From c6c1422c8dfb6ac16b4a60b39710217d40266a9c Mon Sep 17 00:00:00 2001
From: Darek <darek.bidek@gmail.com>
Date: Mon, 8 Aug 2022 17:06:13 -0400
Subject: [PATCH 01/22] Removing inkscape

---
 base-notebook/jupyter_server_config.py  |  3 +++
 minimal-notebook/Dockerfile             |  2 --
 tests/minimal-notebook/test_inkscape.py | 19 -------------------
 3 files changed, 3 insertions(+), 21 deletions(-)
 delete mode 100644 tests/minimal-notebook/test_inkscape.py

diff --git a/base-notebook/jupyter_server_config.py b/base-notebook/jupyter_server_config.py
index ef0380bd35..c8e0d8b73c 100644
--- a/base-notebook/jupyter_server_config.py
+++ b/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
 
diff --git a/minimal-notebook/Dockerfile b/minimal-notebook/Dockerfile
index f7b495f6dd..4a01601aee 100644
--- a/minimal-notebook/Dockerfile
+++ b/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
diff --git a/tests/minimal-notebook/test_inkscape.py b/tests/minimal-notebook/test_inkscape.py
deleted file mode 100644
index 7cdcf2777f..0000000000
--- a/tests/minimal-notebook/test_inkscape.py
+++ /dev/null
@@ -1,19 +0,0 @@
-# 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 test_inkscape(container: TrackedContainer) -> None:
-    """Inkscape shall be installed to be able to convert SVG files."""
-    LOGGER.info("Test that inkscape is working by printing its version ...")
-    logs = container.run_and_wait(
-        timeout=10,
-        tty=True,
-        command=["start.sh", "bash", "-c", "inkscape --version"],
-    )
-    assert "Inkscape" in logs, "Inkscape not installed or not working"

From f59ba42db960b1266befa3ff0e5e0309a75c48cf Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 8 Aug 2022 21:10:43 +0000
Subject: [PATCH 02/22] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 base-notebook/jupyter_server_config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/base-notebook/jupyter_server_config.py b/base-notebook/jupyter_server_config.py
index c8e0d8b73c..c95957cc7b 100644
--- a/base-notebook/jupyter_server_config.py
+++ b/base-notebook/jupyter_server_config.py
@@ -13,7 +13,7 @@
 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'}
+c.InlineBackend.figure_formats = {"png", "jpeg", "svg", "pdf"}
 
 # https://github.com/jupyter/notebook/issues/3130
 c.FileContentsManager.delete_to_trash = False

From c4b286aafb253d3691929e29ca5aac5a1bf7f5a7 Mon Sep 17 00:00:00 2001
From: Darek <darek.bidek@gmail.com>
Date: Tue, 9 Aug 2022 15:25:40 -0400
Subject: [PATCH 03/22] Adding Rprofile to add plot_mimetypes

---
 datascience-notebook/Dockerfile    | 3 +++
 datascience-notebook/Rprofile.site | 5 +++++
 r-notebook/Dockerfile              | 3 +++
 r-notebook/Rprofile.site           | 5 +++++
 4 files changed, 16 insertions(+)
 create mode 100644 datascience-notebook/Rprofile.site
 create mode 100644 r-notebook/Rprofile.site

diff --git a/datascience-notebook/Dockerfile b/datascience-notebook/Dockerfile
index 584d1f5374..9324e49444 100644
--- a/datascience-notebook/Dockerfile
+++ b/datascience-notebook/Dockerfile
@@ -85,6 +85,9 @@ RUN mamba install --quiet --yes \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
+# Add mimetype to specifies how the plot returns from R to the browser.
+COPY --chown=${NB_UID}:${NB_GID} Rprofile.site /opt/conda/lib/R/etc/
+
 # `rpy2` and `r-tidymodels` are not easy to install under aarch64
 RUN set -x && \
     arch=$(uname -m) && \
diff --git a/datascience-notebook/Rprofile.site b/datascience-notebook/Rprofile.site
new file mode 100644
index 0000000000..33bbfe7b3a
--- /dev/null
+++ b/datascience-notebook/Rprofile.site
@@ -0,0 +1,5 @@
+
+# Add mimetype to specifies how the plot returns from R to the browser.
+# https://notebook.community/andrie/jupyter-notebook-samples/Changing%20R%20plot%20options%20in%20Jupyter
+
+options(jupyter.plot_mimetypes = c('text/plain', 'image/svg+xml', 'application/pdf'))
\ No newline at end of file
diff --git a/r-notebook/Dockerfile b/r-notebook/Dockerfile
index 3319a802b3..fa8b9d764c 100644
--- a/r-notebook/Dockerfile
+++ b/r-notebook/Dockerfile
@@ -61,3 +61,6 @@ RUN set -x && \
             fix-permissions "${CONDA_DIR}" && \
             fix-permissions "/home/${NB_USER}"; \
     fi;
+
+# Add mimetype to specifies how the plot returns from R to the browser.
+COPY --chown=${NB_UID}:${NB_GID} Rprofile.site /opt/conda/lib/R/etc/
\ No newline at end of file
diff --git a/r-notebook/Rprofile.site b/r-notebook/Rprofile.site
new file mode 100644
index 0000000000..33bbfe7b3a
--- /dev/null
+++ b/r-notebook/Rprofile.site
@@ -0,0 +1,5 @@
+
+# Add mimetype to specifies 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/svg+xml', 'application/pdf'))
\ No newline at end of file

From 464f035691cdc6711edaec95b9248f876f6a326f Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 9 Aug 2022 19:26:11 +0000
Subject: [PATCH 04/22] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 datascience-notebook/Rprofile.site | 2 +-
 r-notebook/Dockerfile              | 2 +-
 r-notebook/Rprofile.site           | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/datascience-notebook/Rprofile.site b/datascience-notebook/Rprofile.site
index 33bbfe7b3a..551e9aa0e8 100644
--- a/datascience-notebook/Rprofile.site
+++ b/datascience-notebook/Rprofile.site
@@ -2,4 +2,4 @@
 # Add mimetype to specifies 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/svg+xml', 'application/pdf'))
\ No newline at end of file
+options(jupyter.plot_mimetypes = c('text/plain', 'image/svg+xml', 'application/pdf'))
diff --git a/r-notebook/Dockerfile b/r-notebook/Dockerfile
index fa8b9d764c..b1ae785476 100644
--- a/r-notebook/Dockerfile
+++ b/r-notebook/Dockerfile
@@ -63,4 +63,4 @@ RUN set -x && \
     fi;
 
