Installation from source creates changes in the local directory

[awaelchli]

Bug

When installing lightning from source, there remain unstaged changes that show up in git.

Reproduce

1. Clone repo
2. PACKAGE_NAME=lightning_app pip install -e .
3. git status shows file changes for MANIFEST.in, requirements/base.txt, setup.py

Expected behavior

No changed files.

Environment details:

* CUDA:nts/  …uirements.txt
        - GPU:               None
        - available:         False
        - version:           None
* Lightning:
        - lightning:         1.8.0
        - lightning-app:     1.8.0
        - lightning-cloud:   0.5.11
        - lightning-lite:    1.8.0
        - lightning-utilities: 0.3.0
        - pt-lightning-sphinx-theme: 0.0.31
        - torch:             1.12.1
        - torchmetrics:      0.9.2
        - torchvision:       0.13.0
* Packages:
        - absl-py:           1.2.0
        - aiobotocore:       2.3.4
        - aiohttp:           3.8.3
        - aioitertools:      0.11.0
        - aiosignal:         1.2.0
        - alabaster:         0.7.12
        - alembic:           1.8.1
        - altair:            4.2.0
        - antlr4-python3-runtime: 4.9.3
        - anyio:             3.6.1
        - appnope:           0.1.3
        - argon2-cffi:       21.3.0
        - argon2-cffi-bindings: 21.2.0
        - arrow:             1.2.3
        - asgiref:           3.5.2
        - asttokens:         2.0.8
        - async-generator:   1.10
        - async-timeout:     4.0.2
        - attrs:             22.1.0
        - babel:             2.10.3
        - backcall:          0.2.0
        - bcrypt:            4.0.1
        - beautifulsoup4:    4.11.1
        - black:             22.8.0
        - bleach:            5.0.1
        - blessed:           1.19.1
        - blinker:           1.5
        - bokeh:             2.4.3
        - boto3:             1.24.82
        - botocore:          1.24.21
        - bracex:            2.3.post1
        - bravado:           11.0.3
        - bravado-core:      5.17.1
        - cachetools:        5.2.0
        - certifi:           2022.9.14
        - cffi:              1.15.1
        - cfgv:              3.3.1
        - charset-normalizer: 2.1.1
        - click:             8.1.3
        - cloudpickle:       2.1.0
        - codecov:           2.1.12
        - colorama:          0.4.5
        - coloredlogs:       15.0.1
        - comet-ml:          3.31.7
        - commonmark:        0.9.1
        - configobj:         5.0.6
        - coverage:          6.4.2
        - croniter:          1.3.7
        - cryptography:      38.0.1
        - curio:             1.5
        - cycler:            0.11.0
        - databricks-cli:    0.17.3
        - debugpy:           1.6.3
        - decorator:         5.1.1
        - deepdiff:          5.8.1
        - deepspeed:         0.7.3
        - defusedxml:        0.7.1
        - distlib:           0.3.6
        - dnspython:         2.2.1
        - docker:            5.0.3
        - docker-pycreds:    0.4.0
        - docstring-parser:  0.15
        - docutils:          0.17.1
        - dulwich:           0.20.46
        - email-validator:   1.3.0
        - entrypoints:       0.4
        - everett:           3.0.0
        - exceptiongroup:    1.0.0rc9
        - executing:         1.1.0
        - fairscale:         0.4.10
        - fastapi:           0.82.0
        - fastjsonschema:    2.16.2
        - ffmpy:             0.3.0
        - filelock:          3.8.0
        - fire:              0.4.0
        - flake8:            5.0.4
        - flask:             2.2.2
        - flatbuffers:       22.9.24
        - fonttools:         4.37.3
        - frozenlist:        1.3.1
        - fsspec:            2022.7.1
        - future:            0.18.2
        - gcsfs:             2022.7.1
        - gitdb:             4.0.9
        - gitpython:         3.1.27
        - google-api-core:   2.8.2
        - google-auth:       2.12.0
        - google-auth-oauthlib: 0.4.6
        - google-cloud-core: 2.3.2
        - google-cloud-storage: 2.5.0
        - google-crc32c:     1.5.0
        - google-resumable-media: 2.3.3
        - googleapis-common-protos: 1.56.4
        - gradio:            3.6
        - greenlet:          1.1.2
        - grpcio:            1.49.1
        - gunicorn:          20.1.0
        - gym:               0.24.1
        - gym-notices:       0.0.8
        - h11:               0.12.0
        - hjson:             3.1.0
        - httpcore:          0.15.0
        - httptools:         0.5.0
        - httpx:             0.23.0
        - humanfriendly:     10.0
        - hydra-core:        1.2.0
        - identify:          2.5.5
        - idna:              3.4
