Add codespell (workflow and config) to catch typos, fix some caught now (#326)

* Add github action to codespell main on push and PRs

* Add rudimentary codespell config

* Use "size" not "siz" for the variable

AFAIK there is no need to obfuscate as there should be no clash

* ignore mmaped and splitted

* [DATALAD RUNCMD] run codespell throughout but ignore fail

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "codespell -w || :",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

* [DATALAD RUNCMD] Do interactive fixing of some ambigous typos

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "codespell -w -i 3 -C 2",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

Author: yarikoptic

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.pylintrc

@@ -44,7 +44,7 @@ confidence=
 # can either give multiple identifiers separated by comma (,) or put this
 # option multiple times (only on the command line, not in the configuration
 # file where it should appear only once). You can also use "--disable=all" to
-# disable everything first and then reenable specific checks. For example, if
+# disable everything first and then re-enable specific checks. For example, if
 # you want to run only the similarities checker, you can use "--disable=all
 # --enable=similarities". If you want to run only the classes checker, but have
 # no Warning level messages displayed, use "--disable=all --enable=classes

UPGRADE_C_API.rst

@@ -48,7 +48,7 @@ Then, simply generate the header definitions like in this example:
 
 .. code-block:: bash
 
-    scripts/pyslurm_bindgen.py -D /directoy/with/slurm/headers > pyslurm/slurm/header.pxi
+    scripts/pyslurm_bindgen.py -D /directory/with/slurm/headers > pyslurm/slurm/header.pxi
 
 The script outputs everything to `stdout`. Simply redirect the output to the file: :code:`pyslurm/slurm/header.pxi`.
 The headers should now be fully translated.

pyproject.toml

@@ -6,3 +6,10 @@ requires = [
     "Cython>=0.29.30,<3.0",
 ]
 
+
+[tool.codespell]
+skip = '.git,*.pdf,*.svg,*.lock,*.css'
+check-hidden = true
+# ignore-regex = ''
+# ignore some variables etc
+ignore-words-list = 'mmaped,splitted'

pyslurm/core/error.pyx

@@ -51,7 +51,7 @@ def slurm_errno():
 
 
 def get_last_slurm_error():
-    """Get the last slurm error that occured as a tuple of errno and string.
+    """Get the last slurm error that occurred as a tuple of errno and string.
 
     Returns:
         errno (int): The error number

pyslurm/core/job/job.pxd

@@ -1,5 +1,5 @@
 #########################################################################
-# job.pyx - interface to retrieve slurm job informations
+# job.pyx - interface to retrieve slurm job information
 #########################################################################
 # Copyright (C) 2023 Toni Harzendorf <toni.harzendorf@gmail.com>
 #
@@ -353,7 +353,7 @@ cdef class Job:
         kill_on_invalid_dependency (bool):
             Whether the Job should be killed on an invalid dependency.
         spreads_over_nodes (bool):
-            Whether the Job should be spreaded over as many nodes as possible.
+            Whether the Job should be spread over as many nodes as possible.
         power_options (list):
             Options set for Power Management.
         is_cronjob (bool):

pyslurm/core/job/job.pyx

@@ -1,5 +1,5 @@
 #########################################################################
-# job.pyx - interface to retrieve slurm job informations
+# job.pyx - interface to retrieve slurm job information
 #########################################################################
 # Copyright (C) 2023 Toni Harzendorf <toni.harzendorf@gmail.com>
 #

pyslurm/core/job/sbatch_opts.pyx

@@ -40,7 +40,7 @@ class _SbatchOpt():
         self.has_optional_args = has_optional_args
 
 
-# Sorted by occurence in the sbatch manpage - keep in order.
+# Sorted by occurrence in the sbatch manpage - keep in order.
 SBATCH_OPTIONS = [
     _SbatchOpt("A", "account", "account"),
     _SbatchOpt(None, "acctg-freq", "accounting_gather_frequency"),

pyslurm/core/job/step.pxd

@@ -1,5 +1,5 @@
 #########################################################################
-# job/step.pxd - interface to retrieve slurm job step informations
+# job/step.pxd - interface to retrieve slurm job step information
 #########################################################################
 # Copyright (C) 2023 Toni Harzendorf <toni.harzendorf@gmail.com>
 #

pyslurm/core/job/step.pyx

@@ -1,5 +1,5 @@
 #########################################################################
-# job/step.pyx - interface to retrieve slurm job step informations
+# job/step.pyx - interface to retrieve slurm job step information
 #########################################################################
 # Copyright (C) 2023 Toni Harzendorf <toni.harzendorf@gmail.com>
 #