MAINT: Updates for python 3.6 (#58)

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "vendor/sepp-refs"]
+	path = vendor/sepp-refs
+	url = https://github.com/smirarab/sepp-refs.git

ci/recipe/build.sh

@@ -0,0 +1,34 @@
+#!/bin/sh
+
+set -e
+set -x
+
+# extract Silva reference files
+tar xjvf vendor/sepp-refs/silva/sepp-package-silva.tar.bz sepp-package-silva/ref/
+tar xjvf vendor/sepp-refs/silva/sepp-package-silva-2.tar.bz sepp-package-silva/ref/
+tar xjvf vendor/sepp-refs/gg/sepp-package.tar.bz sepp-package/
+
+mv sepp-package-silva/ref/reference-99_otus_aligned_masked1977.fasta-rooted.tre sepp-package/ref/silva12.8_99otus_aligned_masked1977.tre
+mv sepp-package-silva/ref/RAxML_info.99_otus_aligned_masked1977.fasta           sepp-package/ref/silva12.8_99otus_aligned_masked1977.info
+mv sepp-package-silva/ref/99_otus_aligned_masked1977.fasta                      sepp-package/ref/silva12.8_99otus_aligned_masked1977.fasta
+
+if [ "$(uname)" == "Darwin" ]; then
+    rm -rf sepp-package/sepp/tools/bundled/Linux
+fi
+
+# we have an indent error in one of the sepp python source files, which gets fixed here
+patch sepp-package/sepp/sepp/algorithm.py < indent.patch
+
+# change DIR in SEPP wrapper to be relocatable
+patch sepp-package/run-sepp.sh < reloc.patch
+mkdir -p $PREFIX/share/
+mv sepp-package $PREFIX/share/fragment-insertion
+
+# configure SEPP
+cd $PREFIX/share/fragment-insertion/sepp/ && python setup.py config -c ; cd -
+# move SEPP binary into PREFIX/bin and update reference location
+mkdir -p $PREFIX/bin/
+mv $PREFIX/share/fragment-insertion/run-sepp.sh $PREFIX/bin
+cp `cat $PREFIX/share/fragment-insertion/sepp/.sepp/main.config | grep "^path" -m 1 | cut -d "=" -f 2 | xargs dirname`/* $PREFIX/bin/
+
+cp taxonomy_gg99.qza $PREFIX/share/fragment-insertion/ref/ && make install

ci/recipe/conda_build_config.yaml

@@ -0,0 +1,2 @@
+python:
+  - 3.6

ci/recipe/indent.patch

@@ -0,0 +1,11 @@
+--- algorithm.py	2018-06-19 14:19:06.000000000 -0700
++++ algorithm.py.fixindent	2018-06-19 23:59:22.910273892 -0700
+@@ -259,7 +259,7 @@
+                 "ut fragments and re-start. Duplicate names are:\n  '%s'") %
+                 (len(ids_overlap), "'\n  '".join(ids_overlap)))
+
+-       for (k,v) in extra_frags.items():
++        for (k,v) in extra_frags.items():
+             self.root_problem.fragments[k] = v.replace("-","")
+         alg_chunks = self.root_problem.fragments.divide_to_equal_chunks(chunks, max_chunk_size)        
+         ret = []

ci/recipe/meta.yaml

@@ -7,22 +7,21 @@ package:
   version: {{ version }}
 
 source:
-  path: ../..
-
-build:
-  script: cp taxonomy_gg99.qza $PREFIX/share/fragment-insertion/ref/ && make install
+  - path: ../..
+  # Not using the built-in patching mechanism of conda-build, since we aren't
+  # actually patching q2-fragment-insertion, but rather sepp-refs.
+  - path: reloc.patch
+  - path: indent.patch
 
 requirements:
   build:
-    - python 3.5*
+    - python {{ python }}
     - setuptools
-    # Need this in build so that the ref path above exists
-    - fragment-insertion >=4.3.5
+    - java-jdk
 
   run:
-    - python 3.5*
-    - setuptools
-    - fragment-insertion >=4.3.5
+    - python {{ python }}
+    - java-jdk
     - biom-format >=2.1.5,<2.2.0
     - qiime2 {{ release }}.*
     - q2-types {{ release }}.*

ci/recipe/reloc.patch

@@ -0,0 +1,11 @@
+--- run-sepp.sh	2018-06-19 14:19:06.000000000 -0700
++++ run-sepp.sh.reloc	2018-06-20 00:01:16.570464485 -0700
+@@ -107,7 +107,7 @@
+ done
+
+
+-DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
++DIR=/opt/anaconda1anaconda2anaconda3/share/fragment-insertion/
+
+ # Reference tree
+ if [ -z $t ]; then

ci/recipe/run_test.sh

@@ -0,0 +1,9 @@
+#!/bin/sh
+
+set -x
+set -e
+
+# test if new Silva reference files are copied to the right location
+ls $PREFIX/share/fragment-insertion/ref/silva12.8_99otus_aligned_masked1977.tre
+ls $PREFIX/share/fragment-insertion/ref/silva12.8_99otus_aligned_masked1977.info
+ls $PREFIX/share/fragment-insertion/ref/silva12.8_99otus_aligned_masked1977.fasta