Commit Graph

271 Commits

Author SHA1 Message Date
Matthew Honnibal
1c71fdb805 Remove cytoolz usage from spaCy 2018-12-03 02:19:12 +01:00
Ines Montani
f37863093a 💫 Replace ujson, msgpack and dill/pickle/cloudpickle with srsly (#3003)
Remove hacks and wrappers, keep code in sync across our libraries and move spaCy a few steps closer to only depending on packages with binary wheels 🎉

See here: https://github.com/explosion/srsly

    Serialization is hard, especially across Python versions and multiple platforms. After dealing with many subtle bugs over the years (encodings, locales, large files) our libraries like spaCy and Prodigy have steadily grown a number of utility functions to wrap the multiple serialization formats we need to support (especially json, msgpack and pickle). These wrapping functions ended up duplicated across our codebases, so we wanted to put them in one place.

    At the same time, we noticed that having a lot of small dependencies was making maintainence harder, and making installation slower. To solve this, we've made srsly standalone, by including the component packages directly within it. This way we can provide all the serialization utilities we need in a single binary wheel.

    srsly currently includes forks of the following packages:

        ujson
        msgpack
        msgpack-numpy
        cloudpickle



* WIP: replace json/ujson with srsly

* Replace ujson in examples

Use regular json instead of srsly to make code easier to read and follow

* Update requirements

* Fix imports

* Fix typos

* Replace msgpack with srsly

* Fix warning
2018-12-03 01:28:22 +01:00
Ines Montani
ce7eec846b Move CLi-specific Markdown helper to CLI 2018-12-01 04:55:48 +01:00
Ines Montani
40ae499f32 Remove unused helper function
Now imported from wasabi
2018-12-01 04:54:46 +01:00
Ines Montani
37c7c85a86 💫 New JSON helpers, training data internals & CLI rewrite (#2932)
* Support nowrap setting in util.prints

* Tidy up and fix whitespace

* Simplify script and use read_jsonl helper

* Add JSON schemas (see #2928)

* Deprecate Doc.print_tree

Will be replaced with Doc.to_json, which will produce a unified format

* Add Doc.to_json() method (see #2928)

Converts Doc objects to JSON using the same unified format as the training data. Method also supports serializing selected custom attributes in the doc._. space.

* Remove outdated test

* Add write_json and write_jsonl helpers

* WIP: Update spacy train

* Tidy up spacy train

* WIP: Use wasabi for formatting

* Add GoldParse helpers for JSON format

* WIP: add debug-data command

* Fix typo

* Add missing import

* Update wasabi pin

* Add missing import

* 💫 Refactor CLI (#2943)

To be merged into #2932.

## Description
- [x] refactor CLI To use [`wasabi`](https://github.com/ines/wasabi)
- [x] use [`black`](https://github.com/ambv/black) for auto-formatting
- [x] add `flake8` config
- [x] move all messy UD-related scripts to `cli.ud`
- [x] make converters function that take the opened file and return the converted data (instead of having them handle the IO)

### Types of change
enhancement

## Checklist
<!--- Before you submit the PR, go over this checklist and make sure you can
tick off all the boxes. [] -> [x] -->
- [x] I have submitted the spaCy Contributor Agreement.
- [x] I ran the tests, and all new and existing tests passed.
- [x] My changes don't require a change to the documentation, or if they do, I've added all required information.

* Update wasabi pin

* Delete old test

* Update errors

* Fix typo

* Tidy up and format remaining code

* Fix formatting

* Improve formatting of messages

* Auto-format remaining code

* Add tok2vec stuff to spacy.train

* Fix typo

* Update wasabi pin

* Fix path checks for when train() is called as function

* Reformat and tidy up pretrain script

* Update argument annotations

* Raise error if model language doesn't match lang

* Document new train command
2018-11-30 20:16:14 +01:00
Ines Montani
eddeb36c96
💫 Tidy up and auto-format .py files (#2983)
<!--- Provide a general summary of your changes in the title. -->

