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

test/paired/new-results/test.log

@@ -23,17 +23,17 @@ smith-waterman  (writing parameters)
     writing parameters to test/paired/new-results/test/parameters/simu/igh/sw (0.6 sec)
     water time: 0.7  (ig-sw 0.7  processing 0.0)
   writing hmms     removed 16 genes from glfo (leaving v 6  d 18  j 4)
-(0.5 sec)
+(0.6 sec)
 hmm
     reading output
         read 56 hmm output lines with 56 sequences in 56 events  (0 failures)
     writing parameters to test/paired/new-results/test/parameters/simu/igh/hmm (0.5 sec)
-    writing parameters to test/paired/new-results/test/parameters/simu/igh/true (0.5 sec)
+    writing parameters to test/paired/new-results/test/parameters/simu/igh/true (0.4 sec)
          infra time: 1.1
-      hmm step time: 2.1
+      hmm step time: 2.2
   writing hmms     removed 3  genes from glfo (leaving v 6  d 15  j 4)
-(0.3 sec)
-      total time: 3.9
+(0.4 sec)
+      total time: 4.1
 cache-parameters igk:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 run partis cache-parameters --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --is-simu --random-seed 1 --n-procs 10 --infname test/paired/ref-results/test/simu/igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -91,7 +91,7 @@ smith-waterman  (writing parameters)
       kept 14 (0.667) unproductive
         writing sw results to test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml
     writing parameters to test/paired/new-results/test/parameters/simu/igl/sw (0.3 sec)
-    water time: 0.4  (ig-sw 0.4  processing 0.0)
+    water time: 0.4  (ig-sw 0.3  processing 0.0)
   writing hmms     removed 7  genes from glfo (leaving v 3  d 1  j 2)
 (0.1 sec)
 hmm
@@ -103,8 +103,8 @@ hmm
       hmm step time: 0.9
   writing hmms     removed 0  genes from glfo (leaving v 3  d 1  j 2)
 (0.1 sec)
-      total time: 1.7
-      total time: 12.3
+      total time: 1.6
+      total time: 12.6
 partition-new-simu               partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --parameter-dir test/paired/new-results/test/parameters/simu --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --plotdir test/paired/new-results/partition-new-simu-annotation-performance --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/partition-new-simu
   warning ignoring --plot-annotation-performance for paired clustering since it's going to be a bit fiddly to implement
 partition igh:
@@ -122,23 +122,23 @@ smith-waterman
 (0.0 sec)
         water time: 0.1
 hmm
-  caching all 56 naive sequences (1.0s)
+  caching all 56 naive sequences (1.1s)
     collapsed 56 queries into 50 clusters with identical naive seqs (0.0 sec)
-  50 clusters with 10 procs (0.5s)
+  50 clusters with 10 procs (0.6s)
    44 clusters with 7 procs (0.5s)
-   36 clusters with 5 procs (0.4s)
+   36 clusters with 5 procs (0.5s)
    31 clusters with 3 procs (0.3s)
    29 clusters with 2 procs (0.5s)
    23 clusters with 1 proc (0.6s)
    note not merging entire cpath history
-      partition loop time: 2.8
+      partition loop time: 2.9
 getting annotations for final partition
   subcluster annotating 20 clusters with steps:  (0.7s) (0.2s)   plotting performance 
     warning skipped annotation performance evaluation on 1 queries with different true and inferred net shm indel lengths: db63559ea9-igh
 (0.0 sec)
 
