@ -2,15 +2,15 @@ version: "3.8"
 
 services:
   rstudio:
-    image: tschaffter/rstudio:4.0.5
+    image: tschaffter/rstudio:4.1.2
     build:
       context: .
       dockerfile: Dockerfile
     container_name: rstudio
     env_file:
       - .env
     volumes:
-      - .:/home/rstudio/awesome-project:rw
+      - ${PWD}:/home/rstudio/awesome-project:rw
     ports:
       - "${HOST_PORT}:8787"
     command: rstudio