## Description
- [x] Use [`black`](https://github.com/ambv/black) to auto-format all `.py` files.
- [x] Update flake8 config to exclude very large files (lemmatization tables etc.)
- [x] Update code to be compatible with flake8 rules
- [x] Fix various small bugs, inconsistencies and messy stuff in the language data
- [x] Update docs to explain new code style (`black`, `flake8`, when to use `# fmt: off` and `# fmt: on` and what `# noqa` means)

Once #2932 is merged, which auto-formats and tidies up the CLI, we'll be able to run `flake8 spacy` actually get meaningful results.

At the moment, the code style and linting isn't applied automatically, but I'm hoping that the new [GitHub Actions](https://github.com/features/actions) will let us auto-format pull requests and post comments with relevant linting information.

### Types of change
enhancement, code style

## Checklist
<!--- Before you submit the PR, go over this checklist and make sure you can
tick off all the boxes. [] -> [x] -->
- [x] I have submitted the spaCy Contributor Agreement.
- [x] I ran the tests, and all new and existing tests passed.
- [x] My changes don't require a change to the documentation, or if they do, I've added all required information.
2018-11-30 17:03:03 +01:00
Matthew Honnibal
2c37e0ccf6
💫 Use Blis for matrix multiplications (#2966)
Our epic matrix multiplication odyssey is drawing to a close...

I've now finally got the Blis linear algebra routines in a self-contained Python package, with wheels for Windows, Linux and OSX. The only missing platform at the moment is Windows Python 2.7. The result is at https://github.com/explosion/cython-blis

Thinc v7.0.0 will make the change to Blis. I've put a Thinc v7.0.0.dev0 up on PyPi so that we can test these changes with the CI, and even get them out to spacy-nightly, before Thinc v7.0.0 is released. This PR also updates the other dependencies to be in line with the current versions master is using. I've also resolved the msgpack deprecation problems, and gotten spaCy and Thinc up to date with the latest Cython.

The point of switching to Blis is to have control of how our matrix multiplications are executed across platforms. When we were using numpy for this, a different library would be used on pip and conda, OSX would use Accelerate, etc. This would open up different bugs and performance problems, especially when multi-threading was introduced.

With the change to Blis, we now strictly single-thread the matrix multiplications. This will make it much easier to use multiprocessing to parallelise the runtime, since we won't have nested parallelism problems to deal with.

* Use blis

* Use -2 arg to Cython

* Update dependencies

* Fix requirements

* Update setup dependencies

* Fix requirement typo

* Fix msgpack errors

* Remove Python27 test from Appveyor, until Blis works there

* Auto-format setup.py

* Fix murmurhash version
2018-11-27 00:44:04 +01:00
Matthew Honnibal
3e7b214e57 Make pretrain script work with stream from stdin 2018-11-15 22:44:07 +00:00
Matthew Honnibal
6430b1fe64 Restore encoding arg on msgpack-numpy 2018-09-27 15:58:21 +02:00
Matthew Honnibal
8809dc4514 Remove deprecated encoding argument to msgpack 2018-09-27 12:56:23 +02:00
Matthew Honnibal
5afd98dff5 Add a stepping function, for changing batch sizes or learning rates 2018-09-14 18:37:16 +02:00
ines
3c30d1763c Merge branch 'master' into develop 2018-07-21 15:34:18 +02:00
Matthew Honnibal
e0caf3ae8c Fix msgpack for new version 2018-07-20 17:32:00 +02:00
Ines Montani
e7b075565d
💫 Rule-based NER component (#2513)
* Add helper function for reading in JSONL

* Add rule-based NER component

* Fix whitespace

* Add component to factories

* Add tests

* Add option to disable indent on json_dumps compat

Otherwise, reading JSONL back in line by line won't work

* Fix error code
2018-07-18 19:43:16 +02:00
ines
3c3a175018 Merge branch 'master' into develop 2018-05-28 18:37:09 +02:00
ansgar-t
9732988951 escape html in displacy.render (#2378) (closes #2361)
## Description
Fix for issue #2361 :
replace &, <, >, " with &amp;amp; , &amp;lt; , &amp;gt; , &amp;quot; in before rendering svg