     subcluster annotation time 0.9
-      total time: 4.9
+      total time: 5.0
 partition igk:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 run partis partition --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --plot-annotation-performance --max-ccf-fail-frac 0.10 --is-simu --plotdir test/paired/new-results/partition-new-simu-annotation-performance/single-chain/plots/igk --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/ref-results/test/simu/igk.yaml --outfname test/paired/new-results/partition-new-simu/single-chain/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -228,6 +228,7 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
        joint   0.963  0.594
   merge time 0.0
   need to get annotations for 7/15 joint igh clusters
+     tag: v1.0.12
 annotate igh+igk: igh
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 run partis annotate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igh --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igk/input-seqs-igh.fa --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igk/meta-igh.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igk/partition-igh-only-partition.yaml
@@ -245,6 +246,7 @@ hmm
     subcluster annotation time 0.6
       total time: 0.6
   need to get annotations for 13/15 joint igk clusters
+     tag: v1.0.12
 annotate igh+igk: igk
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 run partis annotate --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igk --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igk.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igk/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igk/meta-igk.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igk/partition-igk-only-partition.yaml
@@ -286,6 +288,7 @@ hmm
        joint   1.000  0.611
   merge time 0.0
   need to get annotations for 5/8 joint igh clusters
+     tag: v1.0.12
 annotate igh+igl: igh
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 run partis annotate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igh --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igl/input-seqs-igh.fa --outfname test/paired/new-results/partition-new-simu/igh+igl/partition-igh.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igh/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igl/meta-igh.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igl/partition-igh-only-partition.yaml
@@ -303,6 +306,7 @@ hmm
     subcluster annotation time 0.4
       total time: 0.5
   need to get annotations for 8/8 joint igl clusters
+     tag: v1.0.12
 annotate igh+igl: igl
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 run partis annotate --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --max-ccf-fail-frac 0.10 --only-csv-plots --no-partition-plots --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/partition-new-simu/igh+igl/input-seqs-igl.fa --outfname test/paired/new-results/partition-new-simu/igh+igl/partition-igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/new-results/partition-new-simu/igh+igl/meta-igl.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/partition-new-simu/igh+igl/partition-igl-only-partition.yaml
@@ -331,7 +335,7 @@ hmm
         h   20 --> 23   +3
         k    6 --> 15   +9
         l    3 --> 8    +5
-      total time: 19.9
+      total time: 20.5
 subset-partition-new-simu        partis subset-partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --max-ccf-fail-frac 0.15 --is-simu --n-subsets 2 --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/subset-partition-new-simu
   note: --input-metafnames not specified, so setting to default location test/paired/ref-results/test/simu/meta.yaml
   --input-metafnames: added meta info for 113 sequences from test/paired/ref-results/test/simu/meta.yaml: loci paired-uids
@@ -360,9 +364,12 @@ hmm
    writing merged outputs from 2 subsets to test/paired/new-results/subset-partition-new-simu/merged-subsets
     writing combined h/l info to fasta and meta files in test/paired/new-results/subset-partition-new-simu/merged-subsets
     merging parameters from 2 subdirs (e.g. test/paired/new-results/subset-partition-new-simu/isub-0) to test/paired/new-results/subset-partition-new-simu/merged-subsets
+     tag: v1.0.12
+     tag: v1.0.12
+     tag: v1.0.12
 run partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --max-ccf-fail-frac 0.15 --is-simu --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/subset-partition-new-simu --input-metafnames test/paired/new-results/subset-partition-new-simu/merged-subsets/meta.yaml --input-partition-fname test/paired/new-results/subset-partition-new-simu/merged-subsets --continue-from-input-partition --parameter-dir test/paired/new-results/subset-partition-new-simu/merged-subsets/parameters --ignore-sw-pair-info --refuse-to-cache-parameters --ignore-default-input-metafile
         log: test/paired/new-results/subset-partition-new-simu/merged-partition.log
-      total time: 68.6
+      total time: 69.6
 seed-partition-new-simu          partis partition --dont-write-git-info --paired-loci --paired-indir test/paired/ref-results/test/simu --parameter-dir test/paired/new-results/test/parameters/simu --max-ccf-fail-frac 0.10 --is-simu --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk --seed-loci igh:igk --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/seed-partition-new-simu
    removing seqs very different from seed seq
                            wrong/no     removed      singly         kept   missing
