Merge pull request #40 from Parallel-NetCDF/rename_file_format

wkliao · web-flow · commit 14bc61830708 · 2024-08-09T12:47:21.000-05:00
rename file format strings
diff --git a/examples/collective_write.py b/examples/collective_write.py
@@ -174,7 +174,7 @@ def pnetcdf_io(comm, filename, file_format, length):
     if args.q: verbose = False
 
     if args.k:
-        kind_dict = {'1':None, '2':"64BIT_OFFSET", '5':"64BIT_DATA"}
+        kind_dict = {'1':None, '2':"NETCDF3_64BIT_OFFSET", '5':"NETCDF3_64BIT_DATA"}
         file_format = kind_dict[args.k]
 
     if args.l and int(args.l) > 0:
diff --git a/examples/flexible_api.py b/examples/flexible_api.py
@@ -250,7 +250,7 @@ def pnetcdf_io(filename, file_format):
     if args.q: verbose = False
 
     if args.k:
-        kind_dict = {'1':None, '2':"64BIT_OFFSET", '5':"64BIT_DATA"}
+        kind_dict = {'1':None, '2':"NETCDF3_64BIT_OFFSET", '5':"NETCDF3_64BIT_DATA"}
         file_format = kind_dict[args.k]
 
     filename = args.dir
diff --git a/examples/get_info.py b/examples/get_info.py
@@ -64,7 +64,7 @@ def pnetcdf_io(filename):
         print("{}: example of getting MPI-IO hints".format(os.path.basename(__file__)))
 
     # create a new file using clobber "w" mode
-    f = pnetcdf.File(filename=filename, mode = 'w', file_format = "64BIT_DATA", comm=comm, info=None)
+    f = pnetcdf.File(filename=filename, mode = 'w', file_format = "NETCDF3_64BIT_DATA", comm=comm, info=None)
 
     # exit the define mode
     f.enddef()
diff --git a/examples/get_vara.py b/examples/get_vara.py
@@ -132,7 +132,7 @@ def pnetcdf_io(filename, file_format):
     if args.q: verbose = False
 
     if args.k:
-        kind_dict = {'1':None, '2':"64BIT_OFFSET", '5':"64BIT_DATA"}
+        kind_dict = {'1':None, '2':"NETCDF3_64BIT_OFFSET", '5':"NETCDF3_64BIT_DATA"}
         file_format = kind_dict[args.k]
 
     filename = args.dir
diff --git a/examples/ghost_cell.py b/examples/ghost_cell.py
@@ -173,7 +173,7 @@ def pnetcdf_io(filename, file_format, length):
 
     file_format = None
     if args.k:
-        kind_dict = {'1':None, '2':"64BIT_OFFSET", '5':"64BIT_DATA"}
+        kind_dict = {'1':None, '2':"NETCDF3_64BIT_OFFSET", '5':"NETCDF3_64BIT_DATA"}
         file_format = kind_dict[args.k]
 
     length = 4
diff --git a/examples/global_attribute.py b/examples/global_attribute.py
@@ -131,7 +131,7 @@ def pnetcdf_io(filename, file_format):
 
     file_format = None
     if args.k:
-        kind_dict = {'1':None, '2':"64BIT_OFFSET", '5':"64BIT_DATA"}
+        kind_dict = {'1':None, '2':"NETCDF3_64BIT_OFFSET", '5':"NETCDF3_64BIT_DATA"}
         file_format = kind_dict[args.k]
 
     try:
diff --git a/examples/hints.py b/examples/hints.py
@@ -103,7 +103,7 @@ def pnetcdf_io(filename):
     info1.Set("nc_header_read_chunk_size", "256")
 
     # create a new file for writing
-    f = pnetcdf.File(filename=filename, mode = 'w', file_format = "64BIT_DATA", comm=comm, info=info1)
+    f = pnetcdf.File(filename=filename, mode = 'w', file_format = "NETCDF3_64BIT_DATA", comm=comm, info=info1)
 
