Merge branch 'development' into extract-urls-module

.github/actions/install-icepyx/action.yml

@@ -0,0 +1,19 @@
+name: 'Install icepyx'
+description: 'Install icepyx and dev dependencies'
+
+inputs:
+  python-version:
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - uses: "actions/setup-python@v5"
+      with:
+        python-version: "${{ inputs.python-version }}"
+
+    - name: "Install package and test dependencies"
+      shell: "bash"
+      run: |
+        python -m pip install .
+        python -m pip install -r requirements-dev.txt

.github/workflows/integration_test.yml

@@ -0,0 +1,53 @@
+name: "Integration test"
+# NOTE: We're just running the tests that require earthdata login here; we
+#       don't distinguish between unit and integration tests yet.
+
+on:
+  push:
+    branches:
+      - "main"  # Releases
+      - "development"  # PR merges
+  pull_request:
+    branches:
+      - "main"  # Release pull requests
+  pull_request_review:
+    types:
+      - "submitted"
+    paths:
+      - ".github/**"
+      - "icepyx/**/*.py"
+      - "pyproject.toml"
+      - "requirements*.txt"
+
+
+jobs:
+  test:
+    name: "Integration test"
+    # Job is conditional:
+    # - Do not run on PRs from forks
+    # - Do not run on `pull_request_review` events unless the PR is approved.
+    if: "${{ !github.event.pull_request.head.repo.fork && (github.event.action != 'pull_request_review' || github.event.review.state == 'approved') }}"
+    runs-on: "ubuntu-latest"
+
+    steps:
+      - uses: "actions/checkout@v4"
+        with:
+          fetch-depth: 0
+
+      - uses: "./.github/actions/install-icepyx"
+        with:
+          python-version: "3.12"
+
+      - name: "Run tests"
+        env:
+          EARTHDATA_PASSWORD: "${{ secrets.EARTHDATA_PASSWORD }}"
+          NSIDC_LOGIN: "${{ secrets.EARTHDATA_PASSWORD }}"
+        run: |
+          pytest icepyx/ --verbose --cov app \
+            icepyx/tests/test_behind_NSIDC_API_login.py \
+            icepyx/tests/test_auth.py
+
+      - name: "Upload coverage report"
+        uses: "codecov/[email protected]"
+        with:
+          token: "${{ secrets.CODECOV_TOKEN }}"

.github/workflows/unit_test.yml

@@ -0,0 +1,40 @@
+name: "Unit test"
+# NOTE: We're just skipping the tests requiring earthdata login here; we don't
+#       distinguish yet between unit and integration tests.
+
+on:
+  pull_request:
+  push:
+    branches:
+      - "main"
+      - "development"
+
+
+jobs:
+  test:
+    name: "Unit test (Python ${{ matrix.python-version }})"
+    runs-on: "ubuntu-latest"
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.12"] #NOTE: min and max Python versions supported by icepyx
+
+    steps:
+      - uses: "actions/checkout@v4"
+        with:
+          fetch-depth: 0
+
+      - uses: "./.github/actions/install-icepyx"
+        with:
+          python-version: "${{ matrix.python-version }}"
+
+      - name: "Run tests"
+        run: |
+          pytest icepyx/ --verbose --cov app \
+            --ignore=icepyx/tests/test_behind_NSIDC_API_login.py \
+            --ignore=icepyx/tests/test_auth.py
+
+      - name: "Upload coverage report"
+        uses: "codecov/[email protected]"
+        with:
+          token: "${{ secrets.CODECOV_TOKEN }}"

.pre-commit-config.yaml

@@ -6,9 +6,17 @@ repos:
       - id: check-yaml
       - id: check-added-large-files
         args: ["--maxkb=5000"]
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: debug-statements
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
       - id: end-of-file-fixer
+      - id: mixed-line-ending
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
+      - id: requirements-txt-fixer
 