@@ -423,7 +430,7 @@ hmm
 getting annotations for final partition
   subcluster annotating 2 clusters with steps:  (0.1s) (0.1s) (0.1s) 
     subcluster annotation time 0.2
-      total time: 0.6
+      total time: 0.7
 partition igl:
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
 run partis partition --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/simu/igl --max-ccf-fail-frac 0.10 --random-seed 1 --n-procs 10 --refuse-to-cache-parameters --infname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/input-seqs-igl.fa --outfname test/paired/new-results/seed-partition-new-simu/seeds/3542bd38d8-igh+3542bd38d8-igk/single-chain/partition-igl.yaml --sw-cachefname test/paired/new-results/test/parameters/simu/igl/sw-cache.yaml --input-metafnames test/paired/ref-results/test/simu/meta.yaml
@@ -485,6 +492,7 @@ WARNING using errors instead of sumw2 with weight != 1.0 in Hist::fill_ibin()
   merge time 0.0
      removed 7 unseeded clusters (of 8 total, leaving 1) from igh joint partition
   seed cluster size in best joint partition: 1, excluding seed seq: 0
+     tag: v1.0.12
 annotate igh+igk: igh
     removed 2 arg strs that were specific to action 'partition': --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -506,6 +514,7 @@ hmm
      removed 7 unseeded clusters (of 8 total, leaving 1) from igk joint partition
   need to get annotations for 1/1 joint igk clusters
   seed cluster size in best joint partition: 1, excluding seed seq: 0
+     tag: v1.0.12
 annotate igh+igk: igk
     removed 2 arg strs that were specific to action 'partition': --seed-unique-id 3542bd38d8-igh:3542bd38d8-igk
   note: adding input metafname from default location (test/paired/ref-results/test/simu/meta.yaml)
@@ -552,7 +561,7 @@ hmm
    N clusters with all seqs:
         h   12 --> 1    -11
         k    2 --> 1    -1
-      total time: 9.3
+      total time: 9.4
 get-selection-metrics-new-simu   partis get-selection-metrics --dont-write-git-info --paired-loci --existing-output-run-cfg paired --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/partition-new-simu --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
 get-selection-metrics igh+igk: igh
 run partis get-selection-metrics --locus igh --dont-write-git-info --min-selection-metric-cluster-size 3 --min-paired-cluster-size-to-read 3 --random-seed 1 --n-procs 10 --chosen-ab-fname test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv --refuse-to-cache-parameters --outfname test/paired/new-results/partition-new-simu/igh+igk/partition-igh.yaml
@@ -673,10 +682,10 @@ hmm
     skipped 1/4 clusters that had no uids in common with tree
   writing selection metrics to test/paired/new-results/partition-new-simu/selection-metrics.yaml
       writing 10 chosen abs to test/paired/new-results/get-selection-metrics-new-simu-chosen-abs.csv
-      total time: 5.6
+      total time: 5.9
 cache-parameters-data            partis cache-parameters --dont-write-git-info --paired-loci --infname test/paired-data/all-seqs.fa --parameter-dir test/paired/new-results/test/parameters/data --n-max-queries 100 --random-seed 1 --n-procs 10
   note: --paired-outdir is not set, so there will be no persistent record of the results (except the parameter directory).
-run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/888813/meta.yaml --n-max-queries 100
+run extract-pairing-info.py test/paired-data/all-seqs.fa /tmp/runner/hmms/870150/meta.yaml --n-max-queries 100
   --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
   extract_pairing_info(): read 100 sequences with 48 droplet ids
     droplet id separators (set automatically): _  indices: [0]
@@ -687,9 +696,9 @@ hmm
         2           42     0.875
         3            2     0.042
         4            2     0.042
-run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/888813 --input-metafname /tmp/runner/hmms/888813/meta.yaml --n-max-queries 100
+run split-loci.py test/paired-data/all-seqs.fa --outdir /tmp/runner/hmms/870150 --input-metafname /tmp/runner/hmms/870150/meta.yaml --n-max-queries 100
   --n-max-queries: chose 48 / 48 droplets (first 100, after random shuffling) which had 100 / 100 seqs
-  --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/888813/meta.yaml: paired-uids
+  --input-metafnames: added meta info for 100 sequences from /tmp/runner/hmms/870150/meta.yaml: paired-uids
     read pairing info for 100 seqs from input meta file
   running vsearch on 100 sequences:
     igh:   49 / 100 v annotations (51 failed) with 28 v genes in 0.1 sec
@@ -712,10 +721,10 @@ totals: igh 48 igk 37 igl 15
                2   0.13   h l
                1   0.07   h k
                1   0.07   h h k
-writing to /tmp/runner/hmms/888813/
-  igh: 48 to 888813/igh.fa
-  igk: 37 to 888813/igk.fa
-  igl: 15 to 888813/igl.fa
+writing to /tmp/runner/hmms/870150/
+  igh: 48 to 870150/igh.fa
+  igk: 37 to 870150/igk.fa
+  igl: 15 to 870150/igl.fa
 writing to paired subdirs
     igh+igk:
       igh: 36 / 48 to igh+igk/igh.fa
@@ -724,8 +733,8 @@ writing to paired subdirs
       igh: 15 / 48 to igh+igl/igh.fa
       igl: 15 / 15 to igh+igl/igl.fa
 cache-parameters igh:
-run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/888813/igh.fa --parameter-dir test/paired/new-results/test/parameters/data/igh --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igh/sw-cache.yaml --input-metafnames /tmp/runner/hmms/888813/meta.yaml
-  --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/888813/meta.yaml: paired-uids