     # define dimensions
     dim_z = f.def_dim('Z', NZ*nprocs)
diff --git a/examples/nonblocking_write.py b/examples/nonblocking_write.py
@@ -91,7 +91,7 @@ def pnetcdf_io(filename, length):
 
     # Create the file
     try:
-        f = pnetcdf.File(filename=filename, mode = 'w', format = "64BIT_DATA", comm=comm, info=None)
+        f = pnetcdf.File(filename=filename, mode = 'w', format = "NETCDF3_64BIT_DATA", comm=comm, info=None)
     except OSError as e:
         print("Error at {}:{} ncmpi_create() file {} ({})".format(__file__,inspect.currentframe().f_back.f_lineno, filename, e))
         comm.Abort()
diff --git a/examples/nonblocking_write_def.py b/examples/nonblocking_write_def.py
@@ -92,7 +92,7 @@ def pnetcdf_io(file_name, length):
     write_timing = MPI.Wtime()
 
     # Create the file
-    f = pnetcdf.File(filename=filename, mode = 'w', format = "64BIT_DATA", comm=comm, info=None)
+    f = pnetcdf.File(filename=filename, mode = 'w', format = "NETCDF3_64BIT_DATA", comm=comm, info=None)
 
     # Define dimensions
     dims = []
diff --git a/examples/put_vara.py b/examples/put_vara.py
@@ -149,7 +149,7 @@ def pnetcdf_io(filename, file_format):
 
     file_format = None
     if args.k:
-        kind_dict = {'1':None, '2':"64BIT_OFFSET", '5':"64BIT_DATA"}
+        kind_dict = {'1':None, '2':"NETCDF3_64BIT_OFFSET", '5':"NETCDF3_64BIT_DATA"}
         file_format = kind_dict[args.k]
 
     filename = args.dir
diff --git a/examples/put_varn_int.py b/examples/put_varn_int.py
@@ -175,7 +175,7 @@ def pnetcdf_io(file_name, file_format):
 
     file_format = None
     if args.k:
-        kind_dict = {'1':None, '2':"64BIT_OFFSET", '5':"64BIT_DATA"}
+        kind_dict = {'1':None, '2':"NETCDF3_64BIT_OFFSET", '5':"NETCDF3_64BIT_DATA"}
         file_format = kind_dict[args.k]
 
     filename = args.dir
diff --git a/examples/transpose.py b/examples/transpose.py
@@ -181,7 +181,7 @@ def pnetcdf_io(filename, file_format, length):
 
     file_format = None
     if args.k:
-        kind_dict = {'1':None, '2':"64BIT_OFFSET", '5':"64BIT_DATA"}
+        kind_dict = {'1':None, '2':"NETCDF3_64BIT_OFFSET", '5':"NETCDF3_64BIT_DATA"}
         file_format = kind_dict[args.k]
 
     length = 10
diff --git a/examples/transpose2D.py b/examples/transpose2D.py
@@ -167,7 +167,7 @@ def pnetcdf_io(filename, file_format, length):
 
     file_format = None
     if args.k:
-        kind_dict = {'1':None, '2':"64BIT_OFFSET", '5':"64BIT_DATA"}
+        kind_dict = {'1':None, '2':"NETCDF3_64BIT_OFFSET", '5':"NETCDF3_64BIT_DATA"}
         file_format = kind_dict[args.k]
 
     length = 2
diff --git a/src/pnetcdf/_File.pyx b/src/pnetcdf/_File.pyx
@@ -36,7 +36,7 @@ ctypedef MPI.Info Info
 cdef class File:
     def __init__(self, filename, mode="w", format=None, Comm comm=None, Info info=None, **kwargs):
         """
-        __init__(self, filename, format='64BIT_OFFSET', mode="w", Comm comm=None, Info info=None, **kwargs)
+        __init__(self, filename, format=None, mode="w", Comm comm=None, Info info=None, **kwargs)
 
         The constructor for :class:`pnetcdf.File`.
 
