Drop use of pkg_resources and specify dependencies in pyproject.toml

.github/workflows/tests-workflow.yaml

@@ -32,11 +32,11 @@ jobs:
         id: dependencies
         run: |
           source ci/deps/${{ matrix.config }}.sh
-          echo "CONDA_PYTHON_VERSION=${CONDA_PYTHON_VERSION}" >> $GITHUB_ENV
-          echo "PANDAS_VERSION=${PANDAS_VERSION}" >> $GITHUB_ENV
-          echo "NUMPY_VERSION=${NUMPY_VERSION}" >> $GITHUB_ENV
-          echo "SKLEARN_VERSION=${SKLEARN_VERSION}" >> $GITHUB_ENV
-          echo "NO_SLOW=${NO_SLOW}" >> $GITHUB_ENV
+          echo "CI_PYTHON_VERSION=${CI_PYTHON_VERSION}" >> $GITHUB_ENV
+          echo "CI_PANDAS_VERSION=${CI_PANDAS_VERSION}" >> $GITHUB_ENV
+          echo "CI_NUMPY_VERSION=${CI_NUMPY_VERSION}" >> $GITHUB_ENV
+          echo "CI_SKLEARN_VERSION=${CI_SKLEARN_VERSION}" >> $GITHUB_ENV
+          echo "CI_NO_SLOW=${CI_NO_SLOW}" >> $GITHUB_ENV
           echo "py_version=$(cut -d'.' -f 1-2 <<< ${CONDA_PYTHON_VERSION})" >> $GITHUB_OUTPUT
           echo "requirements=ci/deps/${{ matrix.config }}.sh" >> $GITHUB_OUTPUT
           echo "conda_pkgs=$(${CONDA}/bin/python -c "from conda.base.context import context; print(context.pkgs_dirs[0])")" >> $GITHUB_OUTPUT
@@ -51,11 +51,6 @@ jobs:
         run: |
           sudo chown -R $USER $CONDA
           ci/setup_env.sh ${{ runner.os }}
-      - name: Install Dependencies
-        run: |
-          python3 ci/list-requirements.py requirements/dev.txt > /tmp/conda-req.txt
-          conda install --solver=libmamba -c sebp -n sksurv-test --file /tmp/conda-req.txt
-          conda list -n sksurv-test
       - name: Configure Xcode
         run: |
           sudo xcode-select -s "/Applications/Xcode_13.2.1.app"
@@ -109,11 +104,11 @@ jobs:
           DEPS_CONFIG: py310_pandas14_numpy121_sklearn12
         run: |
           source ci/deps/${DEPS_CONFIG}.sh
-          echo "CONDA_PYTHON_VERSION=${CONDA_PYTHON_VERSION}" >> $GITHUB_ENV
-          echo "PANDAS_VERSION=${PANDAS_VERSION}" >> $GITHUB_ENV
-          echo "NUMPY_VERSION=${NUMPY_VERSION}" >> $GITHUB_ENV
-          echo "SKLEARN_VERSION=${SKLEARN_VERSION}" >> $GITHUB_ENV
-          echo "NO_SLOW=${NO_SLOW}" >> $GITHUB_ENV
+          echo "CI_PYTHON_VERSION=${CI_PYTHON_VERSION}" >> $GITHUB_ENV
+          echo "CI_PANDAS_VERSION=${CI_PANDAS_VERSION}" >> $GITHUB_ENV
+          echo "CI_NUMPY_VERSION=${CI_NUMPY_VERSION}" >> $GITHUB_ENV
+          echo "CI_SKLEARN_VERSION=${CI_SKLEARN_VERSION}" >> $GITHUB_ENV
+          echo "CI_NO_SLOW=${CI_NO_SLOW}" >> $GITHUB_ENV
           echo "requirements=ci/deps/${DEPS_CONFIG}.sh" >> $GITHUB_OUTPUT
           echo "conda_pkgs=$(${CONDA}/bin/python -c "from conda.base.context import context; print(context.pkgs_dirs[0])")" >> $GITHUB_OUTPUT
       - name: Cache downloaded packages
@@ -125,13 +120,6 @@ jobs:
         run: |
           sudo chown -R $USER $CONDA
           ci/setup_env.sh ${{ runner.os }}
-      - name: Install Dependencies
-        run: |
-          python3 ci/list-requirements.py requirements/dev.txt > /tmp/conda-req.txt
-          conda install --solver=libmamba -c sebp -n sksurv-test --file /tmp/conda-req.txt
-          conda install --solver=libmamba -n sksurv-test ipykernel 'matplotlib==3.5.1' nbformat 'seaborn==0.11.2' 'ipython!=8.7.0'
-          conda run -n sksurv-test pip install 'nbval>=0.10.0'
-          conda list -n sksurv-test
       - name: Configure matplotlib
         run: |
           mkdir -p ${XDG_CONFIG_HOME}/matplotlib

