mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-26 06:58:11 +08:00
Compare commits
| Author | SHA1 | Date | |
|---|---|---|---|
 dependabot[bot]
|
e7220bb80d | ||
|
LiudengZhang
|
76a39fcf92 | ||
|
rwbaber
|
5eb3021752 | ||
|
Timmy HuangandClaude Opus 4.5
|
7c7203bdfe | ||
|
rwbaber
|
5ac256fc8b | ||
|
|
2b86f8e600 | ||
|
Timmy Huang
|
0fddcd042a | ||
|
Justin Kiggins
|
eb1dc8944f | ||
|
Ronen
|
fd8b47b78e | ||
|
Ronen
|
487bd13ff8 |
+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 =
|
||||
|
||||
@@ -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${{ matrix.anndata_version }}
|
||||
- name: Install node
|
||||
|
||||
@@ -17,10 +17,10 @@ jobs:
|
||||
- uses: actions/checkout@v4
|
||||
- run: |
|
||||
git fetch --depth=1 origin +${{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
|
||||
@@ -69,20 +69,31 @@ jobs:
|
||||
- name: Install dependencies
|
||||
run: make pydist install-dist dev-env-server
|
||||
- name: Unit tests
|
||||
run: |
|
||||
make unit-test-server unit-test-client
|
||||
bash <(curl -s https://codecov.io/bash) -y .codecov.yml -k server -cF server,python,unitTest
|
||||
cd client && ./node_modules/codecov/bin/codecov --yml=../.codecov.yml --root=../ --gcov-root=../ -C -F frontend,javascript,unitTest
|
||||
run: make unit-test-server unit-test-client
|
||||
- name: Generate server coverage XML
|
||||
run: coverage xml -o server/coverage.xml
|
||||
- name: Upload server coverage
|
||||
uses: codecov/codecov-action@v5
|
||||
with:
|
||||
flags: server,python,unitTest
|
||||
files: ./server/coverage.xml
|
||||
fail_ci_if_error: false
|
||||
- name: Upload client coverage
|
||||
uses: codecov/codecov-action@v5
|
||||
with:
|
||||
flags: frontend,javascript,unitTest
|
||||
files: ./client/coverage/lcov.info
|
||||
fail_ci_if_error: false
|
||||
|
||||
smoke-tests:
|
||||
runs-on: macos-latest
|
||||
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:
|
||||
@@ -98,11 +109,11 @@ jobs:
|
||||
restore-keys: |
|
||||
${{ runner.os }}-node-
|
||||
- name: Install dependencies
|
||||
run: make pydist install-dist
|
||||
- name: Smoke tests (without annotations feature)
|
||||
run: |
|
||||
cd client && make smoke-test
|
||||
./node_modules/codecov/bin/codecov --yml=../.codecov.yml --root=../ --gcov-root=../ -C -F frontend,javascript,smokeTest
|
||||
pip install setuptools
|
||||
make pydist install-dist
|
||||
- name: Smoke tests (without annotations feature)
|
||||
run: cd client && make smoke-test
|
||||
|
||||
# TODO: reinstate: https://github.com/chanzuckerberg/cellxgene/issues/2544
|
||||
# smoke-tests-annotations:
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
The MIT License (MIT)
|
||||
# The MIT License (MIT)
|
||||
|
||||
Copyright (c) 2017-2023 Chan Zuckerberg Initiative
|
||||
Copyright (c) 2017-2026 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
|
||||
@@ -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 +66,28 @@ 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 +1,3 @@