 # Add mimetype to specifies how the plot returns from R to the browser.
-COPY --chown=${NB_UID}:${NB_GID} Rprofile.site /opt/conda/lib/R/etc/
\ No newline at end of file
+COPY --chown=${NB_UID}:${NB_GID} Rprofile.site /opt/conda/lib/R/etc/
diff --git a/r-notebook/Rprofile.site b/r-notebook/Rprofile.site
index 33bbfe7b3a..551e9aa0e8 100644
--- a/r-notebook/Rprofile.site
+++ b/r-notebook/Rprofile.site
@@ -2,4 +2,4 @@
 # Add mimetype to specifies 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/svg+xml', 'application/pdf'))
\ No newline at end of file
+options(jupyter.plot_mimetypes = c('text/plain', 'image/svg+xml', 'application/pdf'))

From 7333d91ca482bb747a2c73707c0d15713a087b25 Mon Sep 17 00:00:00 2001
From: Darek <darek56@yahoo.com>
Date: Wed, 10 Aug 2022 09:23:52 -0400
Subject: [PATCH 05/22] Update datascience-notebook/Dockerfile

Co-authored-by: Ayaz Salikhov <mathbunnyru@users.noreply.github.com>
---
 datascience-notebook/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/datascience-notebook/Dockerfile b/datascience-notebook/Dockerfile
index 9324e49444..3e20cc75ea 100644
--- a/datascience-notebook/Dockerfile
+++ b/datascience-notebook/Dockerfile
@@ -85,7 +85,7 @@ RUN mamba install --quiet --yes \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-# Add mimetype to specifies how the plot returns from R to the browser.
+# Add `mimetype` to specify how the plot returns from R to the browser.
 COPY --chown=${NB_UID}:${NB_GID} Rprofile.site /opt/conda/lib/R/etc/
 
 # `rpy2` and `r-tidymodels` are not easy to install under aarch64

From 1eeed83898928aa88a13b56614e4bc3ca2596e38 Mon Sep 17 00:00:00 2001
From: Darek <darek56@yahoo.com>
Date: Wed, 10 Aug 2022 10:36:58 -0400
Subject: [PATCH 06/22] Update datascience-notebook/Rprofile.site

Co-authored-by: Ayaz Salikhov <mathbunnyru@users.noreply.github.com>
---
 datascience-notebook/Rprofile.site | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/datascience-notebook/Rprofile.site b/datascience-notebook/Rprofile.site
index 551e9aa0e8..a6c0a2f7ee 100644
--- a/datascience-notebook/Rprofile.site
+++ b/datascience-notebook/Rprofile.site
@@ -1,5 +1,4 @@
-
-# Add mimetype to specifies how the plot returns from R to the browser.
+# Add `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/svg+xml', 'application/pdf'))

From 603f07b8bb395d17ca5f3feabb19e90db2d246b6 Mon Sep 17 00:00:00 2001
From: Darek <darek.bidek@gmail.com>
Date: Wed, 17 Aug 2022 12:32:09 -0400
Subject: [PATCH 07/22] Adding R notebook tests

---
 .../data/minetypes_R.ipynb                    | 37 ++++++++++++++++++
 tests/datascience-notebook/test_R_notebook.py | 38 +++++++++++++++++++
 tests/r-notebook/data/minetypes_R.ipynb       | 37 ++++++++++++++++++
 tests/r-notebook/test_R_notebook.py           | 38 +++++++++++++++++++
 4 files changed, 150 insertions(+)
 create mode 100644 tests/datascience-notebook/data/minetypes_R.ipynb
 create mode 100644 tests/datascience-notebook/test_R_notebook.py
 create mode 100644 tests/r-notebook/data/minetypes_R.ipynb
 create mode 100644 tests/r-notebook/test_R_notebook.py

