partis-bcr 1.0.11.post1.dev3__cp312-cp312-manylinux1_x86_64.whl → 1.0.12__cp312-cp312-manylinux1_x86_64.whl

bin/partis-test.py

@@ -299,8 +299,8 @@ class Tester(object):
 
         if ptest == 'simulate':
             argfo['parameter-dir'] = self.paramdir(input_stype, 'data')
-            # if args.no_tree_gen:
-            #     argfo['extras'] += ['--input-simulation-treefname', '%s/test/trees.nwk'%utils.get_partis_dir()]
+            if args.no_tree_gen:
+                argfo['extras'] += ['--input-simulation-treefname', '%s/test/trees.nwk'%utils.get_partis_dir()]
             if args.no_per_base_mutation:
                 argfo['extras'] += ['--no-per-base-mutation']
         else:
@@ -936,7 +936,7 @@ parser.add_argument('--only-bust-current', action='store_true', help='only bust
 parser.add_argument('--paired', action='store_true', help='run paired tests, i.e. with --paired-loci. Note that this doesn\'t test all the things (e.g. seed partitioning) that non-paired does.')
 parser.add_argument('--run-all', action='store_true', help='run all four combinations of tests: paired/non-paired and slow/non-slow (by default only runs one). *Not* for use with --bust-cache, which runs all of them by default.')
 parser.add_argument('--no-simu', action='store_true', help='don\'t run simulation, e.g. if using a minimal install')
-# parser.add_argument('--no-tree-gen', action='store_true', help='if set, use the pre-generated newick file instead of generating trees with R/TreeSim (to avoid R installation)')
+parser.add_argument('--no-tree-gen', action='store_true', help='if set, use the pre-generated newick file instead of generating trees with R/TreeSim (to avoid R installation)')
 parser.add_argument('--no-per-base-mutation', action='store_true', help='use simpler, non-per-base mutation model (to avoid bpp-newlik compilation)')
 parser.add_argument('--ig-or-tr', default='ig')
 parser.add_argument('--print-width', type=int, default=300, help='set to 0 for infinite')

{partis_bcr-1.0.11.post1.dev3.data → partis_bcr-1.0.12.data}/scripts/partis-test.py

@@ -299,8 +299,8 @@ class Tester(object):
 
         if ptest == 'simulate':
             argfo['parameter-dir'] = self.paramdir(input_stype, 'data')
-            # if args.no_tree_gen:
-            #     argfo['extras'] += ['--input-simulation-treefname', '%s/test/trees.nwk'%utils.get_partis_dir()]
+            if args.no_tree_gen:
+                argfo['extras'] += ['--input-simulation-treefname', '%s/test/trees.nwk'%utils.get_partis_dir()]
             if args.no_per_base_mutation:
                 argfo['extras'] += ['--no-per-base-mutation']
         else:
@@ -936,7 +936,7 @@ parser.add_argument('--only-bust-current', action='store_true', help='only bust
 parser.add_argument('--paired', action='store_true', help='run paired tests, i.e. with --paired-loci. Note that this doesn\'t test all the things (e.g. seed partitioning) that non-paired does.')
 parser.add_argument('--run-all', action='store_true', help='run all four combinations of tests: paired/non-paired and slow/non-slow (by default only runs one). *Not* for use with --bust-cache, which runs all of them by default.')
 parser.add_argument('--no-simu', action='store_true', help='don\'t run simulation, e.g. if using a minimal install')
-# parser.add_argument('--no-tree-gen', action='store_true', help='if set, use the pre-generated newick file instead of generating trees with R/TreeSim (to avoid R installation)')
+parser.add_argument('--no-tree-gen', action='store_true', help='if set, use the pre-generated newick file instead of generating trees with R/TreeSim (to avoid R installation)')
 parser.add_argument('--no-per-base-mutation', action='store_true', help='use simpler, non-per-base mutation model (to avoid bpp-newlik compilation)')
 parser.add_argument('--ig-or-tr', default='ig')
 parser.add_argument('--print-width', type=int, default=300, help='set to 0 for infinite')

