Merge pull request #1 from cvxgrp/add-ci-cd

added CI/CD Files and tailored implementation

.github/workflows/build.yml

@@ -0,0 +1,72 @@
+name: Deploy Main
+on:
+  release:
+    types: [published]
+jobs:
+    deploy-pypi:
+        runs-on: ubuntu-latest
+        environment: deployment
+        steps:
+          - name: Checkout Repository
+            uses: actions/checkout@v3
+
+          - name: Install Python
+            uses: actions/setup-python@v3
+            with:
+              python-version: "3.8"
+
+          - name: Install Twine
+            run: sudo pip install twine
+
+          - name: Create the distribution
+            run: |
+              git fetch --prune --unshallow --tags
+              sudo python setup.py sdist bdist_wheel
+          - name: Push to PyPI
+            run: sudo twine upload -u ${{ secrets.PYPI_USERNAME }} -p ${{ secrets.PYPI_PASSWORD }} dist/*
+
+    deploy-conda:
+        runs-on: ubuntu-latest
+        environment: deployment
+# sets default shell to remove need for source to run the conda shell
+        defaults:
+          run:
+            shell: bash -l {0}
+        steps:
+          - name: Checkout Repository
+            uses: actions/checkout@v3
+
+          - name: Install Python
+            uses: actions/setup-python@v3
+            with:
+              python-version: "3.8"
+
+          - name: Install Miniconda
+            uses: conda-incubator/setup-miniconda@v2
+            with:
+              auto-activate-base: true
+              activate-environment: ""
+              miniconda-version: "latest"
+
+          - name: Install the Conda Dependencies
+            run: |
+              conda config --set always_yes yes --set auto_update_conda false
+              conda update conda
+              conda install conda-build
+
+# echo yes before login to prevent anaconda bug breaking automation
+# git tags MUST be fetched otherwise output will be blank
+# bash variables cannot be used in github actions, must use actions specific syntax and methods
+          - name: Build the Anaconda Package
+            id: condabuild
+            run: |
+              conda install anaconda-client
+              conda config --set anaconda_upload no
+              echo yes | anaconda login --username ${{ secrets.ANACONDA_CLOUD_USERNAME }} --password ${{ secrets.ANACONDA_CLOUD_PASSWORD }}
+              git fetch --prune --unshallow --tags
+              VERSION_FROM_GIT_TAG=$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-) conda build . -c pytorch -c stanfordcvxgrp -c conda-forge --numpy 1.22.2
+              echo '::set-output name=gitversion::$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-)'
+          - name: Upload the Anaconda Package
+            id: condaload
+            run: |
+              anaconda upload -u stanfordcvxgrp  /usr/share/miniconda3/conda-bld/noarch/sure-cr-${{ steps.condabuild.outputs.gitversion }}-*.tar.bz2

.github/workflows/test.yml

@@ -0,0 +1,87 @@
+name: Main Test
+on:
+    pull_request:
+    push:
+        branches:
+            - main
+jobs:
+    run-tests:
+        runs-on: ubuntu-latest
+        steps:
+          - name: Checkout Repository
+            uses: actions/checkout@v3
+
+          - name: Install Python
+            uses: actions/setup-python@v3
+
+          - name: Install Dependencies
+            run: |
+              git fetch --prune --unshallow --tags
+              sudo $pythonLocation/bin/python3 -m pip install -r requirements.txt
+              sudo $pythonLocation/bin/python3 -m pip install setuptools --upgrade
+              sudo $pythonLocation/bin/python3 -m pip install pytest
+              sudo $pythonLocation/bin/python3 -m pip install -e .
+# Uncomment and modify once tests have been added to the repo
+#          - name: Run Unit Tests
+#            run: |
+#              sudo $pythonLocation/bin/python3 -m pytest --import-mode=append tests/test_cg.py
+#              sudo $pythonLocation/bin/python3 -m pytest --import-mode=append tests/
+
+    test-build-pypi:
+        needs: run-tests
+        runs-on: ubuntu-latest
+        steps:
+          - name: Checkout Repository
+            uses: actions/checkout@v3
+
+          - name: Install Python
+            uses: actions/setup-python@v3
+            with:
+              python-version: "3.8"
+
+          - name: Install Twine
+            run: sudo pip install twine
+
+          - name: Create the distribution
+            run: |
+              git fetch --prune --unshallow --tags
+              sudo python setup.py sdist bdist_wheel
+    test-build-conda:
+        needs: run-tests
+        runs-on: ubuntu-latest
+# sets default shell to remove need for source to run the conda shell
+        defaults:
+          run:
+            shell: bash -l {0}
+        steps:
+          - name: Checkout Repository
+            uses: actions/checkout@v3
+
+          - name: Install Python
+            uses: actions/setup-python@v3
+            with:
+              python-version: "3.8"
+
+          - name: Install Miniconda
+            uses: conda-incubator/setup-miniconda@v2
+            with:
+              auto-activate-base: true
+              activate-environment: ""
+              miniconda-version: "latest"
+
+          - name: Install the Conda Dependencies
+            run: |
+              conda config --set always_yes yes --set auto_update_conda false
+              conda update conda
+              conda install conda-build
+
+# echo yes before login to prevent anaconda bug breaking automation
+# git tags MUST be fetched otherwise output will be blank
+# bash variables cannot be used in github actions, must use actions specific syntax and methods
+          - name: Build the Anaconda Package
+            id: condabuild
+            run: |
+              conda install anaconda-client
+              conda config --set anaconda_upload no
+              git fetch --prune --unshallow --tags
+              VERSION_FROM_GIT_TAG=$(git tag --list "v*[0-9]" --sort=version:refname | tail -1 | cut -c 2-) conda build . -c pytorch -c stanfordcvxgrp -c conda-forge --numpy 1.22.2

