Merge branch 'bugfix-flake8-sphinx' into 'master'

Fix flake8 and sphinx build issues See merge request webservices/mtg-sift!161
ssec · May 12, 2023 · 18612ab · 18612ab
2 parents 6314ad8 + 4edfc24
commit 18612ab
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diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -17,7 +17,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.9
+          python-version: 3.11
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
@@ -73,10 +73,10 @@ jobs:
         # XXX: We don't currently have OpenGL installation on other platforms
         #os: ["windows-latest", "ubuntu-latest", "macos-latest"]
         os: ["ubuntu-latest"]
-        python-version: ["3.7", "3.10"]
+        python-version: ["3.8", "3.10"]
         experimental: [false]
         include:
-          - python-version: "3.9"
+          - python-version: "3.10"
             os: "ubuntu-latest"
             experimental: true
 

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -9,7 +9,7 @@ repos:
         args:
           - --target-version=py38
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
         language_version: python3

diff --git a/README.md b/README.md
@@ -5,6 +5,7 @@
 ![CI](https://github.com/ssec/sift/actions/workflows/ci.yaml/badge.svg)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2587907.svg)](https://doi.org/10.5281/zenodo.2587907)
 [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/gitterHQ/gitter)
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/ssec/sift/master.svg)](https://results.pre-commit.ci/latest/github/ssec/sift/master)
 
 
 Satellite Information Familiarization Tool (SIFT) was designed by the Space

diff --git a/continuous_integration/environment.yaml b/continuous_integration/environment.yaml
@@ -29,6 +29,7 @@ dependencies:
   - fsspec
   - h5netcdf
   - h5py
+  - hdf5plugin
   - netcdf4
   - pillow
   - pooch

diff --git a/doc/source/api/uwsift.control.rst b/doc/source/api/uwsift.control.rst
@@ -12,30 +12,6 @@ uwsift.control.auto\_update module
    :undoc-members:
    :show-inheritance:
 
-uwsift.control.doc\_ws\_as\_timeline\_scene module
---------------------------------------------------
-
-.. automodule:: uwsift.control.doc_ws_as_timeline_scene
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-uwsift.control.file\_behaviors module
--------------------------------------
-
-.. automodule:: uwsift.control.file_behaviors
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-uwsift.control.layer\_tree module
----------------------------------
-
-.. automodule:: uwsift.control.layer_tree
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 uwsift.control.qml\_utils module
 --------------------------------
 

diff --git a/doc/source/api/uwsift.model.rst b/doc/source/api/uwsift.model.rst
@@ -36,14 +36,6 @@ uwsift.model.document module
    :undoc-members:
    :show-inheritance:
 
-uwsift.model.layer module
--------------------------
-
-.. automodule:: uwsift.model.layer
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 uwsift.model.layer\_item module
 -------------------------------
 

diff --git a/doc/source/api/uwsift.ui.rst b/doc/source/api/uwsift.ui.rst
@@ -12,26 +12,18 @@ uwsift.ui.change\_colormap\_dialog\_ui module
    :undoc-members:
    :show-inheritance:
 
-uwsift.ui.config\_rgb\_layer\_ui module
----------------------------------------
+uwsift.ui.custom\_widgets module
+--------------------------------
 
-.. automodule:: uwsift.ui.config_rgb_layer_ui
+.. automodule:: uwsift.ui.custom_widgets
    :members:
    :undoc-members:
    :show-inheritance:
 
-uwsift.ui.create\_algebraic\_dialog\_ui module
-----------------------------------------------
+uwsift.ui.dataset\_statistics\_widget\_ui module
+------------------------------------------------
 
-.. automodule:: uwsift.ui.create_algebraic_dialog_ui
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-uwsift.ui.custom\_widgets module
---------------------------------
-
-.. automodule:: uwsift.ui.custom_widgets
+.. automodule:: uwsift.ui.dataset_statistics_widget_ui
    :members:
    :undoc-members:
    :show-inheritance:
@@ -44,18 +36,18 @@ uwsift.ui.export\_image\_dialog\_ui module
    :undoc-members:
    :show-inheritance:
 
-uwsift.ui.open\_cache\_dialog\_ui module
-----------------------------------------
+uwsift.ui.layer\_details\_widget\_ui module
+-------------------------------------------
 
-.. automodule:: uwsift.ui.open_cache_dialog_ui
+.. automodule:: uwsift.ui.layer_details_widget_ui
    :members:
    :undoc-members:
    :show-inheritance:
 
-uwsift.ui.open\_file\_wizard\_2\_ui module
-------------------------------------------
+uwsift.ui.open\_cache\_dialog\_ui module
+----------------------------------------
 
-.. automodule:: uwsift.ui.open_file_wizard_2_ui
+.. automodule:: uwsift.ui.open_cache_dialog_ui
    :members:
    :undoc-members:
    :show-inheritance:

diff --git a/doc/source/api/uwsift.view.rst b/doc/source/api/uwsift.view.rst
@@ -1,14 +1,6 @@
 uwsift.view package
 ===================
 
-Subpackages
------------
-
-.. toctree::
-   :maxdepth: 4
-
-   uwsift.view.timeline
-
 Submodules
 ----------
 
@@ -36,18 +28,18 @@ uwsift.view.colormap module
    :undoc-members:
    :show-inheritance:
 
-uwsift.view.colormap\_dialogs module
-------------------------------------
+uwsift.view.colormap\_editor module
+-----------------------------------
 