{partis_bcr-1.0.11.post1.dev3.dist-info → partis_bcr-1.0.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: partis-bcr
-Version: 1.0.11.post1.dev3
+Version: 1.0.12
 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-1.0.11.post1.dev3.dist-info → partis_bcr-1.0.12.dist-info}/RECORD

@@ -26,7 +26,7 @@ bin/makeHtml,sha256=SMMulEmYoU4ve4jlCRNaDuw9f4FS4t8g_FGE7z5Ndb4,1190
 bin/mds-run.py,sha256=rShy5b3oqvFZqhNdVxrtyZ4nw7whK-SKPAYl2thXooU,2003
 bin/parse-output.py,sha256=MzCN5H9yisRjiLcUyfcg78Xvt3Q29qTAU1LpZ6OLMMg,19579
 bin/partis,sha256=QbCbvB8H9Ntm9WR598G_ytP6IvC9dQNo9E2N6anEt7A,225210
-bin/partis-test.py,sha256=GpvCssyBbpzTOWQM_mZMr5GzAQrI7XjAMzmIkkZRBno,64331
+bin/partis-test.py,sha256=xscUK2fRnHwZ0xxzreffdzOmLO7XWEfUi737SA0OnXE,64325
 bin/partis.py,sha256=QbCbvB8H9Ntm9WR598G_ytP6IvC9dQNo9E2N6anEt7A,225210
 bin/plot-gl-set-trees.py,sha256=bgWPBmzzlD_YgWl9nQetGdzmgosXDKyVyfvaHs0VvVc,25695
 bin/plot-hmms.py,sha256=rKhPyWxexMKBt8kmwuM5ebFfFONtREoDlRqs4J52rT8,6560
@@ -303,16 +303,16 @@ data/substitution-profiles/GSSPs_for_VL_genes_with_at_least_300_lineages.txt,sha
 data/substitution-profiles/notes.txt,sha256=-DK9E31YovqOWaXR1Q-LL5KFhjVJcSLwXbriajUq1TA,389
 packages/ham/bcrham,sha256=1g26DafyE_6wglae2TUXc6xkpd2AUp0LDV6Kl_2S7jY,852320
 packages/ig-sw/src/ig_align/ig-sw,sha256=lYbqn7wujB6j1T7BGeeCqw5kwbPFn0213lDfUBmJb98,282048
-partis_bcr-1.0.11.post1.dev3.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
-partis_bcr-1.0.11.post1.dev3.data/scripts/cf-germlines.py,sha256=8_bq0ue3ALFQ-a7-ntnhkbCaBdQ5mlWtQgNeQP_TvcQ,3135
-partis_bcr-1.0.11.post1.dev3.data/scripts/compare-plotdirs.py,sha256=AABVGUOwlLCijjo-wwDLfLHiq80TrFVm8mE-4Zqn5Sg,16370
-partis_bcr-1.0.11.post1.dev3.data/scripts/extract-pairing-info.py,sha256=IGPd4jYpsW3IPgsrxTJrk9jAwUKlb45eX3lOpb8Maos,2941
-partis_bcr-1.0.11.post1.dev3.data/scripts/gctree-run.py,sha256=BfSZCFgqdhUEqVsv2h20o6OkS6KbQgx5tfvBhySRx2U,13950
-partis_bcr-1.0.11.post1.dev3.data/scripts/get-naive-probabilities.py,sha256=WfuglaedP3PF0wpksGiUSvfAg4wJoNlucTPa1Wl9MDo,6916
-partis_bcr-1.0.11.post1.dev3.data/scripts/parse-output.py,sha256=2ArlyFI5zApS33gnApFqvbPvFHqmUmYsh71Amy6lkUE,19565
-partis_bcr-1.0.11.post1.dev3.data/scripts/partis-test.py,sha256=hOqVneQhovWYX0aTIsbvFqSqyJJTDowyMmYRDWEceYg,64317
-partis_bcr-1.0.11.post1.dev3.data/scripts/split-loci.py,sha256=K0WXQYtloL5rs46mwvEXUecqT3iG8bbqwNOTNwfpvzY,20704
-partis_bcr-1.0.11.post1.dev3.dist-info/licenses/COPYING,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+partis_bcr-1.0.12.data/scripts/cf-alleles.py,sha256=AgFLoRfcwuX1InVpE3zG6-unqoCBGOeCTpEl_RZftvU,4723
+partis_bcr-1.0.12.data/scripts/cf-germlines.py,sha256=8_bq0ue3ALFQ-a7-ntnhkbCaBdQ5mlWtQgNeQP_TvcQ,3135
+partis_bcr-1.0.12.data/scripts/compare-plotdirs.py,sha256=AABVGUOwlLCijjo-wwDLfLHiq80TrFVm8mE-4Zqn5Sg,16370
