koronascript 0.1__tar.gz → 0.2.1__tar.gz

{koronascript-0.1 → koronascript-0.2.1}/KoronaScript/KoronaModule.py

@@ -27,11 +27,11 @@ class KoronaModule():
         self._name = name
         self._config = {}
         # Add defaults
-        for k,v in modules_spec[name].items():
+        for k, v in modules_spec[name].items():
             self._config[k] = v
 
         for k in parameters:
-            if k != 'Active' and not k in modules_spec[name]:
+            if k != 'Active' and k not in modules_spec[name]:
                 print(f'Parameter "{k}" not valid for Korona module "{name}" - aborting')
                 exit(-1)
             self._config[k] = parameters[k]
@@ -45,18 +45,18 @@ class KoronaModule():
         for k in self._config:
             if self._config[k] is None:
                 res += f'      <parameter name="{k}"/>\n'
-            elif isinstance(self._config[k],list):
+            elif isinstance(self._config[k], list):
                 res += f'      <parameter name="{k}">'
                 for v in self._config[k]:
-                    res += str(v)+','
-                res = res[:-1] # remove last comma
+                    res += str(v) + ','
+                res = res[:-1]  # remove last comma
                 res += '</parameter>\n'
-            elif isinstance(self._config[k],dict):
+            elif isinstance(self._config[k], dict):
                 res += f'      <parameter name="{k}">\n'
                 # Should maybe call recursively?  Can they be lists or dicts?
-                for key,val in self._config[k].items():
+                for key, val in self._config[k].items():
                     res += f'       <parameter name="{key}">{val}</parameter>\n'
-                res +=  '      </parameter>\n'
+                res += '      </parameter>\n'
             else:
                 res += (f'      <parameter name="{k}">{self._config[k]}</parameter>\n')
         res += ('    </parameters>\n')

{koronascript-0.1 → koronascript-0.2.1}/KoronaScript/Modules.py

@@ -1,6 +1,6 @@
 # Auto-generated, do not edit directly
 # see genmodule.py
-from .Configuration import modules_spec
+
 from .KoronaModule import KoronaModule
 
 class AngleDeletion(KoronaModule):
@@ -292,4 +292,3 @@ class NetcdfWriter(KoronaModule):
     """Writes to a .nc file"""
     def __init__(self, **parameters):
         super().__init__('NetcdfWriter', **parameters)
-

{koronascript-0.1 → koronascript-0.2.1}/KoronaScript/__init__.py

@@ -10,14 +10,17 @@ import subprocess
 import tempfile
 import os
 import sys
-import json
 
-from .KoronaModule import KoronaModule, global_spec
+from .KoronaModule import global_spec
+
+lsss = os.getenv('LSSS')
+if lsss is None:
+    print('KoronaScript: Warning: $LSSS is not set.')
 
 class KoronaScript():
     '''Construct, store, and run a set of Korona modules'''
 
-    def __init__(self, **parameters): # global parameters
+    def __init__(self, **parameters):  # global parameters
         self._module_list = []
         self._config = global_spec
         for k in parameters:
@@ -36,7 +39,7 @@ class KoronaScript():
         cfs.write('<?xml version="1.0" encoding="UTF-8"?>\n\n')
         cfs.write('<ConfigFiles context="Korona">\n')
         cfs.write(f'    <parameter name="ModuleConfiguration" ref="CfsDirectory">{cdsname}</parameter>\n')
-        for k,v in self._config.items():
+        for k, v in self._config.items():
             if v is None:
                 cfs.write(f'    <parameter name="{k}"/>\n')
             else:
@@ -51,7 +54,7 @@ class KoronaScript():
         cds.write('  </modules>\n')
         cds.write('</ModuleContainer>\n')
 
-    def run(self, src, dst):
+    def run(self, src, dst, debug=False):
         '''Save the files (to /tmp?) and call Korona to execute them'''
         cfs, cfsname = tempfile.mkstemp(suffix='.cfs')
         cds, cdsname = tempfile.mkstemp(suffix='.cds')
@@ -60,19 +63,25 @@ class KoronaScript():
                 self.write(cfs=cfsfd, cds=cdsfd, cdsname=cdsname)
 
         # if os.getenv('JAVA_HOME'): (...)
-        lsss = os.getenv('LSSS')
         if lsss is None:
-            print('LSSS environment variable not specified')
+            print('KoronaScript: Error: LSSS environment variable not specified')
             exit(-1)
         os.environ['TOP_INSTALLATION_DIR'] = lsss
 
