refactor: single implicit import of altimetry tools (#68)

* docs: place some imports behind try/except statements

Author: tsutterley

doc/environment.yml

@@ -8,30 +8,22 @@ dependencies:
   - freetype
   - future
   - graphviz
-  - h5py>=2.9=mpi*
   - lxml
   - matplotlib
-  - mpi4py
-  - netCDF4
   - notebook
   - numpy
   - numpydoc
-  - pandas
   - paramiko
   - pip
   - pyproj
   - python>=3.6
   - python-dateutil
   - pyyaml
   - scipy
-  - scikit-learn
   - scp
   - sphinx
   - sphinx_rtd_theme
-  - texlive-core
-  - zarr
   - pip:
     - sphinx-argparse>=0.4
-    - git+https://github.com/tsutterley/yapc.git
     - ..
 

doc/source/api_reference/utilities.rst

@@ -21,6 +21,10 @@ General Methods
 
 .. autofunction:: icesat2_toolkit.utilities.get_hash
 
+.. autofunction:: icesat2_toolkit.utilities.get_git_revision_hash
+
+.. autofunction:: icesat2_toolkit.utilities.get_git_status
+
 .. autofunction:: icesat2_toolkit.utilities.url_split
 
 .. autofunction:: icesat2_toolkit.utilities.s3_client

icesat2_toolkit/convert.py

@@ -1,6 +1,6 @@
 """
 convert.py
-Written by Tyler Sutterley (06/2022)
+Written by Tyler Sutterley (12/2022)
 Utilities for converting ICESat-2 HDF5 files into different formats
 
 PYTHON DEPENDENCIES:
@@ -21,6 +21,7 @@
     time.py: Utilities for calculating time operations
 
 UPDATE HISTORY:
+    Updated 12/2022: place some imports behind try/except statements
     Updated 06/2022: place zarr and pandas imports behind try/except statements
     Updated 04/2022: updated docstrings to numpy documentation format
     Updated 01/2022: added ascii and dataframe outputs for ATL07
@@ -33,26 +34,33 @@
 """
 import os
 import re
-import h5py
 import warnings
 import itertools
 import posixpath
 import numpy as np
 from icesat2_toolkit.convert_delta_time import convert_delta_time
 
+# attempt imports
+try:
+    import h5py
+except ModuleNotFoundError:
+    warnings.filterwarnings("always")
+    warnings.warn("h5py not available")
+    warnings.warn("Some functions will throw an exception if called")
 try:
     import pandas
 except ModuleNotFoundError:
     warnings.filterwarnings("always")
     warnings.warn("pandas not available")
     warnings.warn("Some functions will throw an exception if called")
-
 try:
     import zarr
 except ModuleNotFoundError:
     warnings.filterwarnings("always")
     warnings.warn("zarr not available")
     warnings.warn("Some functions will throw an exception if called")
+# ignore warnings
+warnings.filterwarnings("ignore")
 
 class convert():
     np.seterr(invalid='ignore')

icesat2_toolkit/fit.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 fit.py
-Written by Tyler Sutterley (05/2021)
+Written by Tyler Sutterley (12/2021)
 Utilities for calculating average fits from ATL03 Geolocated Photon Data
 
 PYTHON DEPENDENCIES:
@@ -15,16 +15,26 @@
         https://github.com/scikit-learn/scikit-learn
 
 UPDATE HISTORY:
+    Updated 12/2022: place some imports behind try/except statements
     Updated 04/2022: updated docstrings to numpy documentation format
     Written 05/2021
 """
 import operator
+import warnings
 import itertools
 import numpy as np
 import scipy.stats
 import scipy.signal
 import scipy.optimize
-import sklearn.neighbors
+
+# attempt imports
+try:
+    import sklearn.neighbors
+except (ImportError, ModuleNotFoundError) as e:
+    warnings.filterwarnings("always")
+    warnings.warn("scikit-learn not available")
+# ignore warnings
+warnings.filterwarnings("ignore")
 
