feat: use attempt login for nsidc utilities (#55)

* feat:  add NASA CMR spatial bounding box queries
* feat: update classify photons parameters to match current GSFC version
* feat: updates for uploading to pypi
* refactor: place some imports behind try/except statements

.github/workflows/Dockerfile

@@ -300,6 +300,7 @@ RUN pip3 install --no-cache-dir --no-binary=h5py,cartopy \
         paramiko \
         pyproj \
         python-dateutil \
+        pyYAPC \
         scikit-learn \
         scipy \
         scp \

README.rst

@@ -4,6 +4,7 @@ read-ICESat-2
 
 |Language|
 |License|
+|PyPI Version|
 |Documentation Status|
 |Binder|
 |Pangeo|
@@ -15,6 +16,9 @@ read-ICESat-2
 .. |License| image:: https://img.shields.io/badge/license-MIT-green.svg
    :target: https://github.com/tsutterley/read-ICESat-2/blob/main/LICENSE
 
+.. |PyPI Version| image:: https://img.shields.io/pypi/v/icesat2-toolkit.svg
+   :target: https://pypi.python.org/pypi/icesat2-toolkit/
+
 .. |Documentation Status| image:: https://readthedocs.org/projects/read-icesat-2/badge/?version=latest
    :target: https://read-icesat-2.readthedocs.io/en/latest/?badge=latest
 

doc/source/getting_started/Install.rst

@@ -27,8 +27,8 @@ The ``read-ICESat-2`` installation uses the ``gdal-config`` routines to set the
 Installation
 ############
 
-Presently ``read-ICESat-2`` is only available for use as a
-`GitHub repository <https://github.com/tsutterley/read-ICESat-2>`_.
+``read-ICESat-2`` is available for download from the `GitHub repository <https://github.com/tsutterley/read-ICESat-2>`_,
+and the `Python Package Index (pypi) <https://pypi.org/project/icesat2-toolkit/>`_,
 The contents of the repository can be download as a
 `zipped file <https://github.com/tsutterley/read-ICESat-2/archive/main.zip>`_  or cloned.
 To use this repository, please fork into your own account and then clone onto your system.
@@ -55,6 +55,11 @@ Alternatively can install the utilities directly from GitHub with ``pip``:
 
     python3 -m pip install --user git+https://github.com/tsutterley/read-ICESat-2.git
 
-Executable versions of this repository can also be tested using
-`Binder <https://mybinder.org/v2/gh/tsutterley/read-ICESat-2/main>`_ or
-`Pangeo <https://aws-uswest2-binder.pangeo.io/v2/gh/tsutterley/read-ICESat-2/main?urlpath=lab>`_.
+| This repository can be also tested using `BinderHub <https://github.com/jupyterhub/binderhub>`_ platforms:
+| |Binder| |Pangeo|
+
+.. |Binder| image:: https://mybinder.org/badge_logo.svg
+   :target: https://mybinder.org/v2/gh/tsutterley/read-ICESat-2/main
+
+.. |Pangeo| image:: https://img.shields.io/static/v1.svg?logo=Jupyter&label=PangeoBinderAWS&message=us-west-2&color=orange
+   :target: https://aws-uswest2-binder.pangeo.io/v2/gh/tsutterley/read-ICESat-2/main?urlpath=lab

doc/source/getting_started/Parallel-HDF5.rst

@@ -41,27 +41,27 @@ Dependencies
 
 .. code-block:: bash
 
-    curl -O http://zlib.net/zlib-1.2.11.tar.gz
+    curl -O http://zlib.net/zlib-1.2.12.tar.gz
     export CFLAGS=-fPIC
-    mkdir -p $HOME/packages/zlib/1.2.11
-    ./configure --prefix=$HOME/packages/zlib/1.2.11
+    mkdir -p $HOME/packages/zlib/1.2.12
+    ./configure --prefix=$HOME/packages/zlib/1.2.12
     make
     make install
 
-modulefile for local installation of zlib (``~/privatemodules/zlib/1.2.11``):
+modulefile for local installation of zlib (``~/privatemodules/zlib/1.2.12``):
 
 .. code-block:: tcl
 
     #%Module 1.0
     #
     #  zlib module for use with 'environment-modules' package:
     #
-    module-whatis		"Provides zlib 1.2.11 (local)"
+    module-whatis		"Provides zlib 1.2.12 (local)"
     global              env
-    prepend-path        PATH            $env(HOME)/packages/zlib/1.2.11/bin
-    prepend-path        LD_LIBRARY_PATH $env(HOME)/packages/zlib/1.2.11/lib
-    prepend-path        MANPATH         $env(HOME)/packages/zlib/1.2.11/share/man/
-    append-path         ZLIB_DIR        $env(HOME)/packages/zlib/1.2.11/
+    prepend-path        PATH            $env(HOME)/packages/zlib/1.2.12/bin
+    prepend-path        LD_LIBRARY_PATH $env(HOME)/packages/zlib/1.2.12/lib
+    prepend-path        MANPATH         $env(HOME)/packages/zlib/1.2.12/share/man/
+    append-path         ZLIB_DIR        $env(HOME)/packages/zlib/1.2.12/
 
