Merge pull request #437 from peterjc/read_json_stringio_report

Passing a string to pd.read_json is deprecated

docs/api/conf.py

@@ -17,9 +17,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'pyani'
-copyright = '2019, Author'
-author = 'Author'
+project = "pyani"
+copyright = "2019, Author"
+author = "Author"
 
 
 # -- General configuration ---------------------------------------------------
@@ -28,38 +28,38 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.todo',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.todo",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = 'en'
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "alabaster"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 
 # -- Extension configuration -------------------------------------------------

pyani/run_sge.py

@@ -74,7 +74,7 @@ def build_joblist(jobgraph) -> List:
     :param jobgraph:
     """
     logger = logging.getLogger(__name__)
-    
+
     jobset = set()  # type: Set
     for job in jobgraph:
         jobset = populate_jobset(job, jobset, depth=1)
@@ -136,8 +136,7 @@ def run_dependency_graph(
     logger = logging.getLogger(__name__)
 
     logger.debug("Received jobgraph with %d jobs", len(jobgraph))
-
-
+
     jobs_main = []  # Can be run first, before deps
     jobs_deps = []  # Depend on the main jobs
 
@@ -273,7 +272,7 @@ def submit_safe_jobs(
     """
     logger = logging.getLogger(__name__)
     logger.debug("Received %s jobs", len(jobs))
-    
+
     # Loop over each job, constructing SGE command-line based on job settings
     for job in jobs:
         job.out = root_dir / "stdout"

pyani/scripts/subcommands/subcmd_report.py

@@ -44,6 +44,7 @@
 
 from argparse import Namespace
 from typing import List, NamedTuple
+from io import StringIO
 from pathlib import Path
 
 import pandas as pd
@@ -300,7 +301,7 @@ def subcmd_report(args: Namespace) -> int:
                 ]
             ]:
                 logger.debug("Writing %s results", matdata.name)
-                matrix = pd.read_json(matdata.data)
+                matrix = pd.read_json(StringIO(matdata.data))
                 # Matrix rows and columns are labelled if there's a label dictionary,
                 # and take the dataframe index otherwise
                 matrix = label_results_matrix(matrix, matlabel_dict)