   - repo: https://github.com/codespell-project/codespell
     rev: v2.3.0

README.rst

@@ -7,9 +7,9 @@ icepyx
 
 |JOSS| |Zenodo-all|
 
-Latest release (main branch): |Docs Status main| |Travis main Build Status| |Code Coverage main|
+Latest release (main branch): |Docs Status main| |Unit Tests Status (main)| |Integration Tests Status (main)| |Code Coverage main|
 
-Current development version (development branch): |Docs Status dev| |Travis dev Build Status| |Code Coverage dev| |Pre-commit dev|
+Current development version (development branch): |Docs Status dev| |Unit Tests Status (dev)| |Integration Tests Status (main)| |Code Coverage dev| |Pre-commit dev|
 
 .. |GitHub license| image:: https://img.shields.io/badge/License-BSD%203--Clause-blue.svg
    :target: https://opensource.org/licenses/BSD-3-Clause
@@ -38,11 +38,17 @@ Current development version (development branch): |Docs Status dev| |Travis dev
 .. |Docs Status dev| image:: https://readthedocs.org/projects/icepyx/badge/?version=development
    :target: https://icepyx.readthedocs.io/en/development
 
-.. |Travis main Build Status| image:: https://app.travis-ci.com/icesat2py/icepyx.svg?branch=main
-    :target: https://app.travis-ci.com/icesat2py/icepyx
+.. |Unit Tests Status (main)| image:: https://github.com/icesat2py/icepyx/actions/workflows/unit_test.yml/badge.svg?branch=main
+    :target: https://github.com/icesat2py/icepyx/actions/workflows/unit_test.yml
 
-.. |Travis dev Build Status| image:: https://app.travis-ci.com/icesat2py/icepyx.svg?branch=development
-    :target: https://app.travis-ci.com/icesat2py/icepyx
+.. |Integration Tests Status (main)| image:: https://github.com/icesat2py/icepyx/actions/workflows/integration_test.yml/badge.svg?branch=main
+    :target: https://github.com/icesat2py/icepyx/actions/workflows/integration_test.yml
+
+.. |Unit Tests Status (dev)| image:: https://github.com/icesat2py/icepyx/actions/workflows/unit_test.yml/badge.svg?branch=development
+    :target: https://github.com/icesat2py/icepyx/actions/workflows/unit_test.yml
+
+.. |Integration Tests Status (dev)| image:: https://github.com/icesat2py/icepyx/actions/workflows/integration_test.yml/badge.svg?branch=development
+    :target: https://github.com/icesat2py/icepyx/actions/workflows/integration_test.yml
 
 .. |Code Coverage main| image:: https://codecov.io/gh/icesat2py/icepyx/branch/main/graph/badge.svg
     :target: https://codecov.io/gh/icesat2py/icepyx

doc/source/conf.py

@@ -19,7 +19,6 @@
 
 import icepyx
 
-
 # -- Project information -----------------------------------------------------
 
 project = "icepyx"
@@ -120,10 +119,9 @@ def setup(app):
 
 # this should possibly be moved to the sphinxext directory as a standalone .py file
 # -- custom style for pybtex output -------------------------------------------
-from pybtex.style.formatting.unsrt import Style as UnsrtStyle
-
 # from pybtex.style.labels.alpha import LabelStyle as AlphaLabelStyle
 from pybtex.plugin import register_plugin
+from pybtex.style.formatting.unsrt import Style as UnsrtStyle
 
 # I seem to be unable to figure out how to control what is used for the label. It would
 # make sense if it were fed into this function, which then just formatted it, but I can't figure out from where

doc/source/tracking/pypistats/get_pypi_stats.py

@@ -1,6 +1,7 @@
 import os
-import pypistats
+
 import pandas as pd
+import pypistats
 
 cwd = os.getcwd()
 

doc/source/tracking/traffic/traffic_data_mgmt.py

@@ -1,5 +1,6 @@
-import matplotlib.pyplot as plt
 import os
+
+import matplotlib.pyplot as plt
 import pandas as pd
 
 cwd = os.getcwd()

