diff --git a/.cache/v/cache/lastfailed b/.cache/v/cache/lastfailed
deleted file mode 100644
index 6512ac8..0000000
--- a/.cache/v/cache/lastfailed
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-  "tests/test_suite.py::test_long": true
-}
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index e629ce8..1b0204f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -21,3 +21,15 @@ dist/
 
 # documentation build
 docs/_build/
+
+# PyCharm files 
+.idea/* 
+
+# Python cache
+.cache/* 
+
+# Pytest cache
+.pytest_cache/*
+
+# Mac specifics 
+.DS_Store
diff --git a/.idea/.gitignore b/.idea/.gitignore
deleted file mode 100644
index 73f69e0..0000000
--- a/.idea/.gitignore
+++ /dev/null
@@ -1,8 +0,0 @@
-# Default ignored files
-/shelf/
-/workspace.xml
-# Datasource local storage ignored files
-/dataSources/
-/dataSources.local.xml
-# Editor-based HTTP Client requests
-/httpRequests/
diff --git a/.idea/drep.iml b/.idea/drep.iml
deleted file mode 100644
index 7fef8bd..0000000
--- a/.idea/drep.iml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="PYTHON_MODULE" version="4">
-  <component name="NewModuleRootManager">
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/tests" isTestSource="false" />
-    </content>
-    <orderEntry type="jdk" jdkName="Python 3.7 (drep_v3)" jdkType="Python SDK" />
-    <orderEntry type="sourceFolder" forTests="false" />
-  </component>
-  <component name="PyDocumentationSettings">
-    <option name="format" value="GOOGLE" />
-    <option name="myDocStringFormat" value="Google" />
-    <option name="renderExternalDocumentation" value="true" />
-  </component>
-  <component name="TestRunnerService">
-    <option name="PROJECT_TEST_RUNNER" value="pytest" />
-  </component>
-</module>
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
deleted file mode 100644
index 105ce2d..0000000
--- a/.idea/inspectionProfiles/profiles_settings.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<component name="InspectionProjectProfileManager">
-  <settings>
-    <option name="USE_PROJECT_PROFILE" value="false" />
-    <version value="1.0" />
-  </settings>
-</component>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
deleted file mode 100644
index c198440..0000000
--- a/.idea/misc.xml
+++ /dev/null
@@ -1,4 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.7 (drep_v3)" project-jdk-type="Python SDK" />
-</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
deleted file mode 100644
index dcb3622..0000000
--- a/.idea/modules.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectModuleManager">
-    <modules>
-      <module fileurl="file://$PROJECT_DIR$/.idea/drep.iml" filepath="$PROJECT_DIR$/.idea/drep.iml" />
-    </modules>
-  </component>
-</project>
\ No newline at end of file
diff --git a/.idea/other.xml b/.idea/other.xml
deleted file mode 100644
index 640fd80..0000000
--- a/.idea/other.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="PySciProjectComponent">
-    <option name="PY_SCI_VIEW" value="true" />
-    <option name="PY_SCI_VIEW_SUGGESTED" value="true" />
-  </component>
-</project>
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
deleted file mode 100644
index 94a25f7..0000000
--- a/.idea/vcs.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="VcsDirectoryMappings">
-    <mapping directory="$PROJECT_DIR$" vcs="Git" />
-  </component>
-</project>
\ No newline at end of file
diff --git a/.pytest_cache/v/cache/lastfailed b/.pytest_cache/v/cache/lastfailed
deleted file mode 100644
index 1c88874..0000000
--- a/.pytest_cache/v/cache/lastfailed
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-  "tests/test_suite.py::test_long": true,
-  "tests/test_suite.py::test_quick": true,
-  "tests/test_suite.py::test_short": true,
-  "tests/test_suite.py::test_unit": true
-}
\ No newline at end of file
diff --git a/.pytest_cache/v/cache/nodeids b/.pytest_cache/v/cache/nodeids
deleted file mode 100644
index 1d279d7..0000000
--- a/.pytest_cache/v/cache/nodeids
+++ /dev/null
@@ -1,75 +0,0 @@
-[
-  "tests/tests/test_analyze.py::test_plot_1",
-  "tests/tests/test_analyze.py::test_plot_5_1",
-  "tests/tests/test_analyze.py::test_plot_5_2",
-  "tests/tests/test_analyze.py::test_plot_6_1",
-  "tests/tests/test_analyze.py::test_plotting_functional_1",
-  "tests/tests/test_analyze.py::test_plotting_functional_2",
-  "tests/tests/test_bonus.py::test_drep_scaffold_level",
-  "tests/tests/test_bonus.py::test_drep_scaffold_level_2",