-        java = lsss+'/jre/bin/java'
+        java = os.path.join(*[lsss, 'jre', 'bin', 'java'])
+
+        # "-Xmx${MAX_MEMORY_MB}m" -classpath "t$TOP_INSTALLATION_DIR/lib/jar/*" "-Djava.library.path=$JAVA_LIBRARY_PATH" "-Djna.library.path=$JAVA_LIBRARY_PATH" -XX:-UseGCOverheadLimit -XX:-OmitStackTraceInFastThrow -Dno.marec.incubator=true no.imr.korona.main.KoronaCliMain "$@"
+        javaopts = ['-classpath', os.path.join(*[lsss, "lib", "jar", "*"]), '-Dno.marec.incubator=true']
+        libpath = os.path.join(*[lsss, 'lib', 'native', 'win64'])
+        if os.path.exists(libpath):
+            for v in ['java.library.path', 'jna.library.path']:
+                javaopts.append(f'-D{v}={libpath}')
 
-        # "-Xmx${MAX_MEMORY_MB}m" -classpath "$TOP_INSTALLATION_DIR/lib/jar/*" "-Djava.library.path=$JAVA_LIBRARY_PATH" "-Djna.library.path=$JAVA_LIBRARY_PATH" -XX:-UseGCOverheadLimit -XX:-OmitStackTraceInFastThrow -Dno.marec.incubator=true no.imr.korona.main.KoronaCliMain "$@"
-        javaopts = ['-classpath', f'{lsss}/lib/jar/*', '-Dno.marec.incubator=true', 'no.imr.korona.main.KoronaCliMain']
-        res = subprocess.run([java] + javaopts + ['batch', '--cfs', cfsname, '--source', src, '--destination', dst])
-        print(res.stdout)
+        cmd = [java] + javaopts + ['no.imr.korona.main.KoronaCliMain', 'batch', '--cfs', cfsname, '--source', src, '--destination', dst]
+        if debug: print('Running:\n  ', cmd)
+        res = subprocess.run(cmd, capture_output=True, text=True)
+        if debug: print(res.stdout)
         if res.returncode != 0:
-            print(f'Warning: Java subprocess returned error code {res.returncode}')
-            print('Errors:')
-            print(res.stderr)
+            err_str = f'Korona subprocess returned an error code: {res.returncode}\n' + '----------------------------------------\n' + res.stderr
+            raise Exception(err_str)
+        return res.returncode

{koronascript-0.1 → koronascript-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: koronascript
-Version: 0.1
+Version: 0.2.1
 Summary: Wrapper around Korona modules for processing echosounder data
 Home-page: https://github.com/CRIMAC-WP4-Machine-learning/CRIMAC-KoronaScript
 Author: Ketil Malde
@@ -21,11 +21,16 @@ Download the appropriate version from here:
 
 https://marec.no/tmp/lsss-2.16.0-alpha-20230922-1417-linux.zip
 
+https://marec.no/tmp/lsss-2.18.0-alpha-20240918-0847-linux.zip
+
 https://marec.no/tmp/lsss-2.16.0-alpha-20230922-1417-windows.zip
 
-If you run linux you need to install the netcdf library separately:
+https://marec.no/tmp/lsss-2.18.0-alpha-20240918-0847-windows.zip
+
+If you run linux you need to install the netcdf separately:
+
+`apt-get install libnetcdf` or `sudo apt install libnetcdf-dev`
 
-`apt-get install libnetcdf`
 
 ### Add license 
 
@@ -33,17 +38,17 @@ You need an LSSS licence. The licence have to be added according to the LSSS man
 
 ### Set system variables
 
-This can be set at run time either by setting the LSSS environment
+The `LSSS` environment variable should point to the root directory of your
+LSSS installation.  It can be set at run time either by setting the LSSS environment
 variable in the shell
 ~~~
-export LSSS=~/lsss-2.16.0-alpha/korona
+export LSSS=~/lsss-2.16.0-alpha
 ~~~
-before running your script, or by adding to path 
+before running your script, or by adding it manually from inside Python:
 ~~~
-lsss = '~/lsss-2.16.0-alpha/korona'
+lsss = '~/lsss-2.16.0-alpha'
 os.environ["LSSS"] = lsss
 ~~~
-pointing at the LSSS environment to your script.
 
 # Usage
 

{koronascript-0.1 → koronascript-0.2.1}/README.md

@@ -12,11 +12,16 @@ Download the appropriate version from here:
 
 https://marec.no/tmp/lsss-2.16.0-alpha-20230922-1417-linux.zip
 
+https://marec.no/tmp/lsss-2.18.0-alpha-20240918-0847-linux.zip
+
 https://marec.no/tmp/lsss-2.16.0-alpha-20230922-1417-windows.zip
 
-If you run linux you need to install the netcdf library separately:
+https://marec.no/tmp/lsss-2.18.0-alpha-20240918-0847-windows.zip
+
+If you run linux you need to install the netcdf separately:
+
+`apt-get install libnetcdf` or `sudo apt install libnetcdf-dev`
 
