Merge pull request #528 from icesat2py/development

version 1.1.0 release

.all-contributorsrc

@@ -446,7 +446,10 @@
       "avatar_url": "https://avatars.githubusercontent.com/u/19339926?v=4",
       "profile": "https://whyjz.github.io/",
       "contributions": [
-        "tutorial"
+        "tutorial",
+        "bug",
+        "code",
+        "review"
       ]
     },
     {

.coveragerc

@@ -1,7 +1,6 @@
 [run]
 branch = True
 source = icepyx
-omit = 
+omit =
     setup.py
-    test/*
     doc/*

.flake8

@@ -1,7 +1,7 @@
 [flake8]
 #GOAL: max_line_length = 79 or 99
 max_line_length = 99
-per-file-ignores = 
+per-file-ignores =
     # too many leading '#' for block comment
     */tests/*:E266
     # line too long (several test strs)
@@ -12,7 +12,7 @@ per-file-ignores =
     doc/source/conf.py:E402
 
 # GOAL: remove these ignores
-ignore = 
+ignore =
     # line too long
     E501
     # comparison syntax
@@ -38,4 +38,4 @@ ignore =
 
     # GOAL:
     # syntax check doctests in docstrings
-    # doctests = True
+    # doctests = True

.github/workflows/binder-badge.yml

@@ -8,4 +8,4 @@ jobs:
     steps:
       - uses: manics/action-binderbadge@main
         with:
-          githubToken: ${{ secrets.GITHUB_TOKEN }}
+          githubToken: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/get_pypi_stats.yml

@@ -34,4 +34,4 @@ jobs:
         author_name: learn2phoenix
         message: "Pypi stats auto-update"
         add: "./doc/source/tracking/pypistats/*"
-#         add: "./pypistats/*"
+#         add: "./pypistats/*"

.github/workflows/linter_actions.yml

@@ -11,9 +11,8 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Run black linter
-        uses: psf/black@stable      
+        uses: psf/black@stable
       # use the flake8 linter to annotate improperly formatted code
       # note linter arguments are supplied via the .flake8 config file
       - name: Annotate PR after running flake8
         uses: TrueBrain/actions-flake8@v2
-

.github/workflows/publish_to_pypi.yml

@@ -33,7 +33,7 @@ jobs:
         python-version: 3.9
 
     - name: Install dependencies
-      run: python -m pip install setuptools wheel
+      run: python -m pip install build setuptools wheel
 
     # This step is only necessary for testing purposes and for TestPyPI
     - name: Fix up version string for TestPyPI
@@ -46,7 +46,7 @@ jobs:
 
     - name: Build source and wheel distributions
       run: |
-        python setup.py sdist bdist_wheel
+        python -m build
         echo ""
         echo "Generated files:"
         ls -lh dist/

.github/workflows/traffic_action.yml

@@ -1,7 +1,7 @@
 # temporarily store GitHub traffic data
 # from: https://github.com/marketplace/actions/repository-traffic
 on:
-  schedule: 
+  schedule:
     # runs once a week on sunday
     - cron: "55 23 * * 0"
   # Trigger manually at https://github.com/icesat2py/icepyx/actions/workflows/publish_to_pypi.yml
@@ -20,19 +20,19 @@ jobs:
     - uses: actions/checkout@v3
       with:
         ref: "traffic"
-    
+
     # Calculates traffic and clones and stores in CSV file
-    - name: GitHub traffic 
+    - name: GitHub traffic
       uses: sangonzal/[email protected]
       env:
-        TRAFFIC_ACTION_TOKEN: ${{ secrets.TRAFFIC_ACTION_TOKEN }} 
-    
+        TRAFFIC_ACTION_TOKEN: ${{ secrets.TRAFFIC_ACTION_TOKEN }}
+
     # Custom steps to move files to another dir and format plot
     - name: Move files
       run: |
         pip install matplotlib pandas
         python ./doc/source/tracking/traffic/traffic_data_mgmt.py
-    
+
     # Commits files to repository
     - name: Commit changes
       uses: EndBug/add-and-commit@v9

