partis-bcr 1.0.12.post1.dev3__cp312-cp312-manylinux1_x86_64.whl → 1.0.12.post1.dev4__cp312-cp312-manylinux1_x86_64.whl

{partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: partis-bcr
-Version: 1.0.12.post1.dev3
+Version: 1.0.12.post1.dev4
 Summary: B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference
 Home-page: https://github.com/psathyrella/partis
 Author: Duncan Ralph

{partis_bcr-1.0.12.post1.dev3.dist-info → partis_bcr-1.0.12.post1.dev4.dist-info}/RECORD

@@ -302,18 +302,30 @@ data/substitution-profiles/GSSPs_for_VK_genes_with_at_least_300_lineages.txt,sha
 data/substitution-profiles/GSSPs_for_VL_genes_with_at_least_300_lineages.txt,sha256=CMFb1gk8MbfaMb6y0_qLLiKErrx866C2EafKRSPesB4,184979
 data/substitution-profiles/notes.txt,sha256=-DK9E31YovqOWaXR1Q-LL5KFhjVJcSLwXbriajUq1TA,389
 packages/bpp/bin/bppseqgen,sha256=miMtwBdGjJLBV0d40VfLzqy9X2P9d6xNqFxFopRkepY,202788
+packages/bpp/lib/libbpp-core.a,sha256=bdxvx4Gp9d-occsRcFQy-BTRH8dDJzRn53Yye6nnCHw,6338332
+packages/bpp/lib/libbpp-core.so,sha256=jo7jAS9xCXv4LvxSU37egsO3w5AT-NnQUvd95X8TJ-Y,1992294
+packages/bpp/lib/libbpp-core.so.2,sha256=jo7jAS9xCXv4LvxSU37egsO3w5AT-NnQUvd95X8TJ-Y,1992294
+packages/bpp/lib/libbpp-core.so.2.0.3,sha256=jo7jAS9xCXv4LvxSU37egsO3w5AT-NnQUvd95X8TJ-Y,1992294
+packages/bpp/lib/libbpp-phyl.a,sha256=vZyQgKaB20RkUwNDVXWcY9YJ52FUoArobmPGcYtoBao,29023358
+packages/bpp/lib/libbpp-phyl.so,sha256=n-6JZGenoAnyXxcnm9qffUgcBc7ylsNM8nAvFchLioE,8764566
+packages/bpp/lib/libbpp-phyl.so.9,sha256=n-6JZGenoAnyXxcnm9qffUgcBc7ylsNM8nAvFchLioE,8764566
+packages/bpp/lib/libbpp-phyl.so.9.1.3,sha256=n-6JZGenoAnyXxcnm9qffUgcBc7ylsNM8nAvFchLioE,8764566
+packages/bpp/lib/libbpp-seq.a,sha256=NqDLVwNEvPbdnmOoS6NmCNife9dXWrQ-0ATXM8Rr270,5660348
+packages/bpp/lib/libbpp-seq.so,sha256=bsDlb7oSeDBAvIhuVzeJIBzcewA6IOXwonDgzK2eXGs,1767196
+packages/bpp/lib/libbpp-seq.so.9,sha256=bsDlb7oSeDBAvIhuVzeJIBzcewA6IOXwonDgzK2eXGs,1767196
+packages/bpp/lib/libbpp-seq.so.9.1.3,sha256=bsDlb7oSeDBAvIhuVzeJIBzcewA6IOXwonDgzK2eXGs,1767196
 packages/ham/bcrham,sha256=4Zl5IqQ85_FMz39Dx-O-tgvULN-RVS5U9pCeiTveK-A,852320
 packages/ig-sw/src/ig_align/ig-sw,sha256=lYbqn7wujB6j1T7BGeeCqw5kwbPFn0213lDfUBmJb98,282048
-partis_bcr-1.0.12.post1.dev3.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
-partis_bcr-1.0.12.post1.dev3.data/scripts/cf-germlines.py,sha256=8_bq0ue3ALFQ-a7-ntnhkbCaBdQ5mlWtQgNeQP_TvcQ,3135
-partis_bcr-1.0.12.post1.dev3.data/scripts/compare-plotdirs.py,sha256=AABVGUOwlLCijjo-wwDLfLHiq80TrFVm8mE-4Zqn5Sg,16370
-partis_bcr-1.0.12.post1.dev3.data/scripts/extract-pairing-info.py,sha256=IGPd4jYpsW3IPgsrxTJrk9jAwUKlb45eX3lOpb8Maos,2941
-partis_bcr-1.0.12.post1.dev3.data/scripts/gctree-run.py,sha256=BfSZCFgqdhUEqVsv2h20o6OkS6KbQgx5tfvBhySRx2U,13950
-partis_bcr-1.0.12.post1.dev3.data/scripts/get-naive-probabilities.py,sha256=WfuglaedP3PF0wpksGiUSvfAg4wJoNlucTPa1Wl9MDo,6916
-partis_bcr-1.0.12.post1.dev3.data/scripts/parse-output.py,sha256=2ArlyFI5zApS33gnApFqvbPvFHqmUmYsh71Amy6lkUE,19565
-partis_bcr-1.0.12.post1.dev3.data/scripts/partis-test.py,sha256=ORpG0LjV1PzejY36rO8-Oi3katwOzygDFtcXSst9S_0,64311
-partis_bcr-1.0.12.post1.dev3.data/scripts/split-loci.py,sha256=K0WXQYtloL5rs46mwvEXUecqT3iG8bbqwNOTNwfpvzY,20704
-partis_bcr-1.0.12.post1.dev3.dist-info/licenses/COPYING,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+partis_bcr-1.0.12.post1.dev4.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
+partis_bcr-1.0.12.post1.dev4.data/scripts/cf-germlines.py,sha256=8_bq0ue3ALFQ-a7-ntnhkbCaBdQ5mlWtQgNeQP_TvcQ,3135
+partis_bcr-1.0.12.post1.dev4.data/scripts/compare-plotdirs.py,sha256=AABVGUOwlLCijjo-wwDLfLHiq80TrFVm8mE-4Zqn5Sg,16370
+partis_bcr-1.0.12.post1.dev4.data/scripts/extract-pairing-info.py,sha256=IGPd4jYpsW3IPgsrxTJrk9jAwUKlb45eX3lOpb8Maos,2941
+partis_bcr-1.0.12.post1.dev4.data/scripts/gctree-run.py,sha256=BfSZCFgqdhUEqVsv2h20o6OkS6KbQgx5tfvBhySRx2U,13950
+partis_bcr-1.0.12.post1.dev4.data/scripts/get-naive-probabilities.py,sha256=WfuglaedP3PF0wpksGiUSvfAg4wJoNlucTPa1Wl9MDo,6916
+partis_bcr-1.0.12.post1.dev4.data/scripts/parse-output.py,sha256=2ArlyFI5zApS33gnApFqvbPvFHqmUmYsh71Amy6lkUE,19565
+partis_bcr-1.0.12.post1.dev4.data/scripts/partis-test.py,sha256=ORpG0LjV1PzejY36rO8-Oi3katwOzygDFtcXSst9S_0,64311