+run partis cache-parameters --locus igh --dont-write-git-info --infname /tmp/runner/hmms/870150/igh.fa --parameter-dir test/paired/new-results/test/parameters/data/igh --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igh/sw-cache.yaml --input-metafnames /tmp/runner/hmms/870150/meta.yaml
+  --input-metafnames: added meta info for 48 sequences from /tmp/runner/hmms/870150/meta.yaml: paired-uids
 caching parameters
   vsearch: 48 / 48 v annotations (0 failed) with 27 v genes in 0.0 sec
     keeping 23 / 198 v genes
@@ -753,10 +762,10 @@ hmm
       hmm step time: 3.0
   writing hmms     removed 1  genes from glfo (leaving v 23  d 18  j 6)
 (1.0 sec)
-      total time: 7.5
+      total time: 7.6
 cache-parameters igk:
-run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/888813/igk.fa --parameter-dir test/paired/new-results/test/parameters/data/igk --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igk/sw-cache.yaml --input-metafnames /tmp/runner/hmms/888813/meta.yaml
-  --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/888813/meta.yaml: paired-uids
+run partis cache-parameters --locus igk --dont-write-git-info --infname /tmp/runner/hmms/870150/igk.fa --parameter-dir test/paired/new-results/test/parameters/data/igk --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igk/sw-cache.yaml --input-metafnames /tmp/runner/hmms/870150/meta.yaml
+  --input-metafnames: added meta info for 37 sequences from /tmp/runner/hmms/870150/meta.yaml: paired-uids
 caching parameters
   vsearch: 37 / 37 v annotations (0 failed) with 16 v genes in 0.0 sec
     keeping 16 / 64 v genes
@@ -783,11 +792,11 @@ hmm
          infra time: 1.3
       hmm step time: 1.9
   writing hmms     removed 0  genes from glfo (leaving v 16  d 1  j 7)
-(1.1 sec)
+(1.0 sec)
       total time: 5.7
 cache-parameters igl:
-run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/888813/igl.fa --parameter-dir test/paired/new-results/test/parameters/data/igl --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igl/sw-cache.yaml --input-metafnames /tmp/runner/hmms/888813/meta.yaml
-  --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/888813/meta.yaml: paired-uids
+run partis cache-parameters --locus igl --dont-write-git-info --infname /tmp/runner/hmms/870150/igl.fa --parameter-dir test/paired/new-results/test/parameters/data/igl --random-seed 1 --n-procs 10 --sw-cachefname test/paired/new-results/test/parameters/data/igl/sw-cache.yaml --input-metafnames /tmp/runner/hmms/870150/meta.yaml
+  --input-metafnames: added meta info for 15 sequences from /tmp/runner/hmms/870150/meta.yaml: paired-uids
 caching parameters
   vsearch: 15 / 15 v annotations (0 failed) with 12 v genes in 0.0 sec
     keeping 10 / 80 v genes
@@ -814,199 +823,187 @@ hmm
   writing hmms     removed 0  genes from glfo (leaving v 10  d 1  j 3)
 (0.6 sec)
       total time: 3.5
-      warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/888813/: failed.fa
+      warning expected to remove 1/11 files+dirs that weren't in /tmp/runner/hmms/870150/: failed.fa
       total time: 22.1
-simulate                         partis simulate --dont-write-git-info --paired-loci --parameter-dir test/paired/new-results/test/parameters/data --n-sim-events 10 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --no-per-base-mutation --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/test/simu --indel-frequency 0.2
+simulate                         partis simulate --dont-write-git-info --paired-loci --parameter-dir test/paired/new-results/test/parameters/data --n-sim-events 10 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 1 --n-procs 10 --paired-outdir test/paired/new-results/test/simu --indel-frequency 0.2
 igh+igk: simulating 7 events
-generate-trees igh+igk: igh
-run partis simulate --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igh --n-trees 7 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --no-per-base-mutation --random-seed 2003260051 --indel-frequency 0.2 --generate-trees --outfname test/paired/new-results/test/simu/igh+igk/trees.nwk
-  note: reducing --n-procs to 1 (was 4) so it isn't bigger than --n-sim-events
-  generating 7 trees, n-leaves from geometric distribution with parameter 5.0
-    mean over 7 trees:   depth 0.02051   leaves 5.57
-    writing trees to test/paired/new-results/test/simu/igh+igk/trees.nwk
-      total time: 1.3
+    warning drawing input simulation trees from --input-simulation-treefname *in order* for both heavy and light (rather than randomly, as for single chain)
 simulate igh+igk: igh
-run partis simulate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igh --n-sim-events 7 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --no-per-base-mutation --random-seed 2003260051 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igk/igh.yaml --input-simulation-treefname test/paired/new-results/test/simu/igh+igk/trees.nwk
+run partis simulate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igh --n-sim-events 7 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 2003260051 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igk/igh.yaml
   note: reducing --n-procs to 7 (was 10) so it isn't bigger than --n-sim-events
 simulating
       --> proc 0
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-0.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/938371/trees-sub-0.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 12 seqs in 0.1s (0.1s of which was running bppseqgen)
-      total time: 0.1
+    made 1 event with 10 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.2
 
