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Release for v2.5.0 #204

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merged 70 commits into from
Aug 25, 2022
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d4478ae
Bump versions
johnlees May 12, 2022
100ced0
Change pp-sketchlib args to kwargs
johnlees May 12, 2022
d591238
Typo in a kwarg
johnlees May 12, 2022
3a4c855
Move where recursion limit is set
johnlees May 12, 2022
ca9c93a
Replace dendropy with treeswift and biopython
johnlees May 12, 2022
3f7e6f6
Correct name of midpoint fn
johnlees May 12, 2022
653118c
Revert changes in write_tree()
johnlees May 12, 2022
3a51eb0
Add scale parameter to manual start
johnlees May 12, 2022
f8bf9fe
You need to use two equals signs when you test for equality
johnlees May 12, 2022
c1839a4
Remove flask api code
johnlees May 12, 2022
27ea43c
Replace t-SNE with mandrake
johnlees May 13, 2022
66c3b6c
Remove web test
johnlees May 13, 2022
f2b3003
Mistaken use of n_workers
johnlees May 13, 2022
796c7e0
Fix maxIter type
johnlees May 13, 2022
a416cfc
Add new microreact file and API
johnlees May 16, 2022
eb5e24f
Update microreact docs
johnlees May 16, 2022
f64e8c4
Fix dist QC in assign; check for duplicated names
johnlees May 16, 2022
3eef836
Control installation of pybind11 and boost
richfitz Apr 4, 2022
71e4b6f
Import boost code
richfitz Apr 4, 2022
9ae524a
Control pybind11 installation
richfitz Apr 4, 2022
67dfdbe
Ignore test files
richfitz Apr 4, 2022
80206a9
Add new docker builds
richfitz Apr 5, 2022
f1f7977
Start with extra deps
richfitz Jun 8, 2022
16eb166
Remove flask api code
johnlees May 12, 2022
d4c02f3
Update conda env command for poppipe in docs
johnlees Jun 28, 2022
81a905f
Merge remote-tracking branch 'origin/fix-json-serialisation' into bac…
richfitz Jul 12, 2022
3bbc5ac
Pin minor version
richfitz Jul 12, 2022
4c44de7
Add docs
richfitz Jul 12, 2022
6c60204
added rapidnj installation
muppi1993 Jul 19, 2022
0846398
Try pinning hdf5
richfitz Jul 19, 2022
a4d001f
cleaning up rapidnj installation folder
muppi1993 Jul 19, 2022
5e8da6e
specify numpy version
muppi1993 Jul 19, 2022
ca585f2
Update environment.yml
muppi1993 Jul 20, 2022
19a6e7e
Merge pull request #212 from bacpop/bacpop-36
richfitz Jul 21, 2022
2e5fb03
Update logo
johnlees Aug 3, 2022
e8b63c7
Update docs
johnlees Aug 3, 2022
835bf5f
Fix sample name order in assign QC
johnlees Aug 3, 2022
53f3ae7
Fix some parts of cytoscape visualisation
johnlees Aug 3, 2022
b5f083f
Fix cytoscape subsetting
johnlees Aug 4, 2022
ce336e5
Add docs on sklearn backward compatibility
johnlees Aug 4, 2022
0bc69af
Update visualisation docs with mandrake
johnlees Aug 5, 2022
2d6cf49
Write every component for cytoscape visualisation
johnlees Aug 5, 2022
6181aa4
Improve summary to stderr from lineage networks
johnlees Aug 5, 2022
fec6702
Add the cut algorithm to the poppunk_iterate script
johnlees Aug 11, 2022
d4f7260
Add new pp_iterate functionality to docs
johnlees Aug 11, 2022
02ee4bc
Ignore Ns for read QC
johnlees Aug 12, 2022
00466df
Fix the tree cut code
johnlees Aug 12, 2022
1d43126
Change the search range in multi_boundary
johnlees Aug 12, 2022
a8dfc7f
Fix the multi_refine params
johnlees Aug 12, 2022
229b583
Correct progress when indiv refine fails
johnlees Aug 12, 2022
accae53
Set better range in refine tests; fix boundary check
johnlees Aug 12, 2022
549f20a
Refactor the QC process
johnlees Aug 15, 2022
bda06df
Fix the new qc mode for create-db
johnlees Aug 18, 2022
ca029aa
Start fixing the assign QC
johnlees Aug 18, 2022
5d82cc4
Get assign QC working
johnlees Aug 19, 2022
2fb9b27
Further improve dist QC code
johnlees Aug 22, 2022
2269396
Even further improve dist QC
johnlees Aug 22, 2022
17c7cb0
Add proportion of zeros QC
johnlees Aug 22, 2022
4b0bb03
Add serial assign
johnlees Aug 22, 2022
3422731
Simplify query when novel clusters are found
johnlees Aug 23, 2022
87e7a20
Correct assign when graph updated more than once
johnlees Aug 23, 2022
1cf479a
Remove testing print statements
johnlees Aug 23, 2022
bfc9de9
Add check for queries which link to lots of clusters
johnlees Aug 23, 2022
a0a75b4
Add option to print query betweenness
johnlees Aug 23, 2022
6725b10
Correctly named multi boundary output files
johnlees Aug 23, 2022
91fc91f
Fix some test issues
johnlees Aug 23, 2022
0b14fb6
Fix the tests
johnlees Aug 24, 2022
0d33e47
Merge remote-tracking branch 'origin/bacpop-20' into v250-candidate
johnlees Aug 24, 2022
77479a0
Update test cleaner
johnlees Aug 24, 2022
ce01979
Update docs
johnlees Aug 24, 2022
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Bump versions
johnlees committed May 12, 2022
commit d4478ae5f2370618977214c169cdb46e91458a48
6 changes: 3 additions & 3 deletions PopPUNK/__init__.py
Original file line number Diff line number Diff line change
@@ -3,9 +3,9 @@

'''PopPUNK (POPulation Partitioning Using Nucleotide Kmers)'''

__version__ = '2.4.6'
__version__ = '2.5.0'

# Minimum sketchlib version
SKETCHLIB_MAJOR = 1
SKETCHLIB_MINOR = 7
SKETCHLIB_MAJOR = 2
SKETCHLIB_MINOR = 0
SKETCHLIB_PATCH = 0
2 changes: 1 addition & 1 deletion environment.yml
Original file line number Diff line number Diff line change
@@ -18,7 +18,7 @@ dependencies:
- hdbscan
- rapidnj
- h5py
- pp-sketchlib >=1.7.0
- pp-sketchlib >=2.0.0
- graph-tool >=2.35
- requests
- flask