diff --git a/doc/Makefile b/doc/Makefile index f7866969..f750fb18 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -123,9 +123,9 @@ gh-pages: python gh-pages.py gitwash: - python tools/gitwash/gitwash_dumper.py source scikits-image \ - --project-url=http://scikits-image.org \ - --project-ml-url=http://groups.google.com/group/scikits-image \ - --repo-name=scikits-image \ - --github-user=scikits-image \ + python tools/gitwash/gitwash_dumper.py source scikit-image \ + --project-url=http://scikit-image.org \ + --project-ml-url=http://groups.google.com/group/scikit-image \ + --repo-name=scikit-image \ + --github-user=scikit-image \ --source-suffix=.txt diff --git a/doc/ext/plot2rst.py b/doc/ext/plot2rst.py index 67355289..92978723 100644 --- a/doc/ext/plot2rst.py +++ b/doc/ext/plot2rst.py @@ -9,7 +9,7 @@ To generate your own examples, add this extension to the list of example directory(ies) in `plot2rst_paths` (see below) points to a directory with examples named `plot_*.py` and include an `index.rst` file. -This code was adapted from scikits-image, which took it from scikits-learn. +This code was adapted from scikit-image, which took it from scikit-learn. Options ------- diff --git a/doc/gh-pages.py b/doc/gh-pages.py index 87baddda..ab29959e 100644 --- a/doc/gh-pages.py +++ b/doc/gh-pages.py @@ -30,7 +30,7 @@ from subprocess import Popen, PIPE, CalledProcessError, check_call pages_dir = 'gh-pages' html_dir = 'build/html' pdf_dir = 'build/latex' -pages_repo = 'git@github.com:scikits-image/docs.git' +pages_repo = 'git@github.com:scikit-image/docs.git' #----------------------------------------------------------------------------- # Functions diff --git a/doc/logo/snake_logo.svg b/doc/logo/snake_logo.svg index caa47694..5f9f634f 100644 --- a/doc/logo/snake_logo.svg +++ b/doc/logo/snake_logo.svg @@ -74,7 +74,7 @@ y="278.58533" x="261.22247" id="tspan3152" - sodipodi:role="line">scikits-image + sodipodi:role="line">scikit-image =2.6 or 3.x), NumPy and SciPy can be installed. For more information, visit our website - http://scikits-image.org + http://scikit-image.org or the examples gallery at - http://scikits-image.org/docs/0.3/auto_examples/ + http://scikit-image.org/docs/0.3/auto_examples/ New Features ------------ diff --git a/doc/release/release_0.4.txt b/doc/release/release_0.4.txt index 765b4760..04679271 100644 --- a/doc/release/release_0.4.txt +++ b/doc/release/release_0.4.txt @@ -1,26 +1,26 @@ -Announcement: scikits-image 0.4 +Announcement: scikit-image 0.4 =============================== -We're happy to announce the 0.4 release of scikits-image, an image processing +We're happy to announce the 0.4 release of scikit-image, an image processing toolbox for SciPy. Please visit our examples gallery to see what we've been up to: - http://scikits-image.org/docs/0.4/auto_examples/ + http://scikit-image.org/docs/0.4/auto_examples/ Note that, in this release, we renamed the module from ``scikits.image`` to ``skimage``, to work around name space conflicts with other scikits (similarly, the machine learning scikit is now imported as ``sklearn``). A big shout-out also to everyone currently at SciPy India; have fun, and -remember to join the scikits-image sprint! +remember to join the scikit-image sprint! This release runs under all major operating systems where Python (>=2.6 or 3.x), NumPy and SciPy can be installed. For more information, visit our website - http://scikits-image.org + http://scikit-image.org New Features ------------ diff --git a/doc/release/release_0.5.txt b/doc/release/release_0.5.txt index 74a5b3fe..652f45fa 100644 --- a/doc/release/release_0.5.txt +++ b/doc/release/release_0.5.txt @@ -1,12 +1,12 @@ -Announcement: scikits-image 0.5 +Announcement: scikit-image 0.5 =============================== -We're happy to announce the 0.5 release of scikits-image, our image processing +We're happy to announce the 0.5 release of scikit-image, our image processing toolbox for SciPy. For more information, please visit our website - http://scikits-image.org + http://scikit-image.org New Features ------------ diff --git a/doc/release/release_0.6.txt b/doc/release/release_0.6.txt index 8c525cb7..df2582cc 100644 --- a/doc/release/release_0.6.txt +++ b/doc/release/release_0.6.txt @@ -1,9 +1,9 @@ -Announcement: scikits-image 0.6 +Announcement: scikit-image 0.6 =============================== -We're happy to announce the 6th version of scikits-image! +We're happy to announce the 6th version of scikit-image! -Scikits-image is an image processing toolbox for SciPy that includes algorithms +scikit-image is an image processing toolbox for SciPy that includes algorithms for segmentation, geometric transformations, color space manipulation, analysis, filtering, morphology, feature detection, and more. diff --git a/doc/release/release_0.7.txt b/doc/release/release_0.7.txt index a6b591cb..6637cd51 100644 --- a/doc/release/release_0.7.txt +++ b/doc/release/release_0.7.txt @@ -1,9 +1,9 @@ -Announcement: scikits-image 0.7.0 +Announcement: scikit-image 0.7.0 ================================= -We're happy to announce the 7th version of scikits-image! +We're happy to announce the 7th version of scikit-image! -Scikits-image is an image processing toolbox for SciPy that includes algorithms +scikit-image is an image processing toolbox for SciPy that includes algorithms for segmentation, geometric transformations, color space manipulation, analysis, filtering, morphology, feature detection, and more. @@ -15,7 +15,7 @@ For more information, examples, and documentation, please visit our website New Features ------------ -It's been only 3 months since scikits-image 0.6 was released, but in that short +It's been only 3 months since scikit-image 0.6 was released, but in that short time, we've managed to add plenty of new features and enhancements, including - Geometric image transforms diff --git a/doc/source/_static/default.css_t b/doc/source/_static/default.css_t deleted file mode 100644 index 4497c5e6..00000000 --- a/doc/source/_static/default.css_t +++ /dev/null @@ -1,144 +0,0 @@ -/* This CSS stylesheet is no longer used. Edit agogo.css instead. */ - -/** - * Sphinx stylesheet -- default theme - * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - */ - -@import url("basic.css"); - -/* -- page layout ----------------------------------------------------------- */ - -body { - font-family: {{ theme_bodyfont }}; - font-size: 100%; - background-color: {{ theme_footerbgcolor }}; - color: #000; - margin: 0; - padding: 0; -} - -div.document { - background-color: {{ theme_sidebarbgcolor }}; -} - -div.documentwrapper { - float: left; - width: 100%; -} - -div.bodywrapper { - margin: 0 0 0 230px; -} - -div.body { - background-color: {{ theme_bgcolor }}; - color: {{ theme_textcolor }}; - padding: 0 20px 30px 20px; - overflow: auto; -} - -{%- if theme_rightsidebar|tobool %} -div.bodywrapper { - margin: 0 230px 0 0; -} -{%- endif %} - -div.footer { - color: {{ theme_footertextcolor }}; - width: 100%; - padding: 9px 0 9px 0; - text-align: center; - font-size: 75%; -} - -div.footer a { - color: {{ theme_footertextcolor }}; - text-decoration: underline; -} - -div.related { - background-color: {{ theme_relbarbgcolor }}; - line-height: 30px; - color: {{ theme_relbartextcolor }}; -} - -div.related a { - color: {{ theme_relbarlinkcolor }}; -} - -div.sphinxsidebar { - {%- if theme_stickysidebar|tobool %} - top: 30px; - margin: 0; - position: fixed; - overflow: auto; - height: 100%; - {%- endif %} - {%- if theme_rightsidebar|tobool %} - float: right; - {%- if theme_stickysidebar|tobool %} - right: 0; - {%- endif %} - {%- endif %} -} - -{%- if theme_stickysidebar|tobool %} -/* this is nice, but it it leads to hidden headings when jumping - to an anchor */ -/* -div.related { - position: fixed; -} - -div.documentwrapper { - margin-top: 30px; -} -*/ -{%- endif %} - -div.sphinxsidebar h3 { - font-family: {{ theme_headfont }}; - color: {{ theme_sidebartextcolor }}; - font-size: 1.4em; - font-weight: normal; - margin: 0; - padding: 0; -} - -div.sphinxsidebar h3 a { - color: {{ theme_sidebartextcolor }}; -} - -div.sphinxsidebar h4 { - font-family: {{ theme_headfont }}; - color: {{ theme_sidebartextcolor }}; - font-size: 1.3em; - font-weight: normal; - margin: 5px 0 0 0; - padding: 0; -} - -div.sphinxsidebar p { - color: {{ theme_sidebartextcolor }}; -} - -div.sphinxsidebar p.topless { - margin: 5px 10px 10px 10px; -} - -div.sphinxsidebar ul { - margin: 10px; - padding: 0; - color: {{ theme_sidebartextcolor }}; -} - -div.sphinxsidebar a { - color: {{ theme_sidebarlinkcolor }}; -} - -div.sphinxsidebar input { - border: 1px solid {{ theme_sidebarlinkcolor }}; - font-family: sans-serif; - font-size: 1em; -} diff --git a/doc/source/themes/agogo/static/docversions.js b/doc/source/_static/docversions.js similarity index 70% rename from doc/source/themes/agogo/static/docversions.js rename to doc/source/_static/docversions.js index 30f17f40..660553e0 100644 --- a/doc/source/themes/agogo/static/docversions.js +++ b/doc/source/_static/docversions.js @@ -1,7 +1,5 @@ function insert_version_links() { - var labels = ['dev', '0.7.0', '0.6', '0.5', '0.4', '0.3']; - - document.write('\n'); } diff --git a/doc/source/_static/scikits_image_logo_small.png b/doc/source/_static/scikits_image_logo_small.png deleted file mode 100644 index efd71678..00000000 Binary files a/doc/source/_static/scikits_image_logo_small.png and /dev/null differ diff --git a/doc/source/_templates/layout.html b/doc/source/_templates/layout.html deleted file mode 100644 index 1ddc127c..00000000 --- a/doc/source/_templates/layout.html +++ /dev/null @@ -1,6 +0,0 @@ -{% extends "!layout.html" %} -{% block rootrellink %} -
  • scikits-image home »
    • - {{ super() }} -{% endblock %} - diff --git a/doc/source/_templates/localtoc.html b/doc/source/_templates/localtoc.html index 3a26d6fa..6866649c 100644 --- a/doc/source/_templates/localtoc.html +++ b/doc/source/_templates/localtoc.html @@ -1,8 +1,10 @@ {% if pagename != 'index' %} - {%- if display_toc %} -

