Py open sci review (#89)

* Implementing suggested ruff rules

* isort

* Fix whitespace (many of these were copied from docs example execution - need to confirm it passes docs tests)

* Run test.yml on push to this branch

* Whitespace

* F401 (redundant alias)

* Missed whitespace

* First attempt w/ pre-commit

* Fix indent

* indent/drop name

* Rename .pre-commit-config.yml to .pre-commit-config.yaml

yAml

* Update .pre-commit-config.yaml

fix file structure

* Reduce .pre-commit-config.yaml

Reduce what files it is run on

* Update domains.py

Doesn't need to be raw string (see Batalex pyOpenSci/software-submission#157 (comment))

* Dict doc strings as module level attributes

* Update to main (#88)

* Update domains.py

'Field' -> 'Field***'

* 62   r test ci (#86)

Update test_r.yaml to install conda outside r, specifically miniforge, then run on env from setup with current package (vs pip installing main)

* Update .pre-commit-config.yaml

From issue: pass_filenames: false in the pre-commit config so that the file discovery is done by Ruff taking into account the includes and excludes configured by the user in their pyproject.toml

* Update .pre-commit-config.yaml

Try updating to patch version and specify config in args.

* Update pyproject.toml

try withouth 'docstring-code-format = true' as this may override other settings.

* Update pyproject.toml

Try to get pre-commit to see config

* Update pyproject.toml

Warning message, so it is getting these settings from the toml?

* Update conf.py

E501

* Update basis.py

E501

* Update basis.py

Moved constant doc-string to module level

* Update clean.py

E501

* Update convert.py

E501

* Update conf.py

lint/format edits

* Update pyproject.toml

Without single checking if double is default

* Update pyproject.toml

Will move to one or the other (likely default double for ease), but trying to post-pone to work through diff

* lint/formating

* linted

* W293

* black format/lint

* W605 - try pulling r str out of test doc-string and instead as a comment. Comment shouldn't cause problems but this one has in the past.

* I001 (all whitespace except test_harmonize_WQP.py)

* lint conf file

* lint

* Add white space between module doc-string and imports

* Format: add whitespace after mod doc-string

* Add assert for actual2 - where the characteristics specific function is used instead of the generic.

* Resolved some E501

* Check if new line fails doctest

* Revert to get doc-test passing

* Spread out example df entry

* Spread out dict read out to reduce line length. White space is already normalized for doc-test so this may pass.

* Revert

* Spread out building df for wq_dat.WQCharData example.

* spread out example df for we_date.measure_mask()

* Shotern len of dict for wq_data.replace_unit_str() & wq_data.apply_conversion() examples

* Attempt to skip E501 on this line

* skip rule on line

* Last attempt to ignore line too long in docstrings (3)

* Update pyproject.toml

Drop single quote for lint

* '' -> ""

* Update test.yml

Revert back to testing on main only

.github/workflows/lint.yml

@@ -0,0 +1,26 @@
+name: lint
+
+on:
+  push:
+    branches:
+      [pyOpenSci-review]
+  pull_request:
+    branches:
+      [pyOpenSci-review]
+
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+
+      - uses: pre-commit/[email protected]
+        with:
+          extra_args: --all-files --show-diff-on-failure

.github/workflows/test.yml

@@ -3,7 +3,7 @@ name: test
 on:
   push:
     branches:
-      [main, dev]
+      [main]
   pull_request:
     branches:
       [main]

.pre-commit-config.yaml

@@ -0,0 +1,7 @@
+repos:
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.1
+    hooks:
+    - id: ruff
+      args: ["--fix", "--show-fixes", --config=pyproject.toml]
+    - id: ruff-format

docs/source/conf.py

@@ -9,28 +9,28 @@
 # If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 
+import doctest
 import os
 import sys
-import doctest
 
 sys.path.insert(0, os.path.abspath(".."))
 sys.path.insert(0, os.path.abspath("../.."))
 