diff --git a/tests/datascience-notebook/data/minetypes_R.ipynb b/tests/datascience-notebook/data/minetypes_R.ipynb
new file mode 100644
index 0000000000..539de42d2c
--- /dev/null
+++ b/tests/datascience-notebook/data/minetypes_R.ipynb
@@ -0,0 +1,37 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "# Test for a number of plot_mimetypes available\n",
+    "if (length(getOption(\"jupyter.plot_mimetypes\")) != 3) {\n",
+    "    stop(\"missing jupyter.plot_mimetypes\")\n",
+    "}"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "R",
+   "language": "R",
+   "name": "ir"
+  },
+  "language_info": {
+   "codemirror_mode": "r",
+   "file_extension": ".r",
+   "mimetype": "text/x-r-source",
+   "name": "R",
+   "pygments_lexer": "r",
+   "version": "3.6.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/tests/datascience-notebook/test_R_notebook.py b/tests/datascience-notebook/test_R_notebook.py
new file mode 100644
index 0000000000..730533106b
--- /dev/null
+++ b/tests/datascience-notebook/test_R_notebook.py
@@ -0,0 +1,38 @@
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+import logging
+from pathlib import Path
+
+import pytest  # type: ignore
+
+from tests.conftest import TrackedContainer
+
+LOGGER = logging.getLogger(__name__)
+THIS_DIR = Path(__file__).parent.resolve()
+
+@pytest.mark.parametrize(
+    "test_file", ["minetypes_R"],
+)
+def test_minetypes(container: TrackedContainer, test_file: str) -> None:
+    """Check if R notebooks can be executed"""
+    host_data_dir = THIS_DIR / "data"
+    cont_data_dir = "/home/jovyan/data"
+    output_dir = "/tmp"
+    conversion_timeout_ms = 600
+    LOGGER.info(f"Test that {test_file} notebook can be executed ...")
+    command = (
+        "jupyter nbconvert --to markdown "
+        + f"--ExecutePreprocessor.timeout={conversion_timeout_ms} "
+        + f"--output-dir {output_dir} "
+        + f"--execute {cont_data_dir}/{test_file}.ipynb"
+    )
+    logs = container.run_and_wait(
+        timeout=60,
+        volumes={str(host_data_dir): {"bind": cont_data_dir, "mode": "ro"}},
+        tty=True,
+        command=["start.sh", "bash", "-c", command],
+    )
+
+    expected_file = f"{output_dir}/{test_file}.md"
+    assert expected_file in logs, f"Expected file {expected_file} not generated"
diff --git a/tests/r-notebook/data/minetypes_R.ipynb b/tests/r-notebook/data/minetypes_R.ipynb
new file mode 100644
index 0000000000..539de42d2c
--- /dev/null
+++ b/tests/r-notebook/data/minetypes_R.ipynb
@@ -0,0 +1,37 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "# Test for a number of plot_mimetypes available\n",
+    "if (length(getOption(\"jupyter.plot_mimetypes\")) != 3) {\n",
+    "    stop(\"missing jupyter.plot_mimetypes\")\n",
+    "}"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "R",
+   "language": "R",
+   "name": "ir"
+  },
+  "language_info": {
+   "codemirror_mode": "r",
+   "file_extension": ".r",
+   "mimetype": "text/x-r-source",
+   "name": "R",
+   "pygments_lexer": "r",
+   "version": "3.6.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/tests/r-notebook/test_R_notebook.py b/tests/r-notebook/test_R_notebook.py
new file mode 100644
index 0000000000..730533106b
--- /dev/null
+++ b/tests/r-notebook/test_R_notebook.py
@@ -0,0 +1,38 @@
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+import logging
+from pathlib import Path
+
+import pytest  # type: ignore
+
+from tests.conftest import TrackedContainer
+
+LOGGER = logging.getLogger(__name__)
+THIS_DIR = Path(__file__).parent.resolve()
+
+@pytest.mark.parametrize(
+    "test_file", ["minetypes_R"],
+)
+def test_minetypes(container: TrackedContainer, test_file: str) -> None:
+    """Check if R notebooks can be executed"""
+    host_data_dir = THIS_DIR / "data"
+    cont_data_dir = "/home/jovyan/data"
+    output_dir = "/tmp"
+    conversion_timeout_ms = 600
+    LOGGER.info(f"Test that {test_file} notebook can be executed ...")
+    command = (
+        "jupyter nbconvert --to markdown "
+        + f"--ExecutePreprocessor.timeout={conversion_timeout_ms} "
+        + f"--output-dir {output_dir} "
+        + f"--execute {cont_data_dir}/{test_file}.ipynb"
+    )
+    logs = container.run_and_wait(
+        timeout=60,
+        volumes={str(host_data_dir): {"bind": cont_data_dir, "mode": "ro"}},
+        tty=True,
+        command=["start.sh", "bash", "-c", command],
+    )
+
+    expected_file = f"{output_dir}/{test_file}.md"
+    assert expected_file in logs, f"Expected file {expected_file} not generated"

From 7ee5a396ec5ebc8d6668e03f168ba293a6c8276b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 17 Aug 2022 16:32:53 +0000
Subject: [PATCH 08/22] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/datascience-notebook/test_R_notebook.py | 4 +++-
 tests/r-notebook/test_R_notebook.py           | 4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/tests/datascience-notebook/test_R_notebook.py b/tests/datascience-notebook/test_R_notebook.py
index 730533106b..c3c9d1aeb3 100644
--- a/tests/datascience-notebook/test_R_notebook.py
+++ b/tests/datascience-notebook/test_R_notebook.py
@@ -11,8 +11,10 @@
 LOGGER = logging.getLogger(__name__)
 THIS_DIR = Path(__file__).parent.resolve()
 
+
 @pytest.mark.parametrize(
-    "test_file", ["minetypes_R"],
+    "test_file",
+    ["minetypes_R"],
 )
 def test_minetypes(container: TrackedContainer, test_file: str) -> None:
     """Check if R notebooks can be executed"""
diff --git a/tests/r-notebook/test_R_notebook.py b/tests/r-notebook/test_R_notebook.py
index 730533106b..c3c9d1aeb3 100644
--- a/tests/r-notebook/test_R_notebook.py
+++ b/tests/r-notebook/test_R_notebook.py
@@ -11,8 +11,10 @@
 LOGGER = logging.getLogger(__name__)
 THIS_DIR = Path(__file__).parent.resolve()
 
+
 @pytest.mark.parametrize(
-    "test_file", ["minetypes_R"],
+    "test_file",
+    ["minetypes_R"],
 )
 def test_minetypes(container: TrackedContainer, test_file: str) -> None:
     """Check if R notebooks can be executed"""

From 05b8faf5bcab139bf1a95e0b65a27006e0530715 Mon Sep 17 00:00:00 2001
From: Darek <darek.bidek@gmail.com>
Date: Thu, 18 Aug 2022 11:55:48 -0400
Subject: [PATCH 09/22] Moving Rprofile.site to minimal; Removing duplicate R
 test code

---
 datascience-notebook/Dockerfile               |  3 --
 datascience-notebook/Rprofile.site            |  4 --
 minimal-notebook/Dockerfile                   |  3 ++
 .../Rprofile.site                             |  0
 r-notebook/Dockerfile                         |  5 +--
 tests/R_minetype_check.py                     | 21 ++++++++++
 .../data/minetypes_R.ipynb                    | 37 -----------------
 .../datascience-notebook/test_R_minetypes.py  | 10 +++++
 tests/datascience-notebook/test_R_notebook.py | 40 -------------------
 tests/r-notebook/data/minetypes_R.ipynb       | 37 -----------------
 tests/r-notebook/test_R_minetypes.py          | 10 +++++
 tests/r-notebook/test_R_notebook.py           | 40 -------------------
 12 files changed, 45 insertions(+), 165 deletions(-)
 delete mode 100644 datascience-notebook/Rprofile.site
 rename {r-notebook => minimal-notebook}/Rprofile.site (100%)
 create mode 100644 tests/R_minetype_check.py
 delete mode 100644 tests/datascience-notebook/data/minetypes_R.ipynb
 create mode 100644 tests/datascience-notebook/test_R_minetypes.py
 delete mode 100644 tests/datascience-notebook/test_R_notebook.py
 delete mode 100644 tests/r-notebook/data/minetypes_R.ipynb
 create mode 100644 tests/r-notebook/test_R_minetypes.py
 delete mode 100644 tests/r-notebook/test_R_notebook.py

