* Add check for empty input file to CLI pretrain
* Raise error if JSONL is not a dict or contains neither `tokens` nor `text` key
* Skip empty values for correct pretrain keys and log a counter as warning
* Add tests for CLI pretrain core function make_docs.
* Add a short hint for the `tokens` key to the CLI pretrain docs
* Add success message to CLI pretrain
* Update model loading to fix the tests
* Skip empty values and do not create docs out of it
* Request to add Holmes to spaCy Universe
Dear spaCy team, I would be grateful if you would consider my Python library Holmes for inclusion in the spaCy Universe. Holmes transforms the syntactic structures delivered by spaCy into semantic structures that, together with various other techniques including ontological matching and word embeddings, serve as the basis for information extraction. Holmes supports several use cases including chatbot, structured search, topic matching and supervised document classification. I had the basic idea for Holmes around 15 years ago and now spaCy has made it possible to build an implementation that is stable and fast enough to actually be of use - thank you! At present Holmes supports English and German (I am based in Munich) but could easily be extended to support any other language with a spaCy model.
* Added
<!--- Provide a general summary of your changes in the title. -->
When using `spacy pretrain`, the model is saved only after every epoch. But each epoch can be very big since `pretrain` is used for language modeling tasks. So I added a `--save-every` option in the CLI to save after every `--save-every` batches.
## Description
<!--- Use this section to describe your changes. If your changes required
testing, include information about the testing environment and the tests you
ran. If your test fixes a bug reported in an issue, don't forget to include the
issue number. If your PR is still a work in progress, that's totally fine – just
include a note to let us know. -->
To test...
Save this file to `sample_sents.jsonl`
```
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
{"text": "hello there."}
```
Then run `--save-every 2` when pretraining.
```bash
spacy pretrain sample_sents.jsonl en_core_web_md here -nw 1 -bs 1 -i 10 --save-every 2
```
And it should save the model to the `here/` folder after every 2 batches. The models that are saved during an epoch will have a `.temp` appended to the save name.
At the end the training, you should see these files (`ls here/`):
```bash
config.json model2.bin model5.bin model8.bin
log.jsonl model2.temp.bin model5.temp.bin model8.temp.bin
model0.bin model3.bin model6.bin model9.bin
model0.temp.bin model3.temp.bin model6.temp.bin model9.temp.bin
model1.bin model4.bin model7.bin
model1.temp.bin model4.temp.bin model7.temp.bin
```
### Types of change
<!-- What type of change does your PR cover? Is it a bug fix, an enhancement
or new feature, or a change to the documentation? -->
This is a new feature to `spacy pretrain`.
🌵 **Unfortunately, I haven't been able to test this because compiling from source is not working (cythonize error).**
```
Processing matcher.pyx
[Errno 2] No such file or directory: '/Users/mwu/github/spaCy/spacy/matcher.pyx'
Traceback (most recent call last):
File "/Users/mwu/github/spaCy/bin/cythonize.py", line 169, in <module>
run(args.root)
File "/Users/mwu/github/spaCy/bin/cythonize.py", line 158, in run
process(base, filename, db)
File "/Users/mwu/github/spaCy/bin/cythonize.py", line 124, in process
preserve_cwd(base, process_pyx, root + ".pyx", root + ".cpp")
File "/Users/mwu/github/spaCy/bin/cythonize.py", line 87, in preserve_cwd
func(*args)
File "/Users/mwu/github/spaCy/bin/cythonize.py", line 63, in process_pyx
raise Exception("Cython failed")
Exception: Cython failed
Traceback (most recent call last):
File "setup.py", line 276, in <module>
setup_package()
File "setup.py", line 209, in setup_package
generate_cython(root, "spacy")
File "setup.py", line 132, in generate_cython
raise RuntimeError("Running cythonize failed")
RuntimeError: Running cythonize failed
```
Edit: Fixed! after deleting all `.cpp` files: `find spacy -name "*.cpp" | xargs rm`
## 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.
