From f1eb78a68d8af3921d3f7d47b53830ba08731dce Mon Sep 17 00:00:00 2001 From: Chris Pyles Date: Sun, 18 Sep 2022 13:48:26 -0700 Subject: [PATCH 1/3] updated setup.sh --- .gitignore | 1 + otter/generate/templates/python/setup.sh | 4 +++- otter/generate/templates/r/setup.sh | 6 ++++-- test/test-assign/example-autograder-correct/setup.sh | 4 +++- test/test-assign/gs-autograder-correct/setup.sh | 4 +++- test/test-assign/rmd-autograder-correct/setup.sh | 6 ++++-- test/test-run/autograder/source/setup.sh | 4 +++- .../test-autograder/autograder-correct/setup.sh | 4 +++- .../test-autograder/autograder-custom-env/setup.sh | 4 +++- .../test-autograder/autograder-r-correct/setup.sh | 6 ++++-- .../test-autograder/autograder-token-correct/setup.sh | 4 +++- 11 files changed, 34 insertions(+), 13 deletions(-) diff --git a/.gitignore b/.gitignore index 906581c7c..8358b5fb6 100644 --- a/.gitignore +++ b/.gitignore @@ -22,3 +22,4 @@ docs/_static/notebooks/html arm-Dockerfile htmlcov/ .pytest_cache/ +/sync.sh diff --git a/otter/generate/templates/python/setup.sh b/otter/generate/templates/python/setup.sh index 8a60f9727..026b6b681 100644 --- a/otter/generate/templates/python/setup.sh +++ b/otter/generate/templates/python/setup.sh @@ -3,9 +3,11 @@ if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then apt-get clean apt-get update - apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese + apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese # install wkhtmltopdf + wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb + apt-get install -y /tmp/libssl1.1.deb wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb apt-get install -y /tmp/wkhtmltopdf.deb diff --git a/otter/generate/templates/r/setup.sh b/otter/generate/templates/r/setup.sh index e13b4a72f..bfeec401a 100644 --- a/otter/generate/templates/r/setup.sh +++ b/otter/generate/templates/r/setup.sh @@ -3,10 +3,12 @@ if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then apt-get clean apt-get update - apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese - apt-get install -y libnlopt-dev cmake libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev apt-utils libpoppler-cpp-dev libavfilter-dev libharfbuzz-dev libfribidi-dev imagemagick libmagick++-dev pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese libxft-dev + apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese + apt-get install -y libnlopt-dev cmake libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev apt-utils libpoppler-cpp-dev libavfilter-dev libharfbuzz-dev libfribidi-dev imagemagick libmagick++-dev pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese libxft-dev # install wkhtmltopdf + wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb + apt-get install -y /tmp/libssl1.1.deb wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb apt-get install -y /tmp/wkhtmltopdf.deb diff --git a/test/test-assign/example-autograder-correct/setup.sh b/test/test-assign/example-autograder-correct/setup.sh index 926e3b967..68b283c9e 100644 --- a/test/test-assign/example-autograder-correct/setup.sh +++ b/test/test-assign/example-autograder-correct/setup.sh @@ -3,9 +3,11 @@ if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then apt-get clean apt-get update - apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese + apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese # install wkhtmltopdf + wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb + apt-get install -y /tmp/libssl1.1.deb wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb apt-get install -y /tmp/wkhtmltopdf.deb diff --git a/test/test-assign/gs-autograder-correct/setup.sh b/test/test-assign/gs-autograder-correct/setup.sh index 926e3b967..68b283c9e 100644 --- a/test/test-assign/gs-autograder-correct/setup.sh +++ b/test/test-assign/gs-autograder-correct/setup.sh @@ -3,9 +3,11 @@ if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then apt-get clean apt-get update - apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese + apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese # install wkhtmltopdf + wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb + apt-get install -y /tmp/libssl1.1.deb wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb apt-get install -y /tmp/wkhtmltopdf.deb diff --git a/test/test-assign/rmd-autograder-correct/setup.sh b/test/test-assign/rmd-autograder-correct/setup.sh index d6a7c86b7..8ca1f71fc 100644 --- a/test/test-assign/rmd-autograder-correct/setup.sh +++ b/test/test-assign/rmd-autograder-correct/setup.sh @@ -3,10 +3,12 @@ if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then apt-get clean apt-get update - apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese - apt-get install -y libnlopt-dev cmake libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev apt-utils libpoppler-cpp-dev libavfilter-dev libharfbuzz-dev libfribidi-dev imagemagick libmagick++-dev pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese libxft-dev + apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese + apt-get install -y libnlopt-dev cmake libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev apt-utils libpoppler-cpp-dev libavfilter-dev libharfbuzz-dev libfribidi-dev imagemagick libmagick++-dev pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese libxft-dev # install wkhtmltopdf + wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb + apt-get install -y /tmp/libssl1.1.deb wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb apt-get install -y /tmp/wkhtmltopdf.deb diff --git a/test/test-run/autograder/source/setup.sh b/test/test-run/autograder/source/setup.sh index dcabff747..f401033ad 100644 --- a/test/test-run/autograder/source/setup.sh +++ b/test/test-run/autograder/source/setup.sh @@ -7,9 +7,11 @@ apt-get clean apt-get update apt-get install -y pandoc -apt-get install -y texlive-xetex texlive-fonts-recommended texlive-generic-recommended +apt-get install -y texlive-xetex texlive-fonts-recommended texlive-plain-generic # install wkhtmltopdf +wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb +apt-get install -y /tmp/libssl1.1.deb wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb apt-get install -y /tmp/wkhtmltopdf.deb diff --git a/test/test_generate/test-autograder/autograder-correct/setup.sh b/test/test_generate/test-autograder/autograder-correct/setup.sh index 926e3b967..68b283c9e 100644 --- a/test/test_generate/test-autograder/autograder-correct/setup.sh +++ b/test/test_generate/test-autograder/autograder-correct/setup.sh @@ -3,9 +3,11 @@ if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then apt-get clean apt-get update - apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese + apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese # install wkhtmltopdf + wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb + apt-get install -y /tmp/libssl1.1.deb wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb apt-get install -y /tmp/wkhtmltopdf.deb diff --git a/test/test_generate/test-autograder/autograder-custom-env/setup.sh b/test/test_generate/test-autograder/autograder-custom-env/setup.sh index 926e3b967..68b283c9e 100644 --- a/test/test_generate/test-autograder/autograder-custom-env/setup.sh +++ b/test/test_generate/test-autograder/autograder-custom-env/setup.sh @@ -3,9 +3,11 @@ if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then apt-get clean apt-get update - apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese + apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese # install wkhtmltopdf + wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb + apt-get install -y /tmp/libssl1.1.deb wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb apt-get install -y /tmp/wkhtmltopdf.deb diff --git a/test/test_generate/test-autograder/autograder-r-correct/setup.sh b/test/test_generate/test-autograder/autograder-r-correct/setup.sh index 1e37600f4..126533ddc 100644 --- a/test/test_generate/test-autograder/autograder-r-correct/setup.sh +++ b/test/test_generate/test-autograder/autograder-r-correct/setup.sh @@ -3,10 +3,12 @@ if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then apt-get clean apt-get update - apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese - apt-get install -y libnlopt-dev cmake libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev apt-utils