fixed installation script

pcr2nc/MANIFEST.in

@@ -1 +1,2 @@
 include VERSION
+include pcr2nc_script.py

pcr2nc/README.md

@@ -20,7 +20,7 @@ Ensure you have properly installed the following software:
 - GDAL C library and software
 - netCDF4 C library
 
-Create a python3.5 virtualenv for using the software and activate it.
+Create a python3 virtualenv for using the software and activate it.
 
 If you have virtualenvwrapper:
 ```bash
@@ -32,6 +32,27 @@ Otherwise just execute the activate script
 $ source /path/to/virtualenvs/pcr2nc/bin/activate
 ```
 
+### Install via pip tool
+
+Activate the virtualenv and then:
+
+```bash
+$ pip install pcr2nc
+```
+
+After the install was complete, you still have to install the proper GDAL package,
+according to the version of gdal library that is installed on your machine.
+You will also need C GDAL headers to properly install python GDAL wrapper.
+
+E.g.
+
+```bash
+sudo apt-get install libgdal-dev libgdal
+export CPLUS_INCLUDE_PATH=/usr/include/gdal
+export C_INCLUDE_PATH=/usr/include/gdal
+gdal-config --version  # 2.2.3
+pip install GDAL==2.2.3
+```
 
 ### Install by cloning the repository
 
@@ -65,23 +86,6 @@ $ pip install GDAL==2.1
 $ pip install -r requirements.txt
 ```
 
-### Install via pip tool
-
-Activate the virtualenv and then:
-
-```bash
-$ pip install pcr2nc
-```
-
-After the install was complete, you still have to install the proper GDAL package,
-according to the version of gdal library that is installed on your machine.
-
-E.g.
-
-```bash
-$ pip install GDAL==2.1
-```
-
 ## Usage
 
 > __Note:__ This guide assumes you have installed the program with pip tool.

pcr2nc/VERSION

@@ -1 +1 @@
-0.5
+0.6

pcr2nc/bin/pcr2nc

@@ -0,0 +1,6 @@
+#!/usr/bin/env python
+
+from pcr2nc.main import main_script
+
+if __name__ == '__main__':
+    main_script()

pcr2nc/pcr2nc/main.py

@@ -0,0 +1,65 @@
+"""
+pcr2nc
+A tool that convert PCRaster maps to a netCDF4 mapstack CF-1.7
+"""
+import sys
+import argparse
+import json
+
+import yaml
+try:
+    from yaml import CLoader as Loader, CDumper as Dumper
+except ImportError:
+    from yaml import Loader, Dumper
+
+from pcr2nc.writer import convert
+
+
+class ParserHelpOnError(argparse.ArgumentParser):
+    def error(self, message):
+        sys.stderr.write('error: %s\n' % message)
+        self.print_help()
+        sys.exit(2)
+
+    def add_args(self):
+        required_group = self.add_argument_group('required arguments')
+        required_group.add_argument('-m', '--metadata', help='Path to json/yaml metadata file for NetCDF',
+                                    metavar='metadata', required=True)
+        required_group.add_argument('-i', '--input', required=True,
+                                    help='Path to input dataset. It can be a single PCRaster map, '
+                                         'a folder containing PCRaster maps or a path with wildcards '
+                                         'to use with glob.glob python function',
+                                    metavar='input')
+        self.add_argument('-o', '--output_file', help='Path to netcdf output file.', default='./file.nc',
+                          metavar='output_file')
+
+
+def parse_metadata(metadata_file):
+    if metadata_file.endswith('.yaml') or metadata_file.endswith('.yml'):
+        with open(metadata_file) as f:
+            metadata = yaml.load(f, Loader=Loader)
+    else:
+        # suppose json format
+        with open(metadata_file) as f:
+            metadata = json.load(f)
+    return metadata
+
+
+def main_script():
+    sys.exit(main(sys.argv[1:]))
+
+
+def main(args):
+    parser = ParserHelpOnError(description='Convert PCRaster maps to a NetCDF map stack')
+
+    parser.add_args()
+    parsed_args = parser.parse_args(args)
+    configuration = {'input_set': parsed_args.input,
+                     'output_filename': parsed_args.output_file,
+                     'metadata': parse_metadata(parsed_args.metadata)}
+    # MAIN METHOD
+    convert(configuration)
+
+
+if __name__ == '__main__':
+    main_script()

pcr2nc/pcr2nc/reader.py

@@ -5,11 +5,25 @@
 import os
 import glob
 import re
+import sys
 
-from osgeo import gdal
-from osgeo.gdalconst import GA_ReadOnly
 import numpy as np
 
+try:
+    from osgeo import gdal
