QC modifications

[anleip]

1. Removed type isolate argument
2. Corrected distance plot to show the distances after QC
3. Allows generation of QC folder and files when no sample was removed

[johnlees]

Buildkite error looks transitory:

++ PACKAGE_ROOT=/var/lib/buildkite-agent/builds/reside-bk3-1/mrc-ide/poppunk
++ PACKAGE_NAME=poppunk
++ PACKAGE_ORG=mrcide
++ '[' true = true ']'
++ GIT_SHA=33e48be
++ '[' true = true ']'
++ GIT_BRANCH=qc_modifications
++ TAG_SHA=mrcide/poppunk:33e48be
++ TAG_BRANCH=mrcide/poppunk:qc_modifications
++ TAG_LATEST=mrcide/poppunk:latest
+ docker build --pull --tag mrcide/poppunk:33e48be -f docker/Dockerfile /var/lib/buildkite-agent/builds/reside-bk3-1/mrc-ide/poppunk
[+] Building 11.6s (7/15)                                                                                                                        docker:default
 => [internal] load build definition from Dockerfile                                                                                                       0.0s
 => => transferring dockerfile: 1.67kB                                                                                                                     0.0s
 => [internal] load metadata for docker.io/library/python:3.10                                                                                             0.7s
 => [auth] library/python:pull token for registry-1.docker.io                                                                                              0.0s
 => [internal] load .dockerignore                                                                                                                          0.0s
 => => transferring context: 77B                                                                                                                           0.0s
 => CACHED [ 1/10] FROM docker.io/library/python:3.10@sha256:20ca17b2908b0202fc97510a082177357e7737f16dc231d7508b5a7d0cb96fd3                              0.0s
 => => resolve docker.io/library/python:3.10@sha256:20ca17b2908b0202fc97510a082177357e7737f16dc231d7508b5a7d0cb96fd3                                       0.0s
 => [internal] load build context                                                                                                                          0.0s
 => => transferring context: 89.54kB                                                                                                                       0.0s
 => ERROR [ 2/10] RUN apt-get update &&     apt-get install -y --no-install-recommends                           cmake                           gfortra  10.8s
------
 > [ 2/10] RUN apt-get update &&     apt-get install -y --no-install-recommends                           cmake                           gfortran                           libarmadillo-dev                           libeigen3-dev                           libopenblas-dev                           software-properties-common:
8.550 Hit:1 http://deb.debian.org/debian trixie InRelease
8.552 Get:2 http://deb.debian.org/debian trixie-updates InRelease [47.3 kB]
8.568 Get:3 http://deb.debian.org/debian-security trixie-security InRelease [43.4 kB]
8.603 Get:4 http://deb.debian.org/debian trixie/main amd64 Packages [9670 kB]
8.765 Get:5 http://deb.debian.org/debian trixie-updates/main amd64 Packages [5412 B]
8.769 Get:6 http://deb.debian.org/debian-security trixie-security/main amd64 Packages [71.8 kB]
9.532 Fetched 9838 kB in 9s (1062 kB/s)
9.532 Reading package lists...
10.05 Reading package lists...
10.59 Building dependency tree...
10.73 Reading state information...
10.75 E: Unable to locate package software-properties-common
------
Dockerfile:3
--------------------
   2 |
   3 | >>> RUN apt-get update && \
   4 | >>>     apt-get install -y --no-install-recommends \
   5 | >>>                           cmake \
   6 | >>>                           gfortran \
   7 | >>>                           libarmadillo-dev \
   8 | >>>                           libeigen3-dev \
   9 | >>>                           libopenblas-dev \
  10 | >>>                           software-properties-common
  11 |
--------------------
ERROR: failed to build: failed to solve: process "/bin/sh -c apt-get update &&     apt-get install -y --no-install-recommends                           cmake                           gfortran                           libarmadillo-dev                           libeigen3-dev                           libopenblas-dev                           software-properties-common" did not complete successfully: exit code: 100
🚨 Error: The command exited with status 1
user command error: exit status 1

[johnlees]

Can you also:

• Increase the version number
• Update the docs, so references to the type isolate are removed
• Remove the type isolate selection function

[johnlees]

NB: https://github.com/bacpop/PopPUNK/blob/master/docker/Dockerfile#L10
software-properties-common deprecated