+partis_bcr-1.0.12.post1.dev4.data/scripts/split-loci.py,sha256=K0WXQYtloL5rs46mwvEXUecqT3iG8bbqwNOTNwfpvzY,20704
+partis_bcr-1.0.12.post1.dev4.dist-info/licenses/COPYING,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
 python/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 python/alleleclusterer.py,sha256=x50E_lJMlKPc-CPkdkM1qe4AvVi-mkDJ1cBDxs5L-ms,30551
 python/allelefinder.py,sha256=SgJjopk5ivLOcmTumsWq5PZ05aPZ6zQyjTd1fxeRjaM,80402
@@ -379,9 +391,9 @@ test/new-results/cache-new-partition.csv,sha256=jHVEFlsBiSpjesVSFycef8WPFOc47b2B
 test/new-results/get-selection-metrics-new-simu.yaml,sha256=gePaoouvce-7rcq4_R_yM126SAFmmoqxqhDcjyVQwGs,8670
 test/new-results/multi-annotate-new-simu.yaml,sha256=dBpOYLfvkma-Tfy-DNAxsf7zB8niCRbuFSEbvSvsDLE,37319
 test/new-results/partition-new-simu.yaml,sha256=oQ1MSYpR_1ArYPfoLGYFBwaNDOrCcQ9IY0Rij75CJD8,37726
-test/new-results/run-times.csv,sha256=3Z2RvUmMdeRZ5lP90opf-ffRpHPDhCxshc5OfzkaQpE,255
+test/new-results/run-times.csv,sha256=fn5HD9muyyToSpk3VzjonNzmDYqqwceCtReAOCORy1E,255
 test/new-results/seed-partition-new-simu.yaml,sha256=_OKhRdWnk6Ez1ntXXj3PFnbXZcepKYvtsi5nURN84v0,10671
-test/new-results/test.log,sha256=vs27Bb3zjbGnoFZLJN77BkDIvQdQwB4_PqWwZ_ghT4U,20450
+test/new-results/test.log,sha256=-ajA1OB7cSJzvgn4j9zNfHrl1kir78OeIFpVGHx93e8,20450
 test/new-results/vsearch-partition-new-simu.yaml,sha256=8TCi7_M9ozjXkK82q2vdMD4yUgxwmjjORXPJVmrgReY,36290
 test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv,sha256=ybPnGto_Ly4XhxcAaF48lH-eTqnlFi7GDvJ4f9dXP9Y,153
 test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv,sha256=G1sT72mKm3q7QcXXDsDGdwbD-arhzQBV5k7id54LB_g,166
@@ -503,7 +515,7 @@ test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_ha
 test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv,sha256=mm4bOAHI1yTIte2PooOSreMdTOTommH4cwHIJc1B4_8,97
 test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out,sha256=XcHH5evr0molo9Y8cspuB3_RVy9z61LP47CPYnnJyrE,299
 test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa,sha256=qokRcGSD1p1XlPUBpYFMm8HYpMKfb4ed4d5PwKMVC6E,4377
-test/new-results/partition-new-simu/fasttree/iclust-0/log,sha256=YFV0LHSqsb0vjeByOOmhgKgNpG5E7LnzN3OdUHZufT4,1606
+test/new-results/partition-new-simu/fasttree/iclust-0/log,sha256=aKnvudytZzsjdpSCKLIa1h-LPHnG68UQHk2ygQ6Q0to,1606
 test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out,sha256=5z3K5mwEqkWO2UjHzeQopmc52vsptbIy7eg0dRMoVv0,138
 test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa,sha256=PbcyyZtEcJqvPm8PLFeZDbICNpKJxJCMyfhdV3-dY_I,3061
 test/new-results/partition-new-simu/fasttree/iclust-1/log,sha256=kHcgTG5rI8nO288vbJM7fDs_gImQVbdqnlbLiNb38wg,1603
@@ -975,8 +987,8 @@ test/new-results/test/parameters/simu/true/mute-freqs/IGHV4-4_star_09.csv,sha256
 test/new-results/test/parameters/simu/true/mute-freqs/IGHV4-61_star_01.csv,sha256=kONUU7EHhpBiHqSGDoWdTA5zBjaMYZDo385OHxsD5_w,40111
 test/new-results/test/parameters/simu/true/mute-freqs/IGHV5-51_star_01.csv,sha256=0BOZU7pYns4oh593bGeq2V-qPaLAdH33RodQUnwDmlo,38980
 test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv,sha256=pPLqsoWr7MChKJCeXfFDEo6JS4IG21TgmLzoMi5-vdQ,12593
-test/paired/new-results/run-times.csv,sha256=M_QVoEaKehnXtK-LSKbB3uz2qlezoEARVrabkUG6feA,208
-test/paired/new-results/test.log,sha256=PwBRO6F52IRqoz85USNsU1Q2_zSrmNsATDD-t_DC-nM,84653
+test/paired/new-results/run-times.csv,sha256=sNU7vxUZ5s6Sksg61AZmIWkzlgDGzTzjmohEIVX4FNI,208
+test/paired/new-results/test.log,sha256=zDhGTs4dOZ9O9or35C1VSVpHFgpY-dTpZ7pyrVnptcw,84646
 test/paired/new-results/partition-new-simu/partition-igh.yaml,sha256=qelM_0rtDDwpLWl6_ItvkrXioZ9MI6VMiLPMf6tcbIs,71140
 test/paired/new-results/partition-new-simu/partition-igk.yaml,sha256=9iTcIjgyiVsoADqym9El14fwDT4nU_xu2mWy_UeVHSA,46688
 test/paired/new-results/partition-new-simu/partition-igl.yaml,sha256=XdV7rr3fQJPi3-5NvCxhHI4k5huOja8zxdI9XHWatMQ,23871
@@ -991,13 +1003,13 @@ test/paired/new-results/partition-new-simu/true-pair-clean-performance-unpaired.
 test/paired/new-results/partition-new-simu/true-pair-clean-performance.csv,sha256=EgjeHR05wFVPUvq8acCzf2LhT4c7niHXpEIoc9XyX9Q,178
 test/paired/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out,sha256=PhTFRztnys3BZK9tDAeVNT08qfbpwqVTF-B5yjBIosI,332