-`apt-get install libnetcdf`
 
 ### Add license 
 
@@ -24,17 +29,17 @@ You need an LSSS licence. The licence have to be added according to the LSSS man
 
 ### Set system variables
 
-This can be set at run time either by setting the LSSS environment
+The `LSSS` environment variable should point to the root directory of your
+LSSS installation.  It can be set at run time either by setting the LSSS environment
 variable in the shell
 ~~~
-export LSSS=~/lsss-2.16.0-alpha/korona
+export LSSS=~/lsss-2.16.0-alpha
 ~~~
-before running your script, or by adding to path 
+before running your script, or by adding it manually from inside Python:
 ~~~
-lsss = '~/lsss-2.16.0-alpha/korona'
+lsss = '~/lsss-2.16.0-alpha'
 os.environ["LSSS"] = lsss
 ~~~
-pointing at the LSSS environment to your script.
 
 # Usage
 

{koronascript-0.1 → koronascript-0.2.1}/koronascript.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: koronascript
-Version: 0.1
+Version: 0.2.1
 Summary: Wrapper around Korona modules for processing echosounder data
 Home-page: https://github.com/CRIMAC-WP4-Machine-learning/CRIMAC-KoronaScript
 Author: Ketil Malde
@@ -21,11 +21,16 @@ Download the appropriate version from here:
 
 https://marec.no/tmp/lsss-2.16.0-alpha-20230922-1417-linux.zip
 
+https://marec.no/tmp/lsss-2.18.0-alpha-20240918-0847-linux.zip
+
 https://marec.no/tmp/lsss-2.16.0-alpha-20230922-1417-windows.zip
 
-If you run linux you need to install the netcdf library separately:
+https://marec.no/tmp/lsss-2.18.0-alpha-20240918-0847-windows.zip
+
+If you run linux you need to install the netcdf separately:
+
+`apt-get install libnetcdf` or `sudo apt install libnetcdf-dev`
 
-`apt-get install libnetcdf`
 
 ### Add license 
 
@@ -33,17 +38,17 @@ You need an LSSS licence. The licence have to be added according to the LSSS man
 
 ### Set system variables
 
-This can be set at run time either by setting the LSSS environment
+The `LSSS` environment variable should point to the root directory of your
+LSSS installation.  It can be set at run time either by setting the LSSS environment
 variable in the shell
 ~~~
-export LSSS=~/lsss-2.16.0-alpha/korona
+export LSSS=~/lsss-2.16.0-alpha
 ~~~
-before running your script, or by adding to path 
+before running your script, or by adding it manually from inside Python:
 ~~~
-lsss = '~/lsss-2.16.0-alpha/korona'
+lsss = '~/lsss-2.16.0-alpha'
 os.environ["LSSS"] = lsss
 ~~~
-pointing at the LSSS environment to your script.
 
 # Usage
 

{koronascript-0.1 → koronascript-0.2.1}/koronascript.egg-info/SOURCES.txt

@@ -1,12 +1,13 @@
 README.md
+setup.cfg
 setup.py
 KoronaScript/Configuration.py
 KoronaScript/KoronaModule.py
 KoronaScript/Modules.py
 KoronaScript/__init__.py
-configuration/korona-info.json
 koronascript.egg-info/PKG-INFO
 koronascript.egg-info/SOURCES.txt
 koronascript.egg-info/dependency_links.txt
 koronascript.egg-info/not-zip-safe
-koronascript.egg-info/top_level.txt
+koronascript.egg-info/top_level.txt
+tests/test_examples.py

koronascript-0.2.1/setup.cfg

@@ -0,0 +1,7 @@
+[flake8]
+ignore = E302,E501,E203,E701
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

{koronascript-0.1 → koronascript-0.2.1}/setup.py

@@ -1,7 +1,7 @@
 from setuptools import setup
 
 setup(name='koronascript',
-      version='0.1',
+      version='0.2.1',
       description='Wrapper around Korona modules for processing echosounder data',
       long_description=open('README.md').read(),
       long_description_content_type='text/markdown',

koronascript-0.2.1/tests/test_examples.py

@@ -0,0 +1,15 @@
+import os
+import examples.channelRemoval as CR
+
+TESTDATA = 'test_data/EK60'
+
+def test_get_data():
+    if not os.path.exists(TESTDATA):
+        # Get test data from pyEchoLab examples:
+        os.system('mkdir -p test_data && cd test_data && wget --recursive --no-parent -nH --cut-dirs=6 ftp://ftp.ngdc.noaa.gov/pub/outgoing/mgg/wcd/pyEcholab_data/examples/EK60')
+
+def test_channelRemoval():
+    """This fails to fail if no data is present"""
+    CR.ks.run('test_data/EK60', 'test_out/cr_out')
+
+

koronascript-0.1/MANIFEST.in

@@ -1 +0,0 @@
-include configuration/korona-info.json