diff --git a/datascience-notebook/Dockerfile b/datascience-notebook/Dockerfile
index 3e20cc75ea..584d1f5374 100644
--- a/datascience-notebook/Dockerfile
+++ b/datascience-notebook/Dockerfile
@@ -85,9 +85,6 @@ RUN mamba install --quiet --yes \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-# Add `mimetype` to specify how the plot returns from R to the browser.
-COPY --chown=${NB_UID}:${NB_GID} Rprofile.site /opt/conda/lib/R/etc/
-
 # `rpy2` and `r-tidymodels` are not easy to install under aarch64
 RUN set -x && \
     arch=$(uname -m) && \
diff --git a/datascience-notebook/Rprofile.site b/datascience-notebook/Rprofile.site
deleted file mode 100644
index a6c0a2f7ee..0000000000
--- a/datascience-notebook/Rprofile.site
+++ /dev/null
@@ -1,4 +0,0 @@
-# Add `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/svg+xml', 'application/pdf'))
diff --git a/minimal-notebook/Dockerfile b/minimal-notebook/Dockerfile
index 4a01601aee..6a6e4f6f54 100644
--- a/minimal-notebook/Dockerfile
+++ b/minimal-notebook/Dockerfile
@@ -38,3 +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 ${NB_UID}
+
+# Add R mimetype option to specifies how the plot returns from R to the browser
+COPY --chown=${NB_UID}:${NB_GID} Rprofile.site /opt/conda/lib/R/etc/
\ No newline at end of file
diff --git a/r-notebook/Rprofile.site b/minimal-notebook/Rprofile.site
similarity index 100%
rename from r-notebook/Rprofile.site
rename to minimal-notebook/Rprofile.site
diff --git a/r-notebook/Dockerfile b/r-notebook/Dockerfile
index b1ae785476..a7499a0ee4 100644
--- a/r-notebook/Dockerfile
+++ b/r-notebook/Dockerfile
@@ -60,7 +60,4 @@ RUN set -x && \
             mamba clean --all -f -y && \
             fix-permissions "${CONDA_DIR}" && \
             fix-permissions "/home/${NB_USER}"; \
-    fi;
-
-# Add mimetype to specifies how the plot returns from R to the browser.
-COPY --chown=${NB_UID}:${NB_GID} Rprofile.site /opt/conda/lib/R/etc/
+    fi;
\ No newline at end of file
diff --git a/tests/R_minetype_check.py b/tests/R_minetype_check.py
new file mode 100644
index 0000000000..9f809a9456
--- /dev/null
+++ b/tests/R_minetype_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 minetypes_check(container: TrackedContainer) -> None:
+    """Check if Rscript command can be executed"""
+    LOGGER.info(f"Test that R command can be executed ...")
+    Rcommand = "if (length(getOption(\"jupyter.plot_mimetypes\")) != 3) {stop(\"missing jupyter.plot_mimetypes\")}"
+    logs = container.run_and_wait(
+        timeout=60,
+        tty=True,
+        command=["Rscript", "-e", Rcommand],
+    )
+    LOGGER.debug(f"{logs=}")
+    assert len(logs) == 0, f"Command {Rcommand=} failed"
+
+    return logs
\ No newline at end of file
diff --git a/tests/datascience-notebook/data/minetypes_R.ipynb b/tests/datascience-notebook/data/minetypes_R.ipynb
deleted file mode 100644
index 539de42d2c..0000000000
--- a/tests/datascience-notebook/data/minetypes_R.ipynb
+++ /dev/null
@@ -1,37 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "# Test for a number of plot_mimetypes available\n",
-    "if (length(getOption(\"jupyter.plot_mimetypes\")) != 3) {\n",
-    "    stop(\"missing jupyter.plot_mimetypes\")\n",
-    "}"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "R",
-   "language": "R",
-   "name": "ir"
-  },
-  "language_info": {
-   "codemirror_mode": "r",
-   "file_extension": ".r",
-   "mimetype": "text/x-r-source",
-   "name": "R",
-   "pygments_lexer": "r",
-   "version": "3.6.3"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}
diff --git a/tests/datascience-notebook/test_R_minetypes.py b/tests/datascience-notebook/test_R_minetypes.py
new file mode 100644
index 0000000000..a17041a3ef
--- /dev/null
+++ b/tests/datascience-notebook/test_R_minetypes.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_minetype_check import minetypes_check
+
+def test_minetypes(container: TrackedContainer) -> None:
+    """Check if Rscript command for minetypes can be executed"""
+    logs=minetypes_check(container)
+    assert len(logs) == 0, f"Command R command failed"
\ No newline at end of file
diff --git a/tests/datascience-notebook/test_R_notebook.py b/tests/datascience-notebook/test_R_notebook.py
deleted file mode 100644
index c3c9d1aeb3..0000000000
--- a/tests/datascience-notebook/test_R_notebook.py
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright (c) Jupyter Development Team.
-# Distributed under the terms of the Modified BSD License.
-
-import logging
-from pathlib import Path
-
-import pytest  # type: ignore
-
-from tests.conftest import TrackedContainer
-
-LOGGER = logging.getLogger(__name__)
-THIS_DIR = Path(__file__).parent.resolve()
-
-
-@pytest.mark.parametrize(
-    "test_file",
-    ["minetypes_R"],
-)
-def test_minetypes(container: TrackedContainer, test_file: str) -> None:
-    """Check if R notebooks can be executed"""
-    host_data_dir = THIS_DIR / "data"
-    cont_data_dir = "/home/jovyan/data"
-    output_dir = "/tmp"
-    conversion_timeout_ms = 600
-    LOGGER.info(f"Test that {test_file} notebook can be executed ...")
-    command = (
-        "jupyter nbconvert --to markdown "
-        + f"--ExecutePreprocessor.timeout={conversion_timeout_ms} "
-        + f"--output-dir {output_dir} "
-        + f"--execute {cont_data_dir}/{test_file}.ipynb"
-    )
-    logs = container.run_and_wait(
-        timeout=60,
-        volumes={str(host_data_dir): {"bind": cont_data_dir, "mode": "ro"}},
-        tty=True,
-        command=["start.sh", "bash", "-c", command],
-    )
-
-    expected_file = f"{output_dir}/{test_file}.md"
-    assert expected_file in logs, f"Expected file {expected_file} not generated"
diff --git a/tests/r-notebook/data/minetypes_R.ipynb b/tests/r-notebook/data/minetypes_R.ipynb
deleted file mode 100644
index 539de42d2c..0000000000
--- a/tests/r-notebook/data/minetypes_R.ipynb
+++ /dev/null
@@ -1,37 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "# Test for a number of plot_mimetypes available\n",
-    "if (length(getOption(\"jupyter.plot_mimetypes\")) != 3) {\n",
-    "    stop(\"missing jupyter.plot_mimetypes\")\n",
-    "}"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "R",
-   "language": "R",
-   "name": "ir"
-  },
-  "language_info": {
-   "codemirror_mode": "r",
-   "file_extension": ".r",
-   "mimetype": "text/x-r-source",
-   "name": "R",
-   "pygments_lexer": "r",
-   "version": "3.6.3"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}
diff --git a/tests/r-notebook/test_R_minetypes.py b/tests/r-notebook/test_R_minetypes.py
new file mode 100644
index 0000000000..a17041a3ef
--- /dev/null
+++ b/tests/r-notebook/test_R_minetypes.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_minetype_check import minetypes_check
+
+def test_minetypes(container: TrackedContainer) -> None:
+    """Check if Rscript command for minetypes can be executed"""
+    logs=minetypes_check(container)
+    assert len(logs) == 0, f"Command R command failed"
\ No newline at end of file
diff --git a/tests/r-notebook/test_R_notebook.py b/tests/r-notebook/test_R_notebook.py
deleted file mode 100644
index c3c9d1aeb3..0000000000
--- a/tests/r-notebook/test_R_notebook.py
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright (c) Jupyter Development Team.
-# Distributed under the terms of the Modified BSD License.
-
-import logging
-from pathlib import Path
-
-import pytest  # type: ignore
-
-from tests.conftest import TrackedContainer
-
-LOGGER = logging.getLogger(__name__)
-THIS_DIR = Path(__file__).parent.resolve()
-
-
-@pytest.mark.parametrize(
-    "test_file",
-    ["minetypes_R"],
-)
-def test_minetypes(container: TrackedContainer, test_file: str) -> None:
-    """Check if R notebooks can be executed"""
-    host_data_dir = THIS_DIR / "data"
-    cont_data_dir = "/home/jovyan/data"
-    output_dir = "/tmp"
-    conversion_timeout_ms = 600
-    LOGGER.info(f"Test that {test_file} notebook can be executed ...")
-    command = (
-        "jupyter nbconvert --to markdown "
-        + f"--ExecutePreprocessor.timeout={conversion_timeout_ms} "
-        + f"--output-dir {output_dir} "
-        + f"--execute {cont_data_dir}/{test_file}.ipynb"
-    )
-    logs = container.run_and_wait(
-        timeout=60,
-        volumes={str(host_data_dir): {"bind": cont_data_dir, "mode": "ro"}},
-        tty=True,
-        command=["start.sh", "bash", "-c", command],
-    )
-
-    expected_file = f"{output_dir}/{test_file}.md"
-    assert expected_file in logs, f"Expected file {expected_file} not generated"

