Commit 74a67a8e authored by Frédéric Santos's avatar Frédéric Santos

Update init file

parent e6e97b92
......@@ -7,6 +7,7 @@ RUN apt-get update && apt-get install software-properties-common
RUN apt-get install -y \
curl \
git \
gnupg \
gpm \
imagemagick \
......@@ -14,6 +15,8 @@ RUN apt-get install -y \
libacl1 \
libasound2 \
libcanberra-gtk3-module \
libcurl4 \
libcurl4-openssl-dev \
liblcms2-2 \
libdbus-1-3 \
libgif7 \
......@@ -25,40 +28,41 @@ RUN apt-get install -y \
libpng16-16 \
librsvg2-2 \
libsm6 \
libssl-dev \
libtiff5 \
libx11-xcb1 \
libxml2 \
libxml++2.6-dev \
libxpm4 \
openssh-client \
texinfo \
&& rm -rf /var/lib/apt/lists/*
# Files:
RUN mkdir /home/article
RUN mkdir /home/article/org_manuscript
COPY ./model5-names.bst /home/article/org_manuscript/model5-names.bst
COPY ./ox-extra.el /home/article/org_manuscript/ox-extra.el
COPY ./init_Santos2020.el /home/article/org_manuscript/init_Santos2020.el
COPY /manuscript_outliers_Santos_2020.org /home/article/org_manuscript/manuscript_outliers_Santos_2020.org
# Install Latex:
RUN add-apt-repository universe
RUN apt-get update && apt-get install -y \
latexmk \
texlive
# R:
#RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
#RUN add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'
#RUN apt-get update && apt-get install -t bionic-cran35 r-base=3.6.2-1eoan
# Install R and the R packages used in the article:
RUN apt-get update && apt-get install r-base=3.6.1-4
RUN R -e "options(repos = \
list(CRAN = 'http://mran.revolutionanalytics.com/snapshot/2020-01-05/')); \
install.packages(c('aplpack', 'FactoMineR', 'mvoutlier', 'quantreg', 'remotes', 'robustbase', 'solitude', 'univOutl'))"
RUN R -e "remotes::install_git('https://gitlab.com/f.santos/anthrostat.git', ref = 'v0.1.2')"
RUN R -e "remotes::install_github('geanes/bioanth', ref = 'b179b396')"
# Install Emacs:
# Install Emacs and its packages:
RUN apt-get install emacs=1:26.3+1-1ubuntu1
RUN emacs --script /home/article/org_manuscript/init_Santos2020.el
# Latex:
RUN apt-get install texlive
RUN R -e "options(repos = \
list(CRAN = 'http://mran.revolutionanalytics.com/snapshot/2020-01-05/')); \
install.packages(c('aplpack', 'devtools', 'FactoMineR', 'mvoutlier', 'quantreg', 'robustbase', 'solitude', 'univOutl'), dep = TRUE)"
RUN R -e "devtools::install_git('https://gitlab.com/f.santos/anthrostat.git', ref = 'v0.1.2')"
RUN R -e "devtools::install_github('geanes/bioanth', ref = 'b179b396')"
# Move the article files to the Docker (/!\ still have to add bibfile):
RUN mkdir /home/article
RUN mkdir /home/article/org_manuscript
COPY ./model5-names.bst /home/article/org_manuscript/model5-names.bst
COPY ./ox-extra.el /home/article/org_manuscript/ox-extra.el
COPY ./init_Santos2020.el /home/article/org_manuscript/init_Santos2020.el
COPY /manuscript_outliers_Santos_2020.org /home/article/org_manuscript/manuscript_outliers_Santos_2020.org
# Launch Emacs:
COPY ./init_Santos2020.el /root/.emacs.d/init.el
......
......@@ -44,9 +44,23 @@
:init
(require 'ess-site)
:config
;; Remove Flymake
(setq ess-use-flymake nil))
;; Remove Flymake:
(setq ess-use-flymake nil)
;; Syntax highlighting:
(setq ess-R-font-lock-keywords '((ess-R-fl-keyword:keywords . t)
(ess-R-fl-keyword:constants . t)
(ess-R-fl-keyword:modifiers . t)
(ess-R-fl-keyword:fun-defs . t)
(ess-R-fl-keyword:assign-ops . t)
(ess-R-fl-keyword:%op% . t)
(ess-fl-keyword:fun-calls . t)
(ess-fl-keyword:numbers . t)
(ess-fl-keyword:operators)
(ess-fl-keyword:delimiters)
(ess-fl-keyword:=)
(ess-R-fl-keyword:F&T . t))))
;; Org-mode settings:
(use-package org
:ensure t
:init
......@@ -100,6 +114,12 @@
:config
(setq show-paren-delay 0)
(show-paren-mode 1))
;; Use polymode:
(use-package poly-org
:ensure t)
(use-package poly-R
:ensure t)
;; LaTeX configuration:
(use-package tex
......@@ -116,3 +136,12 @@
(add-hook 'tex-mode-hook 'tex-pdf-on)
(add-hook 'latex-mode-hook 'tex-pdf-on)
(setq TeX-PDF-mode t))
;; Use 'solarized' theme:
(use-package solarized-theme
:ensure t
:config
(setq solarized-distinct-fringe-background t)
(setq solarized-use-variable-pitch nil)
(setq solarized-scale-org-headlines nil)
(load-theme 'solarized-light t))
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