conda_recipe/meta.yaml

@@ -0,0 +1,46 @@
+{% set name = "SURE-CR" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: {{ environ.get('VERSION_FROM_GIT_TAG') }}
+
+source:
+  git_url: https://github.com/cvxgrp/SURE-CR
+
+build:
+  noarch: python
+  number: 0
+  script: "{{ PYTHON }} -m pip install . --ignore-installed -vv "
+
+requirements:
+  host:
+    - pip
+    - python >=3.6
+    - numpy >=1.17.5
+    - scipy
+    - pytorch
+    - cvxpy
+    - torch-linops
+
+  run:
+    - pip
+    - python >=3.6
+    - numpy >=1.17.5
+    - scipy
+    - pytorch
+    - cvxpy
+    - torch-linops
+
+about:
+  home: https://github.com/cvxgrp/SURE-CR
+  license: APACHEv2
+  license_family: Apache
+  license_file:
+  summary: This package enables tractable evaluation of Stein's Unbiased Risk Estimate on convexly regularized estimators.
+  doc_url:
+  dev_url:
+
+extra:
+  recipe-maintainers:
+    - PTNobel
+    - Thistleman

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools >= 18.0", "wheel"]
+build-backend = "setuptools.build_meta"

requirements.txt

@@ -0,0 +1,6 @@
+numpy>=1.17.5
+scipy
+torch
+cvxpy
+cvxpylayers
+torch-linops

setup.py

@@ -1,12 +1,28 @@
 #!/usr/bin/python
-from setuptools import setup
+import subprocess
+from setuptools import setup, find_packages
 
 with open("README.md", "r") as fh:
    long_description = fh.read()
 
+# get all the git tags from the cmd line that follow our versioning pattern
+git_tags = subprocess.Popen(
+    ["git", "tag", "--list", "v*[0-9]", "--sort=version:refname"],
+    stdout=subprocess.PIPE,
+)
+tags = git_tags.stdout.read()
+git_tags.stdout.close()
+tags = tags.decode("utf-8").split("\n")
+tags.sort()
+
+# PEP 440 won't accept the v in front, so here we remove it, strip the new line and decode the byte stream
+VERSION_FROM_GIT_TAG = tags[-1][1:]
+
 setup(
     name="surecr",
+    version=VERSION_FROM_GIT_TAG,  # Required
     setup_requires=["setuptools>=18.0"],
+    packages=find_packages(exclude=["notebooks"]),  # Required
     install_requires=[
         "numpy >= 1.17.5",
         "scipy",
@@ -15,6 +31,9 @@
         "cvxpylayers",
         "torch-linops",
     ],
+    description="This package enables tractable evaluation of Stein's Unbiased Risk Estimate on convexly regularized estimators.",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
     url="https://github.com/cvxgrp/SURE-CR",
     classifiers=[
         "Programming Language :: Python :: 3",