## Checklist
<!--- Before you submit the PR, go over this checklist and make sure you can
tick off all the boxes. [] -> [x] -->
- [x] I have submitted the spaCy Contributor Agreement.
- [ ] I ran the tests, and all new and existing tests passed.
(As discussed in the comments to #2361)
- [x] My changes don't require a change to the documentation, or if they do, I've added all required information.
2018-05-28 18:36:41 +02:00
Ines Montani
862da5e793 Support pipeline factories via entry points (#2348) 2018-05-22 18:29:45 +02:00
ines
5401c55c75 Merge branch 'master' into develop 2018-05-20 16:49:40 +02:00
ines
5768df4f09 Add SimpleFrozenDict util to use as default function argument 2018-05-20 15:13:37 +02:00
Matthew Honnibal
2c4a6d66fa Merge master into develop. Big merge, many conflicts -- need to review 2018-04-29 14:49:26 +02:00
Ines Montani
3141e04822
💫 New system for error messages and warnings (#2163)
* Add spacy.errors module

* Update deprecation and user warnings

* Replace errors and asserts with new error message system

* Remove redundant asserts

* Fix whitespace

* Add messages for print/util.prints statements

* Fix typo

* Fix typos

* Move CLI messages to spacy.cli._messages

* Add decorator to display error code with message

An implementation like this is nice because it only modifies the string when it's retrieved from the containing class – so we don't have to worry about manipulating tracebacks etc.

* Remove unused link in spacy.about

* Update errors for invalid pipeline components

* Improve error for unknown factories

* Add displaCy warnings

* Update formatting consistency

* Move error message to spacy.errors

* Update errors and check if doc returned by component is None
2018-04-03 15:50:31 +02:00
Matthew Honnibal
8308bbc617 Get msgpack and msgpack_numpy via Thinc, to avoid potential version conflicts 2018-03-29 00:14:55 +02:00
Matthew Honnibal
1f7229f40f Revert "Merge branch 'develop' of https://github.com/explosion/spaCy into develop"
This reverts commit c9ba3d3c2d, reversing
changes made to 92c26a35d4.
2018-03-27 19:23:02 +02:00
Matthew Honnibal
8b7a74570f Revert "Revert "Merge branch 'develop' of https://github.com/explosion/spaCy into develop""
This reverts commit f41e626844.
2018-03-27 19:22:52 +02:00
Matthew Honnibal
f41e626844 Revert "Merge branch 'develop' of https://github.com/explosion/spaCy into develop"
This reverts commit c9ba3d3c2d, reversing
changes made to f57bfbccdc.
2018-03-27 19:22:25 +02:00
Matthew Honnibal
c9ba3d3c2d Merge branch 'develop' of https://github.com/explosion/spaCy into develop 2018-03-27 18:59:08 +02:00
Matthew Honnibal
92c26a35d4 Update get_cuda_stream 2018-03-27 16:42:00 +00:00
Matthew Honnibal
bede11b67c
Improve label management in parser and NER (#2108)
This patch does a few smallish things that tighten up the training workflow a little, and allow memory use during training to be reduced by letting the GoldCorpus stream data properly.

Previously, the parser and entity recognizer read and saved labels as lists, with extra labels noted separately. Lists were used becaue ordering is very important, to ensure that the label-to-class mapping is stable.

We now manage labels as nested dictionaries, first keyed by the action, and then keyed by the label. Values are frequencies. The trick is, how do we save new labels? We need to make sure we iterate over these in the same order they're added. Otherwise, we'll get different class IDs, and the model's predictions won't make sense.

To allow stable sorting, we map the new labels to negative values. If we have two new labels, they'll be noted as having "frequency" -1 and -2. The next new label will then have "frequency" -3. When we sort by (frequency, label), we then get a stable sort.

