Merge pull request #96 from picrust/2.2.0

2.2.0

.gitignore

@@ -7,5 +7,5 @@ testing_datasets/
 .pytest_cache/
 picrust2/default_files/prokaryotic/untracked/
 example_files/old/
-tests/test_data/pathway_pipeline/per_seq_contrib_input/humann2_run/humann2_raw_output
 picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna.COPY
+tests/test_data/pathway_pipeline/per_seq_contrib/humann2_run/*

picrust2-env.yaml

@@ -7,19 +7,19 @@ channels:
 - defaults
 
 dependencies:
-- biom-format=2.1.7
+- biom-format >=2.1.7
 - epa-ng=0.3.5
-- gappa=0.2.0
+- gappa=0.4.0
 - glpk=4.65
-- h5py=2.9.0
+- h5py >=2.9.0
 - hmmer=3.2.1
-- jinja2=2.10.1
-- joblib=0.13.1
-- numpy=1.16.3
-- pandas=0.24.2
-- pytest=4.4.1
-- pytest-cov=2.6.1
+- jinja2 >=2.10.1
+- joblib >=0.13.1
+- numpy >=1.16.2
+- pandas >=0.24.2
+- pytest >=4.4.1
+- pytest-cov >=2.6.1
 - python >=3.5,<3.7
-- r-base=3.5.1
-- r-castor=1.3.6
-- scipy=1.2.1
+- r-base >=3.5.1
+- r-castor=1.4.1
+- scipy >=1.2.1

picrust2/Rscripts/castor_hsp.R

@@ -112,6 +112,7 @@ trait_values <- rbind(trait_values, unknown_df)
 
 # Remove unknown_df object from memory.
 remove(unknown_df)
+gc()
 
 # Order this combined trait table by the order of tips in the tree.
 trait_values <- trait_values[full_tree$tip.label, , drop=FALSE]
@@ -147,6 +148,7 @@ if (hsp_method == "pic" | hsp_method == "scp" | hsp_method == "subtree_average")
 
   # Remove raw predict_out object from memory.
   remove(predict_out)
+  gc()
 
 } else if(hsp_method == "emp_prob" | hsp_method == "mp") {
 

picrust2/__init__.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 __author__ = "The PICRUSt Development Team"
-__copyright__ = "Copyright 2018, PICRUSt Project"
+__copyright__ = "Copyright 2018-2019, PICRUSt Project"
 __license__ = "GPL"
 __url__ = "https://github.com/picrust/picrust2"
-__version__ = "2.1.4-b"
+__version__ = "2.2.0-b"

picrust2/default.py

@@ -2,12 +2,10 @@
 
 __copyright__ = "Copyright 2018-2019, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.1.4-b"
+__version__ = "2.2.0-b"
 
 from os import path
 
-# Default support files packaged with PICRUSt2.
-
 project_dir = path.dirname(path.abspath(__file__))
 
 default_ref_dir = path.join(project_dir, "default_files", "prokaryotic",
@@ -29,9 +27,8 @@
                                 "pathway_mapfiles",
                                 "metacyc_path2rxn_struc_filt_pro.txt")
 
-fungi_pathway_map = path.join(project_dir, "default_files",
-                                           "pathway_mapfiles",
-                                           "metacyc_path2rxn_struc_filt_fungi.txt")
+fungi_pathway_map = path.join(project_dir, "default_files", "pathway_mapfiles",
+                              "metacyc_path2rxn_struc_filt_fungi.txt")
 
 # Inititalize default trait table files for hsp.py.
 prokaryotic_dir = path.join(project_dir, "default_files", "prokaryotic")
@@ -54,7 +51,8 @@
 # Initialize default mapfiles to be used with add_descriptions.py
 map_dir = path.join(project_dir, "default_files", "description_mapfiles")
 
-default_map =    {"METACYC": path.join(map_dir, "metacyc_pathways_info_prokaryotes.txt.gz"),
+default_map = {"METACYC": path.join(map_dir,
+                                "metacyc_pathways_info.txt.gz"),
 
                   "COG": path.join(map_dir, "cog_info.tsv.gz"),
 
@@ -65,4 +63,3 @@
                   "PFAM": path.join(map_dir, "pfam_info.tsv.gz"),
 
                   "TIGRFAM": path.join(map_dir, "tigrfam_info.tsv.gz")}
-