    Contents

    - {{ toc }} - {%- endif %} + {%- if display_toc %} +

    Contents

    +
    + {{ toc|replace('
    + {%- endif %} {% endif %} diff --git a/doc/source/_templates/navbar.html b/doc/source/_templates/navbar.html new file mode 100644 index 00000000..b0fa8026 --- /dev/null +++ b/doc/source/_templates/navbar.html @@ -0,0 +1,5 @@ +
  • Home
    • +
  • Download
    • +
  • Gallery
    • +
  • Documentation
    • +
  • Source
    • diff --git a/doc/source/_templates/navigation.html b/doc/source/_templates/navigation.html index 587d95a1..66244695 100644 --- a/doc/source/_templates/navigation.html +++ b/doc/source/_templates/navigation.html @@ -1,12 +1,22 @@ -{%- block navigation %} - - {% if pagename != 'index' %} -

    Navigation

    -

    - Documentation Home -

    -

     

    - {% endif %} - - -{%- endblock %} +

    {{ _('Navigation') }}

    +
    + +
    +{%- if prev %} +

    {{ _('Previous topic') }}

    +
    + +
    +{%- endif %} +{%- if next %} +

    {{ _('Next topic') }}

    +
    + +
    +{%- endif %} diff --git a/doc/source/_templates/versions.html b/doc/source/_templates/versions.html index a0da9d70..6dbb1962 100644 --- a/doc/source/_templates/versions.html +++ b/doc/source/_templates/versions.html @@ -1,9 +1,9 @@ -{%- block versions %} - -

