Merge pull request #24 from mskcc/feature/add-conda-support

adding conda support

Author: john-ziegler

conda_build_config.yaml

@@ -0,0 +1,7 @@
+python:
+    - 2.7
+    - 3.5
+    - 3.6
+    - 3.7
+    - 3.8
+

meta.yaml

@@ -0,0 +1,45 @@
+{% set version = "0.4.2" %}
+
+
+package:
+  name: mimsi
+  version: {{ version }}
+
+source:
+  url: "https://github.com/mskcc/mimsi/archive/refs/heads/feature/add-conda-support.zip"
+
+
+build:
+  number: 0
+  python: {{ python }}
+  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv "
+
+requirements:
+  host:
+    - python
+    - setuptools
+    - pip
+
+  run:
+    - python
+    - future
+    - nose >=1.3.7
+    - pytorch ==1.4.0
+    - torchvision ==0.5.0
+    - numpy ==1.14.6 # [py==35]
+    - numpy # [py>=36]
+    - numpy # [py==27]
+    - pandas ==0.24.2 # [py==27]
+    - pandas # [py>=35]
+    - pysam
+    - scikit-learn # [py>=35]
+    - scikit-learn >=0.20.0 # [py==27]
+  
+
+
+test:
+  commands:
+    - evaluate_sample --version
+    - analyze --version
+    - create_data --version
+    - mi_msi_train_test --version

requirements.txt

@@ -1,18 +1,16 @@
-future; python_version <= '2.7'
+future
 nose>=1.3.7
-numpy==1.16.5
+numpy==1.14.6; python_version == '3.5'
+numpy>=1.16.5; python_version >= '3.6'
+numpy>=1.16.5; python_version == '2.7'
 pandas==0.24.2; python_version <= '2.7'
 pandas
-pillow>=8.1.1; python_version >= '3.6'
-pillow
-pysam==0.16.0.1
+pysam
 python-dateutil==2.8.1
 scikit-learn>=0.20.0; python_version <= '2.7'
 scikit-learn
 scipy>=1.1.0; python_version <= '2.7'
 scipy
-six==1.11.0
-sklearn==0.0; python_version <= '2.7'
-sklearn
-torch==1.4.0
-torchvision==0.5.0
+torch
+torchvision
+

setup.py

@@ -29,7 +29,7 @@ def most_recent_tag():
 
 setup(
     name="MiMSI",
-    version="v0.4.1",
+    version="v0.4.2",
     description="A deep, multiple instance learning based classifier for identifying Microsatellite Instability from NGS",
     url="https://github.com/mskcc/mimsi",
     author="John Ziegler",