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Main - logged #15
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241208c
main script with more comments
Congm12 96e873f
add comment to hmrf main
Congm12 0cdbcc2
add versions in setup
Congm12 0b66b45
black formatted codes
Congm12 4901b56
add logging and tidy for calicost_main
00813b3
add logging info for hmrf_concatenate_pipeline.
0ecfca4
add logging for hmrfmix_concatenate_pipeline
7eb9ba1
add logging for hmm_NB_BB_nophasing
3b10e3f
adding logging for update params in utils_hmm
a5ddc39
add logging of hmm_NB_BB_nophasing_v2
4d23df4
add logging to hmm_NB_BB_phaseswitch
29235a2
add logging to hmrf and utils_IO.
9686939
add logging to hmrf_pipeline
1da81bf
add logging on Weighted_NegativeBinomial
46f692b
add logging of emission fitting.
b44b999
finish logging utils distribution fitting
a3a569d
set error on MKL thread setting in calicost_supervised.
7641681
fix == bug in setup.py
a08f2e7
fix errors with configuration of inner and outer loops
a51d402
fix issues around string and bracks from additional logging.
849c20f
fix errors around disp=False (statsmodels) and inconsistent conda/pip…
ea22b72
fix issue with multiple loggers.
b6f94b1
fix prefix bug
8eb653c
revert imports & prefix checks.
b657a9e
revert imports in calicost supervised.
e340a40
revert import for hmm_nophasing
25b35d1
revert imports for hmm_NB_BB_nophasing_v2
bdd5056
revert imports for hmm phaseswitch
6cc7e6b
revert imports for hmrf
3d7f0b7
revert imports for utils IO.
3b34e64
revert imports for utils hmm
627d6b9
revert imports for distribution fitting.
06a368b
add utils hmm njit import
d343620
fix calicost supervised imports.
91dfaa2
fix runtime logging.
2c7c9b5
import bug
8303c62
fix spelling mistake
9ed0df5
log comparative likelihoods.
96d6fa3
fix
9d3c141
fix
690fd30
improve runtime logging
c11b253
update utils hmm logging to show n spots.
0a3e3d0
fix logging error from multiple args
7118f8d
fix typo in hmrf logging
41e0740
update logging strings.
ffe9f5d
logging edits
c75ec89
log hmrfmix_reassignment_posterior_concatenate.
8f3eb26
more logging improvements. remove deprecated code.
32c4239
add use defaults statement
3463769
edit logging for ARI and bb diff.
b6a95ad
log neyman pearson.
79796c6
improved logging.
80f9c21
update logging.
bc44623
update logging
64c691d
improve logging
dddc8c9
improved logging
e807de0
fix logging
d1ae926
edit logging
3501640
fix logging
cfad541
fix logging
a321ff6
fix bugs
d4db18d
fix bugs
94c5a15
fix
776eeb0
logging fixes
4d5466a
fix
11f7c93
add Baum-Welch log lines.
9d70901
fix
c91591d
fix logging.
2003e04
log bandwidth
27603ec
fix logging
fafef1f
fix
ee1810e
fix logging
03db264
fix logging bug
cef4eb2
add TODO for gammas in phasing beta binomial
fbbb9b5
fix
3409014
fix
f3c06bc
fix
48a34a4
fix
c58ea89
add hmrf logging
c7d09d9
add cpas
fbfe56b
log phasing baum welch.
8969c35
fix
726bc11
log initial alpha and tau
6f85e89
fix
160ca9c
fix
4a8103f
fix
575ca76
fix
75a9132
fix
35ee342
fix
0b8720a
write Weighted Beta Binom chain file
137e4bb
fix
3d46a85
finishing touches
9ac416b
ABC for emission models
2bd629d
abc for emission models
d4a0599
fix
431936c
fixes
bed12f1
fix
ef27f84
fix chain logging
22bceb7
fix
5787061
gzip chains
16f10e1
fix
0424169
fix
207e873
update instance counts.
f945854
fix
1613259
fix
2218ebf
fix
37eee03
fix
9591ccc
cleanup before adding ARI for HMM states.
af2fa1a
precision on likelihood chain
8416be5
fix
9882e5e
add HMM ARI
0febc15
fix
e0c3712
fix
ec676e6
fix
1b56487
fix
2977647
fix
ea01b9e
make parent dirs for chains
890d4a7
fix
4a1039c
add hamming distances
ec8881b
fixes
d883c34
add # of states for hamming.
6f66d31
fix
28b0b81
fix increment bug.
3463cc3
fix
15de4a7
Merge pull request #10 from michaelJwilson/main_logged_verbose_abc
Congm12 5c95c47
remove examples
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,33 +1,32 @@ | ||
import setuptools | ||
|
||
setuptools.setup( | ||
name='calicost', | ||
version='v1.0.0', | ||
python_requires='>=3.8', | ||
packages=['calicost'], | ||
package_dir={'': 'src'}, | ||
author='Cong Ma', | ||
author_email='[email protected]', | ||
description='Allele-specific CNAs and spatial cancer clone inference', | ||
long_description='CalicoST infers allele-specific copy number aberrations and cancer clones in spatially resolved transcriptomics data', | ||
url='https://github.com/raphael-group/CalicoST', | ||
install_requires=[ | ||
'numpy', | ||
'scipy', | ||
'pandas', | ||
'scikit-learn', | ||
'scanpy', | ||
'anndata', | ||
'numba', | ||
'tqdm', | ||
'statsmodels', | ||
'networkx', | ||
'matplotlib', | ||
'seaborn', | ||
'pysam', | ||
'ete3', | ||
'ipykernel' | ||
], | ||
include_package_data=True | ||
name="calicost", | ||
version="v1.0.0", | ||
python_requires=">=3.8", | ||
packages=["calicost"], | ||
package_dir={"": "src"}, | ||
author="Cong Ma", | ||
author_email="[email protected]", | ||
description="Allele-specific CNAs and spatial cancer clone inference", | ||
long_description="CalicoST infers allele-specific copy number aberrations and cancer clones in spatially resolved transcriptomics data", | ||
url="https://github.com/raphael-group/CalicoST", | ||
install_requires=[ | ||
"numpy==1.24.4", | ||
"scipy==1.11.3", | ||
"pandas==2.1.1", | ||
"scikit-learn==1.3.2", | ||
"scanpy==1.9.6", | ||
"anndata==0.10.3", | ||
"numba==0.60.0", | ||
"tqdm==4.66.1", | ||
"statsmodels==0.14.0", | ||
"networkx==3.2.1", | ||
"matplotlib==3.7.3", | ||
"seaborn==0.12.2", | ||
"pysam==0.22.1", | ||
"ete3==3.1.3", | ||
"ipykernel", | ||
], | ||
include_package_data=True, | ||
) | ||
|
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1 +1 @@ | ||
__version__ = 'v1.0.0' | ||
__version__ = "v1.0.0" | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. How about set the version to v1.1? |
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This corresponds to condo environment name, right? If so, shall we change it back as the README and readthedocs documentations still have
conda activate calicost_env
in the installation instruction.