@@ -53,9 +53,9 @@ cdef class File:
 
         :param format: underlying file format. Only relevant when creating file
 
-            - ``64BIT_OFFSET``: CDF-2 format
-            - ``64BIT_DATA``: CDF-5 format
-            - `None` defaults to default file format (CDF-1 format)
+            - ``NETCDF3_64BIT_OFFSET`` or ``NC_64BIT_OFFSET``: CDF-2 format
+            - ``NETCDF3_64BIT_DATA`` or ``NC_64BIT_DATA``: CDF-5 format
+            - ``NETCDF3_CLASSIC`` or `None` defaults to default file format (CDF-1 format)
 
         :type format: str
 
@@ -79,9 +79,9 @@ cdef class File:
         bytestr = _strencode(filename, encoding=encoding)
         path = bytestr
         if format:
-            supported_formats = ["64BIT_OFFSET", "64BIT_DATA"]
+            supported_formats = ["NETCDF3_64BIT_OFFSET", "NETCDF3_64BIT_DATA", "NETCDF3_CLASSIC", "NC_64BIT_OFFSET", "NC_64BIT_DATA"]
             if format not in supported_formats:
-                msg="underlying file format must be one of `'64BIT_OFFSET'` or `'64BIT_DATA'`"
+                msg="underlying file format must be one of `'NETCDF3_CLASSIC'`, `'NETCDF3_64BIT_OFFSET'` (same as `'NC_64BIT_OFFSET'`) or `'NETCDF3_64BIT_DATA'` (same as `'NC_64BIT_DATA'`)"
                 raise ValueError(msg)
 
         clobber = True
@@ -94,8 +94,8 @@ cdef class File:
             cmode = 0
             if not clobber:
                 cmode = NC_NOCLOBBER
-            if format in ['64BIT_OFFSET', '64BIT_DATA']:
-                file_cmode = NC_64BIT_OFFSET_C if format  == '64BIT_OFFSET' else NC_64BIT_DATA_C
+            if format in ['NETCDF3_64BIT_OFFSET', 'NETCDF3_64BIT_DATA', 'NC_64BIT_OFFSET', 'NC_64BIT_DATA']:
+                file_cmode = NC_64BIT_OFFSET_C if format in ['NETCDF3_64BIT_OFFSET', 'NC_64BIT_OFFSET'] else NC_64BIT_DATA_C
                 cmode = cmode | file_cmode
             with nogil:
                 ierr = ncmpi_create(mpicomm, path, cmode, mpiinfo, &ncid)
diff --git a/test/tst_atts.py b/test/tst_atts.py
@@ -44,7 +44,7 @@
            'emptystratt':EMPTYSTRATT,'intatt':INTATT}
 
 NUM_TESTS = 3
-file_formats = [fmt for fmt in ['64BIT_DATA', '64BIT_OFFSET', None] for i in range(NUM_TESTS)]
+file_formats = [fmt for fmt in ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None] for i in range(NUM_TESTS)]
 
 class AttrTestCase(unittest.TestCase):
 
diff --git a/test/tst_default_format.py b/test/tst_default_format.py
@@ -55,7 +55,7 @@ def setUp(self):
         # inquiry current default (for testing)
         self.new_default = inq_default_format()
         # create CDF-2 netCDF files by overwriting default
-        f = pnetcdf.File(filename=self.file_paths[1], mode = 'w', format = "64BIT_OFFSET", comm=comm, info=None)
+        f = pnetcdf.File(filename=self.file_paths[1], mode = 'w', format = "NC_64BIT_OFFSET", comm=comm, info=None)
         f.close()
         assert validate_nc_file(os.environ.get('PNETCDF_DIR'), self.file_paths[1]) == 0 if os.environ.get('PNETCDF_DIR') is not None else True
         # change default file format back to "CLASSIC"
diff --git a/test/tst_dims.py b/test/tst_dims.py
@@ -15,7 +15,7 @@
 
