adopted absolute import for local packages

.github/workflows/bag_on_linux.yml

@@ -22,9 +22,10 @@ jobs:
     - name: Install dependencies
       run: |
         conda config --add channels conda-forge
-        conda install appdirs cartopy gdal matplotlib-base numpy psutil pyproj qt-material hyo2.abc2
+        conda install appdirs cartopy gdal matplotlib-base numpy psutil pyproj qt-material
         pip install PySide6
         sudo apt-get install -y libegl1
+        pip install hyo2.abc2
         pip install --no-deps .
     - name: Lint with flake8
       run: |

.github/workflows/bag_on_windows.yml

@@ -22,8 +22,10 @@ jobs:
     - name: Install dependencies
       run: |
         conda config --add channels conda-forge
-        conda install appdirs cartopy gdal matplotlib-base numpy psutil pyproj qt-material hyo2.abc2
+        conda install appdirs cartopy gdal matplotlib-base numpy psutil pyproj qt-material
+        conda install h5py dateutil lxml
         pip install PySide6
+        pip install hyo2.abc2
         pip install --no-deps .
     - name: Lint with flake8
       run: |

README.rst

@@ -22,8 +22,8 @@ HydrOffice BAG Tools
     :target: https://www.hydroffice.org/manuals/bag/index.html
     :alt: Latest Documentation
 
-.. image:: https://api.codacy.com/project/badge/Grade/c7551d8f90ba4b0086c7b8dc81376260
-    :target: https://www.codacy.com/app/hydroffice/hyo2_bag/dashboard
+.. image:: https://app.codacy.com/project/badge/Grade/b39ce4141d3e412fa789c7d5ee4971f3
+    :target: https://app.codacy.com/gh/hydroffice/hyo2_bag/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade
     :alt: codacy
 
 .. image:: https://coveralls.io/repos/github/hydroffice/hyo2_bag/badge.svg?branch=master

hyo2/bag/__init__.py

@@ -4,7 +4,7 @@
 """
 
 name = 'BAG'
-__version__ = '1.2.2'
+__version__ = '1.2.3'
 __author__ = '[email protected]'
 __license__ = 'LGPLv3 license'
 __copyright__ = 'Copyright (c) 2024, University of New Hampshire, Center for Coastal and Ocean Mapping'

hyo2/bag/bag.py

@@ -60,7 +60,7 @@ def __init__(self, name, mode='r', driver=None,
         self._str = None
 
     @classmethod
-    def is_bag(cls, bag_path:str, advanced: bool = False) -> bool:
+    def is_bag(cls, bag_path: str, advanced: bool = False) -> bool:
         if not advanced:
             return os.path.splitext(bag_path)[-1].lower() == ".bag"
 
@@ -154,7 +154,7 @@ def elevation_min_max(self) -> Tuple[float, float]:
         # logger.debug('shape: %s, %s' % (rows, cols))
 
         mem_row = cols * 32 / 1024 / 1024
-        mem = mem_row * rows
+        # mem = mem_row * rows
         # logger.debug('estimated memory: %.1f MB' % mem)
         chunk_size = 8096
         chunk_rows = int(chunk_size / mem_row) + 1
@@ -190,7 +190,7 @@ def vr_refinements_shape(self):
         return self[BAGFile._bag_varres_refinements].shape
 
     def vr_elevation_min_max(self) -> Tuple[float, float]:
-        rows, cols = self.vr_refinements_shape()
+        # rows, cols = self.vr_refinements_shape()
         # logger.debug('refinements shape: %s, %s' % (rows, cols))
 
         vr_el = self[BAGFile._bag_varres_refinements][0]['depth']
@@ -253,7 +253,7 @@ def uncertainty_min_max(self) -> Tuple[float, float]:
         # logger.debug('shape: %s, %s' % (rows, cols))
 
