├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── README.md ├── _bookdown.yml ├── _build.sh ├── _output.yml ├── build_book.sh ├── index.Rmd ├── notebook.Rproj ├── preamble.tex ├── ref.bib ├── render_dir ├── DESCRIPTION ├── LICENSE ├── _bookdown.yml ├── _build.sh ├── _output.yml ├── index.Rmd ├── libs.html ├── notebook_render.Rproj ├── preamble.tex ├── ref.bib ├── style.css └── toc.css ├── style.css └── toc.css /.Rbuildignore: -------------------------------------------------------------------------------- 1 | ^.*\.Rproj$ 2 | ^\.Rproj\.user$ 3 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | .Ruserdata 5 | .DS_store 6 | _book/ 7 | notebook.rds 8 | _bookdown_files/ 9 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: placeholder 2 | Title: Does not matter. 3 | Version: 0.0.1 4 | Imports: bookdown 5 | Remotes: rstudio/bookdown 6 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | CC0 1.0 Universal 2 | 3 | Statement of Purpose 4 | 5 | The laws of most jurisdictions throughout the world automatically confer 6 | exclusive Copyright and Related Rights (defined below) upon the creator and 7 | subsequent owner(s) (each and all, an "owner") of an original work of 8 | authorship and/or a database (each, a "Work"). 9 | 10 | Certain owners wish to permanently relinquish those rights to a Work for the 11 | purpose of contributing to a commons of creative, cultural and scientific 12 | works ("Commons") that the public can reliably and without fear of later 13 | claims of infringement build upon, modify, incorporate in other works, reuse 14 | and redistribute as freely as possible in any form whatsoever and for any 15 | purposes, including without limitation commercial purposes. These owners may 16 | contribute to the Commons to promote the ideal of a free culture and the 17 | further production of creative, cultural and scientific works, or to gain 18 | reputation or greater distribution for their Work in part through the use and 19 | efforts of others. 20 | 21 | For these and/or other purposes and motivations, and without any expectation 22 | of additional consideration or compensation, the person associating CC0 with a 23 | Work (the "Affirmer"), to the extent that he or she is an owner of Copyright 24 | and Related Rights in the Work, voluntarily elects to apply CC0 to the Work 25 | and publicly distribute the Work under its terms, with knowledge of his or her 26 | Copyright and Related Rights in the Work and the meaning and intended legal 27 | effect of CC0 on those rights. 28 | 29 | 1. Copyright and Related Rights. A Work made available under CC0 may be 30 | protected by copyright and related or neighboring rights ("Copyright and 31 | Related Rights"). Copyright and Related Rights include, but are not limited 32 | to, the following: 33 | 34 | i. the right to reproduce, adapt, distribute, perform, display, communicate, 35 | and translate a Work; 36 | 37 | ii. moral rights retained by the original author(s) and/or performer(s); 38 | 39 | iii. publicity and privacy rights pertaining to a person's image or likeness 40 | depicted in a Work; 41 | 42 | iv. rights protecting against unfair competition in regards to a Work, 43 | subject to the limitations in paragraph 4(a), below; 44 | 45 | v. rights protecting the extraction, dissemination, use and reuse of data in 46 | a Work; 47 | 48 | vi. database rights (such as those arising under Directive 96/9/EC of the 49 | European Parliament and of the Council of 11 March 1996 on the legal 50 | protection of databases, and under any national implementation thereof, 51 | including any amended or successor version of such directive); and 52 | 53 | vii. other similar, equivalent or corresponding rights throughout the world 54 | based on applicable law or treaty, and any national implementations thereof. 