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Update starfish to 0.3.0 #51354

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Update starfish to 0.3.0 #51354

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62d2eb3
Update starfish to 0.3.0
BiocondaBot Oct 13, 2024
b644db5
Add run_exports
martin-g Oct 14, 2024
3eee14a
update dependencies
mencian Oct 14, 2024
0e426a5
try switching to ubuntu-22.04
bgruening Oct 15, 2024
59e513b
need more sleep
bgruening Oct 16, 2024
97c7591
Update azure-pipeline.yml
bgruening Oct 16, 2024
59d18f2
Update azure-pipeline.yml
bgruening Oct 16, 2024
bfec6fc
Update azure-pipeline.yml
bgruening Oct 17, 2024
b92c21b
Update azure-pipeline.yml
bgruening Oct 17, 2024
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4 changes: 2 additions & 2 deletions .github/workflows/PR.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ concurrency:
jobs:
lint:
name: Lint
runs-on: ubuntu-latest
runs-on: ubuntu-22.04
strategy:
fail-fast: true
max-parallel: 13
Expand Down Expand Up @@ -53,7 +53,7 @@ jobs:

build-linux:
name: Linux Tests
runs-on: ubuntu-latest
runs-on: ubuntu-22.04
strategy:
fail-fast: true
max-parallel: 13
Expand Down
8 changes: 5 additions & 3 deletions azure-pipeline.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ stages:
jobs:
- job: "lint"
pool:
vmImage: "ubuntu-latest"
vmImage: "ubuntu-22.04"
strategy:
maxParallel: 8

Expand Down Expand Up @@ -41,10 +41,12 @@ stages:
- stage: "test_linux"
jobs:
- job: "test_linux"
##timeoutInMinutes: 90 # how long to run the job before automatically cancelling
##cancelTimeoutInMinutes: 40 # how much time to give 'run always even if cancelled tasks' before stopping them
Comment on lines +44 to +45
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💡 Codebase verification

Issues found in azure-pipeline.yml

  1. Timeout Settings:

    • The timeoutInMinutes is set to 360 in both test_linux and test_osx stages, overriding the previously commented-out values of 90 and 40. Please confirm if this increase is intentional to allow longer job durations.

  2. Missing common.sh:

    • In the test_osx stage, the script attempts to source common.sh, which does not exist in the repository. This absence is causing build failures. Please ensure that common.sh is added to the repository or update the pipeline to remove or replace this reference.
🔗 Analysis chain

Verify timeout settings and environment variable changes

  1. Timeout settings:

    • The timeoutInMinutes and cancelTimeoutInMinutes settings are commented out. Please confirm if this is intentional, as it might affect the job's behavior.

  2. Environment variables:

    • New environment variables OSTYPE="linux-gnu" and CI="true" are exported.

These changes might impact the build process. Could you please provide more context on why these changes were made and if they've been tested?

To check the impact of these changes, you can run:

Also applies to: 71-72

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check if these environment variables are used elsewhere in the repository
rg --type yaml 'timeoutInMinutes|cancelTimeoutInMinutes|OSTYPE|CI'

Length of output: 38212

Script:

#!/bin/bash
# Verify the usage and impact of timeout settings and environment variables in azure-pipeline.yml

# Check for timeout settings in azure-pipeline.yml
rg 'timeoutInMinutes|cancelTimeoutInMinutes' azure-pipeline.yml -C 3

# Check where OSTYPE and CI environment variables are set and used in azure-pipeline.yml
rg 'OSTYPE|CI' azure-pipeline.yml -C 3

Length of output: 1371

pool:
vmImage: "ubuntu-latest"
vmImage: "ubuntu-22.04"
strategy:
maxParallel: 8
maxParallel: 2
timeoutInMinutes: 360

steps:
Expand Down
46 changes: 26 additions & 20 deletions recipes/starfish/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,51 +1,57 @@
{% set version = "0.2.2" %}
{% set name = "starfish" %}
{% set version = "0.3.0" %}

package:
name: starfish
name: {{ name }}
version: {{ version }}

source:
url: https://github.com/spacetx/starfish/archive/{{ version }}.tar.gz
sha256: 3183465443420ca068a2235ee754c4d02e787d69784349713b74ecf3f83b82fd
url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/starfish-{{ version }}.tar.gz
sha256: 29152eaa81d396ccc32695e9b1a0271e4f89851cf1f8f13687566b1d03fdd58a

build:
number: 0
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run_exports:
- {{ pin_subpackage("starfish", max_pin="x.x") }}
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noarch: python
script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv"
script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"

requirements:
host:
- python >=3.6
- python >=3.9,<3.12
- pip
run:
- python >=3.6
- python >=3.9,<3.12
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- click
- dataclasses
- docutils <0.21
- h5py
- jsonschema
- matplotlib-base
- numpy !=1.13.0
- pandas >=0.23.4
- jsonschema <4.18
- matplotlib-base <3.8
- mistune ==0.8.4
- numpy <1.25
- regional
- read-roi
- semantic_version
- scikit-image >=0.14.0,!=0.16.0.*,!= 0.16.1.*,!=0.16.2.*,!= 0.17.1.*,!=0.17.2.*
- scikit-image ==0.21
- scikit-learn
- scipy
- showit >=1.1.4
- slicedimage ==4.1.1
- seaborn-base
- showit
- slicedimage
- sympy
- tqdm
- trackpy
- validators
- xarray >=0.14.1
- ipywidgets
- xarray <2023.09
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test:
imports:
- starfish

about:
home: https://github.com/spacetx/starfish
home: "https://github.com/spacetx/starfish"
license: MIT
summary: standardized analysis pipeline for image-based transcriptomics
license_family: MIT
license_file: LICENSE
summary: "Standardized analysis pipeline for image-based transcriptomics."
dev_url: "https://github.com/spacetx/starfish"
doc_url: "https://spacetx-starfish.readthedocs.io/en/latest"