CI: dockers & triggers

Author: Borda

.github/workflows/ci_pkg-install.yml

@@ -2,9 +2,9 @@ name: Install package
 
 # see: https://help.github.com/en/actions/reference/events-that-trigger-workflows
 on:  # Trigger the workflow on push or pull request,  but only for the master branch
-  push:
+  push: {}
+  pull_request:
     branches: [master]
-  pull_request: {}
 
 jobs:
   pkg-check:

.github/workflows/ci_testing.yml

@@ -2,13 +2,13 @@ name: CI testing
 
 # see: https://help.github.com/en/actions/reference/events-that-trigger-workflows
 on:  # Trigger the workflow on push or pull request,  but only for the master branch
-  push:
+  push: {}
+  pull_request:
     branches: [master]
-  pull_request: {}
 
 jobs:
-  pytest:
 
+  pytest:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -17,12 +17,8 @@ jobs:
         python-version: [3.6, 3.9]
         requires: ['latest']
         include:
-          - os: "ubuntu-18.04"
-            python-version: 2.7
-            requires: 'latest'
-          - os: "ubuntu-18.04"
-            python-version: 3.6
-            requires: 'minimal'
+          - {os: "ubuntu-18.04", python-version: 2.7, requires: 'latest'}
+          - {os: "ubuntu-18.04", python-version: 3.6, requires: 'oldest'}
 
     # Timeout: https://stackoverflow.com/a/59076067/4521646
     timeout-minutes: 35
@@ -51,7 +47,7 @@ jobs:
         pip install -U backports.functools_lru_cache
 
     - name: Set min. dependencies
-      if: matrix.requires == 'minimal'
+      if: matrix.requires == 'oldest'
       run: |
         for fpath in ('requirements.txt', 'tests/requirements.txt'):
             req = open(fpath).read().replace('>=', '==')

.github/workflows/docker-builds.yml

@@ -2,8 +2,7 @@ name: Publish Docker Image
 # https://www.docker.com/blog/first-docker-github-action-is-here
 # https://github.com/docker/build-push-action
 on:  # Trigger the workflow on push or pull request, but only for the master branch
-  push:
-    branches: [master]
+  push: {}
   pull_request:
     branches: [master]
     types: [opened, reopened, ready_for_review, synchronize]
@@ -14,22 +13,23 @@ jobs:
     if: github.event.pull_request.draft == false
     runs-on: ubuntu-20.04
     strategy:
+      fail-fast: false
       matrix:
-        python_version: [3.7, 3.8, 3.9]
+        python_version: ["3.7", "3.8", "3.9"]
     steps:
       - name: Checkout
         uses: actions/checkout@v2
       # https://github.com/docker/setup-buildx-action
       # Set up Docker Buildx - to use cache-from and cache-to argument of buildx command
       - uses: docker/setup-buildx-action@v1
       - name: Login to DockerHub
+        if: ${{ github.repository_owner == 'Borda' }}
         uses: docker/login-action@v1
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
 
       - name: Build and Publish to Docker Hub
-        # publish master
         uses: docker/build-push-action@v2
         # https://github.com/docker/build-push-action#cache-to-registry
         with:
@@ -38,6 +38,6 @@ jobs:
           cache-from: type=registry,ref=borda/birl:SOTA-py${{ matrix.python_version }}
           cache-to: type=inline
           file: bm_experiments/Dockerfile
-          push: ${{ github.ref == 'refs/heads/master' }}
+          push: ${{ github.ref == 'refs/heads/master' && github.event_name == 'push' }}
           tags: borda/birl:SOTA-py${{ matrix.python_version }}
         timeout-minutes: 240

.github/workflows/docs-check.yml

@@ -3,9 +3,9 @@ name: "Docs check"
 
 # see: https://help.github.com/en/actions/reference/events-that-trigger-workflows
 on:  # Trigger the workflow on push or pull request,  but only for the master branch
-  push:
+  push: {}
+  pull_request:
     branches: [master]
-  pull_request: {}
 
 jobs:
 