 
 - `szip <https://support.hdfgroup.org/doc_resource/SZIP/>`_
@@ -127,7 +127,7 @@ modulefile for local installation of OpenMPI (``~/privatemodules/mpi/openmpi/4.0
     CC=~/packages/mpi/openmpi/4.0.3/bin/mpicc ./configure \
         --enable-parallel --enable-hl --enable-shared \
         --prefix=$HOME/packages/hdf5/1.10.5 \
-        --with-zlib=$HOME/packages/zlib/1.2.11 \
+        --with-zlib=$HOME/packages/zlib/1.2.12 \
         --with-szip=$HOME/packages/szip/2.1.1
     make
     make check
@@ -143,7 +143,7 @@ modulefile for local installation of HDF5 (``~/privatemodules/hdf5/1.10.5``):
     #
     module-whatis		"Provides hdf5 1.10.5 (local)"
     global              env
-    prereq	$env(HOME)/privatemodules/zlib/1.2.11	$env(HOME)/privatemodules/szip/2.1.1	$env(HOME)/privatemodules/mpi/openmpi/4.0.3
+    prereq	$env(HOME)/privatemodules/zlib/1.2.12	$env(HOME)/privatemodules/szip/2.1.1	$env(HOME)/privatemodules/mpi/openmpi/4.0.3
     prepend-path        PATH            $env(HOME)/packages/hdf5/1.10.5/bin
     prepend-path        LD_LIBRARY_PATH $env(HOME)/packages/hdf5/1.10.5/lib
     prepend-path        MANPATH         $env(HOME)/packages/hdf5/1.10.5/share/man/

environment.yml

@@ -1,26 +1,26 @@
-name: read-ICESat-2
+name: icesat2_toolkit
 channels:
   - conda-forge
 dependencies:
   - python>=3.6
   - notebook
-  - numpy
-  - scipy
-  - scikit-learn
-  - python-dateutil
-  - pandas
-  - pyproj
-  - matplotlib
+  - boto3
   - cartopy
-  - mpi4py
+  - future
   - gdal
   - h5py>=2.9=mpi*
-  - netCDF4 
-  - zarr
-  - future
-  - boto3
   - lxml
+  - matplotlib
+  - mpi4py
+  - netCDF4
+  - numpy
+  - pandas
   - paramiko
+  - pyproj
+  - python-dateutil
+  - scikit-learn
+  - scipy
   - scp
+  - zarr
   - pip:
      - git+https://github.com/tsutterley/yapc.git

icesat2_toolkit/__init__.py

@@ -19,7 +19,6 @@
 import icesat2_toolkit.time
 import icesat2_toolkit.utilities
 import icesat2_toolkit.version
-from icesat2_toolkit.convert import convert
 from icesat2_toolkit.convert_delta_time import convert_delta_time
 from icesat2_toolkit.read_ICESat2_ATL03 import read_HDF5_ATL03, \
     find_HDF5_ATL03_beams, read_HDF5_ATL09, read_HDF5_ATL03_main, read_HDF5_ATL03_beam
@@ -33,4 +32,4 @@
 from icesat2_toolkit.read_ICESat2_ATL12 import read_HDF5_ATL12, \
     find_HDF5_ATL12_beams
 # get version number
-__version__ = icesat2_toolkit.version.version
+__version__ = icesat2_toolkit.version.version

icesat2_toolkit/convert.py

@@ -1,6 +1,6 @@
 """
 convert.py
-Written by Tyler Sutterley (04/2022)
+Written by Tyler Sutterley (06/2022)
 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 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
     Updated 09/2021: added ground track and time to output dataframes
@@ -33,13 +34,26 @@
 import os
 import re
 import h5py
-import zarr
-import pandas
+import warnings
 import itertools
 import posixpath
 import numpy as np
 from icesat2_toolkit.convert_delta_time import convert_delta_time
 
+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")
+
 class convert():
     np.seterr(invalid='ignore')
     def __init__(self, filename=None, reformat=None):

icesat2_toolkit/spatial.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 spatial.py
-Written by Tyler Sutterley (04/2022)
+Written by Tyler Sutterley (06/2022)
 
 Utilities for reading and operating on spatial data
 
@@ -17,6 +17,7 @@
         https://pypi.python.org/pypi/GDAL
 
 UPDATE HISTORY:
+    Updated 06/2022: place netCDF4 import behind try/except statements
     Updated 04/2022: updated docstrings to numpy documentation format
     Updated 01/2022: use iteration breaks in convert ellipsoid function
     Written 11/2021
@@ -28,14 +29,22 @@
 import uuid
 import h5py
 import logging
-import netCDF4
 import warnings
 import numpy as np
+
+try:
+    import netCDF4
+except ModuleNotFoundError:
+    warnings.filterwarnings("always")
+    warnings.warn("netCDF4 not available")
+    warnings.warn("Some functions will throw an exception if called")
+
 try:
     import osgeo.gdal, osgeo.osr, osgeo.gdalconst
 except ModuleNotFoundError:
     warnings.filterwarnings("always")
     warnings.warn("GDAL not available")
+    warnings.warn("Some functions will throw an exception if called")
 
 def case_insensitive_filename(filename):
     """