clean up comments. Note that #39 was already fixed in 4321efe Fixes #39

KoslickiLab · Oct 18, 2023 · fcbd3cd · fcbd3cd
1 parent 91cb8e8
commit fcbd3cd
Showing 1 changed file with 0 additions and 61 deletions.
diff --git a/tests/test_workflow.py b/tests/test_workflow.py
@@ -24,36 +24,6 @@ def test_full_workflow():
                                               "training_sig_files.txt"])))
     # one of the signature files
     expected_files.extend(list(map(lambda x: os.path.join(data_dir, intermediate_dir, "signatures", x), ["04212e93c2172d4df49dc5d8c2973d8b.sig.gz"])))
-    # In testdata/
-    # 20_genomes_trained_config.json
-    # 20_genomes_trained_processed_manifest.tsv
-    # 20_genomes_trained_rep_to_corr_orgas_mapping.tsv
-    # /testdata/20_genomes_trained_intermediate_files$ tree .
-    # .
-    # ├── signatures
-    # │   ├── 04212e93c2172d4df49dc5d8c2973d8b.sig.gz
-    # │   ├── 04f2b0e94f2d1f1f5b8355114b70274e.sig.gz
-    # │   ├── 0661ecab88c3d65d0f10e599a5ba1654.sig.gz
-    # │   ├── 06ebe48d527882bfa9505aba8e31ae23.sig.gz
-    # │   ├── 11fe9a00287c7ad086ebbc463724cf10.sig.gz
-    # │   ├── 16c6c1d37259d83088ab3a4f5b691631.sig.gz
-    # │   ├── 188d55801a78d4773cf6c0b46bca96ba.sig.gz
-    # │   ├── 1a121dca600c6504e88252e81004f0cf.sig.gz
-    # │   ├── 39ea7fd48ee7003587c9c763946d5d6e.sig.gz
-    # │   ├── 45f2675c1dca4ef1a24a05f5b268adbb.sig.gz
-    # │   ├── 7b312fffa3fb35440ba40203ba826c05.sig.gz
-    # │   ├── 8fb9b1a69838a58cc4f31c1e42a5f189.sig.gz
-    # │   ├── 92fb1b3e4baa6c474aff3efb84957687.sig.gz
-    # │   ├── 96cb85214535b0f9723a6abc17097821.sig.gz
-    # │   ├── a136145bee08846ed94c0406df3da2d4.sig.gz
-    # │   ├── b691deddf179ead0a006527330d86dde.sig.gz
-    # │   ├── b7f087146f5cc3121477c29ff003e3d0.sig.gz
-    # │   ├── c39c52d2d088348c950c2afe503b405b.sig.gz
-    # │   ├── c9eb6a9d058df8036ad93bc45d5bf260.sig.gz
-    # │   └── ce54d962851b0fdeefc624300036a133.sig.gz
-    # ├── SOURMASH-MANIFEST.csv
-    # ├── training_multisearch_result.csv
-    # └── training_sig_files.txt
     # remove the files if they exist
     for f in expected_files:
         if exists(f):
@@ -77,37 +47,6 @@ def test_full_workflow():
         os.remove(abundance_file)
     # python ../run_YACHT.py --json testdata/20_genomes_trained_config.json --sample_file testdata/sample.sig.zip --out_file result.xlsx
     cmd = f"python {os.path.join(script_dir, 'run_YACHT.py')} --json {os.path.join(data_dir, '20_genomes_trained_config.json')} --sample_file {sample_sketches} --significance 0.99 --min_coverage 0.001 --out_file {os.path.join(data_dir,abundance_file)} --show_all"
-    print(cmd)
-    # ~/pycharm/YACHT/tests/testdata$ tree 20_genomes_trained_intermediate_files/
-    # 20_genomes_trained_intermediate_files/
-    # ├── organism_sig_file.txt  # <-- new
-    # ├── sample_multisearch_result.csv
-    # ├── sample_sig_file.txt
-    # ├── signatures
-    # │   ├── 04212e93c2172d4df49dc5d8c2973d8b.sig.gz
-    # │   ├── 04f2b0e94f2d1f1f5b8355114b70274e.sig.gz
-    # │   ├── 0661ecab88c3d65d0f10e599a5ba1654.sig.gz
-    # │   ├── 06ebe48d527882bfa9505aba8e31ae23.sig.gz
-    # │   ├── 11fe9a00287c7ad086ebbc463724cf10.sig.gz
-    # │   ├── 16c6c1d37259d83088ab3a4f5b691631.sig.gz
-    # │   ├── 188d55801a78d4773cf6c0b46bca96ba.sig.gz
-    # │   ├── 1a121dca600c6504e88252e81004f0cf.sig.gz
-    # │   ├── 39ea7fd48ee7003587c9c763946d5d6e.sig.gz
-    # │   ├── 45f2675c1dca4ef1a24a05f5b268adbb.sig.gz
-    # │   ├── 7b312fffa3fb35440ba40203ba826c05.sig.gz
-    # │   ├── 8fb9b1a69838a58cc4f31c1e42a5f189.sig.gz
-    # │   ├── 92fb1b3e4baa6c474aff3efb84957687.sig.gz
-    # │   ├── 96cb85214535b0f9723a6abc17097821.sig.gz
-    # │   ├── a136145bee08846ed94c0406df3da2d4.sig.gz
-    # │   ├── b691deddf179ead0a006527330d86dde.sig.gz
-    # │   ├── b7f087146f5cc3121477c29ff003e3d0.sig.gz
-    # │   ├── c39c52d2d088348c950c2afe503b405b.sig.gz
-    # │   ├── c9eb6a9d058df8036ad93bc45d5bf260.sig.gz
-    # │   └── ce54d962851b0fdeefc624300036a133.sig.gz
-    # ├── SOURMASH-MANIFEST.csv
-    # ├── training_multisearch_result.csv
-    # └── training_sig_files.txt
-    # print(cmd)
     res = subprocess.run(cmd, shell=True, check=True)
     # check that no errors were raised
     assert res.returncode == 0