Comments (9)
ok I wrote some code to do this but don't want to expand test suite over the internet to use URIs. @sbooeshaghi how do you run tests locally?
from seqspec.
Hi, could you clarify what you mean by "read seqspec from URI"? Do mean something akin to
seqspec print http://myurl.com/customspec.yaml
?
from seqspec.
Also @detrout setup the testing framework and maybe can comment a bit about it and how to effectively write tests for new functionality.
from seqspec.
You could either use a mocking library
https://pypi.org/project/requests-mock/
or alternatively launch a local HTTP server instance to host a test seqspec.
https://docs.python.org/3/library/http.server.html
https://pytest-httpserver.readthedocs.io/en/latest/
from seqspec.
seqspec print http://myurl.com/customspec.yaml
No, not the seqspec file itself, but rather the the references within it to the fastqs and index files. Ha, which means I think I modified the wrong function.
from seqspec.
Ben asked for test documentation in slack, this look good enough for a pull request?
+Test can be run with
+```bash
+tox
+```
+Which will install pytest and pytest-cov, but requires you have already
+installed tox or
+
+```bash
+pytest --cov=seqspec
+```
+which requires that you install pytest and pytest-cov.
+
+
from seqspec.
those should be in dev-requirements.txt right?
from seqspec.
Yes, the package dependencies are listed in dev-requirements.
Though maybe it doesn't hurt to give people the option to ignore pip install -r dev-requirements (In case they forget it's there. like me)
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onlists can now be supplied a uri
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Related Issues (20)
- PIP-seq HOT 5
- Print not working on Windows HOT 3
- Linker is not a region_type HOT 1
- speck check is allowing different region_type HOT 1
- add "requests" package as dependency?
- missing support for custom read primer definition HOT 6
- 10x-RNA-v3 barcode file HOT 3
- DNA for modalities HOT 3
- getting not unique across all regions error but region_id is unique HOT 4
- Please make an initial release HOT 3
- format chromap potentially is not deterministic as python set() does not have a guaranteed order, HOT 1
- index string should take into account strand information HOT 3
- getting an unexpected keyword argument error in seqspec init HOT 2
- With a seqspec that has only one modality it seems like the library png plot is too short.
- source file for pypi HOT 1
- Feature request: grouping of sequencing runs HOT 2
- using region.max_len for format and check is a problem for nanopore reads HOT 1
- seqspec split error HOT 1
- predefined `sequence_protocol`
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from seqspec.