Merge pull request #73 from nuest/master

Dev update

.travis.yml

@@ -19,9 +19,9 @@ addons:
 before_install:
   - gdal-config --version
   # installation of gdal Python package, see https://stackoverflow.com/a/17311033
-  - export CPLUS_INCLUDE_PATH=/usr/include/gdal
-  - export C_INCLUDE_PATH=/usr/include/gdal
-  - pip install gdal==`gdal-config --version`
+  #- export CPLUS_INCLUDE_PATH=/usr/include/gdal
+  #- export C_INCLUDE_PATH=/usr/include/gdal
+  - pip install pygdal=="`gdal-config --version`.*"
 install:
   - pip install -r requirements.txt
   - pip install -e .

CONTRIBUTING.md

@@ -13,7 +13,7 @@ The following steps assume you are familiar with Python packages.
 
 We follow a _fork and pull_ development model. [Fork](https://help.github.com/en/articles/fork-a-repo), then clone the repo:
 
-```
+```bash
 git clone https://github.com/o2r-project/geoextent.git
 ```
 

README.md

@@ -1,15 +1,15 @@
-[![Build Status](https://travis-ci.org/o2r-project/geoextent.svg?branch=master)](https://travis-ci.org/github/o2r-project/geoextent) [![PyPI version](https://badge.fury.io/py/geoextent.svg)](https://pypi.org/project/geoextent/0.1.0/) 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/o2r-project/geoextent/master)
-
 # geoextent
 
+[![Build Status](https://travis-ci.org/o2r-project/geoextent.svg?branch=master)](https://travis-ci.org/github/o2r-project/geoextent) [![PyPI version](https://badge.fury.io/py/geoextent.svg)](https://pypi.org/project/geoextent/0.1.0/)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/o2r-project/geoextent/master)
+
 Python library for extracting geospatial extent of files and directories with multiple data formats
 
-This project is developed as part of the [DFG-funded](https://o2r.info/about/#funding) research project Opening Reproducible Research (o2r, https://o2r.info).
+This project is developed as part of the [DFG-funded](https://o2r.info/about/#funding) research project Opening Reproducible Research (o2r, [https://o2r.info](https://o2r.info)).
 
 ## Installation
 
-**System requirements**
+### System requirements
 
 Python: `3.x`
 
@@ -18,13 +18,17 @@ On Debian systems, the [UbuntuGIS](https://wiki.ubuntu.com/UbuntuGIS) project of
 
 See the `packages` list in `travis.yml` for a full list of dependencies on Linux.
 
-**Install from PyPI**
+### Install from PyPI
+
+You must install a suitable version of `pygdal` manually first, see [instructions](https://pypi.org/project/pygdal/) and [this related SO thread with different helpful answers](https://gis.stackexchange.com/questions/28966/python-gdal-package-missing-header-file-when-installing-via-pip/124420#124420).
+We use `pygdal` for better compatibility with virtual environments.
 
 ```bash
+# pip install pygdal=="`gdal-config --version`.*"
 pip install geoextent
 ```
 
-**Source installation**
+### Source installation
 
