Get filepaths to downloaded hdf5 granule files

.coveragerc

@@ -0,0 +1,7 @@
+[run]
+branch = True
+source = icepyx
+omit = 
+ setup.py
+ test/*
+ doc/*

.github/workflows/flake8_action.yml

@@ -0,0 +1,17 @@
+# use the flake8 linter to annotate improperly formatted code
+# from: https://github.com/marketplace/actions/run-flake8-on-your-pr-with-annotations
+name: Run flake8 linter on PRs
+
+on:
+ pull_request:
+ branches:
+ - development
+ - master
+jobs:
+ build:
+ runs-on: ubuntu-latest
+ steps:
+ - name: Annotate PR after running flake8
+ uses: TrueBrain/actions-flake8@master
+ with:
+ max_line_length: 88

.pre-commit-config.yaml

@@ -0,0 +1,5 @@
+repos:
+- repo: https://github.com/psf/black
+ rev: stable
+ hooks:
+ - id: black

.travis.yml

@@ -1,21 +1,42 @@
 language: python
 
+install:
+ - pip install -r requirements.txt -r requirements-dev.txt
+ - pip install -e .
+
 stages:
  - name: basic tests
- if: type = push
+ if: type = push OR type = pull_request
  - name: behind Earthdata
  if: branch = master OR commit_message =~ nsidc_tests OR type = cron
 
-#ultimately move basic tests list into a separate script with the list of files to run (then this can be put into a matrix and paralellized as well)
+#ultimately move basic tests list into a separate script with the list of files to run (then this can be put into a matrix and parallellized as well)
 jobs:
  include:
  - stage: basic tests
- script: pytest icepyx/tests/test_APIformatting.py
- icepyx/tests/test_geospatial.py
- icepyx/tests/test_is2ref.py
- icepyx/tests/test_validate_inputs.py
-
+ script: pytest icepyx/ --ignore icepyx/tests/behind_NSIDC_API_login.py
+ after_success: codecov
+
  # - stage: behind Earthdata
- # script: 
+ # script:
  # - export NSIDC_LOGIN=$NSIDC_LOGIN
  # - pytest icepyx/tests/behind_NSIDC_API_login.py
+
+deploy:
+ - provider: pypi
+ server: https://test.pypi.org/legacy/ 
+ username: "__token__"
+ password: $test_PyPI_API_Token
+ on:
+ branch: development
+ condition: commit_message = test_pypi
+ skip_existing: true
+ - provider: pypi
+ username: "__token__"
+ password: $PyPI_API_Token
+ on:
+ branch: master
+ tags: true
+ skip_existing: true
+# script:
+# - export PyPI_API_Token=$PyPI_API_Token

CONTRIBUTORS.rst

@@ -3,15 +3,18 @@ Project Contributors
 
 The following people have made contributions to the project (in alphabetical
 order by last name) and are considered "The icepyx Developers":
-* [Anthony Arendt](https://github.com/aaarendt/) - University of Washington
-* [Shashank Bhushan](https://github.com/ShashankBice) - University of Washington
-* [Raphael Hagen](https://github.com/norlandrhagen) - University of Washington
-* [Scott Henderson](https://github.com/scottyhq) - University of Washington
-* [Zheng Liu](https://github.com/liuzheng-arctic) - University of Washington
-* [Joakim Meyer](https://github.com/jomey) - University of Utah
-* [Fernando Perez](https://github.com/fperez) - University of California, Berkeley
-* [Jessica Scheick](https://github.com/jessicas11) - Unaffiliated (ORCID: [0000-0002-3421-4459](https://www.orcid.org/0000-0002-3421-4459))
-* [Ben Smith](https://github.com/smithb) - University of Washington
-* [Amy Steiker](https://github.com/asteiker) - NSIDC, University of Colorado
-* [Bidhyananda Yadav](https://github.com/bidhya) - Ohio State University
 
+* `Anthony Arendt <https://github.com/aaarendt/>`_ - University of Washington
+* `Shashank Bhushan <https://github.com/ShashankBice>`_ - University of Washington
+* `Raphael Hagen <https://github.com/norlandrhagen>`_ - University of Washington
+* `Scott Henderson <https://github.com/scottyhq>`_ - University of Washington
+* `Thomas Johnson <https://github.com/loudTom>`_ - University College London
+* `Zheng Liu <https://github.com/liuzheng-arctic>`_ - University of Washington
+* `Joachim Meyer <https://github.com/jomey>`_ - University of Utah
+* `Fernando Perez <https://github.com/fperez>`_ - University of California, Berkeley
+* `Jessica Scheick <https://github.com/jessicas11>`_ - Unaffiliated (ORCID: `0000-0002-3421-4459 <https://www.orcid.org/0000-0002-3421-4459>`_)
+* `David Shean <https://github.com/dshean>`_ - University of Washington
+* `Ben Smith <https://github.com/smithb>`_ - University of Washington
+* `Amy Steiker <https://github.com/asteiker>`_ - NSIDC, University of Colorado
+* `Bidhyananda Yadav <https://github.com/bidhya>`_ - Ohio State University
+* `Anna Valentine <https://github.com/annavalentine>`_ - Colorado School of Mines