 # PURPOSE: compress complete list of valid indices into a set of ranges
 def compress_list(i,n):

icesat2_toolkit/read_ICESat2_ATL03.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 u"""
-read_ICESat2_ATL03.py (04/2022)
+read_ICESat2_ATL03.py (12/2022)
 Read ICESat-2 ATL03 and ATL09 data files to calculate average segment surfaces
     ATL03 datasets: Global Geolocated Photons
     ATL09 datasets: Atmospheric Characteristics
@@ -15,6 +15,7 @@
         https://www.h5py.org/
 
 UPDATE HISTORY:
+    Updated 12/2022: place some imports behind try/except statements
     Updated 04/2022: updated docstrings to numpy documentation format
     Updated 10/2021: using python logging for handling verbose output
     Updated 02/2021: add check if input streaming from bytes
@@ -33,11 +34,21 @@
 import os
 import io
 import re
-import h5py
 import logging
+import warnings
 import numpy as np
 import scipy.interpolate
 
+# attempt imports
+try:
+    import h5py
+except ModuleNotFoundError:
+    warnings.filterwarnings("always")
+    warnings.warn("h5py not available")
+    warnings.warn("Some functions will throw an exception if called")
+# ignore warnings
+warnings.filterwarnings("ignore")
+
 # PURPOSE: read ICESat-2 ATL03 HDF5 data files
 def read_HDF5_ATL03(FILENAME, ATTRIBUTES=False, **kwargs):
     """

icesat2_toolkit/read_ICESat2_ATL06.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 u"""
-read_ICESat2_ATL06.py (04/2022)
+read_ICESat2_ATL06.py (12/2022)
 Read ICESat-2 ATL06 (Land Ice Along-Track Height Product) data files
 
 OPTIONS:
@@ -16,6 +16,7 @@
         https://www.h5py.org/
 
 UPDATE HISTORY:
+    Updated 12/2022: place some imports behind try/except statements
     Updated 04/2022: updated docstrings to numpy documentation format
     Updated 10/2021: using python logging for handling verbose output
     Updated 02/2021: add check if input streaming from bytes
@@ -31,10 +32,20 @@
 import os
 import io
 import re
-import h5py
 import logging
+import warnings
 import numpy as np
 
+# attempt imports
+try:
+    import h5py
+except ModuleNotFoundError:
+    warnings.filterwarnings("always")
+    warnings.warn("h5py not available")
+    warnings.warn("Some functions will throw an exception if called")
+# ignore warnings
+warnings.filterwarnings("ignore")
+
 # PURPOSE: read ICESat-2 ATL06 HDF5 data files
 def read_HDF5_ATL06(FILENAME, ATTRIBUTES=False, HISTOGRAM=False,
     QUALITY=False, **kwargs):

icesat2_toolkit/read_ICESat2_ATL07.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 u"""
-read_ICESat2_ATL07.py (04/2022)
+read_ICESat2_ATL07.py (12/2022)
 Read ICESat-2 ATL07 (Sea Ice Height) data files
 
 PYTHON DEPENDENCIES:
@@ -11,6 +11,7 @@
         https://www.h5py.org/
 
 UPDATE HISTORY:
+    Updated 12/2022: place some imports behind try/except statements
     Updated 04/2022: updated docstrings to numpy documentation format
     Updated 10/2021: using python logging for handling verbose output
     Updated 02/2021: add check if input streaming from bytes
@@ -24,10 +25,20 @@
 import os
 import io
 import re
-import h5py
 import logging
+import warnings
 import numpy as np
 
