Adapt/extend codespell config #119

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ruestefa wants to merge 35 commits into MeteoSwiss-APN:main from ruestefa:codespell-config

.github/workflows/blueprint-docs.yml

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+Diff line change
@@ Expand Up / @@ -19,7 +19,7 @@ jobs: @@
         - name: Create new project
           run: |
             # Note: Make sure python_version is consistent with python-version hardcoded above
-            conda run --name blueprint copier --force --vcs-ref=HEAD python_version=3.9 copy . ./docs/example_project
+            conda run --name blueprint copier --force --vcs-ref=HEAD copy . ./docs/example_project
             ls
             echo "==================================="
             ls docs
@@ Expand Down @@

README.md

            
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    @@ -42,18 +42,19 @@ conda create --name blueprint
  
    conda activate blueprint

    conda install "copier<8.0"

    ```

    Make sure to have at least copier version 8.1.0. Otherwise, please update copier.

    ## Create your Python package from our template

    You can now produce your Python package from a copier template by running

    ```

    conda activate blueprint

    copier [email protected]:MeteoSwiss-APN/mch-python-blueprint.git </path/to/destination>

    copier copy [email protected]:MeteoSwiss-APN/mch-python-blueprint.git </path/to/destination>

    ```

    If you need to generate your project from a specific commit hash or branch of the blueprint you can run with --vcs-ref

    ```

    conda activate blueprint

    copier --vcs-ref <branch> [email protected]:MeteoSwiss-APN/mch-python-blueprint.git </path/to/destination>

    copier copy --vcs-ref <branch> [email protected]:MeteoSwiss-APN/mch-python-blueprint.git </path/to/destination>

    ```

    **Warning:**

    @@ -91,7 +92,7 @@ out more about provided development tools and setting up CI/CD pipelines on http
  
    To update your package to the latest version of the underlying meta template, run:

    ```bash

    copier -a .copier-answers.yml -f update

    copier update -a .copier-answers.yml -f update

    ```

    With `-f`, conflicting files are overwritten (which doesn't mean that in the end, the files are changed as those conflicts can be purely internal).

copier.yaml

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+Diff line change
@@ Expand Up / @@ -76,5 +76,5 @@ python_version: @@
     year:
       help: "This year"
-      default: "2022"
+      default: "2023"
       type: str

pyproject.toml

-Original file line number
+Diff line change
@@ Expand Up / @@ -31,5 +31,16 @@ ignore_directives = [ @@
     ]
     [tool.codespell]
-    ignore-words-list = "inout"
-    skip = "requirements/*"
+    ignore-regex = '(\b[A-Z]+\b|.*([#!"]|<!--) *codespell-ignore\b|^ *"image/[a-z]+": ".*",$)'
+    # - Ignore all-uppercase words (acronyms)
+    # - Ignore lines with codespell-ignore comment
+    # - Ignore lines "image/...": "..." (images in *.ipynb files)
+    ignore-words = './tmpl/codespell_ignored_words.txt'
+    # Note: To skip local files by their full path, codespell (v2.2.2) requires
+    # './src/...` when called from the command line but 'src/...' when called via
+    # pre-commit (as local hook); '*src/...` matches both
+    skip = """\
+    .git,\
+    *.codespell-ignore.*,\
+    *requirements/*,\
+    """

requirements/environment.yml

            
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    @@ -1,51 +1,48 @@
  
    name: mch-python-blueprint

    channels:

      - conda-forge

      - defaults

    dependencies:

      - _libgcc_mutex=0.1

      - _openmp_mutex=4.5

      - alabaster=0.7.13

      - babel=2.13.0

      - babel=2.14.0

      - brotli-python=1.1.0

      - bzip2=1.0.8

      - ca-certificates=2023.7.22

      - certifi=2023.7.22

      - ca-certificates=2023.11.17

      - certifi=2023.11.17

      - cffi=1.16.0

      - cfgv=3.3.1

      - charset-normalizer=3.3.1

      - charset-normalizer=3.3.2

      - colorama=0.4.6

      - distlib=0.3.7

      - docutils=0.20.1

      - filelock=3.12.4

      - identify=2.5.30

      - idna=3.4

      - distlib=0.3.8

      - filelock=3.13.1

      - identify=2.5.33

      - idna=3.6

      - imagesize=1.4.1

      - importlib-metadata=6.8.0

      - importlib-metadata=7.0.0

      - jinja2=3.1.2

      - ld_impl_linux-64=2.40

      - libexpat=2.5.0

      - libffi=3.4.2

      - libgcc-ng=13.2.0

      - libgomp=13.2.0

      - libnsl=2.0.1

      - libsqlite=3.43.2

      - libsqlite=3.44.2

      - libstdcxx-ng=13.2.0

      - libuuid=2.38.1

      - libzlib=1.2.13

      - markupsafe=2.1.3

      - ncurses=6.4

      - nodeenv=1.8.0

      - openssl=3.1.3

      - openssl=3.2.0

      - packaging=23.2

      - pip=23.3.1

      - platformdirs=3.11.0

      - pre-commit=3.5.0

      - pip=23.3.2

      - platformdirs=4.1.0

      - pre-commit=3.6.0

      - pycparser=2.21

      - pygments=2.16.1

      - pygments=2.17.2

      - pysocks=1.7.1

      - python=3.12.0

      - python_abi=3.12

      - python=3.10.13

      - python_abi=3.10

      - pytz=2023.3.post1

      - pyyaml=6.0.1

      - readline=8.2

    @@ -60,29 +57,29 @@ dependencies:
  
      - sphinxcontrib-qthelp=1.0.6

      - sphinxcontrib-serializinghtml=1.1.9

      - tk=8.6.13

      - typing-extensions=4.8.0

      - typing_extensions=4.8.0

      - tzdata=2023c

      - ukkonen=1.0.1

      - urllib3=2.0.7

      - virtualenv=20.24.4

      - wheel=0.41.2

      - urllib3=2.1.0

      - virtualenv=20.25.0

      - wheel=0.42.0

      - xz=5.2.6

      - yaml=0.2.5

      - zipp=3.17.0

      - pip:

          - annotated-types==0.6.0

          - copier==7.2.0

          - docutils==0.19

          - dunamai==1.19.0

          - funcy==2.0

          - jinja2-ansible-filters==1.3.2

          - mistune==2.0.5

          - pathspec==0.11.2

          - pathspec==0.12.1

          - plumbum==1.8.2

          - prompt-toolkit==3.0.36

          - pydantic==1.10.13

          - pydantic-core==2.10.1

          - pyyaml-include==1.3.1

          - questionary==2.0.1

          - rstcheck-core==1.0.3

          - sphinx-mdinclude==0.5.3

          - wcwidth==0.2.8

          - types-docutils==0.19.1.9

          - typing-extensions==4.9.0

          - wcwidth==0.2.12

tmpl/README.md.j2

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+Diff line change
@@ Expand Up @@
     ```bash
     tools/setup_env.sh -u -e -n <package_env_name>
     ```
+    *Hint*: Make sure to execute the bash scripts in `tools/` (do not source them as this can lead to issues)!
     *Hint*: If you are the package administrator, it is a good idea to understand what this script does, you can do everything manually with `conda` instructions.
     *Hint*: Use the flag `-m` to speed up the installation using mamba. Of course you will have to install mamba first (we recommend to install mamba into your base
@@ Expand Down @@

tmpl/codespell_ignored_words.txt

-Original file line number
+Diff line change
@@ -0,0 +1,9 @@
+    # German
+    alle
+    ist
+    oder
+    # English
+    pres
+    rime
+    theses
+    trough

tmpl/docs/installation.rst.j2

-Original file line number
+Diff line change
@@ Expand Up / @@ -11,6 +11,7 @@ Preparation @@
     -----------
     To install {{ project_name }} you need a miniconda installation. You can either set up your miniconda installation manually or use the script `tools/setup_miniconda.sh`, which will download and install the latest version of miniconda.
+    Make sure to execute the script (do not source it as this can lead to issues)!
     Installation of dependencies
@@ Expand Down @@

tmpl/pyproject.toml.j2

-Original file line number
+Diff line change
@@ Expand Up / @@ -155,5 +155,16 @@ ignore_directives = [ @@
     ]
     [tool.codespell]
-    ignore-words-list = "inout"
-    skip = "requirements/*"
+    ignore-regex = '(\b[A-Z]+\b|.*([#!"]|<!--) *codespell-ignore\b|^ *"image/[a-z]+": ".*",$)'
+    # - Ignore all-uppercase words (acronyms)
+    # - Ignore lines with codespell-ignore comment
+    # - Ignore lines "image/...": "..." (images in *.ipynb files)
+    ignore-words = './codespell_ignored_words.txt'
+    # Note: To skip local files by their full path, codespell (v2.2.2) requires
+    # './src/...` when called from the command line but 'src/...' when called via
+    # pre-commit (as local hook); '*src/...` matches both
+    skip = """\
+    .git,\
+    *.codespell-ignore.*,\
+    *requirements/*,\
+    """

tmpl/requirements/environment.yml.j2

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+Diff line change
@@ -1,7 +1,6 @@
     name: {{ project_slug }}
     channels:
       - conda-forge
-      - defaults
     dependencies:
       - _libgcc_mutex=0.1
       - _openmp_mutex=4.5
@@ Expand Down @@

tmpl/tools/setup_env.sh.j2

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+Diff line change
@@ Expand Up / @@ -3,6 +3,11 @@ @@
     # Create conda environment with pinned or unpinned requirements
+    if [[ "${BASH_SOURCE[0]}" != "${0}" ]]; then
+      echo "Please simply call the script instead of sourcing it!"
+      return
+    fi
     if [[ "${BASH_SOURCE[0]}" != "${0}" ]]; then
       echo "Please simply call the script instead of sourcing it!"
       return
@@ Expand Down @@

tmpl/tools/setup_miniconda.sh

-Original file line number
+Diff line change
@@ Expand Up / @@ -3,6 +3,11 @@ @@
     # Install miniconda if necessary
+    if [[ "${BASH_SOURCE[0]}" != "${0}" ]]; then
+      echo "Please simply call the script instead of sourcing it!"
+      return
+    fi
     if [[ "${BASH_SOURCE[0]}" != "${0}" ]]; then
       echo "Please simply call the script instead of sourcing it!"
       return
@@ Expand Down @@

tools/update_env.sh

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+Diff line change
@@ Expand Up / @@ -10,7 +10,7 @@ main() @@
         if [[ -d "${tmpdir}" ]]; then
             \rm -rfv "${tmpdir}" || return
         fi
-        copier -f --vcs-ref=HEAD . "${tmpdir}" || return
+        copier copy -f --vcs-ref=HEAD . "${tmpdir}" || return
         # Use script in project to update the root environment file
         local env_name
@@ Expand Down @@

tools/update_tmpl_env.sh

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+Diff line change
@@ Expand Up / @@ -10,7 +10,7 @@ main() @@
         if [[ -d "${tmpdir}" ]]; then
             \rm -rfv "${tmpdir}" || return
         fi
-        copier -f --vcs-ref=HEAD . "${tmpdir}" || return
+        copier copy -f --vcs-ref=HEAD . "${tmpdir}" || return
         # Update the project's environment file
         \cd "${tmpdir}" || return
@@ Expand Down @@

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