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diff --git a/2022/captions/emacsconf-2022-haskell--haskell-code-exploration-with-emacs--yuchen-pei--main.vtt b/2022/captions/emacsconf-2022-haskell--haskell-code-exploration-with-emacs--yuchen-pei--main.vtt new file mode 100644 index 00000000..e2bd489c --- /dev/null +++ b/2022/captions/emacsconf-2022-haskell--haskell-code-exploration-with-emacs--yuchen-pei--main.vtt @@ -0,0 +1,1354 @@ +WEBVTT captioned by anush + +00:00.000 --> 00:03.499 +Today, I will talk about Haskell code exploration for Emacs. + +00:03.500 --> 00:06.499 +What is Haskell? It is a purely functional language. + +00:06.500 --> 00:09.499 +For example, every value in Haskell is immutable. + +00:09.500 --> 00:12.999 +And it is the main compiler of Haskell, GHC. + +00:13.000 --> 00:15.999 +It provides API for the whole compilation pipeline. + +00:16.000 --> 00:00:18.324 +For example, the tools mentioned in this talk, + +00:00:18.424 --> 00:00:19.999 +including hcel and haddorg, + +00:20.000 --> 00:24.499 +they use, they heavily utilize the GHC front-end API + +00:24.500 --> 00:00:26.644 +for parsing and understanding + +00:00:26.744 --> 00:00:29.499 +the identifiers in Haskell source files. + +00:29.500 --> 00:00:31.444 +Roughly speaking, + +00:00:31.544 --> 00:00:34.564 +a Haskell program consists of several parts. + +00:00:34.664 --> 00:00:36.964 +it begins with some front matters, including, + +00:00:37.064 --> 00:00:39.924 +for example, language extensions, + +00:00:40.024 --> 00:00:43.964 +which are optional language features one might want to use + +00:00:44.064 --> 00:00:48.364 +for convenience. + +00:00:48.464 --> 00:00:52.499 +The front matters also contain module exports. + +00:52.500 --> 00:00:55.684 +So for example, here we define, + +00:00:55.784 --> 00:00:57.999 +we declare module F2Md.Config + +00:58.000 --> 00:01:00.884 +for this Haskell source file, + +00:01:00.984 --> 00:01:02.999 +which exports these four identifiers + +01:03.000 --> 01:07.499 +that other source files can use when importing F2Md.Config. + +01:07.500 --> 00:01:10.684 +And the next will be + +00:01:10.784 --> 00:01:13.999 +a block of imports so that we can use libraries + +01:14.000 --> 01:16.999 +and identifiers in these libraries. + +01:17.000 --> 00:01:21.644 +The bulk of a Haskell source file normally is + +00:01:21.744 --> 00:01:22.999 +a list of declarations, + +01:23.000 --> 01:25.999 +including values, types, and instances, and so on. + +01:26.000 --> 00:01:29.084 +The difference between a value and a type is that + +00:01:29.184 --> 00:01:30.499 +the type of a value is a type, + +01:30.500 --> 00:01:33.964 +and the type of a type is a kind. + +00:01:34.064 --> 00:01:38.484 +For example, here's a small block of Haskell source code. + +00:01:38.584 --> 00:01:41.404 +We define Range type + +00:01:41.504 --> 00:01:44.999 +from a lower-end integer to a higher-end integer. + +01:45.000 --> 00:01:51.364 +We also declare a value r of the type Range, + +00:01:51.464 --> 00:01:53.999 +which is Range from 2 to 7, + +01:54.000 --> 00:02:01.004 +because in Haskell, we like to-- + +00:02:01.104 --> 00:02:03.999 +by default, functions can be curried, + +02:04.000 --> 00:02:09.804 +which basically means, by default, we want to utilize + +00:02:09.904 --> 00:02:11.999 +the partial application of functions. + +00:02:12.000 --> 00:02:17.284 +We don't require parens surrounding arguments + +00:02:17.384 --> 00:02:19.364 +when invoking a function. + +00:02:19.464 --> 00:02:22.724 +That makes it possible, if you want, + +00:02:22.725 --> 00:02:24.999 +to write Haskell like Lisp + +02:25.000 --> 02:27.999 +by adding a bit of redundant parens. + +02:28.000 --> 00:02:30.044 +So for example, + +00:02:30.144 --> 00:02:33.684 +here are two blocks of code, one Lisp, one Haskell, + +00:02:33.784 --> 00:02:35.999 +and they look quite similar to each other. + +02:36.000 --> 02:37.999 +What is a code explorer? + +02:38.000 --> 00:02:39.444 +A code explorer is a tool + +00:02:39.544 --> 00:02:42.624 +to browse its code base to its code comprehension. + +00:02:42.724 --> 00:02:45.324 +Code explorer commonly comes with + +00:02:45.424 --> 00:02:46.999 +several functionalities or features, + +02:47.000 --> 00:02:49.244 +including a cross-referencer, + +00:02:49.344 --> 00:02:52.999 +which allows going to definitions of an identifier at points + +02:53.000 --> 00:02:56.444 +or looking up references of an identifier, + +00:02:56.544 --> 00:02:57.999 +like where it is used. + +02:58.000 --> 03:03.999 +So the example in Emacs would be xref. + +03:04.000 --> 00:03:07.604 +Code explorer also would be able to show you + +00:03:07.704 --> 00:03:09.999 +documentation and signatures of identifiers at points. + +03:10.000 --> 00:03:13.884 +In Emacs, that would be eldoc. + +00:03:13.984 --> 00:03:16.999 +It also commonly allows you to search for identifiers. + +03:17.000 --> 00:03:19.884 +Something like that in Emacs + +00:03:19.984 --> 00:03:21.999 +could be describe-function and find-function. + +03:22.000 --> 00:03:24.684 +Code explorer is normally + +00:03:24.784 --> 00:03:27.364 +quite often implemented in two parts, + +00:03:27.464 --> 00:03:27.999 +the indexer and the server, + +03:28.000 --> 00:03:32.484 +where the indexer parses the source code files, + +00:03:32.584 --> 00:03:33.999 +indexes the identifiers, + +03:34.000 --> 00:03:36.284 +and stores the information of identifiers + +00:03:36.384 --> 00:03:37.999 +like the definition, size, and the currencies, + +03:38.000 --> 03:41.999 +either in databases or in files. + +03:42.000 --> 00:03:44.444 +The other part is the server, + +00:03:44.544 --> 00:03:48.999 +which uses the database created by the indexer + +03:49.000 --> 00:03:53.004 +to serve the information of the identifier. + +00:03:53.104 --> 00:03:57.004 +Before I present my solution to code exploring, + +00:03:57.104 --> 00:04:00.999 +some description of prior art is in order. + +04:01.000 --> 00:04:05.284 +There are several tools that you can use + +00:04:05.384 --> 00:04:07.999 +to aid code exploration, + +04:08.000 --> 00:04:13.444 +including tech-based tools like hasktags and hs-tags. + +00:04:13.544 --> 00:04:15.484 +The limitation with these tools + +00:04:15.584 --> 00:04:17.999 +is they are focused on the current projects only + +04:18.000 --> 00:04:19.604 +and do not work + +00:04:19.704 --> 00:04:25.999 +for cross-packaging reference and definition. + +04:26.000 --> 00:04:31.044 +Another problem with the tag-based tools is + +00:04:31.045 --> 00:04:34.684 +they might not handle