.github/workflows/uml_action.yml

@@ -3,6 +3,7 @@ on:
   pull_request_review:
     types: [submitted]
     branches: development
+  workflow_dispatch:
 
 jobs:
   diagrams:
@@ -18,12 +19,13 @@ jobs:
         run: |
           pip install -U pip
           pip install -r requirements.txt
-          pip install icepyx pylint 
+          pip install icepyx pylint
           sudo apt-get install graphviz
       - name: run pyreverse
         run: |
           pyreverse ./icepyx/core -p user_uml -o svg
-          pyreverse ./icepyx/core -f ALL -p dev_uml -o svg
+          pyreverse ./icepyx/quest -p quest_user_uml -o svg
+          pyreverse ./icepyx/core ./icepyx/quest -f ALL -p dev_uml -o svg
           rm ./packages_dev_uml.svg
           mv ./*.svg ./doc/source/user_guide/documentation/
       - name: Commit changes

.mailmap

@@ -19,4 +19,3 @@ David Shean <[email protected]>
 Anna Valentine <[email protected]>
 Bidhyananda Yadav <[email protected]>
 Friedrich Knuth <[email protected]>
-

.pre-commit-config.yaml

@@ -1,7 +1,19 @@
 repos:
 -   repo: https://github.com/psf/black
-    rev: 23.12.0
+    rev: 24.4.2
     hooks:
     - id: black
 
-# you can run `pre-commit autoupdate` to automatically update to the latest version of hooks!
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0  # Use the ref you want to point at
+    hooks:
+    - id: check-added-large-files
+      args: ["--maxkb=5000"]
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+      args: [--markdown-linebreak-ext=md]
+
+ci:
+  autoupdate_schedule: monthly
+
+# you can run `pre-commit autoupdate` to automatically update to the latest version of hooks!

.travis.yml

@@ -28,8 +28,16 @@ jobs:
   include:
     - stage: basic tests
       script: pytest icepyx/ --verbose --cov app --ignore icepyx/tests/test_behind_NSIDC_API_login.py
-      after_success: codecov/codecov-action@v3
-
+      # includes an integrity check of the uploader as recommended by CodeCov
+      after_success:
+        - curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --no-default-keyring --keyring trustedkeys.gpg --import # One-time step
+        - curl -Os https://uploader.codecov.io/latest/linux/codecov
+        - curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM
+        - curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM.sig
+        - gpgv codecov.SHA256SUM.sig codecov.SHA256SUM
+        - shasum -a 256 -c codecov.SHA256SUM
+        - chmod +x codecov
+        - ./codecov -t ${CODECOV_TOKEN}
     - stage: behind Earthdata
       script:
         - export EARTHDATA_PASSWORD=$NSIDC_LOGIN

ATTRIBUTION.rst

@@ -4,7 +4,7 @@ Recognizing Contributions
 =========================
 
 We are extremely grateful to everyone who has contributed to the success of the icepyx community and software.
-This document outlines our goals to give appropriate attribution to all contributors to icepyx in ways that are fair and diverse and supportive of professional goals. 
+This document outlines our goals to give appropriate attribution to all contributors to icepyx in ways that are fair and diverse and supportive of professional goals.
 We define *contributions* broadly as:
 
     Efforts towards achieving icepyx's goals, including (1) writing code, tests, or documentation,
@@ -21,11 +21,11 @@ We recognize contributions in the following ways.
 Contributors List
 -----------------
 
-This project follows the `all-contributors <https://github.com/all-contributors/all-contributors>`_ specification. 
+This project follows the `all-contributors <https://github.com/all-contributors/all-contributors>`_ specification.
 When you contribute to icepyx for the first time or in a new way, you or a maintainer can use the `All Contributors bot
 to open a PR <https://allcontributors.org/docs/en/bot/usage>`_` to recognize your contribution.
 Comment on an existing PR with `@all-contributors please add @<username> for <contributions>`.
-This will add you (or your new contribution type) to the ``CONTRIBUTORS.rst`` file located in the top level directory; 
+This will add you (or your new contribution type) to the ``CONTRIBUTORS.rst`` file located in the top level directory;
 the file is packaged and distributed with icepyx, so each release has a record of contributors and their contribution types.
 
 
@@ -41,8 +41,8 @@ If the user's full name is not available on GitHub, their GitHub handle is used.
 Example Workflows
 -----------------
 
-Many of the example workflows included within icepyx were developed by individuals or small teams for educational or research purposes. 
-We encourage example developers to provide proper recognition for these efforts both within the notebook itself and 
+Many of the example workflows included within icepyx were developed by individuals or small teams for educational or research purposes.
+We encourage example developers to provide proper recognition for these efforts both within the notebook itself and
 by adding contributors to the `Contributors List`_ for attribution as describered herein.
 
