diff --git a/.buildinfo b/.buildinfo index 04f12f3..d1158d5 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 08abfb2f80a9202fc2ea94d0ca8a0d80 +config: 635f7983675768b911a1fe17844e1fb7 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_sources/getting-setup-selfstudy.rst.txt b/_sources/getting-setup-selfstudy.rst.txt index 8d02f64..ec65be0 100644 --- a/_sources/getting-setup-selfstudy.rst.txt +++ b/_sources/getting-setup-selfstudy.rst.txt @@ -2,12 +2,17 @@ Getting Set Up (Self-Study Instructions) ======================================== .. warning:: - You **MUST** have PUMA, ARCHER2 and MOSRS accounts setup before starting this section. + You **MUST** have PUMA2, ARCHER2 and MOSRS accounts setup before starting this section. + +.. warning:: + If you have moved your account over to PUMA2 from the old PUMA server (pumanew), then you should follow these instructions: https://cms.ncas.ac.uk/puma2/ + +.. _archer2: -Setup connection to PUMA & ARCHER2 ----------------------------------- +Set up your ARCHER2 connection +------------------------------ -To use the UM Introduction Tutorials you will first need to ensure you can connect from your local desktop to a both PUMA & ARCHER2. There a multiple ways in which you can do this depending on your desktop platform: +To use the UM Introduction Tutorials you will first need to ensure you can connect from your local desktop to ARCHER2. There a multiple ways in which you can do this depending on your desktop platform: * via `Terminal `_ on GNU/Linux & macOS * via `MobaXTerm `_ on Windows @@ -15,7 +20,7 @@ To use the UM Introduction Tutorials you will first need to ensure you can conne SSH key files ^^^^^^^^^^^^^ -Before you try and connect to PUMA or ARCHER2, you need to make sure that you have the ssh-keys for both platforms available on your computer. +Before you try and connect to ARCHER2, you need to make sure that you have the ssh-keys available on your computer. .. _terminal: @@ -23,38 +28,22 @@ Connecting via a Terminal (GNU/Linux & macOS) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ It is possible to connect via a terminal with an X11 connection (`XQuartz `_ is also required when using macOS) -Login to PUMA: :: - - ssh -Y -i ~/.ssh/id_rsa_puma @192.171.169.138 - -We suggest adding an entry to the ``~/.ssh/config`` file so you don't need to keep typing in the IP address. For example: :: - - Host puma - Hostname 192.171.169.138 - User - IdentityFile ~/.ssh/id_rsa_puma - ForwardX11 yes - ForwardX11Trusted yes - -so that you can then connect using the command: :: - - ssh puma - -In a new terminal window, login to ARCHER2: :: +Login to ARCHER2: :: - ssh -Y -i ~/.ssh/id_rsa_archer @login.archer2.ac.uk + ssh -Y -i ~/.ssh/id_rsa_archer2 @login.archer2.ac.uk -It is also possible to define a ``~/.ssh/config`` file entry for each with the necessary information, if desired. For example: :: +To simplify the login process, you can define a ``~/.ssh/config`` file entry containing the necessary information. For example: :: - Host login.archer2.ac.uk + Host archer2 + Hostname login.archer2.ac.uk User - IdentityFile ~/.ssh/id_rsa_archer + IdentityFile ~/.ssh/id_rsa_archer2 ForwardX11 yes ForwardX11Trusted yes -so that you could then just connect using the command: :: +so that you can connect using just the command: :: - ssh login.archer2.ac.uk + ssh archer2 .. _mobaxterm: @@ -63,12 +52,12 @@ Connecting via MobaXTerm * From Chrome, go to page: https://mobaxterm.mobatek.net/download.html * Under “Home Edition” select “Download now” -* | On next page select **“MobaXterm Home Edition v21.4 (Portable edition)”**. +* | On next page select **“MobaXterm Home Edition v23.3 (Portable edition)”**. | This should download the package. * Click the download icon in the bottom left hand corner. -* | Double-click on the **MobaXterm_Personal_21.4** application file, and select “Extract all”. +* | Double-click on the **MobaXterm_Personal_23.3** application file, and select “Extract all”. | A new