symbols with the same name properly. + +00:04:34.784 --> 00:04:35.999 +Sometimes they get confused, + +04:36.000 --> 00:04:43.324 +and they ask you to choose which definition, + +00:04:43.424 --> 00:04:45.924 +what is the correct definition site, + +00:04:46.024 --> 00:04:49.244 +even though the occurrence of the symbol + +00:04:49.344 --> 00:04:54.999 +or the symbol at point has only one definition ambiguously. + +04:55.000 --> 04:57.999 +Another tool is the haskell-mode. + +04:58.000 --> 00:05:02.684 +It has some limited support for eldoc + +00:05:02.784 --> 00:05:06.604 +by displaying the signature of an identifier at points, + +00:05:06.704 --> 00:05:11.764 +but the identifier has to be something + +00:05:11.864 --> 00:05:14.999 +that is commonly known or sort of built-in + +05:15.000 --> 05:17.999 +or come from the base library of Haskell. + +05:18.000 --> 00:05:20.244 +So for example, + +00:05:20.344 --> 00:05:24.244 +it works for common functions like head and tail. + +00:05:24.344 --> 00:05:26.999 +And you can see that the signature is displayed here. + +05:27.000 --> 00:05:29.564 +However, it does not work for, + +00:05:29.664 --> 00:05:31.804 +let's say, IO. IO is a type. + +00:05:31.904 --> 00:05:32.999 +Maybe that's the reason. + +05:33.000 --> 00:05:37.324 +Let's find another function + +00:05:37.424 --> 00:05:39.999 +that's not from the base library. + +05:40.000 --> 05:41.999 +toJSON is from the Aeson library, + +05:42.000 --> 05:46.999 +so no signature is displayed here. + +05:47.000 --> 00:05:51.164 +It also provides + +00:05:51.264 --> 00:05:53.324 +some sort of goto-declaration functionality + +00:05:53.424 --> 00:05:56.324 +to jump to any declaration in a file. + +00:05:56.424 --> 00:06:00.564 +To do that, one has to first run haskell-decl-scan-mode + +00:06:00.664 --> 00:06:02.999 +to enter this minor mode. + +06:03.000 --> 00:06:08.044 +Then we can run imenu to go to any definition, + +00:06:08.144 --> 00:06:10.999 +to go to any declaration, like getHomeR. + +06:11.000 --> 00:06:13.724 +Apparently, after running that, + +00:06:13.824 --> 00:06:15.999 +we are able to go to definition. + +06:16.000 --> 06:18.999 +So for example, let's see, + +06:19.000 --> 06:21.999 +we want to find definition of getCityJR. + +06:22.000 --> 00:06:25.524 +And indeed, it works + +00:06:25.624 --> 00:06:28.524 +if it's within the same source file, of course. + +00:06:28.624 --> 00:06:31.999 +It still does not work for cross-packaging identifiers. + +06:32.000 --> 00:06:36.924 +So HandlerFor is probably an identifier from servant. + +00:06:37.024 --> 00:06:39.999 +Or no, not necessarily servant. Maybe WAI. + +06:40.000 --> 00:06:43.404 +Anyway, it's another library. + +00:06:43.504 --> 00:06:50.404 +And how about find-references? + +00:06:50.504 --> 00:07:01.124 +find-references also works somehow for this file. + +00:07:01.224 --> 00:07:06.684 +How about WidgetFor? + +00:07:06.784 --> 00:07:13.644 +It works for WidgetFor too. + +00:07:13.744 --> 00:07:17.999 +It has some support for goto-definition and find-references. + +07:18.000 --> 07:25.999 +But as usual, it does not support such things cross-package. + +07:26.000 --> 00:07:27.364 +And finally, we have + +00:07:27.365 --> 00:07:30.999 +the Sledgehammer HLS Haskell language server. + +07:31.000 --> 07:32.999 +It can be used with EGLOT. + +07:33.000 --> 00:07:40.804 +But the problem with HLS, HLS has many many features + +00:07:40.904 --> 00:07:42.844 +because it is a language server, + +00:07:42.944 --> 00:07:50.999 +like renaming, like eldoc for standard libraries, and so on. + +07:51.000 --> 07:56.999 +But the problem with HLS is, one, that it is very, very slow. + +07:57.000 --> 07:59.999 +And I wouldn't use it with my laptop. + +08:00.000 --> 08:04.999 +And two, it also does not support cross-package referencing. + +08:05.000 --> 08:07.999 +In fact, there's an outstanding GitHub issue about this. + +08:08.000 --> 00:08:12.964 +So cross-package referencing and goto-definition + +00:08:13.064 --> 00:08:17.164 +is sort of a common shortfall, + +00:08:17.264 --> 00:08:20.999 +a common problem for these existing Haskell code explorers. + +08:21.000 --> 08:22.999 +Then finally, we also have hoogle and hackage. + +08:23.000 --> 00:08:28.284 +Hoogle is a search engine for Haskell identifiers, + +00:08:28.384 --> 00:08:30.644 +and the results link to Hackage, + +00:08:30.744 --> 00:08:33.604 +which is the Haskell documentation website + +00:08:33.704 --> 00:08:34.999 +for all Haskell libraries. + +08:35.000 --> 00:08:40.004 +Haskell Hackage has functionality + +00:08:40.104 --> 00:08:44.999 +where you can jump to the source code file rendered in HTML, + +08:45.000 --> 00:08:49.444 +and you can click on the identifiers there + +00:08:49.544 --> 00:08:51.524 +to jump to definitions, + +00:08:51.624 --> 00:08:54.044 +but it does not support find references, + +00:08:54.144 --> 00:08:58.999 +and it is rather basic. + +08:59.000 --> 00:09:01.644 +Then I learned about haskell-code-explorer, + +00:09:01.744 --> 00:09:04.999 +which is a fully-fledged Haskell code explorer. + +09:05.000 --> 00:09:07.724 +It is written by someone else. + +00:09:07.824 --> 00:09:09.164 +It is a web application + +00:09:09.264 --> 00:09:11.999 +for exploring Haskell package codebases. + +09:12.000 --> 00:09:16.244 +The official reference instance for haskell-code-explorer + +00:09:16.344 --> 00:09:18.999 +is available at this URL, which I will demo soon. + +09:19.000 --> 09:24.999 +What I did with these packages... I ported it to GHC 9.2. + +09:25.000 --> 00:09:29.044 +I renamed it to hcel because I want to focus on Emacs clients + +00:09:29.144 --> 00:09:30.999 +rather than JavaScript clients, which I will explain later. + +09:31.000 --> 09:36.999 +And I also wrote an Emacs client package, of course. + +09:37.000 --> 00:09:41.404 +This is what haskell-code-explorer looks like. + +00:09:41.504 --> 00:09:46.924 +On the homepage, it is a list of indexed packages + +00:09:47.024 --> 00:09:50.044 +indexed by the indexer. + +00:09:50.144 --> 00:09:53.844 +One can filter it by the package name + +00:09:53.944 --> 00:10:04.999 +or look for identifiers directly across all packages. + +10:05.000 --> 00:10:09.884 +Let's have a look at base. There are three versions. + +00:10:09.984 --> 00:10:14.999 +Let's have a look at the latest version, 4.12.0.0. + +10:15.000 --> 00:10:18.964 +Once entering the package view, + +00:10:19.064 --> 00:10:24.444 +you are shown a list of all modules by their path, + +00:10:24.544 --> 00:10:28.999 +as well as a tree of these module