 ```bash
 git clone https://github.com/o2r-project/geoextent
@@ -34,10 +38,6 @@ pip install -r requirements.txt
 pip install -e .
 ```
 
-**System requirements**
-
-- see `travis.yml`
-
 ## Use
 
 Run

docs/source/changelog.rst

@@ -2,6 +2,13 @@
 Changelog
 =========
 
+0.3.0
+^^^^^
+
+- Add debug option ``--debug`` and environment variable ``GEOEXTENT_DEBUG`` (:pr:`73`)
+- Remove need for ``-input=`` for passing input paths in CLI (:pr:`73`)
+- Switch to ``pygdal`` and update docs (:pr:`73`)
+
 0.2.0
 ^^^^^
 

docs/source/development.rst

@@ -6,7 +6,9 @@ Notes for developers of ``geoextent``.
 Environment
 -----------
 
-All commands in this file assume you work in a virtual environment created with [``virtualenvwrapper``](https://virtualenvwrapper.readthedocs.io/en/latest/install.html) as follows (please keep up to date!):
+All commands in this file assume you work in a virtual environment created with virtualenvwrapper_ as follows (please keep up to date!):
+
+.. _virtualenvwrapper: https://virtualenvwrapper.readthedocs.io/en/latest/install.html
 
 ::
 
@@ -69,6 +71,8 @@ You can also run individual files:
 
 ::
 
+    pytest
+
     pytest tests/test_api.py
 
 Documentation
@@ -180,8 +184,8 @@ Install geoextent from TestPyPI and ensure the package is functional:
     geoextent --help
     geoextent --version
 
-    geoextent -b -t -input= /testdata/geojson/muenster_ring_zeit.geojson
-    geoextent -b -t -input= /testdata/shapefile/gis_osm_buildings_a_free_1.shp
+    geoextent -b -t /testdata/geojson/muenster_ring_zeit.geojson
+    geoextent -b -t /testdata/shapefile/gis_osm_buildings_a_free_1.shp
 
 Alternatively, use Debian Testing container to try out a more recent version of GDAL which matches the current release of the GDAL package on PyPI:
 
@@ -198,6 +202,10 @@ Alternatively, use Debian Testing container to try out a more recent version of
 
     wget https://github.com/o2r-project/geoextent/blob/master/tests/testdata/tif/wf_100m_klas.tif
 
+    geoextent -b muenster_ring_zeit.geojson
+    geoextent --version
+    geoextent --help
+
 
 Upload to PyPI
 ^^^^^^^^^^^^^^

docs/source/howto/cli.rst

@@ -10,7 +10,6 @@ Basics
 .. autoprogram:: geoextent.__main__:argparser
    :prog: \
 
-
 Examples
 --------
 
@@ -31,7 +30,7 @@ Show help message
    :stderr:
 
    import geoextent.__main__ as geoextent
-   geoextent.print_help_fun()
+   geoextent.print_help()
 
 Extract bounding box from a single file
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -41,7 +40,7 @@ Extract bounding box from a single file
 
 ::
 
-   geoextent -b -input= 'muenster_ring_zeit.geojson'
+   geoextent -b muenster_ring_zeit.geojson
 
 Output:
 
@@ -55,9 +54,12 @@ Output:
 Extract time interval from a single file
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+.. note::
+   You can find the file used in the examples of this section from `muenster_ring_zeit <https://raw.githubusercontent.com/o2r-project/geoextent/master/tests/testdata/geojson/muenster_ring_zeit.geojson>`_. Furthermore, for displaying the rendering of the file contents, see `rendered blob <https://github.com/o2r-project/geoextent/blob/master/tests/testdata/geojson/muenster_ring_zeit.geojson>`_.
+
 ::
 
-   geoextent -t -input='file.geojson'
+   geoextent -t muenster_ring_zeit.geojson
 
 Output:
 
@@ -71,13 +73,27 @@ Output:
 Extract both bounding box and time interval from a single file
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+.. note::
+   You can find the file used in the examples of this section from `muenster_ring_zeit <https://raw.githubusercontent.com/o2r-project/geoextent/master/tests/testdata/geojson/muenster_ring_zeit.geojson>`_. Furthermore, for displaying the rendering of the file contents, see `rendered blob <https://github.com/o2r-project/geoextent/blob/master/tests/testdata/geojson/muenster_ring_zeit.geojson>`_.
+
 ::
 
-   geoextent -b -t -input= 'file.geojson'
+   geoextent -b -t muenster_ring_zeit.geojson
 
 .. jupyter-execute::
    :hide-code:
    :stderr:
 
    import geoextent.lib.extent as geoextent
    geoextent.fromFile('../tests/testdata/geojson/muenster_ring_zeit.geojson', True, True)
+
+Debugging
+^^^^^^^^^
+
+You can enable detailed logs by passing the ``--debug`` option, or by setting the environment variable ``GEOEXTENT_DEBUG=1``.
+
+::
+
+   geoextent --debug -b -t muenster_ring_zeit.geojson
+
+   GEOEXTENT_DEBUG=1 geoextent -b -t muenster_ring_zeit.geojson

docs/source/supportedformats/index_supportedformats.rst

@@ -36,7 +36,7 @@ The file used in the example can be in the code repository: `muenster_ring_zeit.
 
 ::
 
-   geoextent -b -t -input= 'muenster_ring_zeit.geojson'
+   geoextent -b -t muenster_ring_zeit.geojson
 
 .. jupyter-execute::
    :hide-code:
@@ -70,7 +70,7 @@ The file used in the example can be obtained from `Zenodo Sandbox record 256820
 
 ::
 
-   geoextent -b -t -input= 'cities_NL.csv'
+   geoextent -b -t cities_NL.csv
 
 .. jupyter-execute::
    :hide-code:
@@ -90,7 +90,7 @@ The file used in the example is available online: `wf_100m_klas.tif <https://git
 
 ::
 
-   geoextent -b -input= 'wf_100m_klas.tif'