.pre-commit-config.yaml

@@ -13,8 +13,13 @@ repos:
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
+      - id: check-case-conflict
       - id: check-yaml
-      - id: pretty-format-json
+      - id: check-toml
+      - id: check-json
+      - id: check-added-large-files
+      - id: check-docstring-first
+      - id: detect-private-key
 
   #- repo: https://github.com/pre-commit/mirrors-autopep8
   #  rev: v1.5.7

bm_experiments/Dockerfile

@@ -10,10 +10,10 @@ SHELL ["/bin/bash", "-c"]
 # for installing tzdata see: https://stackoverflow.com/a/58264927/4521646
 ENV DEBIAN_FRONTEND=noninteractive
 
-RUN apt-get update && \
+RUN apt-get update -qq --fix-missing && \
     apt-get install -y --no-install-recommends software-properties-common && \
     add-apt-repository ppa:deadsnakes/ppa && \
-    apt-get update && \
+    apt-get update -qq --fix-missing && \
     apt-get install -y --no-install-recommends \
         python${PYTHON_VERSION} \
         python${PYTHON_VERSION}-dev \
@@ -45,31 +45,9 @@ RUN apt-get update && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-RUN \
-    # BIRL requirement
-    apt-get update && \
-    apt-get install -y --no-install-recommends \
-        openslide-tools \
-    && \
-
-# Download BIRL from master
-    wget https://github.com/Borda/BIRL/archive/master.zip --progress=bar:force:noscroll && \
-    unzip -q master.zip && \
-    rm master.zip && \
-    mv BIRL-master BIRL && \
-
-# Install BIRL
-    # v46 crashes openslide-python install
-    pip install "setuptools<46" -U && \
-    pip install ./BIRL --no-cache-dir && \
-    python -c "import birl ; print(birl.__version__)" && \
-    mkdir BIRL/Applications && \
-# Cleaning
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/*
-
 ENV BIRL_APPs_PATH="/BIRL/Applications"
 
+RUN mkdir -p $BIRL_APPs_PATH
 
 RUN \
     cd $BIRL_APPs_PATH && \
@@ -84,7 +62,7 @@ RUN \
 ENV ANTs_VERSION="2.3.4"
 
 RUN \
-    apt-get update && \
+    apt-get update -qq && \
     apt-get install -y --no-install-recommends \
         zlib1g-dev \
     && \
@@ -127,7 +105,7 @@ RUN \
 ENV ANTSPY_VERSION="0.2.5"
 
 RUN \
-    apt-get update && \
+    apt-get update -qq && \
     apt-get install -y --no-install-recommends \
         libopenblas-dev \
         liblapack-dev \
@@ -163,8 +141,7 @@ RUN \
 ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$BIRL_APPs_PATH/elastix/lib/"
 
 RUN \
-# add required libs
-    apt-get update && \
+    apt-get update -qq && \
     apt-get install -y --no-install-recommends \
         libtbb-dev \
         libboost-all-dev \
@@ -228,8 +205,7 @@ RUN \
     $BIRL_APPs_PATH/DROP2/dropreg --help
 
 RUN \
-# add required libs
-    apt-get update && \
+    apt-get update -qq && \
     apt-get install -y --no-install-recommends \
         r-base-core \
         r-base-dev \
@@ -258,10 +234,25 @@ RUN \
 # try to run RNiftyReg
     R -e 'library(RNiftyReg)'
 
+COPY ./ /BIRL/
+
+RUN \
+    apt-get update -qq && \
+    apt-get install -y --no-install-recommends \
+        openslide-tools \
+    && \
+# Install BIRL
+    # v46 crashes openslide-python install
+    pip install "setuptools<46" -U && \
+    pip install ./BIRL --no-cache-dir && \
+    python -c "import birl ; print(birl.__version__)" && \
+# Cleaning
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
 
 RUN \
-# show installed applications
-    apt-get update && \
+    apt-get update -qq && \
     apt-get install -y --no-install-recommends \
         tree \
     && \