55 | 56 | 2. Waiver. To the greatest extent permitted by, but not in contravention of, 57 | applicable law, Affirmer hereby overtly, fully, permanently, irrevocably and 58 | unconditionally waives, abandons, and surrenders all of Affirmer's Copyright 59 | and Related Rights and associated claims and causes of action, whether now 60 | known or unknown (including existing as well as future claims and causes of 61 | action), in the Work (i) in all territories worldwide, (ii) for the maximum 62 | duration provided by applicable law or treaty (including future time 63 | extensions), (iii) in any current or future medium and for any number of 64 | copies, and (iv) for any purpose whatsoever, including without limitation 65 | commercial, advertising or promotional purposes (the "Waiver"). Affirmer makes 66 | the Waiver for the benefit of each member of the public at large and to the 67 | detriment of Affirmer's heirs and successors, fully intending that such Waiver 68 | shall not be subject to revocation, rescission, cancellation, termination, or 69 | any other legal or equitable action to disrupt the quiet enjoyment of the Work 70 | by the public as contemplated by Affirmer's express Statement of Purpose. 71 | 72 | 3. Public License Fallback. Should any part of the Waiver for any reason be 73 | judged legally invalid or ineffective under applicable law, then the Waiver 74 | shall be preserved to the maximum extent permitted taking into account 75 | Affirmer's express Statement of Purpose. In addition, to the extent the Waiver 76 | is so judged Affirmer hereby grants to each affected person a royalty-free, 77 | non transferable, non sublicensable, non exclusive, irrevocable and 78 | unconditional license to exercise Affirmer's Copyright and Related Rights in 79 | the Work (i) in all territories worldwide, (ii) for the maximum duration 80 | provided by applicable law or treaty (including future time extensions), (iii) 81 | in any current or future medium and for any number of copies, and (iv) for any 82 | purpose whatsoever, including without limitation commercial, advertising or 83 | promotional purposes (the "License"). The License shall be deemed effective as 84 | of the date CC0 was applied by Affirmer to the Work. Should any part of the 85 | License for any reason be judged legally invalid or ineffective under 86 | applicable law, such partial invalidity or ineffectiveness shall not 87 | invalidate the remainder of the License, and in such case Affirmer hereby 88 | affirms that he or she will not (i) exercise any of his or her remaining 89 | Copyright and Related Rights in the Work or (ii) assert any associated claims 90 | and causes of action with respect to the Work, in either case contrary to 91 | Affirmer's express Statement of Purpose. 92 | 93 | 4. Limitations and Disclaimers. 94 | 95 | a. No trademark or patent rights held by Affirmer are waived, abandoned, 96 | surrendered, licensed or otherwise affected by this document. 97 | 98 | b. Affirmer offers the Work as-is and makes no representations or warranties 99 | of any kind concerning the Work, express, implied, statutory or otherwise, 100 | including without limitation warranties of title, merchantability, fitness 101 | for a particular purpose, non infringement, or the absence of latent or 102 | other defects, accuracy, or the present or absence of errors, whether or not 103 | discoverable, all to the greatest extent permissible under applicable law. 104 | 105 | c. Affirmer disclaims responsibility for clearing rights of other persons 106 | that may apply to the Work or any use thereof, including without limitation 107 | any person's Copyright and Related Rights in the Work. Further, Affirmer 108 | disclaims responsibility for obtaining any necessary consents, permissions 109 | or other rights required for any use of the Work. 110 | 111 | d. Affirmer understands and acknowledges that Creative Commons is not a 112 | party to this document and has no duty or obligation with respect to this 113 | CC0 or use of the Work. 114 | 115 | For more information, please see 116 | 117 | 118 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | Template for a computational lab notebook written using the [bookdown](https://github.com/rstudio/bookdown) R package. 2 | -------------------------------------------------------------------------------- /_bookdown.yml: -------------------------------------------------------------------------------- 1 | book_filename: "notebook" 2 | new_session: yes 3 | -------------------------------------------------------------------------------- /_build.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::gitbook')" 4 | -------------------------------------------------------------------------------- /_output.yml: -------------------------------------------------------------------------------- 1 | bookdown::gitbook: 2 | css: style.css 3 | config: 4 | toc: 5 | before: | 6 |