+# attempt imports
+try:
+    import h5py
+except ModuleNotFoundError:
+    warnings.filterwarnings("always")
+    warnings.warn("h5py not available")
+    warnings.warn("Some functions will throw an exception if called")
+# ignore warnings
+warnings.filterwarnings("ignore")
+
 # PURPOSE: read ICESat-2 ATL07 HDF5 data files
 def read_HDF5_ATL07(FILENAME, ATTRIBUTES=False, **kwargs):
     """

icesat2_toolkit/read_ICESat2_ATL10.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 u"""
-read_ICESat2_ATL10.py (04/2022)
+read_ICESat2_ATL10.py (12/2022)
 Read ICESat-2 ATL10 (Sea Ice Freeboard) data files
 
 PYTHON DEPENDENCIES:
@@ -11,6 +11,7 @@
         https://www.h5py.org/
 
 UPDATE HISTORY:
+    Updated 12/2022: place some imports behind try/except statements
     Updated 04/2022: updated docstrings to numpy documentation format
     Written 12/2021
 """
@@ -19,10 +20,20 @@
 import os
 import io
 import re
-import h5py
 import logging
+import warnings
 import numpy as np
 
+# attempt imports
+try:
+    import h5py
+except ModuleNotFoundError:
+    warnings.filterwarnings("always")
+    warnings.warn("h5py not available")
+    warnings.warn("Some functions will throw an exception if called")
+# ignore warnings
+warnings.filterwarnings("ignore")
+
 # PURPOSE: read ICESat-2 ATL10 HDF5 data files
 def read_HDF5_ATL10(FILENAME, ATTRIBUTES=False, **kwargs):
     """

icesat2_toolkit/read_ICESat2_ATL11.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 u"""
-read_ICESat2_ATL11.py (04/2022)
+read_ICESat2_ATL11.py (12/2022)
 Read ICESat-2 ATL11 (Annual Land Ice Height) data files
 
 OPTIONS:
@@ -18,6 +18,7 @@
         https://www.h5py.org/
 
 UPDATE HISTORY:
+    Updated 12/2022: place some imports behind try/except statements
     Updated 04/2022: updated docstrings to numpy documentation format
     Updated 10/2021: using python logging for handling verbose output
     Updated 03/2021: added function for reading only pair level variables
@@ -32,10 +33,20 @@
 import os
 import io
 import re
-import h5py
 import logging
+import warnings
 import numpy as np
 
+# attempt imports
+try:
+    import h5py
+except ModuleNotFoundError:
+    warnings.filterwarnings("always")
+    warnings.warn("h5py not available")
+    warnings.warn("Some functions will throw an exception if called")
+# ignore warnings
+warnings.filterwarnings("ignore")
+
 # PURPOSE: read ICESat-2 ATL11 HDF5 data files
 def read_HDF5_ATL11(FILENAME, GROUPS=['cycle_stats'], ATTRIBUTES=False,
     REFERENCE=False, CROSSOVERS=False, SUBSETTING=False, **kwargs):

icesat2_toolkit/read_ICESat2_ATL12.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 u"""
-read_ICESat2_ATL12.py (04/2022)
+read_ICESat2_ATL12.py (12/2022)
 Read ICESat-2 ATL12 (Ocean Surface Height) data files
 
 PYTHON DEPENDENCIES:
@@ -11,6 +11,7 @@
         https://www.h5py.org/
 
 UPDATE HISTORY:
+    Updated 12/2022: place some imports behind try/except statements
     Updated 04/2022: updated docstrings to numpy documentation format
     Updated 10/2021: using python logging for handling verbose output
     Updated 02/2021: add check if input streaming from bytes
@@ -23,10 +24,20 @@
 import os
 import io
 import re
-import h5py
 import logging
+import warnings
 import numpy as np
 
+# attempt imports
+try:
+    import h5py
+except ModuleNotFoundError:
+    warnings.filterwarnings("always")
+    warnings.warn("h5py not available")
+    warnings.warn("Some functions will throw an exception if called")
+# ignore warnings
+warnings.filterwarnings("ignore")
+
 # PURPOSE: read ICESat-2 ATL12 HDF5 data files
 def read_HDF5_ATL12(FILENAME, ATTRIBUTES=False, **kwargs):
     """