Update starfish to 0.3.0

.github/workflows/PR.yml

@@ -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
@@ -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

azure-pipeline.yml

@@ -41,6 +41,8 @@ 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
  pool:
  vmImage: "ubuntu-latest"
  strategy:

recipes/starfish/meta.yaml

@@ -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
+ run_exports:
+ - {{ pin_subpackage("starfish", max_pin="x.x") }}
  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
  - 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
 
 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"