 
 NUM_TESTS = 5
-file_formats = [fmt for fmt in ['64BIT_DATA', '64BIT_OFFSET', None] for i in range(NUM_TESTS)]
+file_formats = [fmt for fmt in ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None] for i in range(NUM_TESTS)]
 FILE_NAME = "tst_dims.nc"
 
 LAT_NAME="lat"
diff --git a/test/tst_file_fill.py b/test/tst_file_fill.py
@@ -20,7 +20,7 @@
 import io
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_file_fill.nc"
 
 
diff --git a/test/tst_file_inq.py b/test/tst_file_inq.py
@@ -24,7 +24,7 @@
 import io
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_file_inq.nc"
 xdim=9; ydim=10; zdim = 11
 
diff --git a/test/tst_file_mode.py b/test/tst_file_mode.py
@@ -24,7 +24,7 @@
 
 seed(0)
 # Format of the data file we will create (64BIT_DATA for CDF-5 and 64BIT_OFFSET for CDF-2 and None for CDF-1)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 # Name of the test data file
 file_name = "tst_file_mode.nc"
 xdim = 9
diff --git a/test/tst_rename.py b/test/tst_rename.py
@@ -22,7 +22,7 @@
 
 seed(0)
 # Format of the data file we will create (64BIT_DATA for CDF-5 and 64BIT_OFFSET for CDF-2 and None for CDF-1)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 # Name of the test data file
 file_name = "tst_rename.nc"
 
diff --git a/test/tst_var_bput_var.py b/test/tst_var_bput_var.py
@@ -22,7 +22,7 @@
 import io
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_var_bput_var.nc"
 xdim=9; ydim=10; zdim=11
 data = randint(0,10, size=(xdim,ydim,zdim)).astype('i4')
diff --git a/test/tst_var_bput_var1.py b/test/tst_var_bput_var1.py
@@ -23,7 +23,7 @@
 import io
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_var_bput_var1.nc"
 
 comm = MPI.COMM_WORLD
diff --git a/test/tst_var_bput_vara.py b/test/tst_var_bput_vara.py
@@ -22,7 +22,7 @@
 import io
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_var_bput_vara.nc"
 
 comm = MPI.COMM_WORLD
diff --git a/test/tst_var_bput_varm.py b/test/tst_var_bput_varm.py
@@ -23,7 +23,7 @@
 import io
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_var_bput_varm.nc"
 
 comm = MPI.COMM_WORLD
diff --git a/test/tst_var_bput_varn.py b/test/tst_var_bput_varn.py
@@ -211,7 +211,7 @@ def run_test(format):
 
 if __name__ == '__main__':
     # test CDF-1, CDF-2, CDF-5 classic NetCDF file formats
-    file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+    file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
     for i in range(len(file_formats)):
         try:
             run_test(file_formats[i])
diff --git a/test/tst_var_bput_vars.py b/test/tst_var_bput_vars.py
@@ -22,7 +22,7 @@
 import io
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_var_bput_vars.nc"
 
 comm = MPI.COMM_WORLD
diff --git a/test/tst_var_def_fill.py b/test/tst_var_def_fill.py
@@ -24,7 +24,7 @@
 import numpy.ma as ma
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_var_def_fill.nc"
 
