mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-26 06:58:11 +08:00
Compare commits
10
Commits
| Author | SHA1 | Date | |
|---|---|---|---|
 Roy Zheng
|
96cb19c89b | ||
|
Justin Kiggins
|
eb1dc8944f | ||
|
Ronen
|
fd8b47b78e | ||
|
Ronen
|
487bd13ff8 | ||
|
Ronen
|
eb743efd9a | ||
|
Ronen
|
67d152e108 | ||
|
Timmy Huang
|
c425d2e0b0 | ||
|
Timmy Huangandkaloster
|
7bf5add6ef | ||
|
dependabot[bot]andTimmy Huang
|
4281a8f816 | ||
|
Emanuele Bezzi
|
53e9edfec1 |
+1
-1
@@ -1,5 +1,5 @@
|
||||
[bumpversion]
|
||||
current_version = 1.2.0
|
||||
current_version = 1.3.0
|
||||
commit = True
|
||||
parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<prerel>rc)\.(?P<prerelversion>\d+))?
|
||||
serialize =
|
||||
|
||||
@@ -14,9 +14,9 @@ jobs:
|
||||
docker-build:
|
||||
runs-on: ubuntu-latest
|
||||
steps:
|
||||
- uses: actions/checkout@v2
|
||||
- uses: actions/checkout@v4
|
||||
- name: Set up Python ${{ matrix.python-version }}
|
||||
uses: actions/setup-python@v4
|
||||
uses: actions/setup-python@v5
|
||||
with:
|
||||
python-version: ${{ matrix.python-version }}
|
||||
- name: Build docker image
|
||||
@@ -28,24 +28,23 @@ 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-11]
|
||||
python-version: [3.8, 3.9, 3.10, 3.11]
|
||||
os: [ubuntu-latest, macos-latest, macos-13]
|
||||
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: 3.9
|
||||
- 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
|
||||
# TODO: Do not bother running this if anndata latest version
|
||||
# matches this pinned version, to avoid a redundant test
|
||||
anndata_version: "==0.10.3"
|
||||
anndata_version: "==0.10.9"
|
||||
steps:
|
||||
- uses: actions/checkout@v2
|
||||
- uses: actions/checkout@v4
|
||||
- name: Set up Python ${{ matrix.python-version }}
|
||||
uses: actions/setup-python@v4
|
||||
uses: actions/setup-python@v5
|
||||
with:
|
||||
python-version: ${{ matrix.python-version }}
|
||||
- name: Cache env vars
|
||||
@@ -55,14 +54,14 @@ jobs:
|
||||
run: echo "BREW_CACHE=`brew --cache`" >> $GITHUB_ENV
|
||||
# FIXME: Only working for Linux
|
||||
- name: Python cache
|
||||
uses: actions/cache@v1
|
||||
uses: actions/cache@v4
|
||||
with:
|
||||
path: ${{ env.PIP_CACHE }}
|
||||
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
|
||||
restore-keys: |
|
||||
${{ runner.os }}-pip-
|
||||
- name: Node cache
|
||||
uses: actions/cache@v1
|
||||
uses: actions/cache@v4
|
||||
with:
|
||||
path: ~/.npm
|
||||
key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
|
||||
@@ -70,7 +69,7 @@ jobs:
|
||||
${{ runner.os }}-node-
|
||||
- name: Brew cache (MacOS)
|
||||
if: startsWith(matrix.os, 'macos')
|
||||
uses: actions/cache@v1
|
||||
uses: actions/cache@v4
|
||||
with:
|
||||
path: ${{ env.BREW_CACHE }}
|
||||
key: ${{ runner.os }}-brew-
|
||||
@@ -96,6 +95,7 @@ jobs:
|
||||
# keep same pip pkg versions as in the cxg release
|
||||
sed -i'' -e 's/-r requirements.txt//' server/requirements-dev.txt
|
||||
pip install -r server/requirements-dev.txt
|
||||
pip install --force-reinstall numpy==2.0.1 numba>=0.60.0 pandas flatbuffers==2.0.7
|
||||
- name: Install anndata version per matrix variable
|
||||
run: pip install anndata${{ matrix.anndata_version }}
|
||||
- name: Install node
|
||||
|
||||
@@ -14,15 +14,15 @@ jobs:
|
||||
lint:
|
||||
runs-on: ubuntu-latest
|
||||
steps:
|
||||
- uses: actions/checkout@v2
|
||||
- uses: actions/checkout@v4
|
||||
- run: |
|
||||
git fetch --depth=1 origin +${{github.base_ref}}
|
||||
- name: Set up Python 3.9
|
||||
uses: actions/setup-python@v4
|
||||
- name: Set up Python 3.12
|
||||
uses: actions/setup-python@v5
|
||||
with:
|
||||