-.. automodule:: uwsift.view.colormap_dialogs
+.. automodule:: uwsift.view.colormap_editor
    :members:
    :undoc-members:
    :show-inheritance:
 
-uwsift.view.colormap\_editor module
------------------------------------
+uwsift.view.dataset\_statistics\_pane module
+--------------------------------------------
 
-.. automodule:: uwsift.view.colormap_editor
+.. automodule:: uwsift.view.dataset_statistics_pane
    :members:
    :undoc-members:
    :show-inheritance:
@@ -84,14 +76,6 @@ uwsift.view.open\_file\_wizard module
    :undoc-members:
    :show-inheritance:
 
-uwsift.view.open\_file\_wizard\_2 module
-----------------------------------------
-
-.. automodule:: uwsift.view.open_file_wizard_2
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 uwsift.view.probes module
 -------------------------
 

diff --git a/doc/source/api/uwsift.view.timeline.rst b/doc/source/api/uwsift.view.timeline.rst
diff --git a/doc/source/api/uwsift.workspace.rst b/doc/source/api/uwsift.workspace.rst
@@ -28,14 +28,6 @@ uwsift.workspace.collector module
    :undoc-members:
    :show-inheritance:
 
-uwsift.workspace.goesr\_pug module
-----------------------------------
-
-.. automodule:: uwsift.workspace.goesr_pug
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 uwsift.workspace.guidebook module
 ---------------------------------
 
@@ -52,14 +44,6 @@ uwsift.workspace.importer module
    :undoc-members:
    :show-inheritance:
 
-uwsift.workspace.matrix module
-------------------------------
-
-.. automodule:: uwsift.workspace.matrix
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 uwsift.workspace.metadatabase module
 ------------------------------------
 
@@ -76,6 +60,14 @@ uwsift.workspace.simple\_workspace module
    :undoc-members:
    :show-inheritance:
 
+uwsift.workspace.statistics module
+----------------------------------
+
+.. automodule:: uwsift.workspace.statistics
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 uwsift.workspace.workspace module
 ---------------------------------
 

diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -49,8 +49,6 @@
 ]
 
 autodoc_mock_imports = [
-    "netCDF4",
-    "h5py",
     "pyshp",
     "shapely",
     "rasterio",
@@ -113,7 +111,7 @@ def setup(app):
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:

diff --git a/doc/source/configuration-catalogue-auto_update_mode.rst b/doc/source/configuration-catalogue-auto_update_mode.rst
@@ -1,10 +1,10 @@
 Configuring Catalogue and Auto Update Mode
-------------------------------------------
+==========================================
 
 .. _auto_update_catalogue_config:
 
 Catalogue Query Configuration
-=============================
+-----------------------------
 
 The Catalogue configuration defines a list of "queries".
 
@@ -124,7 +124,7 @@ PRO files have this at the *channel* part of their filenames.
 .. _auto_update_mode_activation:
 
 Activation of Auto Update Mode
-==============================
+------------------------------
 
 To activate the auto update mode the following entry must be available in the
 configuration settings::

diff --git a/doc/source/configuration-default_colormaps.rst b/doc/source/configuration-default_colormaps.rst
@@ -1,5 +1,5 @@
 Configuring a Colormap and its Colorlimits Based on the Dataset Standard Name
--------------------------------------------------------
+-----------------------------------------------------------------------------
 
 SIFT automatically associates a colormap and a value range to a newly
 loaded dataset based on the standard name of each dataset via its internal

diff --git a/doc/source/configuration-points_styles.rst b/doc/source/configuration-points_styles.rst
@@ -49,7 +49,7 @@ The following would be an explicit definition of the default marker style::
         stroke-width: 1px
 
 Configuring Point Styles Based on the Dataset Standard Name
----------------------------------------------------------
+-----------------------------------------------------------
 
 Analogous to the default colormap configuration the style of the markers used to
 render a dataset can (and - since there are no default definitions in the

diff --git a/setup.py b/setup.py
@@ -149,12 +149,12 @@ def run(self):
         add_args = ["git", "add", version_pathname, iss_pathname]
         commit_args = ["git", "commit", "-m", "Bump version from {} to {}".format(version_str, new_version_str)]
         if self.commit:
-            import subprocess
+            import subprocess  # nosec
 
             print("Adding files to git staging area...")
-            subprocess.check_call(add_args)
+            subprocess.check_call(add_args)  # nosec
             print("Committing changes...")
-            subprocess.check_call(commit_args)
+            subprocess.check_call(commit_args)  # nosec
         else:
             commit_args[-1] = '"' + commit_args[-1] + '"'
             print("To appropriate files:")
@@ -165,7 +165,7 @@ def run(self):
         tag_args = ["git", "tag", "-a", new_version_str, "-m", "Version {}".format(new_version_str)]
         if self.tag:
             print("Tagging commit...")
-            subprocess.check_call(tag_args)
+            subprocess.check_call(tag_args)  # nosec
         else:
             tag_args[-1] = '"' + tag_args[-1] + '"'
             print("To tag:")
@@ -222,7 +222,7 @@ def run(self):
         'pygrib;sys_platform=="linux" or sys_platform=="darwin"',
         "ecmwflibs",
         "eccodes",
-        "cfgrib"
+        "cfgrib",
     ],
     tests_requires=["pytest", "pytest-qt", "pytest-mock"],
     python_requires=">=3.8",