    Version

    - - - -{%- endblock %} +

    {{ _('Versions') }}

    +
    + +
    diff --git a/doc/source/cell_profiler.txt b/doc/source/cell_profiler.txt index cf24f53c..13918596 100644 --- a/doc/source/cell_profiler.txt +++ b/doc/source/cell_profiler.txt @@ -4,7 +4,7 @@ CellProfiler BSD license announcement :: From: Vebjorn Ljosa - To: scikits-image@googlegroups.com + To: scikit-image@googlegroups.com Date: June 3, 2010 We have changed the license of some parts of CellProfiler from GNU GPL diff --git a/doc/source/conf.py b/doc/source/conf.py index cb22e6f0..71033adc 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -43,7 +43,7 @@ master_doc = 'index' # General information about the project. project = u'skimage' -copyright = u'2011, the scikits-image team' +copyright = u'2011, the scikit-image team' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the @@ -103,8 +103,7 @@ pygments_style = 'sphinx' # The theme to use for HTML and HTML Help pages. Major themes that come with # Sphinx are currently 'default' and 'sphinxdoc'. -html_theme = 'agogo' -html_style = 'agogo.css' +html_theme = 'scikit-image' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the @@ -121,10 +120,6 @@ html_title = 'skimage v%s docs' % version # A shorter title for the navigation bar. Default is the same as html_title. #html_short_title = None -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -html_logo = "scikits_image_logo_small.png" - # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. @@ -147,9 +142,7 @@ html_static_path = ['_static'] html_sidebars = { '**': ['navigation.html', 'localtoc.html', - 'relations.html', - 'versions.html', - 'searchbox.html'], + 'versions.html'], } # Additional templates that should be rendered to pages, maps page names to diff --git a/doc/source/gitwash/development_workflow.txt b/doc/source/gitwash/development_workflow.txt index b5344da8..47bdead0 100644 --- a/doc/source/gitwash/development_workflow.txt +++ b/doc/source/gitwash/development_workflow.txt @@ -4,14 +4,14 @@ Development workflow #################### -You already have your own forked copy of the scikits-image_ repository, by +You already have your own forked copy of the scikit-image_ repository, by following :ref:`forking`. You have :ref:`set-up-fork`. You have configured git by following :ref:`configure-git`. Now you are ready for some real work. Workflow summary ================ -In what follows we'll refer to the upstream scikits-image ``master`` branch, as +In what follows we'll refer to the upstream scikit-image ``master`` branch, as "trunk". * Don't use your ``master`` branch for anything. Consider deleting it. @@ -22,9 +22,9 @@ In what follows we'll refer to the upstream scikits-image ``master`` branch, as * Name your branch for the purpose of the changes - e.g. ``bugfix-for-issue-14`` or ``refactor-database-code``. * If you can possibly avoid it, avoid merging trunk or any other branches into - your feature branch while you are working. + your feature branch while you are working. * If you do find yourself merging from trunk, consider :ref:`rebase-on-trunk` -* Ask on the `scikits-image mailing list`_ if you get stuck. +* Ask on the `scikit-image mailing list`_ if you get stuck. * Ask for code review! This way of working helps to keep work well organized, with readable history. @@ -81,7 +81,7 @@ what the changes in the branch are for. For example ``add-ability-to-fly``, or git checkout my-new-feature Generally, you will want to keep your feature branches on your public github_ -fork of scikits-image_. To do this, you `git push`_ this new branch up to your +fork of scikit-image_. To do this, you `git push`_ this new branch up to your github repo. Generally (if you followed the instructions in these pages, and by default), git will have a link to your github repo, called ``origin``. You push up to your own repo on github with:: @@ -150,7 +150,7 @@ Ask for your changes to be reviewed or merged When you are ready to ask for someone to review your code and consider a merge: #. Go to the URL of your forked repo, say - ``http://github.com/your-user-name/scikits-image``. + ``http://github.com/your-user-name/scikit-image``. #. Use the 'Switch Branches' dropdown menu near the top left of the page to select the branch with your changes: @@ -192,10 +192,10 @@ If you want to work on some stuff with other people, where you are all committing into the same repository, or even the same branch, then just share it via github. -First fork scikits-image into your account, as from :ref:`forking`. +First fork scikit-image into your account, as from :ref:`forking`. Then, go to your forked repository github page, say -``http://github.com/your-user-name/scikits-image`` +``http://github.com/your-user-name/scikit-image`` Click on the 'Admin' button, and add anyone else to the repo as a collaborator: @@ -204,7 +204,7 @@ collaborator: Now all those people can do:: - git clone git@githhub.com:your-user-name/scikits-image.git + git clone git@githhub.com:your-user-name/scikit-image.git Remember that links starting with ``git@`` use the ssh protocol and are read-write; links starting with ``git://`` are read-only. diff --git a/doc/source/gitwash/following_latest.txt b/doc/source/gitwash/following_latest.txt index 69e5ee13..df0842a0 100644 --- a/doc/source/gitwash/following_latest.txt +++ b/doc/source/gitwash/following_latest.txt @@ -5,12 +5,12 @@ ============================= These are the instructions if you just want to follow the latest -*scikits-image* source, but you don't need to do any development for now. +*scikit-image* source, but you don't need to do any development for now. The steps are: * :ref:`install-git` -* get local copy of the `scikits-image github`_ git repository +* get local copy of the `scikit-image github`_ git repository * update local copy from time to time Get the local copy of the code @@ -18,19 +18,19 @@ Get the local copy of the code From the command line:: - git clone git://github.com/scikits-image/scikits-image.git + git clone git://github.com/scikit-image/scikit-image.git -You now have a copy of the code tree in the new ``scikits-image`` directory. +You now have a copy of the code tree in the new ``scikit-image`` directory. Updating the code ================= From time to time you may want to pull down the latest code. Do this with:: - cd scikits-image + cd scikit-image git pull -The tree in ``scikits-image`` will now have the latest changes from the initial +The tree in ``scikit-image`` will now have the latest changes from the initial repository. .. include:: links.inc diff --git