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chore: add support for python 3.12 (#2694)

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This commit is contained in:
Ronen
2024-09-12 14:16:46 -04:00
committed by GitHub
parent eb743efd9a
commit 487bd13ff8
11 changed files with 66 additions and 59 deletions
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11
.github/workflows/compatibility_tests.yml vendored
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@@ -7,10 +7,6 @@ on:
branches:
- main
# For debug - uncomment below to run on all PRs
# pull_request:
# branches: "*"
env:
JEST_ENV: prod
@@ -32,14 +28,13 @@ jobs:
strategy:
fail-fast: false
matrix:
# note: The `macos-latest` is latest Catalina version, and not Big Sur. So we explicitly ask for Big Sur (`macos-11`)
os: [ubuntu-latest, macos-latest, macos-13]
python-version: ["3.10", "3.11"]
python-version: ["3.10", "3.11", "3.12"]
cellxgene_build: [main, latest]
# add anndata pinned version test for subset of matrix configurations,
# in order to reduce matrix cross-product explosion
include:
- python-version: 3.11
- python-version: 3.12
cellxgene_build: latest
# TODO: dynamically use the literal version in requirements.txt,
# to avoid having to update this in manually in the future
@@ -100,7 +95,7 @@ jobs:
# keep same pip pkg versions as in the cxg release
sed -i'' -e 's/-r requirements.txt//' server/requirements-dev.txt
pip install -r server/requirements-dev.txt
pip install --force-reinstall numpy==2.0.1 numba>=0.60.0 pandas
pip install --force-reinstall numpy==2.0.1 numba>=0.60.0 pandas flatbuffers==2.0.7
- name: Install anndata version per matrix variable
run: pip install anndata${{ matrix.anndata_version }}
- name: Install node

16
.github/workflows/push_tests.yml vendored
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@@ -17,10 +17,10 @@ jobs:
- uses: actions/checkout@v4
- run: |
git fetch --depth=1 origin +${{github.base_ref}}
- name: Set up Python 3.11
- name: Set up Python 3.12
uses: actions/setup-python@v5
with:
python-version: 3.11
python-version: 3.12
- name: Node cache
uses: actions/cache@v4
with:
@@ -46,10 +46,10 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python 3.11 (pyenv) # pyenv needed for mlflow in cli annotate tests
- name: Set up Python 3.12 (pyenv) # pyenv needed for mlflow in cli annotate tests
uses: gabrielfalcao/pyenv-action@v9
with:
default: 3.11
default: 3.12
command: pip install -U pip # upgrade pip after installing python
- run: pip install virtualenv # virtualenv needed for mlflow in cli annotate tests
- name: Python cache
@@ -79,10 +79,10 @@ jobs:
timeout-minutes: 20
steps:
- uses: actions/checkout@v4
- name: Set up Python 3.11
- name: Set up Python 3.12
uses: actions/setup-python@v5
with:
python-version: 3.11
python-version: 3.12
- name: Python cache
uses: actions/cache@v4
with:
@@ -98,7 +98,9 @@ jobs:
restore-keys: |
${{ runner.os }}-node-
- name: Install dependencies
run: make pydist install-dist
run: |
pip install setuptools
make pydist install-dist
- name: Smoke tests (without annotations feature)
run: |
cd client && make smoke-test

17
README.md
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@@ -27,7 +27,7 @@ Whether you need to visualize one thousand cells or one million, CELLxGENE Annot
### Quick start
To install CELLxGENE Annotate you need Python 3.6+. We recommend [installing Annotate into a conda or virtual environment.](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/install.md)
To install CELLxGENE Annotate you need Python 3.10+. We recommend [installing Annotate into a conda or virtual environment.](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/install.md)
Install the package.
@@ -66,22 +66,21 @@ For any errors, [report bugs on Github](https://github.com/chanzuckerberg/cellxg
### Contributing
We warmly welcome contributions from the community! Please see our [contributing guide](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/contribute.md) and don't hesitate to open an issue or send a pull request to improve CELLxGENE Annotate. Please see the [dev_docs](https://github.com/chanzuckerberg/cellxgene/tree/main/dev_docs) for pull request suggestions, unit test details, local documentation preview, and other development specifics.
We warmly welcome contributions from the community! Please see our [contributing guide](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/contribute.md) and don't hesitate to open an issue or send a pull request to improve CELLxGENE Annotate. Please see the [dev_docs](https://github.com/chanzuckerberg/cellxgene/tree/main/dev_docs) for pull request suggestions, unit test details, local documentation preview, and other development specifics.
This project adheres to the Contributor Covenant [code of conduct](https://github.com/chanzuckerberg/.github/blob/master/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to opensource@chanzuckerberg.com.
### Reuse
This project was started with the sole goal of empowering the scientific community to explore and understand their data.
As such, we encourage other scientific tool builders in academia or industry to adopt the patterns, tools, and code from
This project was started with the sole goal of empowering the scientific community to explore and understand their data.
As such, we encourage other scientific tool builders in academia or industry to adopt the patterns, tools, and code from
this project. All code is freely available for reuse under the [MIT license](https://opensource.org/licenses/MIT).
Before extending CELLxGENE Annotate, we encourage you to reach out to us with ideas or questions. It might be possible that an
extension could be directly contributed, which would make it available for a wider audience, or that it's on our
[roadmap](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/roadmap.md) and under active development.
Before extending CELLxGENE Annotate, we encourage you to reach out to us with ideas or questions. It might be possible that an
extension could be directly contributed, which would make it available for a wider audience, or that it's on our
[roadmap](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/roadmap.md) and under active development.
See the [CELLxGENE extensions](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/community-extensions.md) section of our documentation for examples of community use and CELLxGENE extensions.
See the [CELLxGENE extensions](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/community-extensions.md) section of our documentation for examples of community use and CELLxGENE extensions.
### Security