From 461d307f04bcd673f30e392c437626006b1c4122 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 18 Aug 2022 15:58:31 +0000
Subject: [PATCH 10/22] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 minimal-notebook/Dockerfile                    | 2 +-
 r-notebook/Dockerfile                          | 2 +-
 tests/R_minetype_check.py                      | 6 ++++--
 tests/datascience-notebook/test_R_minetypes.py | 5 +++--
 tests/r-notebook/test_R_minetypes.py           | 5 +++--
 5 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/minimal-notebook/Dockerfile b/minimal-notebook/Dockerfile
index 6a6e4f6f54..d685038320 100644
--- a/minimal-notebook/Dockerfile
+++ b/minimal-notebook/Dockerfile
@@ -40,4 +40,4 @@ RUN update-alternatives --install /usr/bin/nano nano /bin/nano-tiny 10
 USER ${NB_UID}
 
 # Add R mimetype option to specifies how the plot returns from R to the browser
-COPY --chown=${NB_UID}:${NB_GID} Rprofile.site /opt/conda/lib/R/etc/
\ No newline at end of file
+COPY --chown=${NB_UID}:${NB_GID} Rprofile.site /opt/conda/lib/R/etc/
diff --git a/r-notebook/Dockerfile b/r-notebook/Dockerfile
index a7499a0ee4..3319a802b3 100644
--- a/r-notebook/Dockerfile
+++ b/r-notebook/Dockerfile
@@ -60,4 +60,4 @@ RUN set -x && \
             mamba clean --all -f -y && \
             fix-permissions "${CONDA_DIR}" && \
             fix-permissions "/home/${NB_USER}"; \
-    fi;
\ No newline at end of file
+    fi;
diff --git a/tests/R_minetype_check.py b/tests/R_minetype_check.py
index 9f809a9456..96640a6f74 100644
--- a/tests/R_minetype_check.py
+++ b/tests/R_minetype_check.py
@@ -2,14 +2,16 @@
 # Distributed under the terms of the Modified BSD License.
 
 import logging
+
 from tests.conftest import TrackedContainer
 
 LOGGER = logging.getLogger(__name__)
 
+
 def minetypes_check(container: TrackedContainer) -> None:
     """Check if Rscript command can be executed"""
     LOGGER.info(f"Test that R command can be executed ...")
-    Rcommand = "if (length(getOption(\"jupyter.plot_mimetypes\")) != 3) {stop(\"missing jupyter.plot_mimetypes\")}"
+    Rcommand = 'if (length(getOption("jupyter.plot_mimetypes")) != 3) {stop("missing jupyter.plot_mimetypes")}'
     logs = container.run_and_wait(
         timeout=60,
         tty=True,
@@ -18,4 +20,4 @@ def minetypes_check(container: TrackedContainer) -> None:
     LOGGER.debug(f"{logs=}")
     assert len(logs) == 0, f"Command {Rcommand=} failed"
 
