Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update docs, add checks for formatting/docs building, and refactor modisco and utils modules #34

Merged
merged 40 commits into from
Oct 9, 2024
Merged
Changes from 1 commit
Commits
Show all changes
40 commits
Select commit Hold shift + click to select a range
bdf9d9f
rm old introduction notebook
LukasMahieu Oct 2, 2024
1788df6
updated introduction notebook
LukasMahieu Oct 2, 2024
45a3b8c
remove old docs
LukasMahieu Oct 2, 2024
3f2161b
rename prediction_bar
LukasMahieu Oct 2, 2024
c98f3d7
formatting
LukasMahieu Oct 2, 2024
c5f14c3
reformat
LukasMahieu Oct 2, 2024
c80f030
reformat
LukasMahieu Oct 4, 2024
d6500ae
docs building and ruff formatting check actions
LukasMahieu Oct 4, 2024
4f15fa8
reformat
LukasMahieu Oct 4, 2024
0c674ef
ruff dependency
LukasMahieu Oct 4, 2024
32991fa
ruff formatting
LukasMahieu Oct 4, 2024
bac1af6
fix import
LukasMahieu Oct 4, 2024
11bd71c
manual docs build action check
LukasMahieu Oct 4, 2024
c57c69d
anndata ref
LukasMahieu Oct 4, 2024
d824c8f
docs formatting
LukasMahieu Oct 4, 2024
ef0518f
rm comment
LukasMahieu Oct 4, 2024
3fc1b7b
fix docs action
LukasMahieu Oct 4, 2024
b2f8c1c
fix docs action
LukasMahieu Oct 4, 2024
d640385
fix docs action
LukasMahieu Oct 4, 2024
b0a1421
update python version
LukasMahieu Oct 4, 2024
573508f
fail on warning
LukasMahieu Oct 4, 2024
82d2d77
fail on warning
LukasMahieu Oct 4, 2024
b9812a0
fail on warning
LukasMahieu Oct 4, 2024
fbffd08
change import enhanceroptimizer
LukasMahieu Oct 4, 2024
cf82cdf
new main module 'utils'
LukasMahieu Oct 7, 2024
4c503fa
move logging to utils
LukasMahieu Oct 7, 2024
d306c09
function moved to utils
LukasMahieu Oct 7, 2024
0fd99f9
move modisco funcs into own module
LukasMahieu Oct 7, 2024
0b248fb
rename id_ to pattern_id for docs
LukasMahieu Oct 8, 2024
b07abe6
modisco to separate module under tools
LukasMahieu Oct 8, 2024
61bc3b9
fix some type hints & checks
LukasMahieu Oct 8, 2024
25ef544
update old function name
LukasMahieu Oct 8, 2024
cd0328d
small docfixes
LukasMahieu Oct 8, 2024
dd2a5fe
update locus scoring docs & remove unused parameter 'coordinates'
LukasMahieu Oct 8, 2024
36b3974
remove plot_ from function names (redundant) and rename plot_patterns…
LukasMahieu Oct 8, 2024
3ab9031
fix seaborn return type
LukasMahieu Oct 8, 2024
858ae02
add example plot images to api docs
LukasMahieu Oct 9, 2024
a8cfbb1
update function names and docstrings in ehnacer code analysis
LukasMahieu Oct 9, 2024
b01f757
Notebook check with new update
nkempynck Oct 9, 2024
ec31d34
Notebook check part 2
nkempynck Oct 9, 2024
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
function moved to utils
LukasMahieu committed Oct 7, 2024
commit d306c09904d121c0156efaaf5da7becaea2a9aa1
2 changes: 1 addition & 1 deletion docs/tutorials/model_training_and_eval.ipynb
Original file line number Diff line number Diff line change
@@ -1458,7 +1458,7 @@
"outputs": [],
"source": [
"bigwig = \"/home/VIB.LOCAL/niklas.kempynck/nkemp/mouse/biccn/bigwigs/bws/Sst.bw\"\n",
"bw_values, midpoints = crested.tl.extract_bigwig_values_per_bp(bigwig, coordinates)"
"bw_values, midpoints = crested.utils.extract_bigwig_values_per_bp(bigwig, coordinates)"
]
},
{