  • Lab notebook
    • 7 | edit: 8 | link: https://github.com/timoast/notebook-template/edit/master/%s 9 | text: "Edit" 10 | search: yes 11 | sharing: no 12 | df_print: paged 13 | max.print: 10 14 | -------------------------------------------------------------------------------- /build_book.sh: -------------------------------------------------------------------------------- 1 | #! /bin/sh 2 | 3 | 4 | usage="$(basename "$0") -- build bookdown book 5 | -h show help and exit 6 | -a upload book to aws" 7 | 8 | amazon=false # check options 9 | while getopts "ah" opt; do 10 | case $opt in 11 | h) printf "$usage\n" 12 | exit 13 | ;; 14 | a) amazon=true 15 | ;; 16 | esac 17 | done 18 | 19 | # get most recent Rmd file 20 | RMDFILE="$(ls -Art *.Rmd | tail -n 1)" 21 | BASENAME=(${RMDFILE//.Rmd/}) 22 | 23 | # generate/update the markdown 24 | Rscript -e "bookdown::preview_chapter('${RMDFILE}')" 25 | 26 | # copy the markdown file and associated files over to other dir 27 | cp _book/${BASENAME}.md ./render_dir/${BASENAME}.Rmd 28 | cp -r _bookdown_files/${BASENAME}_files ./render_dir/_bookdown_files 29 | 30 | # build book 31 | cd ./render_dir/ 32 | Rscript -e "bookdown::render_book('index.Rmd')" 33 | open -a "Safari" _book/index.html 34 | 35 | # upload to aws 36 | if [ $amazon == true ]; then 37 | aws s3 sync _book/ s3://[bucket name] # set bucket name 38 | fi 39 | -------------------------------------------------------------------------------- /index.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Lab notebook" 3 | author: "" 4 | date: "`r format(Sys.Date(), '%Y')`" 5 | site: bookdown::bookdown_site 6 | output: bookdown::gitbook 7 | documentclass: book 8 | bibliography: [ref.bib] 9 | biblio-style: apalike 10 | link-citations: yes 11 | github-repo: timoast/notebook-template 12 | description: "Computational lab notebook" 13 | --- 14 | 15 | # Welcome 16 | 17 | This book is a collection of Rmarkdown documents that contain data analyses I have done in day-to-day work. The book is written using [bookdown](https://bookdown.org/), and there is a very useful bookdown reference book [here](https://bookdown.org/yihui/bookdown/). 18 | 19 | ## Getting started 20 | 21 | Many different R packages are used in this book, if you would like to install some of them run: 22 | 23 | ```{r packages, eval=FALSE} 24 | install.packages(c("dplyr", "ggplot2", "readr", "data.table", 25 | "shiny", "plotly", "bookdown", "RColorBrewer", 26 | "d3heatmap", "devtools", "ggvis", "tidyr")) 27 | ``` 28 | 29 | [Bioconductor](www.bioconductor.org) is also very useful. 30 | 31 | ```{r bioc, eval=FALSE} 32 | source("http://bioconductor.org/biocLite.R") 33 | biocLite() 34 | ``` 35 | -------------------------------------------------------------------------------- /notebook.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: knitr 13 | LaTeX: pdfLaTeX 14 | 15 | AutoAppendNewline: Yes 16 | StripTrailingWhitespace: Yes 17 | 18 | BuildType: Website 19 | -------------------------------------------------------------------------------- /preamble.tex: -------------------------------------------------------------------------------- 1 | \usepackage{booktabs} 2 | \usepackage{amsthm} 3 | \makeatletter 4 | \def\thm@space@setup{% 5 | \thm@preskip=8pt plus 2pt minus 4pt 6 | \thm@postskip=\thm@preskip 7 | } 8 | \makeatother 9 | -------------------------------------------------------------------------------- /ref.bib: -------------------------------------------------------------------------------- 1 | @Book{xie2015, 2 | title = {Dynamic Documents with {R} and knitr}, 3 | author = {Yihui Xie}, 4 | publisher = {Chapman and Hall/CRC}, 5 | address = {Boca Raton, Florida}, 6 | year = {2015}, 7 | edition = {2nd}, 8 | note = {ISBN 978-1498716963}, 9 | url = {http://yihui.name/knitr/}, 10 | } 11 | -------------------------------------------------------------------------------- /render_dir/DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: placeholder 2 | Title: Does not matter. 