-    return logs
\ No newline at end of file
+    return logs
diff --git a/tests/datascience-notebook/test_R_minetypes.py b/tests/datascience-notebook/test_R_minetypes.py
index a17041a3ef..e8a7369fed 100644
--- a/tests/datascience-notebook/test_R_minetypes.py
+++ b/tests/datascience-notebook/test_R_minetypes.py
@@ -4,7 +4,8 @@
 from tests.conftest import TrackedContainer
 from tests.R_minetype_check import minetypes_check
 
+
 def test_minetypes(container: TrackedContainer) -> None:
     """Check if Rscript command for minetypes can be executed"""
-    logs=minetypes_check(container)
-    assert len(logs) == 0, f"Command R command failed"
\ No newline at end of file
+    logs = minetypes_check(container)
+    assert len(logs) == 0, f"Command R command failed"
diff --git a/tests/r-notebook/test_R_minetypes.py b/tests/r-notebook/test_R_minetypes.py
index a17041a3ef..e8a7369fed 100644
--- a/tests/r-notebook/test_R_minetypes.py
+++ b/tests/r-notebook/test_R_minetypes.py
@@ -4,7 +4,8 @@
 from tests.conftest import TrackedContainer
 from tests.R_minetype_check import minetypes_check
 
+
 def test_minetypes(container: TrackedContainer) -> None:
     """Check if Rscript command for minetypes can be executed"""
-    logs=minetypes_check(container)
-    assert len(logs) == 0, f"Command R command failed"
\ No newline at end of file
+    logs = minetypes_check(container)
+    assert len(logs) == 0, f"Command R command failed"

From 60e7001f30a7bc90f49559aa293980b54c293f74 Mon Sep 17 00:00:00 2001
From: Darek <darek.bidek@gmail.com>
Date: Thu, 18 Aug 2022 12:02:19 -0400
Subject: [PATCH 11/22] Fixing flake8 errors

---
 tests/R_minetype_check.py                      | 2 +-
 tests/datascience-notebook/test_R_minetypes.py | 2 +-
 tests/r-notebook/test_R_minetypes.py           | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/R_minetype_check.py b/tests/R_minetype_check.py
index 96640a6f74..166ab2bac3 100644
--- a/tests/R_minetype_check.py
+++ b/tests/R_minetype_check.py
@@ -10,7 +10,7 @@
 
 def minetypes_check(container: TrackedContainer) -> None:
     """Check if Rscript command can be executed"""
-    LOGGER.info(f"Test that R command can be executed ...")
+    LOGGER.info("Test that R command can be executed ...")
     Rcommand = 'if (length(getOption("jupyter.plot_mimetypes")) != 3) {stop("missing jupyter.plot_mimetypes")}'
     logs = container.run_and_wait(
         timeout=60,
diff --git a/tests/datascience-notebook/test_R_minetypes.py b/tests/datascience-notebook/test_R_minetypes.py
index e8a7369fed..acd0ee004b 100644
--- a/tests/datascience-notebook/test_R_minetypes.py
+++ b/tests/datascience-notebook/test_R_minetypes.py
@@ -8,4 +8,4 @@
 def test_minetypes(container: TrackedContainer) -> None:
     """Check if Rscript command for minetypes can be executed"""
     logs = minetypes_check(container)
-    assert len(logs) == 0, f"Command R command failed"
+    assert len(logs) == 0, "Command R command failed"
diff --git a/tests/r-notebook/test_R_minetypes.py b/tests/r-notebook/test_R_minetypes.py
index e8a7369fed..acd0ee004b 100644
--- a/tests/r-notebook/test_R_minetypes.py
+++ b/tests/r-notebook/test_R_minetypes.py
@@ -8,4 +8,4 @@
 def test_minetypes(container: TrackedContainer) -> None:
     """Check if Rscript command for minetypes can be executed"""
     logs = minetypes_check(container)
-    assert len(logs) == 0, f"Command R command failed"
+    assert len(logs) == 0, "Command R command failed"

From 9d946ecdefef0de836098fbace4193b3974a35c1 Mon Sep 17 00:00:00 2001
From: Darek <darek56@yahoo.com>
Date: Thu, 18 Aug 2022 12:03:24 -0400
Subject: [PATCH 12/22] Update minimal-notebook/Dockerfile

Co-authored-by: Ayaz Salikhov <mathbunnyru@users.noreply.github.com>
---
 minimal-notebook/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/minimal-notebook/Dockerfile b/minimal-notebook/Dockerfile
index d685038320..e421750eee 100644
--- a/minimal-notebook/Dockerfile
+++ b/minimal-notebook/Dockerfile
@@ -39,5 +39,5 @@ 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 specifies how the plot returns from R to the browser
+# 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/

From d773f50f593a24d3f0ba846a6da70204a5c2dde7 Mon Sep 17 00:00:00 2001
From: Darek <darek56@yahoo.com>
Date: Thu, 18 Aug 2022 12:04:13 -0400
Subject: [PATCH 13/22] Update minimal-notebook/Rprofile.site

Co-authored-by: Ayaz Salikhov <mathbunnyru@users.noreply.github.com>
---
 minimal-notebook/Rprofile.site | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/minimal-notebook/Rprofile.site b/minimal-notebook/Rprofile.site
index 551e9aa0e8..51e0dc889d 100644
--- a/minimal-notebook/Rprofile.site
+++ b/minimal-notebook/Rprofile.site
@@ -1,5 +1,5 @@
 
-# Add mimetype to specifies how the plot returns from R to the browser.
+# Add 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/svg+xml', 'application/pdf'))

From 231ec60d76f3a08cd8eab0bf9e7d976b416f5924 Mon Sep 17 00:00:00 2001
From: Darek <darek.bidek@gmail.com>
Date: Thu, 18 Aug 2022 12:06:47 -0400
Subject: [PATCH 14/22] Removing empty line

