[WIP] New files for putting icepyx examples on pangeo-gallery

.coveragerc

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

.github/workflows/binderbot.yaml

@@ -0,0 +1,78 @@
+name: Binderbot
+on:
+  # Trigger the workflow on push or pull request,
+  # but only for the master branch
+  push:
+    branches:
+      - development
+      - master
+    paths:
+      - 'examples/*.ipynb'
+      - 'binder-gallery.yaml'
+      - 'doc/source/_static/icepyx_logo.png'
+  pull_request:
+    branches:
+      - development
+      - master
+    paths:
+      - 'examples/*.ipynb'
+      - 'binder-gallery.yaml'
+      - 'doc/source/_static/icepyx_logo.png'
+
+jobs:
+  build:
+    name: Binderbot Build
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: parse config
+        id: parse
+        uses: CumulusDS/[email protected]
+        with:
+          file: binder-gallery.yaml
+          gallery_repository: gallery_repository
+          binder_url: binder_url
+          binder_repo: binder_repo
+          binder_ref: binder_ref
+          binderbot_target_branch: binderbot_target_branch
+      - name: Verify output
+        run: |
+          echo gallery_repository: "${{ steps.parse.outputs.gallery_repository }}"
+          echo binder_url: "${{ steps.parse.outputs.binder_url }}"
+          echo binder_repo: "${{ steps.parse.outputs.binder_repo }}"
+          echo binder_ref: "${{ steps.parse.outputs.binder_ref }}"
+          echo binderbot_target_branch: "${{ steps.parse.outputs.binderbot_target_branch }}"
+      - uses: actions/setup-python@v1
+        with:
+          python-version: '3.8'
+          architecture: 'x64'
+      - name: Install Binderbot from github master
+        run: pip install git+https://github.com/pangeo-gallery/binderbot.git
+      - name: Create Clean Branch
+        run: |
+          git checkout --orphan ${{ steps.parse.outputs.binderbot_target_branch }}
+          git rm --cached -r .
+      - name: Build notebooks using Binderbot
+        run: |
+          python -m binderbot.cli \
+          --binder-url ${{ steps.parse.outputs.binder_url }} \
+          --repo ${{ steps.parse.outputs.binder_repo }} \
+          --ref ${{ steps.parse.outputs.binder_ref }} \
+          examples/*.ipynb
+      - name: Commit files
+        if: github.ref == 'refs/heads/master'
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Action"
+          git add binder-gallery.yaml doc/source/_static/icepyx_logo.png examples/*.ipynb
+          git commit -m "Binderbot output"
+      - name: Push commit
+        if: github.ref == 'refs/heads/master'
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ steps.parse.outputs.binderbot_target_branch }}
+          force: true
+      - name: Trigger repository dispatch on Pangeo Gallery
+        if: github.ref == 'refs/heads/master'
+        run: curl -f https://pangeo-gallery-bot.herokuapp.com/gallery/submodule-dispatch/${{ github.repository }}

.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

.github/workflows/lint_yaml.yaml

@@ -0,0 +1,23 @@
+name: Lint Yaml
+on:
+  push:
+    branches:
+      - master
+    paths:
+      - binder-gallery.yaml
+  pull_request:
+    branches:
+      - master
+    paths:
+      - binder-gallery.yaml
+
+jobs:
+  build:
+    name: Lint Yaml
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: jacobtomlinson/gha-lint-yaml@master
+      with:
+        path: binder-gallery.yaml
+        strict: true

.mailmap

@@ -0,0 +1,22 @@
+Jessica Scheick <[email protected]>
+Jessica Scheick <[email protected]> JessicaS11 <[email protected]>
+Jessica Scheick <[email protected]> Jessica <[email protected]>
+
+Zheng Liu <[email protected]>
+Zheng Liu <[email protected]> liuzheng-arctic <[email protected]>
+
+Raphael Hagen <[email protected]> raphael <[email protected]>
+Fernando Perez <[email protected]>
+Shashank Bhushan <[email protected]>
+Anthony Arendt <[email protected]>
+Scott Henderson <[email protected]>
+Wei Ji <[email protected]>
+Tom Johnson <[email protected]>
+Bruce Wallin <[email protected]> <[email protected]>
+Tyler Sutterley <[email protected]>
+Amy Steiker <[email protected]> asteiker <[email protected]>
+David Shean <[email protected]>
+Anna Valentine <[email protected]>
+Bidhyananda Yadav <[email protected]>
+Friedrich Knuth <[email protected]>
+

.pre-commit-config.yaml

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

.travis.yml

@@ -1,21 +1,44 @@
 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
+      if: commit_message =~ test_pypi
+    skip_existing: true
+    distributions: "sdist bdist_wheel"
+
+# NOTE: the API token on Travis must be set to ALL branches, because a tag build is not considered to be on the master branch: https://travis-ci.community/t/pypi-upload-with-api-token-not-working/5338/5
+- provider: pypi
+    username: "__token__"
+    password: $PyPI_API_Token
+    on:
+      branch: master
+      tags: true
+    skip_existing: true
+    distributions: "sdist bdist_wheel"

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

binder-gallery.yaml

@@ -0,0 +1,9 @@
+---
+name: icepyx examples gallery
+description: >-
+  Examples using icepyx Python tools for obtaining and working with ICESat-2 data
+gallery_repository: pangeo-gallery/pangeo-gallery
+binder_url: "https://mybinder.org"
+binder_repo: icesat2py/icepyx
+binder_ref: master
+binderbot_target_branch: binderbot-built

binder/Dockerfile

@@ -0,0 +1 @@
+FROM uwhackweeks/icesat2:2020.06.15