icepyx/__init__.py

@@ -1,6 +1,6 @@
-from icepyx.core.query import Query, GenQuery
+from _icepyx_version import version as __version__
+
+from icepyx.core.query import GenQuery, Query
 from icepyx.core.read import Read
-from icepyx.quest.quest import Quest
 from icepyx.core.variables import Variables
-
-from _icepyx_version import version as __version__
+from icepyx.quest.quest import Quest

icepyx/conftest.py

@@ -1,6 +1,7 @@
-import icepyx
 import pytest
 
+import icepyx
+
 
 @pytest.fixture(autouse=True)
 def add_ipx(doctest_namespace):

icepyx/core/APIformatting.py

@@ -2,7 +2,6 @@
 
 import datetime as dt
 
-
 # ----------------------------------------------------------------------
 # parameter-specific formatting for display
 # or input to a set of API parameters (CMR or NSIDC)
@@ -122,14 +121,17 @@ def combine_params(*param_dicts):
     """
     Combine multiple dictionaries into one.
 
+    Merging is performed in sequence using `dict.update()`; dictionaries later in the
+    list overwrite those earlier.
+
     Parameters
     ----------
     params : dictionaries
         Unlimited number of dictionaries to combine
 
     Returns
     -------
-    single dictionary of all input dictionaries combined
+    A single dictionary of all input dictionaries combined
 
     Examples
     --------
@@ -209,7 +211,7 @@ def __init__(self, partype, values=None, reqtype=None):
             "CMR",
             "required",
             "subset",
-        ], "You need to submit a valid parametery type."
+        ], "You need to submit a valid parameter type."
         self.partype = partype
 
         if partype == "required":
@@ -411,7 +413,10 @@ def build_params(self, **kwargs):
 
                 for key in opt_keys:
                     if key == "Coverage" and key in kwargs:
-                        # DevGoal: make there be an option along the lines of Coverage=default, which will get the default variables for that product without the user having to input is2obj.build_wanted_wanted_var_list as their input value for using the Coverage kwarg
+                        # DevGoal: make an option along the lines of Coverage=default,
+                        # which will get the default variables for that product without
+                        # the user having to input is2obj.build_wanted_wanted_var_list
+                        # as their input value for using the Coverage kwarg
                         self._fmted_keys.update(
                             {key: _fmt_var_subset_list(kwargs[key])}
                         )

icepyx/core/auth.py

@@ -2,6 +2,7 @@
 import datetime
 
 import earthaccess
+
 from icepyx.core.exceptions import DeprecationError
 
 
@@ -10,8 +11,6 @@ class AuthenticationError(Exception):
     Raised when an error is encountered while authenticating Earthdata credentials
     """
 
-    pass
-
 
 class EarthdataAuthMixin:
     """

icepyx/core/exceptions.py

@@ -3,16 +3,12 @@ class DeprecationError(Exception):
     Class raised for use of functionality that is no longer supported by icepyx.
     """
 
-    pass
-
 
 class QueryError(Exception):
     """
     Base class for Query object exceptions
     """
 
-    pass
-
 
 class NsidcQueryError(QueryError):
     """

icepyx/core/granules.py

@@ -1,15 +1,16 @@
 import datetime
-import requests
-import time
 import io
-import re
 import json
-import numpy as np
 import os
 import pprint
+import re
+import time
 from xml.etree import ElementTree as ET
 import zipfile
 
+import numpy as np
+import requests
+
 import icepyx.core.APIformatting as apifmt
 from icepyx.core.auth import EarthdataAuthMixin
 import icepyx.core.exceptions

icepyx/core/is2ref.py

@@ -1,14 +1,14 @@
-import h5py
 import json
-import numpy as np
-import requests
 import warnings
 from xml.etree import ElementTree as ET
 
 import earthaccess
 
 from icepyx.core.urls import COLLECTION_SEARCH_BASE_URL, EGI_BASE_URL
 
+import h5py
+import numpy as np
+import requests
 
 # ICESat-2 specific reference functions