directory window will open up. -* Double-click **MobaXterm_Personal_21.4** to launch the application. +* Double-click **MobaXterm_Personal_23.3** to launch the application. Next time, navigate to “Downloads” to open the application. @@ -84,94 +73,133 @@ Change the permissions on your ``/home`` and ``/work`` directories to enable the chmod -R g+rX /home/n02/n02/ chmod -R g+rX /work/n02/n02/ -Set up your PUMA environment +.. _puma2: + +Set up your PUMA2 connection ---------------------------- -Login to PUMA from your local desktop. +PUMA2 is accessed from the ARCHER2 login nodes, and you will use the same username and password. -Configure ``~/.profile`` -^^^^^^^^^^^^^^^^^^^^^^^^ -If this is the first time you have used your PUMA account, you will need to create a ``.profile``. Copy our standard one: :: +From an ARCHER2 terminal type: :: - puma$ cd - puma$ cp ~um/um-training/setup/.profile . + archer2$ ssh -Y puma2 -(If you already have a ``.profile``, make sure it includes the lines from the standard file.) +and type your ARCHER2 password when prompted. -Configure access to MOSRS -^^^^^^^^^^^^^^^^^^^^^^^^^ -Run the ``mosrs-setup`` script which will take you through the set up process to access the Met Office Science Repository Service (Remember your MOSRS username is one word; usually firstnamelastname, all in lowercase): :: +You should now be logged into PUMA2. To go back to the ARCHER2 login nodes, type ``exit``. - puma$ ~um/um-training/mosrs-setup +Set up passwordless access to PUMA2 +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Log out of PUMA and back in again (you will get a warning about not being able to find ``~/.ssh/ssh-setup`` this can be ignored and will be resolved in the next step). You should be prompted for your Met Office Science Repository Service password. A new window should then pop up (it may be hidden behind other windows) for ``Rosie`` asking for **Username for 'u' - 'https://code.metoffice.gov.uk/rosie/u'** . Enter your MOSRS username again. +You can set up a passphrase-less ssh-key to allow you to connect to PUMA2 without typing a password or passphrase. -.. note:: The cached password is configured to expire after 12 hours. Simply run the command ``mosrs-cache-password`` to re-cache it if this happens. Also if you know you won't need access to the repositories during a login session then just press return when asked for your MOSRS password. +.. note:: We would never normally advise using an ssh-key without a passphrase, but in this case it is safe to do so since we are already authenticated within the ARCHER2 system. -Configure connection to ARCHER2 -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +From the ARCHER2 login nodes, type: :: -Due to ARCHER2 security and the UM workflow it is necessary to generate a special ssh-key that allows submission of UM suite from PUMA. + archer2$ ssh-keygen -t rsa -f ~/.ssh/id_rsa_puma2 -**i. Generate UM workflow ssh-key** +At the prompt, press enter for an empty passphrase. -Run the following command to generate your ``id_rsa_archerum`` ssh key: :: +Copy the key over to PUMA2: :: - puma$ ssh-keygen -t rsa -b 4096 -C "ARCHER2 UM Workflow" -f ~/.ssh/id_rsa_archerum + archer2$ ssh-copy-id -i ~/.ssh/id_rsa_puma2 puma2 -When prompted to **Enter passphrase**, this should be a fairly complicated and unguessable passphrase. You can use spaces in the passphrase if it helps you to remember it more readily. It is recommended that you don't use your password in case it is hacked. +Type in your ARCHER2 password when prompted. -Your ``id_rsa_archerum`` key will be automatically detected and sent to ARCHER2 to be installed. This may take up to 48 hours, excluding weekends, to become activated and you will receive an email confirmation. +Next, create a file called ``~/.ssh/config`` (if it doesn’t already exist), and add the following lines: :: -.. warning:: - * **DO NOT** use an empty passphrase. This presents a security issue. - * **DO NOT** regenerate your ``id_rsa_archerum`` key once you have a working one in place, unless absolutely necessary. + Host puma2 + IdentityFile ~/.ssh/id_rsa_puma2 + ForwardX11 yes -**ii. Update ssh config file** +Test it works by typing: :: -In your PUMA ``~/.ssh/config`` file add the following section: :: + archer2$ ssh puma2 - Host login.archer2.ac.uk - User - IdentityFile ~/.ssh/id_rsa_archerum - ForwardX11 no - ForwardX11Trusted no +You should not be prompted for your password. Note that this should have set up X11 forwarding, so you no longer need the ``-Y`` option. + +.. warning:: You should never use a passphrase-less key to access the ARCHER2 login nodes, as this is a serious security risk. + +Set up your PUMA2 environment +----------------------------- + +Copy our standard ``.profile`` and ``.bashrc`` files: :: + + puma2$ cd + puma2$ cp ~um1/um-training/puma2/.bash_profile . + puma2$ cp ~um1/um-training/puma2/.bashrc . + +Logout of PUMA2 and back in again to pick up these changes. You will get a warning about not being able to find ``~/.ssh/ssh-setup``. This can be ignored and will be resolved in the next step. -Where ```` should be replaced with your ARCHER2 username. If you don't have a ``~/.ssh/config`` file create one. +You should then be prompted for your Met Office Science Repository Service password, then username. Note that it asks for your **password** first. Remember your MOSRS username is one word; usually firstnamelastname, all in lowercase. + +If the password caching works, you should see: :: + + Subversion password cached + Rosie password cached + +This means you can now access the code and roses suites stored in the Met Office respositories. + +.. note:: The cached password is configured to expire after 12 hours. Simply run the command ``mosrs-cache-password`` to re-cache it if this happens. Also if you know you won't need access to the repositories during a login session then just press return when asked for your MOSRS password. + +Finally, change the permission on your PUMA2 ``/home`` space: :: + + chmod -R g+rX /home/n02/n02/ .. _ssh-setup: -**iii. Set up ssh-agent** +Set up your ssh-agent +--------------------- -Setting up an ``ssh-agent`` allows caching of your ``id_rsa_archerum`` key passphrase for a period of time. :: +In order to submit jobs to ARCHER2 from PUMA2, you will need to set up an ``ssh-agent`` and use it to cache the passphrase to your ARCHER2. - puma$ cp ~um/um-training/setup/ssh-setup ~/.ssh +**i. Copy your ARCHER2 ssh-key pair to PUMA2** -Log out of PUMA and back in again to start up the ``ssh-agent`` process. +Your ARCHER2 key is the one that you use to ssh into the ARCHER2 login nodes. You need to copy both the public and private keys into your ``.ssh/`` directory on PUMA2. -Add your ``id_rsa_archerum`` key to your ``ssh-agent`` by running: :: +Open a new terminal from wherever you originally connected to ARCHER2 in :ref:archer2:, and run the following command :: - puma$ ssh-add ~/.ssh/id_rsa_archerum - Enter passphrase for /home//.ssh/id_rsa: - [TYPE_YOUR_PASSPHRASE] + scp ~/.ssh/id_rsa_archer2* @login.archer2.ac.uk:/home/n02/n02-puma//.ssh -Enter your passphrase when prompted. The ``ssh-agent`` will continue to run even when you log out of PUMA, however, it may stop from time to time, for example if PUMA is rebooted. For instructions on what to do in this situation see :ref:`restarting-agent` in the Appendix. +**ii. Start up your ssh-agent** -**iv. Verify the setup is correct** +Setting up an ``ssh-agent`` allows caching of your ARCHER2 key passphrase for a period of time. + +First copy the ``ssh-setup`` script to your ``.ssh/`` directory. :: + + puma2$ cp ~um/um-training/setup/ssh-setup ~/.ssh -.. note:: Only proceed to this step once your ``id_rsa_archerum`` key has been installed on ARCHER2. +Next log out of PUMA2 and back in again to start up the ``ssh-agent`` process. You should see the following message :: -Log in to ARCHER2 with: :: + Initialising new SSH agent... - puma$ ssh login.archer2.ac.uk +**iii. Add your ARCHER2 key** + +Add your ARCHER2 key to the ``ssh-agent``, by running :: + + puma2$ ssh-add ~/.ssh/id_rsa_archer2 + +Enter your passphrase when prompted. If the passphrase has been cached successfully you should see a message like this: :: + + Identity add: /home/n02/n02//.ssh/id_rsa_archer2 + +The ``ssh-agent`` will continue to run even when you log out of PUMA2, however, it may stop from time to time, for example if PUMA2 is rebooted. For instructions on what to do in this situation see :ref:`restarting-agent` in the Appendix. + +**iv. Configure access to the ARCHER2 login nodes** + +Create a file ``.ssh/config`` (if it doesn't already exist), and add the following lines: :: + + # ARCHER2 login nodes + Host ln* + IdentityFile ~/.ssh/ + +**iv. Verify the setup is correct** -You should not be prompted for your passphrase. The response from ARCHER2 should be: :: +To test this is all working correctly, run: :: - puma$ ssh login.archer2.ac.uk - PTY allocation request failed on channel 0 - Comand rejected by policy. Not in authorised list - Connection to login.archer2.ac.uk closed. + puma2$ rose host-select archer2 -.. note:: It is not possible to start an interactive login session on ARCHER2 from PUMA. For an interactive session you need to login from your local desktop or via your host institution. +This should return one of the login nodes, e.g. ``ln01``. If it returns a message like ``[WARN] ln03: (ssh failed)`` then something has gone wrong with the ssh setup. You are now ready to try running a UM suite! diff --git a/_static/basic.css b/_static/basic.css index be19270..30fee9d 100644 --- a/_static/basic.css +++ b/_static/basic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- basic theme. * - * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -130,7 +130,7 @@ ul.search li a { font-weight: bold; } -ul.search li div.context { +ul.search li p.context { color: #888; margin: 2px 0 0 30px; text-align: left; @@ -222,7 +222,7 @@ table.modindextable td { /* -- general body styles --------------------------------------------------- */ div.body { - min-width: 450px; + min-width: 360px; max-width: 800px; } @@ -237,14 +237,8 @@ a.headerlink { visibility: hidden; } -a.brackets:before, -span.brackets > a:before{ - content: "["; -} - -a.brackets:after, -span.brackets > a:after { - content: "]"; +a:visited { + color: #551A8B; } h1:hover > a.headerlink, @@ -277,25 +271,25 @@ p.rubric { font-weight: bold; } -img.align-left, .figure.align-left, object.align-left { +img.align-left, figure.align-left, .figure.align-left, object.align-left { clear: left; float: left; margin-right: 1em; } -img.align-right, .figure.align-right, object.align-right { +img.align-right, figure.align-right, .figure.align-right, object.align-right { clear: right; float: right; margin-left: 1em; } -img.align-center, .figure.align-center, object.align-center { +img.align-center, figure.align-center, .figure.align-center, object.align-center { display: block; margin-left: auto; margin-right: auto; } -img.align-default, .figure.align-default { +img.align-default, figure.align-default, .figure.align-default { display: block; margin-left: auto; margin-right: auto; @@ -319,7 +313,8 @@ img.align-default, .figure.align-default { /* -- sidebars -------------------------------------------------------------- */ -div.sidebar { +div.sidebar, +aside.sidebar { margin: 0 0 0.5em 1em; border: 1px solid #ddb; padding: 7px; @@ -334,12 +329,16 @@ p.sidebar-title { font-weight: bold; } +nav.contents, +aside.topic, div.admonition, div.topic, blockquote { clear: left; } /* -- topics ---------------------------------------------------------------- */ +nav.contents, +aside.topic, div.topic { border: 1px solid #ccc; padding: 7px; @@ -377,12 +376,18 @@ div.body p.centered { /* -- content of sidebars/topics/admonitions -------------------------------- */ div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, div.topic > :last-child, div.admonition > :last-child { margin-bottom: 0; } div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, div.topic::after, div.admonition::after, blockquote::after { @@ -425,10 +430,6 @@ table.docutils td, table.docutils th { border-bottom: 1px solid #aaa; } -table.footnote td, table.footnote th { - border: 0 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b/_static/doctools.js @@ -2,320 +2,155 @@ * doctools.js * ~~~~~~~~~~~ * - * Sphinx JavaScript utilities for all documentation. + * Base JavaScript utilities for all Sphinx HTML documentation. * - * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ - -/** - * select a different prefix for underscore - */ -$u = _.noConflict(); - -/** - * make the code below compatible with browsers without - * an installed firebug like debugger -if (!window.console || !console.firebug) { - var names = ["log", "debug", "info", "warn", "error", "assert", "dir", - "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace", - "profile", "profileEnd"]; - window.console = {}; - for (var i = 0; i < names.length; ++i) - window.console[names[i]] = function() {}; -} - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. Multiple values per key are supported, - * it will always return arrays of strings for the value parts. - */ -jQuery.getQueryParameters = function(s) { - if (typeof s === 'undefined') - s = document.location.search; - var parts = s.substr(s.indexOf('?') + 1).split('&'); - var result = {}; - for (var i = 0; i < parts.length; i++) { - var tmp = parts[i].split('=', 2); - var key = jQuery.urldecode(tmp[0]); - var value = jQuery.urldecode(tmp[1]); - if (key in result) - result[key].push(value); - else - result[key] = [value]; +"use strict"; + +const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([ + "TEXTAREA", + "INPUT", + "SELECT", + "BUTTON", +]); + +const _ready = (callback) => { + if (document.readyState !== "loading") { + callback(); + } else { + document.addEventListener("DOMContentLoaded", callback); } - return result; }; -/** - * highlight a given string on a jquery object by wrapping it in - * span elements with the given class name. - */ -jQuery.fn.highlightText = function(text, className) { - function highlight(node, addItems) { - if (node.nodeType === 3) { - var val = node.nodeValue; - var pos = val.toLowerCase().indexOf(text); - if (pos >= 0 && - !jQuery(node.parentNode).hasClass(className) && - !jQuery(node.parentNode).hasClass("nohighlight")) { - var span; - var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.className = className; - } - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - node.parentNode.insertBefore(span, node.parentNode.insertBefore( - document.createTextNode(val.substr(pos + text.length)), - node.nextSibling)); - node.nodeValue = val.substr(0, pos); - if (isInSVG) { - var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); - var bbox = node.parentElement.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute('class', className); - addItems.push({ - "parent": node.parentNode, - "target": rect}); - } - } - } - else if (!jQuery(node).is("button, select, textarea")) { - jQuery.each(node.childNodes, function() { - highlight(this, addItems); - }); - } - } - var addItems = []; - var result = this.each(function() { - highlight(this, addItems); - }); - for (var i = 0; i < addItems.length; ++i) { - jQuery(addItems[i].parent).before(addItems[i].target); - } - return result; -}; - -/* - * backward compatibility for jQuery.browser - * This will be supported until firefox bug is fixed. - */ -if (!jQuery.browser) { - jQuery.uaMatch = function(ua) { - ua = ua.toLowerCase(); - - var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || - /(webkit)[ \/]([\w.]+)/.exec(ua) || - /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || - /(msie) ([\w.]