codespell: config, workflow and typos fixed

.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

README.md

@@ -103,7 +103,7 @@ There are a few additional specific advantages to `davos` that go beyond more ty
     typical overhead of setting up a new virtual environment (or container, virtual machine, etc.), installing
     third-party tools, writing and sharing configuration files, and so on.  All of your code *and its dependencies* may
     be contained in a single notebook file.
-  - using onion comments, `davos` can enable mutliple versions of the same package to be used or specified in different
+  - using onion comments, `davos` can enable multiple versions of the same package to be used or specified in different
     parts of the same notebook.  Want to use some deprecated or removed function in `scikit-learn` in one cell, but then
     use one of the latest features in another?  You can!  Just add onion comments specifying which versions of the
     package you want to `smuggle` in which cells of your notebook.

davos/core/config.py

@@ -511,7 +511,7 @@ def _block_greedy_ipython_completer():
     imports.
 
     This is particularly problematic for packages that set
-    `IPython`- or notebook-specific options or behavors on import (like
+    `IPython`- or notebook-specific options or behaviors on import (like
     `davos`) because the autocomplete mechanism imports them *outside*
     the `IPython` environment. To prevent this, `davos` parses the stack
     trace for any calls originating from IPython's autocomple module

paper/main.tex

@@ -440,7 +440,7 @@ \subsubsection{Projects}\label{subsec:projects}
 %By default, projects are notebook-specific, but can also be shared by multiple notebooks, and can be managed interactively from within a Davos-enhanced notebook.
 
 %%%%%%%% JEREMY VERSION %%%%%%%%%
-%Installing new packages in a notebook using standard approaches (e.g., system commmands) affect the
+%Installing new packages in a notebook using standard approaches (e.g., system commands) affect the
 %runtime environment. This could lead to undesired behaviors. For example, running a notebook that
 %installs new packages in the user’s primary system environment might alter their main system installation
 %and/or containerized environment in unexpected ways (e.g., changing package versions, causing conflicts
@@ -792,7 +792,7 @@ \section{Illustrative Example}\label{sec:illustrative-example}
 environments are the same.  However, a common ``advanced'' approach
 entails running the notebook server from a base environment, with
 additional environments each providing their own separate,
-interchangeable IPython kernels.  To accomodate this multi-environment
+interchangeable IPython kernels.  To accommodate this multi-environment
 scenario, on lines 26 and 28, we use the \texttt{pip\_executable} option to control which environments each
 package should be installed to.  Once these two packages are installed
 and imported, line 31 smuggles \texttt{tqdm}~\cite{daCoEtal22}, which
@@ -861,7 +861,7 @@ \section{Impact}
 incorporates its own virtual environment system that isolates
 notebook-installed packages from the runtime environment
 (Sec.~\ref{subsec:projects}). In many setups this feature can eliminate the
-need to set up a seperate virtual environment or container (e.g., in
+need to set up a separate virtual environment or container (e.g., in
 conjunction with a \texttt{requirements.txt}, \texttt{project.toml}, or
 \texttt{environment.yml} file specifying the project's dependencies).
 

paper/old/main-old.tex

@@ -649,7 +649,7 @@ \section{Illustrative Example}\label{sec:illustrative-example}
 environments are the same.  However, a common ``advanced'' approach
 entails running the notebook server from a base environment, with
 additional environments each providing their own separate,
-interchangeable IPython kernels.  To accomodate this multi-environment
+interchangeable IPython kernels.  To accommodate this multi-environment
 scenario, on lines 26 and 28, we use the \texttt{pip\_executable} option to control which environments each
 package should be installed to.  Once these two packages are installed
 and imported, line 31 smuggles \texttt{tqdm}~\cite{daCoEtal22}, which

pyproject.toml

@@ -81,3 +81,9 @@ markers = [
     "ipython_post7: marks tests that should run only if IPython>=7.0.0",
     "timeout: marks tests that should fail after a certain amount of time"
 ]
+
+[tool.codespell]
+skip = '.git,*.pdf,*.svg,*.bst,*.cls'
+ignore-regex = 'doesnt/exist|Ser Davos'
+#
+ignore-words-list = 'covert,dateset'

tests/test__environment_and_init.ipynb

@@ -269,7 +269,7 @@
    "source": [
     "def test_config_properties_accessible_toplevel():\n",
     "    \"\"\"\n",
-    "    test that davos.config fields are accesible from the top-level davos \n",
+    "    test that davos.config fields are accessible from the top-level davos \n",
     "    namespace\n",
     "    \"\"\"\n",
     "    config_fields = ['active', 'auto_rerun', 'confirm_install', \n",

tests/test_core.ipynb

@@ -1159,7 +1159,7 @@
     "    onion comment that constrains the smuggled package version using \n",
     "    multiple specifiers. -v/--verbose are passed in a somewhat \n",
     "    unrealistic way, but it's meant to test isolating the version \n",
-    "    specifier from other arugments both before and after it\n",
+    "    specifier from other arguments both before and after it\n",
     "        `smuggle foo    # pip: -v foo-pkg>=1.0.1,<2 --verbose`\n",
     "    \"\"\"\n",
     "    installer_kwargs = {\n",
@@ -2698,7 +2698,7 @@
     "@mark.timeout(30)\n",
     "def test_smuggle_pip_new():\n",
     "    \"\"\"\n",
-    "    smuggle a package that does't exist locally, using 'pip' as the \n",
+    "    smuggle a package that doesn't exist locally, using 'pip' as the \n",
     "    installer program\n",
     "    \"\"\"\n",
     "    assert not is_installed_include_project('ppca')\n",
@@ -2886,7 +2886,7 @@
     "@mark.timeout(300)\n",
     "def test_smuggle_github_subdirectory():\n",
     "    \"\"\"\n",
-    "    smuggle a package tthat exists as a subdirectory of a larger GitHub \n",
+    "    smuggle a package that exists as a subdirectory of a larger GitHub \n",
     "    repository\n",
     "    \"\"\"\n",
     "    assert not is_installed_include_project('sherlock_helpers')\n",

tests/test_ipython_pre7.ipynb

@@ -399,7 +399,7 @@
    "source": [
     "def test_generate_parser_func_noop():\n",
     "    \"\"\"\n",
-    "    the `IPython<7.0` implementation fo `generate_parser_func` should \n",
+    "    the `IPython<7.0` implementation of `generate_parser_func` should \n",
     "    simply return the single-line parser, untouched\n",
     "    \"\"\"\n",
     "    davos_parser = davos.implementations.full_parser\n",

tests/test_project.ipynb

@@ -113,7 +113,7 @@
     "        `atexit.unregister(<fn>)` compares <fn> to each function in the \n",
     "        list with `==`, and fails silently if <fn> isn't found. This \n",
     "        dummy class records each object it's compared to using `==`, so \n",
-    "        passing it to `atexit.unregister()` will extrac te list of \n",
+    "        passing it to `atexit.unregister()` will extract the list of \n",
     "        currently registered functions.\n",
     "        \"\"\"\n",
     "        def __init__(self):\n",
@@ -840,7 +840,7 @@
     "        f'{_sep.join(initial_installed_pkgs)}'\n",
     "    )\n",
     "    # v4.64.1 was the last version to support Python 3.6\n",
-    "    # pass --ignore-installed to ensure packge gets installed in project \n",
+    "    # pass --ignore-installed to ensure package gets installed in project \n",
     "    # rather than using version in notebook kernel environment, just in \n",
     "    # case the exact requested version is installed there\n",
     "    smuggle tqdm    # pip: tqdm==4.64.1 --ignore-installed\n",