Fix process substitutions

.github/workflows/python-package-conda.yml → .github/workflows/ci.yml

@@ -21,6 +21,6 @@ jobs:
     - name: Install dependencies
       run: |
         conda env update --file environment.yml --name base
-    - name: Test with pytest
+    - name: Run all tests
       run: |
-        make tests
+        make test

attotree/attotree.py

@@ -273,6 +273,14 @@ def attotree(fns, newick_fo, k, s, t, phylogeny_algorithm, fof):
         phylip2_fn = os.path.join(d, "distances.phylip")
         newick1_fn = os.path.join(d, "tree.nw")
         newick2_fo = newick_fo
+        if fof:
+            #This is to make the list of file pass to Mash even with
+            #process substitutions
+            old_fof_fn = fns[0]
+            new_fof_fn = os.path.join(d, "fof.txt")
+            with open(old_fof_fn) as f, open(new_fof_fn, 'w') as g:
+                g.write(f.read())
+            fns = [new_fof_fn]
         mash_triangle(fns, phylip1_fn, k=k, s=s, t=t, fof=fof)
         postprocess_mash_phylip(phylip1_fn, phylip2_fn)
         quicktree(phylip2_fn, newick1_fn, algorithm=phylogeny_algorithm)

tests/02_simple_tree/Makefile

@@ -12,9 +12,11 @@ FASTAS=$(shell tar -tf test_spneumo.tar.xz)
 ## Compare trees ##
 ###################
 
-all: tree.default.nw tree.file_list.nw tree.precomputed.newick
-	diff tree.default.nw tree.precomputed.newick
-	diff tree.file_list.nw tree.precomputed.newick
+all: tree.precomputed.newick tree.default.nw tree.file_list.nw tree.file_list_proc_subst.nw
+	for x in $^; do \
+		2>&1 echo Testing "$$x"; \
+		diff $$x tree.precomputed.newick; \
+	done
 
 ###################################
 # Different ways to compute trees #
@@ -28,6 +30,10 @@ tree.file_list.nw: file_list.txt
 	../../attotree/attotree.py -L "$<"  > "$@.tmp"
 	mv "$@.tmp" "$@"
 
+tree.file_list_proc_subst.nw: file_list.txt
+	../../attotree/attotree.py -L <(head -n 99999 "$<")  > "$@.tmp"
+	mv "$@.tmp" "$@"
+
 tree.precomputed.newick: tree.default.nw
 	cp $< $@