+)/.exec(ua) || - ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || - []; - - return { - browser: match[ 1 ] || "", - version: match[ 2 ] || "0" - }; - }; - jQuery.browser = {}; - jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; -} - /** * Small JavaScript module for the documentation. */ -var Documentation = { - - init : function() { - this.fixFirefoxAnchorBug(); - this.highlightSearchWords(); - this.initIndexTable(); - if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) { - this.initOnKeyListeners(); - } +const Documentation = { + init: () => { + Documentation.initDomainIndexTable(); + Documentation.initOnKeyListeners(); }, /** * i18n support */ - TRANSLATIONS : {}, - PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; }, - LOCALE : 'unknown', + TRANSLATIONS: {}, + PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), + LOCALE: "unknown", // gettext and ngettext don't access this so that the functions // can safely bound to a different name (_ = Documentation.gettext) - gettext : function(string) { - var translated = Documentation.TRANSLATIONS[string]; - if (typeof translated === 'undefined') - return string; - return (typeof translated === 'string') ? translated : translated[0]; + gettext: (string) => { + const translated = Documentation.TRANSLATIONS[string]; + switch (typeof translated) { + case "undefined": + return string; // no translation + case "string": + return translated; // translation exists + default: + return translated[0]; // (singular, plural) translation tuple exists + } }, - ngettext : function(singular, plural, n) { - var translated = Documentation.TRANSLATIONS[singular]; - if (typeof translated === 'undefined') - return (n == 1) ? singular : plural; - return translated[Documentation.PLURALEXPR(n)]; + ngettext: (singular, plural, n) => { + const translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated !== "undefined") + return translated[Documentation.PLURAL_EXPR(n)]; + return n === 1 ? singular : plural; }, - addTranslations : function(catalog) { - for (var key in catalog.messages) - this.TRANSLATIONS[key] = catalog.messages[key]; - this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')'); - this.LOCALE = catalog.locale; + addTranslations: (catalog) => { + Object.assign(Documentation.TRANSLATIONS, catalog.messages); + Documentation.PLURAL_EXPR = new Function( + "n", + `return (${catalog.plural_expr})` + ); + Documentation.LOCALE = catalog.locale; }, /** - * add context elements like header anchor links + * helper function to focus on search bar */ - addContextElements : function() { - $('div[id] > :header:first').each(function() { - $('\u00B6'). - attr('href', '#' + this.id). - attr('title', _('Permalink to this headline')). - appendTo(this); - }); - $('dt[id]').each(function() { - $('\u00B6'). - attr('href', '#' + this.id). - attr('title', _('Permalink to this definition')). - appendTo(this); - }); + focusSearchBar: () => { + document.querySelectorAll("input[name=q]")[0]?.focus(); }, /** - * workaround a firefox stupidity - * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075 + * Initialise the domain index toggle buttons */ - fixFirefoxAnchorBug : function() { - if (document.location.hash && $.browser.mozilla) - window.setTimeout(function() { - document.location.href += ''; - }, 10); - }, - - /** - * highlight the search words provided in the url in the text - */ - highlightSearchWords : function() { - var params = $.getQueryParameters(); - var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : []; - if (terms.length) { - var body = $('div.body'); - if (!body.length) { - body = $('body'); + initDomainIndexTable: () => { + const toggler = (el) => { + const idNumber = el.id.substr(7); + const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); + if (el.src.substr(-9) === "minus.png") { + el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; + toggledRows.forEach((el) => (el.style.display = "none")); + } else { + el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; + toggledRows.forEach((el) => (el.style.display = "")); } - window.setTimeout(function() { - $.each(terms, function() { - body.highlightText(this.toLowerCase(), 'highlighted'); - }); - }, 10); - $('

