Merge branch 'main' into tiledbsoma

Author: hadim

recipes/sophios/meta.yaml

@@ -0,0 +1,65 @@
+{% set name = "sophios" %}
+{% set version = "0.2.2" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/PolusAI/workflow-inference-compiler/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 54e8bd0cfd6b0243bce19c0b878a8506687d737242f6a26a5485f86f2acb787b
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation 
+  number: 0
+
+requirements:
+  host:
+    - python {{ python_min }}
+    - setuptools >=42
+    - pip 
+    - wheel 
+    - versioneer ==0.29
+    - tomli
+  run:
+    - python >={{ python_min }}
+    - python-graphviz
+    - jsonschema
+    - toil
+    - pyyaml
+    - requests <=2.31.0
+    - mergedeep
+    - networkx
+    - cwl-utils >=0.32
+    - typeguard
+    - pydantic >=2.6
+    - pydantic-settings
+    - ruamel.yaml.clib
+    - fastapi
+    - docker-py
+    - podman-py
+    - python-jose
+    - uvicorn
+    - orjson
+
+test:
+  imports:
+    - sophios
+  commands:
+    - pip list
+    - pip check
+  requires:
+    - pip
+    - python {{ python_min }}
+
+about:
+  home: https://pypi.org/project/sophios/
+  summary: DSL for inferring the edges of a CWL workflow DAG
+  dev_url: https://github.com/PolusAI/workflow-inference-compiler
+  license: MIT
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - sameeul

recipes/tiledbsoma/fix-includes.patch recipes/tiledbsoma/fix-lib-build.patch

@@ -10,8 +10,10 @@ source:
   url: https://github.com/single-cell-data/TileDB-SOMA/archive/refs/tags/${{ version }}.zip
   sha256: 1c9b60b14c900e252c30586fcadaeddd455d58df624112ecea62eef24212dc61
   patches:
-    # NOTE: fix failing includes when building a conda package
-    - fix-includes.patch
+    # NOTE:
+    # - fix failing includes
+    # - fix failing linking configuration for tiledbsoma-cli and spdlog
+    - fix-lib-build.patch
 
 build:
   number: 0
@@ -50,15 +52,15 @@ outputs:
       build:
         - ${{ compiler('cxx') }}
         - ${{ stdlib("c") }}
-        - cmake
+        - cmake >=3.21
         - ninja
         - pkg-config
       host:
         - tiledb
         - spdlog >=1.15
         - fmt >=11.0
       run_exports:
-        - ${{ pin_subpackage('libtiledbsoma', upper_bound='x.x.x') }}
+        - ${{ pin_subpackage('libtiledbsoma', exact=True) }}
 
     tests:
       - script:
@@ -136,19 +138,20 @@ outputs:
 
         - ${{ compiler('cxx') }}
         - ${{ stdlib("c") }}
-        - cmake
+        - cmake >=3.21
         - ninja
         - pkg-config
+        - git
       host:
-        - python 3.12.*
+        - python
         - setuptools >=70.1
         - pip
         - pybind11 >=2.10.0
         # libraries
         - libtiledbsoma
         - tiledb
       run:
-        - python 3.12.*
+        - python
         - anndata >=0.10.1
         - attrs >=22.2
         - numpy
@@ -164,6 +167,25 @@ outputs:
           imports:
             - tiledbsoma
           pip_check: true
+      - requirements:
+          run:
+            - pytest
+            - typeguard
+        files:
+          source:
+            - apis/python/tests/
+        script: |
+          # NOTE: we only test a subset of the test suite to avoid long build times but
+          # still make sure the package is working.
+          pytest -vvv \
+            apis/python/tests/test_experiment_basic.py \
+            apis/python/tests/test_type_system.py \
+            apis/python/tests/test_stats.py \
+            apis/python/tests/test_simple.py \
+            apis/python/tests/test_scene.py \
+            apis/python/tests/test_reindexer_api.py \
+            apis/python/tests/test_regression.py \
+            apis/python/tests/test_point_cloud_dataframe.py
 
 about:
   summary: Python and R SOMA APIs using TileDB's cloud-native format. Ideal for single-cell data at any scale.