# HG changeset patch # User Vimalkumar Velayudhan # Date 1440603430 -3600 # Node ID 628f82e72d7202622c6bb729cc60e229c8b720be # Parent 8a87a2c44d099fc96468ac6a0a681122e96521bd Version as released on PyPI 0.1.0 diff -r 8a87a2c44d09 -r 628f82e72d72 .editorconfig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.editorconfig Wed Aug 26 16:37:10 2015 +0100 @@ -0,0 +1,21 @@ +# http://editorconfig.org + +root = true + +[*] +indent_style = space +indent_size = 4 +trim_trailing_whitespace = true +insert_final_newline = true +charset = utf-8 +end_of_line = lf + +[*.bat] +indent_style = tab +end_of_line = crlf + +[LICENSE] +insert_final_newline = false + +[Makefile] +indent_style = tab \ No newline at end of file diff -r 8a87a2c44d09 -r 628f82e72d72 AUTHORS.rst --- a/AUTHORS.rst Fri Aug 21 12:37:54 2015 +0100 +++ b/AUTHORS.rst Wed Aug 26 16:37:10 2015 +0100 @@ -1,1 +1,13 @@ -docs/authors.rst \ No newline at end of file +======= +Credits +======= + +Development Lead +---------------- + +* Vimalkumar Velayudhan + +Contributors +------------ + +None yet. Why not be the first? \ No newline at end of file diff -r 8a87a2c44d09 -r 628f82e72d72 CONTRIBUTING.rst --- a/CONTRIBUTING.rst Fri Aug 21 12:37:54 2015 +0100 +++ b/CONTRIBUTING.rst Wed Aug 26 16:37:10 2015 +0100 @@ -1,1 +1,111 @@ -docs/contributing.rst \ No newline at end of file +============ +Contributing +============ + +Contributions are welcome, and they are greatly appreciated! Every +little bit helps, and credit will always be given. + +You can contribute in many ways: + +Types of Contributions +---------------------- + +Report Bugs +~~~~~~~~~~~ + +Report bugs at https://github.com/vimalkumarvelayudhan/riboplot/issues. + +If you are reporting a bug, please include: + +* Your operating system name and version. +* Any details about your local setup that might be helpful in troubleshooting. +* Detailed steps to reproduce the bug. + +Fix Bugs +~~~~~~~~ + +Look through the GitHub issues for bugs. Anything tagged with "bug" +is open to whoever wants to implement it. + +Implement Features +~~~~~~~~~~~~~~~~~~ + +Look through the GitHub issues for features. Anything tagged with "feature" +is open to whoever wants to implement it. + +Write Documentation +~~~~~~~~~~~~~~~~~~~ + +RiboPlot could always use more documentation, whether as part of the +official RiboPlot docs, in docstrings, or even on the web in blog posts, +articles, and such. + +Submit Feedback +~~~~~~~~~~~~~~~ + +The best way to send feedback is to file an issue at https://github.com/vimalkumarvelayudhan/riboplot/issues. + +If you are proposing a feature: + +* Explain in detail how it would work. +* Keep the scope as narrow as possible, to make it easier to implement. +* Remember that this is a volunteer-driven project, and that contributions + are welcome :) + +Get Started! +------------ + +Ready to contribute? Here's how to set up `riboplot` for local development. + +1. Fork the `riboplot` repo on GitHub. +2. Clone your fork locally:: + + $ git clone git@github.com:your_name_here/riboplot.git + +3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:: + + $ mkvirtualenv riboplot + $ cd riboplot/ + $ python setup.py develop + +4. Create a branch for local development:: + + $ git checkout -b name-of-your-bugfix-or-feature + + Now you can make your changes locally. + +5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox:: + + $ flake8 riboplot tests + $ python setup.py test + $ tox + + To get flake8 and tox, just pip install them into your virtualenv. + +6. Commit your changes and push your branch to GitHub:: + + $ git add . + $ git commit -m "Your detailed description of your changes." + $ git push origin name-of-your-bugfix-or-feature + +7. Submit a pull request through the GitHub website. + +Pull Request Guidelines +----------------------- + +Before