4 Commits

Author	SHA1	Message	Date
kadarakos	c003aac29a	SpanFinder into spaCy from experimental (#12507) ... * span finder integrated into spacy from experimental * black * isort * black * default spankey constant * black * Update spacy/pipeline/spancat.py Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * rename * rename * max_length and min_length as Optional[int] and strict checking * black * mypy fix for integer type infinity * revert line order * implement all comparison operators for inf int * avoid two for loops over all docs by not precomputing * interleave thresholding with span creation * black * revert to not interleaving (relized its faster) * black * Update spacy/errors.py Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * update dosctring * enforce that the gold and predicted documents have the same text * new error for ensuring reference and predicted texts are the same * remove todo * adjust test * black * handle misaligned tokenization * return correct variable * failing overfit test * only use a single spans_key like in spancat * black * remove debug lines * typo * remove comment * remove near duplicate reduntant method * use the 'spans_key' variable name everywhere * Update spacy/pipeline/span_finder.py Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * flaky test fix suggestion, hand set bias terms * only test suggester and test result exhaustively * make it clear that the span_finder_suggester is more general (not specific to span_finder) * Update spacy/tests/pipeline/test_span_finder.py Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Apply suggestions from code review * remove question comment * move preset_spans_suggester test to spancat tests * Add docs and unify default configs for spancat and span finder * Add `allow_overlap=True` to span finder scorer * Fix offset bug in set_annotations * Ignore labels in span finder scorer * Format * Add span_finder to quickstart template * Move settings to self.cfg, store min/max unset as None * Remove debugging * Update docstrings and docs * Update spacy/pipeline/span_finder.py Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Fix imports --------- Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>	2023-06-07 15:52:28 +02:00
kadarakos	d1474fdd91	add explanation about overwriting behaviour (#12464) ... * add explanation about overwriting behaviour * Update website/docs/api/spancategorizer.mdx Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Update website/docs/api/spancategorizer.mdx Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Update website/docs/api/spancategorizer.mdx Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * format --------- Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>	2023-03-27 10:27:11 +02:00
Lj Miranda	913d74f509	Add spancat_singlelabel pipeline for multiclass and non-overlapping span labelling tasks (#11365) ... * [wip] Update * [wip] Update * Add initial port * [wip] Update * Fix all imports * Add spancat_exclusive to pipeline * [WIP] Update * [ci skip] Add breakpoint for debugging * Use spacy.SpanCategorizer.v1 as default archi * Update spacy/pipeline/spancat_exclusive.py Co-authored-by: kadarakos <kadar.akos@gmail.com> * [ci skip] Small updates * Use Softmax v2 directly from thinc * Cache the label map * Fix mypy errors However, I ignored line 370 because it opened up a bunch of type errors that might be trickier to solve and might lead to a more complicated codebase. * avoid multiplication with 1.0 Co-authored-by: kadarakos <kadar.akos@gmail.com> * Update spacy/pipeline/spancat_exclusive.py Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Update component versions to v2 * Add scorer to docstring * Add _n_labels property to SpanCategorizer Instead of using len(self.labels) in initialize() I am using a private property self._n_labels. This achieves implementation parity and allows me to delete the whole initialize() method for spancat_exclusive (since it's now the same with spancat). * Inherit from SpanCat instead of TrainablePipe This commit changes the inheritance structure of Exclusive_Spancat, now it's inheriting from SpanCategorizer than TrainablePipe. This allows me to remove duplicate methods that are already present in the parent function. * Revert documentation link to spancat * Fix init call for exclusive spancat * Update spacy/pipeline/spancat_exclusive.py Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Import Suggester from spancat * Include zero_init.v1 for spancat * Implement _allow_extra_label to use _n_labels To ensure that spancat / spancat_exclusive cannot be resized after initialization, I inherited the _allow_extra_label() method from spacy/pipeline/trainable_pipe.pyx and used self._n_labels instead of len(self.labels) for checking. I think that changing it locally is a better solution rather than forcing each class that inherits TrainablePipe to use the self._n_labels attribute. Also note that I turned-off black formatting in this block of code because it reads better without the overhang. * Extend existing tests to spancat_exclusive In this commit, I extended the existing tests for spancat to include spancat_exclusive. I parametrized the test functions with 'name' (similar var name with textcat and textcat_multilabel) for each applicable test. TODO: Add overfitting tests for spancat_exclusive * Update documentation for spancat * Turn on formatting for allow_extra_label * Remove initializers in default config * Use DEFAULT_EXCL_SPANCAT_MODEL I also renamed spancat_exclusive_default_config into spancat_excl_default_config because black does some not pretty formatting changes. * Update documentation Update grammar and usage Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Clarify docstring for