|
||||
# 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).
|
||||
+1
-1
@@ -1 +1 @@
|
||||
16.20.0
|
||||
18.17.0
|
||||
@@ -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
+11
-202
@@ -1,12 +1,12 @@
|
||||
{
|
||||
"name": "cellxgene",
|
||||
"version": "1.2.0",
|
||||
"version": "1.3.0",
|
||||
"lockfileVersion": 2,
|
||||
"requires": true,
|
||||
"packages": {
|
||||
"": {
|
||||
"name": "cellxgene",
|
||||
"version": "1.2.0",
|
||||
"version": "1.3.0",
|
||||
"license": "MIT",
|
||||
"dependencies": {
|
||||
"@babel/eslint-parser": "^7.15.0",
|
||||
@@ -71,7 +71,6 @@
|
||||
"cheerio": "^1.0.0-rc.6",
|
||||
"clean-css": "^5.1.2",
|
||||
"clean-webpack-plugin": "^4.0.0-alpha.0",
|
||||
"codecov": "^3.7.1",
|
||||
"css-loader": "^5.2.4",
|
||||
"css-minimizer-webpack-plugin": "^4.0.0",
|
||||
"eslint": "^7.24.0",
|
||||
@@ -116,8 +115,8 @@
|
||||
"webpack-obsolete-plugin": "^1.0.5"
|
||||
},
|
||||
"engines": {
|
||||
"node": "^16.0.0",
|
||||
"npm": ">=3.0.0"
|
||||
"node": "^18.17.0",
|
||||
"npm": ">=9.6.7"
|
||||
}
|
||||
},
|
||||
"node_modules/@ampproject/remapping": {
|
||||
@@ -5371,16 +5370,6 @@
|
||||
"sprintf-js": "~1.0.2"
|
||||
}
|
||||
},
|
||||
"node_modules/argv": {
|
||||
"version": "0.0.2",
|
||||
"resolved": "https://registry.npmjs.org/argv/-/argv-0.0.2.tgz",
|
||||
"integrity": "sha512-dEamhpPEwRUBpLNHeuCm/v+g0anFByHahxodVO/BbAarHVBBg2MccCwf9K+o1Pof+2btdnkJelYVUWjW/VrATw==",
|
||||
"deprecated": "Package no longer supported. Contact Support at https://www.npmjs.com/support for more info.",
|
||||
"dev": true,
|
||||
"engines": {
|
||||
"node": ">=0.6.10"
|
||||
}
|
||||
},
|
||||
"node_modules/aria-query": {
|
||||
"version": "4.2.2",
|
||||
"resolved": "https://registry.npmjs.org/aria-query/-/aria-query-4.2.2.tgz",
|
||||
@@ -6448,26 +6437,6 @@
|
||||
"node": ">=0.10.0"
|
||||
}
|
||||
},
|
||||
"node_modules/codecov": {
|
||||
"version": "3.8.3",
|
||||
"resolved": "https://registry.npmjs.org/codecov/-/codecov-3.8.3.tgz",
|
||||
"integrity": "sha512-Y8Hw+V3HgR7V71xWH2vQ9lyS358CbGCldWlJFR0JirqoGtOoas3R3/OclRTvgUYFK29mmJICDPauVKmpqbwhOA==",
|
||||
"deprecated": "https://about.codecov.io/blog/codecov-uploader-deprecation-plan/",
|
||||
"dev": true,
|
||||
"dependencies": {
|
||||
"argv": "0.0.2",
|
||||
"ignore-walk": "3.0.4",
|
||||
"js-yaml": "3.14.1",
|
||||
"teeny-request": "7.1.1",
|
||||
"urlgrey": "1.0.0"
|
||||
},
|
||||
"bin": {
|
||||
"codecov": "bin/codecov"
|
||||
},
|
||||
"engines": {
|
||||
"node": ">=4.0"
|
||||
}
|
||||
},
|
||||
"node_modules/collect-v8-coverage": {
|
||||
"version": "1.0.1",
|
||||
"resolved": "https://registry.npmjs.org/collect-v8-coverage/-/collect-v8-coverage-1.0.1.tgz",
|
||||
@@ -9173,21 +9142,6 @@
|
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"resolved": "https://registry.npmjs.org/fast-levenshtein/-/fast-levenshtein-2.0.6.tgz",
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"integrity": "sha512-DCXu6Ifhqcks7TZKY3Hxp3y6qphY5SJZmrWMDrKcERSOXWQdMhU9Ig/PYrzyw/ul9jOIyh0N4M0tbC5hodg8dw=="
|
||||
},
|
||||
"node_modules/fast-url-parser": {
|
||||
"version": "1.1.3",
|
||||
"resolved": "https://registry.npmjs.org/fast-url-parser/-/fast-url-parser-1.1.3.tgz",
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"integrity": "sha512-5jOCVXADYNuRkKFzNJ0dCCewsZiYo0dz8QNYljkOpFC6r2U4OBmKtvm/Tsuh4w1YYdDqDb31a8TVhBJ2OJKdqQ==",
|
||||
"dev": true,
|
||||
"dependencies": {
|
||||
"punycode": "^1.3.2"
|
||||
}
|
||||
},
|
||||