.github/workflows/tox-workflow.yaml

@@ -15,15 +15,15 @@ jobs:
           sudo apt-get install cmake libenchant-2-dev pandoc tox
       - name: Run Tox
         run: |
-          tox run -e py310-${{ matrix.tox_env }}
+          tox run -e ${{ matrix.tox_env }}
       - name: Archive documentation
         uses: actions/upload-artifact@v3
         with:
           name: documentation
           path: doc/_build/html
         if: ${{ matrix.tox_env == 'docs' }}
       - name: Print debug information
-        run: cat .tox/py310-${{ matrix.tox_env }}/log/*.log
+        run: cat .tox/${{ matrix.tox_env }}/log/*.log
         if: ${{ failure() }}
     strategy:
       fail-fast: false

.readthedocs.yaml

@@ -2,10 +2,10 @@ version: 2
 
 python:
   install:
-    - requirements: doc/docs_requirements.txt
-    - requirements: requirements/prod.txt
     - method: pip
       path: .
+      extra_requirements:
+        - docs
 
 build:
   os: ubuntu-22.04

appveyor.yml

@@ -28,13 +28,16 @@ install:
   - ps: conda init powershell
   - ps: conda config --set always_yes yes --set changeps1 no
   - ps: conda config --set auto_update_conda false
+  - ps: conda config --set notify_outdated_conda false
 #  - ps: conda update --yes --quiet conda
   - ps: conda info -a
 
   # Install the build and runtime dependencies of the project.
-  - cmd: conda env create -n sksurv-test --file ci\appveyor\requirements_%CONDA_PY%.yaml
+  - ps: $envScript=".\ci\appveyor\py$($env:CONDA_PY).ps1"
+  - ps: "& $envScript"
+  - ps: python "ci\render-requirements.py" "ci\deps\requirements.yaml.tmpl" > environment.yaml
+  - ps: conda env create -n sksurv-test --file environment.yaml
   - cmd: call %CONDA_INSTALL_LOCN%\Scripts\activate.bat sksurv-test
-  - cmd: python -m pip install build
   - cmd: conda list
   # Initialize the submodules
   - cmd: git submodule update --init --recursive

ci/appveyor/py310.ps1

@@ -0,0 +1,4 @@
+$env:CI_PYTHON_VERSION="3.10.*"
+$env:CI_PANDAS_VERSION="1.4.*"
+$env:CI_NUMPY_VERSION="1.21.*"
+$env:CI_SKLEARN_VERSION="1.2.*"

ci/appveyor/py311.ps1

@@ -0,0 +1,4 @@
+$env:CI_PYTHON_VERSION="3.11.*"
+$env:CI_PANDAS_VERSION="1.5.*"
+$env:CI_NUMPY_VERSION="1.23.*"
+$env:CI_SKLEARN_VERSION="1.2.*"

ci/appveyor/py38.ps1

@@ -0,0 +1,4 @@
+$env:CI_PYTHON_VERSION="3.8.*"
+$env:CI_PANDAS_VERSION="1.1.*"
+$env:CI_NUMPY_VERSION="1.19.*"
+$env:CI_SKLEARN_VERSION="1.2.*"

ci/appveyor/py39.ps1

@@ -0,0 +1,4 @@
+$env:CI_PYTHON_VERSION="3.9.*"
+$env:CI_PANDAS_VERSION="1.3.*"
+$env:CI_NUMPY_VERSION="1.21.*"
+$env:CI_SKLEARN_VERSION="1.2.*"

ci/deps/py310_pandas14_numpy121_sklearn12.sh

@@ -1,6 +1,6 @@
 # shellcheck shell=sh
-export CONDA_PYTHON_VERSION='3.10.*'
-export PANDAS_VERSION='1.4.*'
-export NUMPY_VERSION='1.21.*'
-export SKLEARN_VERSION='1.2.*'
-export NO_SLOW=true
+export CI_PYTHON_VERSION='3.10.*'
+export CI_PANDAS_VERSION='1.4.*'
+export CI_NUMPY_VERSION='1.21.*'
+export CI_SKLEARN_VERSION='1.2.*'
+export CI_NO_SLOW=true

