Address codefactor complaints (lanl#135)

* Address some codefactor complaints * Disable redefined built-in warning for ord * Skip test if no internet connection * Add note on change in jaxlib/jax versions * Resolve lanl#133
Sibgatulin · Dec 15, 2021 · 0fbc4b9 · 0fbc4b9
1 parent 593e9c2
commit 0fbc4b9
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Showing 43 changed files with 471 additions and 524 deletions.
diff --git a/.github/isbin.sh b/.github/isbin.sh
@@ -16,7 +16,7 @@ for f in $@; do
 	exit 1
     fi
     charset=$(file -b --mime $f | sed -e 's/.*charset=//')
-    if [ ! -L "$f" -a "$charset" = "binary" ]; then
+    if [ ! -L "$f" ] && [ "$charset" = "binary" ]; then
     echo "binary files cannot be commited to the repository"
     echo "raw data and ipynb files should go in scico-data"
 	exit 2

diff --git a/CHANGES.rst b/CHANGES.rst
@@ -8,6 +8,7 @@ Version 0.0.2   (unreleased)
 
 • Additional optimization algorithms: Linearized ADMM and PDHG.
 • Move optimization algorithms into ``optimize`` subpackage.
+• Bump pinned `jaxlib` and `jax` versions to 0.1.70 and 0.2.19 respectively.
 
 
 Version 0.0.1   (2021-11-24)

diff --git a/docs/source/_static/scico.css b/docs/source/_static/scico.css
@@ -61,15 +61,15 @@ dl.citation {
 
 dl.citation > dt {
   background-color: #ffffff !important;
-  border-top: 0px !important;
-  margin: 0 0 0 0 !important;
+  border-top: 0 !important;
+  margin: 0 !important;
   grid-column-start: 1;
   width: 2em;
 }
 
 dl.citation > dd {
-  padding-bottom: 0px !important;
-  margin-bottom: 0px !important;
+  padding-bottom: 0 !important;
+  margin-bottom: 0 !important;
   margin-left: 5px !important;
   grid-column-start: 2;
 }

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -312,8 +312,7 @@ def patched_parse(self):
 
 
 if on_rtd:
-    print("Building on ReadTheDocs")
-    print
+    print("Building on ReadTheDocs\n")
     print("Current working directory: {}".format(os.path.abspath(os.curdir)))
     import numpy as np
 

diff --git a/docs/source/docutil.py b/docs/source/docutil.py
@@ -43,7 +43,7 @@ def package_classes(package):
                 # Get internal module name of class for comparison with working module name
                 try:
                     objmodname = getattr(sys.modules[modname], obj.__name__).__module__
-                except:
+                except Exception:
                     objmodname = None
                 if objmodname == modname:
                     classes.append(modname + "." + obj.__name__)
@@ -80,8 +80,9 @@ def insert_inheritance_diagram(clsqname):
     if not lines:
         return
     # Cut leading whitespace lines
-    for n in range(len(lines)):
-        if lines[n] != "":
+    n = 0
+    for n, line in enumerate(lines):
+        if line != "":
             break
     lines = lines[n:]
     # Define inheritance diagram insertion text

diff --git a/examples/makenotebooks.py b/examples/makenotebooks.py
@@ -11,7 +11,6 @@
 import argparse
 import os
 import re
-import sys
 from pathlib import Path
 from timeit import default_timer as timer
 
@@ -88,8 +87,8 @@ def py_file_to_string(src):
 def script_to_notebook(src, dst):
     """Convert a Python example script into a Jupyter notebook."""
 
-    str = py_file_to_string(src)
-    nb = py_string_to_notebook(str)
+    s = py_file_to_string(src)
+    nb = py_string_to_notebook(s)
     write_notebook(nb, dst)
 
 

diff --git a/examples/scriptcheck.sh b/examples/scriptcheck.sh
@@ -5,7 +5,7 @@
 # Currently only supported under Linux.
 
 # Check for presence of Xvfb tool which is used to avoid plots being displayed.
-if [ ! "`which Xvfb 2>/dev/null`" ]; then
+if [ ! "$(which Xvfb 2>/dev/null)" ]; then
     msg="Warning: required tool Xvfb not found: functionality will be degraded"
     echo $msg >&2
     pid=0
@@ -17,7 +17,7 @@ fi
 
 # Set environment variables and paths. This script is assumed to be run
 # from its root directory.
-export PYTHONPATH=`(cd .. && pwd)`
+export PYTHONPATH=$((cd .. && pwd))
 export PYTHONIOENCODING=utf-8
 d='/tmp/scriptcheck_'$$
 mkdir -p $d
@@ -41,14 +41,15 @@ for f in scripts/*.py; do
 
     # Create temporary copy of script with all algorithm maxiter values set
     # to small number and final input statements commented out.
-    g=$d/`basename $f`
+    g=$d/$(basename $f)
     sed -E -e "$re1$re2$re3" $f > $g
 