 
@@ -58,7 +58,7 @@ we collectively represent the icepyx authors in citations (including Zenodo rele
 
 As described above, a complete list of contributors and their contribution types is available via the `Contributors List`_.
 
-  ** A note about releases <v0.6.4: Prior version releases adhere to authorship guidelines in place at the time, 
+  ** A note about releases <v0.6.4: Prior version releases adhere to authorship guidelines in place at the time,
   listing individual contributors who had manually added their names to `CONTRIBUTORS.rst`.
   Authorship order was alphebetical by last name, except in cases where
   a substantial contribution was made by one or more contributors to a given release. **
@@ -67,25 +67,25 @@ As described above, a complete list of contributors and their contribution types
 Peer-Reviewed Publications (Papers)
 -----------------------------------
 
-We will occasionally prepare manuscripts describing our software and its uses for submission to peer-reviewed journals. 
-These efforts are typically "in addition to" contributions made directly to icepyx (community or repository) and 
+We will occasionally prepare manuscripts describing our software and its uses for submission to peer-reviewed journals.
+These efforts are typically "in addition to" contributions made directly to icepyx (community or repository) and
 thus may have specific author lists.
 To be eligible for authorship on a peer-reviewed publication, contributors must:
 
-  1. Contribute to the development (including code, documentation, and examples) of icepyx. 
+  1. Contribute to the development (including code, documentation, and examples) of icepyx.
   Substantial non-code contributions may constitute eligibility for authorship.
- 
-  2. Contribute ideas, participate in authorship discussions (see next paragraph), write, read, and review the manuscript 
+
+  2. Contribute ideas, participate in authorship discussions (see next paragraph), write, read, and review the manuscript
   in a timely manner, and provide feedback (acknowledgement of review is sufficient, but we'd prefer more).
 
-Author order will be determined based on co-author discussion, led by the publication preparation leader, ideally during the initial 
-planning stages of manuscript preparation (i.e. as soon as an idea matures into a potential manuscript and before writing begins). 
-Authorship will continue to be evaluated throughout the manuscript preparation process. 
-Discussions will consider authorship norms (e.g. How does author order convey participation and prestige? 
-How critical is first authorship to career advancement for each member of the team? 
-Do an individual's contributions meet authorship criteria or are they more suited to acknowledgements?). 
-Author order determination may also consider metrics such as the number of commits since the last major release 
-with an associated paper (``git shortlog vX.0.0...HEAD -sne``), contributions that do not have associated commits, 
+Author order will be determined based on co-author discussion, led by the publication preparation leader, ideally during the initial
+planning stages of manuscript preparation (i.e. as soon as an idea matures into a potential manuscript and before writing begins).
+Authorship will continue to be evaluated throughout the manuscript preparation process.
+Discussions will consider authorship norms (e.g. How does author order convey participation and prestige?
+How critical is first authorship to career advancement for each member of the team?
+Do an individual's contributions meet authorship criteria or are they more suited to acknowledgements?).
+Author order determination may also consider metrics such as the number of commits since the last major release
+with an associated paper (``git shortlog vX.0.0...HEAD -sne``), contributions that do not have associated commits,
 and contributions to the preparation of the manuscript.
 
 
@@ -94,20 +94,20 @@ Motivation and References
 
 Concepts and models of attribution, credit, contribution, and authorship can vary across time, application, and communities.
 `FORCE11 <https://force11.org/>`_ has an entire `Attribution Working Group <https://force11.org/groups/attribution-working-group/>`_ dedicated to working on attribution for research products.
-`URSSI <https://urssi.us/>`_ hosted a workshop in 2019 (`report <https://urssi.us/blog/2019/03/24/report-from-urssi-workshop-on-software-credit-citation-and-metrics/>`_) 
+`URSSI <https://urssi.us/>`_ hosted a workshop in 2019 (`report <https://urssi.us/blog/2019/03/24/report-from-urssi-workshop-on-software-credit-citation-and-metrics/>`_)
 to identify core issues and propose solutions to challenges around software credit.
 For software, current best practices (`e.g. <https://arxiv.org/pdf/2012.13117.pdf>`_) emphasize the importance of having a document
 such as this one to describe an individual community's policies for credit, authorship, and attribution.
-This document is an effort to describe icepyx's policies, with an awareness that they may change 
+This document is an effort to describe icepyx's policies, with an awareness that they may change
 to accomodate community growth, best practices, and feedback.
 
