Feature 2022.02.0

Dockerfile

@@ -1,4 +1,4 @@
-ARG ALPINE_VERSION=3.12.0
+ARG ALPINE_VERSION=3.15.0
 FROM alpine:${ALPINE_VERSION}
 
 RUN apk add --no-cache git python3 python3-dev py-pip build-base
@@ -22,7 +22,7 @@ RUN pip3 install hg-evolve --user --no-cache-dir
 
 # install repo2docker
 COPY --from=0 /tmp/wheelhouse /tmp/wheelhouse
-RUN pip3 install --no-cache-dir /tmp/wheelhouse/*.whl --ignore-installed \
+RUN pip3 install --use-deprecated=legacy-resolver --no-cache-dir /tmp/wheelhouse/*.whl --ignore-installed \
  && pip3 list
 
 # add git-credential helper

docs/source/changelog.rst

@@ -3,6 +3,56 @@ Changelog
 =========
 
 
+Version 2022.02.0
+=================
+
+`Full changelog <https://github.com/jupyterhub/repo2docker/compare/2021.08.0...2022.01.0>`_
+
+New features
+------------
+
+- Update ipywidgets jupyter-offlinenotebook jupyterlab :pr:`1127` by :user:`manics`
+- Allow passing in extra args to Docker initialization :pr:`1124` by :user:`yuvipanda`
+- Allow passing in traitlets via commandline :pr:`1123` by :user:`yuvipanda`
+- Bump default R version to 4.1 :pr:`1107` by :user:`yuvipanda`
+- Update jupyterlab 3.2.5 jupyter-resource-usage 0.6.1 :pr:`1105` by :user:`manics`
+- Get binary R packages from packagemanager.rstudio.com :pr:`1104` by :user:`yuvipanda`
+- Support R 4.1 :pr:`1102` by :user:`yuvipanda`
+- Add command line option to pass extra build args :pr:`1100` by :user:`TimoRoth`
+- Set labels when building image from Dockerfile :pr:`1097` by :user:`TimoRoth`
+- jupyterlab 3.1.17 :pr:`1092` by :user:`minrk`
+- Bump JupyterLab to 3.1.11 :pr:`1081` by :user:`choldgraf`
+- Bootstrap base env with micromamba :pr:`1062` by :user:`wolfv ` 
+- Default UI to JupyterLab :pr:`1035` by :user:`SylvainCorlay`
+
+API changes
+-----------
+
+Bug fixes
+---------
+
+Other merged PRs
+----------------
+
+- Put micromamba in /usr/local/bin and use mamba for installs :pr:`1128` by :user:`minrk`
+- Remove deprecated calls to distutils :pr:`1122` by :user:`minrk`
+- Delete /tmp/downloaded_packages after running install.R :pr:`1119` by :user:`yuvipanda`
+- Use a smaller R library in our tests :pr:`1118` by :user:`yuvipanda`
+- Only get R itself (r-base-core) from apt, not CRAN packages :pr:`1117` by :user:`minrk`
+- set USER root after each directive block :pr:`1115` by :user:`minrk`
+- Say 'apt repository' rather than PPA :pr:`1111` by :user:`yuvipanda`
+- add tests for R conda :pr:`1108` by :user:`aplamada`
+- Add help message to freeze.py :pr:`1106` by :user:`manics`
+- Quieter R builds :pr:`1103` by :user:`yuvipanda`
+- update user_interface doc to reflect that lab is default :pr:`1085` by :user:`minrk`
+- Updates to dev docs + Recommonmark -> MyST Parser :pr:`1082` by :user:`choldgraf`
+- Fix Docker build (again) :pr:`1078` by :user:`manics`
+- [mrg] __init__.py: r_version: fixed description :pr:`1074` by :user:`magnush0lm`
+- Typo fix in utils docstring :pr:`1072` by :user:`jgarte`
+- Rename requirements.py-3.5.txt to requirements.py-3.5.pip :pr:`1061` by :user:`manics`
+- Remove nodesource' nodejs :pr:`847` by :user:`yuvipanda`
+
+
 Version 2021.08.0
 =================
 

repo2docker/__main__.py

@@ -66,6 +66,20 @@ def get_argparser():
         description="Fetch a repository and build a container image"
     )
 
+    argparser.add_argument(
+        "--help-all",
+        dest="help_all",
+        action="store_true",
+        help="Display all configurable options and exit.",
+    )
+
+    argparser.add_argument(
+        "--version",
+        dest="version",
+        action="store_true",
+        help="Print the repo2docker version and exit.",
+    )
+
     argparser.add_argument(
         "--config",
         default="repo2docker_config.py",
@@ -204,15 +218,24 @@ def get_argparser():
 
     argparser.add_argument("--appendix", type=str, help=Repo2Docker.appendix.help)
 