2
client/.nvmrc
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@@ -1 +1 @@
16.20.0
18.17.0

1
client/jest-puppeteer.config.js
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@@ -14,6 +14,7 @@ const DEFAULT_LAUNCH_CONFIG = {
headless: !isHeadful,
args: ["--ignore-certificate-errors", "--ignore-ssl-errors"],
ignoreHTTPSErrors: true,
timeout: 90000,
defaultViewport: {
width: 1280,
height: 960,

4
client/package.json
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@@ -18,8 +18,8 @@
},
"engineStrict": true,
"engines": {
"npm": ">=3.0.0",
"node": "^16.0.0"
"npm": ">=9.6.7",
"node": "^18.17.0"
},
"eslintConfig": {
"extends": "./configuration/eslint/eslint.js"

6
dev_docs/developer_guidelines.md
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@@ -3,7 +3,7 @@
## Requirements
- npm
- Python 3.6+
- Python 3.10+
- Chrome
[See dev section of README](../README.md)
@@ -148,6 +148,6 @@ If you would like to run the smoke tests against a hot-reloaded version of the c
### Tips
- You can also install/launch the server side code from npm scrips (requires python3.6 with virtualenv) with the `scripts/backend_dev` script.
- You can also install/launch the server side code from npm scrips (requires python3.10 with virtualenv) with the `scripts/backend_dev` script.
- Check out [e2e Tests](e2e_tests.md) for more details
- Check out [e2e Tests](e2e_tests.md) for more details