+partis_bcr-1.0.12.data/scripts/extract-pairing-info.py,sha256=IGPd4jYpsW3IPgsrxTJrk9jAwUKlb45eX3lOpb8Maos,2941
+partis_bcr-1.0.12.data/scripts/gctree-run.py,sha256=BfSZCFgqdhUEqVsv2h20o6OkS6KbQgx5tfvBhySRx2U,13950
+partis_bcr-1.0.12.data/scripts/get-naive-probabilities.py,sha256=WfuglaedP3PF0wpksGiUSvfAg4wJoNlucTPa1Wl9MDo,6916
+partis_bcr-1.0.12.data/scripts/parse-output.py,sha256=2ArlyFI5zApS33gnApFqvbPvFHqmUmYsh71Amy6lkUE,19565
+partis_bcr-1.0.12.data/scripts/partis-test.py,sha256=ORpG0LjV1PzejY36rO8-Oi3katwOzygDFtcXSst9S_0,64311
+partis_bcr-1.0.12.data/scripts/split-loci.py,sha256=K0WXQYtloL5rs46mwvEXUecqT3iG8bbqwNOTNwfpvzY,20704
+partis_bcr-1.0.12.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
@@ -371,15 +371,16 @@ test/mobille-igblast-run.py,sha256=YkKISY_lQ8BbV-6lu8uoLXAtyjNayxU1x7RQ6O77phI,1
 test/phylo-naive-run.py,sha256=CVOuyOTbCiFINZHrTcLNvk9j-dqnXu9n9LOWvAAVA44,5303
 test/run-gl-inference.sh,sha256=XK3cs5xQad5LAoVaVp2-3IMJssml8ZBNYPwLRrlW2vg,1408
 test/scoper-run.py,sha256=GzLeaGrh3IPzD9B4KC6GiS0wak8ctL7td2WJmsbb7K8,8672
-test/test.py,sha256=GpvCssyBbpzTOWQM_mZMr5GzAQrI7XjAMzmIkkZRBno,64331
+test/test.py,sha256=xscUK2fRnHwZ0xxzreffdzOmLO7XWEfUi737SA0OnXE,64325
+test/trees.nwk,sha256=aRmh5F2fnICw8De1Pzth5qBEp9GkoYBrzb_WoQVHWzE,20301
 test/new-results/annotate-new-simu.yaml,sha256=vaxN1is6V9RKzjPJI0fhSiutubXJvGXDGqPPvQjXvFw,65701
 test/new-results/cache-new-partition.csv,sha256=jHVEFlsBiSpjesVSFycef8WPFOc47b2BVXeX6XwKFHs,20628
 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=HwmoFvJLgq820-BMwBjCn2iN_tWoCxEVZrm5ahehh_Y,256
+test/new-results/run-times.csv,sha256=2jYjH_jTjEyF8jVWnmkt9qZ0Zs_JOousuPx8BF4G9mQ,255
 test/new-results/seed-partition-new-simu.yaml,sha256=_OKhRdWnk6Ez1ntXXj3PFnbXZcepKYvtsi5nURN84v0,10671
-test/new-results/test.log,sha256=3xTJzk_k4PzpSsuCrRrGskNbsQZBH2BmfoM8tyY38Jk,20372
+test/new-results/test.log,sha256=T-a_BqCXrGJtdHrVh8b1Vrm92w-iTbwX7v5Mh0PGomk,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
@@ -567,7 +568,7 @@ test/new-results/partition-new-simu-annotation-performance/sw/mutation/mute_freq
 test/new-results/partition-new-simu-annotation-performance/sw/mutation/muted_bases.csv,sha256=PHIIaj2iqO9j_2G9QQFo7DKsra61A4_2skRWCeeonxY,152
 test/new-results/partition-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv,sha256=mm4bOAHI1yTIte2PooOSreMdTOTommH4cwHIJc1B4_8,97
 test/new-results/partition-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv,sha256=mm4bOAHI1yTIte2PooOSreMdTOTommH4cwHIJc1B4_8,97
-test/new-results/test/simu.yaml,sha256=KF6xrhqWkUjzExqtYeXvFxGJBCXWr-2PpcNE8Xeu3wo,39704
+test/new-results/test/simu.yaml,sha256=65v1POoth7G0aUMs_KWPE9bk3sR7uj6RTmIwQjRD_74,68547
 test/new-results/test/parameters/data/sw-cache.yaml,sha256=FQKFUD7eS2pIz8FXry2DKj1XyXMfj57I_KX7iQbdhZ4,102890
 test/new-results/test/parameters/data/hmm/all-mean-mute-freqs.csv,sha256=zoYBWsn4UHXmOcodBTsyMlLD9ueg5zLM2DVZVG1z4R0,1280
