Import @109242 2022.05.1

metomi · May 6, 2022 · cce4b99 · cce4b99
1 parent 50cc6cb
commit cce4b99
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Showing 15 changed files with 504 additions and 95 deletions.
diff --git a/admin/install_mule.sh b/admin/install_mule.sh
@@ -7,10 +7,10 @@
 #
 # Mule, UM packing extension and UM library installation script
 #
-# In most cases the modules can be directly installed via the usual 
-# python setuptools methods.  However in some cases this might not be 
+# In most cases the modules can be directly installed via the usual
+# python setuptools methods.  However in some cases this might not be
 # possible, so this script instead builds all modules to a dummy
-# install location in a temporary directory and then copies the 
+# install location in a temporary directory and then copies the
 # results to the chosen destinations.
 #
 set -eu
@@ -86,9 +86,9 @@ while [ $# -gt 3 ] ; do
                      SSTPERT_LIB=$1 ;;
         --wafccb_lib) shift
                      WAFCCB_LIB=$1 ;;
-        --spiral_lib)  
+        --spiral_lib)
                      SPIRAL_LIB="build" ;;
-        --ppibm_lib) 
+        --ppibm_lib)
                      PPIBM_LIB="build" ;;
         --library_lock)
                      LIBRARY_LOCK="lock" ;;
@@ -116,8 +116,13 @@ if [ -n "$PPIBM_LIB" ] ; then
     MODULE_LIST="$MODULE_LIST um_ppibm"
 fi
 
-# A few hardcoded settings
-PYTHONEXEC=${PYTHONEXEC:-python2.7}
+# Find out the version of the current interpreter, since this is what we
+# will be trying to install against
+PYTHONVER=$(python -c "from platform import python_version ; print(python_version())")
+PYTHONEXEC=python$(cut -d . -f-2 <<< $PYTHONVER)
+echo "Installing against Python $PYTHONVER"
+
+# Setup a temporary directory where the install will be initially created
 SCRATCHDIR=$(mktemp -d)
 SCRATCHLIB=$SCRATCHDIR/lib/$PYTHONEXEC/site-packages
 
@@ -129,7 +134,7 @@ if [ ! ${BIN_DEST:0:1} == "/" ] ; then
     BIN_DEST=$PWD/$BIN_DEST
 fi
 
-# Create install directores - they may already exist but should be 
+# Create install directores - they may already exist but should be
 # empty if they do, also check the modules exist in the cwd
 exit=0
 for module in $MODULE_LIST ; do
@@ -176,7 +181,7 @@ if [ -n "$WAFCCB_LIB" ] && [ ! -d $WAFCCB_LIB ] ; then
 fi
 
 # Make a temporary directory to hold the installs
-mkdir -p $SCRATCHLIB 
+mkdir -p $SCRATCHLIB
 ln -s $SCRATCHDIR/lib $SCRATCHDIR/lib64
 
 # The install command will complain if this directory isn't on the path
@@ -196,7 +201,7 @@ wc_root=$(pwd)
 # use ln -r for this or realpath but since they aren't as common as we'd
 # like let's use Python
 function pyrelpath(){
-    $PYTHONEXEC -c "import os.path; print(os.path.relpath(\"$1\",\"$2\"))"
+    python -c "import os.path; print(os.path.relpath(\"$1\",\"$2\"))"
 }
 
 # Packing library first
@@ -214,7 +219,7 @@ else
 fi
 
 echo "Building packing module..."
-$PYTHONEXEC setup.py build_ext --inplace \
+python setup.py build_ext --inplace \
    -I$SHUMLIB/include -L$SHUMLIB/lib -R$rpath
 
 # SSTPert library (if being used)
@@ -235,7 +240,7 @@ if [ -n "$SSTPERT_LIB" ] ; then
     fi
 
     echo "Building sstpert module..."
-    $PYTHONEXEC setup.py build_ext --inplace \
+    python setup.py build_ext --inplace \
         -I$SSTPERT_LIB/include \
         -L$SSTPERT_LIB/lib:$SHUMLIB/lib \
         -R$rpath
@@ -257,7 +262,7 @@ if [ -n "$WAFCCB_LIB" ] ; then
     fi
 
     echo "Building wafccb module..."
-    $PYTHONEXEC setup.py build_ext --inplace \
+    python setup.py build_ext --inplace \
         -I$WAFCCB_LIB/include \
         -L$WAFCCB_LIB/lib \
         -R$rpath
@@ -279,7 +284,7 @@ if [ -n "$SPIRAL_LIB" ] ; then
     fi
 
     echo "Building spiral search module..."
-    $PYTHONEXEC setup.py build_ext --inplace \
+    python setup.py build_ext --inplace \
         -I$SHUMLIB/include \
         -L$SHUMLIB/lib \
         -R$rpath
@@ -301,7 +306,7 @@ if [ -n "$PPIBM_LIB" ] ; then
     fi
 