 test/paired/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa,sha256=uHZPu9HHvPAYd4yBC8o-FOdG0jH4ACJcCMhA4dmvvlY,5918
-test/paired/new-results/partition-new-simu/fasttree/iclust-0/log,sha256=_SaOe_D4V50eJursmfGOSUPkiLwSawm5xxsIl7Z_n9E,1534
+test/paired/new-results/partition-new-simu/fasttree/iclust-0/log,sha256=-zBeSfTWmCs-6IqHOi1F2YADR4zdpLLqoFSUga_hVJY,1534
 test/paired/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out,sha256=TKmB3fknPQhsEkQnHyp37K4pfWGMi76t_lP1QEE0PFM,332
 test/paired/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa,sha256=hea0QDRuHtC6QGk7rioaP-qoH6JotckBqySdtILzyV8,6038
 test/paired/new-results/partition-new-simu/fasttree/iclust-1/log,sha256=Nj5WS8kZzmxjC4_NQzyycO0fgaT0ALuXopckGiyVdto,1535
 test/paired/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out,sha256=8iAGmWkl8Cw1An8YerCdGi3dYbBCqM03erljLmfZch0,234
 test/paired/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa,sha256=XvNc2wDAuQR3Z7JnQF3QYnPxfYpQH3KzP__OfQymTcw,4434
-test/paired/new-results/partition-new-simu/fasttree/iclust-2/log,sha256=quZK42R7Oh2N-UQyXHIOhR01qgx2ZlQ2sk959_j6vY0,1535
+test/paired/new-results/partition-new-simu/fasttree/iclust-2/log,sha256=25KZIP4HeKCMxU4DesdGXYNygTysU6ZT4VMYzmWlgDA,1535
 test/paired/new-results/partition-new-simu/igh+igk/partition-igh-selection-metrics.yaml,sha256=qnyJc6r4fEij37iP8yKvwXdXa6oz1GlprIABjBvEac4,5954
 test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml,sha256=TvdmgfDmKq9FTXSZ8WvsP85OsORW3qB2hqMbGZG7_Ss,43157
 test/paired/new-results/partition-new-simu/igh+igk/partition-igk-selection-metrics.yaml,sha256=1cTAXjSz2J7eW7WYV9a1HOnBArqlO66a9M3HQiMTuA0,4635
@@ -1007,7 +1019,7 @@ test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust
 test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/log,sha256=vO7VmqU3ovUHv5eeBQjBL4_OkUPmSrkzRJA-ygBuRy0,1693
 test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/fasttree.out,sha256=R_clhMra-ApsWz9L57q5eee5ouu2TRfhss6AEPherxA,217
 test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/input-seqs.fa,sha256=_AA1cnLEZd2n60CZ_FRSeUID4yggqfQyBXBbRa0ke5w,2723
-test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log,sha256=5UepSdUakrSNr48Z2u1gFSlD0TP0qsR_oAUlgFsnkHE,1692
+test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log,sha256=h81UNPsuHrMD0xu7yvQLELsttjwQCnlV8MB3joqjNVk,1692
 test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/fasttree.out,sha256=4BPvTBrBWb0QNzUIgOAifNN5zlQn2pwLeHyXL62KKAY,166
 test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/input-seqs.fa,sha256=xmghMTcWRSKgyfKU2rnLHgIF5uDeVXOkQH2xOPKxo-o,2825
 test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-0/log,sha256=WRAXrrNjPEfivA5dkHsOQFrvq-mnZ0O5JfZHg8SxcBY,1693
@@ -1031,34 +1043,34 @@ test/paired/new-results/partition-new-simu/single-chain/partition-igh.yaml,sha25
 test/paired/new-results/partition-new-simu/single-chain/partition-igk.yaml,sha256=o-a0agImpMjjo32u7TaIrHbTW_RXJPkHXD8znweeT8Y,38067
 test/paired/new-results/partition-new-simu/single-chain/partition-igl.yaml,sha256=vEjx11N8dkIpx00_h5_qM4dis3254HeEsza7qkTre4I,18883
 test/paired/new-results/partition-new-simu-annotation-performance/plots.html,sha256=yyz8jow57HiaV1_N9RX0jn6vkR_dY0pkzr8KmBxCYlo,3143
-test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg,sha256=Cn239P2qswzW5iS9_Q_cSj9vl4mqu1BOMCHNeiMOICM,29145
-test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg,sha256=hBAV2un6d2QOFFRIQumXBoGraf-q_O3RvfyzjzePsZE,22992
-test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg,sha256=8QP2Kmowa3bHyoxePFYSN2FQy6WBEFUbWgvNi6EnOeQ,19194
+test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg,sha256=2VJYjzo1sd18kgTQoRAZQzR6USN0EB8cIP85ATuXfVY,29145
+test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg,sha256=YRj7UkSLlADLkrJu_hyXWLuIxqS-p50GXNqpE-uyDyY,22992
+test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg,sha256=0rzMUhZ4n5z5s2L-vZfyFE0kr3MYq_Lcw4xHFLh1qCc,19194
 test/paired/new-results/partition-new-simu-annotation-performance/plots/func-per-drop.csv,sha256=hcFbqQj-_5cXQ7nwQk60LucTJs4Sjwctn8UhwGMrvjk,305
 test/paired/new-results/partition-new-simu-annotation-performance/plots/nonfunc-per-drop.csv,sha256=qBE54p878Cw8hi-DYn-Qq6NXA9go9d5-vDzDLrqc06k,318
