Merge pull request #27 from matt-sd-watson/opt_pytest

Opt pytest

environments/environment.yml

@@ -28,6 +28,7 @@ dependencies:
   - r-heatmaply
   - r-markdown
   - r-essentials
+  - r-plotly
   - r-traminer
   - scipy=1.6.3
   - snakemake

outbreaker/workflows/outbreaker_summary_report.Rmd

@@ -55,6 +55,7 @@ library(tidyverse)
 library(magrittr)
 library(heatmaply)
 library(stringr)
+library(plotly)
 ```
 
 

tests/test_outbreaker.py

@@ -6,27 +6,28 @@
 import pytest
 
 
-@pytest.fixture
+@pytest.fixture(scope = "module")
 def get_data_dir():
     return str(os.path.abspath(os.path.join(os.path.dirname( __file__ ), '..', 'data/')))
 
-@pytest.fixture
+@pytest.fixture(scope = "module")
 def get_alignment_reference(get_data_dir):
     return str(os.path.join(get_data_dir, 'reference', 'ncov_reference.gb'))
 
-@pytest.fixture
+@pytest.fixture(scope = "module")
 def get_focal_sequences(get_data_dir):
     return str(os.path.join(get_data_dir, 'tests/', 'focal_seqs.fa'))
 
-@pytest.fixture
+@pytest.fixture(scope = "module")
 def get_background_sequences(get_data_dir):
     return str(os.path.join(get_data_dir, 'tests/', 'background_seqs.fa'))
 
-@pytest.fixture
+@pytest.fixture(scope = "module")
 def get_names_csv(get_data_dir):
     return str(os.path.join(get_data_dir, 'tests/', 'names.csv'))
 
-@pytest.fixture
+# need to keep fixtures that call built-in tmp_path within same scope as tmp_path (function
+@pytest.fixture(scope = "function")
 def get_renamed_fasta(tmp_path):
     return str(os.path.join(tmp_path, 'pytest_renamed.fa'))
 
@@ -83,19 +84,3 @@ def test_run_with_console_output(self, tmp_path, get_focal_sequences, get_backgr
         assert 'WARNING: the following record has no match in samples IDs and will be kept with the original name: Focal_4' \
                in results.stdout.decode('utf-8')
 
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