     echo "Building ppibm module..."
-    $PYTHONEXEC setup.py build_ext --inplace \
+    python setup.py build_ext --inplace \
         -I$SHUMLIB/include \
         -L$SHUMLIB/lib \
         -R$rpath
@@ -316,7 +321,7 @@ function install(){
     cd $wc_root/$module
 
     echo "Installing $module module to $SCRATCHDIR"
-    $PYTHONEXEC setup.py install --prefix $SCRATCHDIR
+    python setup.py install --prefix $SCRATCHDIR
 }
 
 for module in $MODULE_LIST ; do
@@ -336,7 +341,7 @@ function unpack_and_copy(){
       unzip_dir=$SCRATCHLIB/${module}_unzipped_egg
       unzip $egg -d $unzip_dir
       egg=$unzip_dir
-    fi  
+    fi
 
     destdir=$LIB_DEST/$module
     echo "Installing $module to $destdir"
@@ -346,7 +351,7 @@ function unpack_and_copy(){
     # For the execs, also copy these to the bin directory
     if [ $module == "um_utils" ] || [ $module == "um_sstpert" ] ; then
         echo "Installing $module execs and info to $BIN_DEST/"
-        cp -vr $egg/EGG-INFO $BIN_DEST/$module.egg-info        
+        cp -vr $egg/EGG-INFO $BIN_DEST/$module.egg-info
         cp -vr $SCRATCHDIR/bin/* $BIN_DEST/
     fi
 }
@@ -364,7 +369,7 @@ function cleanup(){
     cd $wc_root/$module
 
     echo "Cleaning $module module"
-    $PYTHONEXEC setup.py clean
+    python setup.py clean
 }
 
 for module in $MODULE_LIST ; do

diff --git a/mule/LICENCE.txt b/mule/LICENCE.txt
@@ -1,5 +1,5 @@
 !-------------------------------------------------------------------------------!
-! (C) Crown Copyright 2020, Met Office. All rights reserved.                    !
+! (C) Crown Copyright 2022, Met Office. All rights reserved.                    !
 !                                                                               !
 ! Redistribution and use in source and binary forms, with or without            !
 ! modification, are permitted provided that the following conditions are met:   !

diff --git a/mule/docs/source/conf.py b/mule/docs/source/conf.py
@@ -48,16 +48,16 @@
 
 # General information about the project.
 project = u'Mule'
-copyright = u'2020, UM Systems Team'
+copyright = u'2022, UM Systems Team'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '2020.01.1'
+version = '2022.05.1'
 # The full version, including alpha/beta/rc tags.
-release = '2020.01.1'
+release = '2022.05.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/mule/lib/mule/__init__.py b/mule/lib/mule/__init__.py
@@ -57,7 +57,7 @@
 from contextlib import contextmanager
 from mule.stashmaster import STASHmaster
 
-__version__ = "2020.01.1"
+__version__ = "2022.05.1"
 
 # UM fixed length header names and positions
 _UM_FIXED_LENGTH_HEADER = [

diff --git a/mule/lib/mule/packing.py b/mule/lib/mule/packing.py
@@ -156,7 +156,8 @@ def _wgdos_pack_field(data, mdi, acc):
                     packed byte data.
 
             """
-            data_bytes = mo_pack.compress_wgdos(data.astype("f4"), acc, mdi)
+            data_buffer = mo_pack.compress_wgdos(data.astype("f4"), acc, mdi)
+            data_bytes = data_buffer.tobytes()
             return data_bytes
 
     except ImportError as err:

diff --git a/um_packing/setup.py b/um_packing/setup.py
@@ -49,26 +49,23 @@ def run(self):
                 elif os.path.isdir(cleanpath[0]):
                     shutil.rmtree(cleanpath[0])
 
+
 setuptools.setup(
     name='um_packing',
-    version='2020.01.1',
+    version='2022.05.1',
     description='Unified Model packing library extension',
     author='UM Systems Team',
     url='https://code.metoffice.gov.uk/trac/um',
     cmdclass={'clean': CleanCommand},
     package_dir={'': 'lib'},
     packages=['um_packing',
               'um_packing.tests'],
-    features={
-        'packing': setuptools.Feature(
-            "SHUMlib Packing library",
-            standard=True,
-            ext_modules=[
-                setuptools.Extension(
-                    'um_packing.um_packing',
-                    ['lib/um_packing/um_packing.c'],
-                    include_dirs=[np.get_include()],
-                    libraries=["shum_byteswap",
-                               "shum_wgdos_packing",
-                               "shum_string_conv",
-                               "shum_constants"])])})
+    ext_modules=[
+        setuptools.Extension(
+            'um_packing.um_packing',
+            ['lib/um_packing/um_packing.c'],
+            include_dirs=[np.get_include()],
+            libraries=["shum_byteswap",
+                       "shum_wgdos_packing",
+                       "shum_string_conv",
+                       "shum_constants"])])
diff --git a/um_ppibm/setup.py b/um_ppibm/setup.py
@@ -52,22 +52,18 @@ def run(self):
 