-    argparser.add_argument("--subdir", type=str, help=Repo2Docker.subdir.help)
+    argparser.add_argument(
+        "--label",
+        dest="labels",
+        action="append",
+        help="Extra label to set on the image, in form name=value",
+        default=[],
+    )
 
     argparser.add_argument(
-        "--version",
-        dest="version",
-        action="store_true",
-        help="Print the repo2docker version and exit.",
+        "--build-arg",
+        dest="build_args",
+        action="append",
+        help="Extra build arg to pass to the build process, in form name=value",
+        default=[],
     )
 
+    argparser.add_argument("--subdir", type=str, help=Repo2Docker.subdir.help)
+
     argparser.add_argument(
         "--cache-from", action="append", default=[], help=Repo2Docker.cache_from.help
     )
@@ -229,15 +252,24 @@ def make_r2d(argv=None):
     if argv is None:
         argv = sys.argv[1:]
 
+    argparser = get_argparser()
+
     # version must be checked before parse, as repo/cmd are required and
     # will spit out an error if allowed to be parsed first.
     if "--version" in argv:
         print(__version__)
         sys.exit(0)
 
-    args = get_argparser().parse_args(argv)
+    if "--help-all" in argv:
+        argparser.print_help()
+        print("\nAll configurable options:\n")
+        Repo2Docker().print_help(classes=True)
+        sys.exit(0)
+
+    args, traitlet_args = argparser.parse_known_args(argv)
 
     r2d = Repo2Docker()
+    r2d.parse_command_line(traitlet_args)
 
     if args.debug:
         r2d.log_level = logging.DEBUG
@@ -246,6 +278,14 @@ def make_r2d(argv=None):
     if args.appendix:
         r2d.appendix = args.appendix
 
+    for l in args.labels:
+        key, _, val = l.partition("=")
+        r2d.labels[key] = val
+
+    for a in args.build_args:
+        key, _, val = a.partition("=")
+        r2d.extra_build_args[key] = val
+
     r2d.repo = args.repo
     r2d.ref = args.ref
 

repo2docker/app.py

@@ -47,6 +47,10 @@ class Repo2Docker(Application):
     name = "jupyter-repo2docker"
     version = __version__
     description = __doc__
+    # disable aliases/flags because we don't use the traitlets for CLI parsing
+    # other than --Class.trait=value
+    aliases = {}
+    flags = {}
 
     @default("log_level")
     def _default_log_level(self):
@@ -239,6 +243,26 @@ def _user_name_default(self):
         """,
     )
 
+    labels = Dict(
+        {},
+        help="""
+        Extra labels to set on the final image.
+
+        Each Label is a key-value pair, with the key being the name of the label
+        and the value its value.
+        """,
+        config=True,
+    )
+
+    extra_build_args = Dict(
+        {},
+        help="""
+        Extra build args to pass to the image build process.
+        This is pretty much only useful for custom Dockerfile based builds.
+        """,
+        config=True,
+    )
+
     json_logs = Bool(
         False,
         help="""
@@ -472,7 +496,7 @@ def json_excepthook(self, etype, evalue, traceback):
             extra=dict(phase="failed"),
         )
 
-    def initialize(self):
+    def initialize(self, *args, **kwargs):
         """Init repo2docker configuration before start"""
         # FIXME: Remove this function, move it to setters / traitlet reactors
         if self.json_logs:
@@ -749,23 +773,28 @@ def build(self):
                 picked_buildpack.labels["repo2docker.repo"] = repo_label
                 picked_buildpack.labels["repo2docker.ref"] = self.ref
 
+                picked_buildpack.labels.update(self.labels)
+
+                build_args = {
+                    "NB_USER": self.user_name,
+                    "NB_UID": str(self.user_id),
+                }
+                if self.target_repo_dir:
+                    build_args["REPO_DIR"] = self.target_repo_dir
+                build_args.update(self.extra_build_args)
+
                 if self.dry_run:
-                    print(picked_buildpack.render())
+                    print(picked_buildpack.render(build_args))
                 else:
                     self.log.debug(
-                        picked_buildpack.render(), extra=dict(phase="building")
+                        picked_buildpack.render(build_args),
+                        extra=dict(phase="building"),
                     )
                     if self.user_id == 0:
                         raise ValueError(
                             "Root as the primary user in the image is not permitted."
                         )
 
-                    build_args = {
-                        "NB_USER": self.user_name,
-                        "NB_UID": str(self.user_id),
-                    }
-                    if self.target_repo_dir:
-                        build_args["REPO_DIR"] = self.target_repo_dir
                     self.log.info(
                         "Using %s builder\n",
                         bp.__class__.__name__,

repo2docker/buildpacks/_r_base.py

@@ -3,66 +3,67 @@
 
 Keeping this in r.py would lead to cyclic imports.
 """
+from ..semver import parse_version as V
 
-# Via https://rstudio.com/products/rstudio/download-server/debian-ubuntu/
-RSTUDIO_URL = "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.2.5001-amd64.deb"
-# This is MD5, because that is what RStudio download page provides!
-RSTUDIO_CHECKSUM = "d33881b9ab786c09556c410e7dc477de"
 
-# Via https://www.rstudio.com/products/shiny/download-server/
-SHINY_URL = "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.12.933-amd64.deb"
-SHINY_CHECKSUM = "9aeef6613e7f58f21c97a4600921340e"
-
-# Version of MRAN to pull devtools from.
-DEVTOOLS_VERSION = "2018-02-01"
+def rstudio_base_scripts(r_version):
+    """Base steps to install RStudio and shiny-server."""
 