 test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.csv,sha256=gXd78-EldIOv2K-BxoAnbGc5AZwVMvkyntT1r_p9hbs,126
-test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg,sha256=nHeK9PXZq9GXlx2Z5s3hv0ZEDFGdjMX4yHxqOkK5LbA,7107
+test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-after.svg,sha256=HKamkChU8TjLj3bbztawfp7_daC2EK9epgqypjfPElc,7107
 test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.csv,sha256=Cs0ubrzBHEZfguO-l9_EO8-tzijl7Ih1APSVTEafBm8,183
-test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg,sha256=KgIaAlxKLOAceB3a4UEBrx36iyczbhdLxOGuuStIfDA,8608
-test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg,sha256=oK91zwj8CPHdISXpbfesvBoADiUq1zPnhNzyRwE7C_I,13540
+test/paired/new-results/partition-new-simu-annotation-performance/plots/paired-seqs-per-seq-before.svg,sha256=FdZ-oh0jgEyuvJHQAhjD1U8ji4k96xrfml96iMgrVJo,8608
+test/paired/new-results/partition-new-simu-annotation-performance/plots/pseq-matrix.svg,sha256=CYDUS9VdPHEfO--LWww8_29lz_66Vy0xanjqbLxHYwQ,13540
 test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.csv,sha256=m73KMZ-S024dBjp6ulZUucAc38ZQwsDXYG2sbJGQMos,180
-test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg,sha256=m7pox4_VWTlORBAptj6Q5JJbDucyoZP13r2NfsdF7zA,7763
+test/paired/new-results/partition-new-simu-annotation-performance/plots/seqs-per-droplet.svg,sha256=0x-Q4b1ISf-Zla4YxYj6awVICbbHYOkcbxMSLIYpGfg,7763
 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.csv,sha256=Apzy9JVSmNsEdPoVZxITXt6FZ4nVcwnrDvjMVw8yH-E,371
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg,sha256=ULPf24DV2_b4VGXX_z1HvCgW0GyhmmIhlpso9I8vNQc,12644
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct-family.svg,sha256=HhjT1hrT4YHfB1voLhs-R1GRQioeVNbZA_dEK95W4jo,12644
 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.csv,sha256=Apzy9JVSmNsEdPoVZxITXt6FZ4nVcwnrDvjMVw8yH-E,371
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg,sha256=OEsmlwWQs9RpZbL4qDD-PsgFOvswVWDBW3Rgee80V3Q,12631
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-correct.svg,sha256=1XuS1gHdhxkGCeKh11f6ScmoekXCkSQ4IRc3rFs38vU,12631
 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.csv,sha256=czqVh4ZxAreW2aCwKTHVad8buECSwn1eKK5RToGuESM,402
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg,sha256=dNWEZf5ep9_TK_Pd2OBfU1heN1xFKJeQnEBO_e5EHbM,12648
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-mispaired.svg,sha256=9Hkv6NCQMhG5ge9elSeWg0HTvpEHPUID2_DRQIj-GTs,12648
 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.csv,sha256=1cg0nJL4pkiPxn3jM1c_31pxKPM47KXGZuVp7v-Qz1M,296
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg,sha256=T_UjRmdNMEpbl8cF0170AFKIdzVf5Ee5bGgmegy_ja4,7249
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-multiple.svg,sha256=lgENBIzzF5WGbOtaas_kY04xeC6eh_nl0iWRqN8V164,7249
 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.csv,sha256=1cg0nJL4pkiPxn3jM1c_31pxKPM47KXGZuVp7v-Qz1M,296
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg,sha256=PP2AXpZy6uoSl2PhIF1XoTdD4CKegdM71ZhDu3rMYIQ,7249
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-near-family.svg,sha256=70W80gymdh8H55dO0Dl52HPDARTqmEoTQYC6Tuuz4CQ,7249
 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.csv,sha256=6H8vsJkv89E5OaepY5bg1DnptEIePK6-C6QjuaBRXv4,337
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg,sha256=48y7s9ChGEfQpBpin9e1UoKbOIWlamGv8PJ5mNPxpp4,13482
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-total.svg,sha256=RsoK1Db2Hju9DpzatwI0OX_yItX0uakwH5LRqK7EsvM,13482
 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.csv,sha256=tzXelx5oSqhgkstNA-6DGK027GYT-M4TXrFGDEWNEcg,405
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg,sha256=rC4mHUcp-ung7_80aETIa_5xFEELEBYkAZSgDECJ2SY,13931
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance-unpaired.svg,sha256=iypP3q37H0cPDGxWerK31TVf9D3ZeYReEL4E_nJEE1U,13931
 test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.csv,sha256=EgjeHR05wFVPUvq8acCzf2LhT4c7niHXpEIoc9XyX9Q,178
-test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg,sha256=_tuaqMdwJCgvK8Hy0Dxl6Q4f_cF8qZkgZFqUCWWQA-8,9771
+test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg,sha256=w13SPcq7qae0Ee8ErOPXlVpA_CcjmVu4KQaawVKvgtk,9771