 setuptools.setup(
     name='um_ppibm',
-    version='2020.01.1',
+    version='2022.05.1',
     description='Unified Model pp conversion utility with IBM number format',
     author='UM Systems Team',
     url='https://code.metoffice.gov.uk/trac/um',
     cmdclass={'clean': CleanCommand},
     package_dir={'': 'lib'},
     packages=['um_ppibm', ],
-    features={
-        'ieee2ibm32': setuptools.Feature(
-            "SHUMlib IBM conversion routine",
-            standard=True,
-            ext_modules=[
-                setuptools.Extension(
-                    'um_ppibm.um_ieee2ibm32',
-                    ['lib/um_ppibm/um_ieee2ibm32.c'],
-                    include_dirs=[np.get_include()],
-                    libraries=["shum_string_conv",
-                               "shum_byteswap",
-                               "shum_data_conv"])])})
+    ext_modules=[
+        setuptools.Extension(
+            'um_ppibm.um_ieee2ibm32',
+            ['lib/um_ppibm/um_ieee2ibm32.c'],
+            include_dirs=[np.get_include()],
+            libraries=["shum_string_conv",
+                       "shum_byteswap",
+                       "shum_data_conv"])])
diff --git a/um_spiral_search/setup.py b/um_spiral_search/setup.py
@@ -49,26 +49,23 @@ def run(self):
                 elif os.path.isdir(cleanpath[0]):
                     shutil.rmtree(cleanpath[0])
 
+
 setuptools.setup(
     name='um_spiral_search',
-    version='2020.01.1',
+    version='2022.05.1',
     description='Unified Model Spiral Search extension',
     author='UM Systems Team',
     url='https://code.metoffice.gov.uk/trac/um',
     cmdclass={'clean': CleanCommand},
     package_dir={'': 'lib'},
     packages=['um_spiral_search',
               'um_spiral_search.tests'],
-    features={
-        'spiralsearch': setuptools.Feature(
-            "UM Spiral Search library",
-            standard=True,
-            ext_modules=[
-                setuptools.Extension(
-                    'um_spiral_search.um_spiral_search',
-                    ['lib/um_spiral_search/um_spiral_search.c'],
-                    include_dirs=[np.get_include()],
-                    libraries=["shum_spiral_search",
-                               "shum_string_conv",
-                               "shum_constants"])
-                ])})
+    ext_modules=[
+        setuptools.Extension(
+            'um_spiral_search.um_spiral_search',
+            ['lib/um_spiral_search/um_spiral_search.c'],
+            include_dirs=[np.get_include()],
+            libraries=["shum_spiral_search",
+                       "shum_string_conv",
+                       "shum_constants"])
+        ])
diff --git a/um_sstpert/setup.py b/um_sstpert/setup.py
@@ -49,28 +49,24 @@ def run(self):
                 elif os.path.isdir(cleanpath[0]):
                     shutil.rmtree(cleanpath[0])
 
+
 setuptools.setup(
     name='um_sstpert',
-    version='2020.01.1',
+    version='2022.05.1',
     description='Unified Model SST-perturbation extension and utility',
     author='UM Systems Team',
     url='https://code.metoffice.gov.uk/trac/um',
     cmdclass={'clean': CleanCommand},
     package_dir={'': 'lib'},
     packages=['um_sstpert'],
-    features={
-        'sstpert': setuptools.Feature(
-            "UM SST-pert library (requires UM Licence)",
-            standard=True,
-            ext_modules=[
-                setuptools.Extension(
-                    'um_sstpert.um_sstpert',
-                    ['lib/um_sstpert/um_sstpert.c'],
-                    include_dirs=[np.get_include()],
-                    libraries=["um_sstpert",
-                               "shum_string_conv",
-                               "shum_constants"])
-                ])},
+    ext_modules=[
+        setuptools.Extension(
+            'um_sstpert.um_sstpert',
+            ['lib/um_sstpert/um_sstpert.c'],
+            include_dirs=[np.get_include()],
+            libraries=["um_sstpert",
+                       "shum_string_conv",
+                       "shum_constants"])],
     entry_points={
         'console_scripts': [
             'mule-sstpert = um_sstpert:_main',

diff --git a/um_utils/docs/source/index.rst b/um_utils/docs/source/index.rst
@@ -20,11 +20,11 @@ This is the documentation for the UM utilities, which use the Mule API.
    um_utils/version
    um_utils/unpack
    um_utils/convpp
+   um_utils/editmask
 
 Indices and tables
 ==================
 
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
-