3 | Version: 0.0.1 4 | Imports: bookdown 5 | Remotes: rstudio/bookdown 6 | -------------------------------------------------------------------------------- /render_dir/LICENSE: -------------------------------------------------------------------------------- 1 | CC0 1.0 Universal 2 | 3 | Statement of Purpose 4 | 5 | The laws of most jurisdictions throughout the world automatically confer 6 | exclusive Copyright and Related Rights (defined below) upon the creator and 7 | subsequent owner(s) (each and all, an "owner") of an original work of 8 | authorship and/or a database (each, a "Work"). 9 | 10 | Certain owners wish to permanently relinquish those rights to a Work for the 11 | purpose of contributing to a commons of creative, cultural and scientific 12 | works ("Commons") that the public can reliably and without fear of later 13 | claims of infringement build upon, modify, incorporate in other works, reuse 14 | and redistribute as freely as possible in any form whatsoever and for any 15 | purposes, including without limitation commercial purposes. These owners may 16 | contribute to the Commons to promote the ideal of a free culture and the 17 | further production of creative, cultural and scientific works, or to gain 18 | reputation or greater distribution for their Work in part through the use and 19 | efforts of others. 20 | 21 | For these and/or other purposes and motivations, and without any expectation 22 | of additional consideration or compensation, the person associating CC0 with a 23 | Work (the "Affirmer"), to the extent that he or she is an owner of Copyright 24 | and Related Rights in the Work, voluntarily elects to apply CC0 to the Work 25 | and publicly distribute the Work under its terms, with knowledge of his or her 26 | Copyright and Related Rights in the Work and the meaning and intended legal 27 | effect of CC0 on those rights. 28 | 29 | 1. Copyright and Related Rights. A Work made available under CC0 may be 30 | protected by copyright and related or neighboring rights ("Copyright and 31 | Related Rights"). Copyright and Related Rights include, but are not limited 32 | to, the following: 33 | 34 | i. the right to reproduce, adapt, distribute, perform, display, communicate, 35 | and translate a Work; 36 | 37 | ii. moral rights retained by the original author(s) and/or performer(s); 38 | 39 | iii. publicity and privacy rights pertaining to a person's image or likeness 40 | depicted in a Work; 41 | 42 | iv. rights protecting against unfair competition in regards to a Work, 43 | subject to the limitations in paragraph 4(a), below; 44 | 45 | v. rights protecting the extraction, dissemination, use and reuse of data in 46 | a Work; 47 | 48 | vi. database rights (such as those arising under Directive 96/9/EC of the 49 | European Parliament and of the Council of 11 March 1996 on the legal 50 | protection of databases, and under any national implementation thereof, 51 | including any amended or successor version of such directive); and 52 | 53 | vii. other similar, equivalent or corresponding rights throughout the world 54 | based on applicable law or treaty, and any national implementations thereof. 