files. + +10:29.000 --> 00:10:32.524 +You can filter by module name or file name, + +00:10:32.624 --> 00:10:34.324 +or you can search for identifier within the same package + +00:10:34.424 --> 00:10:35.999 +or in all packages. + +10:36.000 --> 00:10:43.204 +Let's say we want to learn about Control.Monad. + +00:10:43.304 --> 00:10:46.884 +Now we are in the module view. + +00:10:46.984 --> 00:10:49.804 +The source file is presented to you, + +00:10:49.904 --> 00:10:54.999 +and it has links to identifiers. + +10:55.000 --> 00:11:01.804 +When you hover over them, the documentation shows up, + +00:11:01.904 --> 00:11:04.999 +including the signature where it is defined. + +11:05.000 --> 00:11:10.244 +You can go to its definition or find references. + +00:11:10.344 --> 00:11:20.164 +Let's say we want to go to the definition of Monad. + +00:11:20.264 --> 00:11:25.484 +It jumps to the definition site of the monad type class. + +00:11:25.584 --> 00:11:28.004 +If we click at the definition site, + +00:11:28.104 --> 00:11:32.124 +it brings up a list of references. + +00:11:32.224 --> 00:11:33.644 +On the left, you can choose + +00:11:33.744 --> 00:11:38.999 +which package you want to find references of monad in. + +11:39.000 --> 11:46.999 +Let's look at the random one, avwx. + +11:47.000 --> 00:11:54.044 +Here is a list of results where Monad is used in avwx. + +00:11:54.144 --> 00:11:57.764 +This is a module path. + +00:11:57.864 --> 00:12:06.324 +One can go to any of these results. + +00:12:06.424 --> 00:12:07.844 +We can search for things in all packages + +00:12:07.944 --> 00:12:09.484 +or in the current package. + +00:12:09.584 --> 00:12:12.999 +Let’s say I want to search for "Read" + +12:13.000 --> 00:12:19.244 +I think this is the "Read" that is commonly used in Haskell, + +00:12:19.344 --> 00:12:24.999 +the read type class for parsing strings into values. + +12:25.000 --> 00:12:31.004 +I think that is more or less it. + +00:12:31.104 --> 00:12:34.524 +That is the Haskell Code Explorer web application + +00:12:34.624 --> 00:12:38.204 +in all its glory. + +00:12:38.304 --> 00:12:40.884 +Let's go back to the slides. + +00:12:40.984 --> 00:12:43.364 +That was the web application, + +00:12:43.464 --> 00:12:46.444 +which is basically a JavaScript client + +00:12:46.544 --> 00:12:48.644 +that talks to the server + +00:12:48.744 --> 00:12:50.964 +by sending requests and receiving + +00:12:51.064 --> 00:12:54.999 +and parsing the JSON results or JSON responses. + +12:55.000 --> 00:13:02.404 +Initially, I was interested in hacking the web client. + +00:13:02.504 --> 00:13:04.999 +It uses the ember.js web framework. + +13:05.000 --> 00:13:09.844 +The first thing to do was to npm install ember-cli. + +00:13:09.944 --> 00:13:16.124 +It gives me 12 vulnerabilities, + +00:13:16.224 --> 00:13:18.999 +4 low, 2 moderate, 3 high, 3 critical. + +13:19.000 --> 00:13:26.084 +I don't know how often it is the case + +00:13:26.184 --> 00:13:32.964 +when we don't really care about these nasty vulnerabilities + +00:13:33.064 --> 00:13:35.999 +from Node.js or npm because they are so common. + +13:36.000 --> 00:13:41.044 +I don't quite like that. + +00:13:41.144 --> 00:13:45.364 +Another reason for favoring Emacs clients + +00:13:45.464 --> 00:13:48.999 +over JavaScript clients is user freedom. + +13:49.000 --> 00:13:53.284 +Emacs is geared towards user freedom. + +00:13:53.384 --> 00:14:01.564 +It allows users maximum freedom to customize or mod Emacs. + +00:14:01.664 --> 00:14:07.164 +I think Emacs clients can be a way to fix JavaScript traps, + +00:14:07.264 --> 00:14:14.244 +like using user scripts to replace non-free JavaScript. + +00:14:14.344 --> 00:14:19.484 +There are tools to do that, for example, like Haketilo. + +00:14:19.584 --> 00:14:21.404 +Why write JavaScript replacement + +00:14:21.504 --> 00:14:25.164 +if we can write Elisp replacement? + +00:14:25.264 --> 00:14:31.684 +If we overwrite all kinds of front-ends in Emacs + +00:14:31.784 --> 00:14:34.404 +for commonly-used web applications + +00:14:34.504 --> 00:14:36.999 +like Reddit, Hacker News, what have you, + +14:37.000 --> 00:14:40.804 +then we have an Emacs app store + +00:14:40.904 --> 00:14:43.604 +where we can just install these applications + +00:14:43.704 --> 00:14:51.084 +and browse the web more freely. + +00:14:51.184 --> 00:14:56.044 +Back to hcel, which is the Emacs client I wrote. + +00:14:56.144 --> 00:14:59.084 +I tried to reuse as much of Emacs built-ins as possible, + +00:14:59.184 --> 00:15:03.044 +including eldoc, for showing documentation, + +00:15:03.144 --> 00:15:04.764 +xref for cross-referencer, + +00:15:04.864 --> 00:15:06.999 +compilation-mode for showing search results of identifiers, + +15:07.000 --> 00:15:11.604 +outline-mode for a hierarchical view + +00:15:11.704 --> 00:15:14.284 +of package module identifiers, + +00:15:14.384 --> 00:15:17.999 +sort of a cursor-mode for highlighting identifiers, + +15:18.000 --> 00:15:26.044 +help-mode for displaying quick help for Haskell identifiers, + +00:15:26.144 --> 00:15:27.604 +integration with haddorg, + +00:15:27.704 --> 00:15:31.204 +which I will mention later, etc. + +00:15:31.304 --> 00:15:37.999 +It is available as hcel without the dot on GNU ELPA. + +15:38.000 --> 00:15:40.084 +Time for a demo. + +00:15:40.184 --> 00:15:42.484 +To start using hc.el, surprise surprise, + +00:15:42.584 --> 00:15:45.084 +we run the hcel command. + +00:15:45.184 --> 00:15:46.884 +We are presented with a list of packages + +00:15:46.984 --> 00:15:51.999 +indexed by the hcel indexer. + +15:52.000 --> 00:15:53.964 +This is an outline mode, + +00:15:54.064 --> 00:15:58.724 +so we can tab to list all the modules + +00:15:58.824 --> 00:16:00.999 +represented by the module path. + +16:01.000 --> 00:16:03.404 +We can further tab into the list of identifiers + +00:16:03.504 --> 00:16:04.999 +declared in this module. + +16:05.000 --> 00:16:09.084 +Now it asks whether you want to open module source. + +00:16:09.184 --> 00:16:11.884 +This is because some module source code + +00:16:11.984 --> 00:16:13.999 +can be quite large and it can take a bit of time. + +16:14.000 --> 00:16:17.684 +In this case, the control monad is quite small, + +00:16:17.784 --> 00:16:19.844 +so let's say yes. + +00:16:19.944 --> 00:16:24.004 +We see the list of identifiers. + +00:16:24.104 --> 00:16:27.999 +One can jump to an identifier forever. + +16:28.000 --> 16:32.999 +As you can see, the identifiers at points are highlighted. + +16:33.000 --> 00:16:36.124 +This can be particularly useful + +00:16:36.224 --> 00:16:38.604 +in a large function declaration + +00:16:38.704 --> 00:16:39.999 +where you come to see, for example, + +16:40.000 --> 00:16:44.204 +all the occurrences of an identifier + +00:16:44.304 --> 00:16:47.999 +inside the body of the declaration. + +16:48.000 --> 00:16:50.724 +These are declarations + +00:16:50.824 --> 00:16:52.999 +which in Haskell mode are listed in imenu. + +16:53.000 --> 16:59.999 +We can do the same here in hcel source mode. + +17:00.000 --> 17:05.999 +It lists all the declarations with their signature. + +17:06.000 --> 17:12.999 +Let's say we want to jump to this funny operator. + +17:13.000 --> 00:17:20.324 +It worked and you can also go back and forth + +00:17:20.424 --> 00:17:25.999 +within the declarations by pressing "n" and "p". + +17:26.000 --> 00:17:30.804 +Similarly, you can do something similar in the outline mode + +00:17:30.904 --> 00:17:37.999 +by toggling the follow mode, just like in org-agenda. + +17:38.000 --> 00:17:40.124 +Let's turn it off. + +00:17:40.224 --> 00:17:45.999 +Now, how about find definition references? + +17:46.000 --> 00:17:48.964 +Using xref, + +00:17:49.064 --> 00:17:52.999 +we can jump to the definition of Int and jump back. + +17:53.000 --> 17:55.999 +Jump to Maybe, jump back. + +17:56.000 --> 00:18:00.924 +Let's have a look at references of replicateM. + +00:18:01.024 --> 00:18:03.364 +There are plenty of them. + +00:18:03.464 --> 00:18:08.999 +Maybe we want to check out ghc-lib. + +18:09.000 --> 00:18:11.244 +Here are all the references + +00:18:11.344 --> 00:18:15.999 +and you can of course jump to any of them in the results. + +18:16.000 --> 18:18.999 +Cool. + +18:19.000 --> 00:18:21.764 +You may have already noticed + +00:18:21.864 --> 00:18:27.084 +the eldoc displaying the documentation + +00:18:27.184 --> 00:18:34.804 +and signature of identifiers. + +00:18:34.904 --> 00:18:44.004 +For example, here it shows the signature of replicateM, + +00:18:44.104 --> 00:18:46.999 +where it is defined, and its documentation. + +18:47.000 --> 18:55.999 +We can bring up the eldoc buffer. + +18:56.000 --> 00:18:58.164 +In the eldoc buffer, + +00:18:58.264 --> 00:19:00.084 +there are also links to other identifiers, + +00:19:00.184 --> 00:19:04.444 +which takes you to the definition of these identifiers, + +00:19:04.544 --> 00:19:07.524 +like minBound. + +00:19:07.624 --> 00:19:10.764 +Apparently, this is not working. + +00:19:10.864 --> 00:19:13.004 +I'm pretty sure it maybe works. + +00:19:13.104 --> 00:19:16.999 +Let's go to nothing or just... + +19:17.000 --> 00:19:19.764 +I think those didn't work because + +00:19:19.864 --> 00:19:24.044 +the module source for those identifiers is not open. + +00:19:24.144 --> 00:19:30.204 +Of course, you can search + +00:19:30.304 --> 00:19:32.924 +for any identifiers across all indexed packages + +00:19:33.024 --> 00:19:37.999 +by invoking hcel-global-ids. + +19:38.000 --> 19:41.999 +Let's say we want to search for Read. + +19:42.000 --> 00:19:47.364 +We are presented with a list of results, + +00:19:47.464 --> 00:19:53.999 +which are identifiers starting with Read with capital R. + +19:54.000 --> 00:19:57.204 +They also show where they are defined + +00:19:57.304 --> 00:20:06.999 +and the documentation, just like in eldoc. + +20:07.000 --> 00:20:13.844 +One can also directly jump to the identifier + +00:20:13.944 --> 00:20:19.999 +in the mini-buffer results. + +20:20.000 --> 00:20:21.924 +For example, we want to check out this Read2 + +00:20:22.024 --> 00:20:27.999 +defined in base-4.12.0.0 Data.Functor.Classes + +20:28.000 --> 20:33.999 +There we go. + +20:34.000 --> 00:20:37.764 +Another functionality of hcel + +00:20:37.864 --> 00:20:40.999 +is the help buffer integration. + +20:41.000 --> 00:20:46.564 +We can do hcel-help and then let's say + +00:20:46.565 --> 00:20:52.644 +we want to learn about the read type class. + +00:20:52.744 --> 00:20:55.084 +This is a help buffer + +00:20:55.184 --> 00:21:00.804 +and you can jump to other definitions + +00:21:00.904 --> 00:21:02.364 +within the help buffer + +00:21:02.464 --> 00:21:06.999 +to read the documentation like readsPrec. + +21:07.000 --> 21:10.999 +It says Server version cannot be satistifed. Actual version. + +21:11.000 --> 00:21:14.684 +This means we need to tell hecl + +00:21:14.784 --> 00:21:16.999 +that the server has the correct version. + +21:17.000 --> 00:21:21.644 +hecl-fetch-server-version. + +00:21:21.744 --> 00:21:25.604 +Wait a bit for it to update + +00:21:25.704 --> 00:21:26.999 +the knowledge of the server version. + +21:27.000 --> 21:32.999 +Now you can follow the links, Read, readsPrec. + +21:33.000 --> 21:37.999 +You can do the "l" and "r" to navigate within the history. + +21:38.000 --> 21:42.999 +ReadS, ReadP. + +21:43.000 --> 00:21:45.924 +Just like in the help buffer for elisp code, + +00:21:46.024 --> 00:21:52.999 +you can jump to the definition. + +21:53.000 --> 21:59.999 +I believe that is everything, more or less. + +22:00.000 --> 22:04.999 +That concludes the demo. + +22:05.000 --> 00:22:07.044 +Now let's turn to haddorg, + +00:22:07.144 --> 00:22:08.999 +which is an Org backend for Haddock. + +22:09.000 --> 22:12.999 +Haddock is the documentation generator for Haskell packages. + +22:13.000 --> 00:22:15.044 +For example, + +00:22:15.144 --> 00:22:21.999 +the official Haskell package documentation website Hackage, + +22:22.000 --> 00:22:25.804 +all the documentation there is generated by Haddock + +00:22:25.904 --> 00:22:27.999 +into the HTML format. + +22:28.000 --> 00:22:31.324 +Haddock has several backends + +00:22:31.424 --> 00:22:34.284 +that convert the intermediate representation + +00:22:34.384 --> 00:22:36.964 +called interface to various output formats, + +00:22:37.064 --> 00:22:41.764 +including HTML, LaTeX, and Hugo. + +00:22:41.864 --> 00:22:44.804 +HTML is the main format with a lot of features. + +00:22:44.904 --> 00:22:48.999 +LaTeX is less so, and I don't think it is widely used. + +22:49.000 --> 22:52.999 +Let's have a look at an HTML example. + +22:53.000 --> 00:23:01.084 +This is a PDF because these HTML files can be rather large + +00:23:01.184 --> 00:23:06.999 +and slow down EWW significantly. + +23:07.000 --> 00:23:10.164 +It's faster to convert it to PDF + +00:23:10.264 --> 00:23:16.999 +and read it from pdf-tools. + +23:17.000 --> 00:23:20.764 +Looks like this is as big as it goes. + +00:23:20.864 --> 00:23:26.044 +I hope you can still see it. + +00:23:26.144 --> 00:23:30.044 +Can I still enlarge it a bit more? Maybe. + +00:23:30.144 --> 00:23:32.964 +This is