 test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igh/hmm/boundaries/d_3p_del.csv,sha256=P0iNxvqMk9z8jTIYcGjxfKa-T2JIi3eOSh3eXPEnBvM,318
 test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igh/hmm/boundaries/d_5p_del.csv,sha256=G4CoyPjc1MSkQnVijOv2ysz56zGYG4i-QYelQU-un10,635
 test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igh/hmm/boundaries/dj_insertion.csv,sha256=kLzxSn3wfZysDk4IhTlgvEsvdNbLWYOJgMTz_nqRJHU,233
@@ -1251,7 +1263,7 @@ test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-
 test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igh.yaml,sha256=9Pxnw0p8Ug9ZMVcg7X7RMHURhxpWtpj4h93WuuVS-NY,31446
 test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igk.yaml,sha256=ZPuU2MYn7BLZmOJ6jUiH-oCa3SaZAr0jVMEAePScKxA,14687
 test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igl.yaml,sha256=Ls3u67M8CfP5yaBnfud78p7L9uwH1B0BXGkFwHf48to,6542
-test/paired/new-results/subset-partition-new-simu/merged-partition.log,sha256=ArjchZCcVg5vsBE_w7EIbf1ZEJ3KoPpDlSyvWRs6M08,30272
+test/paired/new-results/subset-partition-new-simu/merged-partition.log,sha256=bvFsdjfBz2UIM4HieUh0LATfADE0z80sXW2s8RvD2CA,30272
 test/paired/new-results/subset-partition-new-simu/partition-igh.yaml,sha256=HgoqpG1_ChEuLNouoAGTWOJTKXDR9TP6y_TFxIMmprI,66188
 test/paired/new-results/subset-partition-new-simu/partition-igk.yaml,sha256=Mwg9UfLe-e0sYsvxNgiepogOj0DxuIUECIktiMu_f-A,46690
 test/paired/new-results/subset-partition-new-simu/partition-igl.yaml,sha256=Wi-WCJfj2dWt0E0eSbKaSnY9zajo9lzpZnIVw7mF9OY,19395
@@ -1275,7 +1287,7 @@ test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml,sha256=ZUaFW7
 test/paired/new-results/subset-partition-new-simu/isub-0/partition-igh.yaml,sha256=AcC85PCqK8Epm4ICu4B8q5eUjtsmlFTQwTkmMhZqQ5I,30562
 test/paired/new-results/subset-partition-new-simu/isub-0/partition-igk.yaml,sha256=TrjOFEnyjqRB1mIbZaG2dDUg0BB7h_YMn7P7NJ4siRA,24486
 test/paired/new-results/subset-partition-new-simu/isub-0/partition-igl.yaml,sha256=fc2SzIWy51agwAZcCTJZAfZW_-ddT-g0celyJsbelgY,7960
-test/paired/new-results/subset-partition-new-simu/isub-0/partition.log,sha256=WRM49yEa8DiOPGEzIWdPSfJpWzG00uEx-VQGZ8gFLAM,24021
+test/paired/new-results/subset-partition-new-simu/isub-0/partition.log,sha256=XCDgGtywIkrpDUOMPEYvfY2VBeJ7r2G5fOq5dj2cDX0,24021
 test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/igh.fa,sha256=vR3IfQGVf6SVv6ls-ebrcQmDTDxNu0nhjizzNbitup4,5852
 test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/igk.fa,sha256=_fxa0GOLuWDb0sfWeO4YbSmIcKwuG4F_4fMxte4dYLE,5107
 test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igh.yaml,sha256=FjL_OaOcNDHHamp3ehFMyAuU4sO4_TMXgEAPlI1kBdw,22125
@@ -1626,7 +1638,7 @@ test/paired/new-results/subset-partition-new-simu/isub-1/meta.yaml,sha256=J_IVfe
 test/paired/new-results/subset-partition-new-simu/isub-1/partition-igh.yaml,sha256=BiuYTVEBQq5uK6kM1ywk5H5q_ebrK7YJ_38iBuRi2eU,45209
 test/paired/new-results/subset-partition-new-simu/isub-1/partition-igk.yaml,sha256=93vPGzB3jaCjPPBEUEvqSqf2axzmd1Ry0P6-YoN7OTg,28793
 test/paired/new-results/subset-partition-new-simu/isub-1/partition-igl.yaml,sha256=rzwVZ9JijOgNZAWVW5MaiYTNW6HtQvsrqKPV_y9NT30,14925
-test/paired/new-results/subset-partition-new-simu/isub-1/partition.log,sha256=A8vZb8SsKlcO8YRva0KUuV5FdQ_CwckAMX00Up3pXIk,23969
+test/paired/new-results/subset-partition-new-simu/isub-1/partition.log,sha256=dKuWoYdH6bXifasH65Kp9JvXE1_eO_D8gfyNeZ4t4BA,23969
 test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/igh.fa,sha256=eLpqTnZF03J8ZANDLzei2lXYLU_qMIPYekhVpRgggfk,8772
 test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/igk.fa,sha256=jWCEqF1B5bXygBLb2BKWKD0rmftFl0c0X5xSEEJOtFA,5868
 test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh.yaml,sha256=7OOGwBLiWX7eI9gab1rd3lhRF12WYe7uyrASBEqL7Eg,27612
@@ -1995,7 +2007,7 @@ test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igk/partiti
 test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igk/partition-igk.yaml,sha256=Ybr2uxzr0wzPyEwrxDWDYif2gFk4UlHNPsXmufeFZhg,50990
 test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igl/partition-igh.yaml,sha256=2ip81MiUa7l716-y86dipwvwM3qg1VWlRQT-__6o4Rw,29796
 test/paired/new-results/subset-partition-new-simu/merged-subsets/igh+igl/partition-igl.yaml,sha256=dIOx35YYPOx2RQ2e2-Qyac5qegCzHf-DyhML42ZXZIA,21443