-#from importlib.metadata import version
-#import harmonize_wq
+# from importlib.metadata import version
+# import harmonize_wq
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'harmonize_wq'
-copyright = '2023, US Environmental Protection Agency'
-author = 'Justin Bousquin (US Environmental Protection Agency)'
+project = "harmonize_wq"
+copyright = "2023, US Environmental Protection Agency"
+author = "Justin Bousquin (US Environmental Protection Agency)"
 
 # ToDO:single source version
 version = "0.4.0"
-#release = version(project)
-#release = harmonize_wq.__version__
-#version = '.'.join(release.split('.')[:2])
+# release = version(project)
+# release = harmonize_wq.__version__
+# version = ".".join(release.split(".")[:2])
 
 
 # -- General configuration ---------------------------------------------------
@@ -49,10 +49,12 @@
 ]
 
 autosummary_generate = True  # Turn on sphinx.ext.autosummary
-html_show_sourcelink = False  # Remove 'view source code' from top of page (for html, not python)
 
-templates_path = ['_templates']
-exclude_patterns = ['_build', '_templates']
+# Remove "view source code" from top of page (for html, not python)
+html_show_sourcelink = False
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "_templates"]
 
 
 # -- Options for HTML output -------------------------------------------------
@@ -62,29 +64,32 @@
 html_static_path = []
 
 # Readthedocs theme (may be useful for actions)
-# on_rtd is whether on readthedocs.org, this line of code grabbed from docs.readthedocs.org...
-#on_rtd = os.environ.get("READTHEDOCS", None) == "True"
-#if not on_rtd:  # only import and set the theme if we're building docs locally
+# This line from docs.readthedocs.org, on_rtd is whether on readthedocs.org
+# on_rtd = os.environ.get("READTHEDOCS", None) == "True"
+# if not on_rtd:  # only import and set the theme if we're building docs locally
 #    import sphinx_rtd_theme
 #    html_theme = "sphinx_rtd_theme"
 #    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
-#html_css_files = ["readthedocs-custom.css"] # Override some CSS settings
+# html_css_files = ["readthedocs-custom.css"] # Override some CSS settings
 
 
 # -- Options for doctest ------------------------------------------------------
 # default to ignoring whitespace
 doctest.testmod(optionflags=doctest.NORMALIZE_WHITESPACE)
 
 # Should enable IGNORE_RESULT option
-IGNORE_RESULT = doctest.register_optionflag('IGNORE_RESULT')
+IGNORE_RESULT = doctest.register_optionflag("IGNORE_RESULT")
 
 OutputChecker = doctest.OutputChecker
+
+
 class CustomOutputChecker(OutputChecker):
     def check_output(self, want, got, optionflags):
         if IGNORE_RESULT & optionflags:
             return True
         return OutputChecker.check_output(self, want, got, optionflags)
 
+
 doctest.OutputChecker = CustomOutputChecker
 
 # -- Options for Napolean output ----------------------------------------------
@@ -99,10 +104,10 @@ def check_output(self, want, got, optionflags):
 
 # -- Options for sphinx-contrib\apidoc ----------------------------------------
 # NOT currently using apidoc
-#apidoc_separate_modules = True
-#apidoc_module_dir = "../harmonize_wq"
-#apidoc_excluded_paths = ["tests"]
-#apidoc_module_first = True
+# apidoc_separate_modules = True
+# apidoc_module_dir = "../harmonize_wq"
+# apidoc_excluded_paths = ["tests"]
+# apidoc_module_first = True
 
 # -- Options for sphinxcontrib-spelling ---------------------------------------
 spelling_lang = "en_US"
@@ -123,25 +128,25 @@ def check_output(self, want, got, optionflags):
     "dataretrieval": (
         "https://doi-usgs.github.io/dataretrieval-python/",
         "https://doi-usgs.github.io/dataretrieval-python/objects.inv",
-        ),
+    ),
     "pint": (
         "https://pint.readthedocs.io/en/stable/",
         "https://pint.readthedocs.io/en/stable/objects.inv",
-        ),
+    ),
     "geopandas": (
         "https://geopandas.org/en/stable/",
         "https://geopandas.org/en/stable/objects.inv",
-        ),
+    ),
     "pandas": (
         "https://pandas.pydata.org/pandas-docs/stable/",
         "https://pandas.pydata.org/pandas-docs/stable/objects.inv",
-        ),
+    ),
     "pyproj": (
         "https://pyproj4.github.io/pyproj/stable/",
         "https://pyproj4.github.io/pyproj/stable/objects.inv",
-        ),
+    ),
     "python": (
         "https://docs.python.org/3",
         "https://docs.python.org/3/objects.inv",
-        ),
-    }
+    ),
+}

harmonize_wq/__init__.py

@@ -1,7 +1,8 @@
-from harmonize_wq import harmonize
-from importlib.metadata import version, PackageNotFoundError
+from importlib.metadata import PackageNotFoundError, version
+
+from harmonize_wq import harmonize as harmonize
 
 try:
-    __version__ = version('harmonize_wq')
+    __version__ = version("harmonize_wq")
 except PackageNotFoundError:
     __version__ = "version-unknown"