a/doc/source/gitwash/forking_hell.txt b/doc/source/gitwash/forking_hell.txt index 58e12fee..02c14b25 100644 --- a/doc/source/gitwash/forking_hell.txt +++ b/doc/source/gitwash/forking_hell.txt @@ -1,13 +1,13 @@ .. _forking: ============================================ -Making your own copy (fork) of scikits-image +Making your own copy (fork) of scikit-image ============================================ You need to do this only once. The instructions here are very similar to the instructions at http://help.github.com/forking/ |emdash| please see that page for more detail. We're repeating some of it here just to give the -specifics for the scikits-image_ project, and to suggest some default names. +specifics for the scikit-image_ project, and to suggest some default names. Set up and configure a github account ====================================== @@ -17,17 +17,17 @@ If you don't have a github account, go to the github page, and make one. You then need to configure your account to allow write access |emdash| see the ``Generating SSH keys`` help on `github help`_. -Create your own forked copy of scikits-image_ +Create your own forked copy of scikit-image_ ============================================= #. Log into your github account. -#. Go to the scikits-image_ github home at `scikits-image github`_. +#. Go to the scikit-image_ github home at `scikit-image github`_. #. Click on the *fork* button: .. image:: forking_button.png Now, after a short pause and some 'Hardcore forking action', you - should find yourself at the home page for your own forked copy of scikits-image_. + should find yourself at the home page for your own forked copy of scikit-image_. .. include:: links.inc diff --git a/doc/source/gitwash/git_intro.txt b/doc/source/gitwash/git_intro.txt index cb8e16cc..8b4d42bc 100644 --- a/doc/source/gitwash/git_intro.txt +++ b/doc/source/gitwash/git_intro.txt @@ -2,11 +2,11 @@ Introduction ============== -These pages describe a git_ and github_ workflow for the scikits-image_ +These pages describe a git_ and github_ workflow for the scikit-image_ project. There are several different workflows here, for different ways of -working with *scikits-image*. +working with *scikit-image*. This is not a comprehensive git reference, it's just a workflow for our own project. It's tailored to the github hosting service. You may well diff --git a/doc/source/gitwash/index.txt b/doc/source/gitwash/index.txt index d0eac669..7d26110e 100644 --- a/doc/source/gitwash/index.txt +++ b/doc/source/gitwash/index.txt @@ -1,6 +1,6 @@ .. _using-git: -Working with *scikits-image* source code +Working with *scikit-image* source code ======================================== Contents: diff --git a/doc/source/gitwash/maintainer_workflow.txt b/doc/source/gitwash/maintainer_workflow.txt index 7e2b21ab..e661784c 100644 --- a/doc/source/gitwash/maintainer_workflow.txt +++ b/doc/source/gitwash/maintainer_workflow.txt @@ -16,7 +16,7 @@ access to the upstream repo. Being a maintainer, you've got read-write access. It's good to have your upstream remote have a scary name, to remind you that it's a read-write remote:: - git remote add upstream-rw git@github.com:scikits-image/scikits-image.git + git remote add upstream-rw git@github.com:scikit-image/scikit-image.git git fetch upstream-rw ******************* @@ -29,7 +29,7 @@ Let's say you have some changes that need to go into trunk The changes are in some branch that you are currently on. For example, you are looking at someone's changes like this:: - git remote add someone git://github.com/someone/scikits-image.git + git remote add someone git://github.com/someone/scikit-image.git git fetch someone git branch cool-feature --track someone/cool-feature git checkout cool-feature diff --git a/doc/source/gitwash/patching.txt b/doc/source/gitwash/patching.txt index acec9fa6..b40118af 100644 --- a/doc/source/gitwash/patching.txt +++ b/doc/source/gitwash/patching.txt @@ -3,7 +3,7 @@ ================ You've discovered a bug or something else you want to change -in scikits-image_ .. |emdash| excellent! +in scikit-image_ .. |emdash| excellent! You've worked out a way to fix it |emdash| even better! @@ -29,9 +29,9 @@ Overview git config --global user.email you@yourdomain.example.com git config --global user.name "Your Name Comes Here" # get the repository if you don't have it - git clone git://github.com/scikits-image/scikits-image.git + git clone git://github.com/scikit-image/scikit-image.git # make a branch for your patching - cd scikits-image + cd scikit-image git branch the-fix-im-thinking-of git checkout the-fix-im-thinking-of # hack, hack, hack @@ -44,7 +44,7 @@ Overview # make the patch files git format-patch -M -C master -Then, send the generated patch files to the `scikits-image +Then, send the generated patch files to the `scikit-image mailing list`_ |emdash| where we will thank you warmly. In detail @@ -57,10 +57,10 @@ In detail git config --global user.name "Your Name Comes Here" #. If you don't already have one, clone a copy of the - scikits-image_ repository:: + scikit-image_ repository:: - git clone git://github.com/scikits-image/scikits-image.git - cd scikits-image + git clone git://github.com/scikit-image/scikit-image.git + cd scikit-image #. Make a 'feature branch'. This will be where you work on your bug fix. It's nice and safe and leaves you with @@ -100,7 +100,7 @@ In detail 0001-BF-added-tests-for-Funny-bug.patch 0002-BF-added-fix-for-Funny-bug.patch - Send these files to the `scikits-image mailing list`_. + Send these files to the `scikit-image mailing list`_. When you are done, to switch back to the main copy of the code, just return to the ``master`` branch:: @@ -115,7 +115,7 @@ more feature branches, you will probably want to switch to development mode. You can do this with the repository you have. -Fork the scikits-image_ repository on github |emdash| :ref:`forking`. +Fork the scikit-image_ repository on github |emdash| :ref:`forking`. Then:: # checkout and refresh master branch from main repo @@ -124,7 +124,7 @@ Then:: # rename pointer to main repository to 'upstream' git remote rename origin upstream # point your repo to default read / write to your fork on github - git remote add origin git@github.com:your-user-name/scikits-image.git + git remote add origin git@github.com:your-user-name/scikit-image.git # push up any branches you've made and want to keep git push origin the-fix-im-thinking-of diff --git a/doc/source/gitwash/set_up_fork.txt b/doc/source/gitwash/set_up_fork.txt index f59aa57a..36153e7d 100644 --- a/doc/source/gitwash/set_up_fork.txt +++ b/doc/source/gitwash/set_up_fork.txt @@ -11,9 +11,9 @@ Overview :: - git clone git@github.com:your-user-name/scikits-image.git - cd scikits-image - git remote add upstream git://github.com/scikits-image/scikits-image.git + git clone git@github.com:your-user-name/scikit-image.git + cd scikit-image + git remote add upstream git://github.com/scikit-image/scikit-image.git In detail ========= @@ -22,8 +22,8 @@ Clone your fork --------------- #. Clone your fork to the local computer with ``git clone - git@github.com:your-user-name/scikits-image.git`` -#. Investigate. Change directory to your new repo: ``cd scikits-image``. Then + git@github.com:your-user-name/scikit-image.git`` +#. Investigate. Change directory to your new repo: ``cd scikit-image``. Then ``git branch -a`` to show you all branches. You'll get something like:: @@ -35,7 +35,7 @@ Clone your fork What remote repository is ``remote/origin``? Try ``git remote -v`` to see the URLs for the remote. They will point to your github fork. - Now you want to connect to the upstream `scikits-image github`_ repository, so + Now you want to connect to the upstream `scikit-image github`_ repository, so you can merge in changes from trunk. .. _linking-to-upstream: @@ -45,11 +45,11 @@ Linking your repository to the upstream repo :: - cd scikits-image - git remote add upstream git://github.com/scikits-image/scikits-image.git + cd scikit-image + git remote add upstream git://github.com/scikit-image/scikit-image.git ``upstream`` here is just the arbitrary name we're using to refer to the -main scikits-image_ repository at `scikits-image github`_. +main scikit-image_ repository at `scikit-image github`_. Note that we've used ``git://`` for the URL rather than ``git@``. The ``git://`` URL is read only. This means we that we can't accidentally @@ -59,10 +59,10 @@ use it to merge into our own code. Just for your own satisfaction, show yourself that you now have a new 'remote', with ``git remote -v show``, giving you something like:: - upstream git://github.com/scikits-image/scikits-image.git (fetch) - upstream git://github.com/scikits-image/scikits-image.git (push) - origin git@github.com:your-user-name/scikits-image.git (fetch) - origin git@github.com:your-user-name/scikits-image.git (push) + upstream git://github.com/scikit-image/scikit-image.git (fetch) + upstream git://github.com/scikit-image/scikit-image.git (push) + origin git@github.com:your-user-name/scikit-image.git (fetch) + origin git@github.com:your-user-name/scikit-image.git (push) .. include:: links.inc diff --git a/doc/source/gitwash/this_project.inc b/doc/source/gitwash/this_project.inc index 0bfd7306..349b92ba 100644 --- a/doc/source/gitwash/this_project.inc +++ b/doc/source/gitwash/this_project.inc @@ -1,5 +1,5 @@ -.. scikits-image -.. _scikits-image: http://scikits-image.org -.. _`scikits-image github`: http://github.com/scikits-image/scikits-image +.. scikit-image +.. _scikit-image: http://scikit-image.org +.. _`scikit-image github`: http://github.com/scikit-image/scikit-image -.. _`scikits-image mailing list`: http://groups.google.com/group/scikits-image +.. _`scikit-image mailing list`: http://groups.google.com/group/scikit-image diff --git a/doc/source/install.txt b/doc/source/install.txt index 5aa3f43f..81652ab1 100644 --- a/doc/source/install.txt +++ b/doc/source/install.txt @@ -1,7 +1,7 @@ Pre-built installation ---------------------- -.. !! Also update scikits-image-web !! +.. !! Also update scikit-image-web !! `Windows binaries `__ @@ -12,37 +12,37 @@ Distribution (EPD) `__ and `Python(x,y) `__. On systems that support setuptools, the package can be installed from the -`Python packaging index `__ using +`Python packaging index `__ using :: - easy_install -U scikits-image + easy_install -U scikit-image or :: - pip -U scikits-image + pip -U scikit-image Installation from source ------------------------ Obtain the source from the git-repository at -`http://github.com/scikits-image/scikits-image -`_. +`http://github.com/scikit-image/scikit-image +`_. by running :: - git clone http://github.com/scikits-image/scikits-image.git + git clone http://github.com/scikit-image/scikit-image.git in a terminal (You will need to have git installed on your machine). If you do not have git installed, you can also download a zipball from -`https://github.com/scikits-image/scikits-image/zipball/master -`_. +`https://github.com/scikit-image/scikit-image/zipball/master +`_. The SciKit can be installed globally using diff --git a/doc/source/overview.txt b/doc/source/overview.txt index 0bd9d658..5a4e6123 100644 --- a/doc/source/overview.txt +++ b/doc/source/overview.txt @@ -1,7 +1,7 @@ Image Processing SciKit ======================= -The `scikits-image `__ SciKit (toolkit for +The `scikit-image `__ SciKit (toolkit for `SciPy `__) extends ``scipy.ndimage`` to provide a versatile set of image processing routines. It is written in the `Python `_ language. @@ -12,15 +12,15 @@ mailing list (address provided below). Homepage -------- -http://scikits-image.org +http://scikit-image.org Source, bugs and patches ------------------------ -http://github.com/scikits-image/scikits-image +http://github.com/scikit-image/scikit-image Mailing List ------------ -http://groups.google.com/group/scikits-image +http://groups.google.com/group/scikit-image Contact ------- diff --git a/doc/source/random_gallery.py b/doc/source/random_gallery.py index 6c5a40a2..47ce89a2 100644 --- a/doc/source/random_gallery.py +++ b/doc/source/random_gallery.py @@ -32,8 +32,8 @@ gallery_div = '''\ examples = glob.glob(os.path.join(example_dir, 'plot_*.py')) images, links = [], [] -image_url = 'http://scikits-image.org/docs/dev/_images/%s.png' -link_url = 'http://scikits-image.org/docs/dev/auto_examples/%s.html' +image_url = 'http://scikit-image.org/docs/dev/_images/%s.png' +link_url = 'http://scikit-image.org/docs/dev/auto_examples/%s.html' for e in examples: e = os.path.basename(e) diff --git a/doc/source/themes/agogo/layout.html b/doc/source/themes/agogo/layout.html deleted file mode 100644 index 260f06bf..00000000 --- a/doc/source/themes/agogo/layout.html +++ /dev/null @@ -1,58 +0,0 @@ -{# - agogo/layout.html - ~~~~~~~~~~~~~~~~~ - - Sphinx layout template for the agogo theme, originally written - by Andi Albrecht. - - :copyright: Copyright 2007-2010 by the Sphinx team, see AUTHORS. - :license: BSD, see LICENSE for details. -#} -{% extends "basic/layout.html" %} -{% set script_files = script_files + ['_static/docversions.js'] %} - -{% block header %} -
    -
    - {%- block headertitle %} - - {%- if logo %} - - {%- endif %} - {#

