feat(Generator): don't install Stencila language packages by default

Currently, the Stencila R package is very slow to install so this turns that off
by default until that is sped up. Partially addresses #40 (still need to add argument on CLI)

src/DockerCompiler.ts

@@ -17,8 +17,9 @@ export default class DockerCompiler {
    * @param source The folder, Dockerfile or `SoftwareEnvironment` to compile
    * @param build Should the Docker image be built?
    * @param comments Should comments be added to the Dockerfile?
+   * @param stencila Should relevant Stencila language packages be installed in the image?
    */
-  async compile (source: string, build: boolean = true, comments: boolean = true): Promise<SoftwareEnvironment | null> {
+  async compile (source: string, build: boolean = true, comments: boolean = true, stencila: boolean = false): Promise<SoftwareEnvironment | null> {
     let folder
     if (source.substring(0, 7) === 'file://') {
       folder = source.substring(7)
@@ -57,7 +58,7 @@ export default class DockerCompiler {
 
       // Generate Dockerfile
       dockerfile = '.Dockerfile'
-      new DockerGenerator(environ, folder).generate(comments)
+      new DockerGenerator(environ, folder).generate(comments, stencila)
     }
 
     if (build) {

src/Generator.ts

@@ -13,8 +13,9 @@ export default class Generator extends Doer {
    * Generate a Dockerfile for a `SoftwareEnvironment` instance
    *
    * @param comments Should a comments be added to the Dockerfile?
+   * @param stencila Should relevant Stencila language packages be installed in the image?
    */
-  generate (comments: boolean = true): string {
+  generate (comments: boolean = true, stencila: boolean = false): string {
     let dockerfile = ''
 
     if (comments) {
@@ -74,10 +75,12 @@ RUN apt-get update \\
 `
     }
 
-    let stencilaInstall = this.stencilaInstall(baseIdentifier)
-    if (stencilaInstall) {
-      if (comments) dockerfile += '\n# This section runs commands to install Stencila execution hosts.'
-      dockerfile += `\nRUN ${stencilaInstall}\n`
+    if (stencila) {
+      let stencilaInstall = this.stencilaInstall(baseIdentifier)
+      if (stencilaInstall) {
+        if (comments) dockerfile += '\n# This section runs commands to install Stencila execution hosts.'
+        dockerfile += `\nRUN ${stencilaInstall}\n`
+      }
     }
 
     // Once everything that needs root permissions is installed, switch the user to non-root for installing the rest of the packages.

tests/DockerCompiler.test.ts

@@ -35,7 +35,7 @@ test('compile:multi-lang', async () => {
   let environ = await compiler.compile('file://' + fixture('multi-lang'), false, false)
 
   // Remove the date from the MRAN line to allow for changing date of test v expected
-  const aptAddMRAN = /(apt-add-repository "deb https:\/\/mran.microsoft.com\/snapshot)\/([\d-]+)\/(bin\/linux\/ubuntu xenial\/)"/
+  const aptAddMRAN = /(apt-add-repository "deb https:\/\/mran.microsoft.com\/snapshot)\/([\d-]+)\/(bin\/linux\/ubuntu bionic-cran35\/)"/
   const actual = fs.readFileSync(fixture('multi-lang/.Dockerfile'), 'utf8').replace(aptAddMRAN, '$1/YYYY-MM-DD/$3')
   const expected = fs.readFileSync(fixture('multi-lang/Dockerfile.expected'), 'utf8').replace(aptAddMRAN, '$1/YYYY-MM-DD/$3')
   expect(actual).toEqual(expected)

tests/PythonGenerator.test.ts

@@ -79,8 +79,6 @@ RUN apt-get update \\
  && apt-get clean \\
  && rm -rf /var/lib/apt/lists/*
 
-RUN pip install --no-cache-dir https://github.com/stencila/py/archive/91a05a139ac120a89fc001d9d267989f062ad374.zip
-
 RUN useradd --create-home --uid 1001 -s /bin/bash dockteruser
 USER dockteruser
 WORKDIR /home/dockteruser

tests/RGenerator.test.ts

@@ -50,16 +50,6 @@ RUN apt-get update \\
  && apt-get clean \\
  && rm -rf /var/lib/apt/lists/*
 
-RUN apt-get update \\
- && apt-get install -y  zlib1g-dev libxml2-dev pkg-config \\
- && apt-get autoremove -y \\
- && apt-get clean \\
- && rm -rf /var/lib/apt/lists/* \\
- && Rscript -e 'install.packages("devtools")' \\
- && Rscript -e 'source("https://bioconductor.org/biocLite.R"); biocLite("graph")' \\
- && Rscript -e 'devtools::install_github("r-lib/pkgbuild")' \\
- && Rscript -e 'devtools::install_github("stencila/r")'
-
 RUN useradd --create-home --uid 1001 -s /bin/bash dockteruser
 USER dockteruser
 WORKDIR /home/dockteruser
@@ -104,16 +94,6 @@ RUN apt-get update \\
  && apt-get clean \\
  && rm -rf /var/lib/apt/lists/*
 
-RUN apt-get update \\
- && apt-get install -y  zlib1g-dev libxml2-dev pkg-config \\
- && apt-get autoremove -y \\
- && apt-get clean \\
- && rm -rf /var/lib/apt/lists/* \\
- && Rscript -e 'install.packages("devtools")' \\
- && Rscript -e 'source("https://bioconductor.org/biocLite.R"); biocLite("graph")' \\
- && Rscript -e 'devtools::install_github("r-lib/pkgbuild")' \\
- && Rscript -e 'devtools::install_github("stencila/r")'
-
 RUN useradd --create-home --uid 1001 -s /bin/bash dockteruser
 USER dockteruser
 WORKDIR /home/dockteruser

tests/fixtures/multi-lang/Dockerfile.expected

@@ -28,18 +28,6 @@ RUN apt-get update \
  && apt-get clean \
  && rm -rf /var/lib/apt/lists/*
 
-RUN npm install [email protected] \
- && pip3 install --no-cache-dir https://github.com/stencila/py/archive/91a05a139ac120a89fc001d9d267989f062ad374.zip \
- && apt-get update \
- && apt-get install -y  zlib1g-dev libxml2-dev pkg-config \
- && apt-get autoremove -y \
- && apt-get clean \
- && rm -rf /var/lib/apt/lists/* \
- && Rscript -e 'install.packages("devtools")' \
- && Rscript -e 'source("https://bioconductor.org/biocLite.R"); biocLite("graph")' \
- && Rscript -e 'devtools::install_github("r-lib/pkgbuild")' \
- && Rscript -e 'devtools::install_github("stencila/r")'
-
 RUN useradd --create-home --uid 1001 -s /bin/bash dockteruser
 USER dockteruser
 WORKDIR /home/dockteruser