Small methods to augment images

.github/workflows/build-documentation.yml

@@ -15,21 +15,30 @@ concurrency:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
-
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+    - uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: '3.10'
+        python-version: 3.9.15
+        channels: conda-forge,defaults
+        channel-priority: strict
+        show-channel-urls: true
+        use-mamba: true
+        environment-file: ci-env.yml
+        activate-environment: deepdisc
     - name: Install dependencies
       run: |
         sudo apt-get update
         python -m pip install --upgrade pip
-        if [ -f docs/requirements.txt ]; then pip install -r docs/requirements.txt; fi
         pip install .
+        pip install 'git+https://github.com/facebookresearch/detectron2.git@80307d2d5e06f06a8a677cc2653f23a4c56402ac'
+        pip install 'git+https://github.com/pmelchior/scarlet.git'
+        pip install .[dev]
+        if [ -f docs/requirements.txt ]; then pip install -r docs/requirements.txt; fi
     - name: Install notebook requirements
       run: |
         sudo apt-get install pandoc

.github/workflows/linting.yml

@@ -16,20 +16,28 @@ concurrency:
 jobs:
   build:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v4
+    - uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: '3.10'
+        python-version: 3.9.15
+        channels: conda-forge,defaults
+        channel-priority: strict
+        show-channel-urls: true
+        use-mamba: true
+        environment-file: ci-env.yml
+        activate-environment: deepdisc
     - name: Install dependencies
       run: |
         sudo apt-get update
         python -m pip install --upgrade pip
         pip install .
+        pip install 'git+https://github.com/facebookresearch/detectron2.git@80307d2d5e06f06a8a677cc2653f23a4c56402ac'
+        pip install 'git+https://github.com/pmelchior/scarlet.git'
         pip install .[dev]
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Analyze code with linter
-
       run: |
         pylint -rn -sn --recursive=y ./src --rcfile=./src/.pylintrc

.github/workflows/pre-commit-ci.yml

@@ -10,23 +10,32 @@ on:
 jobs:
   pre-commit-ci:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     env: 
       SKIP: "check-lincc-frameworks-template-version,pytest-check,no-commit-to-branch,validate-pyproject,check-added-large-files,sphinx-build"
     steps:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 0 
-    - name: Set up Python
-      uses: actions/setup-python@v4
+    - uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: '3.10'
+        python-version: 3.9.15
+        channels: conda-forge,defaults
+        channel-priority: strict
+        show-channel-urls: true
+        use-mamba: true
+        environment-file: ci-env.yml
+        activate-environment: deepdisc
     - name: Install dependencies
       run: |
         sudo apt-get update
         python -m pip install --upgrade pip
         pip install .
+        pip install 'git+https://github.com/facebookresearch/detectron2.git@80307d2d5e06f06a8a677cc2653f23a4c56402ac'
+        pip install 'git+https://github.com/pmelchior/scarlet.git'
         pip install .[dev]
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - uses: pre-commit/[email protected]
       with:
         extra_args: --from-ref ${{ github.event.pull_request.base.sha }} --to-ref ${{ github.event.pull_request.head.sha }}

.github/workflows/publish-to-pypi.yml

@@ -17,18 +17,29 @@ permissions:
 
 jobs:
   deploy:
-
     runs-on: ubuntu-latest
-
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v4
+    - uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: '3.10'
+        python-version: 3.9.15
+        channels: conda-forge,defaults
+        channel-priority: strict
+        show-channel-urls: true
+        use-mamba: true
+        environment-file: ci-env.yml
+        activate-environment: deepdisc
     - name: Install dependencies
       run: |
+        sudo apt-get update
         python -m pip install --upgrade pip
+        pip install .
+        pip install 'git+https://github.com/facebookresearch/detectron2.git@80307d2d5e06f06a8a677cc2653f23a4c56402ac'
+        pip install 'git+https://github.com/pmelchior/scarlet.git'
+        pip install .[dev]
         pip install build
     - name: Build package
       run: python -m build

.github/workflows/smoke-test.yml

@@ -16,25 +16,29 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.9', '3.10']
-
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+    - uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: 3.9.15
+        channels: conda-forge,defaults
+        channel-priority: strict
+        show-channel-urls: true
+        use-mamba: true
+        environment-file: ci-env.yml
+        activate-environment: deepdisc
     - name: Install dependencies
       run: |
         sudo apt-get update
         python -m pip install --upgrade pip
         pip install .
+        pip install 'git+https://github.com/facebookresearch/detectron2.git@80307d2d5e06f06a8a677cc2653f23a4c56402ac'
+        pip install 'git+https://github.com/pmelchior/scarlet.git'
         pip install .[dev]
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: List dependencies
       run: |
         pip list

.github/workflows/testing-and-coverage.yml

@@ -11,25 +11,29 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.9', '3.10']
-
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+    - uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: 3.9.15
+        channels: conda-forge,defaults
+        channel-priority: strict
+        show-channel-urls: true
+        use-mamba: true
+        environment-file: ci-env.yml
+        activate-environment: deepdisc
     - name: Install dependencies
       run: |
         sudo apt-get update
         python -m pip install --upgrade pip
         pip install .
+        pip install 'git+https://github.com/facebookresearch/detectron2.git@80307d2d5e06f06a8a677cc2653f23a4c56402ac'
+        pip install 'git+https://github.com/pmelchior/scarlet.git'
         pip install .[dev]
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Run unit tests with pytest
       run: |
         python -m pytest tests --cov=deepdisc --cov-report=xml

ci-env.yml

@@ -0,0 +1,20 @@
+name: deepdisc
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - python=3.9
+  - astropy
+  - ipykernel
+  - imgaug
+  - numpy
+  - opencv
+  - pybind11
+  - pytorch
+  - torchvision
+  - pip:
+    - autograd
+    - peigen
+    - proxmin