 test/new-results/test/parameters/data/hmm/all-mean-n-muted.csv,sha256=9iQWbgFIVuk3pqNZsBN5wqYspDencYClYX9MiK0gJRQ,2523
@@ -973,8 +974,8 @@ 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=He9aZWw2BudfEJG-YYRvpA6ccqki6uZBNla84f2OxKQ,208
-test/paired/new-results/test.log,sha256=7QbWzBA7yDYtMZOWbUOi70EgH_TQcK3DB7HmQAgpfjA,85873
+test/paired/new-results/run-times.csv,sha256=Ds2dptDMCUjF1eKxvhNBuMdfaCBzsWl4aVwT3V2yTgo,208
+test/paired/new-results/test.log,sha256=JziY1qJ9xPeir9iNr8E1FuQR50JGYF3PyVhkBS-mxNY,84815
 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
@@ -995,7 +996,7 @@ test/paired/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa,sha25
 test/paired/new-results/partition-new-simu/fasttree/iclust-1/log,sha256=ou_xxqXaZukRTI1w7eqlqmq0-kTNCasOjtqgC2mJ85A,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=0B3jw_M5grPDVLkbVo0jzDZr40PZciuapueNAhQD9DU,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
@@ -1005,7 +1006,7 @@ 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=h81UNPsuHrMD0xu7yvQLELsttjwQCnlV8MB3joqjNVk,1692
+test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-1/log,sha256=p-Hb-ZI91nNZFRBKRQpOh1g0Nv_LdPzzAf7qRB-75j4,1692
 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
@@ -1029,34 +1030,34 @@ 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=7qf___hYL13BCPHfGKBKWs5x4SiWOh7YTL6ekqHIlHw,29145
-test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg,sha256=e9OiW39kl1o2YokR0aGsAoJIAtZrPHlIGXFrp6GXRdY,22992
-test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg,sha256=W3kaHW87MhP57nsrah62rCcYA5FbriUq5NjEaiUzfeY,19194
+test/paired/new-results/partition-new-simu-annotation-performance/plots/flcount-matrix.svg,sha256=Xy0lZ4BMGjEf43Qp0Ub3mXO7n3sIQ8lCx5mhMpwT7kw,29145
+test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop-log.svg,sha256=mIuTvywR1ECaAZ_QLERZBnDCWVpc__ODlEDp02QsgE8,22992
+test/paired/new-results/partition-new-simu-annotation-performance/plots/func-non-func-per-drop.svg,sha256=NoTxesqnT3Q-2v8RLwh3gF5YNuWfqwh_yp-EEQevxL0,19194
 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
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 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
@@ -1249,7 +1250,7 @@ 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
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 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
@@ -1273,7 +1274,7 @@ 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=6ZAuNzq2itZ62ykhF5qEEXd8-BnRniTZapLYXeAZWOA,24021
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 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
@@ -1624,7 +1625,7 @@ 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