' + _('Hide Search Matches') + '

') - .appendTo($('#searchbox')); - } - }, - - /** - * init the domain index toggle buttons - */ - initIndexTable : function() { - var togglers = $('img.toggler').click(function() { - var src = $(this).attr('src'); - var idnum = $(this).attr('id').substr(7); - $('tr.cg-' + idnum).toggle(); - if (src.substr(-9) === 'minus.png') - $(this).attr('src', src.substr(0, src.length-9) + 'plus.png'); - else - $(this).attr('src', src.substr(0, src.length-8) + 'minus.png'); - }).css('display', ''); - if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) { - togglers.click(); - } - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords : function() { - $('#searchbox .highlight-link').fadeOut(300); - $('span.highlighted').removeClass('highlighted'); - }, - - /** - * make the url absolute - */ - makeURL : function(relativeURL) { - return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL; - }, + }; - /** - * get the current relative url - */ - getCurrentURL : function() { - var path = document.location.pathname; - var parts = path.split(/\//); - $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() { - if (this === '..') - parts.pop(); - }); - var url = parts.join('/'); - return path.substring(url.lastIndexOf('/') + 1, path.length - 1); + const togglerElements = document.querySelectorAll("img.toggler"); + togglerElements.forEach((el) => + el.addEventListener("click", (event) => toggler(event.currentTarget)) + ); + togglerElements.forEach((el) => (el.style.display = "")); + if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); }, - initOnKeyListeners: function() { - $(document).keydown(function(event) { - var activeElementType = document.activeElement.tagName; - // don't navigate when in search box, textarea, dropdown or button - if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT' - && activeElementType !== 'BUTTON' && !event.altKey && !event.ctrlKey && !event.metaKey - && !event.shiftKey) { - switch (event.keyCode) { - case 37: // left - var prevHref = $('link[rel="prev"]').prop('href'); - if (prevHref) { - window.location.href = prevHref; - return false; + initOnKeyListeners: () => { + // only install a listener if it is really needed + if ( + !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS && + !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS + ) + return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.altKey || event.ctrlKey || event.metaKey) return; + + if (!event.shiftKey) { + switch (event.key) { + case "ArrowLeft": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const prevLink = document.querySelector('link[rel="prev"]'); + if (prevLink && prevLink.href) { + window.location.href = prevLink.href; + event.preventDefault(); } - case 39: // right - var nextHref = $('link[rel="next"]').prop('href'); - if (nextHref) { - window.location.href = nextHref; - return false; + break; + case "ArrowRight": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const nextLink = document.querySelector('link[rel="next"]'); + if (nextLink && nextLink.href) { + window.location.href = nextLink.href; + event.preventDefault(); } + break; } } + + // some keyboard layouts may need Shift to get / + switch (event.key) { + case "/": + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; + Documentation.focusSearchBar(); + event.preventDefault(); + } }); - } + }, }; // quick alias for translations -_ = Documentation.gettext; +const _ = Documentation.gettext; -$(document).ready(function() { - Documentation.init(); -}); +_ready(Documentation.init); diff --git a/_static/documentation_options.js b/_static/documentation_options.js index 2fa8c97..7e4c114 100644 --- a/_static/documentation_options.js +++ b/_static/documentation_options.js @@ -1,12 +1,13 @@ -var 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} -if (!splitQuery) { - function splitQuery(query) { - return query.split(/\s+/); +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings } /** * Search Module */ -var Search = { - - _index : null, - _queued_query : null, - _pulse_status : -1, - - htmlToText : function(htmlString) { - var virtualDocument = document.implementation.createHTMLDocument('virtual'); - var htmlElement = $(htmlString, virtualDocument); - htmlElement.find('.headerlink').remove(); - docContent = htmlElement.find('[role=main]')[0]; - if(docContent === undefined) { - console.warn("Content block not found. Sphinx search tries to obtain it " + - "via '[role=main]'. Could you check your theme or template."); - return ""; - } - return docContent.textContent || docContent.innerText; +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; }, - init : function() { - var params = $.getQueryParameters(); - if (params.q) { - var query = params.q[0]; - $('input[name="q"]')[0].value = query; - this.performSearch(query); - } + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); }, - loadIndex : function(url) { - $.ajax({type: "GET", url: url, data: null, - dataType: "script", cache: true, - complete: function(jqxhr, textstatus) { - if (textstatus != "success") { - document.getElementById("searchindexloader").src = url; - } - }}); - }, + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), - setIndex : function(index) { - var q; - this._index = index; - if ((q = this._queued_query) !== null) { - this._queued_query = null; - Search.query(q); + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); } }, - hasIndex : function() { - return this._index !== null; - }, + hasIndex: () => Search._index !== null, - deferQuery : function(query) { - this._queued_query = query; - }, + deferQuery: (query) => (Search._queued_query = query), - stopPulse : function() { - this._pulse_status = 0; - }, + stopPulse: () => (Search._pulse_status = -1), - startPulse : function() { - if (this._pulse_status >= 0) - return; - function pulse() { - var i; + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { Search._pulse_status = (Search._pulse_status + 1) % 4; - var dotString = ''; - for (i = 0; i < Search._pulse_status; i++) - dotString += '.'; - Search.dots.text(dotString); - if (Search._pulse_status > -1) - window.setTimeout(pulse, 500); - } + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; pulse(); }, /** * perform a search for something (or wait until index is loaded) */ - performSearch : function(query) { + performSearch: (query) => { // create the required interface elements - this.out = $('#search-results'); - this.title = $('

