Joris

Evaluation doesn't consider save_seg_dir of Inference and compares lables to labels

1

## Documentation lacking While I was able to understand training and inference actions from the [configuration file documentation](https://niftynet.readthedocs.io/en/dev/config_spec.html#overview), the evaluation action was less clear. For starters, it's not mentioned in...

flag for app considered ambiguous option to pipx run

3

**Describe the bug** some flag arguments are not possible to provide to the app as they seem to be checked for use with `run` instead of the APP **How to...

source install is always overwritten by pypi package install

1

**Describe the bug** Existing installations from source -at least from conda- are not properly installed as python package. Other python packaging tools such as pip cannot recognize the existing installation....

/kind feature **Description:** Artifacts tracking can be very useful, but turning it on globally in case it's not required or desired for every single run is wasteful. Another example for...

prevent overwriting existing versions on dockerhub

2

I had to make the experience that an image build where we had based from (tagged) 0.19.1 started to fail later, because the image on dockerhub with that tag changed....

My `travis endpoint --github` points correctly to an enterprise github api endpoint. I would expect therefore that `travis open --github` picks up the correct enterprise domain but instead it tries...

The setup.py or setup.cfg should contain info on the license ``` 'License :: OSI Approved :: MIT License', ``` https://packaging.python.org/en/latest/guides/distributing-packages-using-setuptools/?highlight=license#classifiers

Currently, unsuccessful responses are handled in a way that there is an error log and then still a response like dictionary is being returned. The major issue with that is...

programmatically convenient output of `pip index versions`

3

### What's the problem this feature will solve? `pip index versions` is an experimental command that scratches the itch to check latest and available versions from index servers. The output...

The REST API documentation suggests to pass the access token as a url parameter: https://developers.zenodo.org/#quickstart-upload:~:text=deposit/depositions%27%2C-,params%3D%7B%27access_token%27%3A%20ACCESS_TOKEN%7D,-)%0Ar. While this might be handy to have when one doesn't have access to developer environment...