python-version: 3.9
|
||||
python-version: 3.12
|
||||
- name: Node cache
|
||||
uses: actions/cache@v1
|
||||
uses: actions/cache@v4
|
||||
with:
|
||||
path: ~/.npm
|
||||
key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
|
||||
@@ -45,22 +45,22 @@ jobs:
|
||||
unit-test:
|
||||
runs-on: ubuntu-latest
|
||||
steps:
|
||||
- uses: actions/checkout@v2
|
||||
- name: Set up Python 3.9 (pyenv) # pyenv needed for mlflow in cli annotate tests
|
||||
- uses: actions/checkout@v4
|
||||
- name: Set up Python 3.12 (pyenv) # pyenv needed for mlflow in cli annotate tests
|
||||
uses: gabrielfalcao/pyenv-action@v9
|
||||
with:
|
||||
default: 3.9
|
||||
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
|
||||
uses: actions/cache@v1
|
||||
uses: actions/cache@v4
|
||||
with:
|
||||
path: ~/.cache/pip
|
||||
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
|
||||
restore-keys: |
|
||||
${{ runner.os }}-pip-
|
||||
- name: Node cache
|
||||
uses: actions/cache@v1
|
||||
uses: actions/cache@v4
|
||||
with:
|
||||
path: ~/.npm
|
||||
key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
|
||||
@@ -78,27 +78,29 @@ jobs:
|
||||
runs-on: macos-latest
|
||||
timeout-minutes: 20
|
||||
steps:
|
||||
- uses: actions/checkout@v2
|
||||
- name: Set up Python 3.9
|
||||
uses: actions/setup-python@v4
|
||||
- uses: actions/checkout@v4
|
||||
- name: Set up Python 3.12
|
||||
uses: actions/setup-python@v5
|
||||
with:
|
||||
python-version: 3.9
|
||||
python-version: 3.12
|
||||
- name: Python cache
|
||||
uses: actions/cache@v1
|
||||
uses: actions/cache@v4
|
||||
with:
|
||||
path: ~/.cache/pip
|
||||
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
|
||||
restore-keys: |
|
||||
${{ runner.os }}-pip-
|
||||
- name: Node cache
|
||||
uses: actions/cache@v1
|
||||
uses: actions/cache@v4
|
||||
with:
|
||||
path: ~/.npm
|
||||
key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
|
||||
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
|
||||
|
||||
@@ -0,0 +1,20 @@
|
||||
The MIT License (MIT)
|
||||
|
||||
Copyright (c) 2017-2023 Chan Zuckerberg Initiative
|
||||
|
||||
Permission is hereby granted, free of charge, to any person obtaining a copy of
|
||||
this software and associated documentation files (the "Software"), to deal in
|
||||
the Software without restriction, including without limitation the rights to
|
||||
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
|
||||
the Software, and to permit persons to whom the Software is furnished to do so,
|
||||
subject to the following conditions:
|
||||
|
||||
The above copyright notice and this permission notice shall be included in all
|
||||
copies or substantial portions of the Software.
|
||||
|
||||
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
||||
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
|
||||
FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
|
||||
COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
|
||||
IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
|
||||
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
||||
@@ -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.
|
||||
|
||||
@@ -58,7 +58,7 @@ Please [file an issue](https://github.com/chanzuckerberg/cellxgene/issues/new/ch
|
||||
### Finding help
|
||||
|
||||
We'd love to hear from you!
|
||||
For questions, suggestions, or accolades, [join the `#cellxgene-users` channel on the CZI Science Slack](https://join-cellxgene-users.herokuapp.com/) and say "hi!".
|
||||
For questions, suggestions, or accolades, join the `#cellxgene-users` channel on the [CZI Science Community Slack](https://czi.co/science-slack) and say "hi!".