55 | 56 | 2. Waiver. To the greatest extent permitted by, but not in contravention of, 57 | applicable law, Affirmer hereby overtly, fully, permanently, irrevocably and 58 | unconditionally waives, abandons, and surrenders all of Affirmer's Copyright 59 | and Related Rights and associated claims and causes of action, whether now 60 | known or unknown (including existing as well as future claims and causes of 61 | action), in the Work (i) in all territories worldwide, (ii) for the maximum 62 | duration provided by applicable law or treaty (including future time 63 | extensions), (iii) in any current or future medium and for any number of 64 | copies, and (iv) for any purpose whatsoever, including without limitation 65 | commercial, advertising or promotional purposes (the "Waiver"). Affirmer makes 66 | the Waiver for the benefit of each member of the public at large and to the 67 | detriment of Affirmer's heirs and successors, fully intending that such Waiver 68 | shall not be subject to revocation, rescission, cancellation, termination, or 69 | any other legal or equitable action to disrupt the quiet enjoyment of the Work 70 | by the public as contemplated by Affirmer's express Statement of Purpose. 71 | 72 | 3. Public License Fallback. Should any part of the Waiver for any reason be 73 | judged legally invalid or ineffective under applicable law, then the Waiver 74 | shall be preserved to the maximum extent permitted taking into account 75 | Affirmer's express Statement of Purpose. In addition, to the extent the Waiver 76 | is so judged Affirmer hereby grants to each affected person a royalty-free, 77 | non transferable, non sublicensable, non exclusive, irrevocable and 78 | unconditional license to exercise Affirmer's Copyright and Related Rights in 79 | the Work (i) in all territories worldwide, (ii) for the maximum duration 80 | provided by applicable law or treaty (including future time extensions), (iii) 81 | in any current or future medium and for any number of copies, and (iv) for any 82 | purpose whatsoever, including without limitation commercial, advertising or 83 | promotional purposes (the "License"). The License shall be deemed effective as 84 | of the date CC0 was applied by Affirmer to the Work. Should any part of the 85 | License for any reason be judged legally invalid or ineffective under 86 | applicable law, such partial invalidity or ineffectiveness shall not 87 | invalidate the remainder of the License, and in such case Affirmer hereby 88 | affirms that he or she will not (i) exercise any of his or her remaining 89 | Copyright and Related Rights in the Work or (ii) assert any associated claims 90 | and causes of action with respect to the Work, in either case contrary to 91 | Affirmer's express Statement of Purpose. 92 | 93 | 4. Limitations and Disclaimers. 94 | 95 | a. No trademark or patent rights held by Affirmer are waived, abandoned, 96 | surrendered, licensed or otherwise affected by this document. 97 | 98 | b. Affirmer offers the Work as-is and makes no representations or warranties 99 | of any kind concerning the Work, express, implied, statutory or otherwise, 100 | including without limitation warranties of title, merchantability, fitness 101 | for a particular purpose, non infringement, or the absence of latent or 102 | other defects, accuracy, or the present or absence of errors, whether or not 103 | discoverable, all to the greatest extent permissible under applicable law. 104 | 105 | c. Affirmer disclaims responsibility for clearing rights of other persons 106 | that may apply to the Work or any use thereof, including without limitation 107 | any person's Copyright and Related Rights in the Work. Further, Affirmer 108 | disclaims responsibility for obtaining any necessary consents, permissions 109 | or other rights required for any use of the Work. 110 | 111 | d. Affirmer understands and acknowledges that Creative Commons is not a 112 | party to this document and has no duty or obligation with respect to this 113 | CC0 or use of the Work. 114 | 115 | For more information, please see 116 | 117 | 118 | -------------------------------------------------------------------------------- /render_dir/_bookdown.yml: -------------------------------------------------------------------------------- 1 | book_filename: "notebook_render" 2 | new_session: yes 3 | -------------------------------------------------------------------------------- /render_dir/_build.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::gitbook')" 4 | -------------------------------------------------------------------------------- /render_dir/_output.yml: -------------------------------------------------------------------------------- 1 | bookdown::gitbook: 2 | css: style.css 3 | config: 4 | toc: 5 | before: | 6 |
