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vnijsvnijs
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3.3.0
1 parent f1beceb commit e702a28

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lines changed

‎connectorx/Dockerfile

+2-2
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,7 @@ RUN pip3.11 install poetry
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# Cloning the connectorx repo and switching to the 0.3.1 tag
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RUN git clone https://github.com/sfu-db/connector-x.git
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WORKDIR /wheeler/connector-x
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RUN git checkout tags/v0.3.2
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RUN git checkout tags/v0.3.3
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# Installing maturin
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RUN pip3.11 install maturin[patchelf]==0.14.15
@@ -46,7 +46,7 @@ RUN maturin build -m connectorx-python/Cargo.toml -i python3.11 --release
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# the below didn't work for me
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# COPY /wheeler/connector-x/connectorx-python/target/wheels/connectorx-* .
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49-
# use the below to access the wheel in /wheeler/connector-x/connectorx-python/target/wheels/
49+
# use the below to access the wheel in /wheeler/connector-x/connectorx-python/target/wheels/
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# docker run -it -v ./:/root your_user_name/connectorx /bin/bash
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# then navigate to the directory below and copy the wheel to the home directory

‎files/install-rstudio.sh

+2-8
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@@ -47,15 +47,9 @@ if [ "$RSTUDIO_VERSION" = "latest" ]; then
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fi
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if [ "$(uname -m)" != "aarch64" ]; then
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# wget "https://s3.amazonaws.com/rstudio-ide-build/server/$UBUNTU_VERSION/amd64/rstudio-server-2023.12.0-daily-330-amd64.deb" -O "$DOWNLOAD_FILE"
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# wget "https://s3.amazonaws.com/rstudio-ide-build/server/jammy/amd64/rstudio-server-2023.12.0-daily-330-amd64.deb" -O "$DOWNLOAD_FILE"
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wget "https://s3.amazonaws.com/rstudio-ide-build/server/jammy/amd64/rstudio-server-2023.12.0-daily-330-amd64.deb" -O "$DOWNLOAD_FILE"
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# wget "https://s3.amazonaws.com/rstudio-ide-build/server/jammy/amd64/rstudio-server-2023.12.0-369-amd64.deb" -O "$DOWNLOAD_FILE"
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wget "https://s3.amazonaws.com/rstudio-ide-build/server/jammy/amd64/rstudio-server-2023.03.0-548-amd64.deb" -O "$DOWNLOAD_FILE"
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else
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# wget "https://s3.amazonaws.com/rstudio-ide-build/server/$UBUNTU_VERSION/arm64/rstudio-server-2023.05.0-daily-293-arm64.deb" -O "$DOWNLOAD_FILE"
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wget "https://s3.amazonaws.com/rstudio-ide-build/server/jammy/arm64/rstudio-server-2023.12.0-daily-330-arm64.deb" -O "$DOWNLOAD_FILE"
57-
# wget "https://s3.amazonaws.com/rstudio-ide-build/server/jammy/arm64/rstudio-server-2023.12.0-daily-330-arm64.deb" -O "$DOWNLOAD_FILE"
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# wget "https://s3.amazonaws.com/rstudio-ide-build/server/jammy/arm64/rstudio-server-2023.12.0-369-arm64.deb" -O "$DOWNLOAD_FILE"
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wget "https://s3.amazonaws.com/rstudio-ide-build/server/jammy/arm64/rstudio-server-2023.03.0-548-arm64.deb" -O "$DOWNLOAD_FILE"
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fi
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dpkg -i "$DOWNLOAD_FILE"

‎files/setup-arrow.sh

+1-6
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@@ -16,15 +16,10 @@ fi
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NCPUS=${NCPUS:--1}
1818

19-
# R -e "Sys.setenv(ARROW_PARQUET = 'ON', ARROW_WITH_SNAPPY = 'ON', ARROW_R_DEV = TRUE); devtools::install_version('arrow', version='9.0.0.2', repos='${CRAN}', Ncpus=${NCPUS})"
20-
# R -e "Sys.setenv(ARROW_PARQUET = 'ON', ARROW_WITH_SNAPPY = 'ON', ARROW_R_DEV = TRUE, ARROW_USE_PKG_CONFIG=TRUE); install.packages('arrow', repo='${CRAN}', Ncpus=${NCPUS})"
21-
# R -e "Sys.setenv(ARROW_PARQUET = 'ON', ARROW_WITH_SNAPPY = 'ON', ARROW_R_DEV = TRUE); devtools::install_version('arrow', version='10.0.1', repos='${CRAN}', Ncpus=${NCPUS})"
22-
# R -e "Sys.setenv(ARROW_PARQUET = 'ON', ARROW_WITH_SNAPPY = 'ON', ARROW_R_DEV = TRUE); devtools::install_version('arrow', version='11.0.0.3', repos='${CRAN}', Ncpus=${NCPUS})"
23-
# R -e "Sys.setenv(ARROW_PARQUET = 'ON', ARROW_WITH_SNAPPY = 'ON', ARROW_R_DEV = TRUE); remotes::install_version('arrow', version='${PYARROW_VERSION}', repos='${CRAN}', Ncpus=${NCPUS})"
2419
R -e "Sys.setenv(ARROW_PARQUET = 'ON', ARROW_WITH_SNAPPY = 'ON', ARROW_R_DEV = TRUE); install.packages('arrow', version='${PYARROW_VERSION}', repos='${CRAN}', Ncpus=${NCPUS})"
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2621
# these run into issues earlier in the install process so we install them here
27-
R -e "install.packages(c('systemfonts', 'textshaping', 'ragg', 'httpgd', 'tidyverse', 'svglite'), repos='${CRAN}', Ncpus=${NCPUS})"
22+
# R -e "install.packages(c('systemfonts', 'textshaping', 'ragg', 'httpgd', 'tidyverse', 'svglite'), repos='${CRAN}', Ncpus=${NCPUS})"
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2924
# for some reason this part needs to be at the end and does not work when combined with setup-radiant
3025
# library(arrow)

