Linting fixes and CI config for multiple Python 3.9+ (#34)

* Disable fail-fast

* Disable py38 build

* Remove docs workflow and re-add 3.8 to test matrix

* Linting fixes; set default language version to 3.9 in pre-commit

* Use 3.9 as the default CI version

* Update dummy version tag in tests

* Cancel running CI jobs if new changes are pushed to a PR

* Run pre-commit autoupdate and unpin flake8 plugins

* Add a second dummy test that checks top-level imports

* Drop 3.8 support

* Run linting with new black rules and fix warnings stacklevel warning

* Reinforce python3.9 in pre-commit to avoid linting slosh

* Use Python 3.9 compatible type hints for pydantic objects

.github/workflows/testing.yml

@@ -7,6 +7,12 @@ on:
 
   pull_request:
 
+# Cancel running workflows when additional changes are pushed
+# https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#example-using-a-fallback-value
+concurrency:
+  group: ${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
 jobs:
   lint:
     runs-on: ubuntu-latest
@@ -15,7 +21,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
+          python-version: '3.9'
           cache: pip
           cache-dependency-path: pyproject.toml
 
@@ -30,8 +36,9 @@ jobs:
   test:
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11']
 
     steps:
       - uses: actions/checkout@v3
@@ -49,23 +56,3 @@ jobs:
 
       - name: Test
         run: pytest --cov=jobflow_remote --cov-report=xml
-
-  docs:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: actions/setup-python@v4
-        with:
-          python-version: '3.11'
-          cache: pip
-          cache-dependency-path: pyproject.toml
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install .[strict,docs]
-
-      - name: Build
-        run: jupyter-book build docs --path-output docs_build

.pre-commit-config.yaml

@@ -1,25 +1,25 @@
 default_language_version:
-  python: python3
+  python: python3.9
 #exclude: '^src/{{ package_name }}/some/directory/'
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
   - id: check-yaml
   - id: fix-encoding-pragma
     args: [--remove]
   - id: end-of-file-fixer
   - id: trailing-whitespace
 - repo: https://github.com/myint/autoflake
-  rev: v2.0.0
+  rev: v2.2.1
   hooks:
   - id: autoflake
 - repo: https://github.com/psf/black
-  rev: 22.12.0
+  rev: 23.9.1
   hooks:
   - id: black
 - repo: https://github.com/asottile/blacken-docs
-  rev: v1.12.1
+  rev: 1.16.0
   hooks:
   - id: blacken-docs
     additional_dependencies: [black]
@@ -29,18 +29,18 @@ repos:
   hooks:
   - id: isort
 - repo: https://github.com/pycqa/flake8
-  rev: 6.0.0
+  rev: 6.1.0
   hooks:
   - id: flake8
     entry: pflake8
     files: ^src/
     additional_dependencies:
-    - pyproject-flake8==6.0.0
-    - flake8-bugbear==22.12.6
-    - flake8-typing-imports==1.14.0
-    - flake8-docstrings==1.6.0
-    - flake8-rst-docstrings==0.3.0
-    - flake8-rst==0.8.0
+    - pyproject-flake8
+    - flake8-bugbear
+    - flake8-typing-imports
+    - flake8-docstrings
+    - flake8-rst-docstrings
+    - flake8-rst
 - repo: https://github.com/pre-commit/pygrep-hooks
   rev: v1.10.0
   hooks:
@@ -49,7 +49,7 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.991
+  rev: v1.6.0
   hooks:
   - id: mypy
     files: ^src/
@@ -58,13 +58,13 @@ repos:
     - types-pkg_resources==0.1.2
     - types-paramiko
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.2
+  rev: v2.2.6
   hooks:
   - id: codespell
     stages: [commit, commit-msg]
     args: [--ignore-words-list, 'titel,statics,ba,nd,te,nin']
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.3.1
+  rev: v3.15.0
   hooks:
     - id: pyupgrade
       args: [--py38-plus]

doc/source/_static/index-images/image_licences.txt

@@ -1,4 +1,4 @@
 getting_started.svg: https://www.svgrepo.com/svg/393367/rocket (PD Licence)
 user_guide.svg: https://www.svgrepo.com/svg/75531/user-guide (CC0 Licence)
 api.svg: https://www.svgrepo.com/svg/157898/gears-configuration-tool (CC0 Licence)
-contributor.svg: https://www.svgrepo.com/svg/57189/code-programing-symbol (CC0 Licence)
+contributor.svg: https://www.svgrepo.com/svg/57189/code-programing-symbol (CC0 Licence)

doc/source/_static/jobflow_remote.css

@@ -159,4 +159,4 @@ html[data-theme=dark] h3 {
 .sd-btn-secondary:hover, .sd-btn-secondary:focus {
     background-color: var(--matgenix-dark-color) !important;
     border-color: var(--matgenix-dark-color) !important;
-}
+}

doc/source/api/index.rst

@@ -6,4 +6,4 @@ API Reference
 
 This is the API reference
 
-.. include:: jobflow_remote.rst
+.. include:: jobflow_remote.rst

doc/source/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.
 #
@@ -28,6 +27,7 @@
 