|
||||
|
||||
For any errors, [report bugs on Github](https://github.com/chanzuckerberg/cellxgene/issues).
|
||||
|
||||
@@ -66,22 +66,28 @@ 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.
|
||||
|
||||
### Trademarks
|
||||
|
||||
CZ CELLXGENE, CZ CELLXGENE DISCOVER, and CZ CELLXGENE ANNOTATE are trademarks of the Chan Zuckerberg Initiative. All rights reserved.
|
||||
|
||||
Use, reuse, modification, and re-distribution of the source code in this repository is subject to the terms of the applicable open source [license](LICENSE.txt). However, that license does not grant permission to use the trademarks without separate, express permission from the Chan Zuckerberg Initiative.
|
||||
|
||||
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
|
||||
|
||||
|
||||
@@ -0,0 +1,2 @@
|
||||
## Reporting Security Issues
|
||||
If you believe you have found a security issue, please responsibly disclose by contacting us at [security@chanzuckerberg.com](mailto:security@chanzuckerberg.com).
|
||||
@@ -0,0 +1 @@
|
||||
18.17.0
|
||||
@@ -13,7 +13,7 @@ import * as ENV_DEFAULT from "../../../environment.default.json";
|
||||
// a test can take more time to finish, so we don't want
|
||||
// jest to shut off the test too soon
|
||||
jest.setTimeout(2 * 60 * 1000);
|
||||
setDefaultOptions({ timeout: 20 * 1000 });
|
||||
setDefaultOptions({ timeout: 60 * 1000 });
|
||||
|
||||
jest.retryTimes(ENV_DEFAULT.RETRY_ATTEMPTS);
|
||||
|
||||
|
||||
@@ -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,
|
||||
|
||||
Generated
+19212
-2297
File diff suppressed because it is too large
Load Diff
+7
-6
@@ -1,6 +1,6 @@
|
||||
{
|
||||
"name": "cellxgene",
|
||||
"version": "1.2.0",
|
||||
"version": "1.3.0",
|
||||
"license": "MIT",
|
||||
"description": "cellxgene is a web application for the interactive exploration of single cell sequence data.",
|
||||
"repository": "https://github.com/chanzuckerberg/cellxgene",
|
||||
@@ -18,7 +18,8 @@
|
||||
},
|
||||
"engineStrict": true,
|
||||
"engines": {
|
||||
"npm": ">=3.0.0"
|
||||
"npm": ">=9.6.7",
|
||||
"node": "^18.17.0"
|
||||
},
|
||||
"eslintConfig": {
|
||||
"extends": "./configuration/eslint/eslint.js"
|
||||
@@ -77,7 +78,7 @@
|
||||
"whatwg-fetch": "^3.2.0"
|
||||
},
|
||||
"devDependencies": {
|
||||
"@babel/core": "^7.13.16",
|
||||
"@babel/core": "^7.25.2",
|
||||
"@babel/plugin-proposal-class-properties": "^7.10.4",
|
||||
"@babel/plugin-proposal-decorators": "^7.13.15",
|
||||
"@babel/plugin-proposal-export-namespace-from": "^7.10.4",
|
||||
@@ -123,7 +124,7 @@
|
||||
"jest-circus": "^27.0.6",
|
||||
"jest-environment-puppeteer": "^5.0.1",
|
||||
"jest-fetch-mock": "^3.0.3",
|
||||
"jest-puppeteer": "^5.0.1",
|
||||
"jest-puppeteer": "^6.2.0",
|
||||
"json-loader": "^0.5.7",
|
||||
"lint-staged": "^10.2.11",
|
||||
"lodash": "^4.17.21",
|
||||
@@ -134,11 +135,11 @@
|
||||
"lodash.zip": "^4.2.0",
|
||||
"mini-css-extract-plugin": "^1.5.0",
|
||||
"prettier": "^2.0.5",
|
||||
"puppeteer": "^8.0.0",
|
||||
"puppeteer": "^10.4.0",
|
||||
"rimraf": "^3.0.2",
|
||||
"serve-favicon": "^2.5.0",
|
||||
"terser-webpack-plugin": "^5.1.1",
|
||||
"webpack": "^5.88.2",
|
||||
"webpack": "^5.94.0",
|
||||
"webpack-cli": "^4.6.0",
|
||||
"webpack-dev-middleware": "^4.1.0",
