Unverified Commit dc7eda3b authored by Alana's avatar Alana Committed by GitHub
Browse files

Merge branch 'deepchem:master' into bert_to_merge

parents 76a0f7ac 22a8fbd7
......@@ -25,6 +25,7 @@ Please check the option that is related to your PR.
- [ ] Run `yapf -i <modified file>` and check no errors (**yapf version must be 0.22.0**)
- [ ] Run `mypy -p deepchem` and check no errors
- [ ] Run `flake8 <modified file> --count` and check no errors
- [ ] Run `python -m doctest <modified file>` and check no errors
- [ ] I have performed a self-review of my own code
- [ ] I have commented my code, particularly in hard-to-understand areas
- [ ] I have made corresponding changes to the documentation
......
......@@ -143,6 +143,10 @@ The DeepChem project maintains an extensive collection of [tutorials](https://gi
After working through the tutorials, you can also go through other [examples](https://github.com/deepchem/deepchem/tree/master/examples). To apply `deepchem` to a new problem, try starting from one of the existing examples or tutorials and modifying it step by step to work with your new use-case. If you have questions or comments you can raise them on our [gitter](https://gitter.im/deepchem/Lobby).
### Supported Integrations
- [Weights & Biases](https://docs.wandb.ai/guides/integrations/other/deepchem): Track your DeepChem model's training and evaluation metrics.
### Gitter
Join us on gitter at [https://gitter.im/deepchem/Lobby](https://gitter.im/deepchem/Lobby). Probably the easiest place to ask simple questions or float requests for new features.
......
......@@ -25,8 +25,7 @@ class WandbLogger(object):
def __init__(self,
name: Optional[str] = None,
entity: Optional[str] = None,
project: Optional[str] = None,
save_dir: Optional[str] = None,
project: Optional[str] = "deepchem",
mode: Optional[str] = "online",
id: Optional[str] = None,
resume: Optional[Union[bool, str]] = None,
......@@ -43,8 +42,6 @@ class WandbLogger(object):
an entity is a username or team name where you're sending the W&B run
project: str
the name of the project where you're sending the new W&B run
save_dir: str
path where data is saved (wandb dir by default)
mode: str
W&B online or offline mode
id: str
......@@ -67,7 +64,6 @@ class WandbLogger(object):
'Note: Model checkpoints will not be uploaded to W&B in offline mode.\n'
'Please set `mode="online"` if you need to log your model.')
self.save_dir = save_dir
self.save_run_history = save_run_history
# set wandb init arguments
......@@ -77,7 +73,6 @@ class WandbLogger(object):
entity=entity,
mode=mode,
id=id,
dir=save_dir,
resume=resume,
anonymous=anonymous)
self.wandb_init_params.update(**kwargs)
......
......@@ -40,7 +40,7 @@ Whenever you modify a file, run :code:`flake8` on it.
flake8 <modified file> --count
If the command return 0, it means your code pass Flake8 check.
If the command returns 0, it means your code passes the Flake8 check.
Docstrings
----------
......@@ -53,8 +53,12 @@ appropriate, cite the relevant publications.
.. _`numpy`: https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard
All docstrings should follow the `numpy`_ docstring formatting conventions.
All docstrings should follow the `numpy`_ docstring formatting conventions. To
ensure that the code examples in the docstrings are working as expected, run
.. code-block:: bash
python -m doctest <modified file>
Unit Tests
----------
......@@ -91,6 +95,12 @@ while installing the package from source. This will let you see changes that you
make to the source code when you import the package and, in particular, it
allows you to import the new classes/methods for unit tests.
Ensure that the tests pass locally! Check this by running
.. code-block:: bash
python -m pytest <modified file>
Testing Machine Learning Models
-------------------------------
......
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