         mem_row = cols * 32 / 1024 / 1024
-        mem = mem_row * rows
+        # mem = mem_row * rows
         # logger.debug('estimated memory: %.1f MB' % mem)
         chunk_size = 8096
         chunk_rows = int(chunk_size / mem_row) + 1
@@ -282,7 +282,7 @@ def uncertainty_min_max(self) -> Tuple[float, float]:
         return unc_min, unc_max
 
     def vr_uncertainty_min_max(self) -> Tuple[float, float]:
-        rows, cols = self.vr_refinements_shape()
+        # rows, cols = self.vr_refinements_shape()
         # logger.debug('shape: %s, %s' % (rows, cols))
 
         vr_unc = self[BAGFile._bag_varres_refinements][0]['depth_uncrt']

hyo2/bag/base.py

@@ -1,22 +1,10 @@
 import os
-import sys
 import logging
 
-log = logging.getLogger(__name__)
-
 import h5py
 from h5py._hl.base import with_phil
 
-from .helper import BAGError
-
-
-PY3 = sys.version_info[0] == 3
-if PY3:
-    def u(s):
-        return s
-else:
-    def u(s):
-        return unicode(s.replace(r'\\', r'\\\\'), "unicode_escape")
+logger = logging.getLogger(__name__)
 
 
 def is_bag(file_name):
@@ -69,33 +57,31 @@ def __init__(self, name, mode: str = "r", driver=None,
 
     def close(self):
         """ Close the file.  All open objects become invalid """
-        log.debug("closing")
+        logger.debug("closing")
         super(File, self).close()
 
     def flush(self):
         """ Tell the BAG library to flush its buffers. """
-        log.debug("flushing")
+        logger.debug("flushing")
         super(File, self).flush()
 
     @with_phil
     def __repr__(self):
         if not self.id:
-            log.info("closed file")
-            r = u('<BAG file>\n')
+            logger.info("closed file")
+            r = '<BAG file>\n'
             r += "  <status: closed>"
         else:
             # Filename has to be forced to Unicode if it comes back bytes
             # Mode is always a "native" string
             filename = self.filename
             if isinstance(filename, bytes):  # Can't decode fname
                 filename = filename.decode('utf8', 'replace')
-            r = u('<BAG file "%s" (mode %s)>') % (os.path.basename(filename), self.mode)
+            r = '<BAG file "%s" (mode %s)>' % (os.path.basename(filename), self.mode)
             r += "  <status: open>\n"
             r += "  <id: %s>\n" % self.id
             r += "  <name: %s>\n" % self.name
             r += "  <driver: %s>\n" % self.driver
             r += "  <user block size: %s>\n" % self.userblock_size
 
-        if PY3:
-            return r
-        return r.encode('utf8')
+        return r

hyo2/bag/bbox.py

@@ -1,13 +1,13 @@
 import os
 import logging
 
-log = logging.getLogger(__name__)
-
 from osgeo import ogr, osr
-from .meta import Meta
-from .helper import BAGError, Helper
-from . import __version__
+from hyo2.bag.meta import Meta
+from hyo2.bag.helper import BAGError, Helper
+from hyo2.bag import __version__
+
 
+logger = logging.getLogger(__name__)
 ogr.UseExceptions()
 
 
@@ -20,16 +20,15 @@ class Bbox2Gdal(object):
         'shp': ["ESRI Shapefile", "bag.shp"],
     }
 
-    def __init__(self, bag_meta, fmt="kml", title=None, out_file=None):
-        assert isinstance(bag_meta, Meta)
+    def __init__(self, bag_meta: Meta, fmt="kml", title=None, out_file=None):
         self.bag_meta = bag_meta
         if not self.bag_meta.valid_bbox():
             raise BAGError("invalid bbox read in BAG metadata")
 
         self.title = title
         if self.title is None:
             self.title = "Metadata"
-        log.debug("title: %s" % self.title)
+        logger.debug("title: %s" % self.title)
 