|
||||
"webpack-merge": "^5.0.9",
|
||||
|
||||
@@ -16,7 +16,7 @@ const InformationMenu = React.memo((props) => {
|
||||
rel="noopener"
|
||||
/>
|
||||
<MenuItem
|
||||
href="https://join-cellxgene-users.herokuapp.com/"
|
||||
href="https://czi.co/science-slack"
|
||||
target="_blank"
|
||||
icon="chat"
|
||||
text="Chat"
|
||||
|
||||
@@ -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
|
||||
|
||||
@@ -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
|
||||
|
||||
+1
-1
@@ -2,7 +2,7 @@ import logging
|
||||
import sys
|
||||
from server.common.utils.utils import import_plugins
|
||||
|
||||
__version__ = "1.2.0"
|
||||
__version__ = "1.3.0"
|
||||
display_version = "cellxgene v" + __version__
|
||||
|
||||
try:
|
||||
|
||||
@@ -176,7 +176,7 @@ class DatasetConfig(BaseConfig):
|
||||
self.validate_correct_type_of_configuration_attribute("diffexp__top_n", int)
|
||||
|
||||
data_adaptor = self.get_data_adaptor()
|
||||
if self.diffexp__enable and data_adaptor.parameters.get("diffexp_may_be_slow", False):
|
||||
if self.diffexp__enable and data_adaptor.parameters.get("diffexp-may-be-slow", False):
|
||||
context["messagefn"](
|
||||
"CAUTION: due to the size of your dataset, " "running differential expression may take longer or fail."
|
||||
)
|
||||
|
||||
@@ -116,7 +116,7 @@ def _get_type_info(array: Union[np.ndarray, pd.Series, pd.Index]) -> Tuple[np.dt
|
||||
raise TypeError("Unsupported data type.")
|
||||
|
||||
dtype = array.dtype
|
||||
|
||||
|
||||
res = _get_type_info_from_dtype(dtype)
|
||||
if res is not None:
|
||||
return res
|
||||
@@ -140,7 +140,6 @@ def _get_type_info(array: Union[np.ndarray, pd.Series, pd.Index]) -> Tuple[np.dt
|
||||
|
||||
if dtype.kind in ["i", "u"] and _can_cast_array_values_to_int32(array):
|
||||
return (np.int32, {"type": "int32"})
|
||||
|
||||
if dtype.kind == "f":
|
||||
_float64_warning(array.dtype)
|
||||
return (np.float32, {"type": "float32"})
|
||||
|
||||
@@ -211,7 +211,7 @@ class AnndataAdaptor(DataAdaptor):
|
||||
# heuristic
|
||||
n_values = self.data.shape[0] * self.data.shape[1]
|
||||
if (n_values > 1e8 and self.server_config.adaptor__anndata_adaptor__backed is True) or (n_values > 5e8):
|
||||
self.parameters.update({"diffexp_may_be_slow": True})
|
||||
self.parameters.update({"diffexp-may-be-slow": True})
|
||||
|
||||
def _is_valid_layout(self, arr):
|
||||
"""return True if this layout data is a valid array for front-end presentation:
|
||||
|
||||
@@ -1,2 +1,2 @@
|
||||
mlflow==1.27.0
|
||||
mlflow==2.16.0
|
||||
scanpy
|
||||
|
||||
@@ -7,16 +7,17 @@ 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
|
||||
h5py>=3.0.0
|
||||
numba>=0.51.2
|
||||
numpy>1.22
|
||||
numba>=0.60.0
|
||||
numpy==2.0.1
|
||||
packaging>=20.0
|
||||
pandas<2.0.0
|
||||
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
|
||||
|
||||
@@ -14,7 +14,7 @@ with open("server/requirements-annotate.txt") as fh:
|
||||
|
||||
setup(
|
||||
name="cellxgene",
|
||||
version="1.2.0",
|
||||
version="1.3.0",
|
||||
packages=find_packages(),
|
||||
url="https://github.com/chanzuckerberg/cellxgene",
|
||||
license="MIT",
|
||||
@@ -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",
|
||||
],
|
||||
|
||||