---
 minimal-notebook/Rprofile.site | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/minimal-notebook/Rprofile.site b/minimal-notebook/Rprofile.site
index 51e0dc889d..4b287455de 100644
--- a/minimal-notebook/Rprofile.site
+++ b/minimal-notebook/Rprofile.site
@@ -1,5 +1,4 @@
-
-# Add mimetype to specify how the plot returns from R to the browser.
+# 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/svg+xml', 'application/pdf'))

From 80de1936640c20fa09e1cecdaa66e7b2b5e2c27a Mon Sep 17 00:00:00 2001
From: Darek <darek.bidek@gmail.com>
Date: Thu, 18 Aug 2022 12:18:04 -0400
Subject: [PATCH 15/22] Renaming minetypes to  mimetypes

---
 tests/{R_minetype_check.py => R_mimetype_check.py} |  3 +--
 tests/datascience-notebook/test_R_mimetypes.py     | 11 +++++++++++
 tests/datascience-notebook/test_R_minetypes.py     | 11 -----------
 tests/r-notebook/test_R_mimetypes.py               | 11 +++++++++++
 tests/r-notebook/test_R_minetypes.py               | 11 -----------
 5 files changed, 23 insertions(+), 24 deletions(-)
 rename tests/{R_minetype_check.py => R_mimetype_check.py} (91%)
 create mode 100644 tests/datascience-notebook/test_R_mimetypes.py
 delete mode 100644 tests/datascience-notebook/test_R_minetypes.py
 create mode 100644 tests/r-notebook/test_R_mimetypes.py
 delete mode 100644 tests/r-notebook/test_R_minetypes.py

diff --git a/tests/R_minetype_check.py b/tests/R_mimetype_check.py
similarity index 91%
rename from tests/R_minetype_check.py
rename to tests/R_mimetype_check.py
index 166ab2bac3..f525492a0e 100644
--- a/tests/R_minetype_check.py
+++ b/tests/R_mimetype_check.py
@@ -2,13 +2,12 @@
 # Distributed under the terms of the Modified BSD License.
 
 import logging
-
 from tests.conftest import TrackedContainer
 
 LOGGER = logging.getLogger(__name__)
 
 
-def minetypes_check(container: TrackedContainer) -> None:
+def mimetypes_check(container: TrackedContainer) -> str:
     """Check if Rscript command can be executed"""
     LOGGER.info("Test that R command can be executed ...")
     Rcommand = 'if (length(getOption("jupyter.plot_mimetypes")) != 3) {stop("missing jupyter.plot_mimetypes")}'
diff --git a/tests/datascience-notebook/test_R_mimetypes.py b/tests/datascience-notebook/test_R_mimetypes.py
new file mode 100644
index 0000000000..9438ff2b8e
--- /dev/null
+++ b/tests/datascience-notebook/test_R_mimetypes.py
@@ -0,0 +1,11 @@
+# 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 mimetypes_check
+
+
+def test_mimetypes(container: TrackedContainer) -> None:
+    """Check if Rscript command for mimetypes can be executed"""
+    logs = mimetypes_check(container)
+    assert len(logs) == 0, "Command R command failed"
diff --git a/tests/datascience-notebook/test_R_minetypes.py b/tests/datascience-notebook/test_R_minetypes.py
deleted file mode 100644
index acd0ee004b..0000000000
--- a/tests/datascience-notebook/test_R_minetypes.py
+++ /dev/null
@@ -1,11 +0,0 @@
-# Copyright (c) Jupyter Development Team.
-# Distributed under the terms of the Modified BSD License.
-
-from tests.conftest import TrackedContainer
-from tests.R_minetype_check import minetypes_check
-
-
-def test_minetypes(container: TrackedContainer) -> None:
-    """Check if Rscript command for minetypes can be executed"""
-    logs = minetypes_check(container)
-    assert len(logs) == 0, "Command R command failed"
diff --git a/tests/r-notebook/test_R_mimetypes.py b/tests/r-notebook/test_R_mimetypes.py
new file mode 100644
index 0000000000..9438ff2b8e
--- /dev/null
+++ b/tests/r-notebook/test_R_mimetypes.py
@@ -0,0 +1,11 @@
+# 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 mimetypes_check
+
+
+def test_mimetypes(container: TrackedContainer) -> None:
+    """Check if Rscript command for mimetypes can be executed"""
+    logs = mimetypes_check(container)
+    assert len(logs) == 0, "Command R command failed"
diff --git a/tests/r-notebook/test_R_minetypes.py b/tests/r-notebook/test_R_minetypes.py
deleted file mode 100644
index acd0ee004b..0000000000
--- a/tests/r-notebook/test_R_minetypes.py
+++ /dev/null
@@ -1,11 +0,0 @@
-# Copyright (c) Jupyter Development Team.
-# Distributed under the terms of the Modified BSD License.
-
-from tests.conftest import TrackedContainer
-from tests.R_minetype_check import minetypes_check
-
-
-def test_minetypes(container: TrackedContainer) -> None:
-    """Check if Rscript command for minetypes can be executed"""
-    logs = minetypes_check(container)
-    assert len(logs) == 0, "Command R command failed"

From c27d085de0e766f032925a226a53579d4ad6d51a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 18 Aug 2022 16:18:22 +0000
Subject: [PATCH 16/22] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/R_mimetype_check.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/R_mimetype_check.py b/tests/R_mimetype_check.py
index f525492a0e..a749f712d9 100644
--- a/tests/R_mimetype_check.py
+++ b/tests/R_mimetype_check.py
@@ -2,6 +2,7 @@
 # Distributed under the terms of the Modified BSD License.
 
 import logging
+
 from tests.conftest import TrackedContainer
 
 LOGGER = logging.getLogger(__name__)

From 722ef81be2609b70737201c879ecaab4d5919583 Mon Sep 17 00:00:00 2001
From: Darek <darek.bidek@gmail.com>
Date: Fri, 19 Aug 2022 08:02:41 -0400
Subject: [PATCH 17/22] Renaming test module to avoid mypy error

---
 .../{test_R_mimetypes.py => test_mimetypes.py}                    | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename tests/datascience-notebook/{test_R_mimetypes.py => test_mimetypes.py} (100%)

diff --git a/tests/datascience-notebook/test_R_mimetypes.py b/tests/datascience-notebook/test_mimetypes.py
similarity index 100%
rename from tests/datascience-notebook/test_R_mimetypes.py
rename to tests/datascience-notebook/test_mimetypes.py

