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mudata v0.3 #56

Merged
merged 65 commits into from
Jul 8, 2024
Merged

mudata v0.3 #56

merged 65 commits into from
Jul 8, 2024

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gtca
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@gtca gtca commented Sep 11, 2023

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mumichae and others added 15 commits August 15, 2023 20:39
@mumichae
copy temp indexes when dealing with gene duplicates while reading zar…
64e8ef7 
…r file
@gtca
Display (non-default) axis and fix dimensions for nested MuData
6e35697
@gtca
Implement modality structure representation
731df86 
Resolves #44
@gtca
Implement fsspec support for reading HDF5 files
cb5fbad 
Currently fsspec is not a dependency. However both
BufferedReader and OpenFile instances should be accepted
by the HDF5 reader functions.
@gtca
Fix .uns slot for views
8a72074
@gtca
Drop 3.8 from dev CI following anndata
1c9e860
@gtca
Use mod-order in read_zarr
6db768b
@gtca
Merge pull request #49 from mumichae/mumichae-patch-1
716f8d9 
Fix #48
@gtca
Drop dtype in AnnData constructors
1e5beda
@gtca
With names intersecting between modalities,
188371a 
avoid name (pandas index) sorting
when adding new modalities.

Resolves #46.
@gtca
Implement to_anndata() and to_mudata()
7364c10 
Addresses #14.
@gtca
Start the main branch for v0.3
b903a47
@gtca
Add a missing import
9d8d9c9
@gtca
Fix an extra import
cb97898
@gtca
Fix code formatting
d3773f8
@codecov-commenter
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codecov-commenter commented Sep 11, 2023 •
edited
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Codecov Report

Merging #56 (26143ed) into master (280f1a8) will decrease coverage by 0.01%.
The diff coverage is 75.00%.

Additional details and impacted files 
@@            Coverage Diff             @@
##           master      #56      +/-   ##
==========================================
- Coverage   69.12%   69.11%   -0.01%     
==========================================
  Files          14       14              
  Lines        1671     1674       +3     
==========================================
+ Hits         1155     1157       +2     
- Misses        516      517       +1
Files Changed Coverage Δ
mudata/_core/mudata.py 62.68% <66.66%> (+0.01%) ⬆️
mudata/__init__.py 100.00% <100.00%> (ø)

@gtca gtca mentioned this pull request Sep 13, 2023
Closed
gtca added 5 commits July 1, 2024 17:56
@gtca
Ruff is not satisfied with _version.py by Hatch
6fc1178
@gtca
Fix #52 and use DictView as in AnnData
123212b
@gtca
Organize imports
068c575
@gtca
Fix exports
37ec45e
@gtca
Improve pull/push interfaces
e28b60d 
- Add pull=True argument to the update functions
- Handle categorical data with different categories in _pull_attr
- Improve error messages for pull/push operations
gtca added 2 commits July 2, 2024 18:13
@gtca
Increase stacklevel of the DeprecationWarning
12dae06
@gtca
Roll out the new .update() that does not pull columns
6aea821 
- Introduce the new _update_attr() to make the default in later versions
- Use configuration to change pull behaviour on update
  (mudata.set_options(pull_on_update=False))
@gtca gtca mentioned this pull request Jul 3, 2024
Closed
@gtca gtca mentioned this pull request Jul 3, 2024
Open
@gtca gtca merged commit 14e3fac into main Jul 8, 2024
24 checks passed
@gtca gtca deleted the mudata-0.3 branch July 8, 2024 22:26
@gtca gtca restored the mudata-0.3 branch July 8, 2024 22:26
@gtca gtca deleted the mudata-0.3 branch July 8, 2024 22:27
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3 participants
@gtca @codecov-commenter @mumichae