-# IRKernel version - specified as a tag in the IRKernel repository
-IRKERNEL_VERSION = "1.1"
+    # Shiny server (not the package!) seems to be the same version for all R versions
+    shiny_server_url = "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.17.973-amd64.deb"
+    shiny_proxy_version = "1.1"
+    shiny_sha256sum = "80f1e48f6c824be7ef9c843bb7911d4981ac7e8a963e0eff823936a8b28476ee"
 
+    if V(r_version) <= V("4.1"):
+        # Older RStudio and jupyter-rsession-proxy for v4.1 and below
+        rstudio_url = "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.3.959-amd64.deb"
+        rstudio_sha256sum = (
+            "187af05cab1221282487fdc33f4b161484c3228eaade3d6697b1d41c206ee6d9"
+        )
+        rsession_proxy_version = "1.4"
+    else:
+        rstudio_url = "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2021.09.1-372-amd64.deb"
+        rstudio_sha256sum = (
+            "c58df09468870b89f1796445853dce2dacaa0fc5b7bb1f92b036fa8da1d1f8a3"
+        )
+        rsession_proxy_version = "2.0.1"
 
-def rstudio_base_scripts():
-    """Base steps to install RStudio and shiny-server."""
     return [
         (
             "root",
-            # Install RStudio!
+            # we should have --no-install-recommends on all our apt-get install commands,
+            # but here it's important because these recommend r-base,
+            # which will upgrade the installed version of R, undoing our pinned version
             r"""
-                curl --silent --location --fail {rstudio_url} > /tmp/rstudio.deb && \
-                echo '{rstudio_checksum} /tmp/rstudio.deb' | md5sum -c - && \
-                apt-get update && \
-                apt install -y /tmp/rstudio.deb && \
-                rm /tmp/rstudio.deb && \
-                apt-get -qq purge && \
-                apt-get -qq clean && \
-                rm -rf /var/lib/apt/lists/*
-                """.format(
-                rstudio_url=RSTUDIO_URL, rstudio_checksum=RSTUDIO_CHECKSUM
+            curl --silent --location --fail {rstudio_url} > /tmp/rstudio.deb && \
+            curl --silent --location --fail {shiny_server_url} > /tmp/shiny.deb && \
+            echo '{rstudio_sha256sum} /tmp/rstudio.deb' | sha256sum -c - && \
+            echo '{shiny_sha256sum} /tmp/shiny.deb' | sha256sum -c - && \
+            apt-get update > /dev/null && \
+            apt install -y --no-install-recommends /tmp/rstudio.deb /tmp/shiny.deb && \
+            rm /tmp/rstudio.deb && \
+            apt-get -qq purge && \
+            apt-get -qq clean && \
+            rm -rf /var/lib/apt/lists/*
+            """.format(
+                rstudio_url=rstudio_url,
+                rstudio_sha256sum=rstudio_sha256sum,
+                shiny_server_url=shiny_server_url,
+                shiny_sha256sum=shiny_sha256sum,
             ),
         ),
         (
-            "root",
-            # Install Shiny Server!
+            "${NB_USER}",
+            # Install jupyter-rsession-proxy
             r"""
-                curl --silent --location --fail {url} > {deb} && \
-                echo '{checksum} {deb}' | md5sum -c - && \
-                dpkg -i {deb} && \
-                rm {deb}
+                pip install --no-cache \
+                    jupyter-rsession-proxy=={rsession_proxy_version} \
+                    jupyter-shiny-proxy=={shiny_proxy_version}
                 """.format(
-                url=SHINY_URL, checksum=SHINY_CHECKSUM, deb="/tmp/shiny.deb"
+                rsession_proxy_version=rsession_proxy_version,
+                shiny_proxy_version=shiny_proxy_version,
             ),
         ),
-        (
-            "${NB_USER}",
-            # Install nbrsessionproxy
-            r"""
-                pip install --no-cache-dir jupyter-server-proxy==1.4.0 && \
-                pip install --no-cache-dir https://github.com/jupyterhub/jupyter-rsession-proxy/archive/d5efed5455870556fc414f30871d0feca675a4b4.zip && \
-                pip install --no-cache-dir https://github.com/ryanlovett/jupyter-shiny-proxy/archive/47557dc47e2aeeab490eb5f3eeae414cdde4a6a9.zip && \
-                jupyter serverextension enable jupyter_server_proxy --sys-prefix && \
-                jupyter nbextension install --py jupyter_server_proxy --sys-prefix && \
-                jupyter nbextension enable --py jupyter_server_proxy --sys-prefix
-                """,
-        ),
         (
             # Not all of these locations are configurable; so we make sure
             # they exist and have the correct permissions