From c3584cd61d6229205d9861c6f4b4a54b3831d54b Mon Sep 17 00:00:00 2001
From: Darek <darek.bidek@gmail.com>
Date: Fri, 19 Aug 2022 08:13:17 -0400
Subject: [PATCH 18/22] Adding to jupyter.plot_mimetypes

---
 minimal-notebook/Rprofile.site | 2 +-
 tests/R_mimetype_check.py      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/minimal-notebook/Rprofile.site b/minimal-notebook/Rprofile.site
index 4b287455de..3d6a93cc1f 100644
--- a/minimal-notebook/Rprofile.site
+++ b/minimal-notebook/Rprofile.site
@@ -1,4 +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/svg+xml', 'application/pdf'))
+options(jupyter.plot_mimetypes = c('text/plain', 'image/png', 'image/jpeg', 'image/svg+xml', 'application/pdf'))
diff --git a/tests/R_mimetype_check.py b/tests/R_mimetype_check.py
index a749f712d9..7ffc4cac98 100644
--- a/tests/R_mimetype_check.py
+++ b/tests/R_mimetype_check.py
@@ -11,7 +11,7 @@
 def mimetypes_check(container: TrackedContainer) -> str:
     """Check if Rscript command can be executed"""
     LOGGER.info("Test that R command can be executed ...")
-    Rcommand = 'if (length(getOption("jupyter.plot_mimetypes")) != 3) {stop("missing jupyter.plot_mimetypes")}'
+    Rcommand = 'if (length(getOption("jupyter.plot_mimetypes")) != 5) {stop("missing jupyter.plot_mimetypes")}'
     logs = container.run_and_wait(
         timeout=60,
         tty=True,

From 01c85d142daa16da657d4b376afb5b902da12f76 Mon Sep 17 00:00:00 2001
From: Ayaz Salikhov <mathbunnyru@users.noreply.github.com>
Date: Sat, 20 Aug 2022 00:16:18 +0400
Subject: [PATCH 19/22] Update R_mimetype_check.py

---
 tests/R_mimetype_check.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/tests/R_mimetype_check.py b/tests/R_mimetype_check.py
index 7ffc4cac98..cc09d13423 100644
--- a/tests/R_mimetype_check.py
+++ b/tests/R_mimetype_check.py
@@ -8,16 +8,14 @@
 LOGGER = logging.getLogger(__name__)
 
 
-def mimetypes_check(container: TrackedContainer) -> str:
+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=60,
+        timeout=10,
         tty=True,
         command=["Rscript", "-e", Rcommand],
     )
     LOGGER.debug(f"{logs=}")
     assert len(logs) == 0, f"Command {Rcommand=} failed"
-
-    return logs

From da13813876fec4197d4a1aef8cdae1b82551e346 Mon Sep 17 00:00:00 2001
From: Ayaz Salikhov <mathbunnyru@users.noreply.github.com>
Date: Sat, 20 Aug 2022 00:16:50 +0400
Subject: [PATCH 20/22] Update test_mimetypes.py

---
 tests/datascience-notebook/test_mimetypes.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/tests/datascience-notebook/test_mimetypes.py b/tests/datascience-notebook/test_mimetypes.py
index 9438ff2b8e..a2ac55cf06 100644
--- a/tests/datascience-notebook/test_mimetypes.py
+++ b/tests/datascience-notebook/test_mimetypes.py
@@ -2,10 +2,9 @@
 # Distributed under the terms of the Modified BSD License.
 
 from tests.conftest import TrackedContainer
-from tests.R_mimetype_check import mimetypes_check
+from tests.R_mimetype_check import check_r_mimetypes
 
 
 def test_mimetypes(container: TrackedContainer) -> None:
     """Check if Rscript command for mimetypes can be executed"""
-    logs = mimetypes_check(container)
-    assert len(logs) == 0, "Command R command failed"
+    check_r_mimetypes(container)

From d4d054ca267a7b51794928e4dbc4813b1f8cc08b Mon Sep 17 00:00:00 2001
From: Ayaz Salikhov <mathbunnyru@users.noreply.github.com>
Date: Sat, 20 Aug 2022 00:17:19 +0400
Subject: [PATCH 21/22] Update test_R_mimetypes.py

---
 tests/r-notebook/test_R_mimetypes.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/tests/r-notebook/test_R_mimetypes.py b/tests/r-notebook/test_R_mimetypes.py
index 9438ff2b8e..361cb2c4f1 100644
--- a/tests/r-notebook/test_R_mimetypes.py
+++ b/tests/r-notebook/test_R_mimetypes.py
@@ -2,10 +2,9 @@
 # Distributed under the terms of the Modified BSD License.
 
 from tests.conftest import TrackedContainer
-from tests.R_mimetype_check import mimetypes_check
+from tests.R_mimetype_check import check_r_mimetypes
 
 
-def test_mimetypes(container: TrackedContainer) -> None:
+def check_r_mimetypes(container: TrackedContainer) -> None:
     """Check if Rscript command for mimetypes can be executed"""
-    logs = mimetypes_check(container)
-    assert len(logs) == 0, "Command R command failed"
+    check_r_mimetypes(container)

From 45f1a7ca787d3152343827e7474773dd4f45ad16 Mon Sep 17 00:00:00 2001
From: Ayaz Salikhov <mathbunnyru@users.noreply.github.com>
Date: Sat, 20 Aug 2022 00:18:35 +0400
Subject: [PATCH 22/22] Update test_R_mimetypes.py

---
 tests/r-notebook/test_R_mimetypes.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/r-notebook/test_R_mimetypes.py b/tests/r-notebook/test_R_mimetypes.py
index 361cb2c4f1..a2ac55cf06 100644
--- a/tests/r-notebook/test_R_mimetypes.py
+++ b/tests/r-notebook/test_R_mimetypes.py
@@ -5,6 +5,6 @@
 from tests.R_mimetype_check import check_r_mimetypes
 
 
-def check_r_mimetypes(container: TrackedContainer) -> None:
+def test_mimetypes(container: TrackedContainer) -> None:
     """Check if Rscript command for mimetypes can be executed"""
     check_r_mimetypes(container)