Storing frequencies then allows us to make the next nice improvement. Previously we had to iterate over the whole training set, to pre-process it for the deprojectivisation. This led to storing the whole training set in memory. This was most of the required memory during training.

To prevent this, we now store the frequencies as we stream in the data, and deprojectivize as we go. Once we've built the frequencies, we can then apply a frequency cut-off when we decide how many classes to make.

Finally, to allow proper data streaming, we also have to have some way of shuffling the iterator. This is awkward if the training files have multiple documents in them. To solve this, the GoldCorpus class now writes the training data to disk in msgpack files, one per document. We can then shuffle the data by shuffling the paths.

This is a squash merge, as I made a lot of very small commits. Individual commit messages below.

* Simplify label management for TransitionSystem and its subclasses

* Fix serialization for new label handling format in parser

* Simplify and improve GoldCorpus class. Reduce memory use, write to temp dir

* Set actions in transition system

* Require thinc 6.11.1.dev4

* Fix error in parser init

* Add unicode declaration

* Fix unicode declaration

* Update textcat test

* Try to get model training on less memory

* Print json loc for now

* Try rapidjson to reduce memory use

* Remove rapidjson requirement

* Try rapidjson for reduced mem usage

* Handle None heads when projectivising

* Stream json docs

* Fix train script

* Handle projectivity in GoldParse

* Fix projectivity handling

* Add minibatch_by_words util from ud_train

* Minibatch by number of words in spacy.cli.train

* Move minibatch_by_words util to spacy.util

* Fix label handling

* More hacking at label management in parser

* Fix encoding in msgpack serialization in GoldParse

* Adjust batch sizes in parser training

* Fix minibatch_by_words

* Add merge_subtokens function to pipeline.pyx

* Register merge_subtokens factory

* Restore use of msgpack tmp directory

* Use minibatch-by-words in train

* Handle retokenization in scorer

* Change back-off approach for missing labels. Use 'dep' label

* Update NER for new label management

* Set NER tags for over-segmented words

* Fix label alignment in gold

* Fix label back-off for infrequent labels

* Fix int type in labels dict key

* Fix int type in labels dict key

* Update feature definition for 8 feature set

* Update ud-train script for new label stuff

* Fix json streamer

* Print the line number if conll eval fails

* Update children and sentence boundaries after deprojectivisation

* Export set_children_from_heads from doc.pxd

* Render parses during UD training

* Remove print statement

* Require thinc 6.11.1.dev6. Try adding wheel as install_requires

* Set different dev version, to flush pip cache

* Update thinc version

* Update GoldCorpus docs