README.rst

@@ -3,7 +3,7 @@ icepyx
 
 **Python tools for obtaining and working with ICESat-2 data**
 
-|Documentation Status| |GitHub license| |Travis CI Status|
+|Documentation Status| |GitHub license| |Travis CI Status| |Code Coverage|
 
 .. |Documentation Status| image:: https://readthedocs.org/projects/icepyx/badge/?version=latest
  :target: http://icepyx.readthedocs.io/?badge=latest
@@ -14,6 +14,9 @@ icepyx
 .. |Travis CI Status| image:: https://travis-ci.org/icesat2py/icepyx.svg?branch=master
  :target: https://travis-ci.org/icesat2py/icepyx
 
+.. |Code Coverage| image:: https://codecov.io/gh/icesat2py/icepyx/branch/development/graph/badge.svg 
+ :target: https://codecov.io/gh/icesat2py/icepyx
+
 Origin and Purpose
 ------------------
 icepyx is both a software library and a community composed of ICESat-2 data users, developers, and the scientific community. We are working together to develop a shared library of resources - including existing resources, new code, tutorials, and use-cases/examples - that simplify the process of querying, obtaining, analyzing, and manipulating ICESat-2 datasets to enable scientific discovery.
@@ -26,35 +29,56 @@ This project combines and generalizes these scripts into a unified framework, ma
 
 
 .. _`zipped file`: https://github.com/icesat2py/icepyx/archive/master.zip
+.. _`Fiona`: https://pypi.org/project/Fiona/
 
 Installation
 ------------
-Currently icepyx is only available for use as a github repository.
-The contents of the repository can be download as a `zipped file`_ or cloned.
+The simplest way to install icepyx is using pip.
+
+.. code-block::
+
+ pip install icepyx
+
+
+Windows users will need to first install `Fiona`_, please look at the instructions there. Windows users may consider installing Fiona using pipwin
+
+.. code-block::
+
+ pip install pipwin
+ pipwin install Fiona 
 
-To use icepyx, fork this repo to your own account, then ``git clone`` the repo onto your system.
-Provided the location of the repo is part of your $PYTHONPATH,
-you should simply be able to add ``import icepyx`` to your Python document.
 
+Currently, updated packages are not automatically generated with each build. This means it is possible that pip will not install the latest release of icepyx. In this case, icepyx is also available for use via the GitHub repository. The contents of the repository can be download as a `zipped file`_ or cloned.
+
+To use icepyx this way, fork this repo to your own account, then git clone the repo onto your system. 
 To clone the repository:
 
-.. code-block:: none
+.. code-block::
 
  git clone https://github.com/icesat2py/icepyx.git
 
 
-Future developments of icepyx may include pip and conda as simplified installation options.
+Provided the location of the repo is part of your $PYTHONPATH, you should simply be able to add import icepyx to your Python document.
+Alternatively, in a command line or terminal, navigate to the folder in your cloned repository containing setup.py and run
+
+.. code-block::
+
+ pip install -e
+
+
+Future developments of icepyx may include conda as another simplified installation option.
 
 
 Examples (Jupyter Notebooks)
 ----------------------------
 
-.. _`ICESat-2_DAAC_DataAccess_Example`: ICESat-2_DAAC_DataAccess_Example.ipynb
+Listed below are example jupyter-notebooks
 
+`ICESat-2_DAAC_DataAccess_Example <https://github.com/icesat2py/icepyx/blob/master/examples/ICESat-2_DAAC_DataAccess_Example.ipynb>`_
 
-Listed below are example jupyter-notebooks
+`ICESat-2_DAAC_DataAccess2_Subsetting <https://github.com/icesat2py/icepyx/blob/master/examples/ICESat-2_DAAC_DataAccess2_Subsetting.ipynb>`_
 
-ICESat-2_DAAC_DataAccess_Example_
+`ICESat-2_DEM_comparison_Colombia_working <https://github.com/icesat2py/icepyx/blob/master/examples/ICESat-2_DEM_comparison_Colombia_working.ipynb>`_
 
 
 Citing icepyx
@@ -72,7 +96,7 @@ Come join the conversation at: https://discourse.pangeo.io/.
 Search for "icesat-2" under the "science" topic to find us.
 