        - imagesize:         1.4.1
        - importlib-metadata: 4.12.0
        - iniconfig:         1.1.1
        - inquirer:          2.10.0
        - ipykernel:         6.16.0
        - ipyparallel:       8.4.1
        - ipython:           8.5.0
        - ipython-genutils:  0.2.0
        - ipywidgets:        8.0.2
        - isort:             5.10.1
        - itsdangerous:      2.1.2
        - jedi:              0.18.1
        - jinja2:            3.0.3
        - jmespath:          1.0.1
        - joblib:            1.2.0
        - jsonargparse:      4.15.2
        - jsonpointer:       2.3
        - jsonref:           0.2
        - jsonschema:        3.2.0
        - jupyter-client:    7.3.5
        - jupyter-core:      4.11.1
        - jupyterlab-pygments: 0.2.2
        - jupyterlab-widgets: 3.0.3
        - kiwisolver:        1.4.4
        - lightning:         1.8.0
        - lightning-app:     1.8.0
        - lightning-cloud:   0.5.11
        - lightning-lite:    1.8.0
        - lightning-utilities: 0.3.0
        - linkify-it-py:     1.0.3
        - livereload:        2.6.3
        - lxml:              4.9.1
        - mako:              1.2.3
        - markdown:          3.4.1
        - markdown-it-py:    2.1.0
        - markupsafe:        2.1.1
        - matplotlib:        3.5.2
        - matplotlib-inline: 0.1.6
        - mccabe:            0.7.0
        - mdit-py-plugins:   0.3.1
        - mdurl:             0.1.2
        - mistune:           2.0.4
        - mlflow:            1.28.0
        - monotonic:         1.6
        - mpmath:            1.2.1
        - msgpack:           1.0.4
        - multidict:         6.0.2
        - mypy:              0.971
        - mypy-extensions:   0.4.3
        - myst-parser:       0.16.1
        - nbclient:          0.6.8
        - nbconvert:         7.0.0
        - nbformat:          5.6.1
        - nbsphinx:          0.8.9
        - neptune-client:    0.16.7
        - nest-asyncio:      1.5.5
        - ninja:             1.10.2.4
        - nodeenv:           1.7.0
        - notebook:          6.4.12
        - numpy:             1.23.0
        - nvidia-ml-py3:     7.352.0
        - oauthlib:          3.2.1
        - omegaconf:         2.2.3
        - onnxruntime:       1.12.1
        - ordered-set:       4.1.0
        - orjson:            3.8.0
        - outcome:           1.2.0
        - packaging:         21.3
        - pandas:            1.5.0
        - pandoc:            2.2
        - pandocfilters:     1.5.0
        - panel:             0.14.0
        - param:             1.12.2
        - paramiko:          2.11.0
        - parso:             0.8.3
        - pathspec:          0.10.1
        - pathtools:         0.1.2
        - pexpect:           4.8.0
        - pickleshare:       0.7.5
        - pillow:            9.2.0
        - pip:               22.1.2
        - pipdeptree:        2.3.1
        - platformdirs:      2.5.2
        - playwright:        1.22.0
        - pluggy:            1.0.0
        - plumbum:           1.8.0
        - ply:               3.11
        - pre-commit:        2.20.0
        - prometheus-client: 0.14.1
        - prometheus-flask-exporter: 0.20.3
        - promise:           2.3
        - prompt-toolkit:    3.0.31
        - protobuf:          3.19.5
        - psutil:            5.9.2
        - pt-lightning-sphinx-theme: 0.0.31
        - ptyprocess:        0.7.0
        - pure-eval:         0.2.2
        - py:                1.11.0
        - py-cpuinfo:        8.0.0
        - pyarrow:           9.0.0
        - pyasn1:            0.4.8
        - pyasn1-modules:    0.2.8
        - pycodestyle:       2.9.1
        - pycparser:         2.21
        - pycryptodome:      3.15.0
        - pyct:              0.4.8
        - pydantic:          1.10.2
        - pydeck:            0.8.0b3
        - pydeprecate:       0.3.2
        - pydub:             0.25.1
        - pyee:              8.1.0
        - pyflakes:          2.5.0
        - pygame:            2.1.0
        - pygments:          2.13.0
        - pyjwt:             2.5.0
        - pympler:           1.0.1
        - pynacl:            1.5.0
        - pyparsing:         3.0.9
        - pyrsistent:        0.18.1
        - pytest:            7.1.2
        - pytest-asyncio:    0.19.0
        - pytest-cov:        3.0.0
        - pytest-forked:     1.4.0
        - pytest-rerunfailures: 10.2
        - pytest-timeout:    2.1.0
        - python-dateutil:   2.8.2
        - python-dotenv:     0.21.0
        - python-editor:     1.0.4
        - python-multipart:  0.0.5
        - pytz:              2022.2.1
        - pytz-deprecation-shim: 0.1.0.post0
        - pyviz-comms:       2.2.1
        - pyyaml:            6.0