         # get the ogr driver
         self.drv = ogr.GetDriverByName(self.formats[fmt][0])
@@ -40,7 +39,7 @@ def __init__(self, bag_meta, fmt="kml", title=None, out_file=None):
         self.out_file = out_file
         if self.out_file is None:
             self.out_file = os.path.abspath(self.formats[fmt][1])
-            log.debug("output: %s" % self.out_file)
+            logger.debug("output: %s" % self.out_file)
 
         if os.path.exists(self.out_file):
             os.remove(self.out_file)

hyo2/bag/density.py

@@ -1,16 +1,14 @@
 import os
 import logging
-
-log = logging.getLogger(__name__)
-
 import numpy as np
 
 from osgeo import gdal, osr
 from .meta import Meta
-from .helper import BAGError, Helper
-from . import __version__
+from .helper import BAGError
 from .bag import BAGFile
 
+
+logger = logging.getLogger(__name__)
 gdal.UseExceptions()
 
 
@@ -22,29 +20,27 @@ class Density2Gdal(object):
         'xyz': [b"XYZ", "bag.leidos.density.xyz"],
     }
 
-    def __init__(self, bag_density, bag_meta, fmt="geotiff", out_file=None, epsg=None):
+    def __init__(self, bag_density: np.ndarray, bag_meta: Meta, fmt="geotiff", out_file=None, epsg=None):
         """Export the elevation layer in one of the listed formats"""
-        assert isinstance(bag_density, np.ndarray)
-        assert isinstance(bag_meta, Meta)
         self.bag_den = bag_density
         self.bag_meta = bag_meta
 
         # get the IN-MEMORY ogr driver
         self.mem = gdal.GetDriverByName(b"MEM")
         if self.mem is None:
             raise BAGError("%s driver not available.\n" % self.formats[fmt][0])
-        log.debug("format: %s" % fmt)
+        logger.debug("format: %s" % fmt)
 
         # set the output file
         self.out_file = out_file
         if self.out_file is None:
             self.out_file = os.path.abspath(self.formats[fmt][1])
-            log.debug("output: %s" % self.out_file)
+            logger.debug("output: %s" % self.out_file)
 
         if os.path.exists(self.out_file):
             os.remove(self.out_file)
 
-        log.debug("dtype: %s" % self.bag_den.dtype)
+        logger.debug("dtype: %s" % self.bag_den.dtype)
         self.rst = self.mem.Create(utf8_path=self.out_file, xsize=self.bag_meta.cols, ysize=self.bag_meta.rows,
                                    bands=1, eType=gdal.GDT_Float32)
         # GDAL geo-transform refers to the top left corner of the top left pixel of the raster.
@@ -58,7 +54,7 @@ def __init__(self, bag_density, bag_meta, fmt="geotiff", out_file=None, epsg=Non
         if self.bag_meta.wkt_srs is not None:
             self.srs.ImportFromWkt(self.bag_meta.wkt_srs)
         else:
-            log.warning("unable to recover valid spatial reference info")
+            logger.warning("unable to recover valid spatial reference info")
         self.rst.SetProjection(self.srs.ExportToWkt())
         self.bnd.FlushCache()
 
@@ -68,8 +64,8 @@ def __init__(self, bag_density, bag_meta, fmt="geotiff", out_file=None, epsg=Non
         # check if re-projection is required
         if not epsg:
             # if not, we just create a copy in the selected format
-            dst_ds = self.drv.CreateCopy(self.out_file, self.rst)
-            dst_ds = None
+            _ = self.drv.CreateCopy(self.out_file, self.rst)
+            _ = None
             self.rst = None
             return
 