@@ -65,13 +65,13 @@ class EstDistTest(unittest.TestCase):
|
||||
|
||||
# non-finites
|
||||
self.assertEqual(estimate_approximate_distribution(np.array([np.nan])), XApproximateDistribution.NORMAL)
|
||||
self.assertEqual(estimate_approximate_distribution(np.array([np.PINF])), XApproximateDistribution.NORMAL)
|
||||
self.assertEqual(estimate_approximate_distribution(np.array([np.NINF])), XApproximateDistribution.NORMAL)
|
||||
self.assertEqual(estimate_approximate_distribution(np.array([np.inf])), XApproximateDistribution.NORMAL)
|
||||
self.assertEqual(estimate_approximate_distribution(np.array([np.inf])), XApproximateDistribution.NORMAL)
|
||||
self.assertEqual(
|
||||
estimate_approximate_distribution(np.array([np.PINF, np.NINF, 0])), XApproximateDistribution.NORMAL
|
||||
estimate_approximate_distribution(np.array([np.inf, np.inf, 0])), XApproximateDistribution.NORMAL
|
||||
)
|
||||
self.assertEqual(
|
||||
estimate_approximate_distribution(np.array([np.nan, np.PINF, np.NINF])), XApproximateDistribution.NORMAL
|
||||
estimate_approximate_distribution(np.array([np.nan, np.inf, np.inf])), XApproximateDistribution.NORMAL
|
||||
)
|
||||
|
||||
raw = np.random.exponential(scale=1000, size=(50, 3))
|
||||
@@ -82,15 +82,15 @@ class EstDistTest(unittest.TestCase):
|
||||
XApproximateDistribution.COUNT,
|
||||
)
|
||||
self.assertEqual(
|
||||
estimate_approximate_distribution(put(raw, [1], [np.PINF])),
|
||||
estimate_approximate_distribution(put(raw, [1], [np.inf])),
|
||||
XApproximateDistribution.COUNT,
|
||||
)
|
||||
self.assertEqual(
|
||||
estimate_approximate_distribution(put(raw, [1], [np.NINF])),
|
||||
estimate_approximate_distribution(put(raw, [1], [np.inf])),
|
||||
XApproximateDistribution.COUNT,
|
||||
)
|
||||
self.assertEqual(
|
||||
estimate_approximate_distribution(put(raw, [1, 3, 88], [np.nan, np.PINF, np.NINF])),
|
||||
estimate_approximate_distribution(put(raw, [1, 3, 88], [np.nan, np.inf, np.inf])),
|
||||
XApproximateDistribution.COUNT,
|
||||
)
|
||||
self.assertEqual(
|
||||
@@ -103,15 +103,15 @@ class EstDistTest(unittest.TestCase):
|
||||
XApproximateDistribution.NORMAL,
|
||||
)
|
||||
self.assertEqual(
|
||||
estimate_approximate_distribution(put(logged, [1], [np.PINF])),
|
||||
estimate_approximate_distribution(put(logged, [1], [np.inf])),
|
||||
XApproximateDistribution.NORMAL,
|
||||
)
|
||||
self.assertEqual(
|
||||
estimate_approximate_distribution(put(logged, [1], [np.NINF])),
|
||||
estimate_approximate_distribution(put(logged, [1], [np.inf])),
|
||||
XApproximateDistribution.NORMAL,
|
||||
)
|
||||
self.assertEqual(
|
||||
estimate_approximate_distribution(put(logged, [1, 3, 88], [np.nan, np.PINF, np.NINF])),
|
||||
estimate_approximate_distribution(put(logged, [1, 3, 88], [np.nan, np.inf, np.inf])),
|
||||
XApproximateDistribution.NORMAL,
|
||||
)
|
||||
self.assertEqual(
|
||||
|
||||
@@ -16,10 +16,10 @@ class TestJsonifyStrict(unittest.TestCase):
|
||||
jsonify_strict({"nan": [np.nan]})
|
||||
|
||||
with self.assertRaises(ValueError):
|
||||
jsonify_strict({"pinf": [np.PINF]})
|
||||
jsonify_strict({"pinf": [np.inf]})
|
||||
|
||||
with self.assertRaises(ValueError):
|
||||
jsonify_strict({"ninf": [np.NINF]})
|
||||
jsonify_strict({"ninf": [np.inf]})
|
||||
|
||||
