Make loading work_queue and cyvcf2 optional

dadi_cli/GenerateFs.py

@@ -1,5 +1,4 @@
 import dadi, random
-from cyvcf2 import VCF
 
 
 def generate_fs(
@@ -60,11 +59,16 @@ def generate_fs(
         raise ValueError("The lengths of `pop_ids` and `projections` must match.")
 
     if polarized:
-        if not VCF(vcf).contains('AA'):
-            raise ValueError(
-                f'The AA (Ancestral allele) INFO field cannot be found in the header of {vcf}, ' +
-                'but an unfolded frequency spectrum is requested.'
-            )
+        try:
+            from cyvcf2 import VCF
+            if not VCF(vcf).contains('AA'):
+                raise ValueError(
+                    f'The AA (Ancestral allele) INFO field cannot be found in the header of {vcf}, ' +
+                    'but an unfolded frequency spectrum is requested.'
+                )
+        except ModuleNotFoundError:
+            print("Unable to load cyvcf2 and check if ancestral alleles are in provided VCF.\n"+
+                  "Generated FS may be empty if ancestral allele not found.")
 
     if subsample:
         subsample_dict = {}

dadi_cli/parsers/infer_dfe_parsers.py

@@ -1,5 +1,4 @@
 import argparse, glob, pickle, os, random, sys, time, warnings
-import work_queue as wq
 from multiprocessing import Process, Queue
 from dadi_cli.parsers.common_arguments import *
 from dadi_cli.parsers.argument_validation import *
@@ -212,6 +211,10 @@ def _run_infer_dfe(args: argparse.Namespace) -> None:
             bestfits = None
 
         if args.work_queue:
+            try:
+                import work_queue as wq
+            except ModuleNotFoundError:
+                raise ValueError("Work Queue could not be loaded.")
 
             if args.debug_wq:
                 q = wq.WorkQueue(name=args.work_queue[0], debug_log="debug.log", port=args.port)

dadi_cli/parsers/infer_dm_parsers.py

@@ -1,5 +1,4 @@
 import argparse, inspect, nlopt, os, random, sys, time, warnings
-import work_queue as wq
 from multiprocessing import Process, Queue
 from sys import exit
 from dadi_cli.parsers.common_arguments import *
@@ -191,7 +190,10 @@ def _run_infer_dm(args: argparse.Namespace) -> None:
             else:
                 global_algorithm = nlopt.GN_MLSL_LDS
             if args.work_queue:
-
+                try:
+                    import work_queue as wq
+                except ModuleNotFoundError:
+                    raise ValueError("Work Queue could not be loaded.")
                 if args.debug_wq:
                     q = wq.WorkQueue(name=args.work_queue[0], debug_log="debug.log", port=args.port)
                 else:
@@ -346,6 +348,10 @@ def _run_infer_dm(args: argparse.Namespace) -> None:
                        bestfits]
 
         if args.work_queue:
+            try:
+                import work_queue as wq
+            except ModuleNotFoundError:
+                raise ValueError("Work Queue could not be loaded.")
             if args.debug_wq:
                 q = wq.WorkQueue(name=args.work_queue[0], debug_log="debug.log", port=args.port)
             else: