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Merged
merged 5 commits into from
May 22, 2022
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CI: mypy&pyright in manual pre-commit stage #47075

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b9ca491
CI: mypy&pyright in manual pre-commit stage
twoertwein May 20, 2022
cc0c6f0
move mypy+pyright to pre-commit
twoertwein May 20, 2022
d249177
Revert "move mypy+pyright to pre-commit"
twoertwein May 20, 2022
a8ad73f
system+manual
twoertwein May 20, 2022
bc3b01a
Update .pre-commit-config.yaml
twoertwein May 22, 2022
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21 changes: 10 additions & 11 deletions .github/workflows/code-checks.yml
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Expand Up @@ -67,15 +67,6 @@ jobs:
environment-file: ${{ env.ENV_FILE }}
use-only-tar-bz2: true

- name: Install node.js (for pyright)
uses: actions/setup-node@v3
with:
node-version: "16"

- name: Install pyright
# note: keep version in sync with .pre-commit-config.yaml
run: npm install -g [email protected]

- name: Build Pandas
id: build
uses: ./.github/actions/build_pandas
Expand All @@ -96,8 +87,16 @@ jobs:
run: ci/code_checks.sh docstrings
if: ${{ steps.build.outcome == 'success' }}

- name: Run typing validation
run: ci/code_checks.sh typing
- name: Use existing environment for type checking
run: |
echo $PATH >> $GITHUB_PATH
echo "PYTHONHOME=$PYTHONHOME" >> $GITHUB_ENV
echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV

- name: Typing
uses: pre-commit/[email protected]
with:
extra_args: --hook-stage manual --all-files
if: ${{ steps.build.outcome == 'success' }}

- name: Run docstring validation script tests
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20 changes: 17 additions & 3 deletions .pre-commit-config.yaml
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@@ -1,5 +1,7 @@
minimum_pre_commit_version: 2.9.2
minimum_pre_commit_version: 2.15.0
exclude: ^LICENSES/|\.(html|csv|svg)$
# reserve "manual" for mypy and pyright
default_stages: [commit, merge-commit, push, prepare-commit-msg, commit-msg, post-checkout, post-commit, post-merge, post-rewrite]
ci:
autofix_prs: false
repos:
Expand Down Expand Up @@ -31,7 +33,9 @@ repos:
- id: debug-statements
- id: end-of-file-fixer
exclude: \.txt$
stages: [commit, merge-commit, push, prepare-commit-msg, commit-msg, post-checkout, post-commit, post-merge, post-rewrite]
- id: trailing-whitespace
stages: [commit, merge-commit, push, prepare-commit-msg, commit-msg, post-checkout, post-commit, post-merge, post-rewrite]
- repo: https://github.com/cpplint/cpplint
rev: 1.6.0
hooks:
Expand Down Expand Up @@ -84,12 +88,22 @@ repos:
- id: pyright
name: pyright
entry: pyright
# note: assumes python env is setup and activated
language: node
pass_filenames: false
types: [python]
stages: [manual]
# note: keep version in sync with .github/workflows/code-checks.yml
additional_dependencies: ['[email protected]']
additional_dependencies: ['[email protected]']
- repo: local
hooks:
- id: mypy
name: mypy
entry: mypy
# note: assumes python env is setup and activated
language: system
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would it work to use the mypy hook, and add numpy (and whatever else is needed for types) in additional_dependencies? I tried this a while ago and there some were inconsistencies with how mypy runs on the whole project versus as a hook, but if we were able to get it to pass as a hook, then it'd solve a whole bunch of typing headaches

I've seen a bunch of other projects do this, and it seems pretty reliable

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I would like that! I think the only downside is that the current pre-commit run is very fast as it doesn't need to install all the dependencies from environment.yml. I'm not familiar with pre-commit, is there a nice way of sharing the exact dependency versions (basically everything in environment.yml)?

I guess to get pyright working, we would need to use its venv argument to point it to pre-commit/mypy's environment (I don't think pre-commit allows installing python dependencies for a node program).

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does it need to be everything in environment.yml? I would've thought that only a few packages would be necessary, like numpy and maybe pytest

is there a nice way of sharing the exact dependency versions (basically everything in environment.yml)?

I don't think so, other than writing our own script (like the one that checks flake8 versions match)

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does it need to be everything in environment.yml?

Probably almost everything: imported libraries might have type annotations (and pyright explicitly checks that it can find all imported modules).

I think I will just see what a mess it will be :) then we can decide on whether it is worth it or not

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😄 no worries then, system is fine, as long as the stage is manual (it used to not be system, and then there were a tonne of false-positives, and people would tend to just turn off pre-commit)

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@twoertwein twoertwein May 20, 2022 •
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Okay, let's try system for this PR! Two questions:

  1. Does github action create a new shell when executing pre-commit: the system hook doesn't find mypy from the activated conda env?
  2. It would be great to have only pyright and mypy in manual. By default all hooks are in all stages. Could change default_stages, then we need to call pre-commit only once for mypy+pyright (might reduce some overhead). Do you think that would be helpful? If so, what value should default_stages have?

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It is actually not that bad listing all dependencies for mypy, see the latest commit.