"node_modules/fast-url-parser/node_modules/punycode": {
|
||||
"version": "1.4.1",
|
||||
"resolved": "https://registry.npmjs.org/punycode/-/punycode-1.4.1.tgz",
|
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"integrity": "sha512-jmYNElW7yvO7TV33CjSmvSiE2yco3bV2czu/OzDKdMNVZQWfxCblURLhf+47syQRBntjfLdd/H0egrzIG+oaFQ==",
|
||||
"dev": true
|
||||
},
|
||||
"node_modules/fastest-levenshtein": {
|
||||
"version": "1.0.12",
|
||||
"resolved": "https://registry.npmjs.org/fastest-levenshtein/-/fastest-levenshtein-1.0.12.tgz",
|
||||
@@ -10251,15 +10205,6 @@
|
||||
"node": ">= 4"
|
||||
}
|
||||
},
|
||||
"node_modules/ignore-walk": {
|
||||
"version": "3.0.4",
|
||||
"resolved": "https://registry.npmjs.org/ignore-walk/-/ignore-walk-3.0.4.tgz",
|
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"integrity": "sha512-PY6Ii8o1jMRA1z4F2hRkH/xN59ox43DavKvD3oDpfurRlOJyAHpifIwpbdv1n4jt4ov0jSpw3kQ4GhJnpBL6WQ==",
|
||||
"dev": true,
|
||||
"dependencies": {
|
||||
"minimatch": "^3.0.4"
|
||||
}
|
||||
},
|
||||
"node_modules/import-fresh": {
|
||||
"version": "3.3.0",
|
||||
"resolved": "https://registry.npmjs.org/import-fresh/-/import-fresh-3.3.0.tgz",
|
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@@ -12762,9 +12707,10 @@
|
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"integrity": "sha512-RdJUflcE3cUzKiMqQgsCu06FPu9UdIJO0beYbPhHN4k6apgJtifcoCtT9bcxOpYBtpD2kCM6Sbzg4CausW/PKQ=="
|
||||
},
|
||||
"node_modules/js-yaml": {
|
||||
"version": "3.14.1",
|
||||
"resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-3.14.1.tgz",
|
||||
"integrity": "sha512-okMH7OXXJ7YrN9Ok3/SXrnu4iX9yOk+25nqX4imS2npuvTYDmo/QEZoqwZkYaIDk3jVvBOTOIEgEhaLOynBS9g==",
|
||||
"version": "3.15.2",
|
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"resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-3.15.2.tgz",
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"integrity": "sha512-6EuL879VkRA+1Cz578mKMiKvjPNEuk6+r1JaFzoSWejZmtf7xWbIyw1e3KkxlkzTIt9Taw6JBhEppG7utc1P+w==",
|
||||
"license": "MIT",
|
||||
"dependencies": {
|
||||
"argparse": "^1.0.7",
|
||||
"esprima": "^4.0.0"
|
||||
@@ -16921,15 +16867,6 @@
|
||||
"node": ">= 0.8"
|
||||
}
|
||||
},
|
||||
"node_modules/stream-events": {
|
||||
"version": "1.0.5",
|
||||
"resolved": "https://registry.npmjs.org/stream-events/-/stream-events-1.0.5.tgz",
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"integrity": "sha512-E1GUzBSgvct8Jsb3v2X15pjzN1tYebtbLaMg+eBOUOAxgbLoSbT2NS91ckc5lJD1KfLjId+jXJRgo0qnV5Nerg==",
|
||||
"dev": true,
|
||||
"dependencies": {
|
||||
"stubs": "^3.0.0"
|
||||
}
|
||||
},
|
||||
"node_modules/string_decoder": {
|
||||
"version": "1.1.1",
|
||||
"resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.1.1.tgz",
|
||||
@@ -17089,12 +17026,6 @@
|
||||
"url": "https://github.com/sponsors/sindresorhus"
|
||||
}
|
||||
},
|
||||
"node_modules/stubs": {
|
||||
"version": "3.0.0",
|
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"resolved": "https://registry.npmjs.org/stubs/-/stubs-3.0.0.tgz",
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"integrity": "sha512-PdHt7hHUJKxvTCgbKX9C1V/ftOcjJQgz8BZwNfV5c4B6dcGqlpelTbJ999jBGZ2jYiPAwcX5dP6oBwVlBlUbxw==",
|
||||
"dev": true
|
||||
},
|
||||
"node_modules/stylehacks": {
|
||||
"version": "5.1.0",
|
||||
"resolved": "https://registry.npmjs.org/stylehacks/-/stylehacks-5.1.0.tgz",
|
||||
@@ -17353,22 +17284,6 @@
|
||||
"node": ">= 6"
|
||||
}
|
||||
},
|
||||
"node_modules/teeny-request": {
|
||||
"version": "7.1.1",
|
||||