‎files/setup-extra.sh

+5-7
Original file line numberDiff line numberDiff line change
@@ -21,9 +21,9 @@ if [ -f "/opt/conda/bin/R" ]; then
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mamba install --quiet --yes -c conda-forge \
2222
r-raster \
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imagemagick \
24-
libgdal \
24+
libgdal
2525

26-
R -e "install.packages('rgdal', repo='${CRAN}', Ncpus=${NCPUS})"
26+
# R -e "install.packages('rgdal', repo='${CRAN}', Ncpus=${NCPUS})"
2727
else
2828
mamba install --quiet --yes -c conda-forge \
2929
r-raster \
@@ -47,16 +47,14 @@ else
4747
libicu-dev \
4848
&& rm -rf /var/lib/apt/lists/*
4949

50-
R -e "install.packages('rgdal', repo='${CRAN}', Ncpus=${NCPUS})"
50+
# R -e "install.packages('rgdal', repo='${CRAN}', Ncpus=${NCPUS})"
5151
fi
5252

53-
R -e "install.packages(c('magick', 'leaflet', 'stringi', 'profvis'), repo='${CRAN}', Ncpus=${NCPUS})" \
54-
-e "install.packages(c('simmer', 'simmer.plot', 'EnvStats', 'matrixStats'), repo='${CRAN}', Ncpus=${NCPUS})" \
55-
-e "install.packages(c('highcharter', 'viridis'), repo='${CRAN}', Ncpus=${NCPUS})" \
56-
-e "install.packages(c('tidytext', 'wordcloud'), repo='${CRAN}', Ncpus=${NCPUS})" \
53+
# R -e "install.packages(c('magick', 'leaflet', 'stringi', 'profvis'), repo='${CRAN}', Ncpus=${NCPUS})"
5754
R -e "install.packages('devtools', repo='${CRAN}', Ncpus=${NCPUS})" \
5855
-e "remotes::install_github('vnijs/webshot', upgrade = 'never')" \
5956
-e "webshot::install_phantomjs()"
57+
# -e "install.packages(c('tidytext', 'wordcloud'), repo='${CRAN}', Ncpus=${NCPUS})"
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6159
# for Machine Learning with PyTorch and Scikit-Learn
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mamba install --quiet --yes -c conda-forge pytorch-lightning tensorboard zip

‎files/setup-hadoop.sh

+1
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@@ -10,5 +10,6 @@ curl -sL --retry 3 \
1010
| gunzip \
1111
| tar -x --strip-components=1 -C $HADOOP_HOME \
1212
&& rm -rf $HADOOP_HOME/share/doc \
13+
&& ln -s /opt/hadoop/bin/hadoop /usr/bin/hadoop \
1314
&& chown -R ${NB_USER} $HADOOP_HOME \
1415
&& mkdir -p "${HADOOP_HOME}/logs"

‎files/setup-quarto.sh

-1
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@@ -11,7 +11,6 @@ NCPUS=${NCPUS:--1}
1111
UBUNTU_VERSION=${UBUNTU_VERSION:-`lsb_release -sc`}
1212
CRAN=${CRAN:-https://cran.r-project.org}
1313
CRAN_SOURCE=${CRAN/"__linux__/$UBUNTU_VERSION/"/""}
14-
QUARTO_VERSION="1.4.506"
1514

1615
if [ "$(uname -m)" != "aarch64" ]; then
1716
# ln -fs /usr/lib/rstudio-server/bin/quarto/bin/quarto /usr/local/bin