-test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml,sha256=Db_QZH8sHfUS54VNMKl6te_5myvzVeY7Bd52VCh9EhI,140753
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/sw-cache.yaml,sha256=dJjErIdBvvgFM9wVw6Gn9CraOv6gTnm-unEVLnGXLIY,140753
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/all-mean-mute-freqs.csv,sha256=LPJkL33RJZwT1nbvv80p_1r5J6pSyejnAb1rxjB5eU8,912
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/d_gene-probs.csv,sha256=zeYbss9bxXW-xyVRkX6eBeMhPy-qiino5f0xJ5z86DI,233
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/j_gene-probs.csv,sha256=u4L0N-3x-YChG9C2unXpDbDTVzDZgfw3aChq3fHOuSk,63
@@ -2029,7 +2041,7 @@ test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/hmms/IGHV3-33_star_01.yaml,sha256=FU4oDYBlqRgZwlQrbG23AEZneBh-icKPaswTKnXojUI,103996
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/hmms/IGHV3-7_star_01.yaml,sha256=GLt0fNZJsArlWs95oE7v2E-ZKciqmRa6plG-AWAxaCg,104240
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igh/hmm/hmms/IGHV4-39_star_01.yaml,sha256=GGUYeGeP3CaMWhWo4B32FWDF5ohfVAJf8_QwQ9sSkp0,104436
-test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml,sha256=MJTPUkvAD5zSzp5NVJlndgIuVkQ4fyp5DmIbi_wCWDQ,78754
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/sw-cache.yaml,sha256=D-cXgcX_fzCoEIPVGT12NBy7GZ5YfqAbFAbu9xqmgQg,78754
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/all-mean-mute-freqs.csv,sha256=yR5AuVGrcUAOe72bT-nEJap_zn3AwCpaXSrFGELbDyA,740
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/d_gene-probs.csv,sha256=p07NACPyIrtcnGVLP8tHoSHCBiO_H7OazG_siOykHws,28
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/j_gene-probs.csv,sha256=40-_sM8ZQBd6J9r__bewvD1wb3DELCmaRHpLak-xa0s,75
@@ -2048,7 +2060,7 @@ test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/hmms/IGKV2-30_star_01.yaml,sha256=otPu6N94wuSVkMB8R4ZUYp0k0NLTXBreU1OCCc1VYBk,107159
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/hmms/IGKV3-11_star_01.yaml,sha256=dizIw0o2xB1DiUzb_HneMaz3yIIyxS0d2HiPCdwo2fA,102590
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igk/hmm/hmms/IGKV3-15_star_01.yaml,sha256=1z0A-rW4uPkaZ0u-3Vu9fxdBoNqsf8MXfaT6yjkaKxw,103093
-test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml,sha256=MZhvAmjeoRC_uSdYmn5h0JluXlTyiBxTca6xASMMlfg,44439
+test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/sw-cache.yaml,sha256=fRsPKaf1Jnr98CVlbUGv2OzvfMSB_TSFPbu5EW3DcGI,44439
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/hmm/all-mean-mute-freqs.csv,sha256=mhl_3xQduo9KwGA20exKyZmQOOdXC5k5HnFS05ySwb0,693
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/hmm/d_gene-probs.csv,sha256=fJ9zLdtkRjPmYgE7qmoz00lDMlBYXZIvOc-N_WNztlE,28
 test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters/igl/hmm/j_gene-probs.csv,sha256=ng_-k77f0BCTsX-VM_EGVf0CIxPYj59BGGkibFelC60,39
@@ -8427,8 +8439,8 @@ test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV4-NL1_star_01.csv
 test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV5-10-1_star_01.csv,sha256=S075HCAZnbZpAMsXeLMmMXEGVHFs_Euk1XujtFQ46y4,41974
 test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV5-51_star_01.csv,sha256=QJGyDRqD2JezXsuMbNNXGSCM-kjaN2h4QGpgsaqTqXQ,57817
 test/ref-results-slow/test/parameters/simu/true/mute-freqs/IGHV7-4-1_star_02.csv,sha256=k5KeCR5Qa6iEF0IEHR63DDdJStqAjcZxgZOUbKDFNaY,39977
-partis_bcr-1.0.12.post1.dev3.dist-info/METADATA,sha256=xtJwjJ-RYD8RZonfoC-QHhGkgVXfd4HNUv0qe75k-8Y,5019
-partis_bcr-1.0.12.post1.dev3.dist-info/WHEEL,sha256=9ctVpAaKKuiwgjVc8F9LY-Q62ellXuEWF53eQGj3hKI,109
-partis_bcr-1.0.12.post1.dev3.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
-partis_bcr-1.0.12.post1.dev3.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
-partis_bcr-1.0.12.post1.dev3.dist-info/RECORD,,
+partis_bcr-1.0.12.post1.dev4.dist-info/METADATA,sha256=rU54FIDPeQFteTuGG_VMQTHOIpNpUrCPWQcu2kbPAXY,5019
+partis_bcr-1.0.12.post1.dev4.dist-info/WHEEL,sha256=9ctVpAaKKuiwgjVc8F9LY-Q62ellXuEWF53eQGj3hKI,109
+partis_bcr-1.0.12.post1.dev4.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
+partis_bcr-1.0.12.post1.dev4.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
+partis_bcr-1.0.12.post1.dev4.dist-info/RECORD,,