The issue is to programmatically find the python env that pre-commit created for mypy so that pyright can use it as well.

While it is possible to move mypy and later move pyright, I would really like to make sure that pyright uses the same env as mypy, as pyright errors when it encounters any missing modules. It is easy to forget a module, which is then resolved as Any (can hide errors).

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I thought I found an ugly way that should work on linux but it seems that pyright (and probably mypy too?) needs pandas to be compiled for some of its checks, see the error in pre-commit now.

Compiling pandas in the pre-commit is a little bit too much (more dependencies and it takes much longer). Let's go back to the system+manual approach.

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@MarcoGorelli I'm mostly pattern matching when it comes to github action+pre-commit but I found a working system+manual version :)

pass_filenames: false
types: [python]
stages: [manual]
- repo: local
hooks:
- id: flake8-rst
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23 changes: 2 additions & 21 deletions ci/code_checks.sh
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Expand Up @@ -11,11 +11,10 @@
# $ ./ci/code_checks.sh code # checks on imported code
# $ ./ci/code_checks.sh doctests # run doctests
# $ ./ci/code_checks.sh docstrings # validate docstring errors
# $ ./ci/code_checks.sh typing # run static type analysis
# $ ./ci/code_checks.sh single-docs # check single-page docs build warning-free

[[ -z "$1" || "$1" == "code" || "$1" == "doctests" || "$1" == "docstrings" || "$1" == "typing" || "$1" == "single-docs" ]] || \
{ echo "Unknown command $1. Usage: $0 [code|doctests|docstrings|typing]"; exit 9999; }
[[ -z "$1" || "$1" == "code" || "$1" == "doctests" || "$1" == "docstrings" || "$1" == "single-docs" ]] || \
{ echo "Unknown command $1. Usage: $0 [code|doctests|docstrings]"; exit 9999; }

BASE_DIR="$(dirname $0)/.."
RET=0
Expand Down Expand Up @@ -85,24 +84,6 @@ if [[ -z "$CHECK" || "$CHECK" == "docstrings" ]]; then

fi

### TYPING ###
if [[ -z "$CHECK" || "$CHECK" == "typing" ]]; then

echo "mypy --version"
mypy --version

MSG='Performing static analysis using mypy' ; echo $MSG
mypy
RET=$(($RET + $?)) ; echo $MSG "DONE"

# run pyright, if it is installed
if command -v pyright &> /dev/null ; then
MSG='Performing static analysis using pyright' ; echo $MSG
pyright
RET=$(($RET + $?)) ; echo $MSG "DONE"
fi
fi

### SINGLE-PAGE DOCS ###
if [[ -z "$CHECK" || "$CHECK" == "single-docs" ]]; then
python doc/make.py --warnings-are-errors --single pandas.Series.value_counts
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14 changes: 7 additions & 7 deletions doc/source/development/contributing_codebase.rst
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Expand Up @@ -23,19 +23,19 @@ contributing them to the project::

./ci/code_checks.sh

The script validates the doctests, formatting in docstrings, static typing, and
The script validates the doctests, formatting in docstrings, and
imported modules. It is possible to run the checks independently by using the
parameters ``docstring``, ``code``, ``typing``, and ``doctests``
parameters ``docstring``, ``code``, and ``doctests``
(e.g. ``./ci/code_checks.sh doctests``).

In addition, because a lot of people use our library, it is important that we
do not make sudden changes to the code that could have the potential to break
a lot of user code as a result, that is, we need it to be as *backwards compatible*
as possible to avoid mass breakages.

In addition to ``./ci/code_checks.sh``, some extra checks are run by
``pre-commit`` - see :ref:`here <contributing.pre-commit>` for how to
run them.
In addition to ``./ci/code_checks.sh``, some extra checks (including static type
checking) are run by ``pre-commit`` - see :ref:`here <contributing.pre-commit>`
for how to run them.

.. _contributing.pre-commit:

Expand Down Expand Up @@ -260,9 +260,9 @@ pandas uses `mypy <http://mypy-lang.org>`_ and `pyright <https://github.com/micr

.. code-block:: shell

./ci/code_checks.sh typing
pre-commit run --hook-stage manual --all-files

A recent version of ``numpy`` (>=1.21.0) is required for type validation.
in your activated python environment. A recent version of ``numpy`` (>=1.22.0) is required for type validation.

.. _contributing.ci:

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2 changes: 1 addition & 1 deletion environment.yml
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Expand Up @@ -25,7 +25,7 @@ dependencies:
- flake8-comprehensions=3.7.0 # used by flake8, linting of unnecessary comprehensions
- isort>=5.2.1 # check that imports are in the right order
- mypy=0.950
- pre-commit>=2.9.2
- pre-commit>=2.15.0
- pycodestyle # used by flake8
- pyupgrade

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2 changes: 1 addition & 1 deletion requirements-dev.txt
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Expand Up @@ -13,7 +13,7 @@ flake8-bugbear==21.3.2
flake8-comprehensions==3.7.0
isort>=5.2.1
mypy==0.950
pre-commit>=2.9.2
pre-commit>=2.15.0
pycodestyle
pyupgrade
gitpython
Expand Down