    {{ shorttitle|e }}

    #} - {%- endblock %} -
    -
    -{% endblock %} - - - -{% block content %} -
    -
    - {%- block sidebar2 %} - {# We don't want the logo here #} - {%- block sidebarlogo %} {% endblock %} - {{ sidebar() }} - {% endblock %} -
    - {%- block document %} - {{ super() }} - {%- endblock %} -
    -
    -
    -
    -{% endblock %} - -{% block footer %} -
    - {{ super() }} -
    -{% endblock %} - -{% block relbar1 %}{% endblock %} - -{% block relbar2 %}{% endblock %} diff --git a/doc/source/themes/agogo/static/agogo.css_t b/doc/source/themes/agogo/static/agogo.css_t deleted file mode 100644 index f47167c0..00000000 --- a/doc/source/themes/agogo/static/agogo.css_t +++ /dev/null @@ -1,754 +0,0 @@ -/* - * agogo.css_t - * ~~~~~~~~~~~ - * - * Sphinx stylesheet -- agogo theme. - * - * :copyright: Copyright 2007-2010 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * - */ - -* { - margin: 0px; - padding: 0px; -} - - -div.header-wrapper { - border-top: 0px solid #babdb6; - padding: 1em 1em 0; - min-height: 0px; -} - -body { - font-family: {{ theme_bodyfont }}; - font-size: 10pt; - line-height: 1.4em; - color: black; - background-color: {{ theme_bgcolor }}; -} - - -/* Page layout */ - -div.header, div.content, div.footer { - max-width: {{ theme_pagewidth }}; - margin-left: auto; - margin-right: auto; -} - -div.header-wrapper { - border-bottom: 0px solid #2e3436; -} - - -/* Default body styles */ -a { - color: {{ theme_linkcolor }}; -} - -div.bodywrapper a, div.footer a { - text-decoration: underline; -} - -.clearer { - clear: both; -} - -.left { - float: left; -} - -.right { - float: right; -} - -.line-block { - display: block; - margin-top: 1em; - margin-bottom: 1em; -} - -.line-block .line-block { - margin-top: 0; - margin-bottom: 0; - margin-left: 1.5em; -} - -h1, h2, h3, h4 { - font-weight: normal; - color: {{ theme_headercolor2 }}; - margin-bottom: .8em; - clear: left; -} - -h1 { - color: {{ theme_headercolor1 }}; - line-height: 1.1em; - text-align: left; -} - -h2 { - padding-bottom: .5em; - color: {{ theme_headercolor1 }}; - border-bottom: 1px solid {{ theme_headercolor1 }}; -} - -a.headerlink { - visibility: hidden; - color: #dddddd; - padding-left: .3em; -} - -h1:hover > a.headerlink, -h2:hover > a.headerlink, -h3:hover > a.headerlink, -h4:hover > a.headerlink, -h5:hover > a.headerlink, -h6:hover > a.headerlink, -dt:hover > a.headerlink { - visibility: visible; -} - -img { - border: 0; -} - -div.admonition { - margin-top: 10px; - margin-bottom: 10px; - padding: 2px 7px 1px 7px; - border-left: 0.2em solid black; -} - -p.admonition-title { - margin: 0px 10px 5px 0px; - font-weight: bold; -} - -dt:target, .highlighted { - background-color: #fbe54e; -} - -/* Header */ - -div.header {} - -div.header h1 { - font-family: "Trebuchet MS", Helvetica, sans-serif; - font-weight: normal; - font-size: 250%; - letter-spacing: .08em; - line-height: 70px; - margin-bottom: 0; -} - -div.header h1 a { - color: white; -} - -div.header h1 a:hover { - text-decoration: none; -} - -div.header div.rel { - margin-top: 1em; - border-top: 1px solid #AAA; - border-bottom: 1px solid #AAA; - border-radius: 5px; - padding: 3px 1em; -} - -div.header div.rel a { - color: {{ theme_linkcolor }}; - letter-spacing: .05em; - font-weight: bold; -} - -div.logo {} - -img.logo { - border: 0; -} - - -/* Content */ -div.content-wrapper { - background-color: white; - padding: 1em; -} - -div.document { - max-width: {{ theme_documentwidth }}; -} - -div.body { - padding-right: 2em; - min-width: 20em; - overflow: hidden; - font-size: 90%; - text-align: {{ theme_textalign }}; -} - -div.document ul { - margin: 1.5em; - list-style-type: square; -} - -div.document dd { - margin-left: 1.2em; - margin-top: .4em; - margin-bottom: 1em; -} - -div.document .section { - margin-top: 1.7em; -} -div.document .section:first-child { - margin-top: 0px; -} - -div.document div.highlight { - padding: 3px; - background-color: #eeeeec; - border-top: 2px solid #dddddd; - border-bottom: 2px solid #dddddd; - margin-top: .8em; - margin-bottom: .8em; -} - -div.document h2 { - margin-top: .7em; -} - -div.document p { - margin-bottom: 1.5em; -} - -div.document li.toctree-l1 { - margin-bottom: 1em; -} - -div.document .descname { - font-weight: bold; -} - -div.document .docutils.literal { - background-color: #eeeeec; - padding: 1px; -} - -div.document .docutils.xref.literal { - background-color: transparent; - padding: 0px; -} - -div.document blockquote { - margin: 1em; -} - -div.document ol { - margin: 1.5em; -} - - -/* Sidebar */ - -div.sphinxsidebar { - width: {{ theme_sidebarwidth }}; - padding: 0 1em; - float: right; - font-size: .93em; - background-color: white; -} - -div.sphinxsidebar a, div.header a { - text-decoration: none; -} - -div.sphinxsidebar a:hover, div.header a:hover { - text-decoration: underline; -} - -div.sphinxsidebar h3 { - color: #2e3436; - text-transform: uppercase; - font-size: 130%; - letter-spacing: .1em; - margin-bottom: .4em; -} - -div.sphinxsidebar h4 { - margin-bottom: 0; - font-weight: bold; -} - -div.sphinxsidebar .tile { - border: 1px solid #D1DDE2; - border-radius: 10px; - background-color: #E1E8EC; - padding-left: 0.5em; - margin: 1em 0; -} - -div.sphinxsidebar ul { - margin-bottom: 1.5em; - list-style-type: none; -} - -div.sphinxsidebar li.toctree-l1 a { - display: block; - padding: 1px; - border: 1px solid #dddddd; - background-color: #eeeeec; - margin-bottom: .4em; - padding-left: 3px; - color: #2e3436; -} - -div.sphinxsidebar