 .. _`icepyx`: https://github.com/icesat2py/icepyx
-.. _`contribution guidelines`: ./doc/source/development/contribution_guidelines.rst
+.. _`contribution guidelines`: ./doc/source/contributing/contribution_guidelines.rst
 
 Contribute
 ----------
@@ -82,4 +106,4 @@ Check out our `contribution guidelines`_ to see how you can contribute.
 Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms. |Contributor Covenant|
 
 .. |Contributor Covenant| image:: https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg
- :target: code_of_conduct.md
+ :target: code_of_conduct.md

doc/source/conf.py

@@ -12,7 +12,8 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../..'))
+
+sys.path.insert(0, os.path.abspath("../.."))
 import datetime
 
 import icepyx
@@ -21,9 +22,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'icepyx'
+project = "icepyx"
 year = datetime.date.today().year
-copyright = '2019-{}, The icepyx Developers'.format(year)
+copyright = "2019-{}, The icepyx Developers".format(year)
 
 # -- General configuration ---------------------------------------------------
 
@@ -35,24 +36,19 @@
  "sphinx.ext.autosectionlabel",
  "numpydoc",
  "nbsphinx",
- "recommonmark"
-
+ "recommonmark",
 ]
-source_suffix = {
- '.rst': 'restructuredtext',
- '.txt': 'markdown',
- '.md': 'markdown',
-}
+source_suffix = {".rst": "restructuredtext", ".txt": "markdown", ".md": "markdown"}
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['**.ipynb_checkpoints']
+exclude_patterns = ["**.ipynb_checkpoints"]
 
 # location of master document (by default sphinx looks for contents.rst)
-master_doc = 'index'
+master_doc = "index"
 
 
 # -- Configuration options ---------------------------------------------------
@@ -68,24 +64,30 @@
 # html_theme = 'alabaster'
 html_theme = "sphinx_rtd_theme"
 html_theme_options = {
- 'logo_only': True,
- 'display_version': False,
- 'prev_next_buttons_location': None,
- 'navigation_depth': 4,
- 'collapse_navigation': True
+ "logo_only": True,
+ "display_version": False,
+ "prev_next_buttons_location": None,
+ "navigation_depth": 4,
+ "collapse_navigation": True,
 }
-html_logo = '_static/icepyx_v2_oval_orig_nobackgr.png'
-html_favicon = '_static/icepyx_v2_oval_tiny-uml_nobackgr.png'
-html_static_path = ['_static']
+html_logo = "_static/icepyx_v2_oval_orig_nobackgr.png"
+html_favicon = "_static/icepyx_v2_oval_tiny-uml_nobackgr.png"
+html_static_path = ["_static"]
 
 html_context = {
- 'menu_links_name': '',
- 'menu_links': [
- ('<i class="fa fa-github fa-fw"></i> icepyx Github', 'https://github.com/icesat2py/icepyx'),
- ('<i class="fa fa-comments fa-fw"></i> Pangeo Discourse', 'https://discourse.pangeo.io/t/icepyx-python-tools-for-icesat-2-data/404/2')
-
- ]
+ "menu_links_name": "",
+ "menu_links": [
+ (
+ '<i class="fa fa-github fa-fw"></i> icepyx Github',
+ "https://github.com/icesat2py/icepyx",
+ ),
+ (
+ '<i class="fa fa-comments fa-fw"></i> Pangeo Discourse',
+ "https://discourse.pangeo.io/t/icepyx-python-tools-for-icesat-2-data/404/2",
+ ),
+ ],
 }
 
+
 def setup(app):
  app.add_stylesheet("style.css")

doc/source/contributing/contribution_guidelines.rst

@@ -34,27 +34,28 @@ Find the *Issues* tab at the top of GitHub repository and click *New Issue* butt
 Questions and Help
 ------------------
 
-Please do not create issues to ask for help. A faster way to reach the community is through our Science/ICESat-2 subcategory on the `Pangeo discourse <https://discourse.pangeo.io/c/science/icesat-2/16>`_ page. We are excited to have you join an existing conversation or start a new post! Please note that a github login is required to post on the discourse page.
+Please do not create issues to ask for help. A faster way to reach the community is through our Science/ICESat-2 subcategory on the `Pangeo discourse <https://discourse.pangeo.io/c/science/icesat-2/16>`_ page. We are excited to have you join an existing conversation or start a new post! Please note that a GitHub login is required to post on the discourse page.
 