 
 import jobflow_remote
+
 # The short X.Y version
 version = jobflow_remote.__version__
 # The full version, including alpha/beta/rc tags
@@ -49,16 +49,16 @@
     "sphinx.ext.todo",
     "sphinx.ext.viewcode",
     "sphinx.ext.napoleon",  # For Google Python Style Guide
-    'sphinx.ext.coverage',
-    'sphinx.ext.doctest',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.graphviz',
-    'sphinx.ext.ifconfig',
-    'matplotlib.sphinxext.plot_directive',
-    'IPython.sphinxext.ipython_console_highlighting',
-    'IPython.sphinxext.ipython_directive',
-    'sphinx.ext.mathjax',
-    'sphinx_design',
+    "sphinx.ext.coverage",
+    "sphinx.ext.doctest",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.graphviz",
+    "sphinx.ext.ifconfig",
+    "matplotlib.sphinxext.plot_directive",
+    "IPython.sphinxext.ipython_console_highlighting",
+    "IPython.sphinxext.ipython_directive",
+    "sphinx.ext.mathjax",
+    "sphinx_design",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -78,7 +78,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = 'en'
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -95,7 +95,7 @@
 # a list of builtin themes.
 #
 # html_theme = 'sphinx_book_theme'
-html_theme = 'pydata_sphinx_theme'
+html_theme = "pydata_sphinx_theme"
 # html_favicon = '_static/favicon/favicon.ico'
 
 # Theme options are theme-specific and customize the look and feel of a theme
@@ -108,7 +108,7 @@
     #       "image_dark": "index-image/contributor.svg",
     #   },
     "collapse_navigation": True,
-    'announcement': (
+    "announcement": (
         "<p>"
         "Jobflow-Remote is still in beta phase. The API may change at any time."
         "</p>"
@@ -137,14 +137,14 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 html_css_files = ["jobflow_remote.css"]
-html_title = "%s v%s Manual" % (project, version)
-html_last_updated_fmt = '%b %d, %Y'
+html_title = f"{project} v{version} Manual"
+html_last_updated_fmt = "%b %d, %Y"
 # html_css_files = ["numpy.css"]
 html_context = {"default_mode": "light"}
 html_use_modindex = True
 html_copy_source = False
 html_domain_indices = False
-html_file_suffix = '.html'
+html_file_suffix = ".html"
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = "jobflow_remote_doc"

doc/source/dev/index.rst

@@ -4,4 +4,4 @@
 Contributing to Jobflow-Remote
 ##############################
 
-Here are the things that can be done.
+Here are the things that can be done.

doc/source/glossary.rst

@@ -11,4 +11,3 @@ Glossary
 
    Worker
        The description of a given resource where to execute flows.
-

doc/source/index.rst

@@ -102,4 +102,4 @@ Jobflow-Remote is a package to submit jobflow flows remotely.
 
 .. This is not really the index page, that is found in
    _templates/indexcontent.html The toctree content here will be added to the
-   top of the template header
+   top of the template header

doc/source/user/basics.rst

@@ -9,4 +9,3 @@ fundamental Jobflow-Remote ideas and philosophy.
 ..
     .. toctree::
        :maxdepth: 1
-

doc/source/user/building.rst

@@ -4,4 +4,4 @@ Building from source
 ====================
 
 Get the source from the git repository.
-Install it with pip install .
+Install it with pip install .

doc/source/user/whatisjobflowremote.rst

@@ -5,4 +5,4 @@ What is Jobflow-Remote?
 =======================
 
 Jobflow-Remote is ...
-TODO: add the features that it has.
+TODO: add the features that it has.

pyproject.toml

@@ -12,7 +12,6 @@ authors = [{ name = "Guido Petretto", email = "[email protected]" }]
 dynamic = ["version"]
 classifiers = [
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
@@ -24,7 +23,7 @@ classifiers = [
     "Topic :: Other/Nonlisted Topic",
     "Topic :: Scientific/Engineering",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 dependencies =[
     "jobflow[strict]",
     "pydantic<2",
@@ -81,7 +80,7 @@ max-line-length = 88
 max-doc-length = 88
 select = "C, E, F, W, B"
 extend-ignore = "E203, W503, E501, F401, RST21"
-min-python-version = "3.8.0"
+min-python-version = "3.9.0"
 docstring-convention = "numpy"
 rst-roles = "class, func, ref, obj"
 

src/jobflow_remote/cli/flow.py

@@ -171,7 +171,6 @@ def flow_info(
         flow_ids = [jf_id]
 
     with loading_spinner():
-
         jc = JobController()
 
         flows_info = jc.get_flows_info(

src/jobflow_remote/cli/formatting.py

@@ -142,7 +142,6 @@ def format_job_info(job_info: JobInfo, show_none: bool = False):
 
 
 def format_flow_info(flow_info: FlowInfo):
-
     title = f"Flow: {flow_info.name} - {flow_info.flow_id} - {flow_info.state.name}"
     table = Table(title=title)
     table.title_style = "bold"

src/jobflow_remote/cli/job.py

@@ -159,7 +159,6 @@ def job_info(
     db_id, job_id = get_job_db_ids(job_db_id, job_index)
 
     with loading_spinner():
-
         jc = JobController()
 
         job_info = jc.get_job_info(

src/jobflow_remote/cli/utils.py

@@ -205,7 +205,6 @@ def convert_metadata(string_metadata: str | None) -> dict | None:
 
 
 def get_start_date(start_date: datetime | None, days: int | None, hours: int | None):
-
     if start_date and (start_date.year, start_date.month, start_date.day) == (
         1900,
         1,