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Implement continous integration for linting and formatting and adress issues #244

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merged 41 commits into from
Aug 26, 2024
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9a4fa4a
add CI stuff from scilifelab/scilifelab_epps
kedhammar Jun 27, 2024
55ce1d1
add ci packages
kedhammar Jun 27, 2024
429872d
ruff format
kedhammar Jun 27, 2024
80257e3
suppress blame on prev commit
kedhammar Jun 27, 2024
d44f18b
run ci on python 3.12
kedhammar Jun 27, 2024
6b7e397
ruff safe fixes
kedhammar Jun 27, 2024
a894d67
suppress blame
kedhammar Jun 27, 2024
3c757d1
fix most star imports
kedhammar Jun 27, 2024
f6a9c3e
ruff unsafe fixes, passing
kedhammar Jun 27, 2024
ff50c12
remove unused imports
kedhammar Jun 27, 2024
fbc6537
explicate imports
kedhammar Jun 27, 2024
a12a77b
merge duplicate function
kedhammar Jun 27, 2024
de179ab
remove duplicate, autopassing test func
kedhammar Jun 27, 2024
842213a
add isinstance
kedhammar Jun 27, 2024
cfcb7fa
bugfix
kedhammar Jun 27, 2024
a11334d
formatting
kedhammar Jun 27, 2024
c2ffa9e
add types
kedhammar Jun 27, 2024
6539925
remove title from .toml
kedhammar Jun 27, 2024
230f4c5
fix deprecated sphinx extension
kedhammar Jun 27, 2024
09d7048
mypy fixes
kedhammar Jun 27, 2024
ebafb49
tweak gitignore
kedhammar Jun 27, 2024
94126aa
add missing reqs
kedhammar Jun 27, 2024
afe1ca6
ignore typing for dynamically assigned class attribute
kedhammar Jun 28, 2024
af62abb
use public method instead of private method
kedhammar Jun 28, 2024
59b5848
exclude docs/ from type checking
kedhammar Jun 28, 2024
4805e3c
add required type annotation
kedhammar Jun 28, 2024
1b656f7
fix python version and get rid of import ambiguity
kedhammar Jun 28, 2024
5b6472b
prettier
kedhammar Jun 28, 2024
9270660
editorconfig file exclusions
kedhammar Jun 28, 2024
7d09c3b
tru updated pipreqs script
kedhammar Jun 28, 2024
cef46a2
fix version syntax
kedhammar Jun 28, 2024
c2eadcc
try new codecov workflow
kedhammar Jun 28, 2024
5bd64d1
improve pipreqs
kedhammar Jul 1, 2024
e15d0f9
bugfix
kedhammar Jul 1, 2024
52d3177
Merge branch 'master' into ci
aanil Jul 16, 2024
f66fa11
Would ruff accept this
aanil Jul 16, 2024
3c11b2e
Try propitiating ruff again
aanil Jul 16, 2024
9d91d03
And again
aanil Jul 16, 2024
c954e41
Update genologics/lims_utils.py
kedhammar Aug 5, 2024
b036676
bump version
kedhammar Aug 26, 2024
afe846e
typo
kedhammar Aug 26, 2024
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prettier
kedhammar committed Jun 28, 2024
commit 5b6472b4a957717317c736849457859d3ee3e7d7
2 changes: 1 addition & 1 deletion .github/pr_labels.yml
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
version: '1'
version: "1"
invalidStatus: "pending"
labelRule:
values:
5 changes: 2 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
@@ -6,16 +6,16 @@ A basic module for interacting with the Illumina Basespace Clarity LIMS server v
its REST API. The goal is to provide simple access to the most common
entities and their attributes in a reasonably Pythonic fashion.


### Compatibility

From version **1.0.0** the scripts have been ported to support **Python 3**,
and it is backwards compatible with **Python 2** as well. The previous versions
(**<0.4.6**) are only compatible with **Python 2**.

### Design

All instances of Project, Sample, Artifact, etc should be obtained using
the get_* methods of the Lims class, which keeps an internal cache of
the get\_\* methods of the Lims class, which keeps an internal cache of
current instances. The idea is to create one and only one instance in
a running script for representing an item in the database. If one has
more than one instance representing the same item, there is a danger that
@@ -78,7 +78,6 @@ NOTE: The example files rely on specific entities and configurations
on the server, and use base URI, user name and password, so to work
for your server, all these must be reviewed and modified.


### EPPs

The EPPs in use at Scilifelab can be found in the subdirectory 'scripts' of the repository [scilifelab_epps](https://github.com/SciLifeLab/scilifelab_epps/).