you submit a pull request, check that it meets these guidelines: + +1. The pull request should include tests. +2. If the pull request adds functionality, the docs should be updated. Put + your new functionality into a function with a docstring, and add the + feature to the list in README.rst. +3. The pull request should work for Python 2.6, 2.7, 3.3, and 3.4, and for PyPy. Check + https://travis-ci.org/vimalkumarvelayudhan/riboplot/pull_requests + and make sure that the tests pass for all supported Python versions. + +Tips +---- + +To run a subset of tests:: + + $ python -m unittest tests.test_riboplot \ No newline at end of file diff -r 8a87a2c44d09 -r 628f82e72d72 HISTORY.rst --- a/HISTORY.rst Fri Aug 21 12:37:54 2015 +0100 +++ b/HISTORY.rst Wed Aug 26 16:37:10 2015 +0100 @@ -1,1 +1,9 @@ -docs/history.rst \ No newline at end of file +.. :changelog: + +History +======= + +0.1.0 (2015-08-24) +--------------------- + +* First release on PyPI. diff -r 8a87a2c44d09 -r 628f82e72d72 MANIFEST.in --- a/MANIFEST.in Fri Aug 21 12:37:54 2015 +0100 +++ b/MANIFEST.in Wed Aug 26 16:37:10 2015 +0100 @@ -1,11 +1,2 @@ -include AUTHORS.rst -include CONTRIBUTING.rst -include HISTORY.rst -include LICENSE -include README.rst - -recursive-include tests * -recursive-exclude * __pycache__ recursive-exclude * *.py[co] - -recursive-include docs *.rst conf.py Makefile make.bat \ No newline at end of file +exclude riboplot/riboplot_multi.py diff -r 8a87a2c44d09 -r 628f82e72d72 README.rst --- a/README.rst Fri Aug 21 12:37:54 2015 +0100 +++ b/README.rst Wed Aug 26 16:37:10 2015 +0100 @@ -1,1 +1,28 @@ -docs/readme.rst \ No newline at end of file +=============================== +RiboPlot +=============================== + +.. image:: https://img.shields.io/travis/vimalkumarvelayudhan/riboplot.svg + :target: https://travis-ci.org/vimalkumarvelayudhan/riboplot + +.. image:: https://img.shields.io/pypi/v/riboplot.svg + :target: https://pypi.python.org/pypi/riboplot + + +RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format). + +There are two programs in the package: + +**riboplot** + Plot and output read counts (csv) for a single transcript. + +**ribocount** + Output read counts for all transcripts in an alignment. + +For help on using these programs, please refer to :ref:`usage`. + + +Free software: GPL license. + +Documentation: https://riboplot.readthedocs.org. + diff -r 8a87a2c44d09 -r 628f82e72d72 data/css/asc.gif Binary file data/css/asc.gif has changed diff -r 8a87a2c44d09 -r 628f82e72d72 data/css/bg.gif Binary file data/css/bg.gif has changed diff -r 8a87a2c44d09 -r 628f82e72d72 data/css/custom.css --- a/data/css/custom.css Fri Aug 21 12:37:54 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ -.info { - font-weight: normal; -} - -.text-muted { - font-size: 0.6em; - text-align: center; - color: #555555; -} - -#main { - text-align: center; -} - -#page-title { - margin-top: 5%; -} - -/* tables */ -table.tablesorter { - border: 1px solid #eeeeee; -} - -table.tablesorter thead tr .header { - background-image: url(bg.gif); - background-repeat: no-repeat; - background-position: center right; - cursor: pointer; -} - -table.tablesorter thead tr .headerSortUp { - background-image: url(asc.gif); -} - -table.tablesorter thead tr .headerSortDown { - background-image: url(desc.gif); -} - -table.tablesorter thead tr .headerSortDown, table.tablesorter thead tr .headerSortUp { - background-color: #eeeeee; -} - -table.tablesorter tbody { - font-family: monospace; -} - -#overlay { - top: 20px; - left: 50%; - position: absolute; - margin-left: -170px; - width: 250px; - text-align: center; - display: none; - margin-top: -10px; - background: #F6FF00; - color: #515151; - padding: 3px; - border-radius: 5px; - box-shadow: 3px 3px 3px #eeeeee; -} \ No newline at end of file diff -r 8a87a2c44d09 -r 628f82e72d72 data/css/desc.gif Binary file data/css/desc.gif has changed diff -r 8a87a2c44d09 -r 628f82e72d72 data/css/normalize.css --- a/data/css/normalize.css Fri Aug 21 12:37:54 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,427 +0,0 @@ -/*! normalize.css v3.0.2 | MIT License | git.io/normalize */ - -/** - * 1. 