+   geoextent -b wf_100m_klas.tif
 
 .. jupyter-execute::
    :hide-code:
@@ -110,7 +110,7 @@ The file used in the example can be found at Geofabrik: `shapefiles_toulouse.zip
 
 ::
 
-   geoextent 'gis_osm_buildings_a_07_1.shp'
+   geoextent -b gis_osm_buildings_a_07_1.shp
 
 .. jupyter-execute::
    :hide-code:

geoextent/__init__.py

@@ -1,3 +1,3 @@
 name = "geoextent"
 
-__version__ = '0.2.0'
+__version__ = '0.3.0'

geoextent/__main__.py

@@ -4,8 +4,8 @@
 from . import __version__ as current_version
 import logging
 
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger(__name__)
+logging.basicConfig(level=logging.WARNING)
+logger = logging.getLogger("geoextent")
 
 help_description = '''
 geoextent is a Python library for extracting geospatial and temporal extents of a file or a directory of multiple geospatial data formats.
@@ -49,7 +49,7 @@ def get_argparser():
         add_help=False,
         prog='geoextent',
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        usage= "geoextent [-h] [--formats] [--version] [-b] [-t] [-input= '[filepath|input file]']"
+        usage= "geoextent [-h] [--formats] [--version] [--debug] [-b] [-t] [input file]']"
     )
 
     parser.add_argument(
@@ -70,36 +70,41 @@ def get_argparser():
         help='show installed version'
     )
 
+    parser.add_argument(
+        '--debug',
+        help='turn on debug logging, alternatively set environment variable GEOEXTENT_DEBUG=1',
+        action='store_true'
+    )
+
     parser.add_argument(
         '-b', '--bounding-box',
         action='store_true',
+        default=False,
         help='extract spatial extent (bounding box)'
     )
 
     parser.add_argument(
         '-t', '--time-box',
         action='store_true',
+        default=False,
         help='extract temporal extent'
     )
 
     parser.add_argument(
-        '-input=',
+        'files',
         action=readable_file_or_dir,
         default=os.getcwd(),
-        nargs='+',
+        nargs=argparse.REMAINDER,
         help="input file or path"
     )
 
     return parser
 
-def print_help_fun():
+def print_help():
     print(help_description)
     argparser.print_help()
-    print_examples()
-    print_supported_formats()
-
-def print_examples():
     print(help_epilog)
+    print_supported_formats()
 
 def print_supported_formats():
     print(supported_formats)
@@ -113,34 +118,50 @@ def print_version():
 def main():
     # Check if there is no arguments, then print help
     if len(sys.argv[1:])==0:
-        print_help_fun()
+        print_help()
         argparser.exit()
 
-    args = vars(argparser.parse_args())
-    logger.debug('Extracting from inputs %s', args['input='])
-
-    if(args['help']):
-        print_help_fun()
-    elif(args['version']):
+    # version, help, and formats must be checked before parse, as otherwise files are required 
+    # but argpase gives an error if allowed to be parsed first
+    if "--help" in sys.argv:
+        print_help()
+        argparser.exit()
+    if "--version" in sys.argv:
         print_version()
-    elif(args['formats']):
+        argparser.exit()
+    if "--formats" in sys.argv:
         print_supported_formats()
-    else:
-        # Check if file is exists happens in parser validation, see readable_file_or_dir
-        if os.path.isfile(os.path.join(os.getcwd(), args['input='])):
-            output = extent.fromFile(args['input='], bbox = args['bounding_box'], tbox = args['time_box'])
-        if os.path.isdir(os.path.join(os.getcwd(), args['input='])):
-            output = extent.fromDirectory(args['input='], bbox = args['bounding_box'], tbox = args['time_box'])
-
-        if output is None:
-            raise Exception("This file format is not supported")
-
-        # print output
-        if type(output) == list or type(output) == dict:
-            print(str(output))
-        else: 
-            print(output)
+        argparser.exit()
 
+    args = vars(argparser.parse_args())
+    files = args['files']
+    logger.debug('Extracting from inputs %s', files)
+
+    # Set logging level
+    if(args['debug']):
+        logging.getLogger('geoextent').setLevel(logging.DEBUG)
+    if(os.environ.get('GEOEXTENT_DEBUG', None) == "1"):
+        logging.getLogger('geoextent').setLevel(logging.DEBUG)
+
+    # Check if file is exists happens in parser validation, see readable_file_or_dir
+    try:
+        if os.path.isfile(os.path.join(os.getcwd(), files)):
+            output = extent.fromFile(files, bbox = args['bounding_box'], tbox = args['time_box'])
+        if os.path.isdir(os.path.join(os.getcwd(), files)):
+            output = extent.fromDirectory(files, bbox = args['bounding_box'], tbox = args['time_box'])
+    except Exception as e:
+        if(logger.getEffectiveLevel() >= logging.DEBUG):
+            logger.exception(e)
+        sys.exit(1)
+
+    if output is None:
+        raise Exception("Did not find supported files at {}".format(files))
+
+    # print output
+    if type(output) == list or type(output) == dict:
+        print(str(output))
+    else: 
+        print(output)
 
 if __name__ == '__main__':
     main()