ci/deps/py311_pandas15_numpy123_sklearn12.sh

@@ -1,6 +1,6 @@
 # shellcheck shell=sh
-export CONDA_PYTHON_VERSION='3.11.*'
-export PANDAS_VERSION='1.5.*    '
-export NUMPY_VERSION='1.23.*'
-export SKLEARN_VERSION='1.2.*'
-export NO_SLOW=false
+export CI_PYTHON_VERSION='3.11.*'
+export CI_PANDAS_VERSION='1.5.*'
+export CI_NUMPY_VERSION='1.23.*'
+export CI_SKLEARN_VERSION='1.2.*'
+export CI_NO_SLOW=false

ci/deps/py38_pandas10_numpy119_sklearn12.sh

@@ -1,6 +1,6 @@
 # shellcheck shell=sh
-export CONDA_PYTHON_VERSION='3.8.*'
-export PANDAS_VERSION='1.0.*'
-export NUMPY_VERSION='1.19.*'
-export SKLEARN_VERSION='1.2.*'
-export NO_SLOW=false
+export CI_PYTHON_VERSION='3.8.*'
+export CI_PANDAS_VERSION='1.0.*'
+export CI_NUMPY_VERSION='1.19.*'
+export CI_SKLEARN_VERSION='1.2.*'
+export CI_NO_SLOW=false

ci/deps/py39_pandas13_numpy121_sklearn12.sh

@@ -1,6 +1,6 @@
 # shellcheck shell=sh
-export CONDA_PYTHON_VERSION='3.9.*'
-export PANDAS_VERSION='1.3.*'
-export NUMPY_VERSION='1.21.*'
-export SKLEARN_VERSION='1.2.*'
-export NO_SLOW=true
+export CI_PYTHON_VERSION='3.9.*'
+export CI_PANDAS_VERSION='1.3.*'
+export CI_NUMPY_VERSION='1.21.*'
+export CI_SKLEARN_VERSION='1.2.*'
+export CI_NO_SLOW=true

ci/deps/requirements.yaml.tmpl

@@ -0,0 +1,31 @@
+name: sksurv-test
+channels:
+  - sebp
+  - defaults
+dependencies:
+  - coverage
+  - cython>=0.29
+  - ecos
+  - ipykernel
+  - ipython!=8.7.0
+  - joblib
+  - matplotlib>=3.6.2,<3.7
+  - nbformat
+  - numexpr
+  - numpy={CI_NUMPY_VERSION}
+  - osqp!=0.6.0,!=0.6.1
+  - packaging
+  - pandas={CI_PANDAS_VERSION}
+  - pip
+  - pytest
+  - python={CI_PYTHON_VERSION}
+  - scikit-learn={CI_SKLEARN_VERSION}
+  - scipy>=1.3.2
+  - seaborn>=0.11.2,<0.12
+  - setuptools-scm
+  - wheel
+  - pip:
+    - build
+    - importlib-resources>=1.3
+    - nbval>=0.10.0
+    - tomli

ci/render-requirements.py

@@ -0,0 +1,38 @@
+import argparse
+import os
+
+parser = argparse.ArgumentParser()
+parser.add_argument("yaml_file")
+
+
+def get_pinned_packages():
+    pkgs = {
+        "NUMPY",
+        "PANDAS",
+        "SKLEARN",
+        "PYTHON",
+    }
+    pinned = {}
+    for env_name in pkgs:
+        key = f"CI_{env_name}_VERSION"
+        ver = os.environ.get(key, "*")
+        pinned[key] = ver
+    return pinned
+
+
+def render_requirements(filename):
+    pinned = get_pinned_packages()
+    with open(filename) as fin:
+        contents = "".join(fin.readlines())
+
+    return contents.format(**pinned)
+
+
+def main():
+    args = parser.parse_args()
+    req = render_requirements(args.yaml_file)
+    print(req)
+
+
+if __name__ == '__main__':
+    main()

ci/run_tests.sh

@@ -4,7 +4,7 @@ export PYTHONWARNINGS="default"
 
 pytest_opts=("")
 
-if [ "x${NO_SLOW:-false}" != "xtrue" ]; then
+if [ "x${CI_NO_SLOW:-false}" != "xtrue" ]; then
   coverage erase
   rm -f coverage.xml
 else