‎files/setup-radiant.sh

+2-4
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@@ -46,16 +46,14 @@ R -e "install.packages('igraph', repo='${CRAN}', Ncpus=${NCPUS})" \
4646
-e "install.packages(c('httpgd', 'languageserver'), repo='${CRAN}', Ncpus=${NCPUS})" \
4747
-e "remotes::install_github('radiant-rstats/radiant.update', upgrade = 'never')" \
4848
-e "remotes::install_github('vnijs/gitgadget', upgrade = 'never')" \
49-
-e "remotes::install_github('IRkernel/IRkernel', upgrade = 'never')" \
50-
-e "remotes::install_github('IRkernel/IRdisplay', upgrade = 'never')" \
51-
-e "IRkernel::installspec(user=FALSE)" \
5249
-e "remotes::install_github('radiant-rstats/radiant.data', upgrade = 'never')" \
5350
-e "remotes::install_github('radiant-rstats/radiant.design', upgrade = 'never')" \
5451
-e "remotes::install_github('radiant-rstats/radiant.basics', upgrade = 'never')" \
5552
-e "remotes::install_github('radiant-rstats/radiant.model', upgrade = 'never')" \
5653
-e "remotes::install_github('radiant-rstats/radiant.multivariate', upgrade = 'never')" \
5754
-e "remotes::install_github('radiant-rstats/radiant', upgrade = 'never')" \
5855
-e "remotes::install_github('radiant-rstats/radiant.update', upgrade = 'never')" \
59-
-e "install.packages('duckdb', repo='${CRAN}', Ncpus=${NCPUS})"
56+
-e "install.packages('duckdb', repo='${CRAN}', Ncpus=${NCPUS})" \
57+
-e "install.packages(c('dbplyr', 'DBI', 'dtplyr', 'RPostgres', 'RSQLite', 'pool', 'usethis'), repo='${CRAN}', Ncpus=${NCPUS})"
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6159
rm -rf /tmp/downloaded_packages

‎files/setup-tidyverse.sh

+7-5
Original file line numberDiff line numberDiff line change
@@ -42,10 +42,12 @@ NCPUS=${NCPUS:--1}
4242
# fi
4343

4444
# version 0.6.32 (2023-6-26) is causing install issues on 6/7/2023
45-
R -e "install.packages('remotes', repo='${CRAN}', Ncpus=${NCPUS})" \
46-
-e "remotes::install_version('digest', version='0.6.31', repos='${CRAN}', Ncpus=${NCPUS})" \
47-
-e "install.packages(c('ragg', 'rlist'), repo='${CRAN}', Ncpus=${NCPUS})" \
48-
-e "install.packages(c('tidyverse', 'rmarkdown', 'gert', 'usethis'), repo='${CRAN}', Ncpus=${NCPUS})" \
49-
-e "install.packages(c('dbplyr', 'DBI', 'dtplyr', 'RPostgres', 'RSQLite'), repo='${CRAN}', Ncpus=${NCPUS})"
45+
# -e "remotes::install_version('digest', version='0.6.31', repos='${CRAN}', Ncpus=${NCPUS})" \
46+
# -e "install.packages(c('ragg', 'rlist'), repo='${CRAN}', Ncpus=${NCPUS})" \
47+
# -e "install.packages(c('tidyverse', 'rmarkdown', 'gert', 'usethis'), repo='${CRAN}', Ncpus=${NCPUS})" \
48+
# -e "install.packages(c('dbplyr', 'DBI', 'dtplyr', 'RPostgres', 'RSQLite'), repo='${CRAN}', Ncpus=${NCPUS})"
49+
50+
# R -e "install.packages('remotes', repo='${CRAN}', Ncpus=${NCPUS})" \
51+
# -e "install.packages(c('dbplyr', 'DBI', 'dtplyr', 'RPostgres', 'RSQLite', 'pool', 'usethis'), repo='${CRAN}', Ncpus=${NCPUS})"
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5153
rm -rf /tmp/downloaded_packages

‎files/setup.sh

+12
Original file line numberDiff line numberDiff line change
@@ -141,6 +141,18 @@ else
141141
fi
142142
fi
143143

144+
if command -v poetry &> /dev/null; then
145+
echo "Poetry is already installed"
146+
else
147+
echo "Installing Poetry $POETRY_VERSION"
148+
pipx install poetry==$POETRY_VERSION
149+
fi
150+
151+
if [ ! -d "${HOMEDIR}/.rsm-msba/zsh/.oh-my-zsh/plugins/poetry" ]; then
152+
mkdir "${HOMEDIR}/.rsm-msba/zsh/.oh-my-zsh/plugins/poetry" ]
153+
poetry completions zsh > $ZSH_CUSTOM/plugins/poetry/_poetry
154+
fi
155+
144156
if [ ! -f "${HOMEDIR}/.rsm-msba/zsh/.zshrc" ]; then
145157
cp /etc/skel/.zshrc "${HOMEDIR}/.rsm-msba/zsh/.zshrc"
146158
source ~/.rsm-msba/zsh/.zshrc 2>/dev/null

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