CI maintenance (#209)

.github/workflows/pre-commit.yml

@@ -10,6 +10,8 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
+    - uses: actions/checkout@main
+    - uses: actions/setup-python@main
+      with:
+        python-version: '>=3.11'
     - uses: pre-commit/action@main

.pre-commit-config.yaml

@@ -1,4 +1,10 @@
 repos:
+- repo: https://github.com/tdegeus/conda_envfile
+  rev: v0.5.2
+  hooks:
+  - id: conda_envfile_pyproject
+    files: environment.yaml
+    args: [--format]
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.5.0
   hooks:
@@ -8,12 +14,12 @@ repos:
   - id: check-toml
   - id: debug-statements
 - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-  rev: v2.11.0
+  rev: v2.12.0
   hooks:
   - id: pretty-format-yaml
     args: [--preserve-quotes, --autofix, --indent, '2']
   - id: pretty-format-toml
-    args: [--autofix]
+    args: [--autofix, --indent, '4', --trailing-commas]
 - repo: https://github.com/pre-commit/pygrep-hooks
   rev: v1.10.0
   hooks:
@@ -25,35 +31,32 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/psf/black
-  rev: 23.11.0
+  rev: 24.2.0
   hooks:
   - id: black
     args: [--safe, --quiet, --line-length=100]
 - repo: https://github.com/PyCQA/autoflake
-  rev: v2.2.1
+  rev: v2.3.0
   hooks:
   - id: autoflake
     args: [--in-place, --remove-unused-variable]
-- repo: https://github.com/asottile/reorder_python_imports
-  rev: v3.12.0
+- repo: https://github.com/pycqa/isort
+  rev: 5.13.2
   hooks:
-  - id: reorder-python-imports
+  - id: isort
+    name: isort
+    args: ["--force-single-line", "--line-length=100", "--profile=black"]
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.15.0
+  rev: v3.15.1
   hooks:
   - id: pyupgrade
     args: [--py36-plus]
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.1.0
+  rev: 7.0.0
   hooks:
   - id: flake8
     args: ["--max-line-length=100", "--per-file-ignores=shelephant/__init__.py:F401", "--ignore=E203,W503"]
 - repo: https://github.com/asottile/setup-cfg-fmt
   rev: v2.5.0
   hooks:
   - id: setup-cfg-fmt
-- repo: https://github.com/tdegeus/conda_envfile
-  rev: v0.4.2
-  hooks:
-  - id: conda_envfile_parse
-    files: environment.yaml

.readthedocs.yml

@@ -4,9 +4,9 @@ sphinx:
   configuration: docs/conf.py
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-lts-latest
   tools:
-    python: mambaforge-22.9
+    python: mambaforge-latest
 
 conda:
   environment: environment.yaml

pyproject.toml

@@ -5,12 +5,12 @@ requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
 authors = [{name = "Tom de Geus", email = "tom@geus.me"}]
 classifiers = ["License :: OSI Approved :: MIT License"]
 dependencies = [
-  "click",
-  "numpy>=1.15.0",
-  "platformdirs",
-  "prettytable",
-  "pyyaml",
-  "tqdm"
+    "click",
+    "numpy >=1.15.0",
+    "platformdirs",
+    "prettytable",
+    "pyyaml",
+    "tqdm",
 ]
 description = "Simple dataset management"
 dynamic = ["version"]

shelephant/_tests.py

@@ -1,6 +1,7 @@
 """
 Not part of public API.
 """
+
 import os
 import pathlib
 

shelephant/rsync.py

@@ -3,6 +3,7 @@
 
 (c) Tom de Geus, 2021, MIT
 """
+
 import os
 import re
 import subprocess

tests/test_cli.py

@@ -380,9 +380,11 @@ def test_ssh_send(self):
         if not has_ssh:
             raise unittest.SkipTest("'ssh localhost' does not work")
 
-        with tempdir(), shelephant.ssh.tempdir("localhost") as remote, contextlib.redirect_stdout(
-            io.StringIO()
-        ) as sio:
+        with (
+            tempdir(),
+            shelephant.ssh.tempdir("localhost") as remote,
+            contextlib.redirect_stdout(io.StringIO()) as sio,
+        ):
             files = ["foo.txt", "bar.txt", "more.txt", "even_more.txt"]
             check = create_dummy_files(files)
             shelephant_dump(files)
@@ -410,9 +412,11 @@ def test_ssh_send2(self):
         if not has_ssh:
             raise unittest.SkipTest("'ssh localhost' does not work")
 
-        with tempdir(), shelephant.ssh.tempdir("localhost") as remote, contextlib.redirect_stdout(
-            io.StringIO()
-        ) as sio:
+        with (
+            tempdir(),
+            shelephant.ssh.tempdir("localhost") as remote,
+            contextlib.redirect_stdout(io.StringIO()) as sio,
+        ):
             files = ["foo.txt", "bar.txt", "more.txt", "even_more.txt"]
             check = create_dummy_files(files)
             shelephant_dump(files)
@@ -441,9 +445,11 @@ def test_ssh_get(self):
         if not has_ssh:
             raise unittest.SkipTest("'ssh localhost' does not work")
 
-        with tempdir(), shelephant.ssh.tempdir("localhost") as remote, contextlib.redirect_stdout(
-            io.StringIO()
-        ) as sio:
+        with (
+            tempdir(),
+            shelephant.ssh.tempdir("localhost") as remote,
+            contextlib.redirect_stdout(io.StringIO()) as sio,
+        ):
             with cwd(remote):
                 files = ["foo.txt", "bar.txt", "more.txt", "even_more.txt"]
                 check = create_dummy_files(files)
@@ -534,9 +540,11 @@ def test_ssh(self):
         if not has_ssh:
             raise unittest.SkipTest("'ssh localhost' does not work")
 
-        with tempdir(), shelephant.ssh.tempdir("localhost") as remote, contextlib.redirect_stdout(
-            io.StringIO()
-        ) as sio:
+        with (
+            tempdir(),
+            shelephant.ssh.tempdir("localhost") as remote,
+            contextlib.redirect_stdout(io.StringIO()) as sio,
+        ):
             with cwd(remote):
                 files = ["foo.txt", "bar.txt", "more.txt", "even_more.txt"]
                 create_dummy_files(files)