* Remove print statements

* Fix formatting and links [ci skip]
2018-03-19 02:58:08 +01:00
Matthew Honnibal
31b156d60b Fix itershuffle 2018-03-10 22:32:59 +01:00
Johannes Dollinger
012e874d09 Add contributor agreement for emulbreh 2018-02-13 13:40:33 +01:00
Johannes Dollinger
bf94c13382 Don't fix random seeds on import 2018-02-13 12:42:23 +01:00
ines
35653bef3a Add missing import (fixes #1546) 2017-11-10 19:05:18 +01:00
Matthew Honnibal
726f689da4 Fix missing import 2017-11-07 13:20:12 +01:00
ines
8fb48b9b91 Update and document new util functions 2017-11-07 00:22:43 +01:00
Matthew Honnibal
1cab703bba Move minibatch function to util 2017-11-06 23:45:36 +01:00
ines
39e0586192 Add deprecated helper
Uses warning to show DeprecationWarning and custom stack trace
2017-11-01 16:32:36 +01:00
Matthew Honnibal
a7bf38bf31 Remove misleading comment on util.get_cuda_stream() 2017-11-01 13:57:25 +01:00
ines
ea4a41c8fb Tidy up util and helpers 2017-10-27 14:39:09 +02:00
Matthew Honnibal
9baa8fe7ec Convert closure to functools.partial, to promote pickling 2017-10-17 18:20:52 +02:00
Matthew Honnibal
df488274b1 Fix deserialization of vectors 2017-10-16 20:55:00 +02:00
ines
d5418553eb Fix whitespace 2017-10-16 18:30:04 +02:00
ines
6ceadcdb5c Make sure from_disk passes string to numpy (see #1421)
If path is a WindowsPath, numpy does not recognise it as a path and as
a result, doesn't open the file.
https://github.com/numpy/numpy/blob/master/numpy/lib/npyio.py#L369
2017-10-16 18:29:56 +02:00
ines
b39409173e Add disable option and True/False/None values for pipeline 2017-10-07 00:29:08 +02:00
ines
212c8f0711 Implement new Language methods and pipeline API 2017-10-07 00:25:54 +02:00
Matthew Honnibal
f24c2e3a8a Fix evaluate for non-GPU 2017-10-03 22:47:31 +02:00
ines
8dbe49ecb8 Always compare lowercase package names
Otherwise, is_package will return False if model name contains
uppercase characters. See this issue:
https://support.prodi.gy/t/saving-a-trained-ner-model-as-a-loadable-modu
le/46/6
2017-09-29 20:55:17 +02:00
ines
153c2589d4 Revert "Always compare lowercase package names"
This reverts commit 7d77dc490f.
2017-09-29 20:53:36 +02:00
ines
7d77dc490f Always compare lowercase package names
Otherwise, is_package will return False if model name contains
uppercase characters. See this issue:
https://support.prodi.gy/t/saving-a-trained-ner-model-as-a-loadable-modu
le/46/6
2017-09-29 20:52:28 +02:00
Matthew Honnibal
ffda38356a Add util function to enable GPU 2017-09-20 19:16:35 -05:00
ines
68f66aebf8 Use pkg_resources instead of pip for is_package (resolves #1293) 2017-09-16 20:27:59 +02:00
Matthew Honnibal
30e35d9666 Fix syntax error 2017-08-30 17:35:39 -05:00
ines
173089a45a Add more validation for model meta 2017-08-29 11:21:46 +02:00
Matthew Honnibal
ed95009b5c Fix data loading on Python 2 2017-08-18 21:57:06 +02:00
Dan O'Huiginn
ebf5a3ce59 Allow loading with python < 3.6
Don't rely on recent python features to load models