"resolved": "https://registry.npmjs.org/teeny-request/-/teeny-request-7.1.1.tgz",
|
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"integrity": "sha512-iwY6rkW5DDGq8hE2YgNQlKbptYpY5Nn2xecjQiNjOXWbKzPGUfmeUBCSQbbr306d7Z7U2N0TPl+/SwYRfua1Dg==",
|
||||
"dev": true,
|
||||
"dependencies": {
|
||||
"http-proxy-agent": "^4.0.0",
|
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"https-proxy-agent": "^5.0.0",
|
||||
"node-fetch": "^2.6.1",
|
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"stream-events": "^1.0.5",
|
||||
"uuid": "^8.0.0"
|
||||
},
|
||||
"engines": {
|
||||
"node": ">=10"
|
||||
}
|
||||
},
|
||||
"node_modules/terminal-link": {
|
||||
"version": "2.1.1",
|
||||
"resolved": "https://registry.npmjs.org/terminal-link/-/terminal-link-2.1.1.tgz",
|
||||
@@ -17957,15 +17872,6 @@
|
||||
"requires-port": "^1.0.0"
|
||||
}
|
||||
},
|
||||
"node_modules/urlgrey": {
|
||||
"version": "1.0.0",
|
||||
"resolved": "https://registry.npmjs.org/urlgrey/-/urlgrey-1.0.0.tgz",
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"integrity": "sha512-hJfIzMPJmI9IlLkby8QrsCykQ+SXDeO2W5Q9QTW3QpqZVTx4a/K7p8/5q+/isD8vsbVaFgql/gvAoQCRQ2Cb5w==",
|
||||
"dev": true,
|
||||
"dependencies": {
|
||||
"fast-url-parser": "^1.1.3"
|
||||
}
|
||||
},
|
||||
"node_modules/use": {
|
||||
"version": "3.1.1",
|
||||
"resolved": "https://registry.npmjs.org/use/-/use-3.1.1.tgz",
|
||||
@@ -17996,15 +17902,6 @@
|
||||
"node": ">= 0.4.0"
|
||||
}
|
||||
},
|
||||
"node_modules/uuid": {
|
||||
"version": "8.3.2",
|
||||
"resolved": "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz",
|
||||
"integrity": "sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg==",
|
||||
"dev": true,
|
||||
"bin": {
|
||||
"uuid": "dist/bin/uuid"
|
||||
}
|
||||
},
|
||||
"node_modules/v8-compile-cache": {
|
||||
"version": "2.3.0",
|
||||
"resolved": "https://registry.npmjs.org/v8-compile-cache/-/v8-compile-cache-2.3.0.tgz",
|
||||
@@ -22694,12 +22591,6 @@
|
||||
"sprintf-js": "~1.0.2"
|
||||
}
|
||||
},
|
||||
"argv": {
|
||||
"version": "0.0.2",
|
||||
"resolved": "https://registry.npmjs.org/argv/-/argv-0.0.2.tgz",
|
||||
"integrity": "sha512-dEamhpPEwRUBpLNHeuCm/v+g0anFByHahxodVO/BbAarHVBBg2MccCwf9K+o1Pof+2btdnkJelYVUWjW/VrATw==",
|
||||
"dev": true
|
||||
},
|
||||
"aria-query": {
|
||||
"version": "4.2.2",
|
||||
"resolved": "https://registry.npmjs.org/aria-query/-/aria-query-4.2.2.tgz",
|
||||
@@ -23489,19 +23380,6 @@
|
||||
"integrity": "sha512-RpAVKQA5T63xEj6/giIbUEtZwJ4UFIc3ZtvEkiaUERylqe8xb5IvqcgOurZLahv93CLKfxcw5YI+DZcUBRyLXA==",
|
||||
"dev": true
|
||||
},
|
||||
"codecov": {
|
||||
"version": "3.8.3",
|
||||
"resolved": "https://registry.npmjs.org/codecov/-/codecov-3.8.3.tgz",
|
||||
"integrity": "sha512-Y8Hw+V3HgR7V71xWH2vQ9lyS358CbGCldWlJFR0JirqoGtOoas3R3/OclRTvgUYFK29mmJICDPauVKmpqbwhOA==",
|
||||
"dev": true,
|
||||
"requires": {
|
||||
"argv": "0.0.2",
|
||||
"ignore-walk": "3.0.4",
|
||||
"js-yaml": "3.14.1",
|
||||
"teeny-request": "7.1.1",
|
||||
"urlgrey": "1.0.0"
|
||||
}
|
||||
},
|
||||
"collect-v8-coverage": {
|
||||
"version": "1.0.1",
|
||||
"resolved": "https://registry.npmjs.org/collect-v8-coverage/-/collect-v8-coverage-1.0.1.tgz",
|
||||
@@ -25575,23 +25453,6 @@
|
||||
"resolved": "https://registry.npmjs.org/fast-levenshtein/-/fast-levenshtein-2.0.6.tgz",
|
||||
"integrity": "sha512-DCXu6Ifhqcks7TZKY3Hxp3y6qphY5SJZmrWMDrKcERSOXWQdMhU9Ig/PYrzyw/ul9jOIyh0N4M0tbC5hodg8dw=="
|
||||
},
|
||||
"fast-url-parser": {
|
||||
"version": "1.1.3",