        - pyzmq:             24.0.1
        - qtconsole:         5.3.2
        - qtpy:              2.2.0
        - querystring-parser: 1.2.4
        - readchar:          4.0.3
        - requests:          2.28.1
        - requests-oauthlib: 1.3.1
        - requests-toolbelt: 0.9.1
        - rfc3986:           1.5.0
        - rfc3987:           1.3.8
        - rich:              12.6.0
        - rsa:               4.9
        - s3fs:              2022.7.1
        - s3transfer:        0.6.0
        - scikit-learn:      1.1.2
        - scipy:             1.9.1
        - semantic-version:  2.10.0
        - semver:            2.13.0
        - send2trash:        1.8.0
        - sentry-sdk:        1.9.9
        - setproctitle:      1.3.2
        - setuptools:        59.5.0
        - shortuuid:         1.0.9
        - simplejson:        3.17.6
        - six:               1.16.0
        - smmap:             5.0.0
        - sniffio:           1.3.0
        - snowballstemmer:   2.2.0
        - sortedcontainers:  2.4.0
        - soupsieve:         2.3.2.post1
        - sphinx:            4.5.0
        - sphinx-autobuild:  2021.3.14
        - sphinx-autodoc-typehints: 1.14.1
        - sphinx-copybutton: 0.5.0
        - sphinx-multiproject: 1.0.0rc1
        - sphinx-paramlinks: 0.5.4
        - sphinx-togglebutton: 0.3.2
        - sphinxcontrib-applehelp: 1.0.2
        - sphinxcontrib-devhelp: 1.0.2
        - sphinxcontrib-fulltoc: 1.2.0
        - sphinxcontrib-htmlhelp: 2.0.0
        - sphinxcontrib-jsmath: 1.0.1
        - sphinxcontrib-mockautodoc: 0.0.1.dev20130518
        - sphinxcontrib-qthelp: 1.0.3
        - sphinxcontrib-serializinghtml: 1.1.5
        - sqlalchemy:        1.4.41
        - sqlparse:          0.4.3
        - stack-data:        0.5.1
        - starlette:         0.19.1
        - starsessions:      1.3.0
        - streamlit:         1.13.0
        - strict-rfc3339:    0.7
        - swagger-spec-validator: 2.7.6
        - sympy:             1.11.1
        - tabulate:          0.8.10
        - tensorboard:       2.10.1
        - tensorboard-data-server: 0.6.1
        - tensorboard-plugin-wit: 1.8.1
        - termcolor:         2.0.1
        - terminado:         0.15.0
        - testpath:          0.6.0
        - threadpoolctl:     3.1.0
        - tinycss2:          1.1.1
        - toml:              0.10.2
        - tomli:             2.0.1
        - toolz:             0.12.0
        - torch:             1.12.1
        - torchmetrics:      0.9.2
        - torchvision:       0.13.0
        - tornado:           6.2
        - tqdm:              4.64.1
        - traitlets:         5.4.0
        - trio:              0.21.0
        - types-protobuf:    3.20.4
        - types-pyyaml:      6.0.12
        - types-requests:    2.28.11
        - types-setuptools:  65.3.0
        - types-six:         1.16.21
        - types-ujson:       5.5.0
        - types-urllib3:     1.26.25
        - typing-extensions: 4.3.0
        - tzdata:            2022.4
        - tzlocal:           4.2
        - uc-micro-py:       1.0.1
        - ujson:             5.5.0
        - urllib3:           1.26.12
        - uvicorn:           0.17.6
        - uvloop:            0.17.0
        - validators:        0.20.0
        - virtualenv:        20.16.5
        - wandb:             0.13.3
        - watchfiles:        0.17.0
        - watchgod:          0.8.2
        - wcmatch:           8.4.1
        - wcwidth:           0.2.5
        - webcolors:         1.12
        - webencodings:      0.5.1
        - websocket-client:  1.4.1
        - websockets:        10.1
        - werkzeug:          2.2.2
        - wheel:             0.37.1
        - widgetsnbextension: 4.0.3
        - wrapt:             1.14.1
        - wurlitzer:         3.0.2
        - yarl:              1.8.1
        - zipp:              3.8.1
* System:
        - OS:                Darwin
        - architecture:
                - 64bit
                - 
        - processor:         arm
        - python:            3.9.13
        - version:           Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:37 PDT 2022; root:xnu-8020.121.3~4/RELEASE_ARM64_T6000

cc @carmocca @akihironitta @Borda

[awaelchli]

@Borda for visibility. I'm not sure whether it is expected.

[carmocca]

This is basically done. We still write changes to requirements/base.txt but it has been added to .gitignore in #15558 so it's not a high priority. We can keep this open if we want to avoid that too

[carmocca]

For reference, this is the problematic piece of code: https://github.com/Lightning-AI/lightning/blob/c53dc205ed0c1911295a2f741781920b840808d7/.actions/setup_tools.py#L176-L189. We would want to find a solution like the one in #15549