     # Run temporary script.
     python $g > /dev/null 2>&1
 
-    # Print status message.
-    if [ $? = 0 ]; then
+    # Run temporary script and print status message.
+    if python $g > /dev/null 2>&1
+    then
 	printf "%-50s %s\n" $f succeeded
     else
 	printf "%-50s %s\n" $f FAILED

diff --git a/misc/conda/install_conda.sh b/misc/conda/install_conda.sh
@@ -8,7 +8,7 @@ URLROOT=https://repo.continuum.io/miniconda/
 INSTLINUX=Miniconda3-latest-Linux-x86_64.sh
 INSTMACOSX=Miniconda3-latest-MacOSX-x86_64.sh
 
-SCRIPT=`basename $0`
+SCRIPT=$(basename $0)
 USAGE=$(cat <<-EOF
 Usage: $SCRIPT [-h] [-y] install_path
           [-h] Display usage information
@@ -36,32 +36,32 @@ if [ ! $# -eq 1 ] ; then
     exit 1
 fi
 
-OS=`uname -a | cut -d ' ' -f 1`
+OS=$(uname -a | cut -d ' ' -f 1)
 case "$OS" in
     Linux)    SOURCEURL=$URLROOT$INSTLINUX;;
     Darwin)   SOURCEURL=$URLROOT$INSTMACOSX;;
     *)        echo "Error: unsupported operating system $OS" >&2; exit 2;;
 esac
 
-if [ ! "`which wget 2>/dev/null`" ]; then
+if [ ! "$(which wget 2>/dev/null)" ]; then
     has_wget=0
 else
     has_wget=1
 fi
 
-if [ ! "`which curl 2>/dev/null`" ]; then
+if [ ! "$(which curl 2>/dev/null)" ]; then
     has_curl=0
 else
     has_curl=1
 fi
 
-if [ $has_curl -eq 0 -a $has_wget -eq 0 ]; then
+if [ $has_curl -eq 0 ] && [ $has_wget -eq 0 ]; then
     echo "Error: neither curl nor wget found; at least one required" >&2
     exit 3
 fi
 
 INSTALLROOT=$1
-if [ ! -d "$INSTALLROOT" -o ! -w "$INSTALLROOT" ]; then
+if [ ! -d "$INSTALLROOT" ] || [ ! -w "$INSTALLROOT" ]; then
     echo "Error: installation root path \"$INSTALLROOT\" is not a directory "\
 	 "or is not writable"  >&2
     exit 4
@@ -77,7 +77,7 @@ fi
 if [ "$AGREE" == "no" ]; then
     read -r -p "Confirm conda installation in root path $INSTALLROOT [y/N] "\
 	 CNFRM
-    if [ "$CNFRM" != 'y' -a "$CNFRM" != 'Y' ]; then
+    if [ "$CNFRM" != 'y' ] && [ "$CNFRM" != 'Y' ]; then
 	echo "Cancelling installation"
 	exit 6
     fi

diff --git a/misc/conda/make_conda_env.sh b/misc/conda/make_conda_env.sh
@@ -14,7 +14,7 @@
 # Run with -h flag for usage information
 set -e  # exit when any command fails
 
-SCRIPT=`basename $0`
+SCRIPT=$(basename $0)
 USAGE=$(cat <<-EOF
 Usage: $SCRIPT [-h] [-y] [-g] [-p python_version] [-c cuda_version]
        [-e env_name] [-j jaxlib_url]
@@ -34,7 +34,7 @@ GPU=no
 CUVER=""
 JLVER="0.1.71"
 PYVER="3.8"
-ENVNM=py`echo $PYVER | sed -e 's/\.//g'`
+ENVNM=py$(echo $PYVER | sed -e 's/\.//g')
 
 # Project requirements files
 REQUIRE=$(cat <<-EOF
@@ -54,31 +54,29 @@ EOF
 
 OPTIND=1
 while getopts ":hygc:p:e:j:" opt; do
-  case $opt in
-      c|p|e|j) if [ -z "$OPTARG" -o "${OPTARG:0:1}" = "-" ] ; then
-           echo "Error: option -$opt requires an argument" >&2
+    case $opt in
+	c|p|e|j) if [ -z "$OPTARG" ] || [ "${OPTARG:0:1}" = "-" ] ; then
+		     echo "Error: option -$opt requires an argument" >&2
+		     echo "$USAGE" >&2
+		     exit 1
+		 fi
+		 ;;&
+	h) echo "$USAGE"; exit 0;;
+	y) AGREE=yes;;
+	g) GPU=yes;;
+	c) CUVER=$OPTARG;;
+	p) PYVER=$OPTARG;;
+	e) ENVNM=$OPTARG;;
+	j) JAXURL=$OPTARG;;
+	:) echo "Error: option -$OPTARG requires an argument" >&2
 	   echo "$USAGE" >&2
-           exit 1
-       fi
+	   exit 1
+	   ;;
+	\?) echo "Error: invalid option -$OPTARG" >&2
+	    echo "$USAGE" >&2
+	    exit 1
+	    ;;
   esac
-  case $opt in
-    h) echo "$USAGE"; exit 0;;
-    y) AGREE=yes;;
-    g) GPU=yes;;
-    c) CUVER=$OPTARG;;
-    p) PYVER=$OPTARG;;
-    e) ENVNM=$OPTARG;;
-    j) JAXURL=$OPTARG;;
-    :) echo "Error: option -$OPTARG requires an argument" >&2
-       echo "$USAGE" >&2
-       exit 1
-       ;;
-   \?) echo "Error: invalid option -$OPTARG" >&2
-       echo "$USAGE" >&2
-       exit 1
-       ;;
-  esac
-
 done
 