def test_jsonify_numpy_ndarray(self):
|
||||
values = {
|
||||
|
||||
@@ -42,7 +42,7 @@ class TestTypeConversionUtils(unittest.TestCase):
|
||||
with self.assertRaises(TypeError):
|
||||
get_schema_type_hint_from_dtype(np.dtype(dtype))
|
||||
|
||||
for dtype in [np.float16, np.float32, np.float64]:
|
||||
for dtype in [np.float32, np.float64]:
|
||||
self.assertEqual(get_schema_type_hint_from_dtype(np.dtype(dtype)), {"type": "float32"})
|
||||
|
||||
for dtype in [np.dtype(object), np.dtype(str)]:
|
||||
@@ -123,17 +123,18 @@ int_OK_cases = [
|
||||
|
||||
float_OK_cases = [
|
||||
{
|
||||
"test_case": "float_OK_cases",
|
||||
"data": data,
|
||||
"expected_encoding_dtype": np.float32,
|
||||
"expected_schema_hint": {"type": "float32"},
|
||||
"logs": None if data.dtype != np.float64 else {"level": logging.WARNING, "output": "may lose precision"},
|
||||
"logs": None if dtype == np.float32 else {"level": logging.WARNING, "output": "may lose precision"},
|
||||
}
|
||||
for dtype in [np.float16, np.float32, np.float64]
|
||||
for dtype in [np.float32, np.float64]
|
||||
for data in [
|
||||
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.NINF, -1, np.NZERO, 0, np.PZERO, 1, np.PINF, 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),
|
||||
]
|
||||
@@ -198,12 +199,13 @@ category_numeric_OK_cases = [
|
||||
# numeric, no NA/NaN, float
|
||||
*[
|
||||
{
|
||||
"test_case": "numeric, no NA/NaN, float",
|
||||
"data": data,
|
||||
"expected_encoding_dtype": np.float32,
|
||||
"expected_schema_hint": {"type": "categorical"},
|
||||
"logs": {"level": logging.WARNING, "output": "may lose precision"},
|
||||
"logs": None if dtype == np.float32 else {"level": logging.WARNING, "output": "may lose precision"},
|
||||
}
|
||||
for dtype in [np.float16, np.float32, np.float64]
|
||||
for dtype in [np.float32, np.float64]
|
||||
for data in [
|
||||
pd.Series(np.array([0, 1, 2], dtype=dtype), dtype="category"),
|
||||
pd.Series(np.array([0, 1, 2], dtype=dtype), dtype="category").cat.remove_categories([1]),
|
||||
@@ -213,10 +215,11 @@ category_numeric_OK_cases = [
|
||||
# numeric, has NA-induced cast to float32
|
||||
*[
|
||||
{
|
||||
"test_case": "numeric, has NA-induced cast to float32",
|
||||
"data": data,
|
||||
"expected_encoding_dtype": np.float32,
|
||||
"expected_schema_hint": {"type": "categorical"},
|
||||
"logs": {"level": logging.WARNING, "output": "may lose precision"},
|
||||
"logs": None if dtype == np.float32 else {"level": logging.WARNING, "output": "may lose precision"},
|
||||
}
|
||||
for dtype in [
|
||||
np.int8,
|
||||
@@ -227,7 +230,6 @@ category_numeric_OK_cases = [
|
||||
np.uint32,
|
||||
np.int64,
|
||||
np.uint64,
|
||||
np.float16,
|
||||
np.float32,
|
||||
np.float64,
|
||||
]
|
||||
@@ -312,7 +314,6 @@ class TestTypeInference(unittest.TestCase, AssertNoLog):
|
||||
self.assertEqual(encoding_dtype, self.expected_encoding_dtype)
|
||||
self.assertEqual(schema_hint, self.expected_schema_hint)
|
||||
self.assertIn(logs["output"], logger.output[0])
|
||||
|
||||
else:
|
||||
with self.assertNoLogs(logging.getLogger(), logging.WARNING):
|
||||
encoding_dtype, schema_hint = get_dtype_and_schema_of_array(self.data)
|
||||
|
||||
Reference in New Issue
Block a user