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hello,can you help me ? #29

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1db4060
fix s2_t_hat calculation
ilia-kats Jan 15, 2020
1727ab2
First port of SpatialDE to gpflow + tensorflow
ilia-kats Jan 28, 2020
c125580
remove apparently unused file
ilia-kats Jan 29, 2020
ef72229
fix s2_t_hat calculation
ilia-kats Jan 15, 2020
2f0737b
remove apparently unused file
ilia-kats Jan 29, 2020
8a0c4f4
add option to use score test instead of LRT test
ilia-kats Mar 5, 2020
ded3891
Merge branch 'master' of https://github.com/ilia-kats/SpatialDE
ilia-kats Mar 5, 2020
1e570ae
do not fit multiple GPs for multiple kernels
ilia-kats Mar 17, 2020
d8f03a4
enable pickling of frozen models, improve power spectrum plot
ilia-kats Mar 18, 2020
cdec422
fix deleted function in __init__.py
ilia-kats Mar 18, 2020
22717c6
implement an optimizer based on tensorflow probability, add some minor
ilia-kats Mar 20, 2020
84cae8b
full refactor
ilia-kats Mar 23, 2020
09c441d
minor bugfixes
ilia-kats Mar 24, 2020
781aba7
refactor score tests in prepration for NB null model
ilia-kats Mar 27, 2020
b09ad95
testing negative binomial null model
ilia-kats Mar 30, 2020
dd1d203
performance: perform score test once per gene and model
ilia-kats Mar 30, 2020
9a19a45
Merge branch 'gpflow'
ilia-kats Mar 31, 2020
5a6902b
fix up some merge issues
ilia-kats Mar 31, 2020
db545ad
fully integrate gpflow into spatialde
ilia-kats Apr 6, 2020
b687830
robustify against singular matrices, some bugfixes
ilia-kats Apr 7, 2020
f9d400b
NB score test: use proper MLE for mean and dispersion
ilia-kats Apr 14, 2020
a0b3227
clean up obsolete functions
ilia-kats Apr 14, 2020
9714c83
setup: bump version, add gpflow dependency
ilia-kats Apr 14, 2020
11ef99e
remove deleted function from __init__.py
ilia-kats Apr 14, 2020
88cf687
increase minimum lengthscale for automatically generated kernel space
ilia-kats Apr 15, 2020
fbd166d
bugfixes for spectral mixture kernel
ilia-kats Apr 15, 2020
2217ff2
work around negative variances
ilia-kats Apr 15, 2020
599abb4
NB score test: initialize alpha MLE with MoM estimator
ilia-kats Apr 15, 2020
8809ddf
score test: do score test before GP fitting
ilia-kats Jun 2, 2020
0e4b883
add tissue segmentation functionality
ilia-kats Jun 2, 2020
fd44a3c
tissue segmentation: fix some variable names left over from testing
ilia-kats Jun 2, 2020
62597ea
major refactor
ilia-kats Jun 4, 2020
a1749f5
add missing type hinting imports
ilia-kats Jun 4, 2020
065ea38
implement reader for 10x SpaceRanger output
ilia-kats Jun 4, 2020
0d24dec
score test: fix the case where data are subset due to several
ilia-kats Jun 4, 2020
1d32da8
full sparse matrix support
ilia-kats Jun 4, 2020
27bcc40
score test: fix testing multiple kernels
ilia-kats Jun 5, 2020
fd76bcd
simplify kernels + distance cache
ilia-kats Jun 5, 2020
ff61793
tissue segmentation: fix off-by-one error
ilia-kats Jun 8, 2020
3fc4f73
tissue segmentation: fix elbo calculation
ilia-kats Jun 9, 2020
7404517
more tissue segmentation fixes
ilia-kats Jun 12, 2020
be9ff05
tissue segmentation: some more elbo fixes
ilia-kats Jun 19, 2020
28a5477
fix sizefactor calculation for sparse matrices
ilia-kats Jul 8, 2020
5014f93
space ranger import: properly handle duplicate gene names
ilia-kats Jul 8, 2020
1694543
tissue segmentation: properly log about not using spatial information
ilia-kats Jul 9, 2020
389cc57
tissue segmentation: tighten convergence tolerance
ilia-kats Jul 10, 2020
8e088d3
properly handle AnnData files with duplicate gene names in the
ilia-kats Jul 14, 2020
76630fe
make score test work with scipy 1.5
ilia-kats Jul 14, 2020
b568612
port AEH to tensorflow with Dirichlet Process prior
ilia-kats Sep 2, 2020
eb78e70
also export SpatialPatterns class
ilia-kats Sep 2, 2020
f3905b5
aeh: clean up some imports
ilia-kats Sep 2, 2020
468360e
tissue segmentation: fix class pruning
ilia-kats Sep 7, 2020
4c44a7a
tissue segmentation: adjust alpha hyperprior
ilia-kats Sep 7, 2020
8068e0a
aeh: discard unused classes after optimization
ilia-kats Sep 7, 2020
75898a2
implement SVCA model
ilia-kats Oct 8, 2020
d2dd0bf
score test: use gpflow.default_float() consistently