@@ -87,6 +83,6 @@ def __init__(self, bag_density, bag_meta, fmt="geotiff", out_file=None, epsg=Non
                                           0.125  # error threshold --> use same value as in gdalwarp
                                           )
         # Create the final warped raster
-        dst_ds = self.drv.CreateCopy(self.out_file, tmp_ds)
-        dst_ds = None
+        _ = self.drv.CreateCopy(self.out_file, tmp_ds)
+        _ = None
         self.rst = None

hyo2/bag/elevation.py

@@ -1,15 +1,15 @@
 import os
 import logging
 
-log = logging.getLogger(__name__)
-
 import numpy as np
-
 from osgeo import gdal, osr
-from .meta import Meta
-from .helper import BAGError
-from .bag import BAGFile
 
+from hyo2.bag.meta import Meta
+from hyo2.bag.helper import BAGError
+from hyo2.bag.bag import BAGFile
+
+
+logger = logging.getLogger(__name__)
 gdal.UseExceptions()
 
 
@@ -21,29 +21,27 @@ class Elevation2Gdal:
         'xyz': ["XYZ", "bag.elevation.xyz"],
     }
 
-    def __init__(self, bag_elevation, bag_meta, fmt="geotiff", out_file=None, epsg=None):
+    def __init__(self, bag_elevation: np.ndarray, bag_meta: Meta, fmt="geotiff", out_file=None, epsg=None):
         """Export the elevation layer in one of the listed formats"""
-        assert isinstance(bag_elevation, np.ndarray)
-        assert isinstance(bag_meta, Meta)
         self.bag_elv = bag_elevation
         self.bag_meta = bag_meta
 
         # get the IN-MEMORY ogr driver
         self.mem = gdal.GetDriverByName("MEM")
         if self.mem is None:
             raise BAGError("%s driver not available.\n" % self.formats[fmt][0])
-        log.debug("format: %s" % fmt)
+        logger.debug("format: %s" % fmt)
 
         # set the output file
         self.out_file = out_file
         if self.out_file is None:
             self.out_file = os.path.abspath(self.formats[fmt][1])
-            log.debug("output: %s" % self.out_file)
+            logger.debug("output: %s" % self.out_file)
 
         if os.path.exists(self.out_file):
             os.remove(self.out_file)
 
-        log.debug("dtype: %s" % self.bag_elv.dtype)
+        logger.debug("dtype: %s" % self.bag_elv.dtype)
         self.rst = self.mem.Create(utf8_path=self.out_file, xsize=self.bag_meta.cols, ysize=self.bag_meta.rows,
                                    bands=1, eType=gdal.GDT_Float32)
         # GDAL geo-transform refers to the top left corner of the top left pixel of the raster.
@@ -57,7 +55,7 @@ def __init__(self, bag_elevation, bag_meta, fmt="geotiff", out_file=None, epsg=N
         if self.bag_meta.wkt_srs is not None:
             self.srs.ImportFromWkt(self.bag_meta.wkt_srs)
         else:
-            log.warning("unable to recover valid spatial reference info")
+            logger.warning("unable to recover valid spatial reference info")
         self.rst.SetProjection(self.srs.ExportToWkt())
         self.bnd.FlushCache()
 
@@ -67,8 +65,8 @@ def __init__(self, bag_elevation, bag_meta, fmt="geotiff", out_file=None, epsg=N
         # check if re-projection is required
         if not epsg:
             # if not, we just create a copy in the selected format
-            dst_ds = self.drv.CreateCopy(self.out_file, self.rst)
-            dst_ds = None
+            _ = self.drv.CreateCopy(self.out_file, self.rst)
+            _ = None
             self.rst = None
             return
 
@@ -86,7 +84,6 @@ def __init__(self, bag_elevation, bag_meta, fmt="geotiff", out_file=None, epsg=N
                                           0.125  # error threshold --> use same value as in gdalwarp
                                           )
         # Create the final warped raster
-        dst_ds = self.drv.CreateCopy(self.out_file, tmp_ds)
-        dst_ds = None
+        _ = self.drv.CreateCopy(self.out_file, tmp_ds)
+        _ = None
         self.rst = None
-