Merge pull request #340 from kipoi/sharedenvupdate

Shared env update (moving tensorflow, keras) to conda from pip where ever possible

shared/envs/kipoi-py3-keras1.2.yaml

@@ -10,18 +10,16 @@ dependencies:
 - pysam=0.15.3
 - python=3.7
 - genomelake==0.1.4
-- numpy
-- pandas
 - cython=0.29.28
 - pip=21.3.1
+- tensorflow=1.14
 - pip:
+  - keras==1.2.2 # keras 1.2.2 is not available with python 3.7 in conda-forge
   - pyvcf==0.4.3
   - kipoi_veff
   - kipoi_interpret
   - kipoi
   - kipoiseq
-  - tensorflow==1.15
-  - keras==1.2.2
   - deepcpg==1.0.4
   - h5py==3.6.0
   - protobuf==3.20

shared/envs/kipoi-py3-keras2-tf1.yaml

@@ -22,25 +22,20 @@ dependencies:
 - pybedtools=0.8.1
 - pysam=0.15.3
 - joblib=1.1.0
+- tensorflow=1.14
 - pip:
+  - keras==2.1.6 # Only FactorNet can not work with keras 2.2.4 wich is the least available option in conda-forge with python=3.7. Keeping keras in pip.
   - scikit-learn==0.19.2
   - gtfparse>=1.0.7
   - pyvcf==0.4.3
   - kipoi_veff
   - kipoi_interpret
   - kipoi
   - kipoiseq
-  - tensorflow==1.15
-  - keras==2.1.6
   - gffutils==0.10.1
   - pyfaidx==0.6.4
-  # - scikit-learn
   - intervaltree==2.1.0
-  # - sklearn-pandas
   - tqdm==4.64.0
-  # - mmsplice
-  - numpy
   - concise>=0.6.6
-  # other 
   - ipykernel==6.13.0
   - protobuf==3.20

shared/envs/kipoi-py3-keras2-tf2.yaml

@@ -1,6 +1,5 @@
 name: kipoi-py3-keras2-tf2
 channels:
-- pytorch
 - bioconda
 - conda-forge
 - defaults
@@ -22,23 +21,8 @@ dependencies:
 - pysam=0.17
 - joblib=1.1.0
 - scikit-learn=1.0.2
+- tensorflow
+- keras
 - pip:
-  - gtfparse>=1.0.7
-  - pyvcf==0.4.3
-  - kipoi_veff
-  - kipoi_interpret
   - kipoi
-  - kipoiseq
-  - tensorflow
-  - keras
-  - gffutils==0.10.1
-  - pyfaidx==0.6.4
-  # - scikit-learn
-  - intervaltree==2.1.0
-  # - sklearn-pandas
-  - tqdm==4.64.0
-  # - mmsplice
-  - concise>=0.6.6
-  # other 
-  - ipykernel==6.13.0
-  - protobuf==3.20
+  - kipoiseq