 shift $((OPTIND-1))
@@ -88,46 +86,46 @@ if [ ! $# -eq 0 ] ; then
     exit 1
 fi
 
-if [ ! "`which conda 2>/dev/null`" ]; then
+if [ ! "$(which conda 2>/dev/null)" ]; then
     echo "Error: conda command required but not found" >&2
     exit 2
 fi
 
 # Not available on BSD systems such as OSX: install via MacPorts etc.
-if [ ! "`which realpath 2>/dev/null`" ]; then
+if [ ! "$(which realpath 2>/dev/null)" ]; then
     echo "Error: realpath command required but not found" >&2
     exit 3
 fi
 
-OS=`uname -a | cut -d ' ' -f 1`
+OS=$(uname -a | cut -d ' ' -f 1)
 case "$OS" in
-    Linux)    SOURCEURL=$URLROOT$INSTLINUX; SED=sed;;
-    Darwin)   SOURCEURL=$URLROOT$INSTMACOSX; SED=gsed;;
+    Linux)    SOURCEURL=$URLROOT$INSTLINUX; SED="sed";;
+    Darwin)   SOURCEURL=$URLROOT$INSTMACOSX; SED="gsed";;
     *)        echo "Error: unsupported operating system $OS" >&2; exit 4;;
 esac
-if [ "$OS" == "Darwin" -a "$GPU" == yes ]; then
+if [ "$OS" == "Darwin" ] && [ "$GPU" == yes ]; then
     echo "Error: GPU-enabled jaxlib installation not supported under OSX" >&2
     exit 5
 fi
 if [ "$OS" == "Darwin" ]; then
-    if [ ! "`which gsed 2>/dev/null`" ]; then
+    if [ ! "$(which gsed 2>/dev/null)" ]; then
 	echo "Error: gsed command required but not found" >&2
 	exit 6
     fi
 fi
 
-if [ "$GPU" == "yes" -a "$CUVER" == "" ]; then
-    if [ "`which nvcc`" == "" ]; then
+if [ "$GPU" == "yes" ] && [ "$CUVER" == "" ]; then
+    if [ "$(which nvcc)" == "" ]; then
 	echo "Error: GPU-enabled jaxlib requested but CUDA version not"\
 	     "specified and could not be automatically determined" >&2
 	exit 7
     else
-	CUVER=`nvcc --version | grep -o 'release [0-9][0-9]*\.[[0-9][0-9]*' \
-                              | sed -e 's/release //' -e 's/\.//'`
+	CUVER=$(nvcc --version | grep -o 'release [0-9][0-9]*\.[[0-9][0-9]*' \
+                              | sed -e 's/release //' -e 's/\.//')
     fi
 fi
 
-CONDAHOME=`conda info --base`
+CONDAHOME=$(conda info --base)
 ENVDIR=$CONDAHOME/envs/$ENVNM
 if [ -d "$ENVDIR" ]; then
     echo "Error: environment $ENVNM already exists"
@@ -138,7 +136,7 @@ if [ "$AGREE" == "no" ]; then
     RSTR="Confirm creation of conda environment $ENVNM with Python $PYVER"
     RSTR="$RSTR [y/N] "
     read -r -p "$RSTR" CNFRM
-    if [ "$CNFRM" != 'y' -a "$CNFRM" != 'Y' ]; then
+    if [ "$CNFRM" != 'y' ] && [ "$CNFRM" != 'Y' ]; then
 	echo "Cancelling environment creation"
 	exit 9
     fi
@@ -201,7 +199,7 @@ conda install $CONDA_FLAGS $CONDAREQ ipython
 # Utility ffmpeg is required by imageio for reading mp4 video files
 # it can also be installed via the system package manager, .e.g.
 #    sudo apt install ffmpeg
-if [ "`which ffmpeg`" = '' ]; then
+if [ "$(which ffmpeg)" = '' ]; then
     conda install $CONDA_FLAGS ffmpeg
 fi