test/new-results/partition-new-simu/fasttree/iclust-0/log

@@ -18,6 +18,6 @@ CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
 ML-NNI round 2: LogLk = -655.501 NNIs 1 max delta 0.00 Time 0.03
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -655.501 NNIs 1 max delta 0.00 Time 0.04 (final)
+ML-NNI round 3: LogLk = -655.501 NNIs 1 max delta 0.00 Time 0.03 (final)
 Optimize all lengths: LogLk = -655.501 Time 0.04
-Total time: 0.05 seconds Unique: 8/12 Bad splits: 0/5
+Total time: 0.04 seconds Unique: 8/12 Bad splits: 0/5

test/new-results/run-times.csv

@@ -1,10 +1,10 @@
 name,seconds
-cache-parameters-simu,5.2
+cache-parameters-simu,5.1
 annotate-new-simu,2.0
-multi-annotate-new-simu,1.9
+multi-annotate-new-simu,1.8
 partition-new-simu,3.1
-seed-partition-new-simu,1.7
+seed-partition-new-simu,1.6
 vsearch-partition-new-simu,1.9
-get-selection-metrics-new-simu,1.5
-cache-parameters-data,6.2
-simulate,7.3
+get-selection-metrics-new-simu,1.4
+cache-parameters-data,6.1
+simulate,7.0

