Fix ci (#12)

* Remove log file redirect

* Add missing quotation

* Add miniconda version

* Try v3

* Add latest

* try miniforge?

* fix architecture conda-incubator/setup-miniconda#344

* Pin macos-13

* Remove latest

* ok try macos-12...

.github/workflows/test.yml

@@ -17,12 +17,12 @@ jobs:
     strategy:
           fail-fast: false
           matrix:
-            os: [ubuntu-latest, macos-latest]
+            os: [ubuntu-latest, macos-12]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2.2.0
+        uses: conda-incubator/setup-miniconda@v3
         with:
           environment-file: ./lemur.yml
           activate-environment: lemur-env
@@ -38,7 +38,7 @@ jobs:
                      -d ./examples/example-db 
                      --tax-path ./examples/example-db/taxonomy.tsv 
                      -r species 
-                     --verbose > ./examples/example-output/example.log 2>&1;
+                     --verbose;
 
       - name: Check that output was produced
         id: check_files

lemur

@@ -670,7 +670,7 @@ class LemurRunEnv():
         criteria has been met, stopping once it has.'''
         n_reads = len(set(self.P_rgs_df.reset_index()["Read_ID"]))
         if n_reads == 0:
-            self.log(f"No alignments available for EM algorithm.\nVerify SAM file, {self.self.args.output}P_rgs_df_raw.tsv, and consider lowering --min-aln-len-ratio or --fidelity flags., logging.ERROR)
+            self.log(f"No alignments available for EM algorithm.\nVerify SAM file, {self.self.args.output}P_rgs_df_raw.tsv, and consider lowering --min-aln-len-ratio or --fidelity flags.", logging.ERROR)
             exit(1)
         else:
             self.low_abundance_threshold = 1. / n_reads