       --> proc 1
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-1.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/938371/trees-sub-1.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 3 seqs in 0.2s (0.0s of which was running bppseqgen)
-      total time: 0.2
+    made 1 event with 8 seqs in 0.2s (0.1s of which was running bppseqgen)
+      total time: 0.3
 
       --> proc 2
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-2.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/938371/trees-sub-2.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 3 seqs in 0.0s (0.0s of which was running bppseqgen)
-      total time: 0.1
+    made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.2
 
       --> proc 3
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-3.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/938371/trees-sub-3.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 2 seqs in 0.1s (0.0s of which was running bppseqgen)
-      total time: 0.1
+    made 1 event with 6 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.2
 
       --> proc 4
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-4.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/938371/trees-sub-4.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
+    made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
       total time: 0.1
 
       --> proc 5
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-5.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/938371/trees-sub-5.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 9 seqs in 0.1s (0.0s of which was running bppseqgen)
-      total time: 0.1
+    made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.2
 
       --> proc 6
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/390989/trees-sub-6.nwk
+    resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/938371/trees-sub-6.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 8 seqs in 0.1s (0.0s of which was running bppseqgen)
-      total time: 0.1
+    made 1 event with 13 seqs in 0.1s (0.1s of which was running bppseqgen)
+      total time: 0.2
 
-   read 7 events with 39 seqs from 7 .yaml files
-      total time: 4.1
+   read 7 events with 40 seqs from 7 .yaml files
+      total time: 4.2
 simulate igh+igk: igk
-run partis simulate --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igk --n-sim-events 7 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --no-per-base-mutation --random-seed 2077655082 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igk/igk.yaml --input-simulation-treefname test/paired/new-results/test/simu/igh+igk/trees.nwk
+run partis simulate --locus igk --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igk --n-sim-events 7 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 2077655082 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igk/igk.yaml
   note: reducing --n-procs to 7 (was 10) so it isn't bigger than --n-sim-events
 simulating
       --> proc 0
     reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-0.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/129826/trees-sub-0.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 12 seqs in 0.1s (0.1s of which was running bppseqgen)
+    made 1 event with 10 seqs in 0.1s (0.1s of which was running bppseqgen)
       total time: 0.1
 
       --> proc 1
     reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-1.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/129826/trees-sub-1.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 3 seqs in 0.0s (0.0s of which was running bppseqgen)
-      total time: 0.1
+    made 1 event with 8 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.2
 
