Remove inkscape package from the minimal-notebook (#1765)

* Removing inkscape

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Adding Rprofile to add plot_mimetypes

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Update datascience-notebook/Dockerfile

Co-authored-by: Ayaz Salikhov <mathbunnyru@users.noreply.github.com>

* Update datascience-notebook/Rprofile.site

Co-authored-by: Ayaz Salikhov <mathbunnyru@users.noreply.github.com>

* Adding R notebook tests

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Moving Rprofile.site to minimal;
Removing duplicate R test code

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Fixing flake8 errors

* Update minimal-notebook/Dockerfile

Co-authored-by: Ayaz Salikhov <mathbunnyru@users.noreply.github.com>

* Update minimal-notebook/Rprofile.site

Co-authored-by: Ayaz Salikhov <mathbunnyru@users.noreply.github.com>

* Removing empty line

* Renaming minetypes to  mimetypes

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Renaming test module to avoid mypy error

* Adding to jupyter.plot_mimetypes

* Update R_mimetype_check.py

* Update test_mimetypes.py

* Update test_R_mimetypes.py

* Update test_R_mimetypes.py

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Ayaz Salikhov <mathbunnyru@users.noreply.github.com>

Author: 3 people

base-notebook/jupyter_server_config.py

@@ -12,6 +12,9 @@
 c.ServerApp.port = 8888
 c.ServerApp.open_browser = False
 
+# to output both image/svg+xml and application/pdf plot formats in the notebook file
+c.InlineBackend.figure_formats = {"png", "jpeg", "svg", "pdf"}
+
 # https://github.com/jupyter/notebook/issues/3130
 c.FileContentsManager.delete_to_trash = False
 

minimal-notebook/Dockerfile

@@ -21,8 +21,6 @@ RUN apt-get update --yes && \
     tzdata \
     unzip \
     vim-tiny \
-    # Inkscape is installed to be able to convert SVG files
-    inkscape \
     # git-over-ssh
     openssh-client \
     # less is needed to run help in R
@@ -40,3 +38,6 @@ RUN update-alternatives --install /usr/bin/nano nano /bin/nano-tiny 10
 
 # Switch back to jovyan to avoid accidental container runs as root
 USER ${NB_UID}
+
+# Add R mimetype option to specify how the plot returns from R to the browser
+COPY --chown=${NB_UID}:${NB_GID} Rprofile.site /opt/conda/lib/R/etc/

minimal-notebook/Rprofile.site

@@ -0,0 +1,4 @@
+# Add R mimetype to specify how the plot returns from R to the browser.
+# https://notebook.community/andrie/jupyter-notebook-samples/Changing%20R%20plot%20options%20in%20Jupyter
+
+options(jupyter.plot_mimetypes = c('text/plain', 'image/png', 'image/jpeg', 'image/svg+xml', 'application/pdf'))

tests/R_mimetype_check.py

@@ -0,0 +1,21 @@
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+import logging
+
+from tests.conftest import TrackedContainer
+
+LOGGER = logging.getLogger(__name__)
+
+
+def check_r_mimetypes(container: TrackedContainer) -> None:
+    """Check if Rscript command can be executed"""
+    LOGGER.info("Test that R command can be executed ...")
+    Rcommand = 'if (length(getOption("jupyter.plot_mimetypes")) != 5) {stop("missing jupyter.plot_mimetypes")}'
+    logs = container.run_and_wait(
+        timeout=10,
+        tty=True,
+        command=["Rscript", "-e", Rcommand],
+    )
+    LOGGER.debug(f"{logs=}")
+    assert len(logs) == 0, f"Command {Rcommand=} failed"

tests/datascience-notebook/test_mimetypes.py

@@ -0,0 +1,10 @@
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+from tests.conftest import TrackedContainer
+from tests.R_mimetype_check import check_r_mimetypes
+
+
+def test_mimetypes(container: TrackedContainer) -> None:
+    """Check if Rscript command for mimetypes can be executed"""
+    check_r_mimetypes(container)

tests/minimal-notebook/test_inkscape.py

@@ -0,0 +1,10 @@
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+from tests.conftest import TrackedContainer
+from tests.R_mimetype_check import check_r_mimetypes
+
+
+def test_mimetypes(container: TrackedContainer) -> None:
+    """Check if Rscript command for mimetypes can be executed"""
+    check_r_mimetypes(container)