update github actions and add black linter for PRs (#475)

- update pypi action to use OIDC trusted publisher mgmt
- generalize the flake8 action to a general linting action and add black
- put flake8 config parameters into a separate file (.flake8)
- update versions of actions/pre-commit hooks
- specify uml updates only need to run on PRs to development
- do not run uml updates on PRs into main #449)
- update docs config files to be compliant
- temporarily ignore many flake8 error codes until legacy files are updated

.flake8

@@ -0,0 +1,41 @@
+[flake8]
+#GOAL: max_line_length = 79 or 99
+max_line_length = 99
+per-file-ignores = 
+    # too many leading '#' for block comment
+    */tests/*:E266
+    # line too long (several test strs)
+    test_granules.py:E501
+    # imported but unused
+    __init__.py:F401
+    # import not at top of file
+    doc/source/conf.py:E402
+
+# GOAL: remove these ignores
+ignore = 
+    # line too long
+    E501
+    # comparison syntax
+    E711
+    # comparison syntax
+    E712
+    # comparison syntax in tests
+    E714
+    # comparison syntax in tests
+    E721
+    # bare except
+    E722
+    # ambiguous var name
+    E741
+    # imported but unused
+    F401
+    # unable to detect undefined names
+    F403
+    # assigned and unused (in tests)
+    F841
+    # line break before binary operator
+    W503
+
+    # GOAL:
+    # syntax check doctests in docstrings
+    # doctests = True

.github/workflows/linter_actions.yml

@@ -0,0 +1,19 @@
+name: Run linters on PRs
+
+on:
+  pull_request:
+    branches:
+      - development
+      - main
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Run black linter
+        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

@@ -51,12 +51,13 @@ jobs:
 
     - name: Publish to Test PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
+      permissions:
+        id-token: write
       with:
-        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
         repository_url: https://test.pypi.org/legacy/
 
     - name: Publish to PyPI
       if: startsWith(github.ref, 'refs/tags')
+      permissions:
+        id-token: write
       uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/uml_action.yml

@@ -2,6 +2,7 @@ name: Update UML diagrams
 on:
   pull_request_review:
     types: [submitted]
+    branches: development
 
 jobs:
   diagrams:

.pre-commit-config.yaml

@@ -1,5 +1,7 @@
 repos:
 -   repo: https://github.com/psf/black
-    rev: 22.6.0
+    rev: 23.12.0
     hooks:
-    - id: black
+    - id: black
+
+# you can run `pre-commit autoupdate` to automatically update to the latest version of hooks!

doc/source/conf.py

@@ -10,12 +10,12 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
+import datetime
 import os
 import sys
 
 sys.path.insert(0, os.path.abspath("../.."))
 sys.path.insert(0, os.path.abspath("../sphinxext"))
-import datetime
 
 import icepyx
 
@@ -121,7 +121,8 @@ 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.style.labels.alpha import LabelStyle as AlphaLabelStyle
 from pybtex.plugin import register_plugin
 
 # I seem to be unable to figure out how to control what is used for the label. It would

doc/sphinxext/announce.py

@@ -17,9 +17,20 @@
 
 The output is utf8 rst.
 
-Custom extension from the Pandas library: https://github.com/pandas-dev/pandas/blob/1.1.x/doc/sphinxext/announce.py
+Custom extension from the Pandas library:
+https://github.com/pandas-dev/pandas/blob/1.1.x/doc/sphinxext/announce.py
 Copied 10 August 2020 and subsequently modified.
-Specifically, get_authors was adjusted to check for a .mailmap file and use the git through the command line in order to utilize it if present. Using a mailmap file is currently not possible in gitpython (from git import Repo), and the recommended solution is to bring in the mailmap file yourself and use it to modify the author list (i.e. replicate the functionality that already exists in git). This felt a bit out of time-scope for right now. Alternatively, the git-fame library (imported as gitfame) uses the mailmap file and compiles statistics, but the python wrapper for this command line tool was taking forever. So, I've reverted to using os.system to use git behind the scenes instead.
+Specifically, get_authors was adjusted to check for a .mailmap file
+and use the git through the command line in order to utilize it if present.
+Using a mailmap file is currently not possible in gitpython
+(from git import Repo), and the recommended solution is to
+bring in the mailmap file yourself and use it to modify the author list
+(i.e. replicate the functionality that already exists in git).
+This felt a bit out of time-scope for right now.
+Alternatively, the git-fame library (imported as gitfame)
+uses the mailmap file and compiles statistics,
+but the python wrapper for this command line tool was taking forever.
+So, I've reverted to using os.system to use git behind the scenes instead.
 
 Dependencies
 ------------
@@ -76,7 +87,6 @@ def get_authors(revision_range):
     # "Co-authored by" commits, which come from backports by the bot,
     # and one for regular commits.
     if ".mailmap" in os.listdir(this_repo.git.working_dir):
-
         xpr = re.compile(r"Co-authored-by: (?P<name>[^<]+) ")
 
         gitcur = list(os.popen("git shortlog -s " + revision_range).readlines())
@@ -94,7 +104,6 @@ def get_authors(revision_range):
         pre = set(pre)
 
     else:
-
         xpr = re.compile(r"Co-authored-by: (?P<name>[^<]+) ")
         cur = set(
             xpr.findall(