' + _('Searching') + '

').appendTo(this.out); - this.dots = $('').appendTo(this.title); - this.status = $('

 

').appendTo(this.out); - this.output = $('

Note that fcm revert will undo ALL changes to a file relative to your branch. Therefore if you’ve made several uncommitted changes, fcm revert will undo them all, not just the last one.

- -
-

Committing changes

+ +
+

Committing changes

The change in your working copy remains local until you commit it to the repository where it becomes permanent. If you are planning to make a large number of changes, you are encouraged to commit regularly to your branch at appropriate intervals. Make sure you are in the top level directory of the working copy and then type:

puma$ fcm commit
@@ -430,9 +347,9 @@

Committing changes -

Getting information about your branch

+

+
+

Getting information about your branch

If you need to find out information about your (or another user’s) branches, you can use the fcm branch info command.

In the directory where you checked out the code, type:

puma$ fcm branch-info
@@ -456,9 +373,9 @@ 
Getting information about your branch
-
Testing that your branch works

+
+
+

Testing that your branch works

Now that you have made a branch you can use it in the suite you were running earlier. Go back to the section where you added an existing branch to your suite and add your new branch as well.

Save and then Run your suite.

If you have followed the tutorial scenario so far you should find that your suite fails during the fcm extract of code. In the job.err file for the fcm_make task you will see an error message like this:

@@ -485,15 +402,15 @@

Testing that your branch worksHint

Remember not all run output is in the job.out or job.err files. You may need to look in the pe_output directory too.

- -
-

Viewing your changes in Trac

+ +
+

Viewing your changes in Trac

Making a change to your branch results in a changeset which is basically a record of the changes. One way of viewing the changeset you have just created is to click on Timeline in Trac. The Timeline view is a sequential record of all events in the repository. Near the top, you should see changesets for the creation of your branch, and the subsequent commit for the code changes you made. The changesets are numbered corresponding to the revision of your branch which would have been displayed in the GUI when you did a fcm commit or `fcm branch info. To see all the details click on the line ‘Changeset[xxx]…’ relating to your changeset. Alternatively, if you enter the number of the changeset “[xxx]” into the search box at the top right, it will take you directly to the numbered changeset. Your changeset should look something like this:

_images/fcm_changeset.png -
- -
-

4.5. Documenting your change

+ + +
+

4.5. Documenting your change

Go back to the Trac ticket you created for your code change and add some documentation as follows:

Preview and Submit your ticket to save the changes. Check the link you added works.

-
-
-

4.6. Tidying Up

+ +
+

4.6. Tidying Up

If your development is destined for the UM trunk, then once you have finished your code changes and it has been tested and reviewed, your branch will be committed to the project shared package branch by the project owner. Once this has been done and there are no problems, your branch is essentially redundant. If no other users are using this branch in their suites it can be deleted.

For the purposes of this tutorial, you can now proceed to delete your branch. When you delete a branch, it becomes invisible from the HEAD revision, but will continue to exist in the repository should you want to refer to it in the future.

List branches owned by you

@@ -526,9 +443,9 @@

4.6. Tidying UpYou will be prompted to edit the commit message file. Again a standard template is automatically supplied for the commit. Add your commit message, save your changes and exit the editor.

Answer y when you are prompted to go ahead and delete this branch.

Your working copy is now pointing to a branch that no longer exists at the HEAD revision of the repository. It is possible to keep this working copy, create a new branch and switch your working copy to point to the new branch. Otherwise, you can remove your working copy by issuing a careful rm -rf command.

-

-
-

4.7. Version Control of Suites

+ +
+

4.7. Version Control of Suites

Just like the model code, your UM suites are also under version control in a subversion repository called roses-u which is on the MOSRS. Once you have a working copy of your suite under ~/roses you can use FCM commands in the same way as for your source code branches; i.e. commit changes, diff changes, etc.

- - + + - -