 We do not attempt to identify contribution levels through the number of commits made to the repository (e.g. ``git shortlog -sne``)
 or active engagement on GitHub (e.g. through issues, discussions, and pull requests) and Discourse.
-The latter is difficult to quantify, and the use of squash merges into the development branch can mask the relative complexity 
+The latter is difficult to quantify, and the use of squash merges into the development branch can mask the relative complexity
 of various contributions and does not necessarily capture significant conceptual contributions.
 
 
-Copyright notice: Preparation of this document and our credit policies was inspired in part by these `authorship guidelines <https://github.com/fatiando/contributing/blob/master/AUTHORSHIP.md>`_ provided by `Fatiando a Terra <https://github.com/fatiando>`_ 
+Copyright notice: Preparation of this document and our credit policies was inspired in part by these `authorship guidelines <https://github.com/fatiando/contributing/blob/master/AUTHORSHIP.md>`_ provided by `Fatiando a Terra <https://github.com/fatiando>`_
 and `The Turing Way <https://the-turing-way.netlify.app/community-handbook/acknowledgement/acknowledgement-members.html>`_.
 We encourage potential contributors to consider the resources provided by the `NASA High Mountain Asia Team (HiMAT) <https://highmountainasia.github.io/team-collaboration/authorship/>`_
 and established or emerging best practices in their community.

CITATION.cff

@@ -32,4 +32,4 @@ license: BSD-3-Clause
 identifiers:
   - description: "All archived versions of icepyx."
     type: doi
-    value: 10.5281/zenodo.7729175
+    value: 10.5281/zenodo.7729175

CITATION.rst

@@ -7,7 +7,7 @@ icepyx
 ------
 
 This community and software is developed with the goal of supporting science applications.
-Thus, our contributors (including those who have developed the packages used within icepyx) 
+Thus, our contributors (including those who have developed the packages used within icepyx)
 and maintainers justify their efforts and demonstrate the impact of their work through citations.
 
 If you have used icepyx in your work, please consider citing our library.
@@ -30,16 +30,16 @@ A bibtex version for users working in Latex::
   publisher = {Zenodo},
   url = "https://github.com/icesat2py/icepyx",
   }
-    
+
 For more information on the "icepyx Developers", please see our `Attribution Guidelines <https://icepyx.readthedocs.io/en/latest/contributing/attribution_link.html>`_.
 See our docs for a `full list of contributors <https://icepyx.readthedocs.io/en/latest/contributing/contributors_link.html>`_ and their contribution types.
 
 icepyx Dependencies
 -------------------
-If you have used one of the included packages to extend your data analysis capabilities within icepyx, 
-please consider additionally citing that work, because it represents an independent software contribution to the open-source community. 
-`SciPy <https://www.scipy.org/index.html>`_ provides a `helpful resource <https://www.scipy.org/citing.html>`_ for citing 
-packages within the SciPy ecosystem (including Matplotlib, NumPy, pandas, and SciPy). 
+If you have used one of the included packages to extend your data analysis capabilities within icepyx,
+please consider additionally citing that work, because it represents an independent software contribution to the open-source community.
+`SciPy <https://www.scipy.org/index.html>`_ provides a `helpful resource <https://www.scipy.org/citing.html>`_ for citing
+packages within the SciPy ecosystem (including Matplotlib, NumPy, pandas, and SciPy).
 Links to citation information for other commonly used packages are below.
 
 - `fiona <https://github.com/Toblerity/Fiona/blob/master/CITATION.txt>`_
@@ -52,4 +52,4 @@ Links to citation information for other commonly used packages are below.
 ICESat-2 Data
 -------------
 ICESat-2 data citation depends on the exact dataset used.
-Citation information for each data product can be found through the `NSIDC website <https://nsidc.org/data/icesat-2/data-sets>`_.
+Citation information for each data product can be found through the `NSIDC website <https://nsidc.org/data/icesat-2/data-sets>`_.