Fixes Issue #1271
2017-08-17 15:15:47 +00:00
ines
ea167e14db Fix model package loading from link 2017-06-05 13:10:49 +02:00
ines
dd6dc4c120 Update spacy.load() helper functions 2017-06-05 13:02:31 +02:00
ines
7db1a0e83e Make sure printed values are always strings 2017-06-04 21:27:20 +02:00
ines
070e026ed9 Ensure path on read_json 2017-06-04 20:44:37 +02:00
ines
e1e73936b1 Raise correct error 2017-06-04 20:44:27 +02:00
ines
4c2bbc3ccc Add add_lookups util function 2017-06-03 19:44:47 +02:00
ines
924c58bde3 Fix serialization of optional elements 2017-06-02 18:18:17 +02:00
Matthew Honnibal
1d18cedae8 Fiddle with msgpack bytes vs unicode 2017-06-01 10:48:43 -05:00
Matthew Honnibal
3ff7d7fcef Merge for updated requirements 2017-06-01 04:57:47 -05:00
Matthew Honnibal
ae8010b526 Move weight serialization to Thinc 2017-06-01 02:56:12 -05:00
Matthew Honnibal
c8a58cfcf8 Fix Python2/3 load bug 2017-05-31 15:21:44 -05:00
Matthew Honnibal
8dfb9546f0 Merge branch 'develop' of https://github.com/explosion/spaCy into develop 2017-05-31 07:21:14 -05:00
Matthew Honnibal
92f9e5cc9a Silence env_opt, and fix serialization for GPU 2017-05-31 07:14:11 -05:00
Matthew Honnibal
33e5ec737f Fix to/from disk methods 2017-05-31 13:43:10 +02:00
Matthew Honnibal
2a061e2777 Fix serialisation, for reals this time 2017-05-29 17:52:08 -05:00
Matthew Honnibal
35d981241f Fix model deserialization 2017-05-29 14:46:31 -05:00
Matthew Honnibal
5b29f227ae Fix serialization 2017-05-29 14:35:53 -05:00
Matthew Honnibal
1e6df0a2a1 Merge branch 'develop' of https://github.com/explosion/spaCy into develop 2017-05-29 14:30:12 -05:00
ines
08382f21e3 Pass model meta to nlp object in load_model 2017-05-29 20:44:11 +02:00
Matthew Honnibal
f1acdaab55 Fix serialization of weight offsets 2017-05-29 13:23:11 -05:00
Matthew Honnibal
c044e9c21c Merge branch 'develop' of https://github.com/explosion/spaCy into develop 2017-05-29 08:41:02 -05:00
Matthew Honnibal
aa4c33914b Work on serialization 2017-05-29 08:40:45 -05:00
ines
567485a818 Fix and document model loading with pipeline and overrides 2017-05-29 14:10:10 +02:00
Matthew Honnibal
deac7eb01c Fix for serialization 2017-05-29 13:54:18 +02:00
Matthew Honnibal
04c32aa091 Fix for serialization 2017-05-29 13:53:32 +02:00
Matthew Honnibal
a1960c2d09 Fix for serialization 2017-05-29 13:47:42 +02:00
Matthew Honnibal
7b06bb896e Fix for serialization 2017-05-29 13:42:55 +02:00
Matthew Honnibal
f4aafca222 Merge changes to test_misc 2017-05-29 12:26:02 +02:00
Matthew Honnibal
ff26aa6c37 Work on to/from bytes/disk serialization methods 2017-05-29 11:45:45 +02:00
ines
df920ba0e7 Add tests for displaCy and util functions and fix util typo 2017-05-29 10:51:19 +02:00
Matthew Honnibal
c91b121aeb Move serialization functions to util 2017-05-29 10:13:42 +02:00
Matthew Honnibal
6dad4117ad Work on serialization for models 2017-05-29 01:37:57 +02:00
ines
c1983621fb Update util functions for model loading 2017-05-28 00:22:40 +02:00
ines
c8543c8237 Fix formatting and docstrings and remove deprecated function 2017-05-28 00:22:40 +02:00
ines
51882c4984 Fix formatting 2017-05-26 12:37:45 +02:00
Matthew Honnibal
80cf42e33b Fix compounding and decaying utils 2017-05-25 17:15:39 -05:00
Matthew Honnibal
b9cea9cd93 Add compounding and decaying functions 2017-05-25 16:16:10 -05:00
ines
b5fb43fdd8 Allow sys.exit status as exits keyword arg in util.prints() 2017-05-22 12:29:15 +02:00
Matthew Honnibal
5db89053aa Merge docstrings 2017-05-21 13:46:23 -05:00
Matthew Honnibal
0731971bfc Add itershuffle utility function. Maybe belongs in thinc 2017-05-21 09:05:05 -05:00
ines
3871157d84 Update spacy.util documentation 2017-05-21 01:12:09 +02:00
Matthew Honnibal
238be0f16a Merge branch 'develop' of https://github.com/explosion/spaCy into develop 2017-05-18 08:32:22 -05:00
Matthew Honnibal
c214c0decb Improve env_opt reporting 2017-05-18 08:32:03 -05:00
ines
489d2fb4ba Add is_in_jupyter() helper for displaCy (see #1058) 2017-05-18 14:13:14 +02:00
ines
abf0188b0a Move cupy and CudaStream to compat 2017-05-18 14:12:45 +02:00
Matthew Honnibal
fc8d3a112c Add util.env_opt support: Can set hyper params through environment variables. 2017-05-18 04:36:53 -05:00