From ed183a50fe6757c52770f03f9d10ddf1fef4fabd Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Tue, 8 Oct 2024 15:00:36 +0100 Subject: [PATCH 1/2] Passing a string to pd.read_json is deprecated This was fixed in subcmd_plot.py during #425 --- pyani/scripts/subcommands/subcmd_report.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pyani/scripts/subcommands/subcmd_report.py b/pyani/scripts/subcommands/subcmd_report.py index f62aecbe..2d6378a1 100644 --- a/pyani/scripts/subcommands/subcmd_report.py +++ b/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) From 42b3c01929c13fd4e0d1cc0473c5b1be37a25772 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Tue, 8 Oct 2024 15:05:44 +0100 Subject: [PATCH 2/2] Ran black via pre-commit setup --- docs/api/conf.py | 22 +++++++++++----------- pyani/run_sge.py | 7 +++---- 2 files changed, 14 insertions(+), 15 deletions(-) diff --git a/docs/api/conf.py b/docs/api/conf.py index fbdccbe5..adfb7c71 100644 --- a/docs/api/conf.py +++ b/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 --------------------------------------------------- @@ -28,25 +28,25 @@ # 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 ------------------------------------------------- @@ -54,12 +54,12 @@ # 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 ------------------------------------------------- diff --git a/pyani/run_sge.py b/pyani/run_sge.py index 4473756a..8c14ba05 100644 --- a/pyani/run_sge.py +++ b/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"