Merge pull request #75 from kipoi/minorfixes

Minor fixes

.github/workflows/release-workflow.yml

@@ -34,7 +34,7 @@ jobs:
         mkdir -p /home/runner/singularity/
         sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev pkg-config
         python -m pip install --upgrade pip
-        pip install -e .
+        pip install .
     - name: Build and test ${{ matrix.image }}
       shell: bash -l {0}
       run: |
@@ -97,7 +97,7 @@ jobs:
         mkdir -p /home/runner/singularity/
         sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev pkg-config
         python -m pip install --upgrade pip
-        pip install -e .
+        pip install .
     - name: Build sharedpy3keras2 and kipoi-base-env
       shell: bash -l {0}
       run: |

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

@@ -40,7 +40,7 @@ jobs:
       run: |
         sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev pkg-config
         python -m pip install --upgrade pip
-        pip install -e .
+        pip install .
     - name: Sync with kipoi model repo
       shell: bash -l {0}
       run: |

.github/workflows/test-images.yml

@@ -22,7 +22,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install flake8 
-        pip install -e .
+        pip install .
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -63,7 +63,7 @@ jobs:
         mkdir -p /home/runner/singularity/
         sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev pkg-config
         python -m pip install --upgrade pip
-        pip install -e .
+        pip install .
     - name: Test with pytest
       shell: bash -l {0}
       run: |
@@ -85,7 +85,7 @@ jobs:
       run: |
         sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev pkg-config
         python -m pip install --upgrade pip
-        pip install -e .
+        pip install .
     - name: Test kipoi_containers and send coverage report to coveralls.io
       run: |-
         pip install coveralls

README.md

@@ -70,7 +70,7 @@ kipoi predict Basset \
 
 - Install [singularity](https://sylabs.io/guides/3.0/user-guide/installation.html)
 
-- Install kipoi_containers using ```pip install -e .```
+- Install kipoi_containers using ```pip install .```
 
 ## Environment variables
 

kipoi_containers/update_all_singularity_images.py

@@ -25,7 +25,7 @@ def run_update(docker_image: str) -> None:
     kipoi_containers/container-info/model-group-to-singularity.json will be
     updated.
     """
-    click.echo(f"Testing {docker_image}")
+    click.echo(f"Updating {docker_image}")
     model_group_to_singularity_dict = populate_json(
         MODEL_GROUP_TO_SINGULARITY_JSON
     )

setup.py

@@ -36,7 +36,7 @@
         boilerplate you need to create a Python package.",
     entry_points={
         "console_scripts": [
-            "update_all_singularity=kipoi_containers.update_all_singularity_containers:run_update",
+            "update_all_singularity=kipoi_containers.update_all_singularity_images:run_update",
         ],
     },
     install_requires=requirements,