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Normalize vertical alignment of `progress` in Chrome, Firefox, and Opera. - */ - -audio, -canvas, -progress, -video { - display: inline-block; /* 1 */ - vertical-align: baseline; /* 2 */ -} - -/** - * Prevent modern browsers from displaying `audio` without controls. - * Remove excess height in iOS 5 devices. - */ - -audio:not([controls]) { - display: none; - height: 0; -} - -/** - * Address `[hidden]` styling not present in IE 8/9/10. - * Hide the `template` element in IE 8/9/11, Safari, and Firefox < 22. - */ - -[hidden], -template { - display: none; -} - -/* Links - ========================================================================== */ - -/** - * Remove the gray background color from active links in IE 10. - */ - -a { - background-color: transparent; -} - -/** - * Improve readability when focused and also mouse hovered in all browsers. - */ - -a:active, -a:hover { - outline: 0; -} - -/* Text-level semantics - ========================================================================== */ - -/** - * Address styling not present in IE 8/9/10/11, Safari, and Chrome. - */ - -abbr[title] { - border-bottom: 1px dotted; -} - -/** - * Address style set to `bolder` in Firefox 4+, Safari, and Chrome. - */ - -b, -strong { - font-weight: bold; -} - -/** - * Address styling not present in Safari and Chrome. - */ - -dfn { - font-style: italic; -} - -/** - * Address variable `h1` font-size and margin within `section` and `article` - * contexts in Firefox 4+, Safari, and Chrome. - */ - -h1 { - font-size: 2em; - margin: 0.67em 0; -} - -/** - * Address styling not present in IE 8/9. - */ - -mark { - background: #ff0; - color: #000; -} - -/** - * Address inconsistent and variable font size in all browsers. - */ - -small { - font-size: 80%; -} - -/** - * Prevent `sub` and `sup` affecting `line-height` in all browsers. - */ - -sub, -sup { - font-size: 75%; - line-height: 0; - position: relative; - vertical-align: baseline; -} - -sup { - top: -0.5em; -} - -sub { - bottom: -0.25em; -} - -/* Embedded content - ========================================================================== */ - -/** - * Remove border when inside `a` element in IE 8/9/10. - */ - -img { - border: 0; -} - -/** - * Correct overflow not hidden in IE 9/10/11. - */ - -svg:not(:root) { - overflow: hidden; -} - -/* Grouping content - ========================================================================== */ - -/** - * Address margin not present in IE 8/9 and Safari. - */ - -figure { - margin: 1em 40px; -} - -/** - * Address differences between Firefox and other browsers. - */ - -hr { - -moz-box-sizing: content-box; - box-sizing: content-box; - height: 0; -} - -/** - * Contain overflow in all browsers. - */ - -pre { - overflow: auto; -} - -/** - * Address odd `em`-unit font size rendering in all browsers. - */ - -code, -kbd, -pre, -samp { - font-family: monospace, monospace; - font-size: 1em; -} - -/* Forms - ========================================================================== */ - -/** - * Known limitation: by default, Chrome and Safari on OS X allow very limited - * styling of `select`, unless a `border` property is set. - */ - -/** - * 1. Correct color not being inherited. - * Known issue: affects color of disabled elements. - * 2. Correct font properties not being inherited. - * 3. Address margins set differently in Firefox 4+, Safari, and Chrome. - */ - -button, -input, -optgroup, -select, -textarea { - color: inherit; /* 1 */ - font: inherit; /* 2 */ - margin: 0; /* 3 */ -} - -/** - * Address `overflow` set to `hidden` in IE 8/9/10/11. - */ - -button { - overflow: visible; -} - -/** - * Address inconsistent `text-transform` inheritance for `button` and `select`. - * All other form control elements do not inherit `text-transform` values. - * Correct `button` style inheritance in Firefox, IE 8/9/10/11, and Opera. - * Correct `select` style inheritance in Firefox. - */ - -button, -select { - text-transform: none; -} - -/** - * 1. Avoid the WebKit bug in Android 4.0.* where (2) destroys native `audio` - * and `video` controls. - * 2. Correct inability to style clickable `input` types in iOS. - * 3. Improve usability and consistency of cursor style between image-type - * `input` and others. - */ - -button, -html input[type="button"], /* 1 */ -input[type="reset"], -input[type="submit"] { - -webkit-appearance: button; /* 2 */ - cursor: pointer; /* 3 */ -} - -/** - * Re-set default cursor for disabled elements. - */ - -button[disabled], -html input[disabled] { - cursor: default; -} - -/** - * Remove inner padding and border in Firefox 4+. - */ - -button::-moz-focus-inner, -input::-moz-focus-inner { - border: 0; - padding: 0; -} - -/** - * Address Firefox 4+ setting `line-height` on `input` using `!important` in - * the UA stylesheet. - */ - -input { - line-height: normal; -} - -/** - * It's recommended that you don't attempt to style these elements. - * Firefox's implementation doesn't respect box-sizing, padding, or width. - * - * 1. Address box sizing set to `content-box` in IE 8/9/10. - * 2. 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Address `box-sizing` set to `border-box` in Safari and Chrome - * (include `-moz` to future-proof). - */ - -input[type="search"] { - -webkit-appearance: textfield; /* 1 */ - -moz-box-sizing: content-box; - -webkit-box-sizing: content-box; /* 2 */ - box-sizing: content-box; -} - -/** - * Remove inner padding and search cancel button in Safari and Chrome on OS X. - * Safari (but not Chrome) clips the cancel button when the search input has - * padding (and `textfield` appearance). - */ - -input[type="search"]::-webkit-search-cancel-button, -input[type="search"]::-webkit-search-decoration { - -webkit-appearance: none; -} - -/** - * Define consistent border, margin, and padding. - */ - -fieldset { - border: 1px solid #c0c0c0; - margin: 0 2px; - padding: 0.35em 0.625em 0.75em; -} - -/** - * 1. Correct `color` not being inherited in IE 8/9/10/11. - * 2. Remove padding so people aren't caught out if they zero out fieldsets. - */ - -legend { - border: 0; /* 1 */ - padding: 0; /* 2 */ -} - -/** - * Remove default vertical scrollbar in IE 8/9/10/11. - */ - -textarea { - overflow: auto; -} - -/** - * Don't inherit the `font-weight` (applied by a rule above). - * NOTE: the default cannot safely be changed in Chrome and Safari on OS X. - */ - -optgroup { - font-weight: bold; -} - -/* Tables - ========================================================================== */ - -/** - * Remove most spacing between table cells. - */ - -table { - border-collapse: collapse; - border-spacing: 0; -} - -td, -th { - padding: 0; -} \ No newline at end of file diff -r 8a87a2c44d09 -r 628f82e72d72 data/css/skeleton.css --- a/data/css/skeleton.css Fri Aug 21 12:37:54 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,419 +0,0 @@ -/* -* Skeleton V2.0.4 -* Copyright 2014, Dave Gamache -* www.getskeleton.com -* Free to use under the MIT license. -* http://www.opensource.org/licenses/mit-license.php -* 12/29/2014 -*/ - - -/* Table of contents -–––––––––––––––––––––––––––––––––––––––––––––––––– -- Grid -- Base Styles -- Typography -- Links -- Buttons -- Forms -- Lists -- Code -- Tables -- Spacing -- Utilities -- Clearing -- Media Queries -*/ - - -/* Grid -–––––––––––––––––––––––––––––––––––––––––––––––––– */ -.container { - position: relative; - width: 100%; - max-width: 960px; - margin: 0 auto; - padding: 0 20px; - box-sizing: border-box; } -.column, -.columns { - width: 100%; - float: left; - box-sizing: border-box; } - -/* For devices larger than 400px */ -@media (min-width: 400px) { - .container { - width: 85%; - padding: 0; } -} - -/* For devices larger than 550px */ -@media (min-width: 550px) { - .container { - width: 80%; } - .column, - .columns { - margin-left: 4%; } - .column:first-child, - .columns:first-child { - margin-left: 0; } - - .one.column, - .one.columns { width: 4.66666666667%; } - .two.columns { width: 13.3333333333%; } - .three.columns { width: 22%; } - .four.columns { width: 30.6666666667%; } - .five.columns { width: 39.3333333333%; } - .six.columns { width: 48%; } - .seven.columns { width: 56.6666666667%; } - .eight.columns { width: 65.3333333333%; } - .nine.columns { width: 74.0%; } - .ten.columns { width: 82.6666666667%; } - .eleven.columns { width: 91.3333333333%; } - .twelve.columns { width: 100%; margin-left: 0; } - - .one-third.column { width: 30.6666666667%; } - .two-thirds.column { width: 65.3333333333%; } - - .one-half.column { width: 48%; } - - /* Offsets */ - .offset-by-one.column, - .offset-by-one.columns { margin-left: 8.66666666667%; } - .offset-by-two.column, - .offset-by-two.columns { margin-left: 17.3333333333%; } - .offset-by-three.column, - .offset-by-three.columns { margin-left: 26%; } - .offset-by-four.column, - .offset-by-four.columns { margin-left: 34.6666666667%; } - .offset-by-five.column, - .offset-by-five.columns { margin-left: 43.3333333333%; } - .offset-by-six.column, - .offset-by-six.columns { margin-left: 52%; } - .offset-by-seven.column, - .offset-by-seven.columns { margin-left: 60.6666666667%; } - .offset-by-eight.column, - .offset-by-eight.columns { margin-left: 69.3333333333%; } - .offset-by-nine.column, - .offset-by-nine.columns { margin-left: 78.0%; } - .offset-by-ten.column, - .offset-by-ten.columns { margin-left: 86.6666666667%; } - .offset-by-eleven.column, - .offset-by-eleven.columns { margin-left: 95.3333333333%; } - - .offset-by-one-third.column, - .offset-by-one-third.columns { margin-left: 34.6666666667%; } - .offset-by-two-thirds.column, - .offset-by-two-thirds.columns { margin-left: 69.3333333333%; } - - .offset-by-one-half.column, - .offset-by-one-half.columns { margin-left: 52%; } - -} - - -/* Base Styles -–––––––––––––––––––––––––––––––––––––––––––––––––– */ -/* NOTE -html is set to 62.5% so that all the REM measurements throughout Skeleton -are based on 10px sizing. 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- border-color: #888; - outline: 0; } -.button.button-primary, -button.button-primary, -input[type="submit"].button-primary, -input[type="reset"].button-primary, -input[type="button"].button-primary { - color: #FFF; - background-color: #33C3F0; - border-color: #33C3F0; } -.button.button-primary:hover, -button.button-primary:hover, -input[type="submit"].button-primary:hover, -input[type="reset"].button-primary:hover, -input[type="button"].button-primary:hover, -.button.button-primary:focus, -button.button-primary:focus, -input[type="submit"].button-primary:focus, -input[type="reset"].button-primary:focus, -input[type="button"].button-primary:focus { - color: #FFF; - background-color: #1EAEDB; - border-color: #1EAEDB; } - - -/* Forms -–––––––––––––––––––––––––––––––––––––––––––––––––– */ -input[type="email"], -input[type="number"], -input[type="search"], -input[type="text"], -input[type="tel"], -input[type="url"], -input[type="password"], -textarea, -select { - height: 38px; - padding: 6px 10px; 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