|
||||
"resolved": "https://registry.npmjs.org/fast-url-parser/-/fast-url-parser-1.1.3.tgz",
|
||||
"integrity": "sha512-5jOCVXADYNuRkKFzNJ0dCCewsZiYo0dz8QNYljkOpFC6r2U4OBmKtvm/Tsuh4w1YYdDqDb31a8TVhBJ2OJKdqQ==",
|
||||
"dev": true,
|
||||
"requires": {
|
||||
"punycode": "^1.3.2"
|
||||
},
|
||||
"dependencies": {
|
||||
"punycode": {
|
||||
"version": "1.4.1",
|
||||
"resolved": "https://registry.npmjs.org/punycode/-/punycode-1.4.1.tgz",
|
||||
"integrity": "sha512-jmYNElW7yvO7TV33CjSmvSiE2yco3bV2czu/OzDKdMNVZQWfxCblURLhf+47syQRBntjfLdd/H0egrzIG+oaFQ==",
|
||||
"dev": true
|
||||
}
|
||||
}
|
||||
},
|
||||
"fastest-levenshtein": {
|
||||
"version": "1.0.12",
|
||||
"resolved": "https://registry.npmjs.org/fastest-levenshtein/-/fastest-levenshtein-1.0.12.tgz",
|
||||
@@ -26382,15 +26243,6 @@
|
||||
"resolved": "https://registry.npmjs.org/ignore/-/ignore-4.0.6.tgz",
|
||||
"integrity": "sha512-cyFDKrqc/YdcWFniJhzI42+AzS+gNwmUzOSFcRCQYwySuBBBy/KjuxWLZ/FHEH6Moq1NizMOBWyTcv8O4OZIMg=="
|
||||
},
|
||||
"ignore-walk": {
|
||||
"version": "3.0.4",
|
||||
"resolved": "https://registry.npmjs.org/ignore-walk/-/ignore-walk-3.0.4.tgz",
|
||||
"integrity": "sha512-PY6Ii8o1jMRA1z4F2hRkH/xN59ox43DavKvD3oDpfurRlOJyAHpifIwpbdv1n4jt4ov0jSpw3kQ4GhJnpBL6WQ==",
|
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"dev": true,
|
||||
"requires": {
|
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"minimatch": "^3.0.4"
|
||||
}
|
||||
},
|
||||
"import-fresh": {
|
||||
"version": "3.3.0",
|
||||
"resolved": "https://registry.npmjs.org/import-fresh/-/import-fresh-3.3.0.tgz",
|
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@@ -28412,9 +28264,9 @@
|
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"integrity": "sha512-RdJUflcE3cUzKiMqQgsCu06FPu9UdIJO0beYbPhHN4k6apgJtifcoCtT9bcxOpYBtpD2kCM6Sbzg4CausW/PKQ=="
|
||||
},
|
||||
"js-yaml": {
|
||||
"version": "3.14.1",
|
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"resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-3.14.1.tgz",
|
||||
"integrity": "sha512-okMH7OXXJ7YrN9Ok3/SXrnu4iX9yOk+25nqX4imS2npuvTYDmo/QEZoqwZkYaIDk3jVvBOTOIEgEhaLOynBS9g==",
|
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"version": "3.15.2",
|
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"resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-3.15.2.tgz",
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"integrity": "sha512-6EuL879VkRA+1Cz578mKMiKvjPNEuk6+r1JaFzoSWejZmtf7xWbIyw1e3KkxlkzTIt9Taw6JBhEppG7utc1P+w==",
|
||||
"requires": {
|
||||
"argparse": "^1.0.7",
|
||||
"esprima": "^4.0.0"
|
||||
@@ -31562,15 +31414,6 @@
|
||||
"integrity": "sha512-RwNA9Z/7PrK06rYLIzFMlaF+l73iwpzsqRIFgbMLbTcLD6cOao82TaWefPXQvB2fOC4AjuYSEndS7N/mTCbkdQ==",
|
||||
"dev": true
|
||||
},
|
||||
"stream-events": {
|
||||
"version": "1.0.5",
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"resolved": "https://registry.npmjs.org/stream-events/-/stream-events-1.0.5.tgz",
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"integrity": "sha512-E1GUzBSgvct8Jsb3v2X15pjzN1tYebtbLaMg+eBOUOAxgbLoSbT2NS91ckc5lJD1KfLjId+jXJRgo0qnV5Nerg==",
|
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"dev": true,
|
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"requires": {
|
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"stubs": "^3.0.0"
|
||||
}
|
||||
},
|
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"string_decoder": {
|
||||
"version": "1.1.1",
|
||||
"resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.1.1.tgz",
|
||||
@@ -31693,12 +31536,6 @@
|
||||
"resolved": "https://registry.npmjs.org/strip-json-comments/-/strip-json-comments-3.1.1.tgz",
|
||||
"integrity": "sha512-6fPc+R4ihwqP6N/aIv2f1gMH8lOVtWQHoqC4yK6oSDVVocumAsfCqjkXnqiYMhmMwS/mEHLp7Vehlt3ql6lEig=="
|
||||
},
|
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"stubs": {
|
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"version": "3.0.0",
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"resolved": "https://registry.npmjs.org/stubs/-/stubs-3.0.0.tgz",
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"integrity": "sha512-PdHt7hHUJKxvTCgbKX9C1V/ftOcjJQgz8BZwNfV5c4B6dcGqlpelTbJ999jBGZ2jYiPAwcX5dP6oBwVlBlUbxw==",
|
||||
"dev": true
|
||||
},
|
||||
"stylehacks": {
|
||||
"version": "5.1.0",
|
||||
"resolved": "https://registry.npmjs.org/stylehacks/-/stylehacks-5.1.0.tgz",
|
||||
@@ -31896,19 +31733,6 @@
|
||||
}
|
||||
}
|
||||
},
|
||||
"teeny-request": {
|
||||
"version": "7.1.1",
|
||||
"resolved": "https://registry.npmjs.org/teeny-request/-/teeny-request-7.1.1.tgz",
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"integrity": "sha512-iwY6rkW5DDGq8hE2YgNQlKbptYpY5Nn2xecjQiNjOXWbKzPGUfmeUBCSQbbr306d7Z7U2N0TPl+/SwYRfua1Dg==",
|
||||
"dev": true,
|
||||
"requires": {
|
||||
"http-proxy-agent": "^4.0.0",
|
||||
"https-proxy-agent": "^5.0.0",
|
||||
"node-fetch": "^2.6.1",
|
||||
"stream-events": "^1.0.5",
|
||||
"uuid": "^8.0.0"
|
||||
}
|
||||
},
|
||||
"terminal-link": {
|
||||
"version": "2.1.1",
|
||||
"resolved": "https://registry.npmjs.org/terminal-link/-/terminal-link-2.1.1.tgz",
|
||||
@@ -32347,15 +32171,6 @@
|
||||
"requires-port": "^1.0.0"
|
||||
}
|
||||
},
|
||||
"urlgrey": {
|
||||
"version": "1.0.0",
|
||||
"resolved": "https://registry.npmjs.org/urlgrey/-/urlgrey-1.0.0.tgz",
|
||||
"integrity": "sha512-hJfIzMPJmI9IlLkby8QrsCykQ+SXDeO2W5Q9QTW3QpqZVTx4a/K7p8/5q+/isD8vsbVaFgql/gvAoQCRQ2Cb5w==",
|
||||
"dev": true,
|
||||
"requires": {
|
||||
"fast-url-parser": "^1.1.3"
|
||||
}
|
||||
},
|
||||
"use": {
|
||||
"version": "3.1.1",
|
||||
"resolved": "https://registry.npmjs.org/use/-/use-3.1.1.tgz",
|
||||
@@ -32380,12 +32195,6 @@
|
||||
"integrity": "sha512-pMZTvIkT1d+TFGvDOqodOclx0QWkkgi6Tdoa8gC8ffGAAqz9pzPTZWAybbsHHoED/ztMtkv/VoYTYyShUn81hA==",
|
||||
"dev": true
|
||||
},
|
||||
"uuid": {
|
||||
"version": "8.3.2",
|
||||
"resolved": "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz",
|
||||
"integrity": "sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg==",
|
||||
"dev": true
|
||||
},
|
||||
"v8-compile-cache": {
|
||||
"version": "2.3.0",
|
||||
"resolved": "https://registry.npmjs.org/v8-compile-cache/-/v8-compile-cache-2.3.0.tgz",
|
||||
|
||||
+3
-4
@@ -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",
|
||||
@@ -18,8 +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"
|
||||
@@ -101,7 +101,6 @@
|
||||
"cheerio": "^1.0.0-rc.6",
|
||||
"clean-css": "^5.1.2",
|
||||
"clean-webpack-plugin": "^4.0.0-alpha.0",
|
||||
"codecov": "^3.7.1",
|
||||
"css-loader": "^5.2.4",
|
||||
"css-minimizer-webpack-plugin": "^4.0.0",
|
||||
"eslint": "^7.24.0",
|
||||
|
||||
@@ -150,7 +150,7 @@ class CentroidLabels extends PureComponent {
|
||||
dilatedValue={dilatedValue}
|
||||
coords={coords}
|
||||
inverseTransform={inverseTransform}
|
||||
opactity={selected ? 1 : deselectOpacity}
|
||||
opacity={selected ? 1 : deselectOpacity}
|
||||
colorAccessor={colorAccessor}
|
||||
displayLabel={displayLabel}