Servant.Server. + +00:23:33.064 --> 00:23:35.999 +It is a module in the servant-server package. + +23:36.000 --> 23:41.999 +It is a widely used package for writing servers. + +23:42.000 --> 00:23:49.804 +It starts with a heading, which is the name of the module, + +00:23:49.904 --> 00:23:52.684 +and the table of contents. + +00:23:52.784 --> 00:23:55.999 +Then a heading: Run an wai application from an API. + +23:56.000 --> 00:24:00.804 +Under this heading, there are all the relevant identifiers + +00:24:00.904 --> 00:24:08.524 +that is concerned with running a WAI application from API, + +00:24:08.624 --> 00:24:13.204 +including serve, which is one of the main entry points + +00:24:13.304 --> 00:24:15.524 +for a Servant.Server. + +00:24:15.624 --> 00:24:21.604 +It has a signature linkable to the other identifiers, + +00:24:21.704 --> 00:24:23.004 +the documentation, + +00:24:23.104 --> 00:24:26.644 +an example with a Haskell source code block. + +00:24:26.744 --> 00:24:30.999 +That's what HTML output looks like. + +24:31.000 --> 00:24:33.924 +As I mentioned, + +00:24:34.024 --> 00:24:35.804 +there are several downsides or drawbacks with that, + +00:24:35.904 --> 00:24:40.999 +like the HTML files can be huge and slow down EWW. + +24:41.000 --> 00:24:46.124 +Also, every module is an HTML of itself, + +00:24:46.224 --> 00:24:48.284 +and there's also an HTML for the package + +00:24:48.384 --> 00:24:49.999 +with a list of all the modules. + +24:50.000 --> 00:24:54.644 +Whereas the Org backend + +00:24:54.744 --> 00:25:04.164 +is better in that it is much more compact. + +00:25:04.264 --> 00:25:07.404 +All the modules under the same package + +00:25:07.504 --> 00:25:10.684 +are included in one Org file + +00:25:10.784 --> 00:25:12.999 +as sub-headings, level 2 headings. + +25:13.000 --> 00:25:19.404 +So, servant-server, Servant.Server, that is the module. + +00:25:19.504 --> 00:25:21.844 +So basically, this level 2 heading + +00:25:21.944 --> 00:25:24.999 +contains all the information in this PDF. + +25:25.000 --> 25:28.999 +Run the WAI application from API, serve. + +25:29.000 --> 00:25:39.124 +It has a signature that links to other identifiers + +00:25:39.224 --> 00:25:41.999 +and the documentation that's also linkable. + +25:42.000 --> 00:25:47.124 +The Haskell source block is now an Org source block, + +00:25:47.224 --> 00:25:49.404 +and you can do all sorts of interesting things + +00:25:49.504 --> 00:25:52.644 +with it using org-babel. + +00:25:52.744 --> 00:25:55.999 +Let's check the links as server. + +25:56.000 --> 25:59.999 +Right, so the link works. + +26:00.000 --> 00:26:05.284 +Application, right, Request. + +00:26:05.384 --> 00:26:08.284 +It also supports cross-packaging package linking, + +00:26:08.384 --> 00:26:12.204 +so following the link to request + +00:26:12.304 --> 00:26:17.524 +takes us from servant-server package Org documentation + +00:26:17.624 --> 00:26:24.684 +to the WAI Org documentation. + +00:26:24.784 --> 00:26:27.444 +Another nice thing with Org documentation + +00:26:27.544 --> 00:26:32.644 +is that you can use Org functions + +00:26:32.744 --> 00:26:40.444 +like org-goto to jump to any identifiers. + +00:26:40.544 --> 00:26:45.804 +Let's say we want to jump to application. + +00:26:45.904 --> 00:26:49.999 +We have toApplication. So it jumpts to toApplication. + +26:50.000 --> 00:26:53.924 +I guess application is not an identifier, + +00:26:54.024 --> 00:26:55.724 +yes, it is more like a type alias, + +00:26:55.824 --> 00:26:58.564 +that's why we couldn't find it. + +00:26:58.664 --> 00:27:00.999 +So that is haddorg. + +27:01.000 --> 00:27:06.004 +And of course, I implemented a bit of integration + +00:27:06.104 --> 00:27:08.444 +between haddorg and hcel + +00:27:08.544 --> 00:27:11.204 +so that we can jump from one to the other. + +00:27:11.304 --> 00:27:14.999 +Let's go back to servant. + +27:15.000 --> 27:23.999 +Let's see, ServerT. + +27:24.000 --> 00:27:27.004 +Maybe we want to check out + +00:27:27.104 --> 00:27:31.844 +the source code definition of ServerT. + +00:27:31.944 --> 00:27:36.164 +To find out exactly what sort of type alias it is, + +00:27:36.264 --> 00:27:43.084 +like what is the alias (or type synonym) + +00:27:43.184 --> 00:27:49.404 +We run hcel-identifier-at-point-- + +00:27:49.504 --> 00:27:52.244 +sorry, hcel-haddorg-to-hcel-definition... + +00:27:52.344 --> 00:27:54.999 +Oh, we have an HTTP error. + +27:55.000 --> 27:58.999 +Typ ServerT not found in module src/Servant/Server.hs + +27:59.000 --> 00:28:01.124 +Why? Well, this is because + +00:28:01.125 --> 00:28:04.844 +the HCEL server only understands, + +00:28:04.944 --> 00:28:07.724 +it only has knowledge of identifiers + +00:28:07.824 --> 00:28:11.999 +that is defined in the original source file. + +28:12.000 --> 00:28:17.084 +So, it is not aware of, say, + +00:28:17.184 --> 00:28:20.999 +identifiers that are re-exported in the module. + +28:21.000 --> 00:28:25.724 +Most likely, Servant.Server module re-exports ServerT + +00:28:25.824 --> 00:28:28.604 +from another module. + +00:28:28.704 --> 00:28:29.644 +We will probably have better luck + +00:28:29.744 --> 00:28:34.999 +looking into some internal modules like this one. + +28:35.000 --> 28:38.999 +Let's try this type class HasContextEntry. + +28:39.000 --> 28:41.999 +So this time it worked. + +28:42.000 --> 00:28:44.244 +And, of course, we can go the other direction + +00:28:44.344 --> 00:28:47.999 +from hecl to haddorg. + +28:48.000 --> 00:28:51.484 +Let's say if we want to display named context + +00:28:51.584 --> 00:28:53.999 +in the haddorg documentation + +28:54.000 --> 00:29:01.524 +so that we can read about, other identifiers documentation + +00:29:01.624 --> 00:29:03.999 +that is related to named context. + +29:04.000 --> 29:07.999 +We do hecl-identifier-at-point-to-haddorg + +29:08.000 --> 29:13.999 +And it does take us to the server-server old file. + +29:14.000 --> 29:17.999 +Okay. + +29:18.000 --> 29:20.999 +And that concludes my presentation. + +29:21.000 --> 00:29:23.484 +You can find hecl in GNU Elpa, + +00:29:23.584 --> 00:29:24.999 +and you can also find the source code, + +29:25.000 --> 00:29:27.364 +as well as the source of haddorg + +00:29:27.464 --> 00:29:29.764 +and instructions on how to generate org documentation + +00:29:29.864 --> 00:29:32.999 +using haddorg in my cgit instance. + +29:33.000 --> 00:29:36.684 +Thank you for your attention. + +00:29:36.784 --> 00:29:37.999 +I hope you enjoy the rest of the conference. + +29:38.000 --> 29:51.000 +Thank you. diff --git