Conda-based Dockerfile & new exit status for unexpected errors

zavolanlab / htsinfer

Infer metadata for your downstream analysis straight from your RNA-seq data

Apache License 2.0

10 stars 22 forks source link

Description

The Dockerfile now (or rather, again) uses Conda to build the environment
Unexpected errors, just like expected errors, now lead to the tool exiting with status code 2

Fixes #143 Fixes #144

Type of change

Please delete options that are not relevant.

[x] Bug fix (non-breaking change which fixes an issue)

Checklist

Please carefully read these items and tick them off if the statements are true or do not apply.

[x] I have performed a self-review of my own code
[x] My code follows the existing coding style, lints and generates no new warnings
[x] I have added type annotations to all function/method signatures, and I have added type annotations for any local variables that are non-trivial, potentially ambiguous or might otherwise benefit from explicit typing.
[x] I have commented my code in hard-to-understand areas
[x] I have added ["Google-style docstrings"] to all new modules, classes, methods/functions or updated previously existing ones
[x] I have added tests that prove my fix is effective or that my feature works
[x] New and existing unit tests pass locally with my changes and I have not reduced the code coverage relative to the previous state
[x] I have updated any sections of the app's documentation that are affected by the proposed changes

If for some reason you are unable to tick off all boxes, please leave a comment explaining the issue you are facing so that we can work on it together.

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (54b54a3) 99.80% compared to head (0ec70d0) 99.80%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## dev #142 +/- ## ======================================= Coverage 99.80% 99.80% ======================================= Files 12 12 Lines 1042 1047 +5 ======================================= + Hits 1040 1045 +5 Misses 2 2 ``` | [Files Changed](https://app.codecov.io/gh/zavolanlab/htsinfer/pull/142?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab) | Coverage Δ | | |---|---|---| | [htsinfer/cli.py](https://app.codecov.io/gh/zavolanlab/htsinfer/pull/142?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-aHRzaW5mZXIvY2xpLnB5) | `100.00% <100.00%> (ø)` | |

zavolanlab / htsinfer