Exclusive_SpanCategorizer * Remove mypy ignore and typecast labels to list * Fix documentation API * Use a single variable for tests * Update defaults for number of rows Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Put back initializers in spancat config Whenever I remove model.scorer.init_w and model.scorer.init_b, I encounter an error in the test: SystemError: <method '__getitem__' of 'dict' objects> returned a result with an error set. My Thinc version is 8.1.5, but I can't seem to check what's causing the error. * Update spancat_exclusive docstring * Remove init_W and init_B parameters This commit is expected to fail until the new Thinc release. * Require thinc>=8.1.6 for serializable Softmax defaults * Handle zero suggestions to make tests pass I'm not sure if this is the most elegant solution. But what should happen is that the _make_span_group function MUST return an empty SpanGroup if there are no suggestions. The error happens when the 'scores' variable is empty. We cannot get the 'predicted' and other downstream vars. * Better approach for handling zero suggestions * Update website/docs/api/spancategorizer.md Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Update spancategorizer headers * Apply suggestions from code review Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Add default value in negative_weight in docs * Add default value in allow_overlap in docs * Update how spancat_exclusive is constructed In this commit, I added the following: - Put the default values of negative_weight and allow_overlap in the default_config dictionary. - Rename make_spancat -> make_exclusive_spancat * Run prettier on spancategorizer.mdx * Change exactly one -> at most one * Add suggester documentation in Exclusive_SpanCategorizer * Add suggester to spancat docstrings * merge multilabel and singlelabel spancat * rename spancat_exclusive to singlelable * wire up different make_spangroups for single and multilabel * black * black * add docstrings * more docstring and fix negative_label * don't rely on default arguments * black * remove spancat exclusive * replace single_label with add_negative_label and adjust inference * mypy * logical bug in configuration check * add spans.attrs[scores] * single label make_spangroup test * bugfix * black * tests for make_span_group with negative labels * refactor make_span_group * black * Update spacy/tests/pipeline/test_spancat.py Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * remove duplicate declaration * Update spacy/pipeline/spancat.py Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * raise error instead of just print * make label mapper private * update docs * run prettier * Update website/docs/api/spancategorizer.mdx Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Update website/docs/api/spancategorizer.mdx Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Update spacy/pipeline/spancat.py Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Update spacy/pipeline/spancat.py Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Update spacy/pipeline/spancat.py Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Update spacy/pipeline/spancat.py Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * don't keep recomputing self._label_map for each span * typo in docs * Intervals to private and document 'name' param * Update spacy/pipeline/spancat.py Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Update spacy/pipeline/spancat.py Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * add Tag to new features * replace tags * revert * revert * revert * revert * Update website/docs/api/spancategorizer.mdx Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Update website/docs/api/spancategorizer.mdx Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * prettier * Fix merge * Update website/docs/api/spancategorizer.mdx * remove references to 'single_label' * remove old paragraph * Add spancat_singlelabel to config template * Format * Extend init config tests --------- Co-authored-by: kadarakos <kadar.akos@gmail.com> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>	2023-03-09 10:30:59 +01:00
Sofie Van Landeghem	554df9ef20	Website migration from Gatsby to Next (#12058) ... * Rename all MDX file to `.mdx` * Lock current node version (#11885) * Apply Prettier (#11996) * Minor website fixes (#11974) [ci skip] * fix table * Migrate to Next WEB-17 (#12005) * Initial commit * Run `npx create-next-app@13 next-blog` * Install MDX packages Following: 77b5f79a4d/packages/next-mdx/readme.md * Add MDX to Next * Allow Next to handle `.md` and `.mdx` files. * Add VSCode extension recommendation * Disabled TypeScript strict mode for now * Add prettier * Apply Prettier to all files * Make sure to use correct Node version * Add basic implementation for `MDXRemote` * Add experimental Rust MDX parser * Add `/public` * Add SASS support * Remove default pages and styling * Convert to module This allows to use `import/export` syntax * Add import for custom components * Add ability to load plugins * Extract function This will make the next commit easier to read * Allow to handle directories for page creation * Refactoring * Allow to parse subfolders for pages * Extract logic * Redirect `index.mdx` to parent directory * Disabled ESLint during builds * Disabled typescript during build * Remove Gatsby from `README.md` * Rephrase Docker part of `README.md` * Update project structure in `README.md` * Move and rename plugins * Update plugin for wrapping sections * Add dependencies for plugin * Use plugin * Rename wrapper type * Simplify unnessary adding of id to sections The slugified section ids are useless, because they can not be referenced anywhere anyway. The navigation only works if the section has the same id as the heading. * Add