       --> proc 2
     reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-2.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/129826/trees-sub-2.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 3 seqs in 0.0s (0.0s of which was running bppseqgen)
+    made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
       total time: 0.1
 
       --> proc 3
     reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-3.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/129826/trees-sub-3.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
+    made 1 event with 6 seqs in 0.1s (0.0s of which was running bppseqgen)
       total time: 0.1
 
       --> proc 4
     reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-4.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/129826/trees-sub-4.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
-      total time: 0.0
+    made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
+      total time: 0.2
 
       --> proc 5
     reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-5.nwk
+    resetting --n-trees from 10 to 14 to match trees read from /tmp/runner/hmms/129826/trees-sub-5.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 9 seqs in 0.1s (0.0s of which was running bppseqgen)
+    made 1 event with 1 seqs in 0.1s (0.0s of which was running bppseqgen)
       total time: 0.2
 
       --> proc 6
     reco params: test/paired/new-results/test/parameters/data/igk/hmm     shm params: test/paired/new-results/test/parameters/data/igk/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/780025/trees-sub-6.nwk
+    resetting --n-trees from 10 to 16 to match trees read from /tmp/runner/hmms/129826/trees-sub-6.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 8 seqs in 0.1s (0.0s of which was running bppseqgen)
+    made 1 event with 13 seqs in 0.1s (0.1s of which was running bppseqgen)
       total time: 0.1
 
-   read 7 events with 39 seqs from 7 .yaml files
+   read 7 events with 40 seqs from 7 .yaml files
       total time: 4.1
 igh+igl: simulating 3 events
-generate-trees igh+igl: igh
-run partis simulate --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igh --n-trees 3 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --no-per-base-mutation --random-seed 982264879 --indel-frequency 0.2 --generate-trees --outfname test/paired/new-results/test/simu/igh+igl/trees.nwk
-  note: reducing --n-procs to 1 (was 4) so it isn't bigger than --n-sim-events
-  generating 3 trees, n-leaves from geometric distribution with parameter 5.0
-    mean over 3 trees:   depth 0.05242   leaves 9.00
-    writing trees to test/paired/new-results/test/simu/igh+igl/trees.nwk
-      total time: 1.3
+    warning drawing input simulation trees from --input-simulation-treefname *in order* for both heavy and light (rather than randomly, as for single chain)
 simulate igh+igl: igh
-run partis simulate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igh --n-sim-events 3 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --no-per-base-mutation --random-seed 982264879 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igl/igh.yaml --input-simulation-treefname test/paired/new-results/test/simu/igh+igl/trees.nwk
+run partis simulate --locus igh --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igh --n-sim-events 3 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 982264879 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igl/igh.yaml
   note: reducing --n-procs to 3 (was 10) so it isn't bigger than --n-sim-events
 simulating
       --> proc 0
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/99260/trees-sub-0.nwk
+    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/373835/trees-sub-0.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 14 seqs in 0.1s (0.0s of which was running bppseqgen)
+    made 1 event with 10 seqs in 0.1s (0.0s of which was running bppseqgen)
       total time: 0.1
 
       --> proc 1
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/99260/trees-sub-1.nwk
+    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/373835/trees-sub-1.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 3 seqs in 0.0s (0.0s of which was running bppseqgen)
+    made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
       total time: 0.1
 
       --> proc 2
     reco params: test/paired/new-results/test/parameters/data/igh/hmm     shm params: test/paired/new-results/test/parameters/data/igh/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/99260/trees-sub-2.nwk
+    resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/373835/trees-sub-2.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 10 seqs in 0.1s (0.0s of which was running bppseqgen)
+    made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
       total time: 0.1
 