li.toctree-l2 a { - background-color: transparent; - border: none; - margin-left: 1em; - border-bottom: 1px solid #dddddd; -} - -div.sphinxsidebar li.toctree-l3 a { - background-color: transparent; - border: none; - margin-left: 2em; - border-bottom: 1px solid #dddddd; -} - -div.sphinxsidebar li.toctree-l2:last-child a { - border-bottom: none; -} - -div.sphinxsidebar li.toctree-l1.current a { - border-right: 5px solid {{ theme_headerlinkcolor }}; -} - -div.sphinxsidebar li.toctree-l1.current li.toctree-l2 a { - border-right: none; -} - -div.sidebarblock { - padding-bottom: .4em; - border-bottom: 1px solid #AAA; - margin-bottom: .8em; -} - -ul.versions li { - color: gray; - list-style: circle inside; -} - -ul.versions li#current { - list-style: disc inside; -} - -/* Footer */ - -div.footer-wrapper { - padding-top: 10px; - padding-bottom: 10px; -} - -div.footer { - border-top: 2px solid #aaa; - text-align: right; -} - -div.footer, div.footer a { - color: #888a85; -} - -.figure { - float: left; - margin: 1em; -} - -.figure img { - display: block; - margin-left: auto; - margin-right: auto; - max-height: 150px; -} - -.figure .caption { - width: 200px; - text-align: center !important; -} - - -/* Styles copied from basic theme */ - -img.align-left, .figure.align-left, object.align-left { - clear: left; - float: left; - margin-right: 1em; -} - -img.align-right, .figure.align-right, object.align-right { - clear: right; - float: right; - margin-left: 1em; -} - -img.align-center, .figure.align-center, object.align-center { - display: block; - margin-left: auto; - margin-right: auto; -} - -.align-left { - text-align: left; -} - -.align-center { - clear: both; - text-align: center; -} - -.align-right { - text-align: right; -} - -/* -- search page ----------------------------------------------------------- */ - -ul.search { - margin: 10px 0 0 20px; - padding: 0; -} - -ul.search li { - padding: 5px 0 5px 20px; - background-image: url(file.png); - background-repeat: no-repeat; - background-position: 0 7px; -} - -ul.search li a { - font-weight: bold; -} - -ul.search li div.context { - color: #888; - margin: 2px 0 0 30px; - text-align: left; -} - -ul.keywordmatches li.goodmatch a { - font-weight: bold; -} - -/* -- index page ------------------------------------------------------------ */ - -table.contentstable p.biglink { - line-height: 150%; -} - -table.contentstable, table.contentstable td, table.contentstable th { - border-style: none; -} - -div.body table.contentstable p { - margin: 0.5em; - text-align: left; -} - -table.contentstable a { - text-decoration: none; - font-size: 120%; -} - -a.biglink { - font-size: 1.3em; -} - -span.linkdescr { - font-style: italic; - padding-top: 5px; - font-size: 90%; -} - -/* -- general index --------------------------------------------------------- */ - -table.indextable td { - text-align: left; - vertical-align: top; -} - -table.indextable dl, table.indextable dd { - margin-top: 0; - margin-bottom: 0; -} - -table.indextable tr.pcap { - height: 10px; -} - -table.indextable tr.cap { - margin-top: 10px; - background-color: #f2f2f2; -} - -img.toggler { - margin-right: 3px; - margin-top: 3px; - cursor: pointer; -} - -/* -- viewcode extension ---------------------------------------------------- */ - -.viewcode-link { - float: right; -} - -.viewcode-back { - float: right; - font-family:: {{ theme_bodyfont }}; -} - -div.viewcode-block:target { - margin: -1px -3px; - padding: 0 3px; - background-color: #f4debf; - border-top: 1px solid #ac9; - border-bottom: 1px solid #ac9; -} - -span.strike { text-decoration: line-through; } - -/* -- body styles ----------------------------------------------------------- */ - -a { - color: {{ theme_linkcolor }}; - text-decoration: none; -} - -a:visited { - color: {{ theme_visitedlinkcolor }}; - text-decoration: none; -} - -a:hover { - text-decoration: underline; -} - -div.body h1, -div.body h2, -div.body h3, -div.body h4, -div.body h5, -div.body h6 { - font-family: {{ theme_headfont }}; - background-color: {{ theme_headbgcolor }}; - font-weight: normal; - color: {{ theme_headtextcolor }}; - border-bottom: 1px solid #ccc; - margin: 20px 20px 10px 0px; - padding: 3px 0 3px 0px; -} - -div.body h1 { margin-top: 0; font-size: 180%; } -div.body h2 { font-size: 150%; } -div.body h3 { font-size: 130%; } -div.body h4 { font-size: 120%; } -div.body h5 { font-size: 110%; } -div.body h6 { font-size: 100%; } - -a.headerlink { - color: {{ theme_headlinkcolor }}; - font-size: 0.8em; - padding: 0 4px 0 4px; - text-decoration: none; -} - -a.headerlink:hover { - background-color: {{ theme_headlinkcolor }}; - color: white; -} - -div.body p, div.body dd, div.body li { - text-align: justify; - line-height: 130%; -} - -div.admonition p.admonition-title + p { - display: inline; -} - -div.note { - background-color: #eee; - border: 1px solid #ccc; -} - -div.seealso { - background-color: #ffc; - border: 1px solid #ff6; -} - -div.topic { - background-color: #eee; -} - -div.warning { - background-color: #ffe4e4; - border: 1px solid #f66; -} - -p.admonition-title { - display: inline; -} - -p.admonition-title:after { - content: ":"; -} - -pre { - padding: 1em; - margin-bottom: 0.5em; - background-color: {{ theme_codebgcolor }}; - color: {{ theme_codetextcolor }}; - line-height: 120%; - border: 0px solid #ac9; - border-left: none; - border-right: none; -} - -sup { - font-size: x-small; - line-height: 0; -} - -tt { - background-color: #ecf0f3; - padding: 0 1px 0 1px; - font-size: 