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 test/paired/new-results/subset-partition-new-simu/isub-1/igh+igk/partition-igh.yaml,sha256=7OOGwBLiWX7eI9gab1rd3lhRF12WYe7uyrASBEqL7Eg,27612
@@ -1993,7 +1994,7 @@ 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
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@@ -2027,7 +2028,7 @@ 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
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 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
@@ -2046,7 +2047,7 @@ 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
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 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
@@ -3058,15 +3059,15 @@ test/paired/new-results/test/parameters/simu/igl/true/mute-freqs/IGLJ3_star_02.c
 test/paired/new-results/test/parameters/simu/igl/true/mute-freqs/IGLV1-40_star_01.csv,sha256=p3PWsVLEeD2PICWmIxgpUGuT3JOxQTslQzU6_LrBvBI,41802
 test/paired/new-results/test/parameters/simu/igl/true/mute-freqs/IGLV2-14_star_04.csv,sha256=AZk7s8pua4urPiGRa88MRVK3xZI4q-lWgBiAuy8S6Ko,39100
 test/paired/new-results/test/parameters/simu/igl/true/mute-freqs/IGLV2-23_star_02.csv,sha256=NNCfbwB78nBRyZxpP6CerXnVqbmxjZYupYkdYMYsvL4,38044
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 test/paired/ref-results/get-selection-metrics-new-simu-chosen-abs.csv,sha256=pPLqsoWr7MChKJCeXfFDEo6JS4IG21TgmLzoMi5-vdQ,12593
 test/paired/ref-results/run-times.csv,sha256=hFA6Pz-Qw3UzqYiKjObhgKAYIK9g0PnNqjGy2RCjOQQ,238
 test/paired/ref-results/test.log,sha256=Ju_Oo1TSl2_R9KQvtFuHdYxJGjL9WbBtFy2SpqT9Tlg,85256
@@ -8425,8 +8426,8 @@ 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-1.0.11.post1.dev3.dist-info/METADATA,sha256=hVIsGVEKaXzw2a3-qkeSsEhwaKo3LZeuXAntvK14MrE,5019
-partis_bcr-1.0.11.post1.dev3.dist-info/WHEEL,sha256=9ctVpAaKKuiwgjVc8F9LY-Q62ellXuEWF53eQGj3hKI,109
-partis_bcr-1.0.11.post1.dev3.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
-partis_bcr-1.0.11.post1.dev3.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
-partis_bcr-1.0.11.post1.dev3.dist-info/RECORD,,
+partis_bcr-1.0.12.dist-info/METADATA,sha256=3SDt4TXOVYyoZ-i6O20NxsmLxdWVxzbmc4wfcXSfU0M,5008
+partis_bcr-1.0.12.dist-info/WHEEL,sha256=9ctVpAaKKuiwgjVc8F9LY-Q62ellXuEWF53eQGj3hKI,109
+partis_bcr-1.0.12.dist-info/entry_points.txt,sha256=Q-AkAQ91YwiKNHruS32ACdY4_IQdpZhpij2EuVDmdnM,44
+partis_bcr-1.0.12.dist-info/top_level.txt,sha256=J-z0poNcsv31IHB413--iOY8LoHBKiTHeybHX3abokI,7
+partis_bcr-1.0.12.dist-info/RECORD,,

test/new-results/run-times.csv

@@ -1,10 +1,10 @@
 name,seconds
 cache-parameters-simu,5.2
 annotate-new-simu,2.0
-multi-annotate-new-simu,1.8
-partition-new-simu,3.0
-seed-partition-new-simu,1.6
+multi-annotate-new-simu,1.9
+partition-new-simu,3.1
+seed-partition-new-simu,1.7
 vsearch-partition-new-simu,1.9
 get-selection-metrics-new-simu,1.4
-cache-parameters-data,6.2
-simulate,12.7
+cache-parameters-data,6.1
+simulate,7.2