Support new format of MiSeq sample sheets

.flake8

@@ -33,7 +33,6 @@ per-file-ignores =
     micall/tests/test_cigar_tools.py: E704,W503
     micall/tests/test_consensus_aligner.py: F841,E126,W504,E701,F401
     micall/tests/test_contig_stitcher.py: W503
-    micall/tests/test_error_metrics_parser.py: E231
     micall/tests/test_fastq_g2p.py: W293
     micall/tests/test_hcv_reference_tree.py: W293
     micall/tests/test_hcv_rules_import.py: E241
@@ -77,6 +76,5 @@ per-file-ignores =
     micall/utils/report_amino.py: W504
     micall/utils/sam_g2p_simplify.py: W293,E265,E303,E305
     micall/utils/sample_fastq.py: E305
-    micall/utils/sample_sheet_parser.py: E275,W504
     micall/utils/scan_run_folders.py: W504
     micall/utils/v3loop_alignment_scores/plot.py: W293

.github/workflows/build-and-test.yml

@@ -118,11 +118,14 @@ jobs:
       - name: Singularity build
         run: sudo singularity build micall.simg Singularity
 
+      - name: Install python packages
+        run: pip install multicsv
+
       - name: Singularity test
         run: python release_test_microtest.py micall.simg
 
       - name: Upload Singularity Image
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: micall.simg
           path: micall.simg

.mypy.ini

@@ -65,7 +65,6 @@ exclude = (?x)
     ^micall/utils/sample_fastq[.]py$|
     ^micall/utils/sample_project_summary[.]py$|
     ^micall/utils/samples_from_454[.]py$|
-    ^micall/utils/sample_sheet_parser[.]py$|
     ^micall/utils/scan_run_folders[.]py$|
     ^micall/utils/seed_alignments[.]py$|
     ^micall/utils/spring_beads[.]py$|

micall/tests/test_error_metrics_parser.py

@@ -1,7 +1,7 @@
 from io import BytesIO, StringIO
 from struct import pack
 from unittest import TestCase
-from micall.monitor.error_metrics_parser import read_errors, write_phix_csv,\
+from micall.monitor.error_metrics_parser import read_errors, write_phix_csv, \
     read_records