plugin for custom attributes on Markdown elements * Add plugin to readd support for tables * Add plugin to fix problem with wrapped images For more details see this issue: https://github.com/mdx-js/mdx/issues/1798 * Add necessary meta data to pages * Install necessary dependencies * Remove outdated MDX handling * Remove reliance on `InlineList` * Use existing Remark components * Remove unallowed heading Before `h1` components where not overwritten and would never have worked and they aren't used anywhere either. * Add missing components to MDX * Add correct styling * Fix broken list * Fix broken CSS classes * Implement layout * Fix links * Fix broken images * Fix pattern image * Fix heading attributes * Rename heading attribute `new` was causing some weird issue, so renaming it to `version` * Update comment syntax in MDX * Merge imports * Fix markdown rendering inside components * Add model pages * Simplify anchors * Fix default value for theme * Add Universe index page * Add Universe categories * Add Universe projects * Fix Next problem with copy Next complains when the server renders something different then the client, therfor we move the differing logic to `useEffect` * Fix improper component nesting Next doesn't allow block elements inside a `<p>` * Replace landing page MDX with page component * Remove inlined iframe content * Remove ability to inline HTML content in iFrames * Remove MDX imports * Fix problem with image inside link in MDX * Escape character for MDX * Fix unescaped characters in MDX * Fix headings with logo * Allow to export static HTML pages * Add prebuild script This command is automatically run by Next * Replace `svg-loader` with `react-inlinesvg` `svg-loader` is no longer maintained * Fix ESLint `react-hooks/exhaustive-deps` * Fix dropdowns * Change code language from `cli` to `bash` * Remove unnessary language `none` * Fix invalid code language `markdown_` with an underscore was used to basically turn of syntax highlighting, but using unknown languages know throws an error. * Enable code blocks plugin * Readd `InlineCode` component MDX2 removed the `inlineCode` component > The special component name `inlineCode` was removed, we recommend to use `pre` for the block version of code, and code for both the block and inline versions Source: https://mdxjs.com/migrating/v2/#update-mdx-content * Remove unused code * Extract function to own file * Fix code syntax highlighting * Update syntax for code block meta data * Remove unused prop * Fix internal link recognition There is a problem with regex between Node and browser, and since Next runs the component on both, this create an error. `Prop `rel` did not match. Server: "null" Client: "noopener nofollow noreferrer"` This simplifies the implementation and fixes the above error. * Replace `react-helmet` with `next/head` * Fix `className` problem for JSX component * Fix broken bold markdown * Convert file to `.mjs` to be used by Node process * Add plugin to replace strings * Fix custom table row styling * Fix problem with `span` inside inline `code` React doesn't allow a `span` inside an inline `code` element and throws an error in dev mode. * Add `_document` to be able to customize `<html>` and `<body>` * Add `lang="en"` * Store Netlify settings in file This way we don't need to update via Netlify UI, which can be tricky if changing build settings. * Add sitemap * Add Smartypants * Add PWA support * Add `manifest.webmanifest` * Fix bug with anchor links after reloading There was no need for the previous implementation, since the browser handles this nativly. Additional the manual scrolling into view was actually broken, because the heading would disappear behind the menu bar. * Rename custom event I was googeling for ages to find out what kind of event `inview` is, only to figure out it was a custom event with a name that sounds pretty much like a native one. 🫠 * Fix missing comment syntax highlighting * Refactor Quickstart component The previous implementation was hidding the irrelevant lines via data-props and dynamically generated CSS. This created problems with Next and was also hard to follow. CSS was used to do what React is supposed to handle. The new implementation simplfy filters the list of children (React elements) via their props. * Fix syntax highlighting for Training Quickstart * Unify code rendering * Improve error logging in Juniper * Fix Juniper component * Automatically generate "Read Next" link * Add Plausible * Use recent DocSearch component and adjust styling * Fix images * Turn of image optimization > Image Optimization using Next.js' default loader is not compatible with `next export`. We currently deploy to Netlify via `next export` * Dont build pages starting with `_` * Remove unused files * Add Next plugin to Netlify * Fix button layout MDX automatically adds `p` tags around text on a new line and Prettier wants to put the text on a new line. Hacking with JSX string. * Add 404 page * Apply Prettier * Update Prettier for `package.json` Next sometimes wants to patch `package-lock.json`. The old Prettier setting indended with 4 spaces, but Next always indends with 2 spaces. Since `npm install` automatically uses the indendation from `package.json` for `package-lock.json` and to avoid the format switching back and forth, both files are now set to 2 spaces. * Apply Next patch to `package-lock.json` When starting the dev server Next would warn `warn - Found lockfile missing swc dependencies, patching...` and update the `package-lock.json`. These are the patched changes. * fix link Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * small backslash fixes * adjust to new style Co-authored-by: Marcus Blättermann <marcus@essenmitsosse.de>	2023-01-11 17:30:07 +01:00