libpoppler-cpp-dev libavfilter-dev libharfbuzz-dev libfribidi-dev imagemagick libmagick++-dev pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese libxft-dev + apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese + apt-get install -y libnlopt-dev cmake libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev apt-utils libpoppler-cpp-dev libavfilter-dev libharfbuzz-dev libfribidi-dev imagemagick libmagick++-dev pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese libxft-dev # install wkhtmltopdf + wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb + apt-get install -y /tmp/libssl1.1.deb wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb apt-get install -y /tmp/wkhtmltopdf.deb diff --git a/test/test_generate/test-autograder/autograder-token-correct/setup.sh b/test/test_generate/test-autograder/autograder-token-correct/setup.sh index 926e3b967..68b283c9e 100644 --- a/test/test_generate/test-autograder/autograder-token-correct/setup.sh +++ b/test/test_generate/test-autograder/autograder-token-correct/setup.sh @@ -3,9 +3,11 @@ if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then apt-get clean apt-get update - apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese + apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese # install wkhtmltopdf + wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb + apt-get install -y /tmp/libssl1.1.deb wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb apt-get install -y /tmp/wkhtmltopdf.deb From 0b0882111cfc3b33da9b03c21caf9603f476f698 Mon Sep 17 00:00:00 2001 From: Chris Pyles Date: Sun, 18 Sep 2022 14:19:03 -0700 Subject: [PATCH 2/3] pin R>=4.0.0 --- environment.yml | 2 +- otter/generate/templates/r/environment.yml | 4 ++-- test/test-assign/rmd-autograder-correct/environment.yml | 4 ++-- .../test-autograder/autograder-r-correct/environment.yml | 4 ++-- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/environment.yml b/environment.yml index 4a8aee073..740296150 100644 --- a/environment.yml +++ b/environment.yml @@ -4,7 +4,7 @@ channels: - defaults dependencies: - python>=3.6 - - r-base + - r-base>=4.0.0 - r-essentials - r-devtools - pip diff --git a/otter/generate/templates/r/environment.yml b/otter/generate/templates/r/environment.yml index 2e86bfa01..12e236b30 100644 --- a/otter/generate/templates/r/environment.yml +++ b/otter/generate/templates/r/environment.yml @@ -6,8 +6,8 @@ dependencies: - python=3.7 - pip - nb_conda_kernels - - r-base - - r-essentials + - r-base>=4.0.0 + - r-essentials - r-devtools - libgit2 - libgomp diff --git a/test/test-assign/rmd-autograder-correct/environment.yml b/test/test-assign/rmd-autograder-correct/environment.yml index 0bd9b54ac..b0f3d05a4 100644 --- a/test/test-assign/rmd-autograder-correct/environment.yml +++ b/test/test-assign/rmd-autograder-correct/environment.yml @@ -6,8 +6,8 @@ dependencies: - python=3.7 - pip - nb_conda_kernels - - r-base - - r-essentials + - r-base>=4.0.0 + - r-essentials - r-devtools - libgit2 - libgomp diff --git a/test/test_generate/test-autograder/autograder-r-correct/environment.yml b/test/test_generate/test-autograder/autograder-r-correct/environment.yml index 0bd9b54ac..b0f3d05a4 100644 --- a/test/test_generate/test-autograder/autograder-r-correct/environment.yml +++ b/test/test_generate/test-autograder/autograder-r-correct/environment.yml @@ -6,8 +6,8 @@ dependencies: - python=3.7 - pip - nb_conda_kernels - - r-base - - r-essentials + - r-base>=4.0.0 + - r-essentials - r-devtools - libgit2 - libgomp From 5fb908327821cec901573ce35cdd20a856d84965 Mon Sep 17 00:00:00 2001 From: Chris Pyles Date: Mon, 19 Sep 2022 21:09:13 -0700 Subject: [PATCH 3/3] changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 52eeda4ab..2102c6e21 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,7 @@ * Close temporary file handle before removal when checking tests in `otter.Notebook.export` * Fixed bug caused by unspecified encoding in Windows JSON loads per [#524](https://github.com/ucbds-infra/otter-grader/issues/524) +* Updated autograder zip `setup.sh` file and `r-base` version per [#514](https://github.com/ucbds-infra/otter-grader/issues/514) **v4.0.1:**