a/2022/captions/emacsconf-2022-jupyter--edit-live-jupyter-notebook-cells-with-emacs--blaine-mooers--main.vtt b/2022/captions/emacsconf-2022-jupyter--edit-live-jupyter-notebook-cells-with-emacs--blaine-mooers--main.vtt new file mode 100644 index 00000000..e51ef23b --- /dev/null +++ b/2022/captions/emacsconf-2022-jupyter--edit-live-jupyter-notebook-cells-with-emacs--blaine-mooers--main.vtt @@ -0,0 +1,792 @@ +WEBVTT captioned by sachac + +NOTE Introduction + +00:00:00.000 --> 00:00:03.839 +Hi, my name is Blaine Mooers. + +00:00:03.840 --> 00:00:05.399 +I'm an associate professor of biochemistry + +00:00:05.400 --> 00:00:08.199 +at the University of Oklahoma Health Sciences Center + +00:00:08.200 --> 00:00:09.759 +in Oklahoma City. + +00:00:09.760 --> 00:00:11.999 +I'm going to talk about the use of Emacs + +00:00:12.000 --> 00:00:16.239 +to edit live Jupyter notebook cells + +00:00:16.240 --> 00:00:20.519 +as well as text areas on web pages. + +00:00:20.520 --> 00:00:22.519 +So like a lot of technical workers, + +00:00:22.520 --> 00:00:24.879 +I find myself having to write prose + +00:00:24.880 --> 00:00:28.679 +in text areas on web pages, + +00:00:28.680 --> 00:00:31.719 +as well as working with code + +00:00:31.720 --> 00:00:36.999 +in Jupyter notebooks and Colab notebooks, + +00:00:37.000 --> 00:00:39.319 +and often I have wished for + +00:00:39.320 --> 00:00:43.479 +the full power of Emacs while doing so. + +NOTE GhostText and Atomic Chrome + +00:00:43.480 --> 00:00:45.319 +Well, now that is possible. + +00:00:45.320 --> 00:00:46.799 +Actually, there are several solutions + +00:00:46.800 --> 00:00:49.039 +that have been available for some time. + +00:00:49.040 --> 00:00:50.399 +I'm going to talk about one solution + +00:00:50.400 --> 00:00:55.319 +that I'm familiar with and has worked out for me. + +00:00:55.320 --> 00:00:58.119 +So this requires the use of two software packages, + +00:00:58.120 --> 00:01:01.599 +GhostText and Atomic Chrome. + +00:01:01.600 --> 00:01:04.239 +GhostText is an extension for the web browser, + +00:01:04.240 --> 00:01:07.279 +whereas Atomic Chrome is a package for Emacs. + +00:01:07.280 --> 00:01:10.879 +You have to have both of these. + +00:01:10.880 --> 00:01:13.399 +So Chrome is for the editor side + +00:01:13.400 --> 00:01:18.919 +and GhostText handles the browser side. + +NOTE GhostText + +00:01:18.920 --> 00:01:22.479 +The GhostText extension is available + +00:01:22.480 --> 00:01:26.799 +in the Chrome web store. + +00:01:26.800 --> 00:01:29.519 +And GhostText is represented by this icon, + +00:01:29.520 --> 00:01:31.519 +which has a ghost in front of the capital letter T. + +00:01:31.520 --> 00:01:36.399 +It is being developed by Federico Brigante. + +00:01:36.400 --> 00:01:41.239 +He is a very prolific JavaScript developer. + +00:01:41.240 --> 00:01:44.279 +He has a web page committed to GhostText, + +00:01:44.280 --> 00:01:47.199 +as well as a GitHub site. + +00:01:47.200 --> 00:01:50.159 +So here's an example of GhostText. + +00:01:50.160 --> 00:01:54.839 +This is a snapshot from a session + +00:01:54.840 --> 00:02:01.279 +that I had while editing LaTeX on the Overleaf website. + +00:02:01.280 --> 00:02:03.759 +Overleaf is this web service + +00:02:03.760 --> 00:02:09.719 +that empowers the editing of LaTeX documents on the web. + +00:02:09.720 --> 00:02:14.039 +So I have clicked on this GhostText icon in the toolbar. + +00:02:14.040 --> 00:02:17.039 +I had already opened up Emacs, + +00:02:17.040 --> 00:02:19.879 +and I had the Atomic Chrome server running. + +00:02:19.880 --> 00:02:21.799 +So a connection was established, + +00:02:21.800 --> 00:02:28.599 +as indicated by this blue border around this text area. + +00:02:28.600 --> 00:02:30.519 +And as soon as that appeared, + +00:02:30.520 --> 00:02:35.319 +the text appeared in a buffer inside of Emacs. + +00:02:35.320 --> 00:02:40.159 +So I have overlaid the area where normally the compiled PDF + +00:02:40.160 --> 00:02:43.919 +would appear in an Overleaf session. + +00:02:43.920 --> 00:02:47.679 +So I'm using a configuration for LaTeX that I developed, + +00:02:47.680 --> 00:02:52.159 +which is available through the MooersLab GitHub site. + +00:02:52.160 --> 00:02:55.919 +I also gave a talk about how I use LaTeX in Emacs + +00:02:55.920 --> 00:02:58.839 +at the Berlin Emacs meetup in August. + +00:02:58.840 --> 00:03:00.039 +This talk was not recorded, + +00:03:00.040 --> 00:03:05.119 +but the slides are available on this website. + +NOTE Live coding demo + +00:03:05.120 --> 00:03:09.519 +So I would like to now switch to a little live coding + +00:03:09.520 --> 00:03:12.359 +to make this a little more interesting. + +00:03:12.360 --> 00:03:22.439 +So I start my day at this other website called 750Words. + +00:03:22.440 --> 00:03:25.279 +This site just takes plain text, + +00:03:25.280 --> 00:03:28.559 +but I like to write in LaTeX. + +00:03:28.560 --> 00:03:31.519 +So GhostText came to my rescue + +00:03:31.520 --> 00:03:34.479 +when I started using this everyday last May. + +00:03:34.480 --> 00:03:37.239 +So I clicked on the GhostText icon. + +00:03:37.240 --> 00:03:39.759 +It highlighted that area in blue. + +00:03:39.760 --> 00:03:41.839 +There's some boilerplate + +00:03:41.840 --> 00:03:45.919 +that I like to start my day with. + +00:03:45.920 --> 00:03:50.599 +I like to get a list of my deadlines + +00:03:50.600 --> 00:03:54.239 +that are coming up, as shown here, + +00:03:54.240 --> 00:03:55.839 +for the next several months. + +00:03:55.840 --> 00:03:59.399 +And then I have landed at this tab stop. + +00:03:59.400 --> 00:04:04.239 +And so I had issued a tab trigger + +00:04:04.240 --> 00:04:09.519 +which inserted this almost 50 lines of text + +00:04:09.520 --> 00:04:13.639 +from a snippet through Yasnippet. + +00:04:13.640 --> 00:04:17.479 +And then I'll change this text to whatever. + +00:04:17.480 --> 00:04:29.279 +And then I can hit TAB to move to the next site. + +00:04:29.280 --> 00:04:38.439 +I was dead tired last night, so I fell asleep at my desk, + +00:04:38.440 --> 00:04:42.439 +and whatever. So I just keep on going + +00:04:42.440 --> 00:04:47.319 +and then hit TAB again and enter my "To Be Done" items. + +00:04:47.320 --> 00:04:50.239 +And then what I love about Emacs is that + +00:04:50.240 --> 00:04:56.119 +you can hit C-c C-j to insert a new item and so forth, + +00:04:56.120 --> 00:05:03.239 +so you can extend the list. + +00:05:03.240 --> 00:05:05.079 +Initially, I just have 10 items. + +00:05:05.080 --> 00:05:08.839 +I'm going to have more. And on I go, + +00:05:08.840 --> 