-   read 3 events with 27 seqs from 3 .yaml files
-      total time: 2.0
+   read 3 events with 13 seqs from 3 .yaml files
+      total time: 2.1
 simulate igh+igl: igl
-run partis simulate --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igl --n-sim-events 3 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --no-per-base-mutation --random-seed 1083609742 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igl/igl.yaml --input-simulation-treefname test/paired/new-results/test/simu/igh+igl/trees.nwk
+run partis simulate --locus igl --dont-write-git-info --parameter-dir test/paired/new-results/test/parameters/data/igl --n-sim-events 3 --n-trees 10 --n-leaf-distribution geometric --n-leaves 5 --min-observations-per-gene 5 --mean-cells-per-droplet 1.25 --constant-cells-per-droplet --fraction-of-reads-to-remove 0.15 --input-simulation-treefname /home/runner/work/partis/partis/test/trees.nwk --no-per-base-mutation --random-seed 1083609742 --n-procs 10 --indel-frequency 0.2 --choose-trees-in-order --outfname test/paired/new-results/test/simu/igh+igl/igl.yaml
   note: reducing --n-procs to 3 (was 10) so it isn't bigger than --n-sim-events
 simulating
       --> proc 0
     reco params: test/paired/new-results/test/parameters/data/igl/hmm     shm params: test/paired/new-results/test/parameters/data/igl/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/63603/trees-sub-0.nwk
+    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/635551/trees-sub-0.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 14 seqs in 0.1s (0.0s of which was running bppseqgen)
+    made 1 event with 10 seqs in 0.0s (0.0s of which was running bppseqgen)
       total time: 0.1
 
       --> proc 1
     reco params: test/paired/new-results/test/parameters/data/igl/hmm     shm params: test/paired/new-results/test/parameters/data/igl/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/63603/trees-sub-1.nwk
+    resetting --n-trees from 10 to 33 to match trees read from /tmp/runner/hmms/635551/trees-sub-1.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 3 seqs in 0.0s (0.0s of which was running bppseqgen)
-      total time: 0.0
+    made 1 event with 2 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
 
       --> proc 2
     reco params: test/paired/new-results/test/parameters/data/igl/hmm     shm params: test/paired/new-results/test/parameters/data/igl/hmm
-    resetting --n-trees from 10 to 1 to match trees read from /tmp/runner/hmms/63603/trees-sub-2.nwk
+    resetting --n-trees from 10 to 34 to match trees read from /tmp/runner/hmms/635551/trees-sub-2.nwk
       using bpp uniform mutation with path /home/runner/work/partis/partis/packages/bpp
-    made 1 event with 10 seqs in 0.0s (0.0s of which was running bppseqgen)
-      total time: 0.0
+    made 1 event with 1 seqs in 0.0s (0.0s of which was running bppseqgen)
+      total time: 0.1
 
-   read 3 events with 27 seqs from 3 .yaml files
-      total time: 2.2
+   read 3 events with 13 seqs from 3 .yaml files
+      total time: 2.0
 igh+igk: synchronizing heavy and light chain simulation trees and rewriting output files in test/paired/new-results/test/simu/igh+igk/
 igh+igl: synchronizing heavy and light chain simulation trees and rewriting output files in test/paired/new-results/test/simu/igh+igl/
   concatenating heavy chain loci:
-      h starting with 7 annotations (39 seqs)
-      k starting with 7 annotations (39 seqs)
-      h adding 3 annotations (27 seqs) for total 7 (39)
-      l starting with 3 annotations (27 seqs)
+      h starting with 7 annotations (40 seqs)
+      k starting with 7 annotations (40 seqs)
+      h adding 3 annotations (13 seqs) for total 7 (40)
+      l starting with 3 annotations (13 seqs)
     finished with:
-     h: 10 annotations (66 seqs)
-  apportioned 132 seqs among 52 droplets (mean/2 1.3): 4 2 2 2 2 4 2 2 2 2 2 2 4 2 2 2 4 4 2 2 4 2 2 2 2 2 2 4 2 2 4 2 4 2 2 2 2 2 2 2 2 2 4 4 2 4 2 2 2 4 4 2
-  removed 19 / 132 = 0.14 seqs from outfos (leaving 7 / 113 unpaired)
+     h: 10 annotations (53 seqs)
+  apportioned 106 seqs among 42 droplets (mean/2 1.3): 2 2 2 4 4 2 4 4 4 4 2 2 2 4 2 2 2 2 2 2 2 2 2 2 4 2 4 2 2 2 2 2 4 4 2 2 2 2 2 2 2 2
+  removed 15 / 106 = 0.14 seqs from outfos (leaving 9 / 91 unpaired)
     writing combined h/l info to fasta and meta files in test/paired/new-results/test/simu
-      total time: 22.8
+      total time: 17.6

test/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')