1em; -} - -table { - border-collapse: collapse; - margin-bottom: 1em; - margin-top: 1em; -} - -table, th, td { - border: 1px solid #ccc; -} - -th, td { - padding: 5px; -} - -th { - color: #333; - background-color: #eee; -} - -#api-reference ul:first-child { - float: left; - width: 35em; - margin-top: 0; - padding-top: 0; - list-style: none; - overflow: auto; -} - -#api-reference li { - float: left; - position: relative; - margin-right: 1em; - width: 17em; - padding: 0; -} - -.field-list { - font-size: 80%; -} - -/* ----------------- Example Gallery ----------------- */ - -.gallery { - height: 200px; -} - -.gallery p.caption a{ - text-decoration: none; -} - -/* ----------------- Coverage States ----------------- */ -span.missing{ - color: #000; - background-color: #ff5840; - border-color: #A77272; - font-weight: bold; -} -span.partial{ - color: #806600; - background-color: #ffc343; - font-weight: bold; -} -span.done{ - color: #106600; - background-color: #60f030; - border-color: #4F8530; - font-weight: bold; -} -span.na{ - color: #A8A8A8; - border-color: #4F8530; -} - -table.coverage { - border: solid 1px; -} - -td.missing-bar{ - color: #ff5840; - background-color: #ff5840; - border-color: #A77272; - font-weight: normal; - font-style: normal; -} -td.partial-bar{ - color: #ffc343; - background-color: #ffc343; - font-weight: normal; - font-style: normal; -} -td.done-bar{ - color: #60f030; - background-color: #60f030; - border-color: #4F8530; - font-weight: normal; - font-style: normal; -} -td.na-bar{ - color: #FFF; - background-color: #FFF; - border-color: #4F8530; - font-weight: normal; - font-style: normal; -} - -/* Adjust doc headers such as Notes, References, etc. */ -p.rubric { - font-weight: bold; - font-size: 120%; -} - -/* Math */ -img.math { - vertical-align: middle; -} - -div.body div.math p { - text-align: center; -} - -span.eqno { - float: right; -} diff --git a/doc/source/themes/agogo/theme.conf b/doc/source/themes/agogo/theme.conf deleted file mode 100644 index a991e5c0..00000000 --- a/doc/source/themes/agogo/theme.conf +++ /dev/null @@ -1,19 +0,0 @@ -[theme] -inherit = basic -stylesheet = agogo.css -pygments_style = tango - -[options] -bodyfont = "Verdana", Arial, sans-serif -pagewidth = 70em -documentwidth = 55em -sidebarwidth = 14em -bgcolor = white -headerbg = url(bgtop.png) top left repeat-x -footerbg = url(bgfooter.png) top left repeat-x -linkcolor = #FC852B -headercolor1 = #555 -headercolor2 = #555 -headerlinkcolor = #fcaf3e -codebgcolor = #EEE -textalign = justify diff --git a/doc/source/themes/scikit-image/layout.html b/doc/source/themes/scikit-image/layout.html new file mode 100644 index 00000000..58424f2f --- /dev/null +++ b/doc/source/themes/scikit-image/layout.html @@ -0,0 +1,113 @@ +{# + scikit-image/layout.html + ~~~~~~~~~~~~~~~~~ + + Sphinx layout template for the scikit-image theme, written by + Johannes Schönberger. + +#} + +{%- set url_root = pathto('', 1) %} +{# XXX necessary? #} +{%- if url_root == '#' %}{% set url_root = '' %}{% endif %} +{%- if not embedded and docstitle %} + {%- set titlesuffix = " — "|safe + docstitle|e %} +{%- else %} + {%- set titlesuffix = "" %} +{%- endif %} + +{%- macro script() %} + + + + {%- for scriptfile in script_files %} + + {%- endfor %} +{%- endmacro %} + +{%- macro css() %} + + + + + {%- for cssfile in css_files %} + + {%- endfor %} +{%- endmacro %} + + + + + {%- block htmltitle %} + {{ title|striptags|e }}{{ titlesuffix }} + {%- endblock %} + {{ metatags }} + {{ css() }} + {{ script() }} + {%- if hasdoc('about') %} + + {%- endif %} + {%- if hasdoc('genindex') %} + + {%- endif %} + {%- if hasdoc('search') %} + + {%- endif %} + {%- if hasdoc('copyright') %} + + {%- endif %} + + {%- if parents %} + + {%- endif %} + {%- if next %} + + {%- endif %} + {%- if prev %} + + {%- endif %} + + + {%- block extrahead %}{% endblock %} + + + +
    +
    +
    +
      + {% include 'navbar.html' %} +
    +
    + + + +
    +
    +
    +
    +
    + {% block body %}{% endblock %} +
    +
    + {%- for sidebartemplate in sidebars %} + {%- include sidebartemplate %} + {%- endfor %} +
    +
    +
    + + © Copyright the scikit-image development team. + Created using Bootstrap and Sphinx. + +
    + + diff --git a/doc/source/themes/scikit-image/search.html b/doc/source/themes/scikit-image/search.html new file mode 100644 index 00000000..61520e6b --- /dev/null +++ b/doc/source/themes/scikit-image/search.html @@ -0,0 +1,46 @@ +{# + basic/search.html + ~~~~~~~~~~~~~~~~~ + + Template for the search page. + + :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. + :license: BSD, see LICENSE for details. +#} +{% extends "layout.html" %} +{% set title = _('Search') %} +{% set script_files = script_files + ['_static/searchtools.js'] %} +{% set script_files = script_files + ['searchindex.js'] %} +{% block body %} +

    {{ _('Search') }}

    +
    + +

    + {% trans %}Please activate JavaScript to enable the search + functionality.{% endtrans %} +

    +
    +

    + {% trans %}From here you can search these documents. Enter your search + words into the box in the navigation bar and press "Enter". Note that the + search function will automatically search for all of the words. Pages + containing fewer words won't appear in the result list.{% endtrans %} +

    + {% if search_performed %} + {% if not search_results %} +

    {{ _('Your search did not match any results.') }}

    + {% endif %} + {% endif %} +
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