 Other Resources
 ^^^^^^^^^^^^^^^
-- We are currently working on compiling a list of resources for working with ICESat-2 data (in the meantime, check out the `2019 ICESat-2 Hackweek repo <https://github.com/ICESAT-2HackWeek>`_ and `consider applying for this year's Hackweek <https://icesat-2hackweek.github.io/>`_) 
+- Check out our :ref:`ICESat-2 Open-Source Resources Guide<resource_ref_label>` for a host of tools and code for getting and working with ICESat-2 data
+- The `2019 ICESat-2 Hackweek Tutorial repo <https://github.com/ICESAT-2HackWeek/ICESat2_hackweek_tutorials>`_ and [in progress] `2020 ICESat-2 Hackweek Tutorial repo <https://github.com/ICESAT-2HackWeek/2020_ICESat-2_Hackweek_Tutorials>`_ are great resources for learning basic Python and development skills, learning about ICESat-2 data, setting up a computational environment, and finding and analyzing ICESat-2 datasets.
 - A great set of `interactive tutorials <https://learngitbranching.js.org>`_ for learning and practicing using git
 - Let us know about the helpful tools you've found by posting on our discourse forum as indicated above (`Questions and Help`_)!
 
 
 Adding Examples
 ---------------
-We are delighted you'd like to contribute your `icepyx <https://github.com/icesat2py/icepyx>`_ example! Examples may be in the form of executable scripts or interactive Jupyter Notebooks. Please make sure that each example has a descriptive name so someone not familiar with your project understands its general behavior. Fully working examples should be submitted using a pull request to the "examples" branch, following the steps outlined below for `Contributing Code`_.
+We are delighted you'd like to contribute your `icepyx <https://github.com/icesat2py/icepyx>`_ example! Examples may be in the form of executable scripts or interactive Jupyter Notebooks. Please make sure that each example has a descriptive name so someone not familiar with your project understands its general behavior. Fully working examples should be submitted using a pull request to the "development" branch, following the steps outlined below for `Contributing Code`_.
 
 
 Contributing Code
 -----------------
-We follow a standard git workflow for code changes and additions. All submitted code, including our own, goes through the pull request process; no changes are pushed directly to the *master* branch. This allows our continuous integration (testing) process to ensure that the code is up to our standards and passes all of our tests (i.e. doesn't break what's already there and working). It also means that the *master* branch remains stable even as new features are being developed.
+We follow a standard git workflow for code changes and additions. All submitted code, including our own, goes through the pull request process; no changes are pushed directly to the *master* or *development* branches. This allows our continuous integration (testing) process to ensure that the code is up to our standards and passes all of our tests (i.e. doesn't break what's already there and working). By having a *development* branch for daily work, we enable the *master* branch to remain stable between releases even as new features are being added.
 
 First Steps
 ^^^^^^^^^^^
-Before you even begin writing code, please first check out our issues page. Someone may already be working on the same problem, and you may be able to contribute directly to their efforts. If not, create a new issue to describe what you plan to do.
+Before you begin writing code, please first check out our issues page. Someone may already be working on the same problem, and you may be able to contribute directly to their efforts. If not, create a new issue to describe what you plan to do.
 
 General Guidelines
 ^^^^^^^^^^^^^^^^^^
@@ -75,14 +76,15 @@ We encourage users to follow the `git pull request workflow <https://www.asmeure
  - Clone the repository
  - Fork the repo to your personal GitHub account
  - Add your fork as a remote
+ - Add yourself to `CONTRIBUTORS.rst` (see `Attribution for Contributions`_)
 
-(each time you make changes)
+(each time you are going to make changes)
 
- - Update the master
- - Create a branch
+ - Update the development branch
+ - Create a new branch
  - Make your changes and commit them to the branch
  - Push your changes to your fork
- - Make a pull request (on GitHub)
+ - Make a pull request (on GitHub; pull requests will automatically be made against the development branch)
  - Push any additional, relevant changes to the same pull request (this will happen automatically if you push the changes to the same branch from which you made the pull request)
 
 Licensing

doc/source/getting_started/citation_link.rst

@@ -1,4 +1 @@
-Citing icepyx
-=============
-
 .. include:: ../../../CITATION.rst

doc/source/getting_started/example_link.rst

@@ -1,4 +1,4 @@
 Examples
 ========
 
-.. include:: ../../examples/examples.rst
+.. include:: ../../../examples/examples.rst