intermediate kipoiseq version

.circleci/config.yml

@@ -6,34 +6,34 @@ variables:
     run:
       name: Update conda
       command: |
-        conda install python=3.6 -y
-        conda update --yes conda
-        conda update setuptools
-        conda config --add channels bioconda
-        conda config --add channels conda-forge
+        conda install -c conda-forge mamba -y
+        mamba env create -f environment.yaml
+        source activate mmsplice_dev
   install_mmsplice: &install_mmsplice
     run:
       name: Install mmsplice
       command: |
-        conda install cyvcf2 -y
-        conda install cython -y
-        conda install pybigwig -y
+        source activate mmsplice_dev
         pip install -e '.'
-        pip install pytest pytest-runner pytest-benchmark
   install_dependencies: &install_dependencies
     run:
       name: Install dependencies not in miniconda3
       command: |
+        source activate mmsplice_dev
         apt-get update && \
         apt-get install -y build-essential libz-dev libcurl3-dev gcc libssl-dev libbz2-dev
   test_cli: &test_cli
     run:
       name: Test cli
-      command: mmsplice
+      command: |
+        source activate mmsplice_dev
+        mmsplice
   run_tests: &run_tests
     run:
       name: Run tests
-      command: pytest
+      command: |
+        source activate mmsplice_dev
+        pytest
   install_docker: &install_docker
     run:
       name: Install Docker client

.gitignore

@@ -109,7 +109,7 @@ variant_effect_output.txt
 variant_effect_output.txt_summary.html
 variant_effect_output.txt_warnings.txt
 *-env/
-env*
+# env*
 notebooks/pred.csv
 notebooks/pred_exon.csv
 tests/data/test-out.vcf

environment.yaml

@@ -0,0 +1,22 @@
+name: mmsplice_dev
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - 'python=3.7'
+  - 'cython'
+  - 'pybigwig'
+  - 'setuptools'
+  - 'kipoiseq>=0.7,<0.8'
+  - 'cyvcf2'
+  - 'tensorflow'
+  - 'scipy'
+  - 'pandas'
+  - 'pyfaidx'
+  - 'tqdm'
+  - 'click'
+  - 'pyranges>=0.0.71'
+  - 'pip'
+  - 'pytest'
+  - 'pytest-runner'
+  - 'pytest-benchmark'

setup.py

@@ -13,7 +13,7 @@
 
 requirements = [
     'setuptools',
-    'kipoiseq>=0.7',
+    'kipoiseq>=0.7,<0.8',
     'cyvcf2',
     'tensorflow',
     'scipy',