-  "tests/tests/test_bonus.py::test_drep_scaffold_level_3",
-  "tests/tests/test_bonus.py::test_drep_scaffold_level_4",
-  "tests/tests/test_bonus.py::test_drep_scaffold_level_5",
-  "tests/tests/test_bonus.py::test_parse_stb",
-  "tests/tests/test_bonus.py::test_parse_stb_2",
-  "tests/tests/test_bonus.py::test_parse_stb_3",
-  "tests/tests/test_choose.py::test_centrality_1",
-  "tests/tests/test_choose.py::test_centrality_2",
-  "tests/tests/test_choose.py::test_choose_1",
-  "tests/tests/test_choose.py::test_choose_2",
-  "tests/tests/test_choose.py::test_choose_3",
-  "tests/tests/test_cluster.py::test_all_vs_all_mash",
-  "tests/tests/test_cluster.py::test_cluster_functional_1",
-  "tests/tests/test_cluster.py::test_cluster_functional_2",
-  "tests/tests/test_cluster.py::test_cluster_functional_3",
-  "tests/tests/test_cluster.py::test_cluster_functional_4",
-  "tests/tests/test_cluster.py::test_cluster_mash_database",
-  "tests/tests/test_cluster.py::test_compare_genomes",
-  "tests/tests/test_cluster.py::test_fastANI",
-  "tests/tests/test_cluster.py::test_genome_hierarchical_clustering",
-  "tests/tests/test_cluster.py::test_goANI",
-  "tests/tests/test_cluster.py::test_goANI2",
-  "tests/tests/test_cluster.py::test_list_genome_load",
-  "tests/tests/test_cluster.py::test_skipsecondary",
-  "tests/tests/test_cluster.py::test_time_compare_genomes",
-  "tests/tests/test_dereplicate.py::test_dereplicate_1",
-  "tests/tests/test_dereplicate.py::test_dereplicate_2",
-  "tests/tests/test_dereplicate.py::test_dereplicate_3",
-  "tests/tests/test_dereplicate.py::test_dereplicate_4",
-  "tests/tests/test_dereplicate.py::test_dereplicate_5",
-  "tests/tests/test_dereplicate.py::test_dereplicate_6",
-  "tests/tests/test_dereplicate.py::test_dereplicate_7",
-  "tests/tests/test_dereplicate.py::test_dereplicate_8",
-  "tests/tests/test_dereplicate.py::test_dereplicate_9",
-  "tests/tests/test_evaluate.py::test_tertiary_clustering_1",
-  "tests/tests/test_evaluate.py::test_tertiary_clustering_2",
-  "tests/tests/test_filter.py::test_calc_genome_info",
-  "tests/tests/test_filter.py::test_chdb_to_genomeInfo",
-  "tests/tests/test_filter.py::test_filer_functional_1",
-  "tests/tests/test_filter.py::test_filer_functional_2",
-  "tests/tests/test_filter.py::test_filer_functional_3",
-  "tests/tests/test_filter.py::test_filer_functional_4",
-  "tests/tests/test_filter.py::test_run_checkm",
-  "tests/tests/test_filter.py::test_run_checkm2",
-  "tests/tests/test_filter.py::test_validate_genomeInfo",
-  "tests/tests/test_greedy.py::test_greedy_secondary_clustering_1",
-  "tests/tests/test_greedy.py::test_greedy_secondary_clustering_2",
-  "tests/tests/test_greedy.py::test_multiround_primary_clustering_1",
-  "tests/tests/test_greedy.py::test_multiround_primary_clustering_2",
-  "tests/tests/test_greedy.py::test_multiround_primary_clustering_3",
-  "tests/tests/test_greedy.py::test_multiround_primary_clustering_4",
-  "tests/tests/test_rerun.py::test_unit_1",
-  "tests/tests/test_rerun.py::test_unit_2",
-  "tests/tests/test_rerun.py::test_unit_3",
-  "tests/tests/test_rerun.py::test_unit_4",
-  "tests/tests/test_rerun.py::test_unit_5",
-  "tests/tests/test_rerun.py::test_unit_6",
-  "tests/tests/test_rerun.py::test_unit_7",
-  "tests/tests/test_taxonomy.py::test_taxonomy_1",
-  "tests/tests/test_taxonomy.py::test_taxonomy_2",
-  "tests/tests/test_taxonomy.py::test_taxonomy_3",
-  "tests/tests/test_taxonomy.py::test_taxonomy_4",
-  "tests/tests/test_unit.py::test_compare_dfs",
-  "tests/tests/test_unit.py::test_n50",
-  "tests/tests/test_unit.py::test_scoring"
-]
\ No newline at end of file
diff --git a/.pytest_cache/v/cache/stepwise b/.pytest_cache/v/cache/stepwise
deleted file mode 100644
index 0637a08..0000000
--- a/.pytest_cache/v/cache/stepwise
+++ /dev/null
@@ -1 +0,0 @@
-[]
\ No newline at end of file
diff --git a/bin/dRep b/bin/dRep
index 1f12247..98685f2 100755
--- a/bin/dRep
+++ b/bin/dRep
@@ -18,9 +18,9 @@ import sys
 
 if sys.version_info[0] < 3:
     print('''
-    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-    !!! you're running dRep with python2- you need python 3 !!!
-    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!''')
+    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+    !!! you're running dRep with python2 - you need python 3 !!!
+    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!''')
     sys.exit(1)
 
 import drep.argumentParser