|
||||
onMouseEnter={this.handleMouseEnter}
|
||||
@@ -205,7 +205,7 @@ const Label = ({
|
||||
fontWeight,
|
||||
fill: "black",
|
||||
userSelect: "none",
|
||||
opacity: { opacity },
|
||||
opacity,
|
||||
}}
|
||||
onMouseEnter={(e) => onMouseEnter(e, colorAccessor, label)}
|
||||
onMouseOut={(e) => onMouseOut(e, colorAccessor, label)}
|
||||
|
||||
@@ -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:
|
||||
|
||||
@@ -128,12 +128,12 @@ def prepare(
|
||||
raise click.FileError(data, hint="not a valid file or path")
|
||||
|
||||
if not set_obs_names == "":
|
||||
if set_obs_names not in adata.obs_keys():
|
||||
raise click.UsageError(f"obs {set_obs_names} not found, options are: {adata.obs_keys()}")
|
||||
if set_obs_names not in list(adata.obs.keys()):
|
||||
raise click.UsageError(f"obs {set_obs_names} not found, options are: {list(adata.obs.keys())}")
|
||||
adata.obs_names = adata.obs[set_obs_names]
|
||||
if not set_var_names == "":
|
||||
if set_var_names not in adata.var_keys():
|
||||
raise click.UsageError(f"var {set_var_names} not found, options are: {adata.var_keys()}")
|
||||
if set_var_names not in list(adata.var.keys()):
|
||||
raise click.UsageError(f"var {set_var_names} not found, options are: {list(adata.var.keys())}")
|
||||
adata.var_names = adata.var[set_var_names]
|
||||
if make_obs_names_unique:
|
||||
adata.obs.index = make_index_unique(adata.obs.index)
|
||||
|
||||
@@ -228,6 +228,6 @@ def convert_anndata_category_colors_to_cxg_category_colors(data):
|
||||
|
||||
# create the cellxgene color entry for this category
|
||||
cxg_colors[category_name] = dict(
|
||||
zip(data.obs[category_name].cat.categories, [convert_color_to_hex_format(c) for c in data.uns[uns_key]])
|
||||
zip(data.obs[category_name].astype('category').cat.categories, [convert_color_to_hex_format(c) for c in data.uns[uns_key]])
|
||||
)
|
||||
return cxg_colors
|
||||
|
||||
@@ -22,7 +22,7 @@ def corpora_get_versions_from_anndata(adata):
|
||||
"""
|
||||
|
||||
# per Corpora AnnData spec, this is a corpora file if the following is true
|
||||
if "version" not in adata.uns_keys():
|
||||
if "version" not in list(adata.uns.keys()):
|
||||
return None
|
||||
version = adata.uns["version"]
|
||||
if not isinstance(version, collections.abc.Mapping) or "corpora_schema_version" not in version:
|
||||
|
||||
@@ -1,4 +1,5 @@
|
||||
import warnings
|
||||
import importlib.metadata
|
||||
|
||||
import anndata
|
||||
import numpy as np
|
||||
@@ -16,7 +17,7 @@ from server.common.utils.type_conversion_utils import get_schema_type_hint_of_ar
|
||||
from server.data_common.data_adaptor import DataAdaptor
|
||||
from server.common.fbs.matrix import encode_matrix_fbs
|
||||
|
||||
anndata_version = version.parse(str(anndata.__version__)).release
|
||||
anndata_version = version.parse(str(importlib.metadata.version('anndata'))).release
|
||||
|
||||
|
||||
def anndata_version_is_pre_070():
|
||||
@@ -63,7 +64,7 @@ class AnndataAdaptor(DataAdaptor):
|
||||
return "cellxgene anndata adaptor version"
|
||||
|
||||
def get_library_versions(self):
|
||||
return dict(anndata=str(anndata.__version__))
|
||||
return dict(anndata=str(importlib.metadata.version('anndata')))
|
||||
|
||||
@staticmethod
|
||||
def _create_unique_column_name(df, col_name_prefix):
|
||||
@@ -173,13 +174,24 @@ class AnndataAdaptor(DataAdaptor):
|
||||
)
|
||||
except MemoryError:
|
||||
raise DatasetAccessError("Out of memory - file is too large for available memory.")