test/new-results/test.log

@@ -28,10 +28,10 @@ hmm
     writing parameters to test/new-results/test/parameters/simu/hmm (0.6 sec)
     writing parameters to test/new-results/test/parameters/simu/true (0.6 sec)
          infra time: 1.3
-      hmm step time: 1.9
+      hmm step time: 1.8
   writing hmms     removed 0  genes from glfo (leaving v 7  d 5  j 3)
 (0.5 sec)
-      total time: 3.9
+      total time: 3.8
 annotate-new-simu                partis annotate --dont-write-git-info --infname test/ref-results/test/simu.yaml --parameter-dir test/new-results/test/parameters/simu --sw-cachefname test/new-results/test/parameters/simu/sw-cache.yaml --plot-annotation-performance --is-simu --plotdir test/new-results/annotate-new-simu-annotation-performance --only-csv-plots --random-seed 1 --n-procs 10 --outfname test/new-results/annotate-new-simu.yaml
 annotating    (with test/new-results/test/parameters/simu/hmm)
 smith-waterman
@@ -201,7 +201,7 @@ smith-waterman  (writing parameters)
       kept 16 (0.320) unproductive
         writing sw results to test/new-results/test/parameters/data/sw-cache.yaml
     writing parameters to test/new-results/test/parameters/data/sw (0.8 sec)
-    water time: 1.0  (ig-sw 0.9  processing 0.0)
+    water time: 0.9  (ig-sw 0.9  processing 0.0)
   writing hmms     removed 15 genes from glfo (leaving v 18  d 22  j 7)
 (0.8 sec)
 hmm
@@ -212,31 +212,31 @@ hmm
       hmm step time: 2.2
   writing hmms     removed 6  genes from glfo (leaving v 15  d 19  j 7)
 (0.7 sec)
-      total time: 4.9
+      total time: 4.8
 simulate                         partis simulate --dont-write-git-info --parameter-dir test/new-results/test/parameters/data --n-sim-events 10 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 1 --n-procs 10 --outfname test/new-results/test/simu.yaml --indel-frequency 0.2
 simulating
       --> proc 0
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 6 seqs in 0.1s (0.0s of which was running bppseqgen)
-      total time: 0.2
+      total time: 0.3
 
       --> proc 1
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 5 seqs in 0.1s (0.1s of which was running bppseqgen)
+    made 1 event with 5 seqs in 0.2s (0.1s of which was running bppseqgen)
       total time: 0.3
 
       --> proc 2
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 2 seqs in 0.1s (0.1s of which was running bppseqgen)
+    made 1 event with 2 seqs in 0.2s (0.1s of which was running bppseqgen)
       total time: 0.3
 
       --> proc 3
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 11 seqs in 0.3s (0.1s of which was running bppseqgen)
+    made 1 event with 11 seqs in 0.2s (0.1s of which was running bppseqgen)
       total time: 0.4
 
       --> proc 4
@@ -249,7 +249,7 @@ simulating
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 22 seqs in 0.3s (0.2s of which was running bppseqgen)
-      total time: 0.4
+      total time: 0.5
 
       --> proc 6
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
@@ -260,14 +260,14 @@ simulating
       --> proc 7
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 3 seqs in 0.1s (0.0s of which was running bppseqgen)
+    made 1 event with 3 seqs in 0.1s (0.1s of which was running bppseqgen)
       total time: 0.2
 
       --> proc 8
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
     made 1 event with 5 seqs in 0.2s (0.0s of which was running bppseqgen)
-      total time: 0.3
+      total time: 0.2
 
       --> proc 9
     reco params: test/new-results/test/parameters/data/hmm     shm params: test/new-results/test/parameters/data/hmm
@@ -276,4 +276,4 @@ simulating
       total time: 0.3
 
    read 10 events with 74 seqs from 10 .yaml files
-      total time: 6.0
+      total time: 5.8

test/paired/new-results/partition-new-simu/fasttree/iclust-0/log

@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.666 so that average rate = 1.0
 CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
-ML-NNI round 2: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.07
+ML-NNI round 2: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.06
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.08 (final)
-Optimize all lengths: LogLk = -1661.140 Time 0.09
-Total time: 0.10 seconds Unique: 8/8 Bad splits: 0/5
+ML-NNI round 3: LogLk = -1661.140 NNIs 0 max delta 0.00 Time 0.07 (final)
+Optimize all lengths: LogLk = -1661.140 Time 0.07
+Total time: 0.08 seconds Unique: 8/8 Bad splits: 0/5

test/paired/new-results/partition-new-simu/fasttree/iclust-2/log

@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.641 so that average rate = 1.0
 CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
-ML-NNI round 2: LogLk = -1274.921 NNIs 0 max delta 0.00 Time 0.04
+ML-NNI round 2: LogLk = -1274.921 NNIs 0 max delta 0.00 Time 0.05
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -1274.921 NNIs 0 max delta 0.00 Time 0.04 (final)
-Optimize all lengths: LogLk = -1274.921 Time 0.05
-Total time: 0.05 seconds Unique: 6/6 Bad splits: 0/3
+ML-NNI round 3: LogLk = -1274.921 NNIs 0 max delta 0.00 Time 0.06 (final)
+Optimize all lengths: LogLk = -1274.921 Time 0.06
+Total time: 0.07 seconds Unique: 6/6 Bad splits: 0/3

test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log

@@ -16,8 +16,8 @@ Switched to using 20 rate categories (CAT approximation)
 Rate categories were divided by 0.658 so that average rate = 1.0
 CAT-based log-likelihoods may not be comparable across runs
 Use -gamma for approximate but comparable Gamma(20) log-likelihoods
-ML-NNI round 2: LogLk = -794.522 NNIs 0 max delta 0.00 Time 0.03
+ML-NNI round 2: LogLk = -794.522 NNIs 0 max delta 0.00 Time 0.02
 Turning off heuristics for final round of ML NNIs (converged)
-ML-NNI round 3: LogLk = -794.513 NNIs 0 max delta 0.00 Time 0.04 (final)
-Optimize all lengths: LogLk = -794.513 Time 0.04
-Total time: 0.05 seconds Unique: 7/7 Bad splits: 0/4
+ML-NNI round 3: LogLk = -794.513 NNIs 0 max delta 0.00 Time 0.03 (final)
+Optimize all lengths: LogLk = -794.513 Time 0.03
+Total time: 0.04 seconds Unique: 7/7 Bad splits: 0/4