 # file value to be set for each variable
diff --git a/test/tst_var_get_var.py b/test/tst_var_get_var.py
@@ -18,7 +18,7 @@
 import io
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_var_get_var.nc"
 xdim=9; ydim=10; zdim=11
 # generate numpy array to write to the netCDF variable
diff --git a/test/tst_var_get_var1.py b/test/tst_var_get_var1.py
@@ -18,7 +18,7 @@
 import io
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_var_get_var1.nc"
 
 comm = MPI.COMM_WORLD
diff --git a/test/tst_var_get_vara.py b/test/tst_var_get_vara.py
@@ -18,7 +18,7 @@
 import io
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_var_get_vara.nc"
 
 
diff --git a/test/tst_var_get_varm.py b/test/tst_var_get_varm.py
@@ -19,7 +19,7 @@
 
 seed(0)
 # Format of the data file we will create (64BIT_DATA for CDF-5 and 64BIT_OFFSET for CDF-2)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 # Name of the test data file
 file_name = "tst_var_get_varm.nc"
 
diff --git a/test/tst_var_get_varn.py b/test/tst_var_get_varn.py
@@ -14,7 +14,7 @@
 import argparse
 
 
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_var_get_varn.nc"
 
 
diff --git a/test/tst_var_get_vars.py b/test/tst_var_get_vars.py
@@ -19,7 +19,7 @@
 import io
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_var_get_vars.nc"
 
 
diff --git a/test/tst_var_iget_var.py b/test/tst_var_iget_var.py
@@ -20,7 +20,7 @@
 import io
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_var_iget_var.nc"
 xdim=9; ydim=10; zdim=11
 # values to be written to netCDF variables
diff --git a/test/tst_var_iget_var1.py b/test/tst_var_iget_var1.py
@@ -20,7 +20,7 @@
 import io
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_var_iget_var1.nc"
 
 comm = MPI.COMM_WORLD
diff --git a/test/tst_var_iget_vara.py b/test/tst_var_iget_vara.py
@@ -20,7 +20,7 @@
 import io
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_var_iget_vara.nc"
 
 comm = MPI.COMM_WORLD
diff --git a/test/tst_var_iget_varm.py b/test/tst_var_iget_varm.py
@@ -20,7 +20,7 @@
 import io
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_var_iget_varm.nc"
 
 comm = MPI.COMM_WORLD
diff --git a/test/tst_var_iget_varn.py b/test/tst_var_iget_varn.py
@@ -20,7 +20,7 @@
 import io
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_var_iget_varn.nc"
 
 comm = MPI.COMM_WORLD
diff --git a/test/tst_var_iget_vars.py b/test/tst_var_iget_vars.py
@@ -20,7 +20,7 @@
 import io
 
 seed(0)
-file_formats = ['64BIT_DATA', '64BIT_OFFSET', None]
+file_formats = ['NC_64BIT_DATA', 'NC_64BIT_OFFSET', None]
 file_name = "tst_var_iget_vars.nc"
 
 comm = MPI.COMM_WORLD
diff --git a/test/tst_var_indexer.py b/test/tst_var_indexer.py
diff --git a/test/tst_var_iput_var.py b/test/tst_var_iput_var.py
diff --git a/test/tst_var_iput_var1.py b/test/tst_var_iput_var1.py
diff --git a/test/tst_var_iput_vara.py b/test/tst_var_iput_vara.py
diff --git a/test/tst_var_iput_varm.py b/test/tst_var_iput_varm.py
diff --git a/test/tst_var_iput_varn.py b/test/tst_var_iput_varn.py
diff --git a/test/tst_var_iput_vars.py b/test/tst_var_iput_vars.py
diff --git a/test/tst_var_put_var.py b/test/tst_var_put_var.py
diff --git a/test/tst_var_put_var1.py b/test/tst_var_put_var1.py
diff --git a/test/tst_var_put_vara.py b/test/tst_var_put_vara.py
diff --git a/test/tst_var_put_varm.py b/test/tst_var_put_varm.py
diff --git a/test/tst_var_put_varn.py b/test/tst_var_put_varn.py
diff --git a/test/tst_var_put_vars.py b/test/tst_var_put_vars.py
diff --git a/test/tst_var_rec_fill.py b/test/tst_var_rec_fill.py
diff --git a/test/tst_var_string.py b/test/tst_var_string.py
diff --git a/test/tst_var_type.py b/test/tst_var_type.py
diff --git a/test/tst_wait.py b/test/tst_wait.py