  • Lab notebook
    • 7 | edit: 8 | link: https://github.com/timoast/notebook/edit/master/%s 9 | text: "Edit" 10 | search: yes 11 | sharing: no 12 | df_print: paged 13 | max.print: 10 14 | includes: 15 | in_header: libs.html 16 | -------------------------------------------------------------------------------- /render_dir/index.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Lab notebook" 3 | author: "" 4 | date: "2017" 5 | site: bookdown::bookdown_site 6 | output: bookdown::gitbook 7 | documentclass: book 8 | bibliography: [ref.bib] 9 | biblio-style: apalike 10 | link-citations: yes 11 | github-repo: timoast/notebook-template 12 | description: "Computational lab notebook" 13 | --- 14 | 15 | # Welcome 16 | 17 | This book is a collection of Rmarkdown documents that contain data analyses I have done in day-to-day work. The book is written using [bookdown](https://bookdown.org/), and there is a very useful bookdown reference book [here](https://bookdown.org/yihui/bookdown/). 18 | 19 | ## Getting started 20 | 21 | Many different R packages are used in this book, if you would like to install some them run: 22 | 23 | 24 | ```r 25 | install.packages(c("dplyr", "ggplot2", "readr", "data.table", 26 | "shiny", "plotly", "bookdown", "RColorBrewer", 27 | "d3heatmap", "devtools", "ggvis", "tidyr")) 28 | ``` 29 | 30 | [Bioconductor](www.bioconductor.org) is also very useful. 31 | 32 | 33 | ```r 34 | source("http://bioconductor.org/biocLite.R") 35 | biocLite() 36 | ``` 37 | -------------------------------------------------------------------------------- /render_dir/libs.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | -------------------------------------------------------------------------------- /render_dir/notebook_render.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: knitr 13 | LaTeX: pdfLaTeX 14 | 15 | AutoAppendNewline: Yes 16 | StripTrailingWhitespace: Yes 17 | 18 | BuildType: Website 19 | -------------------------------------------------------------------------------- /render_dir/preamble.tex: -------------------------------------------------------------------------------- 1 | \usepackage{booktabs} 2 | \usepackage{amsthm} 3 | \makeatletter 4 | \def\thm@space@setup{% 5 | \thm@preskip=8pt plus 2pt minus 4pt 6 | \thm@postskip=\thm@preskip 7 | } 8 | \makeatother 9 | -------------------------------------------------------------------------------- /render_dir/ref.bib: -------------------------------------------------------------------------------- 1 | @Book{xie2015, 2 | title = {Dynamic Documents with {R} and knitr}, 3 | author = {Yihui Xie}, 4 | publisher = {Chapman and Hall/CRC}, 5 | address = {Boca Raton, Florida}, 6 | year = {2015}, 7 | edition = {2nd}, 8 | note = {ISBN 978-1498716963}, 9 | url = {http://yihui.name/knitr/}, 10 | } 11 | -------------------------------------------------------------------------------- /render_dir/style.css: -------------------------------------------------------------------------------- 1 | .rmdcaution, .rmdimportant, .rmdnote, .rmdtip, .rmdwarning { 2 | padding: 1em 1em 1em 4em; 3 | margin-bottom: 10px; 4 | background: #f5f5f5 5px center/3em no-repeat; 5 | } 6 | .rmdcaution { 7 | background-image: url("../images/caution.png"); 8 | } 9 | .rmdimportant { 10 | background-image: url("../images/important.png"); 11 | } 12 | .rmdnote { 13 | background-image: url("../images/note.png"); 14 | } 15 | .rmdtip { 16 | background-image: url("../images/tip.png"); 17 | } 18 | .rmdwarning { 19 | background-image: url("../images/warning.png"); 20 | } 21 | p.caption { 22 | color: #777; 23 | margin-top: 10px; 24 | } 25 | p code { 26 | white-space: inherit; 27 | } 28 | pre { 29 | word-break: normal; 30 | word-wrap: normal; 31 | } 32 | pre code { 33 | white-space: inherit; 34 | } 35 | p.flushright { 36 | text-align: right; 37 | } 38 | blockquote > p:last-child { 39 | text-align: right; 40 | } 41 | blockquote > p:first-child { 42 | text-align: inherit; 43 | } 44 | .header-section-number { 45 | padding-right: .2em; 46 | font-weight: 500; 47 | } 48 | .level1 .header-section-number { 49 | display: inline-block; 50 | border-bottom: 3px solid; 51 | } 52 | .level1 h1 { 53 | border-bottom: 1px solid; 54 | } 55 | h1, h2, h3, h4, h5, h6 { 56 | font-weight: normal; 57 | } 58 | h1.title { 59 | font-weight: 700; 60 | } 61 | .book .book-body .page-wrapper .page-inner section.normal strong { 62 | font-weight: 500; 63 | } 64 | -------------------------------------------------------------------------------- /render_dir/toc.css: -------------------------------------------------------------------------------- 1 | #TOC ul, 2 | #TOC li, 3 | #TOC span, 4 | #TOC a { 5 | margin: 0; 6 | padding: 0; 7 | position: relative; 8 | } 9 | #TOC { 10 | line-height: 1; 11 | border-radius: 5px 5px 0 0; 12 | background: #141414; 13 | background: linear-gradient(to bottom, #333333 0%, #141414 100%); 14 | border-bottom: 2px solid #0fa1e0; 15 | width: auto; 16 | } 17 | #TOC:after, 18 | #TOC ul:after { 19 | content: ''; 20 | display: block; 21 | clear: both; 22 | } 23 | #TOC a { 24 | background: #141414; 25 | background: linear-gradient(to bottom, #333333 0%, #141414 100%); 26 | color: #ffffff; 27 | display: block; 28 | padding: 19px 20px; 29 | text-decoration: none; 30 | text-shadow: none; 31 | } 32 | #TOC ul { 33 | list-style: none; 34 | } 35 | #TOC > ul > li { 36 | display: inline-block; 37 | float: left; 38 | margin: 0; 39 | } 40 | #TOC > ul > li > a { 41 | color: #ffffff; 42 | } 43 | #TOC > ul > li:hover:after { 44 | content: ''; 45 | display: block; 46 | width: 0; 47 | height: 0; 48 | position: absolute; 49 | left: 50%; 50 | bottom: 0; 51 | border-left: 10px solid transparent; 52 | border-right: 10px solid transparent; 53 | border-bottom: 10px solid #0fa1e0; 54 | margin-left: -10px; 55 | } 56 | #TOC > ul > li:first-child > a { 57 | border-radius: 5px 0 0 0; 58 | } 59 | #TOC.align-right > ul > li:first-child > a, 60 | #TOC.align-center > ul > li:first-child > a { 61 | border-radius: 0; 62 | } 63 | #TOC.align-right > ul > li:last-child > a { 64 | border-radius: 0 5px 0 0; 65 | } 66 | #TOC > ul > li.active > a, 67 | #TOC > ul > li:hover > a { 68 | color: #ffffff; 69 | box-shadow: inset 0 0 3px #000000; 70 | background: #070707; 71 | background: linear-gradient(to bottom, #262626 0%, #070707 100%); 72 | } 73 | #TOC .has-sub { 74 | z-index: 1; 75 | } 76 | #TOC .has-sub:hover > ul { 77 | display: block; 78 | } 79 | #TOC .has-sub ul { 80 | display: none; 81 | position: absolute; 82 | width: 200px; 83 | top: 100%; 84 | left: 0; 85 | } 86 | #TOC .has-sub ul li a { 87 | background: #0fa1e0; 88 | border-bottom: 1px dotted #31b7f1; 89 | filter: none; 90 | display: block; 91 | line-height: 120%; 92 | padding: 10px; 93 | color: #ffffff; 94 | } 95 | #TOC .has-sub ul li:hover a { 96 | background: #0c7fb0; 97 | } 98 | #TOC ul ul li:hover > a { 99 | color: #ffffff; 100 | } 101 | #TOC .has-sub .has-sub:hover > ul { 102 | display: block; 103 | } 104 | #TOC .has-sub .has-sub ul { 105 | display: none; 106 | position: absolute; 107 | left: 100%; 108 | top: 0; 109 | } 110 | #TOC .has-sub .has-sub ul li a { 111 | background: #0c7fb0; 112 | border-bottom: 1px dotted #31b7f1; 113 | } 114 | #TOC .has-sub .has-sub ul li a:hover { 115 | background: #0a6d98; 116 | } 117 | #TOC ul ul li.last > a, 118 | #TOC ul ul li:last-child > a, 119 | #TOC ul ul ul li.last > a, 120 | #TOC ul ul ul li:last-child > a, 121 | #TOC .has-sub ul li:last-child > a, 122 | #TOC .has-sub ul li.last > a { 123 | border-bottom: 0; 124 | } 125 | -------------------------------------------------------------------------------- /style.css: -------------------------------------------------------------------------------- 1 | .rmdcaution, .rmdimportant, .rmdnote, .rmdtip, .rmdwarning { 2 | padding: 1em 1em 1em 4em; 3 | margin-bottom: 10px; 4 | background: #f5f5f5 5px center/3em no-repeat; 5 | } 6 | .rmdcaution { 7 | background-image: url("../images/caution.png"); 8 | } 9 | .rmdimportant { 10 | background-image: url("../images/important.png"); 11 | } 12 | .rmdnote { 13 | background-image: url("../images/note.png"); 14 | } 15 | .rmdtip { 16 | background-image: url("../images/tip.png"); 17 | } 