Merge 1853a15 into 1e01735

.github/workflows/release-workflow.yml

@@ -18,14 +18,14 @@ jobs:
       GITHUB_TOKEN: ${{ secrets.GITHUBPAT }}
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
-    - name: Install conda environment py39
+        python-version: '3.10'
+    - name: Install conda environment py310
       uses: conda-incubator/setup-miniconda@v2
       with:
-        activate-environment: py39
+        activate-environment: py310
         environment-file: environment.ubuntu.singularity.yml
         auto-activate-base: false
     - name: Install dependencies
@@ -62,14 +62,14 @@ jobs:
       GITHUB_TOKEN: ${{ secrets.GITHUBPAT }}
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
-    - name: Install conda environment py39
+        python-version: '3.10'
+    - name: Install conda environment py310
       uses: conda-incubator/setup-miniconda@v2
       with:
-        activate-environment: py39
+        activate-environment: py310
         environment-file: environment.ubuntu.singularity.yml
         auto-activate-base: false
     - name: Install dependencies
@@ -94,11 +94,11 @@ jobs:
       GITHUB_TOKEN: ${{ secrets.GITHUBPAT }}
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
-    - name: Install conda environment py39
+        python-version: '3.10'
+    - name: Install conda environment py310
       uses: conda-incubator/setup-miniconda@v2
       with:
         activate-environment: py39
@@ -134,14 +134,14 @@ jobs:
       GITHUB_TOKEN: ${{ secrets.GITHUBPAT }}
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
-    - name: Install conda environment py39
+        python-version: '3.10'
+    - name: Install conda environment py310
       uses: conda-incubator/setup-miniconda@v2
       with:
-        activate-environment: py39
+        activate-environment: py310
         environment-file: environment.ubuntu.singularity.yml
         auto-activate-base: false
     - name: Install dependencies

.github/workflows/sync-with-model-repo.yml

@@ -22,14 +22,14 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: '3.10'
     - name: Install conda dependencies
       uses: conda-incubator/setup-miniconda@v2
       with:
-        activate-environment: py39
+        activate-environment: py310
         environment-file: environment.ubuntu.singularity.yml
         auto-activate-base: false
     - name: Install pip dependencies

.github/workflows/test-images.yml

@@ -14,10 +14,10 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - uses: psf/black@stable
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: '3.10'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -47,16 +47,16 @@ jobs:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: '3.10'
     - name: Install
       uses: conda-incubator/setup-miniconda@v2
       with:
-        activate-environment: py39
+        activate-environment: py310
         environment-file: environment.ubuntu.singularity.yml
-        python-version: 3.9
+        python-version: '3.10'
         auto-activate-base: false
     - name: Install dependencies
       shell: bash -l {0}
@@ -78,10 +78,10 @@ jobs:
       ZENODO_ACCESS_TOKEN: ${{ secrets.ZENODOACCESSTOKEN }}
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: '3.10'
     - name: Install dependencies
       run: |
         sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev pkg-config

dockerfiles/environment.kipoi.yml

@@ -4,10 +4,9 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - python=3.9
+  - python=3.10
   - pip
   - pkgconfig
   - conda-forge::hdf5
   - pip:
-    - kipoi
-
+    - git+https://github.com/kipoi/kipoi.git #TODO: Add back when kipoi when py3.10 version is available

environment.ubuntu.singularity.yml

@@ -1,9 +1,9 @@
-name: py39
+name: py310
 channels:
   - bioconda
   - conda-forge
   - defaults
 dependencies:
   - pip
   - singularity>=3.5
-  - python=3.9
+  - python=3.10

setup.py

@@ -13,7 +13,6 @@
     "ruamel.yaml.clib",
     "pandas",
     "spython",
-    "kipoi",
     "pre-commit",
     "click",
 ]
@@ -39,7 +38,10 @@
             "update_all_singularity=kipoi_containers.update_all_singularity_images:run_update",
         ],
     },
-    install_requires=requirements,
+    install_requires=[
+        requirements,
+        "kipoi @ https://github.com/kipoi/kipoi/archive/master.tar.gz",
+    ],
     license="MIT license",
     include_package_data=True,
     keywords="kipoi_containers",