54
dev_docs/developer_scripts.md
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@@ -11,9 +11,10 @@ $PROJECT_ROOT`.
### Build
**Usage:** from the `$PROJECT_ROOT` directory run:
* `make build` builds whole app client and server
* `make build-client` runs webpack build
* `make build-for-server-dev` builds client and copies output directly into
- `make build` builds whole app client and server
- `make build-client` runs webpack build
- `make build-for-server-dev` builds client and copies output directly into
source tree (only for server devlopment)
### Clean
@@ -21,17 +22,19 @@ $PROJECT_ROOT`.
Deletes generated files.
**Usage:** from the `$PROJECT_ROOT` directory run:
* `make clean` cleans everything including node modules (means build with take
- `make clean` cleans everything including node modules (means build with take
a while
* `make clean-lite` cleans built directories
* `make clean-server` cleans source tree
- `make clean-lite` cleans built directories
- `make clean-server` cleans source tree
### Distribution
Creates distribution for python module to upload to pypi.
**Usage:** from the `$PROJECT_ROOT` directory run:
* `make pydist` builds code and then builds sdist
- `make pydist` builds code and then builds sdist
### Release
@@ -42,16 +45,18 @@ See `release_process.md`.
Installs requirements files.
**Usage:** from the `$PROJECT_ROOT` directory run:
* `make dev-env` installs requirements and requirments-dev (for building code)
- `make dev-env` installs requirements and requirments-dev (for building code)
### Installing cellxgene packages
**Usage:** from the `$PROJECT_ROOT` directory:
* `install-dev` - installs from local source tree
* `install-release-test` - installs from test pypi
* `install-release` - installs from pypi
* `install-dist` - installs from local dist folder
* `uninstall` - uninstalls cellxgene
- `install-dev` - installs from local source tree
- `install-release-test` - installs from test pypi
- `install-release` - installs from pypi
- `install-dist` - installs from local dist folder
- `uninstall` - uninstalls cellxgene
## Client-level scripts
@@ -62,8 +67,9 @@ Installs requirements files.
**About** Serve the current client javascript independently from the `server` code.
**Requires**
* The server to be running. Best way to do this is with [backend_dev](#backend_dev).
* `make ci` to install the necessary node modules
- The server to be running. Best way to do this is with [backend_dev](#backend_dev).
- `make ci` to install the necessary node modules
**Usage:** from the `$PROJECT_ROOT/client` directory run `make start-frontend`
@@ -75,23 +81,24 @@ the FE developer gets the current version of the backend with a single command
and no knowledge of python necessary. It creates and activates a virtual
environment and installs cellxgene from the current branch.
**Requires** `Python3.6+`, `virtual-env`, `pip`
**Requires** `Python3.10+`, `virtual-env`, `pip`
**Usage:** from the `$PROJECT_ROOT` directory run `./scripts/backend_dev`
**Options:**
* In parallel, you can then launch the node development server to serve the
- In parallel, you can then launch the node development server to serve the
current state of the FE with [`start-frontend`](#start-frontend), usually in
a different terminal tab.
* You can also select a specific dataset using `DATASET=<dataset path> ./scripts/backend_dev`.
* You can also use `CXG_OPTIONS` to pass options to the `cellxgene launch`
- You can also select a specific dataset using `DATASET=<dataset path> ./scripts/backend_dev`.
- You can also use `CXG_OPTIONS` to pass options to the `cellxgene launch`
command, as in `CXG_OPTIONS='--disable-annotations' ./scripts/backend_dev`.
**Breakdown**
| command | purpose |
| ---------------------------------------- | ---------------------------------------------------------- |
| python3.6 -m venv cellxgene | creates cellxgene virtual environment |
| python3.12 -m venv cellxgene | creates cellxgene virtual environment |
| source cellxgene/bin/activate | activates virtual environment |
| yes \| pip uninstall cellxgene \|\| true | uninstalls cellxgene (if installed) |
| pip install -e . | installs current local version of cellxgene |
@@ -102,14 +109,15 @@ environment and installs cellxgene from the current branch.
Methods used to test the client javascript code
**Usage:** from the `$PROJECT_ROOT/client` directory run:
* `make unit-test` Runs all unit tests. It excludes any tests in the e2e
- `make unit-test` Runs all unit tests. It excludes any tests in the e2e
folder. This is used by travis to run unit tests.
* `make smoke-test` Starts backend development server and runs end to end
- `make smoke-test` Starts backend development server and runs end to end
tests. This is what travis runs. It depends on the `e2e` and the
`backend-dev` targets. One starts the server, the other runs the tests. If
developing a front-end feature and just checking if tests pass, this is
probabaly the one you want to run.
* `npm run e2e` Runs backend tests without starting the server. You will need to
- `npm run e2e` Runs backend tests without starting the server. You will need to
start the rest api separately with the pbmc3k.h5ad file. Note you can use
the `JEST_ENV` environment variable to change how JEST runs in the browser.
The test runs against `localhost:3000` by default. You can use the

5
server/requirements.txt
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@@ -7,7 +7,7 @@ Flask-Cors>=3.0.9
Flask-RESTful>=0.3.6
flask-server-timing>=0.1.2
flask-talisman>=0.7.0
flatbuffers>=1.11.0,<2.0.0 # cellxgene is not compatible with 2.0.0. Requires migration
flatbuffers==2.0.7
flatten-dict>=0.2.0
fsspec>0.8.0
gunicorn>=20.0.4
@@ -19,4 +19,5 @@ pandas>=2.2.2
PyYAML>=5.4 # CVE-2020-14343
requests>=2.22.0
s3fs==0.4.2
scipy>=1.4
scipy>=1.4
setuptools

7
setup.py
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@@ -24,7 +24,7 @@ setup(
long_description=long_description,
long_description_content_type="text/markdown",
install_requires=requirements,
python_requires=">=3.6",
python_requires=">=3.10",
include_package_data=True,
zip_safe=False,
classifiers=[
@@ -37,8 +37,9 @@ setup(
"Operating System :: MacOS :: MacOS X",
"Programming Language :: JavaScript",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3 :: Only",
"Topic :: Scientific/Engineering :: Bio-Informatics",
],

2
test/unit/utils/test_type_conversion_utils.py
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@@ -134,7 +134,7 @@ float_OK_cases = [
np.arange(-128, 1000, dtype=dtype),
pd.Series(np.arange(-128, 1000, dtype=dtype)),
pd.Index(np.arange(-129, 1000, dtype=dtype)),
np.array([-np.nan, np.inf, -1, 0.0, 0, 0.0, 1, np.inf, np.nan], dtype=dtype),
np.array([-np.nan, -np.inf, -1, -0.0, 0, 0.0, 1, np.inf, np.nan], dtype=dtype),
np.array([np.finfo(dtype).min, 0, np.finfo(dtype).max], dtype=dtype),
sparse.csr_matrix((10, 100), dtype=dtype),
]