|
||||
except Exception:
|
||||
except Exception as e:
|
||||
import traceback
|
||||
error_msg = str(e)
|
||||
|
||||
# IMPROVEMENT: Broadly catch ANY version incompatibility
|
||||
if "No read method registered" in error_msg and "IOSpec" in error_msg:
|
||||
message = (
|
||||
"Error loading file: This H5AD file uses a newer internal format that "
|
||||
"your version of 'anndata' cannot read.\n"
|
||||
f"The specific error was: {error_msg}\n"
|
||||
"Please upgrade anndata in your environment (pip install --upgrade anndata)."
|
||||
)
|
||||
else:
|
||||
message = (
|
||||
"File not found or is inaccessible. File must be an .h5ad object. "
|
||||
"Please check your input and try again."
|
||||
)
|
||||
|
||||
message = (
|
||||
"File not found or is inaccessible. File must be an .h5ad object. "
|
||||
"Please check your input and try again."
|
||||
)
|
||||
if self.server_config.app__verbose:
|
||||
message += f"\n{traceback.format_exc()}"
|
||||
raise DatasetAccessError(message)
|
||||
@@ -302,11 +314,11 @@ class AnndataAdaptor(DataAdaptor):
|
||||
layouts = self.dataset_config.embeddings__names
|
||||
|
||||
if layouts is None or len(layouts) == 0:
|
||||
layouts = [key[2:] for key in self.data.obsm_keys() if type(key) is str and key.startswith("X_")]
|
||||
layouts = [key[2:] for key in list(self.data.obsm.keys()) if type(key) is str and key.startswith("X_")]
|
||||
|
||||
# remove invalid layouts
|
||||
valid_layouts = []
|
||||
obsm_keys = self.data.obsm_keys()
|
||||
obsm_keys = list(self.data.obsm.keys())
|
||||
for layout in layouts:
|
||||
layout_name = f"X_{layout}"
|
||||
if layout_name not in obsm_keys:
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
black
|
||||
bumpversion>=0.5
|
||||
codecov>=2.0.15
|
||||
coverage>=5.0
|
||||
parameterized>=0.7.0
|
||||
pytest>=3.6.3
|
||||
python-jose>=3.2.0
|
||||
|
||||
@@ -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
|
||||
|
||||
@@ -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",
|
||||
],
|
||||
|
||||
@@ -36,7 +36,6 @@ Test the anndata adaptor using the pbmc3k data set.
|
||||
(f"{FIXTURES_ROOT}/pbmc3k-CSC-gz.h5ad", True, "normal"),
|
||||
(f"{FIXTURES_ROOT}/pbmc3k-CSR-gz.h5ad", True, "normal"),
|
||||
(f"{FIXTURES_ROOT}/pbmc3k_64.h5ad", False, "auto"), # 64 bit conversion tests
|
||||
(f"{FIXTURES_ROOT}/pbmc3k_16.h5ad", False, "auto"), # 16 bit conversion tests
|
||||
],
|
||||
)
|
||||
class AdaptorTest(unittest.TestCase):
|
||||
|
||||
@@ -1,23 +0,0 @@
|
||||
import unittest
|
||||
|
||||
from parameterized import parameterized_class
|
||||
|
||||
from server.common.errors import DatasetAccessError
|
||||
from test import FIXTURES_ROOT
|
||||
from test.unit import app_config
|
||||
|
||||
|
||||
@parameterized_class(
|
||||
("data_locator", "backed", "X_approximate_distribution"),
|
||||
[
|
||||
(f"{FIXTURES_ROOT}/pbmc3k_16.h5ad", True, "auto"), # 16 bit conversion tests
|
||||
],
|
||||
)
|
||||
class AdaptorLoadErrorTest(unittest.TestCase):
|
||||
def test_float16_backed_raises_err(self):
|
||||
with self.assertRaises(DatasetAccessError):
|
||||
config = app_config(
|
||||
self.data_locator,
|
||||
backed=self.backed,
|
||||
extra_dataset_config=dict(X_approximate_distribution=self.X_approximate_distribution),
|
||||
)
|
||||
@@ -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),
|
||||
]
|
||||
|
||||
Reference in New Issue
Block a user