00:05:12.359 +using the full power of LaTeX. + +00:05:12.360 --> 00:05:16.119 +So I have configured Atomic Chrome + +00:05:16.120 --> 00:05:19.999 +so it will recognize this website as a – + +00:05:20.000 --> 00:05:21.399 +it will open up this website – + +00:05:21.400 --> 00:05:26.159 +the connection to this website with this buffer + +00:05:26.160 --> 00:05:36.559 +in the LaTeX major mode. To turn this off, + +00:05:36.560 --> 00:05:40.319 +we can close – simply just close the buffer + +00:05:40.320 --> 00:05:42.959 +and that will shut things down. + +00:05:42.960 --> 00:05:46.399 +On the browser side, you can right-click on the icon + +00:05:46.400 --> 00:05:49.039 +and disconnect GhostText on this page. + +NOTE Editing code cells + +00:05:49.040 --> 00:05:53.639 +Okay, let's go to a different situation. + +00:05:53.640 --> 00:05:57.359 +This is not a feature that's advertised by the developer, + +00:05:57.360 --> 00:06:00.119 +but I discovered that you can edit code cells + +00:06:00.120 --> 00:06:02.799 +(or any kind of cell for that matter) + +00:06:02.800 --> 00:06:04.439 +in a Jupyter Notebook. + +00:06:04.440 --> 00:06:05.719 +However, we have a challenge here. + +00:06:05.720 --> 00:06:09.319 +We have three text areas open – three code cells. + +00:06:09.320 --> 00:06:14.759 +So if we click on the GhostText icon, + +00:06:14.760 --> 00:06:17.479 +these three areas will show up in green + +00:06:17.480 --> 00:06:19.119 +and we'll be prompted to select the one + +00:06:19.120 --> 00:06:20.279 +that we want to activate. + +00:06:20.280 --> 00:06:22.359 +We want to activate the one with text. + +00:06:22.360 --> 00:06:31.399 +So then we can go in here and make edits, of course, + +00:06:31.400 --> 00:06:33.359 +and you can do this in Emacs + +00:06:33.360 --> 00:06:35.639 +or we can do it in the browser. It doesn't matter. + +00:06:35.640 --> 00:06:38.359 +You saw me editing in Emacs, + +00:06:38.360 --> 00:06:40.359 +but we can also make the edits + +00:06:40.360 --> 00:06:44.879 +in the text area of the browser + +00:06:44.880 --> 00:06:47.519 +and they will show up immediately in Emacs. + +00:06:47.520 --> 00:06:54.439 +So we could change the case of that M and that's going to – + +00:06:54.440 --> 00:06:59.279 +shows up over here. Okay, we can run this code. + +00:06:59.280 --> 00:07:03.439 +So this is R, one of the three major + +00:07:03.440 --> 00:07:05.159 +programming languages for data science. + +00:07:05.160 --> 00:07:07.319 +At least, Jupyter is supposed to be + +00:07:07.320 --> 00:07:13.479 +a combination of Julia, Python, and R. + +00:07:13.480 --> 00:07:17.559 +So we're running mcmc to get the posterior distribution + +00:07:17.560 --> 00:07:21.119 +and we're going to plot those out with this pyplots package, + +00:07:21.120 --> 00:07:24.079 +and we have these beautiful plots showing the median + +00:07:24.080 --> 00:07:27.039 +of the posterior distribution for four variables in – + +00:07:27.040 --> 00:07:31.559 +four parameters in the CARS data set, + +00:07:31.560 --> 00:07:38.039 +which is available – built into the R package. + +00:07:38.040 --> 00:07:45.559 +And then these shaded areas are the 80% interval. + +00:07:45.560 --> 00:07:49.159 +Okay. Oops. + +NOTE Python + +00:07:49.160 --> 00:08:07.639 +So now for the Python side, + +00:08:07.640 --> 00:08:13.359 +here's an example in which I'm going to actually + +00:08:13.360 --> 00:08:18.679 +insert a snippet of that cell + +00:08:18.680 --> 00:08:27.279 +and then I'm going to enter nvlig for nglview ligand, + +00:08:27.280 --> 00:08:43.319 +and just hit enter. Oops. Hit TAB, excuse me, + +00:08:43.320 --> 00:08:47.999 +and we don't need this line of code, so delete that. + +00:08:48.000 --> 00:08:52.199 +Yep, we want to load up this pdb file + +00:08:52.200 --> 00:08:54.279 +that's in this subdirectory. + +00:08:54.280 --> 00:08:56.919 +So the pdb file is a plain text file + +00:08:56.920 --> 00:08:58.839 +that contains atomic coordinates + +00:08:58.840 --> 00:09:00.159 +of protein crystal structure. + +00:09:00.160 --> 00:09:02.999 +This protein happens to be important in cancer + +00:09:03.000 --> 00:09:09.079 +and we have – we screened by docking 55,000 compounds + +00:09:09.080 --> 00:09:10.679 +on a supercomputer + +00:09:10.680 --> 00:09:12.743 +and then we did MD [molecular dynamics] simulations + +00:09:12.744 --> 00:09:14.159 +of the top 10 [actually 20] leads. + +00:09:14.160 --> 00:09:18.319 +Twelve of them had the compound remain bound + +00:09:18.320 --> 00:09:19.679 +during the period of the simulation, + +00:09:19.680 --> 00:09:22.559 +so those have some potential for – + +00:09:22.560 --> 00:09:25.159 +and require experimental validation. + +00:09:25.160 --> 00:09:28.639 +So we'll run this chunk of code, + +00:09:28.640 --> 00:09:30.839 +and this will give a view of the molecule + +00:09:30.840 --> 00:09:36.479 +that we can interact with by using the mouse. + +00:09:36.480 --> 00:09:39.879 +But I want to share this with my colleague. + +00:09:39.880 --> 00:09:42.919 +My colleague is not set up to use Jupyter, + +00:09:42.920 --> 00:09:46.959 +but instead we can write this out to a HTML file, + +00:09:46.960 --> 00:09:48.319 +which I have loaded up already. + +00:09:48.320 --> 00:09:55.319 +And so we can actually – perhaps. + +00:09:55.320 --> 00:10:01.679 +We click on these two arrows pointing at each other, + +00:10:01.680 --> 00:10:05.159 +and we can get a full screen view of this molecule + +00:10:05.160 --> 00:10:10.439 +and he can identify each atom in this structure. + +00:10:10.440 --> 00:10:12.719 +Over a thousand atoms present. + +00:10:12.720 --> 00:10:14.959 +We're just hovering over a specific atom. + +00:10:14.960 --> 00:10:27.759 +So shown in gray is the ligand that is bound. Okay. + +00:10:27.760 --> 00:10:32.079 +So we still have this box selected + +00:10:32.080 --> 00:10:36.559 +and we still have these two different – + +00:10:36.560 --> 00:10:40.519 +so for each of the – our selected text areas + +00:10:40.520 --> 00:11:03.839 +we have a separate – we have a separate buffer open. Okay. + +NOTE Julia + +00:11:03.840 --> 00:11:06.839 +To wrap things up here, here's an example of using – + +00:11:06.840 --> 00:11:08.919 +with evolving Julia code. + +00:11:08.920 --> 00:11:12.919 +And so this Julia code in this cell is in a Emacs buffer. + +00:11:12.920 --> 00:11:19.279 +So you've got an idea now, I think. + +00:11:19.280 --> 00:11:23.759 +So in terms of plain text areas like in Overleaf + +00:11:23.760 --> 00:11:27.519 +and then these cells in Jupyter