ilia-kats Oct 8, 2020
fe9e67b
clean up repository, modernize setup
ilia-kats Oct 8, 2020
5a7472f
black-ify
ilia-kats Oct 8, 2020
f13a046
fix importing pip-installed SpatialDE
ilia-kats Oct 9, 2020
4bbe4b4
move kernels to _internal, set up basic sphinx-docs
ilia-kats Oct 9, 2020
f09094d
replace old README
ilia-kats Oct 9, 2020
2dd0fb2
SVCA: allow running fit_spatial_interactions without testing first
ilia-kats Oct 12, 2020
0d6b7c8
svca.fit_spatial_interactions: properly initialize kernel
ilia-kats Oct 13, 2020
262dec6
svca: better initialization
ilia-kats Oct 15, 2020
81a7038
svca: use squared exponential kernel (faster)
ilia-kats Oct 19, 2020
5b93d99
svca: performance optimization
ilia-kats Oct 20, 2020
916e0e3
svca: fix test (got broken in previous commit)
ilia-kats Oct 22, 2020
8c3d7c8
fix spatially variable genes test
ilia-kats Nov 4, 2020
6cc9e16
tissue segmentation: write the labels to the AnnData as pd.Categorical
ilia-kats Nov 5, 2020
f3a853f
Merge branch 'master' of https://github.com/ilia-kats/SpatialDE into …
ilia-kats Nov 5, 2020
e93cef6
svca: handle sparse matrices
ilia-kats Nov 6, 2020
3c15d79
aeh: save spatial patterns into adata.obs
ilia-kats Nov 11, 2020
267fd68
when working with AnnData, allow the user to specify the layer
ilia-kats May 17, 2021
714a63c
make setting a different default_float work for score test
ilia-kats Jun 28, 2021
4da263e
make caching the distance matrices optional
ilia-kats Jun 28, 2021
ec40f5a
add docstrings, adjust Sphinx config
ilia-kats Aug 27, 2021
603fbaf
docs: use custom template for classes
ilia-kats Aug 30, 2021
6bd6d1c
auto-build docs on push
ilia-kats Aug 30, 2021
13eddb8
update black version
ilia-kats Aug 31, 2021
f9ff81f
test: improve speed for AnnData with lots of metadata
ilia-kats Sep 21, 2021
37e22ad
tissue segmentation: don't crash when no coordinates are found
ilia-kats Oct 1, 2021
d1bbc5f
workflow: use Python 3.9 for docs (no NumPy wheels for 3.10 yet)
ilia-kats Oct 26, 2021
44d5dbe
docs workflow: debug
ilia-kats Oct 26, 2021
0345513
docs workflow: explicitly install missing NaiveDE dep
ilia-kats Oct 26, 2021
bc8ee56
docs workflow: remove debug step
ilia-kats Oct 26, 2021
906c5e7
README: add docs badge
ilia-kats Oct 26, 2021
78da0ac
fixes for GPflow 2.1
ilia-kats Nov 10, 2021
a3d5ec7
add layer argument to GP fitting
ilia-kats Jan 9, 2023
0e27c17
some more bugfixes, black-ify
ilia-kats Jan 9, 2023
cde7720
update pre-commit action
ilia-kats Jan 9, 2023
c5aa9cd
update pre-commit config
ilia-kats Jan 9, 2023
42b076c
allow specifying a .obs column to use as size factor for normalization
ilia-kats Jan 12, 2023
a69ba45
fix SGPR model
ilia-kats Jan 13, 2023
25f96b6
fit_fast: add parameter to enable/disable sparse GPs
ilia-kats Jan 13, 2023
3703cef
Add `.test` for Normal distribution (#1)
jykr Dec 20, 2024
6dbdb55
update sphinx-docs-to-gh-pages version
ilia-kats Dec 20, 2024
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29 changes: 29 additions & 0 deletions .github/workflows/docs.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,29 @@
name: docs
on: [push]

jobs:
docs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
with:
python-version: "3.9"
- name: Cache pip
uses: actions/cache@v2
with:
# This path is specific to Ubuntu
path: ~/.cache/pip
# Look to see if there is a cache hit for the corresponding requirements file
key: ${{ runner.os }}-pip-${{ hashFiles('setup.cfg') }}
restore-keys: |
${{ runner.os }}-pip-
${{ runner.os }}-
- run: pip install .[docs]
- run: pip install patsy # missing dep of NaiveDE
- name: Running the Sphinx to gh-pages Action
uses: uibcdf/[email protected]
with:
branch: master
dir_docs: docs/source
sphinxopts: ''
13 changes: 13 additions & 0 deletions .github/workflows/pre-commit.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
name: pre-commit

on:
pull_request:
push:

jobs:
pre-commit:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
- uses: pre-commit/[email protected]
6 changes: 6 additions & 0 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
repos:
- repo: https://github.com/psf/black
rev: 22.12.0
hooks:
- id: black
language_version: python3
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