Merge pull request #36 from BerriJ/dev

Adds pybind11 + carma config

.devcontainer/devcontainer.json

@@ -62,7 +62,7 @@
                     "CMAKE_TOOLCHAIN_FILE": "/usr/vcpkg/scripts/buildsystems/vcpkg.cmake"
                 },
                 // Python
-                // "python.dataScience.notebookFileRoot": "${workspaceFolder}/code",
+                "jupyter.notebookFileRoot": "${workspaceFolder}",
                 "python.pythonPath": "/usr/bin/python3",
                 "python.dataScience.interactiveWindowMode": "perFile",
                 "python.dataScience.sendSelectionToInteractiveWindow": true,

Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:jammy@sha256:2b7412e6465c3c7fc5bb21d3e6f1917c167358449fecac8176c6e496e5c1f05f
+FROM ubuntu:jammy@sha256:6042500cf4b44023ea1894effe7890666b0c5c7871ed83a97c36c76ae560bb9b
 
 SHELL ["/bin/bash", "-c"]
 
@@ -32,9 +32,9 @@ RUN echo "ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula sele
     git \
     build-essential \
     cmake \
+    ninja-build \
     ccache \
-    libboost-all-dev \
-    libarmadillo-dev \
+    gfortran \
     netbase \
     zip \
     unzip \
@@ -74,14 +74,16 @@ RUN chmod +x install_scripts/install_phantomjs.sh &&\
     install_scripts/install_phantomjs.sh
 
 # Install vcpkg C++ dependency manager
-# RUN git clone --depth=1 https://github.com/Microsoft/vcpkg /usr/local/vcpkg \
-#     && rm -rf /usr/local/vcpkg/.git \
-#     && cd /usr/local/vcpkg \
-#     && ./bootstrap-vcpkg.sh \
-#     && ./vcpkg integrate install \
-#     && chown --recursive $USERNAME:$USERNAME /usr/local/vcpkg
-# 
-# ENV PATH="/usr/local/vcpkg:${PATH}"
+RUN git clone --depth=1 https://github.com/Microsoft/vcpkg /usr/local/vcpkg \
+    && rm -rf /usr/local/vcpkg/.git \
+    && cd /usr/local/vcpkg \
+    && ./bootstrap-vcpkg.sh \
+    && ./vcpkg integrate install \
+    && /usr/local/vcpkg/vcpkg install armadillo \
+    && /usr/local/vcpkg/vcpkg install pybind11 \
+    && chown --recursive $USERNAME:$USERNAME /usr/local/vcpkg
+
+ENV PATH="/usr/local/vcpkg:${PATH}"
 
 # Install Python CARMA
 RUN git clone --depth=1 https://github.com/RUrlus/carma.git /usr/local/carma \
@@ -91,7 +93,7 @@ RUN git clone --depth=1 https://github.com/RUrlus/carma.git /usr/local/carma \
     && cd build \
     && cmake -DCARMA_INSTALL_LIB=ON .. \
     && cmake --build . --config Release --target install \
-    && chown --recursive $USERNAME:$USERNAME /usr/local/carma
+    && rm -rf /usr/local/carma
 
 # Install Python
 COPY package_lists/python_packages.txt /package_lists/python_packages.txt
@@ -131,7 +133,7 @@ ENV R_VERSION=4.3.2
 
 # Set RSPM snapshot see:
 # https://packagemanager.posit.co/client/#/repos/cran/setup?r_environment=other&snapshot=2023-10-04&distribution=ubuntu-22.04
-ENV R_REPOS=https://packagemanager.posit.co/cran/__linux__/jammy/2023-10-04
+ENV R_REPOS=https://packagemanager.posit.co/cran/__linux__/jammy/2024-02-02
 
 COPY install_scripts/install_r.sh /install_scripts/install_r.sh
 COPY package_lists/r_packages.txt /package_lists/r_packages.txt

install_scripts/install_r.sh

@@ -11,6 +11,7 @@ BUILDDEPS="libssl-dev"
 
 RUNDEPS="ca-certificates \
       less \
+      jq \
       libatlas-base-dev \
       libxml2-dev \
       vim-tiny \

package_lists/python_packages.txt

@@ -20,7 +20,7 @@ numpy
 pandas
 plotly
 properscoring
-pybind11[global]
+Pyarrow
 pylint
 pyparsing==2.4.7
 pytest

package_lists/r_packages.txt

@@ -42,13 +42,14 @@ ggthemes
 gifski
 glmnet
 gridExtra
+grImport2
 gt
 Hmisc
 htmlwidgets
-httpgd
 igraph
 inline
 inspectdf
+jqr
 kableExtra
 knitr
 languageserver
@@ -85,7 +86,6 @@ RcppParallel
 RcppProgress
 RCurl
 reactable
-renderthis
 reshape2
 reticulate
 rgenoud

package_lists/r_packages_github.txt

@@ -1,4 +1,7 @@
 BerriJ/strsplit.fix
 GreenGrassBlueOcean/RefinitivR
+jhelvy/renderthis
 ManuelHentschel/vscDebugger@*release
+nx10/httpgd
+sjp/grConvert
 stenevang/sftp