Notebooks, + +00:11:27.520 --> 00:11:30.959 +these are other areas that can be edited + +00:11:30.960 --> 00:11:37.919 +like in the text areas within Outlook Webmail and Gmail. + +00:11:37.920 --> 00:11:42.639 +Instead of having to point with the mouse + +00:11:42.640 --> 00:11:43.519 +or click with the mouse, + +00:11:43.520 --> 00:11:48.079 +one can also use keybindings or keyboard shortcuts. + +00:11:48.080 --> 00:11:51.599 +So here are the ones for three major operating systems. + +NOTE How does GhostText work? + +00:11:51.600 --> 00:11:54.639 +So how does GhostText work? + +00:11:54.640 --> 00:11:57.199 +Main thing is you have to open up Emacs + +00:11:57.200 --> 00:11:59.679 +and get this Atomic Chrome server running. + +00:11:59.680 --> 00:12:03.119 +And then with it up and going, + +00:12:03.120 --> 00:12:06.679 +GhostText will be able to – has to be activated + +00:12:06.680 --> 00:12:09.639 +and it will find the GhostText server + +00:12:09.640 --> 00:12:15.079 +through the localhost port 4001. + +00:12:15.080 --> 00:12:19.039 +Put that into the web browser. + +00:12:19.040 --> 00:12:21.639 +If you navigate to that port, + +00:12:21.640 --> 00:12:23.719 +you'll get output that looks like this + +00:12:23.720 --> 00:12:25.639 +if everything's working well. + +00:12:25.640 --> 00:12:27.919 +Otherwise, you'll get a error message + +00:12:27.920 --> 00:12:30.519 +and it should have a port socket – + +00:12:30.520 --> 00:12:34.319 +a web socket port number. + +00:12:34.320 --> 00:12:36.319 +It will not be the same every time. + +NOTE Supported web browsers + +00:12:36.320 --> 00:12:42.319 +So these are the supported web browsers + +00:12:42.320 --> 00:12:45.359 +in addition to Chrome. These are supported + +00:12:45.360 --> 00:12:47.279 +and likewise anything in these – + +00:12:47.280 --> 00:12:49.879 +any browser related to these + +00:12:49.880 --> 00:12:53.079 +can probably use these extensions. + +00:12:53.080 --> 00:12:56.359 +For example, the Brave browser will use Chrome extension + +00:12:56.360 --> 00:13:01.679 +and the Firefox browser extension works with WaterFox. + +00:13:01.680 --> 00:13:05.239 +These are the supported editors. + +00:13:05.240 --> 00:13:10.199 +Each editor has its own extension + +00:13:10.200 --> 00:13:15.719 +and this GhostText was initially developed for SublimeText. + +00:13:15.720 --> 00:13:17.919 +So if you have SublimeText, + +00:13:17.920 --> 00:13:21.959 +then you can use its smooth operation as positive control + +00:13:21.960 --> 00:13:24.999 +when things go wrong with Emacs. + +NOTE Atomic Chrome configuration + +00:13:25.000 --> 00:13:29.479 +This is Atomic. This is a GitHub site for Atomic Chrome. + +00:13:29.480 --> 00:13:33.159 +Atomic Chrome is available for installation through Melpa. + +00:13:33.160 --> 00:13:40.319 +This is my configuration for Atomic Chrome. + +00:13:40.320 --> 00:13:45.519 +So I have this setup so the server starts whenever I log in, + +00:13:45.520 --> 00:13:50.319 +and I have it set up so that default major mode is Python + +00:13:50.320 --> 00:13:55.559 +to deal with the Jupyter notebooks and Colab notebooks. + +00:13:55.560 --> 00:13:57.719 +And then I have major modes + +00:13:57.720 --> 00:13:59.839 +for these other websites defined below. + +00:13:59.840 --> 00:14:06.079 +This is a testing site so the developer has made + +00:14:06.080 --> 00:14:08.119 +to help with troubleshooting. + +00:14:08.120 --> 00:14:11.159 +He also has a protocol on his website + +00:14:11.160 --> 00:14:13.559 +to follow during troubleshooting. + +NOTE Precautions + +00:14:13.560 --> 00:14:16.639 +So here are some precautions. + +00:14:16.640 --> 00:14:19.079 +You'll find that GhostText doesn't work with Pluto. + +00:14:19.080 --> 00:14:21.239 +Pluto is a new computational notebook + +00:14:21.240 --> 00:14:23.479 +for working with Julia. + +00:14:23.480 --> 00:14:27.039 +My suggestion would be just to run IJulia in Jupyter. + +00:14:27.040 --> 00:14:31.999 +It also doesn't work, of course, with RStudio. + +00:14:32.000 --> 00:14:35.199 +Even though RStudio sort of resembles + +00:14:35.200 --> 00:14:38.999 +a web page, web browser, it's not. + +00:14:39.000 --> 00:14:41.359 +Of course, you can always run R, + +00:14:41.360 --> 00:14:48.239 +as you've just seen, using the IPy kernel. + +00:14:48.240 --> 00:14:52.239 +I will also caution you that if you use the Emacs server, + +00:14:52.240 --> 00:14:53.519 +you may run into issues + +00:14:53.520 --> 00:14:57.999 +with the server competing with the port 4001. + +00:14:58.000 --> 00:15:01.919 +So instead, you should probably configure the Emacs server + +00:15:01.920 --> 00:15:04.999 +to use a specific port. + +00:15:05.000 --> 00:15:07.639 +So far – although I haven't done that myself – + +00:15:07.640 --> 00:15:10.999 +so far, I haven't found any conflicts + +00:15:11.000 --> 00:15:13.479 +with the Org Roam user interface. + +NOTE Conclusions + +00:15:13.480 --> 00:15:20.919 +So my conclusions are: GhostText allows you to edit prose + +00:15:20.920 --> 00:15:24.439 +with your favorite major mode + +00:15:24.440 --> 00:15:28.119 +in the text areas of web pages + +00:15:28.120 --> 00:15:31.079 +and in the cells of Jupyter notebooks. + +00:15:31.080 --> 00:15:34.359 +This allows you to tap into snippets + +00:15:34.360 --> 00:15:37.519 +and thereby save time as you have – probably have – + +00:15:37.520 --> 00:15:39.719 +hopefully got an idea of. + +NOTE Thanks + +00:15:39.720 --> 00:15:44.039 +I'd like to thank my friends and mentors + +00:15:44.040 --> 00:15:46.599 +who've helped me out during my second year + +00:15:46.600 --> 00:15:49.359 +in my Emacs learning spiral. + +00:15:49.360 --> 00:15:55.839 +These include my local colleagues. + +00:15:55.840 --> 00:15:58.679 +We meet once a month in the Oklahoma Data Science Workshop. + +00:15:58.680 --> 00:16:01.719 +Last July, I gave a presentation about GhostText. + +00:16:01.720 --> 00:16:08.359 +And then also my friends at Berlin and Austin Emacs meetups + +00:16:08.360 --> 00:16:12.959 +and in the UK research software engineer + +00:16:12.960 --> 00:16:17.599 +Emacs research Slack channel. + +00:16:17.600 --> 00:16:18.919 +So I don't attend these every month, + +00:16:18.920 --> 00:16:21.439 +but I try to make the meetings as often as I can. + +00:16:21.440 --> 00:16:25.399 +Then I'm supported by the following grants, + +00:16:25.400 --> 00:16:28.359 +which allow me to spend + +00:16:28.360 --> 00:16:30.679 +at least some time each day in Emacs. + +00:16:30.680 --> 00:16:34.960 +I'll be happy to take any questions. |