MTN setup CI to validate dependencies

.github/workflows/check_deps.py

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+"""Script to check that `requirements.txt` and `environment.yml` are synced.
+This script requires `pyyaml` to read `environment.yml`. It checks that all
+packages listed as dependencies in it are also present in one of
+`requirements.txt` or `extra_libraries.txt`.
+As there might be some discrepency between package names in `pip` and `conda`,
+one can add the name of the corresponding conda package as a comment on the
+same line as a requirement in `requirements.txt` to ensure proper matching.
+For instance, if one add the following line in `requirements.txt`
+> tensorflow-gpu  # tensorflow
+it will match a dependency `tensorflow` in the `environment.yml`.
+"""
+
+import yaml
+
+
+def preprocess_pip_deps(lines):
+
+    deps = []
+    for dep in lines:
+        dep = dep.strip()
+        if len(dep) == 0 or dep.startswith('#'):
+            continue
+
+        # If there is a comment on the same line use this to declare compat
+        # with conda install name. Note that if two packages are to be
+        # installed with conda, they can be added on the same line separated
+        # with a space.
+        deps.extend(dep.split('#')[-1].strip().split())
+    return deps
+
+
+def assert_same_deps(deps_pip, deps_conda):
+    "Check the two dependencies are the same with an explicit error message."
+    deps_pip = set(deps_pip)
+    deps_conda = set(deps_conda) - {'pip'}
+    # For requirements fetched via git, need to add parsing:
+    # environment.yml uses git+https://, requirements.txt uses git+git://
+    deps_pip = fix_req_set(deps_pip)
+    deps_conda = fix_req_set(deps_conda)
+
+    missing = deps_pip.symmetric_difference(deps_conda)
+
+    assert len(missing) == 0, (
+        f"Missing dependency {deps_pip.difference(deps_conda)} in `environment.yml` and "
+        f"dependencies {deps_conda.difference(deps_pip)} in `requirements.txt`"
+    )
+    return
+
+
+def fix_req_set(req_set: set):
+    '''
+    Parses through the input set and replaces entries starting with 'git+git://' or 'git+https://' with entries with
+    those fields removed.
+    Parameters
+    ----------
+    req_set : set
+        Set containing the requirements to fix.
+
+    Returns
+    -------
+    set
+        Set with entries starting with 'git+git://' or 'git+https://' removed.
+    '''
+    returned_set = set()
+    for req in req_set:
+        returned_set.add(remove_git_prefix(req))
+    return returned_set
+
+
+def remove_git_prefix(req_name: str) -> str:
+    '''
+    For strings starting with either git+git:// or git+https://, remove these and return the remainder.
+    Parameters
+    ----------
+    req_name : str
+        String from which to remove the git prefix, if present.
+
+    Returns
+    -------
+    str
+        String without the git prefix.
+    '''
+    if(req_name.startswith('git+')):
+        # More generally, can use req_name[req_name.index('//')+2:], but would
+        # do more than is stated in the docstring.
+        if(req_name.startswith('git+git://')):
+            return req_name.replace('git+git://', '')
+        elif(req_name.startswith('git+https://')):
+            return req_name.replace('git+https://', '')
+    return req_name
+
+
+if __name__ == '__main__':
+
+    # Load deps from envrionment.yml
+    with open('environment.yml') as f:
+        conf = yaml.load(f, Loader=yaml.FullLoader)
+
+    deps_conda = conf['dependencies']
+    deps_conda = deps_conda[:-1] + deps_conda[-1]['pip']
+
+    deps_pip = []
+    for requirement_file in ['requirements.txt', 'extra_libraries.txt']:
+        with open(requirement_file) as f:
+            deps_pip += preprocess_pip_deps(f.readlines())
+
+    assert_same_deps(deps_pip, deps_conda)

.github/workflows/install.yml

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+name: Check Extra Install
+
+on:
+  push:
+    branches:
+      - '**'
+  create:
+    branches:
+      - 'master'
+    tags:
+      - '**'
+
+jobs:
+  pip_install:
+    name: Check extra install with pip
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+
+    - name: Pip install extra_libraries
+      run: pip install -r extra_libraries.txt
+
+  conda_install:
+    name: Check extra install with conda
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: s-weigand/setup-conda@v1
+    - name: Install mamba
+      run: conda install -y -c conda-forge mamba
+    - name: Conda install environment.yml
+      run: mamba env create -f environment.yml -n test_env
+
+  check_same_deps:
+    name: Check pip and conda install same env
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Setup Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: Install dependencies
+        run: pip install pyyaml
+      - name: Check same requirements
+        run: python .github/workflows/check_deps.py

.github/workflows/testing.yml

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+name: 'build'
+on:
+  push:
+    branches:
+      - master
+      - main
+  pull_request:
+    branches:
+      - master
+      - main
+
+jobs:
+  build_conda:
+    name: RAMP tests
+    runs-on: "ubuntu-latest"
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: anaconda-client-env
+          environment-file: environment.yml
+          python-version: 3.8
+          auto-activate-base: false
+      - run: |
+          export RAMP_TEST_MODE=true  # to have download_data.py just download the dummy dataset
+          python download_data.py
+          ramp-test --quick-test
+  build_pip:
+    name: Linux pip
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 nbconvert[test]
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install git+https://github.com/AlexandreHutton/stroke
+    - name: Test
+      run: |
+        flake8 *.py submissions/*/*.py
+        export RAMP_TEST_MODE=true  # to have download_data.py just download the dummy dataset
+        python download_data.py
+        ramp-test --quick-test
+        ramp-test --submission sample --quick-test
+        jupyter nbconvert --execute stroke_lesions_starting_kit.ipynb --to html --ExecutePreprocessor.kernel_name=python3