18 | .rmdwarning { 19 | background-image: url("../images/warning.png"); 20 | } 21 | p.caption { 22 | color: #777; 23 | margin-top: 10px; 24 | } 25 | p code { 26 | white-space: inherit; 27 | } 28 | pre { 29 | word-break: normal; 30 | word-wrap: normal; 31 | } 32 | pre code { 33 | white-space: inherit; 34 | } 35 | p.flushright { 36 | text-align: right; 37 | } 38 | blockquote > p:last-child { 39 | text-align: right; 40 | } 41 | blockquote > p:first-child { 42 | text-align: inherit; 43 | } 44 | .header-section-number { 45 | padding-right: .2em; 46 | font-weight: 500; 47 | } 48 | .level1 .header-section-number { 49 | display: inline-block; 50 | border-bottom: 3px solid; 51 | } 52 | .level1 h1 { 53 | border-bottom: 1px solid; 54 | } 55 | h1, h2, h3, h4, h5, h6 { 56 | font-weight: normal; 57 | } 58 | h1.title { 59 | font-weight: 700; 60 | } 61 | .book .book-body .page-wrapper .page-inner section.normal strong { 62 | font-weight: 500; 63 | } 64 | -------------------------------------------------------------------------------- /toc.css: -------------------------------------------------------------------------------- 1 | #TOC ul, 2 | #TOC li, 3 | #TOC span, 4 | #TOC a { 5 | margin: 0; 6 | padding: 0; 7 | position: relative; 8 | } 9 | #TOC { 10 | line-height: 1; 11 | border-radius: 5px 5px 0 0; 12 | background: #141414; 13 | background: linear-gradient(to bottom, #333333 0%, #141414 100%); 14 | border-bottom: 2px solid #0fa1e0; 15 | width: auto; 16 | } 17 | #TOC:after, 18 | #TOC ul:after { 19 | content: ''; 20 | display: block; 21 | clear: both; 22 | } 23 | #TOC a { 24 | background: #141414; 25 | background: linear-gradient(to bottom, #333333 0%, #141414 100%); 26 | color: #ffffff; 27 | display: block; 28 | padding: 19px 20px; 29 | text-decoration: none; 30 | text-shadow: none; 31 | } 32 | #TOC ul { 33 | list-style: none; 34 | } 35 | #TOC > ul > li { 36 | display: inline-block; 37 | float: left; 38 | margin: 0; 39 | } 40 | #TOC > ul > li > a { 41 | color: #ffffff; 42 | } 43 | #TOC > ul > li:hover:after { 44 | content: ''; 45 | display: block; 46 | width: 0; 47 | height: 0; 48 | position: absolute; 49 | left: 50%; 50 | bottom: 0; 51 | border-left: 10px solid transparent; 52 | border-right: 10px solid transparent; 53 | border-bottom: 10px solid #0fa1e0; 54 | margin-left: -10px; 55 | } 56 | #TOC > ul > li:first-child > a { 57 | border-radius: 5px 0 0 0; 58 | } 59 | #TOC.align-right > ul > li:first-child > a, 60 | #TOC.align-center > ul > li:first-child > a { 61 | border-radius: 0; 62 | } 63 | #TOC.align-right > ul > li:last-child > a { 64 | border-radius: 0 5px 0 0; 65 | } 66 | #TOC > ul > li.active > a, 67 | #TOC > ul > li:hover > a { 68 | color: #ffffff; 69 | box-shadow: inset 0 0 3px #000000; 70 | background: #070707; 71 | background: linear-gradient(to bottom, #262626 0%, #070707 100%); 72 | } 73 | #TOC .has-sub { 74 | z-index: 1; 75 | } 76 | #TOC .has-sub:hover > ul { 77 | display: block; 78 | } 79 | #TOC .has-sub ul { 80 | display: none; 81 | position: absolute; 82 | width: 200px; 83 | top: 100%; 84 | left: 0; 85 | } 86 | #TOC .has-sub ul li a { 87 | background: #0fa1e0; 88 | border-bottom: 1px dotted #31b7f1; 89 | filter: none; 90 | display: block; 91 | line-height: 120%; 92 | padding: 10px; 93 | color: #ffffff; 94 | } 95 | #TOC .has-sub ul li:hover a { 96 | background: #0c7fb0; 97 | } 98 | #TOC ul ul li:hover > a { 99 | color: #ffffff; 100 | } 101 | #TOC .has-sub .has-sub:hover > ul { 102 | display: block; 103 | } 104 | #TOC .has-sub .has-sub ul { 105 | display: none; 106 | position: absolute; 107 | left: 100%; 108 | top: 0; 109 | } 110 | #TOC .has-sub .has-sub ul li a { 111 | background: #0c7fb0; 112 | border-bottom: 1px dotted #31b7f1; 113 | } 114 | #TOC .has-sub .has-sub ul li a:hover { 115 | background: #0a6d98; 116 | } 117 | #TOC ul ul li.last > a, 118 | #TOC ul ul li:last-child > a, 119 | #TOC ul ul ul li.last > a, 120 | #TOC ul ul ul li:last-child > a, 121 | #TOC .has-sub ul li:last-child > a, 122 | #TOC .has-sub ul li.last > a { 123 | border-bottom: 0; 124 | } 125 | --------------------------------------------------------------------------------