fix: pip install mikado now works

Changed the requiremnts.txt and a scipy import so pip won't fail. This was tested with python 3.8 and 3.9.
EI-CoreBioinformatics · Jun 6, 2023 · 9129dbf · 9129dbf
1 parent c8f6b7c
commit 9129dbf
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Showing 3 changed files with 7 additions and 5 deletions.
diff --git a/environment.yml b/environment.yml
@@ -23,8 +23,8 @@ dependencies:
   - pyyaml>=5.1.2
   - scipy>=1.3.1
   - snakemake-minimal>=5.7.0
-  - sqlalchemy>=1.4.0
-  - sqlalchemy-utils>=0.34.1
+  - sqlalchemy==1.4.48
+  - sqlalchemy-utils==0.34.1
   - sqlite
   - tabulate>=0.8.5
   - wheel

diff --git a/requirements.txt b/requirements.txt
@@ -11,8 +11,8 @@ pysam>=0.15.3
 pyyaml>=5.1.2
 scipy>=1.3.1
 snakemake>=5.7.0
-sqlalchemy>=1.4.0
-sqlalchemy-utils>=0.37
+sqlalchemy==1.4.48
+sqlalchemy-utils==0.37
 tabulate>=0.8.5
 pytest>=5.4.1
 python-rapidjson>=1.0.0

diff --git a/setup.py b/setup.py
@@ -12,8 +12,10 @@
 import re
 import sys
 import numpy as np
-from scipy._build_utils import numpy_nodepr_api
 
+### See comment here https://github.com/cython/cython/issues/2498
+numpy_nodepr_api = dict(define_macros=[("NPY_NO_DEPRECATED_API",
+                                        "NPY_1_9_API_VERSION")])
 
 here = path.abspath(path.dirname("__file__"))