+    from osgeo.gdalconst import GA_ReadOnly
+except (ModuleNotFoundError, ImportError) as e:
+    print("""
+    [!] GDAL is not installed. Please, install GDAL binaries and libraries for your system and then install the relative pip package.
+    [!] Important note: you have to install same version of GDAL for its python interface. You also need to install GDAL C headers.
+    [!] sudo apt-get install libgdal-dev libgdal
+    [!] export CPLUS_INCLUDE_PATH=/usr/include/gdal
+    [!] export C_INCLUDE_PATH=/usr/include/gdal
+    [!] To know your gdal version execute `gdal-config --version` ex. 2.2.3
+    [!] pip install GDAL==2.2.3
+    """)
+    sys.exit(1)
+
 
 class PCRasterMap:
     """

pcr2nc/setup.py

@@ -32,8 +32,6 @@
 import os
 from setuptools import setup, find_packages
 
-
-packages_deps = ['numpy>=1.15', 'pyyaml', 'netCDF4>=1.3.1']
 current_dir = os.path.dirname(os.path.abspath(__file__))
 readme_file = os.path.join(current_dir, 'README.md')
 version_file = os.path.join(current_dir, 'VERSION')
@@ -44,36 +42,38 @@
 with open(version_file, 'r') as f:
     version = f.read()
 
-setup_args = dict(name='pcr2nc',
-                  version=version,
-                  packages=find_packages(),
-                  description='Convert PCRaster files to netCDF4',
-                  long_description=long_description,
-                  long_description_content_type='text/markdown',
-                  install_requires=packages_deps,
-                  author="Domenico Nappo",
-                  author_email="domenico.nappo@gmail.com",
-                  keywords=['netCDF4', 'PCRaster', 'mapstack'],
-                  license='EUPL 1.2',
-                  url='https://github.com/ec-jrc/lisflood-model',
-                  entry_points={'console_scripts': ['pcr2nc = pcr2nc_script:main_script']},
-                  zip_safe=True,
-                  classifiers=[
-                      # complete classifier list: http://pypi.python.org/pypi?%3Aaction=list_classifiers
-                      'Development Status :: 4 - Beta',
-                      'Intended Audience :: Developers',
-                      'Intended Audience :: Education',
-                      'Intended Audience :: Other Audience',
-                      'Intended Audience :: Science/Research',
-                      'License :: OSI Approved :: European Union Public Licence 1.2 (EUPL 1.2)',
-                      'Operating System :: Unix',
-                      'Operating System :: POSIX',
-                      'Operating System :: Microsoft :: Windows',
-                      'Operating System :: MacOS :: MacOS X',
-                      'Programming Language :: Python',
-                      'Programming Language :: Python :: 3',
-                      'Topic :: Scientific/Engineering :: Physics',
-                  ],
+setup_args = dict(
+    name='pcr2nc',
+    version=version,
+    packages=find_packages(),
+    description='Convert PCRaster files to netCDF4',
+    long_description=long_description,
+    long_description_content_type='text/markdown',
+    install_requires=['numpy>=1.15', 'pyyaml', 'netCDF4>=1.3.1'],
+    author="Domenico Nappo",
+    author_email="domenico.nappo@gmail.com",
+    keywords=['netCDF4', 'PCRaster', 'mapstack'],
+    license='EUPL 1.2',
+    url='https://github.com/ec-jrc/lisflood-model',
+    # entry_points={'console_scripts': ['pcr2nc = pcr2nc_script:main_script']},
+    scripts=['bin/pcr2nc'],
+    zip_safe=True,
+    classifiers=[
+          # complete classifier list: http://pypi.python.org/pypi?%3Aaction=list_classifiers
+          'Development Status :: 4 - Beta',
+          'Intended Audience :: Developers',
+          'Intended Audience :: Education',
+          'Intended Audience :: Other Audience',
+          'Intended Audience :: Science/Research',
+          'License :: OSI Approved :: European Union Public Licence 1.2 (EUPL 1.2)',
+          'Operating System :: Unix',
+          'Operating System :: POSIX',
+          'Operating System :: Microsoft :: Windows',
+          'Operating System :: MacOS :: MacOS X',
+          'Programming Language :: Python',
+          'Programming Language :: Python :: 3',
+          'Topic :: Scientific/Engineering :: Physics',
+    ],
 )
 
 setup(**setup_args)